diff --git a/app/assets/javascripts/components/staticDropdownOptions/options.js b/app/assets/javascripts/components/staticDropdownOptions/options.js
index 3c51610ae..3ebdf5aea 100644
--- a/app/assets/javascripts/components/staticDropdownOptions/options.js
+++ b/app/assets/javascripts/components/staticDropdownOptions/options.js
@@ -427,12 +427,24 @@ export const kindOptions = [{
},{
label: "13C NMR",
value: "13C NMR"
+},{
+ label: "15N NMR",
+ value: "15N NMR"
+},{
+ label: "NMR",
+ value: "NMR"
},{
label: "Mass",
value: "Mass"
},{
label: "IR",
value: "IR"
+},{
+ label: 'Raman',
+ value: 'Raman'
+},{
+ label: 'UV-VIS',
+ value: 'UV-VIS'
},{
label: "EA",
value: "EA"
@@ -452,6 +464,77 @@ export const kindOptions = [{
label: "Others",
value: "Others"
}];
+ // { label: 'no method', value: 'no_method'},
+ // { label: 'Others', value: 'others' },
+ //
+ // { label: '1H NMR CDCl3 250', value: 'NMR/1H/CDCl3/250'},
+ // { label: '1H NMR CDCl3 300', value: 'NMR/1H/CDCl3/300'},
+ // { label: '1H NMR CDCl3 400', value: 'NMR/1H/CDCl3/400'},
+ // { label: '1H NMR CDCl3 500', value: 'NMR/1H/CDCl3/500'},
+ //
+ //
+ // { label: '1H NMR C6D6 250', value: 'NMR/1H/C6D6/250'},
+ // { label: '1H NMR C6D6 300', value: 'NMR/1H/C6D6/300'},
+ // { label: '1H NMR C6D6 400', value: 'NMR/1H/C6D6/400'},
+ //
+ //
+ // { label: '1H NMR MeOD 250', value: 'NMR/1H/MeOD/250'},
+ // { label: '1H NMR MeOD 300', value: 'NMR/1H/MeOD/300'},
+ // { label: '1H NMR MeOD 400', value: 'NMR/1H/MeOD/400'},
+ //
+ //
+ // { label: '1H NMR DMSO 250', value: 'NMR/1H/DMSO/250'},
+ // { label: '1H NMR DMSO 300', value: 'NMR/1H/DMSO/300'},
+ // { label: '1H NMR DMSO 400', value: 'NMR/1H/DMSO/400'},
+ //
+ //
+ // { label: '13C NMR CDCl3 62.5', value: 'NMR/13C/CDCl3/62.5'},
+ // { label: '13C NMR CDCl3 75', value: 'NMR/13C/CDCl3/75'},
+ // { label: '13C NMR CDCl3 100', value: 'NMR/13C/CDCl3/100'},
+ // { label: '13C NMR CDCl3 125', value: 'NMR/13C/CDCl3/125'},
+ //
+ //
+ // { label: '13C NMR C6D6 62.5', value: 'NMR/13C/C6D6/62.5'},
+ // { label: '13C NMR C6D6 75', value: 'NMR/13C/C6D6/75'},
+ // { label: '13C NMR C6D6 100', value: 'NMR/13C/C6D6/100'},
+ //
+ // { label: '13C NMR MeOD 62.5', value: 'NMR/13C/MeOD/62.5'},
+ // { label: '13C NMR MeOD 75', value: 'NMR/13C/MeOD/75'},
+ // { label: '13C NMR MeOD 100', value: 'NMR/13C/MeOD/100'},
+ //
+ //
+ // { label: '13C NMR DMSO 62.5', value: 'NMR/13C/DMSO/62.5'},
+ // { label: '13C NMR DMSO 75', value: 'NMR/13C/DMSO/75'},
+ // { label: '13C NMR DMSO 100', value: 'NMR/13C/DMSO/100'},
+ //
+ //
+ // { label: '19F NMR acetone 400', value: 'NMR/19F/acetone/400'},
+ // { label: '19F NMR CDCl3 367', value: 'NMR/19F/CDCl3/367'},
+ // { label: '19F NMR MeOD 367', value: 'NMR/19F/MeOD/367'},
+ // { label: '19F NMR C6D6 367', value: 'NMR/19F/C6D6/367'},
+ //
+ //
+ // { label: 'H-H COSY NMR CDCl3', value: 'NMR/HHCOSY/CDCl3'},
+ // { label: 'H-H COSY NMR DMSO', value: 'NMR/HHCOSY/DMSO'},
+ // { label: 'H-H COSY NMR methanol', value: 'NMR/HHCOSY/methanol'},
+ //
+ // { label: 'H-C COSY NMR CDCl3', value: 'NMR/HCCOSY/CDCl3'},
+ // { label: 'H-C COSY NMR DMSO', value: 'NMR/HCCOSY/DMSO'},
+ // { label: 'H-C COSY NMR methanol', value: 'NMR/HCCOSY/methanol'},
+ //
+ // { label: 'DEPT 135', value: 'DEPT/135'},
+ // { label: 'DEPT 90', value: 'DEPT/90'},
+ // { label: 'DEPT 45', value: 'DEPT/45'},
+ //
+ // { label: 'IR', value: 'IR'},
+ // { label: 'Mass EI', value: 'Mass/EI'},
+ // { label: 'Mass GCMS', value: 'Mass/GCMS'},
+ // { label: 'Raman', value: 'Raman'},
+ // { label: 'UV-VIS', value: 'UV-VIS'},
+ // { label: 'TLC', value: 'TLC'},
+ // { label: 'Xray', value: 'Xray'},
+ // { label: 'Additional material', value: 'additional'},
+// ];
export const rolesOptions = [{
label: 'General Procedure',
diff --git a/app/assets/javascripts/components/stores/ElementStore.js b/app/assets/javascripts/components/stores/ElementStore.js
index 6dcfd39a3..b5ae41a79 100644
--- a/app/assets/javascripts/components/stores/ElementStore.js
+++ b/app/assets/javascripts/components/stores/ElementStore.js
@@ -12,6 +12,7 @@ import ElementActions from '../actions/ElementActions';
import CollectionActions from '../actions/CollectionActions';
import UIActions from '../actions/UIActions';
import UserActions from '../actions/UserActions';
+import RepositoryActions from '../actions/RepositoryActions';
import UIStore from './UIStore';
import ClipboardStore from './ClipboardStore';
import Sample from '../models/Sample';
@@ -226,13 +227,23 @@ class ElementStore {
handleUpdateLinkedElement: [
ElementActions.updateReaction,
ElementActions.updateSample,
+ RepositoryActions.publishSample,
+ RepositoryActions.publishReaction,
+ RepositoryActions.publishSampleReserveDois,
+ RepositoryActions.publishReactionReserveDois,
+ RepositoryActions.reviewPublish,
+ ],
+ handleRefreshSyncCollections: [
+ RepositoryActions.reviewPublish,
+ RepositoryActions.publishSample,
+ RepositoryActions.publishReaction,
],
handleUpdateElement: [
// ElementActions.updateReaction,
// ElementActions.updateSample,
ElementActions.updateWellplate,
ElementActions.updateScreen,
- ElementActions.updateResearchPlan
+ ElementActions.updateResearchPlan,
],
handleRefreshComputedProp: ElementActions.refreshComputedProp,
})
@@ -617,6 +628,10 @@ class ElementStore {
this.handleUpdateElement(element);
}
+ handleRefreshSyncCollections() {
+ CollectionActions.fetchSyncInCollectionRoots();
+ }
+
handleUpdateSampleForWellplate(wellplate) {
// UserActions.fetchCurrentUser()
this.state.currentElement = null;
@@ -1072,7 +1087,11 @@ class ElementStore {
&& previous.tag.taggable_data.reaction_id;
const openedReaction = selecteds.find(el => SameEleTypId(el, { type: 'reaction', id: rId }));
if (openedReaction) {
- openedReaction.updateMaterial(previous);
+ const freeze = (openedReaction && openedReaction.publication && openedReaction.publication.taggable_data &&
+ openedReaction.publication.taggable_data.scheme_only === true && (openedReaction.publication.state !== 'declined' || openedReaction.publication.state !== 'withdrawn')) || false;
+ if (freeze === false) {
+ openedReaction.updateMaterial(previous);
+ }
if (previous.isPendingToSave) {
openedReaction.changed = previous.isPendingToSave;
}
diff --git a/app/assets/javascripts/components/stores/LoadingStore.js b/app/assets/javascripts/components/stores/LoadingStore.js
index 5b6a8fc20..086b27252 100644
--- a/app/assets/javascripts/components/stores/LoadingStore.js
+++ b/app/assets/javascripts/components/stores/LoadingStore.js
@@ -3,6 +3,8 @@ import LoadingActions from '../actions/LoadingActions';
import ReportActions from '../actions/ReportActions';
import ElementActions from '../actions/ElementActions';
import InboxActions from '../actions/InboxActions';
+import RepositoryActions from '../actions/RepositoryActions';
+import PublicActions from '../actions/PublicActions';
class LoadingStore {
constructor() {
@@ -26,6 +28,9 @@ class LoadingStore {
ElementActions.createResearchPlan,
ElementActions.updateResearchPlan,
InboxActions.fetchInbox,
+ RepositoryActions.reviewPublish,
+ PublicActions.updateComment,
+ PublicActions.reviewPublish,
],
});
}
diff --git a/app/assets/javascripts/components/stores/PublicStore.js b/app/assets/javascripts/components/stores/PublicStore.js
new file mode 100644
index 000000000..b9a612a9f
--- /dev/null
+++ b/app/assets/javascripts/components/stores/PublicStore.js
@@ -0,0 +1,425 @@
+import Aviator from 'aviator';
+import alt from '../alt';
+import PublicActions from '../actions/PublicActions';
+import SearchActions from '../actions/ElementActions';
+import UIActions from '../actions/UIActions';
+
+class PublicStore {
+ constructor() {
+ this.molecules = [];
+ this.reactions = [];
+ this.page = 1;
+ this.pages = 1;
+ this.perPage = 10;
+ this.selectType;
+ this.selectState;
+ this.selectEmbargoId;
+ this.publishedStatics = [];
+ this.lastPublished;
+ this.lastPublishedSample;
+ this.guestPage = "";
+ this.currentElement = null;
+ this.queryId = -1;
+ this.news = {};
+ this.articles = [];
+ this.howto = {};
+ this.howtos = [];
+ this.bundles = [];
+
+ this.bindListeners({
+ handleGetMolecules: PublicActions.getMolecules,
+ handleGetReactions: PublicActions.getReactions,
+ handleSearchMolecules: PublicActions.getSearchMolecules,
+ handleSearchReactions: PublicActions.getSearchReactions,
+ handlePublishedStatics: PublicActions.publishedStatics,
+ handleLastPublished: PublicActions.lastPublished,
+ handleLastPublishedSample: PublicActions.lastPublishedSample,
+ handleOpenRepositoryPage: PublicActions.openRepositoryPage,
+ handleDisplayDataset: PublicActions.displayDataset,
+ handleDisplayMolecule: PublicActions.displayMolecule,
+ handleDisplayReaction: PublicActions.displayReaction,
+ handleReceiveSearchresult: SearchActions.fetchBasedOnSearchSelectionAndCollection,
+ handleClearSearchSelection: [UIActions.selectCollection, UIActions.selectSyncCollection],
+ handleClose: PublicActions.close,
+ handleArticles: PublicActions.articles,
+ handleEditArticle: PublicActions.editArticle,
+ handleDisplayArticle: PublicActions.displayArticle,
+ handleHowTos: PublicActions.howtos,
+ handleEditHowTo: PublicActions.editHowTo,
+ handleDisplayHowTo: PublicActions.displayHowTo,
+ handleGetElements: PublicActions.getElements,
+ handleGetEmbargoElements: PublicActions.getEmbargoElements,
+ handleDisplayReviewReaction: PublicActions.displayReviewReaction,
+ handleDisplayReviewSample: PublicActions.displayReviewSample,
+ handelReviewPublish: PublicActions.reviewPublish,
+ handelUpdateComment: PublicActions.updateComment,
+ handleFetchBundles: PublicActions.fetchEmbargoBundle,
+ handleDisplayEmbargoElement: PublicActions.displayReviewEmbargo,
+ handleEmbargoRelease: [PublicActions.releaseEmbargo, PublicActions.deleteEmbargo],
+ handleEmbargoMove: PublicActions.moveEmbargo,
+ });
+ }
+
+
+ handleClose({ deleteEl }) {
+ this.setState({
+ currentElement: null
+ });
+ if (this.guestPage === 'embargo') {
+ Aviator.navigate('/embargo', { silent: true });
+ } else if (this.guestPage === 'review') {
+ Aviator.navigate('/review', { silent: true });
+ } else {
+ Aviator.navigate('/publications', { silent: true });
+ }
+ }
+
+ handleClearSearchSelection(){
+ PublicActions.getMolecules.defer();
+ }
+
+ handleGetMolecules(results) {
+ const { molecules, page, pages, perPage } = results;
+ this.setState({ molecules, page, pages, perPage });
+ }
+
+ handleGetReactions(results) {
+ const { reactions, page, pages, perPage } = results;
+ this.setState({ reactions, page, pages, perPage });
+ }
+
+ handleSearchMolecules(results) {
+ const { molecules, page, perPage, totalElements } = results;
+ let { pages } = results;
+ if (totalElements && perPage) {
+ pages = Math.ceil(totalElements / perPage);
+ }
+ this.setState({
+ molecules, page, pages, perPage
+ });
+ }
+
+ handleSearchReactions(results) {
+ const {
+ reactions, page, perPage, totalElements
+ } = results;
+ let { pages } = results;
+ if (totalElements && perPage) {
+ pages = Math.ceil(totalElements / perPage);
+ }
+ this.setState({
+ reactions, page, pages, perPage
+ });
+ }
+
+ handlePublishedStatics(publishedStatics) {
+ if (publishedStatics) {
+ this.setState({ publishedStatics });
+ }
+ }
+
+ handleLastPublished(lastPublished) {
+ if (lastPublished) {
+ this.setState({ lastPublished });
+ }
+ }
+
+ handleLastPublishedSample(lastPublishedSample){
+ if (lastPublishedSample) {
+ this.setState({ lastPublishedSample });
+ }
+ }
+
+ handleOpenRepositoryPage(page) {
+ this.setState({ guestPage: page, currentElement: null });
+ }
+
+ handleDisplayDataset(result) {
+ this.setState({
+ guestPage: 'publications',
+ elementType: 'dataset',
+ queryId: result.id,
+ currentElement: result.dataset
+ });
+ Aviator.navigate(`/publications/datasets/${result.id}`,
+ { silent: true });
+ }
+
+ handleDisplayMolecule(moleculeList) {
+ this.setState({
+ guestPage: 'publications',
+ elementType: 'molecule',
+ queryId: moleculeList.id,
+ currentElement: moleculeList.moleculeData
+ });
+ Aviator.navigate(`/publications/molecules/${moleculeList.id}`, { silent: true });
+ }
+
+ handleDisplayReaction(reactionList) {
+ this.setState({
+ guestPage: 'publications',
+ elementType: 'reaction',
+ queryId: reactionList.id,
+ currentElement: reactionList.reactionData
+ });
+ Aviator.navigate(`/publications/reactions/${reactionList.id}`, { silent: true });
+ }
+
+ handleReceiveSearchresult(result) {
+ this.setState({ ...result.publicMolecules });
+ }
+
+ handleArticles(result) {
+ this.setState({
+ guestPage: 'newsroom',
+ articles: result.data
+ });
+ }
+
+ handleEditArticle(result) {
+ const news = result.data;
+ news.key = result.key;
+ news.article = news.article ? news.article : [];
+ this.setState({
+ guestPage: 'newseditor',
+ news,
+ });
+ }
+
+ handleDisplayArticle(result) {
+ const news = result.data;
+ news.key = result.key;
+ this.setState({
+ guestPage: 'newsreader',
+ news,
+ });
+ }
+
+ handleHowTos(result) {
+ this.setState({
+ guestPage: 'howto',
+ howtos: result.data
+ });
+ }
+
+ handleEditHowTo(result) {
+ const howto = result.data;
+ howto.key = result.key;
+ howto.article = howto.article ? howto.article : [];
+ this.setState({
+ guestPage: 'howtoeditor',
+ howto,
+ });
+ }
+
+ handleDisplayHowTo(result) {
+ const howto = result.data;
+ howto.key = result.key;
+ this.setState({
+ guestPage: 'howtoreader',
+ howto,
+ });
+ }
+
+ handleGetElements(results) {
+ const { elements, page, perPage, pages, selectType, selectState } = results;
+ this.setState({ elements, page, perPage, pages, selectType, selectState });
+ }
+
+ handleGetEmbargoElements(results) {
+ const { elements, current_user, embargo_id } = results;
+ this.setState({
+ selectEmbargoId: embargo_id,
+ elements,
+ currentElement: null,
+ currentUser: current_user
+ });
+ }
+
+ handelUpdateComment(result) {
+ this.setState({ commentInfo: result.comments });
+ }
+
+ handelReviewPublish(results) {
+ let newState = '';
+ switch (results.action) {
+ case 'Submit':
+ newState = 'pending';
+ break;
+ case 'Review':
+ newState = 'reviewed';
+ break;
+ case 'Accept':
+ newState = 'completed';
+ break;
+ case 'Reject':
+ newState = 'rejected';
+ break;
+ default:
+ newState = 'pending';
+ }
+
+ if (results.action == 'Comments') {
+ this.setState({
+ commentInfo: results.comments,
+ summaryInfo: results.summary,
+ feedbackInfo: results.feedback
+ });
+ } else {
+ this.setState({
+ pubState: newState,
+ commentInfo: results.comments,
+ summaryInfo: results.summary,
+ feedbackInfo: results.feedback
+ });
+ }
+
+ PublicActions.getElements(this.selectType || 'All', this.selectState || 'pending', this.page, this.perPage);
+ }
+
+ handleDisplayReviewReaction(result) {
+ let comments = {};
+ let summary = '';
+ let feedback = '';
+ let pubState = '';
+
+ if (result.element && result.element.reviewLevel === 0) {
+ Aviator.navigate('/home');
+ } else {
+ if (result.element && result.element.reaction &&
+ result.element.reaction.publication) {
+ const { publication } = result.element.reaction;
+ pubState = publication.state;
+
+ if (publication.review) {
+ const pr = publication.review;
+ comments = pr.comments ? pr.comments : {};
+ summary = pr.summary ? pr.summary : '';
+ feedback = pr.feedback ? pr.feedback : '';
+ }
+ }
+
+ this.setState({
+ guestPage: 'review',
+ elementType: 'reaction',
+ queryId: result.id,
+ currentElement: result.element,
+ commentInfo: comments,
+ summaryInfo: summary,
+ feedbackInfo: feedback,
+ submitter: result.element.pub_name,
+ reviewLevel: result.element.reviewLevel,
+ pubState
+ });
+ Aviator.navigate(`/review/review_reaction/${result.id}`, { silent: true });
+ }
+ }
+
+ handleDisplayReviewSample(result) {
+ let comments = {};
+ let summary = '';
+ let feedback = '';
+ let pubState = '';
+ if (result.element && result.element.reviewLevel === 0) {
+ Aviator.navigate('/home');
+ } else {
+ if (result.element &&
+ result.element.publication) {
+ const { publication } = result.element;
+ pubState = publication.state;
+
+ if (publication.review) {
+ const pr = publication.review;
+ comments = pr.comments ? pr.comments : {};
+ summary = pr.summary ? pr.summary : '';
+ feedback = pr.feedback ? pr.feedback : '';
+ }
+ }
+ this.setState({
+ guestPage: 'review',
+ elementType: 'sample',
+ queryId: result.id,
+ currentElement: result.element,
+ commentInfo: comments,
+ summaryInfo: summary,
+ feedbackInfo: feedback,
+ submitter: result.element.pub_name,
+ reviewLevel: result.element.reviewLevel,
+ pubState
+ });
+ Aviator.navigate(`/review/review_sample/${result.id}`, { silent: true });
+ }
+ }
+
+ handleFetchBundles(result) {
+ const cols = result.repository;
+ const { current_user } = result;
+ const bundles = [];
+ if (cols && cols.length > 0) {
+ cols.forEach((col) => {
+ bundles.push({ value: col.id, name: col.label, label: col.label });
+ });
+ this.setState({
+ bundles, current_user, elements: [], currentElement: null
+ });
+ } else {
+ this.setState({
+ bundles: [], current_user, elements: [], currentElement: null
+ });
+ }
+ }
+
+ handleDisplayEmbargoElement(result) {
+ let comments = {};
+ let summary = '';
+ let feedback = '';
+ let pubState = '';
+
+ if (result.element && result.element.reviewLevel === 0) {
+ Aviator.navigate('/home/');
+ } else {
+ if (result.element &&
+ result.element.publication) {
+ const { publication } = result.element;
+ pubState = publication.state;
+
+ if (publication.review) {
+ const pr = publication.review;
+ comments = pr.comments ? pr.comments : {};
+ summary = pr.summary ? pr.summary : '';
+ feedback = pr.feedback ? pr.feedback : '';
+ }
+ }
+
+ const elementType = (result.element.sample ? 'sample' : 'reaction');
+
+ this.setState({
+ guestPage: 'embargo',
+ elementType,
+ queryId: result.id,
+ currentElement: result.element,
+ commentInfo: comments,
+ summaryInfo: summary,
+ feedbackInfo: feedback,
+ pubState,
+ reviewLevel: result.element.reviewLevel
+ });
+ Aviator.navigate(`/embargo/${elementType}/${result.id}`, { silent: true });
+ }
+ }
+
+ handleEmbargoRelease(result) {
+ PublicActions.fetchEmbargoBundle();
+ }
+
+ handleEmbargoMove(results) {
+ const { col_id, is_new_embargo, new_embargo, message } = results.result;
+ if (is_new_embargo === true) {
+ this.bundles.push({value: new_embargo.id, name: new_embargo.label, label: new_embargo.label });
+ }
+ alert(message);
+ PublicActions.getEmbargoElements(col_id);
+ }
+}
+
+export default alt.createStore(PublicStore, 'PublicStore')
diff --git a/app/assets/javascripts/components/stores/ReportStore.js b/app/assets/javascripts/components/stores/ReportStore.js
index 381840bc7..f17b8c42e 100644
--- a/app/assets/javascripts/components/stores/ReportStore.js
+++ b/app/assets/javascripts/components/stores/ReportStore.js
@@ -61,6 +61,7 @@ class ReportStore {
this.prdAtts = [];
this.attThumbNails = [];
this.fileName = '';
+ this.dois = [];
this.bindListeners({
handleUpdateSplSettings: ReportActions.updateSplSettings,
@@ -318,6 +319,9 @@ class ReportStore {
case 'rxn_list_html':
prefix = 'Reaction_List_';
break;
+ case 'doi_list_xlsx':
+ prefix = 'DOI_List_';
+ break;
default:
prefix = '';
break;
@@ -353,6 +357,7 @@ class ReportStore {
let ext = 'docx';
switch (template) {
case 'rxn_list_xlsx':
+ case 'doi_list_xlsx':
ext = 'xlsx';
break;
case 'rxn_list_csv':
diff --git a/app/assets/javascripts/components/stores/UIStore.js b/app/assets/javascripts/components/stores/UIStore.js
index 36321480d..017c0dfcb 100644
--- a/app/assets/javascripts/components/stores/UIStore.js
+++ b/app/assets/javascripts/components/stores/UIStore.js
@@ -3,6 +3,7 @@ import alt from '../alt';
import UIActions from '../actions/UIActions';
import ElementActions from '../actions/ElementActions';
+import PublicActions from '../actions/PublicActions';
import ElementStore from './ElementStore';
import UserStore from './UserStore';
import ArrayUtils from '../utils/ArrayUtils';
@@ -103,6 +104,7 @@ class UIStore {
handleSetFromDate: UIActions.setFromDate,
handleSetToDate: UIActions.setToDate,
handleSetProductOnly: UIActions.setProductOnly,
+ handleSelectPublicCollection: PublicActions.selectPublicCollection,
});
}
@@ -376,6 +378,11 @@ class UIStore {
this.state.productOnly = productOnly;
this.handleSelectCollection(this.state.currentCollection, true);
}
+
+ handleSelectPublicCollection(result) {
+ this.state.currentCollection = result;
+ this.state.isSync = result.is_sync;
+ }
}
export default alt.createStore(UIStore, 'UIStore');
diff --git a/app/assets/javascripts/components/stores/UserStore.js b/app/assets/javascripts/components/stores/UserStore.js
index 90c1f5e87..7184ec8cb 100644
--- a/app/assets/javascripts/components/stores/UserStore.js
+++ b/app/assets/javascripts/components/stores/UserStore.js
@@ -37,7 +37,7 @@ class UserStore {
handleFetchCurrentUser(result) {
this.state.currentUser = result
- }
+ }
handleFetchProfile(result) {
this.state.profile = result;
diff --git a/app/assets/javascripts/components/users/AuthorModal.js b/app/assets/javascripts/components/users/AuthorModal.js
new file mode 100644
index 000000000..8ce17612c
--- /dev/null
+++ b/app/assets/javascripts/components/users/AuthorModal.js
@@ -0,0 +1,516 @@
+import React, { Component } from 'react';
+import PropTypes from 'prop-types';
+import { Col, OverlayTrigger, Tooltip, Modal, Button, Table, Panel, Form, FormControl, FormGroup, ControlLabel } from 'react-bootstrap';
+import { findIndex, filter } from 'lodash';
+import UsersFetcher from '../fetchers/UsersFetcher';
+import PublicFetcher from '../fetchers/PublicFetcher';
+import SelectionField from '../common/SelectionField';
+import DeleteConfirmBtn from '../common/DeleteConfirmBtn';
+
+const sortList = data => data.sort((a, b) => a.name.localeCompare(b.name));
+const addUserTooltip = Save to my collaboration;
+const removeAffTooltip = Remove this affiliation;
+const addAffTooltip = Add new affiliation;
+
+const lineAff = (g, aff, onDeleteAff, handleInputChange) => {
+
+ let removeBtn = '';
+ if (g.type === 'Collaborator') {
+ removeBtn = (
+
+
+
+ );
+ }
+
+
+ return (
+
+ | {aff.department} |
+ {aff.organization} |
+ {aff.country} |
+
+ { removeBtn }
+ |
+
+ );
+}
+
+export default class AuthorModal extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ countries: [],
+ organizations: [],
+ departments: [],
+ authors: [],
+ users: [],
+ fields: {},
+ showNewUser: false
+ };
+ this.handleInputChange = this.handleInputChange.bind(this);
+ this.findUsers = this.findUsers.bind(this);
+ this.handleAddUser = this.handleAddUser.bind(this);
+ this.handleHide = this.handleHide.bind(this);
+ this.onAddAff = this.onAddAff.bind(this);
+ this.onDeleteAff = this.onDeleteAff.bind(this);
+ }
+
+ componentDidMount() {
+ UsersFetcher.fetchMyCollaborations()
+ .then((result) => {
+ if (result.authors && result.authors.length > 0) {
+ this.setState({ authors: sortList(result.authors) });
+ } else {
+ this.setState({ authors: [], users: [], fields: {}, showNewUser: false });
+ }
+ });
+ PublicFetcher.affiliations('countries').then((result) => {
+ const affOption = result.affiliations.map(a => ({ label: a, value: a })).filter(a => a.value && a.value.length > 1);
+ this.setState({ countries: affOption });
+ });
+ PublicFetcher.affiliations('organizations').then((result) => {
+ const affOption = result.affiliations.map(a => ({ label: a, value: a })).filter(a => a.value && a.value.length > 1);
+ this.setState({ organizations: affOption });
+ });
+ PublicFetcher.affiliations('departments').then((result) => {
+ const affOption = result.affiliations.map(a => ({ label: a, value: a })).filter(a => a.value && a.value.length > 1);
+ this.setState({ departments: affOption });
+ });
+ }
+
+ componentDidUpdate() {
+ }
+
+ handleHide() {
+ this.setState({ users: [], fields: {}, showNewUser: false });
+ this.props.onHide();
+ }
+
+ // inputs of create new group
+ handleInputChange(type, ev) {
+ let { fields } = this.state;
+ switch (type) {
+ case 'firstName':
+ fields.firstName = ev.currentTarget.value;
+ break;
+ case 'lastName':
+ fields.lastName = ev.currentTarget.value;
+ break;
+ case 'abbr':
+ fields.abbr = ev.currentTarget.value;
+ break;
+ case 'country':
+ fields.country = ev && ev.value;
+ break;
+ case 'organization':
+ fields.organization = ev && ev.value;
+ break;
+ case 'department':
+ fields.department = ev && ev.value;
+ break;
+ case 'search_key':
+ fields.search_key = ev.currentTarget.value;
+ break;
+ default:
+ if (typeof fields === 'undefined') {
+ fields = {};
+ }
+ fields[type] = ev && ev.value;
+ }
+ this.setState({ fields });
+ }
+
+ findUsers() {
+ const { fields } = this.state;
+ if ((!fields.firstName || fields.firstName.trim() === '') && (!fields.lastName || fields.lastName.trim() === '')) {
+ alert('Please input First Name or Last Name');
+ return false;
+ }
+ UsersFetcher.fetchUsersByNameFirst(fields.lastName || '', fields.firstName || '')
+ .then((result) => {
+ if (result.users && result.users.length > 0) {
+ this.setState({
+ users: sortList(result.users),
+ showNewUser: false,
+ fields: {}
+ });
+ } else {
+ this.setState({ showNewUser: true, users: [] });
+ }
+ });
+ return true;
+ }
+
+ handleAddUser(u) {
+ const { authors } = this.state;
+ UsersFetcher.AddMyCollaboration({ id: u.id })
+ .then((result) => {
+ authors.push(result.user);
+ this.setState({
+ authors: sortList(authors), users: [], fields: {}, showNewUser: false
+ });
+ });
+ }
+
+ createAdd() {
+ const { fields, authors } = this.state;
+
+ const nilFields = [];
+ if (!fields.firstName || fields.firstName.trim() === '') {
+ nilFields.push('First Name');
+ }
+ if (!fields.lastName || fields.lastName.trim() === '') {
+ nilFields.push('Last Name');
+ }
+ if (!fields.country || fields.country.trim() === '') {
+ nilFields.push('Country');
+ }
+ if (!fields.organization || fields.organization.trim() === '') {
+ nilFields.push('Organization');
+ }
+ if (!fields.department || fields.department.trim() === '') {
+ nilFields.push('Department');
+ }
+ if (nilFields.length > 0) {
+ alert(`Please input ${nilFields.join()}!`);
+ return false;
+ }
+
+ UsersFetcher.createAddMyCollaboration(fields)
+ .then((result) => {
+ if (result.error) {
+ alert(result.error);
+ } else {
+ authors.push(result.user);
+ this.setState({
+ authors: sortList(authors), users: [], fields: {}
+ });
+ }
+ });
+ return true;
+ }
+
+ handleDeleteCollaborator(c) {
+ const { authors } = this.state;
+ UsersFetcher.deleteCollaboration({ id: c.id })
+ .then((result) => {
+ if (result.error) {
+ alert(result.error);
+ } else {
+ this.setState({
+ authors: filter(authors, o => o.id !== c.id)
+ });
+ }
+ });
+ }
+
+ onAddAff(g) {
+ const { authors, fields } = this.state;
+ const department = fields[`${g.id}@line_department`];
+ const organization = fields[`${g.id}@line_organization`];
+ const country = fields[`${g.id}@line_country`];
+ const params = { id: g.id, department, organization, country };
+
+
+ UsersFetcher.addCollaboratorAff(params)
+ .then((result) => {
+ if (result.error) {
+ alert(result.error);
+ } else {
+ const idx = findIndex(authors, o => o.id === result.user.id);
+ authors.splice(idx, 1, result.user);
+ fields[`${g.id}@line_department`] = '';
+ fields[`${g.id}@line_organization`] = '';
+ fields[`${g.id}@line_country`] = '';
+ this.setState({ authors, fields });
+ }
+ });
+ }
+
+ onDeleteAff(a, g) {
+ const { authors } = this.state;
+
+ const params = { user_id: g.id, aff_id: a.id };
+
+ UsersFetcher.deleteCollaboratorAff(params)
+ .then((result) => {
+ if (result.error) {
+ alert(result.error);
+ } else {
+ const idx = findIndex(authors, o => o.id === result.user.id);
+ authors.splice(idx, 1, result.user);
+
+ this.setState({ authors });
+ }
+ });
+ }
+
+ render() {
+ const { authors, users, showNewUser } = this.state;
+
+ const modalStyle = {
+ overflowY: 'auto',
+ };
+
+ let tbody = '';
+
+ const searchTbody = (users || []).map(g => (
+
+
+ |
+
+
+
+
+ |
+ {g.name} |
+ {g.affiliations && g.affiliations.length > 0 ? g.affiliations[0].department : ''} |
+ {g.affiliations && g.affiliations.length > 0 ? g.affiliations[0].organization : ''} |
+ {g.affiliations && g.affiliations.length > 0 ? g.affiliations[0].country : ''} |
+
+
+ ));
+
+ if (Object.keys(authors).length <= 0) {
+ tbody = '';
+ } else {
+ tbody = authors.map(g => (
+
+
+ |
+ this.handleDeleteCollaborator(g)}
+ />
+
+ |
+ {g.name} |
+
+
+
+ {
+ g.affiliations && g.affiliations.length > 0 ?
+ g.affiliations.map(a =>
+ lineAff(g, a, this.onDeleteAff, this.handleInputChange)) : ' '
+ }
+ {
+ g.type === 'Collaborator' ?
+ (
+
+ |
+
+ |
+
+
+ |
+
+
+ |
+
+
+
+
+ |
+
+ ) : ' '
+ }
+
+
+ |
+
+
+ ));
+ }
+
+ let newAff = '';
+ if (showNewUser === true) {
+ newAff = (
+
+ );
+ }
+
+ const newUserPanel = (
+
+
+
+ Add new collaborator
+
+
+
+
+
+
+
+ {newAff}
+
+
+
+ );
+
+ return (
+
+
+ My Collaboration
+
+
+
+ { newUserPanel }
+
+
+
+ Search Result
+
+
+
+
+
+
+ | Action |
+ Name |
+ Department |
+ Organization |
+ Country |
+
+
+ { searchTbody }
+
+
+
+
+
+
+ My Collaboration
+
+
+
+
+
+
+ | Action |
+ Name |
+
+
+
+ | Department |
+ Organization |
+ Country |
+ |
+
+
+ |
+
+
+ { tbody }
+
+
+
+
+ {/*
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ */}
+ {/*
+
+ Content
+ {quill}
+
+
+ Description
+
+
+ */}
+
+
+
this.props.onChange(container)}
+ />
+
+
{ XHome.count && XHome.count > 0
? extraHomes().map((Annex, i) =>
)
- :
-
-
-
-
-
-
+ : (
+
+
+
+
+
+
+
+ {this.renderGuestPage()}
+
+
+ {this.renderNavFooter()}
+
+ )
}
Repository
const NavHead = () => {
- let isHome = window.location.href.match(/\/home/)
+ const isHome = window.location.href.match(/\/home/)
return(
-
-
-
-
-
-
-
-
+
+
+
+
+
)
}
-NavHead.propTypes = {
-}
-
export default NavHead;
diff --git a/app/assets/javascripts/libHome/Navigation.js b/app/assets/javascripts/libHome/Navigation.js
new file mode 100644
index 000000000..09fbcc1bf
--- /dev/null
+++ b/app/assets/javascripts/libHome/Navigation.js
@@ -0,0 +1,136 @@
+import React from 'react';
+import { Nav, Navbar, NavItem, Label } from 'react-bootstrap';
+import UserAuth from '../components/UserAuth';
+import ManagingActions from '../components/managing_actions/ManagingActions';
+import ContextActions from '../components/contextActions/ContextActions';
+import UserStore from '../components/stores/UserStore';
+import UIStore from '../components/stores/UIStore';
+import UserActions from '../components/actions/UserActions';
+import UIActions from '../components/actions/UIActions';
+import ElementActions from '../components/actions/ElementActions';
+import NavNewSession from './NavNewSession';
+import NavHead from './NavHead';
+import DocumentHelper from '../components/utils/DocumentHelper';
+import NavigationModal from '../components/NavigationModal';
+import PublicActions from '../components/actions/PublicActions';
+
+export default class Navigation extends React.Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ currentUser: null,
+ modalProps: {
+ show: false,
+ title: '',
+ component: '',
+ action: null,
+ listSharedCollections: false,
+ }
+ };
+ this.onChange = this.onChange.bind(this);
+ this.onUIChange = this.onUIChange.bind(this);
+ // this.toggleCollectionTree = this.toggleCollectionTree.bind(this)
+ }
+
+ componentDidMount() {
+ UIStore.listen(this.onUIChange);
+ UserStore.listen(this.onChange);
+ UserActions.fetchCurrentUser();
+ }
+
+ componentWillUnmount() {
+ UIStore.unlisten(this.onUIChange);
+ UserStore.unlisten(this.onChange);
+ }
+
+ onChange(state) {
+ const newId = state.currentUser ? state.currentUser.id : null;
+ const oldId = this.state.currentUser ? this.state.currentUser.id : null;
+ if (newId !== oldId) { this.setState({ currentUser: state.currentUser }); }
+ }
+
+ onUIChange(state) {
+ this.setState({
+ modalProps: state.modalParams,
+ });
+ }
+
+ // toggleCollectionTree() {
+ // this.props.toggleCollectionTree();
+ // }
+
+ token() { return DocumentHelper.getMetaContent("csrf-token") }
+
+ updateModalProps(modalProps) { this.setState({ modalProps }); }
+
+ navHeader() {
+ return (
+
+
+ {/* */}
+
+
+
+
+ )
+ }
+
+ render() {
+ const { modalProps, currentUser } = this.state;
+
+ let userBar = ();
+ if (currentUser) {
+ userBar = ();
+ } else {
+ userBar = ();
+ }
+ // const logo = 
+ return (
+
+
+
+ Aviator.navigate('/home')} >
+ Chemotion-Repository
+
+
+
+
+ {userBar}
+
+
+
+ );
+ }
+}
diff --git a/app/assets/javascripts/libHome/RepoAbout.js b/app/assets/javascripts/libHome/RepoAbout.js
new file mode 100644
index 000000000..c9acbacd1
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoAbout.js
@@ -0,0 +1,164 @@
+import React from 'react';
+import { Col, Row, Panel } from 'react-bootstrap';
+
+const RepoAbout = () => {
+ const bodyStyle = {
+ maxHeight: 'calc(100vh - 262px)',
+ overflowY: 'auto',
+ backgroundColor: '#f5f5f5',
+ borderRadius: '6px',
+ padding: '30px',
+ textAlign: 'center'
+ };
+
+ return (
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ );
+};
+
+const CardIcons = () =>
+ (
+
+ );
+
+const CardAbout = () =>
+ (
+
+
This development is part of the work of the Stefan Bräse group at the KIT.
+
+
Brief project description
+
+
This project aims for the development of a freely available
+ infrastructure for research data management through the development
+ of two independent IT systems namely an electronic laboratory notebook
+ (ELN) and a chemistry web repository. With the tools that will be
+ established by our project group it will be possible to integrate
+ modern web-techniques into the routine work of academic researchers,
+ thereby increasing the amount of available data and improving the
+ quality of the information obtained and published.
+
+
The aim of this project is to make a substantial contribution to
+ securing research results in a cost-effective and simple manner,
+ and to optimally network in particular chemists (initially with each
+ other and in a second step with other disciplines). The new model
+ provides a combination of recording and documentation as well as
+ publication and storage of data sets.
+
+
The necessary IT structures for modern documentation of
+ research data are developed within the scope of this project,
+ will be summarized in an electronic laboratory notebook (ELN) and will
+ be provided and distributed as OPEN SOURCE. The ELN will be completed
+ by the establishment and hosting of the web-repository, for which a
+ direct connection to the ELN enables a fast and easy transfer of
+ selected research information.
+
+
Free access and free use by academic researchers is
+ one principle of this project allowing and promoting collaborative
+ work and scientific exchange among scientists.
+
+
+
+
Imprint
+
Karlsruhe Institute of Technology
+
Leader of the research group
+
Prof. Stefan Bräse
+
Institute of Organic Chemistry
+
Fritz-Haber-Weg 6, Geb. 30.42
+
76131 Karlsruhe
+
Germany
+
+
Institute of Biological and Chemical Systems – Functional Molecular Systems (IBCS-FMS)
+
Hermann-von-Helmholtz-Platz 1, Geb. 341
+
76344 Eggenstein-Leopoldshafen
+
Phone: +49 721 608 42903
+
Fax: +49 721 608 48581
+
+
+
Homepage Prof. Bräse
+
+
Office Campus North (KIT)
+
Dr. Nicole Jung, Dr. Pierre Tremouilhac
+
Institute of Organic Chemistry
+
Institute of Biological and Chemical Systems – Functional Molecular Systems
+
Hermann-von-Helmholtz-Platz 1
+
76344 Eggenstein-Leopoldshafen
+
Germany
+
Phone: +49 721 608 24697
+
+
Authors
+
Prof. Stefan Braese
+
Dr. Nicole Jung, Dr. Pierre Tremouilhac
+
+
Copyright Notices
+
+
+ During the submission process, the submitter of a publication can choose,
+ between several CC licenses, which license to apply to the submitted work.
+ As the result, the content of this repository database
+ (including the submitted publication files) is partly licensed under:
+
+
+ -
+
+
+ Creative Commons Attribution-ShareAlike 4.0 International License (default),
+
+ -
+
+
+ Creative Commons Attribution 4.0 International License, and
+
+ -
+
+
+ Creative Commons Universal License
+
+
+
+ The source code of the chemotion REPOSITORY web server and client is currently licensed under the GNU Affero General Public License v3.0.
+ The code can be found on github.
+
+
DOI®, DOI.ORG®, and shortDOI® are trademarks of the International DOI Foundation.
+
+
+
+
Content
+
+
+ All texts, pictures and other information published here are subject to
+ copyright. The logo may not be used without the prior consent
+ of the working group.
+ A change of the logo is not permitted. The contents of our website are
+ created with the utmost care. Nevertheless, no guarantee for topicality
+ and completeness can be taken over. The Compound Platform does not
+ assume any responsibility for any web content connected by a link,
+ as this is not its own content.
+
+
+
+ ID:
+
+
+);
+ChemotionId.propTypes = {
+ id: PropTypes.number.isRequired,
+ type: PropTypes.oneOf(['sample', 'reaction']).isRequired
+};
+
+const SchemeWord = () => (scheme);
+
+
+const AuthorTitle = (authorIds) => {
+ if (authorIds && authorIds.length > 1) {
+ return 'Authors:';
+ }
+ if (authorIds && authorIds.length === 1) {
+ return 'Author:';
+ }
+ return '';
+}
+
+const NewsroomTemplate = {
+ title: '', content: {}, article: []
+};
+
+const RequiredLabel = (props) => {
+ return (
+ This field is required for publication}
+ >
+
+
+ );
+};
+
+RequiredLabel.propTypes = {
+ placement: PropTypes.oneOf(['top', 'right', 'bottom', 'left']).isRequired
+};
+
+const HomeFeature = (props) => {
+ return (
+
+
{props.title}
+
+ {props.intro}
+
+
) : ( (1H {msg})
);
+ } else if (container.extended_metadata.kind.split('|')[0].trim() === chmoConversions.nmr_13c.termId) {
+ const msg = cNmrCheckMsg(sample.molecule.sum_formular, nmrStr);
+ return msg === '' ? (
) : ( (13C {msg})
);
+ }
+ return '';
+};
+
+// the requirements for file types as given
+const isFileTypePass = (analysisType, attachments) => {
+ const baseType = ['jpg', 'jpeg', 'png', 'tiff'];
+ const nmrType = ['jcamp', 'dx', 'jdx'];
+ let files = [];
+ switch (analysisType) {
+ case '1H NMR':
+ case chmoConversions.nmr_1h.termId:
+ case '13C NMR':
+ case chmoConversions.nmr_13c.termId:
+ case '15N NMR':
+ case 'NMR':
+ case 'IR':
+ case chmoConversions.ir.termId:
+ files = attachments.filter(f => baseType.includes(f.filename.split('.').pop().toLowerCase()) && !f.is_deleted);
+ if (files.length < 1) return false;
+ files = attachments.filter(f => nmrType.includes(f.filename.split('.').pop().toLowerCase()) && !f.is_deleted);
+ if (files.length < 1) return false;
+ break;
+ case 'EA':
+ case chmoConversions.ea.termId:
+ case 'X-Ray':
+ case 'Crystall-Structure':
+ case chmoConversions.crystal_structure.termId:
+ files = attachments.filter(f => baseType.includes(f.filename.split('.').pop().toLowerCase()) && !f.is_deleted);
+ if (files.length < 1) return false;
+ break;
+ default:
+ break;
+ }
+ return true;
+};
+
+// at least one dataset has to be attached
+// in dataset: instrument has to be given
+const isDatasetPass = (analysis) => {
+ const dataset = analysis.children;
+ const attachments = dataset.filter(d => d.attachments.length > 0 && !d.is_deleted);
+ if (attachments.length < 1) return false;
+ const instruments = dataset.filter(d => d.extended_metadata && (d.extended_metadata.instrument || '').trim() !== '' && !d.is_deleted);
+ if (instruments.length < 1) return false;
+ const analysisType = (analysis.extended_metadata.kind || '').split('|').shift().trim();
+ const files = attachments.filter(d => isFileTypePass(analysisType, d.attachments));
+ if (files.length < 1) return false;
+ return true;
+};
+
+const isNmrPass = (analysis, sample) => {
+ const nmrStr = analysis.extended_metadata && contentToText(analysis.extended_metadata.content);
+ const nmrType = analysis.extended_metadata && (analysis.extended_metadata.kind || '').split('|').shift().trim();
+ if (nmrType !== '1H NMR' && nmrType !== '13C NMR' && nmrType !== chmoConversions.nmr_1h.termId && nmrType !== chmoConversions.nmr_13c.termId) return true;
+ if (nmrType === '1H NMR' || nmrType === chmoConversions.nmr_1h.termId) {
+ return hNmrCheckMsg(sample.molecule.sum_formular, nmrStr) === '';
+ } else if (nmrType === '13C NMR' || nmrType === chmoConversions.nmr_13c.termId) {
+ return cNmrCheckMsg(sample.molecule.sum_formular, nmrStr) === '';
+ }
+ return true;
+};
+
+const DownloadMetadataBtn = (l) => {
+ const contentUrl = `/api/v1/public/metadata/download?type=${l.type}&id=${l.id}`;
+ return (
+ download published metadata}
+ >
+
+
+ );
+};
+
+const DownloadDOICsv = (e, a) => {
+ const dataToCsvURI = data => encodeURI(`data:text/csv;charset=utf-8,${data.map(row => row.join(',')).join('\n')}`);
+ const dois = [];
+ dois.push(['Reserved DOIs', '']);
+ dois.push(['', '']);
+
+ if (e.tag.taggable_data.reserved_doi) dois.push([e.type.charAt(0).toUpperCase() + e.type.slice(1), `DOI: ${e.tag.taggable_data.reserved_doi}`]);
+ a.forEach((an) => {
+ if (an.extended_metadata.reserved_doi) dois.push([`${an.name} - ${an.extended_metadata.kind}`, `DOI: ${an.extended_metadata.reserved_doi}`]);
+ });
+
+ if (e.type === 'reaction') {
+ // product(sample)
+ if (e.products !== null && e.products.length > 0) {
+ e.products.forEach((p) => {
+ if (p.tag.taggable_data.reserved_doi) dois.push([`Product ${p.name}`, `DOI: ${p.tag.taggable_data.reserved_doi}`]);
+ p.analysisArray().forEach((an) => {
+ if (an.extended_metadata.reserved_doi) dois.push([`${an.name} - ${an.extended_metadata.kind}`, `DOI: ${an.extended_metadata.reserved_doi}`]);
+ });
+ });
+ }
+ }
+ Utils.downloadFile({ contents: dataToCsvURI(dois), name: 'export_dois.csv' });
+};
+
+class EmbargoCom extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ isShow: false
+ };
+ this.handleEmbargoChange = this.handleEmbargoChange.bind(this);
+ }
+
+ handleEmbargoChange(e) {
+ this.props.onEmbargoChange(e.value);
+ }
+
+ handleLicenseChange(e) {
+ this.props.onLicenseChange(e.value);
+ }
+
+ handleCC0ConsentChange(e, type) {
+ this.props.onCC0ConsentChange(e.target.checked, type);
+ }
+
+ render() {
+ const defaultBundles = [
+ { value: '-1', name: 'no', label: 'No embargo' },
+ { value: '0', name: 'new', label: '--Create a new Embargo Bundle--' },
+ ];
+ const licenses = [
+ { name: 'CC BY-SA', value: 'CC BY-SA', label: 'CC BY-SA' },
+ { name: 'CC BY', value: 'CC BY', label: 'CC BY' },
+ { name: 'CC0', value: 'CC0', label: 'CC0' }
+ ];
+
+ const bundles = defaultBundles.concat(this.props.opts);
+ const description = [
+ 'Please use the embargo if you do not wish your data to be published as soon as they are processed but want to release them yourself at a later stage.',
+ 'Please use one bundle for data that belongs to the same publication.',
+ 'If you create data for more than one publication, please take care that you assign the data to the right bundle.'
+ ].join(' ');
+ const { isShow } = this.state;
+ const embargoDesc = isShow ? (
+
+ Embargo Bundle: {description}
+
+ ) : (null);
+
+ const cc0Consent1 = 'I hereby waive all copyright and related or neighboring rights together with all associated claims and causes of action with respect to this work to the extent possible under the law.';
+ const cc0Consent2 = 'I have read and understand the terms and intended legal effect of CC0, and hereby voluntarily elect to apply it to this work.';
+ const deed = (
+
+ {LicenseLegalCode(this.props.selectedLicense)}
+ {
+ this.props.selectedLicense === 'CC0' ?
+ (
+
+ this.handleCC0ConsentChange(e, 'consent1')}>
+ {cc0Consent1}
+
+ this.handleCC0ConsentChange(e, 'consent2')}>
+ {cc0Consent2}
+
+
+ )
+ :
+ (null)
+ }
+
+
+ {embargoDesc}
+ {deed}
+
+ Choose the publication type as Full or Scheme-Only}>
+
+
+ props.onChange(e)}
+ />
+
+ );
+};
+
+PublishTypeAs.propTypes = {
+ options: PropTypes.arrayOf(PropTypes.string),
+ selected: PropTypes.string,
+ onChange: PropTypes.func.isRequired,
+};
+
+PublishTypeAs.defaultProps = {
+ options: [],
+ selected: 'full',
+};
+
+
+const ElStateLabel = (state) => {
+ let stateStyle;
+ switch (state) {
+ case 'reviewed':
+ stateStyle = 'info';
+ break;
+ case 'pending':
+ stateStyle = 'warning';
+ break;
+ case 'accepted':
+ stateStyle = 'success';
+ break;
+ default:
+ stateStyle = 'default';
+ }
+ return ;
+};
+
+
+const MoveEmbargoedBundle = (element, onMoveClick) => {
+ return (
+ Move to another embargoed bundle}>
+
+
+ );
+};
+
+const ElSubmitTime = (submitAt) => {
+ const time = new Date(submitAt);
+ return `${time.getDate()}-${time.getMonth() + 1}-${time.getFullYear()} ${time.getHours()}:${time.getMinutes()} `;
+};
+
+const SvgPath = (svg, type) => {
+ if (svg && svg !== '***') {
+ if (type === 'Reaction') {
+ return `/images/reactions/${svg}`;
+ }
+ return `/images/samples/${svg}`;
+ }
+ return 'images/wild_card/no_image_180.svg';
+};
+
+const ElAspect = (e, onClick, user = null, currentElement = null, onMoveClick) => {
+ if (!e) {
+ return '';
+ }
+ let listClass;
+ if (e.type === 'Reaction') {
+ listClass = (currentElement !== null && currentElement.reaction && currentElement.reaction.id === e.id) ? 'list_focus_on' : 'list_focus_off';
+ } else {
+ listClass = (currentElement !== null && currentElement.sample && currentElement.sample.id === e.id) ? 'list_focus_on' : 'list_focus_off';
+ }
+ const schemeOnly = (e && e.scheme_only === true) || false;
+ return (
+ onClick(e.type.toLowerCase(), e.id)}
+ >
+ |
+
+ {schemeOnly ? : ''} {e.title}
+
+ By {e.published_by} at
+ {ElSubmitTime(e.submit_at)} {user !== null && user.type === 'Anonymous' ? '' : ElStateLabel(e.state)}
+ {user !== null && user.type === 'Anonymous' ? '' : MoveEmbargoedBundle(e, onMoveClick)}
+
+
+
+ |
+
+ );
+};
+
+const SampleExactMW = (em) => {
+ if (em) {
+ return ({em.toFixed(6)} g⋅mol-1);
+ }
+ return '';
+};
+
+const DateFormatYMDLong = (params) => {
+ const dateTime = new Date(params);
+ const options = {
+ year: 'numeric', month: 'long', day: 'numeric', timeZone: 'UTC'
+ };
+ return dateTime.toLocaleDateString('en-GB', options);
+};
+
+const DateFormatDMYTime = (dt) => {
+ if (dt == null || typeof dt === 'undefined') return '';
+ try {
+ const m = moment(dt, 'DD/MM/YYYY HH:mm:ss');
+ if (m.isValid()) {
+ return dt;
+ }
+ const dtJSON = new Date(dt).toJSON();
+ const dtISO = new Date(Date.parse(dt)).toISOString();
+ if (dtISO === dtJSON) {
+ return moment.parseZone(new Date(Date.parse(dt))).utc().format('DD/MM/YYYY HH:mm:ss').toString();
+ }
+ return '';
+ } catch (e) {
+ return '';
+ }
+};
+
+const EditorTips = () => {
+ return (
+
+ {/* - Use Preview to see how your work will look like.
*/}
+ - Use to open a text editor and add into the content.
+ - Use to open a image editor and add into the content.
+ - Use to change the section order.
+ - Use to remove the section from the content.
+ - In text editor, use to link to the url.
+
+ );
+};
+
+const BackSoonPage = () => {
+ return (
+
+
We’ll be back soon!
+
+
+ Sorry for the inconvenience but we’re performing some maintenance at the moment.
+
+
+ If you need to you can always contact us, otherwise we’ll be back online shortly!
+
+
— ComPlat Team
+
;
+};
+
+const IconToMyDB = ({
+ id, type, tooltipTitle = 'Link to My DB', isLogin = false
+}) => {
+ if (isLogin) {
+ return (
+ {tooltipTitle}}>
+
+
+
+
+ );
+ }
+ return ();
+};
+
+IconToMyDB.propTypes = {
+ id: PropTypes.number.isRequired,
+ type: PropTypes.string.isRequired,
+ tooltipTitle: PropTypes.string,
+ isLogin: PropTypes.bool,
+}
+
+IconToMyDB.defaultProps = {
+ tooltipTitle: 'Link to My DB',
+ isLogin: false
+}
+
+const SidToPubChem = ({ sid }) => {
+ let labelStyle = {
+ // display: 'inline-block',
+ marginLeft: '2px',
+ marginRight: '2px',
+ //position: 'absolute',
+ fontSize: 'xx-large'
+ };
+ if (!sid || isNaN(sid)) {
+ labelStyle.WebkitFilter = "grayscale(100%)"
+ }
+ const handleOnClick = (e) => {
+ if (sid && !isNaN(sid)){
+ window.open("https://pubchem.ncbi.nlm.nih.gov/substance/" + sid, '_blank')
+ }
+ e.stopPropagation()
+ }
+
+ if (sid && !isNaN(sid)){
+ return (
+
+ 
+
+ )
+ }else {
+ return
+ }
+}
+
+SidToPubChem.propTypes = {
+ sid: PropTypes.string
+}
+
+const ElementIcon = (elementType) => {
+ switch (elementType) {
+ case 'Reaction':
+ return ;
+ case 'Sample':
+ return ;
+ default:
+ return ;
+ }
+};
+
+const AnalysesTypeJoinLabel = (analyses, type) => {
+ const regExp = /\(([^)]+)\)/;
+ const analysesTypeJoin = analyses.map((analysis) => {
+ let kind = (regExp.exec(analysis.extended_metadata['kind'] || '') || ['']).pop().trim();
+ if (kind === '') {
+ kind = (analysis.extended_metadata['kind'] || '').split('|').pop().trim();
+ }
+ return kind;
+ }).join(', ');
+
+ return analysesTypeJoin === '' ? analysesTypeJoin :
+ (
+
+ {ElementIcon(type)}{' '}{analysesTypeJoin}
+
+ );
+};
+
+const PreviewImage = (container) => {
+ const rawImg = container.preview_img;
+ const noAttSvg = '/images/wild_card/no_attachment.svg';
+ const noAvaSvg = '/images/wild_card/not_available.svg';
+ switch (rawImg) {
+ case null:
+ case undefined:
+ return noAttSvg;
+ case 'not available':
+ return noAvaSvg;
+ default:
+ return `data:image/png;base64,${rawImg}`;
+ }
+};
+
+const CalcDuration = (reaction) => {
+ let duration = null;
+
+ if (reaction.duration && !!reaction.duration.match(/\d+/)) {
+ return reaction.duration;
+ }
+
+ if (reaction.timestamp_start && reaction.timestamp_stop) {
+ const start = moment(reaction.timestamp_start, 'DD-MM-YYYY HH:mm:ss');
+ const stop = moment(reaction.timestamp_stop, 'DD-MM-YYYY HH:mm:ss');
+ if (start < stop) {
+ duration = moment.preciseDiff(start, stop);
+ }
+ }
+ if (duration == null) {
+ return '';
+ }
+ return duration;
+};
+
+const AuthorList = ({ creators, affiliationMap }) => {
+ return (
+
+ {creators.map(
+ (creator, i) => (
+
+ {i === 0 ? null : ' - '}{creator.name}
+
+ {creator.affiliationIds && creator.affiliationIds.map(e => affiliationMap[e]).sort().join()}
+
+
+ )
+ )}
+
+ );
+};
+
+AuthorList.propTypes = {
+ creators: PropTypes.array,
+ affiliationMap: PropTypes.object,
+};
+
+AuthorList.defaultProps = {
+ creators: [],
+ affiliationMap: {},
+};
+
+const ContributorInfo = ({ contributor }) => {
+ if (!contributor.name) {
+ return ;
+ }
+ return (
+
+
+ Contributor: {contributor.name}
+
+
+ {contributor.affiliations && contributor.affiliations.map(
+ (e, i) =>
{i + 1}. {e}
+ )}
+
+
+ {names.map(
+ (e, i) => (i === 0 ? null :
{i}. {e}
)
+ )}
+
{this.props.text}
+
+ );
+ }
+}
+
+class ClipboardCopyBtn extends Component {
+ constructor(props) {
+ super(props)
+ this.clipboard = new Clipboard('.clipboardBtn');
+ }
+
+ render() {
+ return (
+ copy to clipboard}
+ >
+
+
+ );
+ }
+}
+
+
+
+const MoleculeInfo = ({ molecule, sample_svg_file='' }) => {
+ let svgPath = `/images/molecules/${molecule.molecule_svg_file}`;
+ if (sample_svg_file && sample_svg_file != '') {
+ svgPath = `/images/samples/${sample_svg_file}`;
+ }
+ const tagData = molecule.tag && molecule.tag.taggable_data;
+ const pubchemInfo = {
+ pubchem_tag: { pubchem_cid: tagData && tagData.pubchem_cid }
+ };
+ const nameOrFormula = molecule.iupac_name && molecule.iupac_name !== ''
+ ? IUPAC Name: {molecule.iupac_name} ()
+ : Formula:
;
+ return (
+
+
+
+
+
+ {nameOrFormula}
+
+ Canonical Smiles:
+ Inchi:
+ Inchikey:
+ Exact Mass: {SampleExactMW(molecule.exact_molecular_weight)}
+
+
+ Crosslinks:
+
+
+
+
+
+
+ );
+};
+
+class RenderAnalysisHeader extends Component {
+ constructor(props) {
+ super();
+ }
+
+ render() {
+ const svgPath = `/images/samples/${this.props.element.sample_svg_file}`;
+ let doiLink = '';
+ if (this.props.isPublic) {
+ doiLink = this.props.element.tag && this.props.element.tag.taggable_data && this.props.element.tag.taggable_data.publication && this.props.element.tag.taggable_data.publication.doi;
+ } else {
+ doiLink = (this.props.element.doi && this.props.element.doi.full_doi) || '';
+ }
+
+ const nameOrFormula = this.props.element.molecule.iupac_name && this.props.element.molecule.iupac_name !== ''
+ ? IUPAC Name: {this.props.element.molecule.iupac_name} ()
+ : Formula: ;
+
+ const iupacUserDefined = this.props.element.showed_name == this.props.element.molecule.iupac_name
+ ?
+ : Name: {this.props.element.showed_name}
;
+
+
+ const rinchiStyle = { borderStyle: 'none', boxShadow: 'none' };
+ const crsId = (this.props.element.publication && this.props.element.publication.id) || '';
+ return (
+
+
+
+
+
+
+
+
+
+
+ Product
+ {nameOrFormula}
+ {iupacUserDefined}
+
+ Canonical Smiles:
+ Inchi:
+ Inchikey:
+ Exact Mass: {SampleExactMW(this.props.element.molecule.exact_molecular_weight)}
+ DOI:
+ {
+ this.props.isPublic ?
+ (
+
+
+
+
+
+ )
+ :
+ (
+
+ {doiLink}
+
+ )
+ }
+
+
+ ID:
+
+
+
+
+
+
+
| {matType} |
);
+ }
+ return (
+
+ {title}
+
+ | {label} |
+ {isPublic ? sample.sum_formular : sample.molecule.sum_formular} |
+ {sample.mat_group === 'solvents' ? ' ' : isPublic ? sample.dmv: !sample.has_molarity && !sample.has_density ? '- / -' : sample.has_density ? + sample.density + ' / - ' : ' - / ' + sample.molarity_value + sample.molarity_unit} |
+ {sample.mat_group === 'solvents' ? ' - ' : materialCalc(sample.amount_g, 1, 3)} |
+ {materialCalc(sample.amount_l, 1000, 3)} |
+ {sample.mat_group === 'solvents' ? ' - ' : materialCalc(sample.amount_mol, 1000, 3)} |
+ {equivYield(sample, sumSolvents, isPublic)} |
+
+
+ );
+ })
+ : null
+ )
+ };
+
+ const table = dataRows => (
+
+
+
+ | IUPAC |
+ Formula |
+ Density/Molarity |
+ Amount(g) |
+ Volume(ml) |
+ Amount(mmol) |
+ Equiv/Yield |
+
+
+ {dataRows}
+
+ );
+
+ return (
+
+
+ { }}>
+
+
+
+ {table(rows(schemes))}
+
+
+
+
+
+ );
+}
+
+const ReactionRinChiKey = ({
+ reaction, toggle, show, bodyAttrs
+}) => {
+ const showIndicatorRinchi = (show) ? 'glyphicon-chevron-down' : 'glyphicon-chevron-right';
+ return (
+
+
+ { }}>
+
+
+
+ RInChI
+
+
+
+ Long-RInChIKey
+
+
+
+ Short-RInChIKey
+
+
+
+ Web-RInChIKey
+
+
+
+
+
+
+ );
+}
+
+const ReactionProperties = ({
+ reaction, toggle, show, bodyAttrs
+}) => {
+ const showIndicatorProp = (show) ? 'glyphicon-chevron-down' : 'glyphicon-chevron-right';
+ return (
+
+
+ { }}>
+
+
+
+
+ Status: {reaction.status}
+
+
+ Temperature: {reaction.temperature && reaction.temperature.userText !== '' ? `${reaction.temperature.userText} ${reaction.temperature.valueUnit}` : ''}
+
+
+ Duration: {CalcDuration(reaction)}
+
+
+
+
+
+
+ );
+}
+
+const ReactionTlc = ({
+ reaction, toggle, show, bodyAttrs
+}) => {
+ const showIndicatorTlc = (show) ? 'glyphicon-chevron-down' : 'glyphicon-chevron-right';
+ return (
+
+
+ { }}>
+
+
+
+ Solvents (parts)
+ {reaction.tlc_solvents || ''}
+
+
+ Rf-Value
+ {reaction.rf_value || ''}
+
+
+ TLC-Description
+
+
+ {reaction.tlc_description || ''}
+
+
+
+
+
+
+
+ );
+}
+
+const InputFieldYield = (props) => {
+ return (
+
+
+ props.onInputChange(props.product, event)}
+ />
+ %
+
+
+ );
+};
+
+const InputFieldDuration = props =>
+ (
+
+ );
+
+const InputFieldTemperture = props =>
+ (
+
+ );
+
+const ReactionTableEdit = ({
+ reaction, bodyAttrs, isPublic = true,
+ onInputChange
+}) => {
+ let schemes = [];
+ let sumSolvents = 0.0;
+
+ if (isPublic) {
+ schemes = reaction.schemes;
+ } else {
+ reaction.starting_materials.map((s) => {
+ const ns = new Sample(s)
+ ns.mat_group = 'starting_materials';
+ schemes.push(ns);
+ });
+ reaction.reactants.map((s) => {
+ const ns = new Sample(s)
+ ns.mat_group = 'reactants';
+ schemes.push(ns);
+ });
+ reaction.products.map((s) => {
+ const ns = new Sample(s)
+ ns.mat_group = 'products';
+ schemes.push(ns);
+ });
+ reaction.solvents.map((s) => {
+ const ns = new Sample(s)
+ sumSolvents += ns.amount_l;
+ ns.mat_group = 'solvents';
+ schemes.push(ns);
+ });
+ }
+
+ const materialCalc = (target, multi, precision) => (target ? (target * multi).toFixed(precision) : '0');
+ const equivYield = (s, sumSolvents = 1.0, isPublic = true) => {
+ let val = 0;
+ switch (s.mat_group) {
+ case 'products':
+ val = materialCalc(s.equivalent * 100, 1, 0);
+ break;
+ default:
+ return ;
+ }
+ return (
+
+ );
+ };
+
+ const rows = (samples) => {
+ let currentType = '';
+
+ return (
+ typeof samples !== 'undefined'
+ ? samples.map((sample, i) => {
+ const matType = sample.mat_group && sample.mat_group[0].toUpperCase() + sample.mat_group.replace('_', ' ').slice(1);
+ let label = isPublic ? sample.iupac_name : sample.molecule_iupac_name;
+ if (sample.mat_group === 'solvents') label = sample.external_label;
+ let title = null;
+ if (currentType !== sample.mat_group) {
+ currentType = sample.mat_group;
+ title = (| {matType} |
);
+ }
+ return (
+
+ {title}
+
+ | {label} |
+ {isPublic ? sample.sum_formular : sample.molecule.sum_formular} |
+ |
+ |
+ |
+ |
+ {equivYield(sample, sumSolvents, isPublic)} |
+
+
+ );
+ })
+ : null
+ )
+ };
+
+ const table = dataRows => (
+
+
+
+ | IUPAC |
+ Formula |
+ Density/Molarity |
+ Amount(g) |
+ Volume(ml) |
+ Amount(mmol) |
+ Equiv/Yield |
+
+
+ {dataRows}
+
+ );
+
+ return (
+
+
+ { }}>
+
+
+
+ {table(rows(schemes))}
+
+
+
+
+
+ );
+};
+
+const ReactionPropertiesEdit = ({
+ reaction, bodyAttrs,
+ onInputChange, onUnitChange
+}) =>
+ (
+
+
+ { }}>
+
+
+
+
+ Status{reaction.status}
+
+
+
+
+
+
+
+
+
+
+
+
+ );
+
+const ReactionSchemeOnlyInfo = ({
+ reaction, isPublic = true, schemeDesc,
+ onYieldChange, onPropertiesChange, onUnitChange
+}) => {
+ const svgPath = `/images/reactions/${reaction.reaction_svg_file}`;
+
+ const bodyAttrs = {
+ style: {
+ fontSize: '90%',
+ paddingBottom: 'unset'
+ }
+ };
+
+ return (
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { onPropertiesChange('schemeDesc'); }}
+ >
+ add the description field?
+
+
+
+
+
+
+
+
+
+
+ );
+};
+
+const ReactionInfo = ({ reaction, toggleScheme, showScheme, isPublic = true,
+ toggleRinchi, showRinchi,
+ toggleProp, showProp,
+ toggleTlc, showTlc,
+ schemeOnly = false, onToggle = () => {}
+ }) => {
+ const svgPath = `/images/reactions/${reaction.reaction_svg_file}`;
+ const content = reaction.description;
+ const additionInfo = reaction.observation;
+
+ const contentlength = (content && content.ops && content.ops.length > 0 && content.ops[0].insert) ? content.ops[0].insert.trim().length : 0;
+ const additionlength = (additionInfo && additionInfo.ops && additionInfo.ops.length > 0 && additionInfo.ops[0].insert) ? additionInfo.ops[0].insert.trim().length : 0;
+
+ const descQV = contentlength > 0 ?
+ (Description:) : null;
+ const addQV = additionlength > 0 ?
+ (Additional information for publication and purification details: ) : null;
+
+
+ const bodyAttrs = {
+ style: {
+ fontSize: '90%',
+ paddingBottom: 'unset'
+ }
+ };
+
+ if (schemeOnly) {
+ return (
+
+ );
+ }
+
+ return (
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ {descQV}
+
+
+ {addQV}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ );
+};
+
+const AnalysisHeaderSample = ({ sample, sampleType }) => {
+ const svgPath = `/images/samples/${sample.sample_svg_file}`;
+ const doiLink = sample.pubchem_tag.chemotion ? sample.pubchem_tag.chemotion.doi : '';
+ const rinchiStyle = { borderStyle: 'none', boxShadow: 'none', textAlign: 'left' };
+ return (
+
+
+
+
+
+
+ {sampleType}
+ DOI:
+
+
+
+
+
+
+ );
+};
+AnalysisHeaderSample.propTypes = {
+ sample: PropTypes.instanceOf(Sample).isRequired,
+ sampleType: PropTypes.string,
+};
+
+AnalysisHeaderSample.defaultProps = {
+ sample: {},
+ sampleType: '',
+};
+
+class RenderPublishAnalysesPanel extends Component {
+ header() {
+ const { analysis, isPublic } = this.props;
+ const content = analysis.extended_metadata['content'];
+ const previewImg = PreviewImage(analysis);
+ const kind = (analysis.extended_metadata['kind'] || '').split('|').pop().trim();
+
+ let hasPop = true;
+ let fetchNeeded = false;
+ let fetchId = 0;
+ let fetchFilename = '';
+ if (analysis.preview_img && analysis.preview_img !== undefined && analysis.preview_img !== 'not available') {
+ const containerAttachments = filter(analysis.children, o => o.attachments.length > 0);
+ const atts = flatMap(map(containerAttachments, 'attachments'));
+ const imageThumb = filter(atts, o => o.thumb === true && startsWith(o.content_type, 'image/'));
+ if (imageThumb && imageThumb.length > 0) {
+ fetchNeeded = true;
+ fetchId = imageThumb[0].id;
+ fetchFilename = imageThumb[0].filename;
+ }
+ } else {
+ hasPop = false;
+ }
+
+ const doiLink = (isPublic === false) ? (
+
+ DOI:
+ {analysis.dataset_doi}
+
+ ) : (
+
+ DOI:
+
+
+
+
+ )
+
+ return (
+
+
+
+
+
+
+
+ {kind}
+
+ {doiLink}
+
+ ID:
+
+
+
+
+
+
+
+
+
+
+
+ {this.header()}
+
+ Datasets
+
+
+
+ );
+ }
+}
+
+class RenderPublishAnalyses extends Component {
+ constructor(props) {
+ super(props);
+ }
+
+ header() {
+ const analysis = this.props.analysis;
+ const content = analysis.extended_metadata['content'];
+ const rawImg = analysis.preview_img;
+ const noAttSvg = '/images/wild_card/no_attachment.svg';
+ const noAvaSvg = '/images/wild_card/not_available.svg';
+ let previewImg = rawImg;
+ switch (rawImg) {
+ case null:
+ case undefined:
+ previewImg = noAttSvg;
+ break;
+ case 'not available':
+ previewImg = noAvaSvg;
+ break;
+ default:
+ previewImg = `data:image/png;base64,${rawImg}`;
+ }
+
+ const kind = (analysis.extended_metadata['kind'] || '').split('|').pop().trim();
+
+ let hasPop = true;
+ let fetchNeeded = false;
+ let fetchId = 0;
+ let fetchFilename = '';
+ if (analysis.preview_img && analysis.preview_img !== undefined && analysis.preview_img !== 'not available') {
+ const containerAttachments = filter(analysis.children, o => o.attachments.length > 0);
+ const atts = flatMap(map(containerAttachments, 'attachments'));
+ const imageThumb = filter(atts, o => o.thumb === true && startsWith(o.content_type, 'image/'));
+ if (imageThumb && imageThumb.length > 0) {
+ fetchNeeded = true;
+ fetchId = imageThumb[0].id;
+ fetchFilename = imageThumb[0].filename;
+ }
+ } else {
+ hasPop = false;
+ }
+
+ return (
+
+
+
+
+
+
+
+ DOI:
+
+
+
+
+
+ ID:
+
+
+
+
+ Content:
+
+
+
+
+
+
+
Published on {formattedTime}
+ {IconLicense(this.props.license, (this.props.publication.author_ids.length > 1))}
+
+
+ {kind}
+
+ {ElementIcon(elementType)}
+
+
+ Author{this.props.publication.author_ids && (this.props.publication.author_ids.length > 1) ? 's' : ''}:
+
+
+
+
+
+
+ {this.header()}
+
+ Datasets
+
+
+
+
+
+ );
+ }
+}
+
+RenderPublishAnalyses.propTypes = {
+ analysis: PropTypes.object.isRequired,
+ expanded: PropTypes.bool.isRequired,
+ elementType: PropTypes.string.isRequired,
+ license: PropTypes.string.isRequired,
+ publication: PropTypes.shape({
+ author_ids: PropTypes.arrayOf(PropTypes.number),
+ creators: PropTypes.arrayOf(PropTypes.object),
+ affiliation_ids: PropTypes.arrayOf(PropTypes.array),
+ affiliations: PropTypes.object,
+ published_at: PropTypes.string,
+ }).isRequired
+};
+
+class PublishAnalysesTag extends Component {
+ constructor(props) {
+ super(props);
+ const { reaction, analysis, analysesType, product } = props;
+ this.state = {
+ reaction,
+ analysis,
+ analysesType,
+ product
+ };
+ this.handleCheck = this.handleCheck.bind(this);
+ }
+
+ handleCheck(e, elementType) {
+ if (e.extended_metadata.publish && (e.extended_metadata.publish === true || e.extended_metadata.publish === 'true')) {
+ e.extended_metadata.publish = false;
+ } else {
+ e.extended_metadata.publish = true;
+ }
+ this.props.handleAnalysesChecked(e, elementType);
+ }
+
+ generateTitle() {
+ const {
+ reaction, analysis, analysesType, product
+ } = this.state;
+ const kind = (analysis.extended_metadata.kind || '').split('|').pop().trim();
+ const { content } = analysis.extended_metadata;
+ const status = analysis.extended_metadata.status || '';
+ const previewImg = PreviewImage(analysis);
+ const typeMissing = !analysis.extended_metadata.kind || ((analysis.extended_metadata.kind || '').split('|').length < 2);
+
+ let statusMissing = false;
+ let nmrMissing = false;
+ let datasetMissing = false;
+ if (analysesType === 'Product') {
+ statusMissing = (analysis.extended_metadata.status || '') !== 'Confirmed';
+ nmrMissing = !isNmrPass(analysis, product);
+ datasetMissing = !isDatasetPass(analysis);
+ }
+ const constructBtnTip = () => {
+ const tip = [];
+ if (typeMissing || statusMissing || nmrMissing || datasetMissing) {
+ if (typeMissing) tip.push('Type is invalid.');
+ if (statusMissing) tip.push('Status must be Confirmed.');
+ if (nmrMissing) tip.push('Content is invalid, NMR Check fails.');
+ if (datasetMissing) {
+ tip.push('Dataset is incomplete. Please check that: ');
+ tip.push('1. for NMR, Mass, or IR analyses, at least one dataset has been attached with an image and a jcamp files.');
+ tip.push('2. the instrument field is not empty.');
+ }
+ return tip.join('\r\n');
+ }
+ return 'publish this analysis';
+ };
+ const btnTip = constructBtnTip();
+
+ let statusChk = false;
+ let statusMsg = '';
+ let typeChk = false;
+ if (analysesType === 'Product') {
+ statusChk = (status !== 'Confirmed' || nmrMissing);
+ statusMsg = nmrMsg(product, analysis);
+ typeChk = (kind === '');
+ }
+
+ if (!analysis.extended_metadata.kind) {
+ analysis.extended_metadata.publish = false;
+ }
+ const isPublish = (analysis.extended_metadata.publish && (analysis.extended_metadata.publish === true || analysis.extended_metadata.publish === 'true')
+ && !statusMissing && !nmrMissing && !datasetMissing) || false;
+ let analysesIcon = '';
+ switch (analysesType) {
+ case 'Reaction':
+ analysesIcon = ;
+ break;
+ case 'Product':
+ analysesIcon = ;
+ break;
+ default:
+ analysesIcon = '';
+ }
+
+ return (
+
+
+
+
+
+
+
+ {analysesIcon}
+
+
+
+ {btnTip}}
+ >
+
+ { this.handleCheck(analysis, analysesType); }}
+ disabled={typeMissing || statusMissing || nmrMissing || datasetMissing}
+ defaultChecked={isPublish}
+ >
+ {
+ (typeMissing || statusMissing || nmrMissing || datasetMissing) ?
+ Add to publication
+ :
+ Add to publication
+ }
+
+
+
+
+
+
+
+ {analysis.name}
+
+ {
+ typeChk ?
+
Type: {kind}
+ :
+
Type: {kind}
+ }
+ {
+ statusChk ?
+
Status: {status} {statusMsg}
+ :
+
Status: {status} {statusMsg}
+ }
+
+
+ Content:
+
+
+
+
+
+
+
+
+ {datasetView}
+
+
+
+ );
+};
+
+DatasetDetail.propTypes = {
+ element: PropTypes.object.isRequired,
+};
+
+const ClosePanel = ({ element }) => (
+
+ Close}
+ >
+
+
+
+);
+
+ClosePanel.propTypes = {
+ element: PropTypes.object.isRequired,
+};
+
+const CommentBtn = (props) => {
+ const {
+ canComment,
+ reviewLevel,
+ submitter,
+ pubState,
+ comments,
+ onShow,
+ field,
+ orgInfo
+ } = props;
+
+ if (!canComment) return '';
+ return (
+
+ onShow(true, field, orgInfo)}
+ />
+
+ );
+};
+
+CommentBtn.propTypes = {
+ canComment: PropTypes.bool.isRequired,
+ reviewLevel: PropTypes.number.isRequired,
+ submitter: PropTypes.string.isRequired,
+ pubState: PropTypes.string.isRequired,
+ comments: PropTypes.object.isRequired,
+ onShow: PropTypes.func.isRequired,
+ field: PropTypes.string.isRequired,
+ orgInfo: PropTypes.string.isRequired
+};
+
+const Doi = (props) => {
+ const {
+ type, id, doi, isPublished
+ } = props;
+
+ let data = '';
+
+ if (isPublished) {
+ data = (
+
+
+
+
+
+ );
+ } else {
+ data = (
+
+ {doi.full_doi}
+
+ );
+ }
+
+ return (
+
+ DOI:
+ {data}
+
+ );
+};
+
+Doi.propTypes = {
+ type: PropTypes.string.isRequired,
+ id: PropTypes.number.isRequired,
+ doi: PropTypes.oneOfType([
+ PropTypes.string,
+ PropTypes.object,
+ ]).isRequired,
+ isPublished: PropTypes.bool.isRequired,
+};
+
+const DateInfo = (props) => {
+ const {
+ pubData, tagData, isPublished
+ } = props;
+
+ let time = '';
+ let formattedTime = '';
+
+ if (isPublished) {
+ time = new Date(tagData && (tagData.published_at || tagData.doi_reg_at));
+ formattedTime = `${time.getDate()}-${time.getMonth() + 1}-${time.getFullYear()} `;
+ return (Published on {formattedTime});
+ }
+
+ time = new Date(pubData && pubData.updated_at);
+ formattedTime = `${time.getDate()}-${time.getMonth() + 1}-${time.getFullYear()} `;
+ return (Submitted on {formattedTime});
+};
+
+DateInfo.propTypes = {
+ pubData: PropTypes.object.isRequired,
+ tagData: PropTypes.object.isRequired,
+ isPublished: PropTypes.bool.isRequired,
+};
+
+export {
+ AnalysisHeaderSample,
+ AnalysesTypeJoinLabel,
+ AffiliationList,
+ AuthorList,
+ AuthorTitle,
+ BackSoonPage,
+ CalcDuration,
+ ChemotionId,
+ ClipboardCopyLink,
+ ClipboardCopyBtn,
+ ClosePanel,
+ CommentBtn,
+ ContributorInfo,
+ DateFormatYMDLong,
+ DateFormatDMYTime,
+ DatasetDetail,
+ DateInfo,
+ Doi,
+ DownloadDOICsv,
+ DownloadMetadataBtn,
+ EditorTips,
+ ElementIcon,
+ ElStateLabel,
+ ElSubmitTime,
+ ElAspect,
+ EmbargoCom,
+ IconLicense,
+ IconToMyDB,
+ isNmrPass,
+ isDatasetPass,
+ HomeFeature,
+ MoleculeInfo,
+ NewsroomTemplate,
+ PreviewImage,
+ PublishAnalysesTag,
+ PublishTypeAs,
+ ReactionSchemeOnlyInfo,
+ ReactionInfo,
+ ReactionTable,
+ ReactionRinChiKey,
+ ReactionProperties,
+ ReactionTlc,
+ RenderAnalysisHeader,
+ RenderPublishAnalyses,
+ RenderPublishAnalysesPanel,
+ RequiredLabel,
+ SchemeWord,
+ SidToPubChem,
+ ShowIndicator,
+ SvgPath,
+ ToggleIndicator,
+};
diff --git a/app/assets/javascripts/libHome/RepoContact.js b/app/assets/javascripts/libHome/RepoContact.js
new file mode 100644
index 000000000..028a6eadb
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoContact.js
@@ -0,0 +1,43 @@
+import React from 'react';
+import { Well, Col, Row } from 'react-bootstrap';
+
+const RepoContact = () => {
+ const cpmail = nicole.jungioc.kit.edu;
+ const institute = 'Institute of Biological and Chemical Systems – Functional Molecular Systems (IBCS-FMS)';
+ return (
+
+
+
+
+
+
+
+ Complat
|
+ | {institute} |
+ | Hermann-von-Helmholtz-Platz 1 |
+ | Building 341 |
+ | 76344 Eggenstein-Leopoldshafen |
+ Germany
|
+ | Dr. Nicole Jung |
+ | +49 721 608 24697 |
+ | {cpmail} |
+
+
+
+
+
+
+
+
+
+
+
+ {container.children.map((datasetContainer) => {
+ return (
+
+ this.handleModalOpen(datasetContainer)}
+ disabled
+ />
+
+ );
+ })}
+
+
+ this.handleModalHide()}
+ show={modal.show}
+ readOnly
+ dataset_container={modal.dataset_container}
+ disabled
+ />
+
+ );
+ }
+ return (
+
+
+ There are currently no Datasets.
+
+
+ );
+ }
+}
diff --git a/app/assets/javascripts/libHome/RepoDirective.js b/app/assets/javascripts/libHome/RepoDirective.js
new file mode 100644
index 000000000..8712595b1
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoDirective.js
@@ -0,0 +1,41 @@
+import React from 'react';
+import { Col, Row, Panel } from 'react-bootstrap';
+import { Parser } from 'html-to-react';
+
+export default class RepoDirective extends React.Component {
+ constructor() {
+ super();
+ this.state = {
+ content:
+ };
+ }
+
+ componentDidMount() {
+ fetch('/directives/directives.html', { credentials: 'same-origin' })
+ .then(res => res.text())
+ .then((html) => {
+ // const parser = new HtmlToReactParser();
+ this.setState({ content: Parser().parse(html) });
+ })
+ .catch((errorMessage) => { console.log(errorMessage); });
+ }
+
+ render() {
+ return (
+
+
+
+
+
+ Directive to use the service
+
+
+ {this.state.content}
+
+
+
+
+
+ );
+ }
+};
diff --git a/app/assets/javascripts/libHome/RepoElementDetails.js b/app/assets/javascripts/libHome/RepoElementDetails.js
new file mode 100644
index 000000000..abf6329ee
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoElementDetails.js
@@ -0,0 +1,70 @@
+import React, { Component } from 'react';
+import PublicStore from '../components/stores/PublicStore';
+import { DatasetDetail } from './RepoCommon';
+import RepoReactionDetails from './RepoReactionDetails';
+import RepoSampleDetails from './RepoSampleDetails';
+
+export default class RepoElementDetails extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ currentElement: {}
+ };
+ this.onStoreChange = this.onStoreChange.bind(this);
+ }
+
+ componentDidMount() {
+ PublicStore.listen(this.onStoreChange);
+ }
+
+ componentWillUnmount() {
+ PublicStore.unlisten(this.onStoreChange);
+ }
+
+ onStoreChange(state) {
+ this.setState(prevState => ({ ...prevState, ...state }));
+ }
+
+ switchTypeRender() {
+ const { currentElement, elementType } = this.state;
+
+ if (typeof (currentElement) === 'undefined' || !currentElement) {
+ return ;
+ }
+
+ switch (elementType) {
+ case 'dataset': return ;
+ case 'molecule': return (
+ );
+ case 'reaction': return (
+ );
+ default: return ;
+ }
+ }
+
+ render() {
+ return (
+
+ {this.switchTypeRender()}
+
+ );
+ }
+}
diff --git a/app/assets/javascripts/libHome/RepoEmbargo.js b/app/assets/javascripts/libHome/RepoEmbargo.js
new file mode 100644
index 000000000..7a5f934c7
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoEmbargo.js
@@ -0,0 +1,278 @@
+import React, { Component } from 'react';
+import { Table, Col, Row, Navbar, DropdownButton, MenuItem, ButtonGroup, Button, ButtonToolbar, Modal, Panel } from 'react-bootstrap';
+import Select from 'react-select';
+import { findIndex, filter } from 'lodash';
+import RepoEmbargoDetails from './RepoEmbargoDetails';
+import PublicActions from '../components/actions/PublicActions';
+import PublicStore from '../components/stores/PublicStore';
+import { ElAspect } from './RepoCommon';
+import { ConfirmModal } from '../components/common/ConfirmModal';
+
+const renderMenuItems = (bundles) => {
+ if (bundles.length < 1) return ;
+ const menu = bundles.map(bundle => (
+
+ ));
+ return menu;
+};
+
+export default class RepoEmbargo extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ elements: [],
+ current_user: {},
+ currentElement: null,
+ moveElement: {},
+ newEmbargo: null,
+ selectEmbargo: null,
+ bundles: [],
+ showConfirmModal: false,
+ showMoveModal: false,
+ };
+ this.onChange = this.onChange.bind(this);
+ this.handleElementSelection = this.handleElementSelection.bind(this);
+ this.handleEmbargoAccount = this.handleEmbargoAccount.bind(this);
+ this.handleEmbargoRelease = this.handleEmbargoRelease.bind(this);
+ this.handleEmbargoDelete = this.handleEmbargoDelete.bind(this);
+ this.handleMoveEmbargo = this.handleMoveEmbargo.bind(this);
+ this.handleMoveShow = this.handleMoveShow.bind(this);
+ this.handleMoveClose = this.handleMoveClose.bind(this);
+ this.loadBundles = this.loadBundles.bind(this);
+ this.handleEmbargoChange = this.handleEmbargoChange.bind(this);
+ }
+
+ componentDidMount() {
+ PublicStore.listen(this.onChange);
+ this.loadBundles();
+ }
+
+ componentWillUnmount() {
+ PublicStore.unlisten(this.onChange);
+ }
+
+ onChange(state) {
+ this.setState(prevState => ({ ...prevState, ...state }));
+ if (this.state.selectEmbargo !== null) {
+ const vaildSelect = state.bundles.find(b => b.value === this.state.selectEmbargo.value);
+ if (typeof (vaildSelect) === 'undefined') {
+ this.setState({ selectEmbargo: null });
+ }
+ }
+ }
+
+ onClickDelete() {
+ this.setState({ showConfirmModal: true });
+ }
+
+
+ handleMoveShow(element) {
+ this.setState({
+ showMoveModal: true,
+ moveElement: element
+ });
+ }
+
+ handleMoveClose() {
+ this.setState({ showMoveModal: false, moveElement: {} });
+ }
+
+ handleEmbargoChange(selectedValue) {
+ if (selectedValue) {
+ this.setState({ newEmbargo: selectedValue });
+ }
+ }
+
+ handleElementSelection(eventKey, event) {
+ const { bundles } = this.state;
+ const selectEmbargo = bundles.find(b => b.value === eventKey);
+ this.setState({ selectEmbargo });
+ PublicActions.getEmbargoElements(eventKey);
+ }
+
+ handleEmbargoAccount() {
+ const { selectEmbargo } = this.state;
+
+ if (selectEmbargo === null) {
+ alert('Please select an embargo first!');
+ } else {
+ PublicActions.generateEmbargoAccount(selectEmbargo.value);
+ alert(`A temporary account for [${selectEmbargo.label}] has been created. The details have been sent to you by e-mail.`);
+ }
+ }
+
+ handleEmbargoRelease() {
+ const { selectEmbargo } = this.state;
+
+ if (selectEmbargo === null) {
+ alert('Please select an embargo first!');
+ } else {
+ PublicActions.releaseEmbargo(selectEmbargo.value);
+ alert(`The embargo on [${selectEmbargo.label}] has been released!`);
+ }
+ }
+
+ handleEmbargoDelete(shouldPerform) {
+ if (shouldPerform) {
+ const { selectEmbargo } = this.state;
+ if (selectEmbargo === null) {
+ alert('Please select an embargo first!');
+ } else {
+ PublicActions.deleteEmbargo(selectEmbargo.value);
+ }
+ }
+ this.setState({ showConfirmModal: false });
+ }
+
+ handleMoveEmbargo() {
+ const { selectEmbargo, moveElement, newEmbargo } = this.state;
+ PublicActions.moveEmbargo(selectEmbargo.value, newEmbargo, moveElement);
+ this.setState({ showMoveModal: false });
+ }
+
+ loadBundles() {
+ PublicActions.fetchEmbargoBundle();
+ }
+
+ renderSearch(bundles) {
+ const { selectEmbargo, elements, current_user } = this.state;
+ const acceptedEl = ((typeof (elements) !== 'undefined' && elements) || []).filter(e => e.state === 'accepted');
+ const customClass = '.btn-unified';
+ const actionButtons = current_user.type === 'Anonymous' ? :
+ (
+
+
+
+
+
+ );
+ const filterDropdown = (
+
+
+ {renderMenuItems(bundles)}
+
+ {actionButtons}
+
+ );
+
+ return (
+
+ {filterDropdown}
+
+ );
+ }
+
+
+ // render modal
+ renderMoveModal() {
+ const { showMoveModal, selectEmbargo, moveElement, bundles } = this.state;
+ const defaultBundles = [
+ { value: '0', name: 'new', label: '--Create a new Embargo Bundle--' },
+ ];
+ const allBundles = defaultBundles.concat(filter(bundles, b => b.name !== (selectEmbargo == null ? '' : selectEmbargo.name)));
+
+ return (
+
+
+ {moveElement.type}: [{moveElement.title}]
+
+
+
+
+
+
+ Move {moveElement.type} [{moveElement.title}] from Embargo Bundle [{selectEmbargo && selectEmbargo.label}] to :
+
+
+
+
+
+
+
+
+
+
+ {this.renderSearch(bundles)}
+
+
+
+
+
+
+ {((typeof (elements) !== 'undefined' && elements) || []).map(r => ElAspect(r, PublicActions.displayReviewEmbargo, currentUser, currentElement, this.handleMoveShow)) }
+
+
+
+
+ );
+ }
+}
diff --git a/app/assets/javascripts/libHome/RepoEmbargoDetails.js b/app/assets/javascripts/libHome/RepoEmbargoDetails.js
new file mode 100644
index 000000000..89d33cae8
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoEmbargoDetails.js
@@ -0,0 +1,47 @@
+import React, { Component } from 'react';
+import PublicStore from '../components/stores/PublicStore';
+import RepoReactionDetails from './RepoReactionDetails';
+import RepoSampleDetails from './RepoSampleDetails';
+
+export default class RepoEmbargoDetails extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ element: props.element
+ };
+
+ this.onStoreChange = this.onStoreChange.bind(this);
+ }
+
+ componentDidMount() {
+ PublicStore.listen(this.onStoreChange);
+ }
+
+ componentWillUnmount() {
+ PublicStore.unlisten(this.onStoreChange);
+ }
+
+ onStoreChange(state) {
+ this.setState(prevState => ({ ...prevState, ...state }));
+ }
+
+ switchTypeRender() {
+ const { currentElement, elementType } = this.state;
+
+ if (typeof (currentElement) === 'undefined' || !currentElement) {
+ return ;
+ }
+ switch (elementType) {
+ case 'reaction': return ;
+ case 'sample': return ;
+ default: return ;
+ }
+ }
+
+ render() {
+ return (
+
+ {this.switchTypeRender()}
+
);
+ }
+}
diff --git a/app/assets/javascripts/libHome/RepoHome.js b/app/assets/javascripts/libHome/RepoHome.js
new file mode 100644
index 000000000..512a53cc3
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoHome.js
@@ -0,0 +1,476 @@
+import React, {Component} from 'react'
+import { Label, Col, Row, Panel, ButtonToolbar, Button, Carousel, Thumbnail, Table, Well} from 'react-bootstrap'
+import SVG from 'react-inlinesvg'
+
+import PublicActions from '../components/actions/PublicActions'
+import PublicStore from '../components/stores/PublicStore'
+import { HomeFeature } from './RepoCommon';
+
+const PartnersInfo = (info) => {
+ const { header, img, content } = info
+ const imgSrc = `/images/repo/${img}`
+
+ return (
+
+
+
+ );
+}
+
+const Infos = [
+ {
+ header: "Database API",
+ img: "OAI.png",
+ content: "The molecule and dataset metadata are available via a low-barrier mechanism for repository interopability.",
+ }, {
+ header: "KIT Stiftung",
+ img: "KITStiftung.png",
+ content: "The KIT foundation honors excellent contributions to chemistry research with the Chemotion Award.",
+ }, {
+ header: "re3data",
+ img: "re3data.png",
+ content: "Karlsruhe Institute of Technology Registry of Research Data Repositories",
+ }, {
+ header: "Inchitrust",
+ img: "InChITRUST.png",
+ content: "The KIT has a Supporter Membership.",
+ }, {
+ header: "Datacite",
+ img: "DataCite.png",
+ content: "Helping you to find, access, and reuse data.",
+ }, {
+ header: "Pubmed",
+ img: "pubchem.jpg",
+ content: "All compounds are automatically registered with PubChem.",
+ }, {
+ header: "Thomson Reuters",
+ img: "DCIbadge.png",
+ content: "Datasets are automatically registered at the Data Citation Index.",
+ }, {
+ header: "DFG",
+ img: "ri_logo.png",
+ content: "Listed in the DFG catalogue for Research Infrastructures.",
+ }
+]
+
+const timeInterval = (date) => {
+ if (!date) { return null; }
+ switch (typeof date) {
+ case 'number':
+ break;
+ case 'string':
+ date = +new Date(date);
+ break;
+ case 'object':
+ if (date.constructor === Date) date = date.getTime();
+ break;
+ default:
+ date = +new Date();
+ }
+ let seconds = Math.floor((new Date() - date) / 1000);
+ let intrvlTypes = [
+ [31536000, 'year', 'a'],
+ [2592000, 'month', 'a'],
+ [604800, 'week', 'a'],
+ [86400, 'day', 'a'],
+ [3600, 'hour', 'an'],
+ [60, 'minute', 'a'],
+ [1, 'second', 'a'],
+ ]
+ let intrvlCount = 0
+ let intrvlType = intrvlTypes.find((e) => {
+ intrvlCount = Math.floor(seconds / e[0])
+ return intrvlCount >= 1
+ })
+ return `${intrvlCount === 1 ? intrvlType[2] : intrvlCount} ${intrvlType[1]}${intrvlCount > 1 ? 's' : ''} ago`;
+}
+
+const CardLatestPublish = ({ lastPublished }) => {
+ if (lastPublished) {
+ const { sample, reaction } = lastPublished;
+ const svgPathSample = sample.sample_svg_file
+ ? `/images/samples/${sample.sample_svg_file}`
+ : `/images/molecules/${sample.molecule.molecule_svg_file}`;
+ const pubTagSample = sample.tag || {};
+ const svgPathReaction = reaction
+ ? `/images/reactions/${reaction.reaction_svg_file}`
+ : '/images/no_image_180.svg';
+ const pubTagReaction = reaction.tag || {};
+ const spanStyle = {
+ color: 'black', textShadow: 'none', textAlign: 'justify', fontSize: 'medium'
+ };
+
+
+ return (
+
+ );
+ }
+ return ;
+};
+
+const CardSample = ({ lastPublishedSample }) => {
+ const sample = lastPublishedSample;
+ let svgPath = '/images/no_image_180.svg';
+ // let href = ''
+
+ if (sample) {
+ svgPath = sample.svgPath
+ ? `/images/samples/${sample.sample_svg_file}`
+ : `/images/molecules/${sample.molecule.molecule_svg_file}`
+ // href = `/molecules/${sample.molecule.id}`;
+ const pubTag = sample.tag && sample.tag.taggable_data['publication'] || {}
+
+ return (
+
+
+
+
Published { timeInterval(pubTag.published_at || pubTag.doi_reg_at || pubTag.queued_at)} by {pubTag.creators[0].name}
+
+
+
+
+
+
+
+
+
+
+ )
+}
+
+const CardIntro = () => {
+ return (
+
+ )
+}
+
+const ImgTitle = () => {
+ return (
+
+
+
+
+
+
+ Repository for molecules, reactions and research data
+
+
+
+ Visibility and Impact
+
+ -
+ Publish your structures, attach your characterization data, and make them citable via DOI
+
+ -
+ Automated registration at various scientific data providers
+
+ -
+ Long-term archival - from scientists for scientists
+
+ -
+
+ Now, publish your Reactions
+
+
+
+
+ )
+}
+
+const StaticsBoard = (params) => {
+ const { publishedStatics } = params;
+ if (publishedStatics && publishedStatics.length !== 0) {
+ const stsSample = publishedStatics.find(p => (p.el_type === 'sample' && p.ex_type === 'sample'));
+ const stsSampleReview = publishedStatics.find(p => (p.el_type === 'sample' && p.ex_type === 'sample-review'));
+ const stsSampleEmbargo = publishedStatics.find(p => (p.el_type === 'sample' && p.ex_type === 'sample-embargo'));
+ const stsReaction = publishedStatics.find(p => (p.el_type === 'reaction' && p.ex_type === 'reaction'));
+ const stsReactionReview = publishedStatics.find(p => (p.el_type === 'reaction' && p.ex_type === 'reaction-review'));
+ const stsReactionEmbargo = publishedStatics.find(p => (p.el_type === 'reaction' && p.ex_type === 'reaction-embargo'));
+ const stsAnalysis = publishedStatics.filter(p => p.el_type === 'analysis');
+ const stsAnalysisSort = stsAnalysis.sort((a, b) => a.e_cnt - b.e_cnt).reverse();
+ const stsAnalysisCnt = stsAnalysisSort
+ .map(e => Number(e.e_cnt)).reduce((accumulator, currentValue) => accumulator + currentValue);
+
+ const csInfo = {
+ borderBottomWidth: '6px', paddingLeft: 'unset', paddingRight: 'unset', borderColor: '#3a9fd3', marginBottom: '10px'
+ };
+ const csHead = {
+ backgroundColor: 'unset', color: 'unset', fontSize: '2rem', border: 'none', textAlign: 'center', paddingLeft: 'unset', paddingRight: 'unset'
+ };
+
+ return (
+
+
+
+
+
+ Samples
+
+
+
+
+ published
+ {stsSample.e_cnt}
+ {stsSampleReview.e_cnt} under review
+ {stsSampleEmbargo.e_cnt} under embargo
+
+
+
+
+
+
+
+ Reactions
+
+
+
+
+ published
+ {stsReaction.e_cnt}
+ {stsReactionReview.e_cnt} under review
+ {stsReactionEmbargo.e_cnt} under embargo
+
+
+
+
+
+
+
+ Analyses
+
+
+
+
+ {stsAnalysisCnt}
+ Top 3:
+
+ {stsAnalysisSort[0].e_cnt} {stsAnalysisSort[0].ex_type}
+ {stsAnalysisSort[1].e_cnt} {stsAnalysisSort[1].ex_type}
+ {stsAnalysisSort[2].e_cnt} {stsAnalysisSort[2].ex_type}
+
+
+
+
+
+ );
+ }
+ return ;
+};
+
+class RepoHome extends Component {
+ constructor(props) {
+ super()
+ this.state = {
+ };
+ this.onChange = this.onChange.bind(this);
+ }
+
+ componentDidMount() {
+ PublicStore.listen(this.onChange);
+ PublicActions.lastPublished();
+ PublicActions.publishedStatics();
+ }
+
+ componentWillUnmount() {
+ PublicStore.unlisten(this.onChange);
+ }
+
+ onChange(PublicState) {
+ if (PublicState.lastPublished || PublicState.publishedStatics) {
+ this.setState(prevState => ({
+ ...prevState,
+ lastPublished: PublicState.lastPublished,
+ publishedStatics: PublicState.publishedStatics
+ }));
+ }
+ }
+
+ render() {
+ const features = {
+ metadata: {
+ fa: 'fa fa-file-code-o',
+ title: 'Metadata',
+ intro: 'Keep your research data findable and accessible and collect descriptions about the data. Based on DataCite Metadata Scheme 4.0.'
+ },
+ doi: {
+ fa: 'fa fa-id-card-o',
+ title: 'DOI',
+ intro: 'Tie Digital Object Identifier (DOI) to your research data. This registers your data in DataCite and makes it identifiable, searchable and citable.'
+ },
+ license: {
+ fa: 'fa fa-creative-commons',
+ title: 'Licenses',
+ intro: 'Choose which license is suitable for your research data to allow others to re-use your data.'
+ },
+ embargo: {
+ fa: 'fa fa-ban',
+ title: 'Embargo',
+ intro: 'Put an embargo on your data. This allows you to delay the publication of your research data. You can release to make your research data visible to the public whenever you are ready.'
+ },
+ // usage: {
+ // fa: 'fa fa-bar-chart',
+ // title: 'Usage',
+ // intro: 'Assess your research data and track the published research data......'
+ // },
+ // oai: {
+ // fa: 'fa fa-tasks',
+ // title: 'OAI Provider',
+ // intro: 'Exposes your research data using the Open Archives Initative Protocol for Metadata Harvesting (OAI-PMH). OAI-PMH is a protocol developed for harvesting metadata and we support representing the metadata of your published research data.'
+ // },
+ dataQuality: {
+ fa: 'fa fa-diamond',
+ title: 'Data Quality',
+ intro: 'Release your research data and pass an internal review that ensures data quality.'
+ },
+ peer: {
+ fa: 'fa fa-external-link',
+ title: 'Peer review',
+ intro: 'Before publication, you can share your data with external reviewers or the publishers.'
+ },
+ store: {
+ fa: 'fa fa-database',
+ title: 'Storage',
+ intro: 'Hosted by an experienced data center, Chemotion repository can store your research data reliably and securely.'
+ },
+ api: {
+ fa: 'fa fa-connectdevelop',
+ title: 'APIs',
+ intro: 'With Chemotion APIs, transfer data easily from your ELN to the repository.'
+ }
+ };
+
+ return (
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Features
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Partners, Affiliations, APIs
+
+
+
+
+
+
+
+ { Infos.map((info, index) => PartnersInfo(info, index)) }
+
+
+
+
+
+
+
+ );
+ }
+}
+
+export default RepoHome;
diff --git a/app/assets/javascripts/libHome/RepoHowTo.js b/app/assets/javascripts/libHome/RepoHowTo.js
new file mode 100644
index 000000000..00c109964
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoHowTo.js
@@ -0,0 +1,177 @@
+import React, { Component } from 'react';
+import { Col, Row } from 'react-bootstrap';
+import { orderBy } from 'lodash';
+import PublicActions from '../components/actions/PublicActions';
+import PublicStore from '../components/stores/PublicStore';
+import ArticleFetcher from '../components/fetchers/ArticleFetcher';
+import { BackSoonPage, DateFormatYMDLong } from '../libHome/RepoCommon';
+
+const renderEditRead = (article, isEditor) => {
+ if (isEditor === true) {
+ return (
+
+ );
+ }
+
+ return (
+
+ );
+};
+
+
+const mainImage = (howto) => {
+ let imageUrl = '';
+ if (typeof (howto) !== 'undefined' && howto
+ && typeof (howto.cover_image) !== 'undefined' && howto.cover_image) {
+ imageUrl = `/howto/${howto.cover_image}`;
+ }
+ return (
+
+ {
+ imageUrl === '' ?
+
+
+ HOW TO
+
+
+ :
+
+ }
+
+
+
+
+
+ ) :
+
+
+
+
+
;
+ }
+}
+
+const NewsColSmall = (param) => {
+ const { howto, isEditor } = param;
+ return (
+
+
+
+
{mainImage(howto)}
+
+
+
+
{howto.title}
+
+
+ {howto.firstParagraph}
+
+
+
+
+
+ {renderEditRead(howto, isEditor)}
+
+
+
+
+ {howto.creator_name}
+ Published on {DateFormatYMDLong(howto.published_at ? howto.published_at : howto.created_at)}
+ , updated on {DateFormatYMDLong(howto.updated_at ? howto.updated_at : howto.published_at)}
+
+
+
+
+
+ {
+ howtos.map(a => ())
+ }
+
+
+
+
+ ) : ;
+};
+
diff --git a/app/assets/javascripts/libHome/RepoHowTo/EditorBtn.js b/app/assets/javascripts/libHome/RepoHowTo/EditorBtn.js
new file mode 100644
index 000000000..a503ce392
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoHowTo/EditorBtn.js
@@ -0,0 +1,67 @@
+
+import React from 'react';
+import PropTypes from 'prop-types';
+import { Button, Tooltip, OverlayTrigger } from 'react-bootstrap';
+import uuid from 'uuid';
+
+const fa = klass => ();
+const FaBtn = props => (
+ {props.tip}}>
+
+
+);
+FaBtn.propTypes = {
+ tip: PropTypes.string.isRequired,
+ txt: PropTypes.string.isRequired,
+ fa: PropTypes.string,
+ place: PropTypes.string,
+ bsStyle: PropTypes.string,
+ bsSize: PropTypes.string,
+ onClick: PropTypes.func,
+};
+FaBtn.defaultProps = {
+ fa: '',
+ place: 'top',
+ bsStyle: 'primary',
+ bsSize: 'small',
+ onClick: null,
+};
+
+const EditorBtn = props => (
+
+ props.onClick('txt')} />
+ props.onClick('img')} />
+
+);
+
+EditorBtn.propTypes = {
+ onClick: PropTypes.func,
+};
+
+EditorBtn.defaultProps = {
+ onClick: null,
+};
+
+const EditorBaseBtn = props => (
+
+ {/* */}
+ props.onClick('save')} />
+ props.onClick('delete')} />
+
+);
+
+EditorBaseBtn.propTypes = {
+ onClick: PropTypes.func,
+};
+
+EditorBaseBtn.defaultProps = {
+ onClick: null,
+};
+
+module.exports = {
+ FaBtn,
+ EditorBtn,
+ EditorBaseBtn,
+};
diff --git a/app/assets/javascripts/libHome/RepoHowTo/EditorImage.js b/app/assets/javascripts/libHome/RepoHowTo/EditorImage.js
new file mode 100644
index 000000000..b1f1609f4
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoHowTo/EditorImage.js
@@ -0,0 +1,43 @@
+import React, { Component } from 'react';
+import PropTypes from 'prop-types';
+import Dropzone from 'react-dropzone';
+
+export default class EditorImage extends Component {
+ handleDrop(files) {
+ if (files && files.length > 0) {
+ this.props.onChange('pfad', files);
+ }
+ }
+ render() {
+ return (
+
+
this.handleDrop(files)}
+ className="dropzone"
+ >
+ {
+ this.props.pfad !== '' ?
+
+
+
Drop Files, or Click to Select.
+ }
+
+
+ this.handleChange(e)}
+ extraToolbarOptions={[['link'], [{ align: '' }, { align: 'center' }, { align: 'right' }, { align: 'justify' }]]}
+ />
+
+ );
+ }
+}
+
+EditorRichText.propTypes = {
+ quill: PropTypes.object,
+ onChange: PropTypes.func,
+};
+
+EditorRichText.defaultProps = {
+ quill: null,
+ onChange: null,
+};
diff --git a/app/assets/javascripts/libHome/RepoHowTo/EditorStelle.js b/app/assets/javascripts/libHome/RepoHowTo/EditorStelle.js
new file mode 100644
index 000000000..1af6593d7
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoHowTo/EditorStelle.js
@@ -0,0 +1,84 @@
+import React, { Component } from 'react';
+import PropTypes from 'prop-types';
+import { Row, Col } from 'react-bootstrap';
+import RepoHowToDragSource from '../RepoHowToDragSource';
+import RepoHowToDropTarget from '../RepoHowToDropTarget';
+import EditorRichText from '../RepoHowTo/EditorRichText';
+import EditorImage from '../RepoHowTo/EditorImage';
+import { FaBtn } from './EditorBtn';
+
+export default class EditorStelle extends Component {
+ handleChange(t, e) {
+ this.props.onChange(t, e, this.props.sid);
+ }
+
+ renderComponent() {
+ let label = '';
+ let component = ;
+ switch (this.props.stelle.art) {
+ case 'txt':
+ label = (Text Section
);
+ component =
+ ( this.handleChange(t, e)}
+ sid={this.props.sid}
+ editor_type={this.props.editor_type}
+ />);
+ break;
+ case 'img':
+ label = (Image Section
);
+ component =
+ ( this.handleChange(t, e)}
+ sid={this.props.sid}
+ editor_type={this.props.editor_type}
+ />);
+ break;
+ default:
+ }
+
+ return (
+
+ {label}
+ {component}
+
+ );
+ }
+
+ render() {
+ return (
+
+
+
+
+
+
+ this.props.onRemove(this.props.sid)} />
+
+
+ {this.renderComponent()}
+
+
+ );
+ }
+}
+
+EditorStelle.propTypes = {
+ sid: PropTypes.number.isRequired,
+ stelle: PropTypes.shape({
+ art: PropTypes.string,
+ quill: PropTypes.object,
+ pfad: PropTypes.string,
+ }).isRequired,
+ onDrop: PropTypes.func.isRequired,
+ onRemove: PropTypes.func.isRequired,
+ onChange: PropTypes.func.isRequired,
+ editor_type: PropTypes.string.isRequired,
+};
+
diff --git a/app/assets/javascripts/libHome/RepoHowToDragSource.js b/app/assets/javascripts/libHome/RepoHowToDragSource.js
new file mode 100644
index 000000000..0873b66a2
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoHowToDragSource.js
@@ -0,0 +1,21 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import { DragSource } from 'react-dnd';
+import DragDropItemTypes from '../components/DragDropItemTypes';
+
+const listSource = {
+ beginDrag(props) { return { sid: props.sid, stelle: props.stelle }; },
+};
+
+const collectSource = (connect, monitor) => ({
+ connectDragSource: connect.dragSource(),
+ isDragging: monitor.isDragging(),
+});
+
+const RepoHowToDragSource = ({ connectDragSource }) => connectDragSource();
+
+export default DragSource(DragDropItemTypes.HOWTO, listSource, collectSource)(RepoHowToDragSource);
+
+RepoHowToDragSource.propTypes = {
+ connectDragSource: PropTypes.func.isRequired,
+};
diff --git a/app/assets/javascripts/libHome/RepoHowToDropTarget.js b/app/assets/javascripts/libHome/RepoHowToDropTarget.js
new file mode 100644
index 000000000..09efb95a6
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoHowToDropTarget.js
@@ -0,0 +1,41 @@
+import React, { Component } from 'react';
+import PropTypes from 'prop-types';
+import { DropTarget } from 'react-dnd';
+import DragDropItemTypes from '../components/DragDropItemTypes';
+
+const stelleTarget = {
+ drop(targetProps, monitor) {
+ const targetTag = { sid: targetProps.sid, stelle: targetProps.stelle };
+ const sourceProps = monitor.getItem();
+ const sourceTag = { sid: sourceProps.sid, stelle: sourceProps.stelle };
+ if (targetTag.sid !== sourceTag.sid) {
+ targetProps.onDrop({ sourceTag, targetTag });
+ }
+ }
+};
+
+const stelleDropCollect = (connect, monitor) => ({
+ connectDropTarget: connect.dropTarget(),
+ isOver: monitor.isOver(),
+ canDrop: monitor.canDrop()
+});
+
+
+class RepoHowToDropTarget extends Component {
+ render() {
+ const { connectDropTarget, isOver, canDrop } = this.props;
+ const className = `editor-field-drop-target${isOver ? ' is-over' : ''}${canDrop ? ' can-drop' : ''}`;
+ return connectDropTarget();
+ }
+}
+
+export default DropTarget(
+ DragDropItemTypes.HOWTO,
+ stelleTarget, stelleDropCollect
+)(RepoHowToDropTarget);
+
+RepoHowToDropTarget.propTypes = {
+ connectDropTarget: PropTypes.func.isRequired,
+ isOver: PropTypes.bool.isRequired,
+ canDrop: PropTypes.bool.isRequired,
+};
diff --git a/app/assets/javascripts/libHome/RepoHowToEditor.js b/app/assets/javascripts/libHome/RepoHowToEditor.js
new file mode 100644
index 000000000..7feca87b5
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoHowToEditor.js
@@ -0,0 +1,435 @@
+import React, { Component } from 'react';
+import { Alert, Jumbotron, Row, Col, Form, FormGroup, FormControl, ControlLabel, Button, InputGroup } from 'react-bootstrap';
+import Dropzone from 'react-dropzone';
+import moment from 'moment';
+import ArticleFetcher from '../components/fetchers/ArticleFetcher';
+import NewsPreviewModal from '../components/common/NewsPreviewModal';
+import PublicStore from '../components/stores/PublicStore';
+import { ConfirmModal } from '../components/common/ConfirmModal';
+import Attachment from '../components/models/Attachment';
+import { EditorTips, DateFormatDMYTime } from '../libHome/RepoCommon';
+import { contentToText } from '../components/utils/quillFormat';
+import { EditorBtn, EditorBaseBtn } from './RepoHowTo/EditorBtn';
+import EditorStelle from './RepoHowTo/EditorStelle';
+
+const extractIntro = (article) => {
+ const result = article.filter(a => a.art === 'txt');
+ if (result.length < 1) {
+ return '';
+ }
+ return (contentToText(result[0].quill) || '').slice(0, 1500);
+};
+
+const confirmText = (
+ Are you sure that you want to delete this ?
+);
+
+const stelle = props => ({ art: props.art || '', quill: props.quill || null, pfad: props.pfad || '' });
+
+export default class RepoHowToEditor extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ howto: PublicStore.getState().howto && PublicStore.getState().howto.key ? { ...PublicStore.getState().howto } : { title: '', content: {}, article: [] },
+ message: { type: '', content: '' },
+ showPreview: false,
+ showDeleteModal: false
+ };
+
+ this.onInputChange = this.onInputChange.bind(this);
+ this.onClickPreview = this.onClickPreview.bind(this);
+ this.onClickCurrentTime = this.onClickCurrentTime.bind(this);
+ this.onClickClose = this.onClickClose.bind(this);
+ this.onClickSave = this.onClickSave.bind(this);
+ this.onClickDelete = this.onClickDelete.bind(this);
+ this.handleDismiss = this.handleDismiss.bind(this);
+ this.onChange = this.onChange.bind(this);
+ this.onShowDeleteModal = this.onShowDeleteModal.bind(this);
+ this.onEditorBtnClick = this.onEditorBtnClick.bind(this);
+ }
+
+ componentDidMount() {
+ PublicStore.listen(this.onChange);
+ }
+
+ componentWillUnmount() {
+ PublicStore.unlisten(this.onChange);
+ }
+
+ onEditorBtnClick(e) {
+ const { howto } = this.state;
+ howto.article.push(stelle({ art: e }));
+ this.setState(howto);
+ }
+
+ onEditorBaseBtnClick(e) {
+ switch (e) {
+ case 'save':
+ this.onClickSave();
+ break;
+ case 'delete':
+ this.onShowDeleteModal();
+ break;
+ default:
+ }
+ }
+
+ onStelleDrop(e) {
+ const { howto } = this.state;
+ const { article } = howto;
+
+ article[e.sourceTag.sid] = e.targetTag.stelle;
+ article[e.targetTag.sid] = e.sourceTag.stelle;
+
+ howto.article = article;
+ this.setState(howto);
+ }
+
+ onStelleRemove(e) {
+ const { howto } = this.state;
+ howto.article.splice(e, 1);
+ this.setState(howto);
+ }
+
+ onStelleInputChange(art, e, sid) {
+ const { howto } = this.state;
+ switch (art) {
+ case 'quill':
+ howto.article[sid].quill = e;
+ this.setState(howto);
+ break;
+ case 'pfad':
+ this.handleImage(e, sid);
+ break;
+ default:
+ break;
+ }
+ }
+
+ onChange(state) {
+ if (state.howto && state.howto.key) {
+ this.setState(prevState => ({
+ ...prevState, howto: state.howto
+ }));
+ } else {
+ this.setState(prevState => ({
+ ...prevState, howto: { title: '', content: {}, article: [] }
+ }));
+ }
+ }
+
+ onInputChange(type, event) {
+ const { howto } = this.state;
+ switch (type) {
+ case 'title':
+ howto.title = event.currentTarget.value;
+ break;
+ case 'content':
+ howto.content = event;
+ break;
+ case 'published_at':
+ howto.published_at = event.currentTarget.value.trim();
+ break;
+ case 'updated_at':
+ howto.updated_at = event.currentTarget.value.trim();
+ break;
+ default:
+ break;
+ }
+ this.setState({ howto });
+ }
+
+ onClickCurrentTime(type) {
+ const currentTime = new Date().toLocaleString('en-GB').split(', ').join(' ');
+ const wrappedEvent = { currentTarget: { value: currentTime } };
+ this.onInputChange(type, wrappedEvent);
+ }
+
+ onClickPreview() {
+ this.setState({ showPreview: true });
+ }
+
+ onClickClose() {
+ this.setState({ showPreview: false });
+ }
+
+ onClickSave() {
+ const { howto } = this.state;
+ let m = moment(howto.published_at, 'DD/MM/YYYY HH:mm:ss');
+ if (howto.published_at && howto.published_at !== '' && !m.isValid()) {
+ howto.published_at = DateFormatDMYTime(howto.published_at);
+ }
+ m = moment(howto.published_at, 'DD/MM/YYYY HH:mm:ss');
+
+ if ((typeof howto.title === 'undefined') || !howto.title || howto.title.trim() === '') {
+ this.setState({ message: { type: 'danger', content: 'Ooops! Title can not be empty!' } });
+ } else if (howto.published_at && howto.published_at !== '' && !m.isValid()) {
+ this.setState({ message: { type: 'danger', content: 'Ooops! Published On is invalid !' } });
+ } else {
+ howto.firstParagraph = extractIntro(howto.article);
+ ArticleFetcher.createOrUpdateHowTo(howto)
+ .then((result) => {
+ if (result.error) {
+ this.setState({ message: { type: 'danger', content: `Ooops! You got an error! ${result.error}` } });
+ } else {
+ this.setState({
+ howto: { title: '', content: {}, article: [] },
+ message: { type: 'success', content: 'Send to How-To successfully!' }
+ });
+ }
+ });
+ }
+ }
+
+ onShowDeleteModal() {
+ this.setState({ showDeleteModal: true });
+ }
+
+ onClickDelete(isDelete) {
+ if (isDelete) {
+ const { howto } = this.state;
+ ArticleFetcher.deleteHowTo(howto)
+ .then((result) => {
+ if (result.error) {
+ this.setState({ message: { type: 'danger', content: `Ooops! You got an error! ${result.error}` } });
+ } else {
+ this.setState({ howto: { title: '', content: {}, article: [] }, message: { type: 'success', content: 'Deleted successfully!' } });
+ }
+ });
+ }
+ this.setState({ showDeleteModal: false });
+ }
+
+ handleImage(files, sid) {
+ const { howto } = this.state;
+ const image = Attachment.fromFile(files[0]);
+ ArticleFetcher.updateEditorImage(image, 'howto')
+ .then((result) => {
+ if (result.error) {
+ this.setState({ message: { type: 'danger', content: `Ooops! You got an error! ${result.error}` } });
+ } else {
+ howto.article[sid].pfad = result.pfad_image;
+ this.setState(howto);
+ }
+ });
+ }
+
+ handleDismiss() {
+ this.setState({ message: { type: '', content: '' } });
+ }
+
+ deleteNewButton() {
+ const { howto } = this.state;
+ if (typeof (howto.key) === 'undefined' || !howto.key || howto.key === 'new') {
+ return (
+
+ );
+ }
+ return (
+
+ );
+ }
+
+ coverImage() {
+ let imageUrl = '';
+ const { howto } = this.state;
+ if (typeof (howto) !== 'undefined' && howto &&
+ typeof (howto.cover_image) !== 'undefined' && howto.cover_image) {
+ imageUrl = `/howto/${howto.cover_image}`;
+ }
+
+ return (
+
+
How-To Cover
+
Click on the image to change the cover
+
+ this.handleFileDrop(files)}
+ style={{ height: '100%', width: '100%', border: '3px dashed lightgray' }}
+ >
+ {
+ imageUrl === '' ?
+
+
+ HOW TO
+
+
+ :
+
+ }
+
+
+
+ {m.content}
+
+
+ :
+
+ );
+ };
+
+ const tPublished = howto.published_at == null ? '' : DateFormatDMYTime(howto.published_at);
+ const tUpdated = howto.updated_at == null ? '' : DateFormatDMYTime(howto.updated_at);
+ const stelles = howto.article.map((s, i) => {
+ return (
+ this.onStelleDrop(e)}
+ onRemove={e => this.onStelleRemove(e)}
+ onChange={(art, e, sid) => this.onStelleInputChange(art, e, sid)}
+ editor_type="howto"
+ />
+ );
+ });
+
+ return (
+
+
+
+
+
+
+
+ {renderAlert(message)}
+ How-To Editor
+
+ Give Chemotion readers some advice
+
+
+
+
+
+
+ {this.coverImage()}
+
+
+ Published on
+
+ this.onInputChange('published_at', event)}
+ />
+
+
+
+
+ Updated on
+
+ this.onInputChange('updated_at', event)}
+ />
+
+
+
+
+
+ Tips:
+
+
+
+
+
+
+
+ HOW TO
+
+
+ );
+ }
+
+ return (
+
+
+
+ );
+ }
+
+ render() {
+ const { howto } = this.state;
+ return (
+
+
+
+
+
+
+
+ {howto.title}
+
+
+ {howto.creator_name}
+
+
Published on {DateFormatYMDLong(howto.published_at ? howto.published_at : howto.created_at)},
+ updated on {DateFormatYMDLong(howto.updated_at ? howto.updated_at : howto.published_at)}
+
+
+
+
+
+
+
+ {
+ howto.article ?
+ howto.article.map((s) => {
+ if (s.art === 'txt') {
+ return
;
+ }
+ if (s.art === 'img') {
+ return (
+
+
+
+
+ );
+ }
+ }) :
+ }
+
+ );
+ }
+}
diff --git a/app/assets/javascripts/libHome/RepoNewsEditor.js b/app/assets/javascripts/libHome/RepoNewsEditor.js
new file mode 100644
index 000000000..99218a3f8
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoNewsEditor.js
@@ -0,0 +1,427 @@
+import React, { Component } from 'react';
+import { Alert, Jumbotron, Row, Col, Form, FormGroup, FormControl, ControlLabel, Button, InputGroup } from 'react-bootstrap';
+import Dropzone from 'react-dropzone';
+import moment from 'moment';
+import ArticleFetcher from '../components/fetchers/ArticleFetcher';
+import NewsPreviewModal from '../components/common/NewsPreviewModal';
+import PublicStore from '../components/stores/PublicStore';
+import { ConfirmModal } from '../components/common/ConfirmModal';
+import Attachment from '../components/models/Attachment';
+import { EditorTips, DateFormatDMYTime, NewsroomTemplate } from '../libHome/RepoCommon';
+import { contentToText } from '../components/utils/quillFormat';
+import { EditorBtn, EditorBaseBtn } from './RepoHowTo/EditorBtn';
+import EditorStelle from './RepoHowTo/EditorStelle';
+
+const extractIntro = (article) => {
+ const result = article.filter(a => a.art === 'txt');
+ if (result.length < 1) {
+ return '';
+ }
+ return (contentToText(result[0].quill) || '').slice(0, 1500);
+};
+
+const confirmText = (
+ Are you sure that you want to delete this ?
+);
+
+const stelle = props => ({ art: props.art || '', quill: props.quill || null, pfad: props.pfad || '' });
+
+export default class RepoNewsEditor extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ news: PublicStore.getState().news && PublicStore.getState().news.key ? { ...PublicStore.getState().news } : NewsroomTemplate,
+ message: { type: '', content: '' },
+ showPreview: false,
+ showDeleteModal: false
+ };
+
+ this.onInputChange = this.onInputChange.bind(this);
+ this.onClickPreview = this.onClickPreview.bind(this);
+ this.onClickCurrentTime = this.onClickCurrentTime.bind(this);
+ this.onClickClose = this.onClickClose.bind(this);
+ this.onClickSave = this.onClickSave.bind(this);
+ this.onClickDelete = this.onClickDelete.bind(this);
+ this.handleDismiss = this.handleDismiss.bind(this);
+ this.onChange = this.onChange.bind(this);
+ this.onShowDeleteModal = this.onShowDeleteModal.bind(this);
+ this.onEditorBtnClick = this.onEditorBtnClick.bind(this);
+ }
+
+ componentDidMount() {
+ PublicStore.listen(this.onChange);
+ }
+
+ componentWillUnmount() {
+ PublicStore.unlisten(this.onChange);
+ }
+
+ onEditorBtnClick(e) {
+ const { news } = this.state;
+ news.article.push(stelle({ art: e }));
+ this.setState(news);
+ }
+
+ onEditorBaseBtnClick(e) {
+ switch (e) {
+ case 'save':
+ this.onClickSave();
+ break;
+ case 'delete':
+ this.onShowDeleteModal();
+ break;
+ default:
+ }
+ }
+
+ onStelleDrop(e) {
+ const { news } = this.state;
+ const { article } = news;
+
+ article[e.sourceTag.sid] = e.targetTag.stelle;
+ article[e.targetTag.sid] = e.sourceTag.stelle;
+
+ news.article = article;
+ this.setState(news);
+ }
+
+ onStelleRemove(e) {
+ const { news } = this.state;
+ news.article.splice(e, 1);
+ this.setState(news);
+ }
+
+ onStelleInputChange(art, e, sid) {
+ const { news } = this.state;
+ switch (art) {
+ case 'quill':
+ news.article[sid].quill = e;
+ this.setState(news);
+ break;
+ case 'pfad':
+ this.handleImage(e, sid);
+ break;
+ default:
+ break;
+ }
+ }
+
+ onChange(state) {
+ if (state.news && state.news.key) {
+ this.setState(prevState => ({
+ ...prevState, news: state.news
+ }));
+ } else {
+ this.setState(prevState => ({
+ ...prevState, news: NewsroomTemplate
+ }));
+ }
+ }
+
+ onInputChange(type, event) {
+ const { news } = this.state;
+ switch (type) {
+ case 'title':
+ news.title = event.currentTarget.value;
+ break;
+ case 'content':
+ news.content = event;
+ break;
+ case 'published_at':
+ news.published_at = event.currentTarget.value.trim();
+ break;
+ case 'updated_at':
+ news.updated_at = event.currentTarget.value.trim();
+ break;
+ default:
+ break;
+ }
+ this.setState({ news });
+ }
+
+ onClickCurrentTime(type) {
+ const currentTime = new Date().toLocaleString('en-GB').split(', ').join(' ');
+ const wrappedEvent = { currentTarget: { value: currentTime } };
+ this.onInputChange(type, wrappedEvent);
+ }
+
+ onClickPreview() {
+ this.setState({ showPreview: true });
+ }
+
+ onClickClose() {
+ this.setState({ showPreview: false });
+ }
+
+ onClickSave() {
+ const { news } = this.state;
+ let m = moment(news.published_at, 'DD/MM/YYYY HH:mm:ss');
+ if (news.published_at && news.published_at !== '' && !m.isValid()) {
+ news.published_at = DateFormatDMYTime(news.published_at);
+ }
+ m = moment(news.published_at, 'DD/MM/YYYY HH:mm:ss');
+
+ if ((typeof news.title === 'undefined') || !news.title || news.title.trim() === '') {
+ this.setState({ message: { type: 'danger', content: 'Ooops! Title can not be empty!' } });
+ } else if (news.published_at && news.published_at !== '' && !m.isValid()) {
+ this.setState({ message: { type: 'danger', content: 'Ooops! Published On is invalid !' } });
+ } else {
+ news.firstParagraph = extractIntro(news.article);
+ ArticleFetcher.createOrUpdate(news)
+ .then((result) => {
+ if (result.error) {
+ this.setState({ message: { type: 'danger', content: `Ooops! You got an error! ${result.error}` } });
+ } else {
+ this.setState({
+ news: NewsroomTemplate,
+ message: { type: 'success', content: 'Send to Newsroom successfully!' }
+ });
+ }
+ });
+ }
+ }
+
+ onShowDeleteModal() {
+ this.setState({ showDeleteModal: true });
+ }
+
+ onClickDelete(isDelete) {
+ if (isDelete) {
+ const { news } = this.state;
+ ArticleFetcher.delete(news)
+ .then((result) => {
+ if (result.error) {
+ this.setState({ message: { type: 'danger', content: `Ooops! You got an error! ${result.error}` } });
+ } else {
+ this.setState({ news: NewsroomTemplate, message: { type: 'success', content: 'Deleted successfully!' } });
+ }
+ });
+ }
+ this.setState({ showDeleteModal: false });
+ }
+
+ handleImage(files, sid) {
+ const { news } = this.state;
+ const image = Attachment.fromFile(files[0]);
+ ArticleFetcher.updateEditorImage(image, 'newsroom')
+ .then((result) => {
+ if (result.error) {
+ this.setState({ message: { type: 'danger', content: `Ooops! You got an error! ${result.error}` } });
+ } else {
+ news.article[sid].pfad = result.pfad_image;
+ this.setState(news);
+ }
+ });
+ }
+
+ handleDismiss() {
+ this.setState({ message: { type: '', content: '' } });
+ }
+
+ deleteNewButton() {
+ const { news } = this.state;
+ if (typeof (news.key) === 'undefined' || !news.key || news.key === 'new') {
+ return (
+
+ );
+ }
+ return (
+
+ );
+ }
+
+ coverImage() {
+ let imageUrl = '/images/chemnews.png';
+ const { news } = this.state;
+ if (typeof (news) !== 'undefined' && news &&
+ typeof (news.cover_image) !== 'undefined' && news.cover_image) {
+ imageUrl = `/newsroom/${news.cover_image}`;
+ }
+
+ return (
+
+
News Cover
+
Click on the image to change the cover
+
+ this.handleFileDrop(files)}
+ style={{ height: '100%', width: '100%', border: '3px dashed lightgray' }}
+ >
+
+
+
+
+ {m.content}
+
+
+ :
+
+ );
+ };
+
+ const tPublished = news.published_at == null ? '' : DateFormatDMYTime(news.published_at);
+ const tUpdated = news.updated_at == null ? '' : DateFormatDMYTime(news.updated_at);
+
+ const stelles = news.article.map((s, i) => {
+ return (
+ this.onStelleDrop(e)}
+ onRemove={e => this.onStelleRemove(e)}
+ onChange={(art, e, sid) => this.onStelleInputChange(art, e, sid)}
+ editor_type="newsroom"
+ />
+ );
+ });
+
+ return (
+
+
+
+
+
+
+
+ {renderAlert(message)}
+ Newsroom Editor
+
+ Chemotion NEWS
+
+
+
+
+
+
+ {this.coverImage()}
+
+
+ Published on
+
+ this.onInputChange('published_at', event)}
+ />
+
+
+
+
+ Updated on
+
+ this.onInputChange('updated_at', event)}
+ />
+
+
+
+
+
+ Tips:
+
+
+
+
+
+
+
+
+
+
+
+ Chemotion News
+
+
+
+
+
+
+
+ {news.title}
+
+
+ {news.creator_name}
+ {DateFormatYMDLong(news.published_at ? news.published_at : news.created_at)}
+
+
+
+ {this.coverImage()}
+
+
+
+
+
+
+
+
+
+ {
+ news.article ?
+ news.article.map((s) => {
+ if (s.art === 'txt') {
+ return
;
+ }
+ if (s.art === 'img') {
+ return (
+
+
+
+
+ );
+ }
+ }) :
+ }
+
+
+
+ );
+ }
+}
diff --git a/app/assets/javascripts/libHome/RepoNewsroom.js b/app/assets/javascripts/libHome/RepoNewsroom.js
new file mode 100644
index 000000000..19e9f6020
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoNewsroom.js
@@ -0,0 +1,186 @@
+import React, { Component } from 'react';
+import { Col, Row } from 'react-bootstrap';
+import { orderBy, slice } from 'lodash';
+import PublicActions from '../components/actions/PublicActions';
+import PublicStore from '../components/stores/PublicStore';
+import ArticleFetcher from '../components/fetchers/ArticleFetcher';
+import { BackSoonPage, DateFormatYMDLong } from '../libHome/RepoCommon';
+
+const renderEditRead = (article, isEditor) => {
+ if (isEditor === true) {
+ return (
+
+ );
+ }
+
+ return (
+
+ );
+};
+
+
+const mainImage = (article) => {
+ let imageUrl = '/images/chemnews.png';
+ if (typeof (article) !== 'undefined' && article
+ && typeof (article.cover_image) !== 'undefined' && article.cover_image) {
+ imageUrl = `/newsroom/${article.cover_image}`;
+ }
+ return (
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ) : |
;
+ }
+}
+
+const LatestNews = ({ article, isEditor }) => {
+ return (
+
+
Latest
+
{mainImage(article)}
+
+
+
{article.title}
+
+
+ {article.firstParagraph}
+
+
+
+ {renderEditRead(article, isEditor)}
+
+
+
+
+
+ {article.creator_name}
+ {DateFormatYMDLong(article.published_at ? article.published_at : article.created_at)}
+
+
+
+
+
+
+
+
+ {
+ articles.map(a => ())
+ }
+
+
+
+
+
+ ) : ;
+};
+
+const NewsTBox = ({ article, isEditor }) => {
+ return (
+
+ -
+
+
{article.title}
+ {article.firstParagraph}
+
+
+ {article.creator_name}
+ {renderEditRead(article, isEditor)}
+
+
+ {DateFormatYMDLong(article.published_at ? article.published_at : article.created_at)}
+
+
+
+ );
+};
diff --git a/app/assets/javascripts/libHome/RepoPubl.js b/app/assets/javascripts/libHome/RepoPubl.js
new file mode 100644
index 000000000..e8e2b3e92
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoPubl.js
@@ -0,0 +1,713 @@
+import React, { Component } from 'react';
+import SVG from 'react-inlinesvg';
+import {
+ Pagination, Table, Form, Col, Row, InputGroup, ButtonGroup, Button,
+ Glyphicon, Grid, Radio, DropdownButton, MenuItem,
+ FormGroup, FormControl, Nav, Navbar, Tooltip, OverlayTrigger,
+ Tabs, Tab
+} from 'react-bootstrap';
+import Select from 'react-select';
+import uuid from 'uuid';
+import UIActions from '../components/actions/UIActions';
+import PublicActions from '../components/actions/PublicActions';
+import PublicStore from '../components/stores/PublicStore';
+import PubchemLabels from '../components/PubchemLabels';
+import RepoElementDetails from './RepoElementDetails';
+import SuggestionsFetcher from '../components/fetchers/SuggestionsFetcher';
+import PublicFetcher from '../components/fetchers/PublicFetcher';
+import AutoCompleteInput from '../components/search/AutoCompleteInput';
+import StructureEditorModal from '../components/structure_editor/StructureEditorModal';
+import Formula from '../components/common/Formula';
+
+
+const pubchemTag = (molecule) => {
+ if (molecule && molecule.tag &&
+ molecule.tag.taggable_data && molecule.tag.taggable_data.pubchem_cid) {
+ return {
+ pubchem_tag: { pubchem_cid: molecule.tag.taggable_data.pubchem_cid }
+ };
+ }
+ return false;
+};
+
+const renderReaction = (element, currentElement) => {
+ const listClass = (currentElement !== null && currentElement.id === element.id) ? 'list_focus_on' : 'list_focus_off';
+ return (
+ PublicActions.displayReaction(element.id)}
+ >
+ |
+
+
+
+ |
+
+ );
+};
+
+export default class RepoPubl extends Component {
+ constructor(props) {
+ super(props);
+
+ this.state = {
+ // ...PublicStore.getState(),
+ page: 1,
+ perPage: 10,
+ showStructureEditor: false,
+ isSearch: false,
+ defaultSearchValue: null,
+ selectType: 'all',
+ inputDisabled: false,
+ queryMolfile: null,
+ searchType: 'similar',
+ tanimotoThreshold: 0.7,
+ listType: 'reaction',
+ advFlag: false,
+ advType: 'Authors',
+ advValue: [],
+ selectUsers: [],
+ key: uuid.v4(),
+ showSearch: false
+ };
+
+ this.onChange = this.onChange.bind(this);
+ this.changeSort = this.changeSort.bind(this);
+ this.handleClearSearchSelection = this.handleClearSearchSelection.bind(this);
+ this.handleStructureEditorCancel = this.handleStructureEditorCancel.bind(this);
+ this.handleSelectAdvValue = this.handleSelectAdvValue.bind(this);
+ this.showAdvancedSearch = this.showAdvancedSearch.bind(this);
+ this.closeAdvancedSearch = this.closeAdvancedSearch.bind(this);
+ this.renderAdvancedSearch = this.renderAdvancedSearch.bind(this);
+ this.advSearchClick = this.advSearchClick.bind(this);
+ this.handleSelectAdvType = this.handleSelectAdvType.bind(this);
+ this.loadAdvValuesByName = this.loadAdvValuesByName.bind(this);
+ this.handleElementSelection = this.handleElementSelection.bind(this);
+ this.handleShowSearch = this.handleShowSearch.bind(this);
+ }
+
+ componentDidMount() {
+ PublicActions.selectPublicCollection.defer();
+ PublicStore.listen(this.onChange);
+ PublicActions.getReactions.defer();
+ }
+
+ componentWillUnmount() {
+ PublicStore.unlisten(this.onChange);
+ }
+
+ onChange(state) {
+ this.setState(prevState => ({ ...prevState, ...state }));
+ }
+
+ handleSearchTypeChange(e) {
+ this.setState({ searchType: e.target && e.target.value });
+ }
+
+ handleStructureEditorCancel() {
+ this.setState({ isSearch: false });
+ this.hideStructureEditor();
+ }
+
+ showStructureEditor() {
+ this.setState({ showStructureEditor: true });
+ }
+
+ hideStructureEditor() {
+ this.setState({ showStructureEditor: false });
+ }
+
+ showAdvancedSearch() {
+ this.setState({ advFlag: true });
+ }
+
+ handleSelectAdvType(val) {
+ if (val) { this.setState({ advType: val, advValue: null }); }
+ }
+
+ onPerPageChange(e) {
+ this.setState({ perPage: e.target.value }, () => this.getList());
+ }
+
+ getList(ps = {}) {
+ const {
+ advFlag, advType, advValue,
+ isSearch,
+ selectType, selection,
+ page, perPage,
+ } = this.state;
+ let params = {
+ advFlag,
+ advType,
+ advValue,
+ elementType: selectType,
+ page,
+ perPage,
+ selection,
+ ...ps
+ };
+ if (isSearch) {
+ switch (this.state.listType) {
+ case 'reaction':
+ PublicActions.getSearchReactions(params);
+ break;
+ case 'sample':
+ PublicActions.getSearchMolecules(params);
+ break;
+ case 'scheme':
+ params = { ...params, collectionId: 'schemeOnly' };
+ PublicActions.getSearchReactions(params);
+ break;
+ default:
+ }
+ return;
+ }
+ switch (this.state.listType) {
+ case 'reaction':
+ params = { ...params, schemeOnly: false };
+ PublicActions.getReactions(params);
+ break;
+ case 'sample':
+ PublicActions.getMolecules(params);
+ break;
+ case 'scheme':
+ params = { ...params, schemeOnly: true };
+ PublicActions.getReactions(params);
+ break;
+ default:
+ PublicActions.getReactions(params);
+ }
+ UIActions.clearSearchSelection();
+ }
+
+ handleClearSearchSelection() {
+ this.setState({
+ defaultSearchValue: null,
+ searchType: 'similar',
+ tanimotoThreshold: 0.7,
+ queryMolfile: null,
+ isSearch: false,
+ key: uuid.v4(),
+ page: 1
+ }, () => this.getList());
+ }
+
+ handleElementSelection(event) {
+ this.setState({ selectType: event.toLowerCase() });
+ }
+
+ handleShowSearch() {
+ const { showSearch, advFlag } = this.state;
+ this.setState({ showSearch: !showSearch, advFlag: !advFlag });
+ }
+
+ closeAdvancedSearch() {
+ this.setState({ advType: 'Authors', advValue: null, page: 1 }, () => this.getList());
+ }
+
+
+ loadAdvValuesByName(input) {
+ if (!input || input.length < 3) {
+ return Promise.resolve({ options: [] });
+ }
+ return PublicFetcher.fetchAdvancedValues(this.state.advType, input)
+ .then(res => ({
+ options: res.result
+ .map(u => ({
+ value: u.key,
+ name: u.name,
+ label: u.label
+ }))
+ })).catch((errorMessage) => {
+ console.log(errorMessage);
+ });
+ }
+
+ changeSort(e) {
+ this.setState({
+ // isSearch: false,
+ // defaultSearchValue: null,
+ page: 1,
+ listType: e
+ }, () => this.getList());
+ }
+
+
+ renderMolecule(molecule) {
+ const {
+ advFlag, advType, advValue, currentElement
+ } = this.state;
+ const pubchemInfo = pubchemTag(molecule);
+ const svgPathSample = molecule.sample_svg_file
+ ? `/images/samples/${molecule.sample_svg_file}`
+ : `/images/molecules/${molecule.molecule_svg_file}`;
+ const listClass = (currentElement !== null && currentElement.molecule && currentElement.molecule.id === molecule.id) ? 'list_focus_on' : 'list_focus_off';
+ return (
+ PublicActions.displayMolecule(molecule.id, advFlag, advType, advValue)}
+ >
+ |
+
+
+
+
+
+
+ {molecule.iupac_name}
+ {pubchemInfo ? : null }
+
+ |
+
+ );
+ }
+
+ renderMenuItems() {
+ const elements = [
+ 'All', 'Samples', 'Reactions'
+ ];
+
+ const menu = elements.map(element => (
+
+ ));
+
+ return menu;
+ }
+
+
+ handleTanimotoChange(e) {
+ const val = e.target && e.target.value;
+ if (!isNaN(val - val)) {
+ this.setState({ tanimotoThreshold: val });
+ }
+ }
+
+ handleSelectionChange(selection) {
+ this.setState({
+ isSearch: true,
+ selection,
+ page: 1
+ }, () => this.getList());
+ }
+
+ structureSearch(molfile) {
+ const {
+ page,
+ perPage,
+ searchType,
+ selectType,
+ tanimotoThreshold
+ } = this.state;
+
+ const tanimoto = (tanimotoThreshold <= 0 || tanimotoThreshold > 1) ? 0.3 : tanimotoThreshold;
+ const selection = {
+ molfile,
+ search_type: searchType,
+ tanimoto_threshold: tanimoto,
+ search_by_method: 'structure',
+ structure_search: true
+ };
+
+ this.setState(
+ {
+ isSearch: true,
+ selection,
+ page: 1,
+ defaultSearchValue: 'structure',
+ queryMolfile: molfile
+ },
+ () => PublicActions.getSearchMolecules({ // NB: use getList instead?
+ elementType: selectType,
+ page,
+ perPage,
+ selection,
+ })
+ );
+ }
+
+ handleStructureEditorSave(molfile) {
+ this.hideStructureEditor();
+ if (molfile) {
+ const molfileLines = molfile.match(/[^\r\n]+/g);
+ if (molfileLines && molfileLines[1].trim()[0] !== 0) {
+ this.structureSearch(molfile);
+ } else {
+ // TODO: clear search?
+ }
+ }
+ }
+
+ perPageInput() {
+ const { perPage } = this.state;
+ return (
+
+ );
+ }
+
+ onPaginationSelect(eventKey) {
+ const { pages } = this.state;
+ if (eventKey > 0 && eventKey <= pages) {
+ this.setState({ page: eventKey }, () => this.getList());
+ }
+ }
+
+ pagination() {
+ const { page, pages } = this.state;
+ const items = [];
+ const minPage = Math.max(page - 2, 1);
+ const maxPage = Math.min(minPage + 4, pages);
+ items.push( this.onPaginationSelect(1)} />);
+ if (page > 1) {
+ items.push( this.onPaginationSelect(page - 1)} />);
+ }
+ for (let tpage = minPage; tpage <= maxPage; tpage += 1) {
+ items.push((
+ this.onPaginationSelect(tpage)}
+ >
+ {tpage}
+
+ ));
+ }
+
+ if (pages > maxPage) {
+ items.push();
+ }
+ if (page !== pages) {
+ items.push( this.onPaginationSelect(page + 1)} />);
+ }
+ items.push( this.onPaginationSelect(pages)} />);
+
+ return ;
+ }
+
+
+ renderSwitch() {
+ const { listType } = this.state;
+ return (
+
+
+
+
+
+ );
+ }
+
+ renderSelectValues() {
+ const { advValue } = this.state;
+ return (
+
+ );
+ }
+
+ handleSelectAdvValue(val) {
+ if (val) {
+ this.setState({ advValue: val });
+ }
+ }
+
+ advSearchClick() {
+ this.setState({ page: 1 }, () => this.getList());
+ }
+
+ renderAdvancedSearch() {
+ const { advFlag, advType, advValue } = this.state;
+ if (advFlag === true) {
+ this.listOptions = [
+ {
+ value: 'Authors',
+ label: 'by authors'
+ },
+ {
+ value: 'Ontologies',
+ label: 'by analysis type'
+ }
+ ];
+ return (
+
+
+
+
+
+
+
+
+
+ Advanced Search}>
+
+
+ Reset Advanced Search}>
+
+
+
+
+
+
+
+
+
+ { this.searchSubstructureRadio = input; }}
+ value="sub"
+ checked={this.state.searchType === 'sub'}
+ onChange={e => this.handleSearchTypeChange(e)}
+ >
+ Substructure Search
+
+
+
+
+ );
+
+ const inputAttributes = {
+ placeholder: 'IUPAC, InChI, SMILES, ...',
+ style: { minWidth: 168, maxWidth: 268 }
+ };
+
+ const suggestionsAttributes = {
+ style: {
+ marginTop: 15,
+ width: 398,
+ maxHeight: 400
+ }
+ };
+
+ const searchTooltip = Select search type;
+
+ const innerDropdown = (
+
+ }
+ >
+ {this.renderMenuItems()}
+
+
+ );
+
+ return (
+
+
+
+
+ {
+ this.state.showSearch ?
+ (
+
+
+
+
SuggestionsFetcher.fetchSuggestionsForCurrentUser(
+ this.state.selectType.toLowerCase(), input, 'public', false)}
+ ref={(input) => { this.autoComplete = input; }}
+ onSelectionChange={selection => this.handleSelectionChange(selection)}
+ buttonBefore={innerDropdown}
+ buttonAfter={buttonAfter}
+ />
+
+ ) :
+ (
+
+ )
+ }
+
+
+
+
+
+
+
+
+
+
+
+ {this.pagination()}
+ {this.perPageInput()}
+
+
+
+
+
+
+
+
+
+ );
+ }
+}
diff --git a/app/assets/javascripts/libHome/RepoReactionDetails.js b/app/assets/javascripts/libHome/RepoReactionDetails.js
new file mode 100644
index 000000000..786e59478
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoReactionDetails.js
@@ -0,0 +1,556 @@
+import React, { Component } from 'react';
+import SVG from 'react-inlinesvg';
+import {
+ Panel,
+ Row,
+ Col,
+ Jumbotron,
+} from 'react-bootstrap';
+import PropTypes from 'prop-types';
+import { head, filter } from 'lodash';
+import ArrayUtils from '../components/utils/ArrayUtils';
+import {
+ AuthorList,
+ AuthorTitle,
+ AffiliationList,
+ CalcDuration,
+ ChemotionId,
+ ClosePanel,
+ CommentBtn,
+ ContributorInfo,
+ DateInfo,
+ Doi,
+ ReactionTable,
+ ReactionRinChiKey,
+ ReactionProperties,
+ ReactionTlc,
+ RenderAnalysisHeader,
+ RenderPublishAnalysesPanel,
+ IconLicense,
+ IconToMyDB,
+ AnalysesTypeJoinLabel,
+ SchemeWord,
+} from './RepoCommon';
+import LoadingActions from '../components/actions/LoadingActions';
+import PublicActions from '../components/actions/PublicActions';
+import QuillViewer from '../components/QuillViewer';
+import { Citation, literatureContent, RefByUserInfo } from '../components/LiteratureCommon';
+import RepoReactionSchemeInfo from './RepoReactionSchemeInfo';
+import RepoReviewButtonBar from './RepoReviewButtonBar';
+import RepoCommentModal from '../components/common/RepoCommentModal';
+import RepoReviewModal from '../components/common/RepoReviewModal';
+
+export default class RepoReactionDetails extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ showScheme: true,
+ showRinchi: false,
+ showProp: true,
+ showTlc: true,
+ showSA: true,
+ showRA: {},
+ showReviewModal: false,
+ btnAction: '',
+ showCommentModal: false,
+ commentField: '',
+ originInfo: '',
+ };
+
+ this.toggleScheme = this.toggleScheme.bind(this);
+ this.toggleRinchi = this.toggleRinchi.bind(this);
+ this.toggleProp = this.toggleProp.bind(this);
+ this.toggleTlc = this.toggleTlc.bind(this);
+ this.toggleSA = this.toggleSA.bind(this);
+ this.toggleRA = this.toggleRA.bind(this);
+ this.handleToggle = this.handleToggle.bind(this);
+ this.handleReviewBtn = this.handleReviewBtn.bind(this);
+ this.handleSubmitReview = this.handleSubmitReview.bind(this);
+ this.handleCommentBtn = this.handleCommentBtn.bind(this);
+ this.handleSubmitComment = this.handleSubmitComment.bind(this);
+ }
+
+ toggleScheme() {
+ const { showScheme } = this.state;
+ this.setState({ showScheme: !showScheme });
+ }
+
+ toggleRinchi() {
+ const { showRinchi } = this.state;
+ this.setState({ showRinchi: !showRinchi });
+ }
+
+ toggleProp() {
+ const { showProp } = this.state;
+ this.setState({ showProp: !showProp });
+ }
+
+ toggleTlc() {
+ const { showTlc } = this.state;
+ this.setState({ showTlc: !showTlc });
+ }
+
+ toggleSA() {
+ const { showSA } = this.state;
+ this.setState({ showSA: !showSA });
+ }
+
+ toggleRA(idx = -1) {
+ const { showRA } = this.state;
+ if (idx in showRA && showRA[idx] === false) {
+ showRA[idx] = true;
+ } else {
+ showRA[idx] = false;
+ }
+ this.setState({ showRA });
+ }
+
+ handleToggle(type) {
+ switch (type) {
+ case 'Scheme':
+ this.toggleScheme();
+ break;
+ case 'Rinchi':
+ this.toggleRinchi();
+ break;
+ case 'Prop':
+ this.toggleProp();
+ break;
+ default:
+ break;
+ }
+ }
+
+ handleReviewBtn(showReviewModal, btnAction) {
+ this.setState({ showReviewModal, btnAction });
+ }
+
+ handleSubmitReview(elementId, comments, summary, feedback, action) {
+ LoadingActions.start();
+ PublicActions.reviewPublish(elementId, 'reaction', comments, summary, feedback, action);
+ this.setState({ showReviewModal: false });
+ }
+
+ handleCommentBtn(show, field, orgInfo) {
+ this.setState({
+ showCommentModal: show,
+ commentField: field,
+ originInfo: orgInfo
+ });
+ }
+
+ handleSubmitComment(elementId, elementType, field, comment, origInfo) {
+ LoadingActions.start();
+ const cinfo = {};
+ if (typeof (cinfo[field]) === 'undefined') {
+ cinfo[field] = {};
+ }
+ const today = new Date();
+ const d = `${today.getDate()}-${today.getMonth() + 1}-${today.getFullYear()} `;
+ const t = `${today.getHours()}:${today.getMinutes() + 1}:${today.getSeconds()} `;
+ const dt = `${d} ${t}`;
+ if (this.props.reviewLevel === 2) {
+ cinfo[field].feedback = comment;
+ cinfo[field].origInfo = origInfo;
+ cinfo[field].feedback_time = dt;
+ } else {
+ cinfo[field].comment = comment;
+ cinfo[field].origInfo = origInfo;
+ cinfo[field].comment_time = dt;
+ }
+
+ PublicActions.updateComment(elementId, elementType, cinfo);
+ this.setState({ showCommentModal: false });
+ }
+
+ reactionInfo(reaction) {
+ const {
+ showScheme, showRinchi, showProp, showTlc
+ } = this.state;
+ const {
+ canComment,
+ reviewLevel,
+ submitter,
+ pubState,
+ comments,
+ } = this.props;
+
+ const svgPath = `/images/reactions/${reaction.reaction_svg_file}`;
+ const content = reaction.description;
+ const additionInfo = reaction.observation;
+
+ const descContent = (content && content.ops && content.ops.length > 0
+ && content.ops[0].insert) ? content.ops[0].insert.trim() : '';
+ let descQV = (
+ Description:
+ );
+ if (descContent === '') descQV = '';
+
+ const addinfoContent = (additionInfo && additionInfo.ops && additionInfo.ops.length > 0 &&
+ additionInfo.ops[0].insert) ? additionInfo.ops[0].insert.trim() : '';
+ let addQV = (
+ Additional information for publication and purification details:
+
+ );
+ if (addinfoContent === '') addQV = '';
+
+ const temperature = reaction.temperature ? `${reaction.temperature.userText} ${reaction.temperature.valueUnit}` : '';
+ const duration = CalcDuration(reaction);
+ const properties = `Status:[${reaction.status}]; Temperature:[${temperature}]; Duration: [${duration}]`;
+ const tlc = `Solvents (parts):[${reaction.tlc_solvents || ''}]; Rf-Value:[${reaction.rf_value || ''}]; TLC-Description: [${reaction.tlc_description || ''}]`;
+
+ const bodyAttrs = {
+ style: {
+ fontSize: '90%',
+ paddingBottom: 'unset'
+ }
+ };
+ const schemeOnly = (reaction && reaction.publication && reaction.publication.taggable_data &&
+ reaction.publication.taggable_data.scheme_only === true) || false;
+ if (schemeOnly) {
+ if (canComment) {
+ return (
+
+ );
+ }
+ return (
+
+ );
+ }
+ return (
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ {descQV}
+
+
+
+ {addQV}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ );
+ }
+
+ renderAnalysisView(container, type, product = null, idx = -1, isLogin = false) {
+ if (typeof (container) === 'undefined' || !container) {
+ return ;
+ }
+
+ const analyses = ArrayUtils.sortArrByIndex(head(filter(container.children, o => o.container_type === 'analyses')).children);
+ const show = this.state.showRA[idx];
+ if (typeof (analyses) === 'undefined' || !analyses || analyses.length === 0) {
+ return ;
+ }
+
+ const productHeader = (typeof (product) !== 'undefined' && product) ? : ;
+
+ const analysesView = analyses.map((analysis) => {
+ const kind = analysis.extended_metadata && analysis.extended_metadata.kind && analysis.extended_metadata['kind'].split('|').pop().trim();
+ return (
+
+
+
+
+ );
+ });
+
+ return (
+
+
this.toggleRA(idx)}
+ >
+ Analyses
+
+
+
+ {AnalysesTypeJoinLabel(analyses, type)}
+
+
{ }}>
+
+
+ {productHeader}
+ {analysesView}
+
+
+
+
+ {this.renderAnalysisView(product.container, 'Sample', product, idx, isLogin)}
+
+ ));
+ }
+
+ render() {
+ const {
+ reaction,
+ isPublished,
+ canComment,
+ reviewLevel,
+ submitter,
+ pubState,
+ comments,
+ summary,
+ feedback,
+ canClose,
+ } = this.props;
+ let { buttons } = this.props;
+
+ if (typeof (reaction) === 'undefined' || !reaction) {
+ return ;
+ }
+
+ const taggData = (reaction && reaction.publication && reaction.publication.taggable_data) || {};
+ const pubData = (reaction && reaction.publication) || {};
+ const doi = (reaction && reaction.doi) || {};
+
+ const aId = [].concat.apply([], taggData.affiliation_ids);
+ const affiliationMap = {};
+ const { literatures } = reaction;
+ const references = literatures ? literatures.map(lit => (
+
+
+
+
+
+ )) : [];
+ const refArray = [];
+ let referencesText = '';
+ if (literatures) {
+ literatures.forEach((lit) => {
+ const content = literatureContent(lit, true);
+ refArray.push(content);
+ });
+ referencesText = refArray.join('');
+ }
+
+ let aCount = 0;
+ aId.map((e) => {
+ if (!affiliationMap[e]) {
+ aCount += 1;
+ affiliationMap[e] = aCount;
+ }
+ });
+ const license = taggData.license || 'CC BY-SA';
+
+ const schemeOnly = (reaction && reaction.publication && reaction.publication.taggable_data &&
+ reaction.publication.taggable_data.scheme_only === true) || false;
+
+ let showDOI = ;
+ if (schemeOnly) {
+ buttons = ['Decline', 'Comments', 'Accept'];
+ showDOI = '';
+ }
+
+ const idyLogin = typeof reaction.isLogin === 'undefined' ? true : reaction.isLogin;
+
+ return (
+
+
+
+ {
+ canComment ?
+ : ''
+ }
+ {canClose ? : ''}
+
+ {schemeOnly ? : ''}
+
+ {IconLicense(license, (taggData.author_ids && (taggData.author_ids.length > 1)))}
+
+
+
+
+ {AuthorTitle(taggData.author_ids)}
+
+
+
+ {showDOI}
+
+
+
+ Reference{references.length > 1 ? 's' : null}:
+
+
+
+
+ {this.reactionInfo(reaction)}
+
+ {schemeOnly ? '' : this.renderAnalysisView(reaction.container, 'Reaction')}
+ {schemeOnly ? '' : this.renderProductAnalysisView(reaction.products, idyLogin)}
+
+
+ {
+ canComment ? (
+
+ this.setState({ showCommentModal: false })}
+ />
+ this.setState({ showReviewModal: false })}
+ />
+
+ ) : ''
+ }
+
+
+
+
+
+
+
+
+ props.onToggle('Scheme')}
+ show={props.showScheme}
+ isPublic
+ bodyAttrs={props.bodyAttrs}
+ />
+
+
+
+
+
+ {descQV}
+
+
+
+
+
+ props.onToggle('Rinchi')}
+ show={props.showRinchi}
+ bodyAttrs={props.bodyAttrs}
+ />
+
+
+
+
+ );
+};
+
+RepoReactionSchemeInfo.propTypes = {
+ reaction: PropTypes.object.isRequired,
+ svgPath: PropTypes.string.isRequired,
+ showScheme: PropTypes.bool.isRequired,
+ showRinchi: PropTypes.bool.isRequired,
+ showProp: PropTypes.bool.isRequired,
+ bodyAttrs: PropTypes.object.isRequired,
+ onToggle: PropTypes.func.isRequired,
+ comments: PropTypes.object,
+ reviewLevel: PropTypes.number,
+ pubState: PropTypes.string,
+ submitter: PropTypes.string,
+ propInfo: PropTypes.string,
+ onComment: PropTypes.func,
+ canComment: PropTypes.bool,
+};
+
+RepoReactionSchemeInfo.defaultProps = {
+ comments: {},
+ reviewLevel: 0,
+ pubState: '',
+ submitter: '',
+ propInfo: '',
+ onComment: () => {},
+ canComment: false
+};
+
+export default RepoReactionSchemeInfo;
diff --git a/app/assets/javascripts/libHome/RepoReview.js b/app/assets/javascripts/libHome/RepoReview.js
new file mode 100644
index 000000000..620fcabd5
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoReview.js
@@ -0,0 +1,236 @@
+import React, { Component } from 'react';
+import SVG from 'react-inlinesvg';
+import { Table, Col, Row, Navbar, DropdownButton, MenuItem, ButtonGroup, Pagination, Form, FormGroup, InputGroup, FormControl } from 'react-bootstrap';
+import RepoReviewDetails from './RepoReviewDetails';
+import PublicActions from '../components/actions/PublicActions';
+import PublicStore from '../components/stores/PublicStore';
+import { IconToMyDB, SvgPath, ElStateLabel, ElSubmitTime, SchemeWord } from './RepoCommon';
+
+const renderElement = (e, currentElement) => {
+ if (e.type === 'Reaction') {
+ const listClass = (currentElement !== null && currentElement.reaction && currentElement.reaction.id === e.id) ? 'list_focus_on' : 'list_focus_off';
+ const schemeOnly = (e && e.scheme_only === true) || false;
+ return (
+ PublicActions.displayReviewReaction(e.id)}
+ >
+ |
+
+ {schemeOnly ? : ''} {e.title}
+
+ By {e.published_by} at
+ {ElSubmitTime(e.submit_at)} {ElStateLabel(e.state)} {ElStateLabel(e.embargo)}
+
+
+
+ |
+
+ );
+ }
+ const listClass = (currentElement !== null && currentElement.sample && currentElement.sample.id === e.id) ? 'list_focus_on' : 'list_focus_off';
+ return (
+ PublicActions.displayReviewSample(e.id)}
+ >
+ |
+
+ {e.title}
+
+ By {e.published_by} at
+ {ElSubmitTime(e.submit_at)} {ElStateLabel(e.state)} {ElStateLabel(e.embargo)}
+
+
+
+ |
+
+ );
+};
+
+const defaultState = 'pending';
+
+export default class RepoReview extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ page: 1,
+ perPage: 10,
+ elements: [],
+ currentElement: null,
+ selectType: 'All',
+ selectState: defaultState
+ };
+ this.onChange = this.onChange.bind(this);
+ this.handleElementSelection = this.handleElementSelection.bind(this);
+ }
+
+ componentDidMount() {
+ PublicStore.listen(this.onChange);
+ PublicActions.getElements.defer();
+ }
+
+ componentWillUnmount() {
+ PublicStore.unlisten(this.onChange);
+ }
+
+ onChange(state) {
+ this.setState(prevState => ({ ...prevState, ...state }));
+ }
+
+ handleElementSelection(t, event) {
+ const { page, perPage } = this.state;
+ if (t === 'type') {
+ this.setState({ selectType: event });
+ PublicActions.getElements(event,this.state.selectState, 1, perPage);
+ } else if (t === 'state') {
+ this.setState({ selectState: event });
+ PublicActions.getElements(this.state.selectType, event, 1, perPage);
+ }
+ }
+
+
+ onPerPageChange(e) {
+ const { page, selectType, selectState } = this.state;
+ const perPage = e.target.value;
+ this.setState({ perPage });
+ PublicActions.getElements(selectType, selectState, page, perPage);
+ }
+
+ perPageInput() {
+ const { perPage } = this.state;
+ return (
+
+ );
+ }
+
+ onPaginationSelect(eventKey) {
+ const { pages, perPage, selectType, selectState } = this.state;
+ if (eventKey > 0 && eventKey <= pages) {
+ PublicActions.getElements(selectType, selectState, eventKey, perPage);
+ }
+ }
+
+ pagination() {
+ const { page, pages } = this.state;
+ const items = [];
+ const minPage = Math.max(page - 2, 1);
+ const maxPage = Math.min(minPage + 4, pages);
+ items.push( this.onPaginationSelect(1)} />);
+ if (page > 1) {
+ items.push( this.onPaginationSelect(page - 1)} />);
+ }
+ for (let tpage = minPage; tpage <= maxPage; tpage += 1) {
+ items.push((
+ this.onPaginationSelect(tpage)}
+ >
+ {tpage}
+
+ ));
+ }
+
+ if (pages > maxPage) {
+ items.push();
+ }
+ if (page !== pages) {
+ items.push( this.onPaginationSelect(page + 1)} />);
+ }
+ items.push( this.onPaginationSelect(pages)} />);
+
+ return ;
+ }
+
+ renderMenuItems(t, elements) {
+ const menu = elements.map(element => (
+
+ ));
+ return menu;
+ }
+
+ renderSearch() {
+ const customClass = '.btn-unified';
+ const optSearchType = ['All', 'Samples', 'Reactions'];
+ const optSearchState = ['pending', 'reviewed', 'accepted'];
+
+ const filterDropdown = (
+
+
+ {this.renderMenuItems('type', optSearchType)}
+
+
+ {this.renderMenuItems('state', optSearchState)}
+
+
+ );
+
+ return (
+
+ {filterDropdown}
+
+ );
+ }
+
+ render() {
+ const { elements, currentElement } = this.state;
+ return (
+
+
+
+ {this.renderSearch()}
+
+
+
+
+
+
+ {((typeof (elements) !== 'undefined' && elements) || []).map(r => renderElement(r, currentElement)) }
+
+
+
+
+
+ {this.pagination()}
+ {this.perPageInput()}
+
+
+
+ );
+ }
+}
diff --git a/app/assets/javascripts/libHome/RepoReviewButtonBar.js b/app/assets/javascripts/libHome/RepoReviewButtonBar.js
new file mode 100644
index 000000000..88d13bae8
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoReviewButtonBar.js
@@ -0,0 +1,129 @@
+import React from 'react';
+import {
+ Button,
+ ButtonToolbar,
+ OverlayTrigger,
+ Tooltip
+} from 'react-bootstrap';
+import PropTypes from 'prop-types';
+import RepoMetadataModal from '../components/common/RepoMetadataModal';
+
+const showButton = (btn, func, reviewLevel, pubState) => {
+ let title = btn;
+ let btnBsStyle = '';
+ let btnIcon = '';
+ let btnTooltip = '';
+ switch (btn) {
+ case 'Accept':
+ btnBsStyle = 'primary';
+ btnIcon = 'fa fa-paper-plane';
+ btnTooltip = 'Accept publication';
+ break;
+ case 'Review':
+ btnBsStyle = 'info';
+ btnIcon = 'fa fa-exchange';
+ btnTooltip = 'Review publication, modification required for submittor';
+ break;
+ case 'Submit':
+ btnBsStyle = 'info';
+ btnIcon = 'fa fa-play';
+ btnTooltip = 'Submit for publication';
+ break;
+ case 'Decline':
+ btnBsStyle = 'default';
+ btnIcon = 'fa fa-eject';
+ if (reviewLevel === 2) {
+ btnTooltip = 'Withdraw publication';
+ title = 'Withdraw';
+ } else if (reviewLevel === 3) {
+ btnTooltip = 'Reject publication';
+ title = 'Reject';
+ }
+ break;
+ default:
+ break;
+ }
+ return ((reviewLevel === 3 && pubState === 'pending' && btn !== 'Submit') || (reviewLevel === 2 && pubState === 'reviewed' && (btn === 'Submit' || btn === 'Decline'))) ? (
+ {btnTooltip}}
+ >
+
+
+ ) : ;
+};
+
+const showCommentButton = (btn, func, comments, summary, feedback) => {
+ let hasComments = false;
+ if (Object.keys(comments).length > 0
+ || (summary && summary.length > 0)
+ || (feedback && feedback.length > 0)) {
+ hasComments = true;
+ }
+ return (
+
+ );
+};
+
+const RepoReviewButtonBar = props =>
+ (
+
+ {
+ props.buttons.filter(b => b === 'Comments').map(b =>
+ showCommentButton(b, props.buttonFunc, props.comments, props.summary, props.feedback))
+ }
+ {
+ props.buttons.filter(b => b !== 'Comments').map(b =>
+ showButton(b, props.buttonFunc, props.reviewLevel, props.pubState))
+ }
+
+
+ );
+
+RepoReviewButtonBar.propTypes = {
+ element: PropTypes.shape({
+ id: PropTypes.number,
+ elementType: PropTypes.string
+ }).isRequired,
+ buttons: PropTypes.arrayOf(PropTypes.string),
+ buttonFunc: PropTypes.func,
+ reviewLevel: PropTypes.number,
+ pubState: PropTypes.string,
+ comments: PropTypes.object,
+ summary: PropTypes.string,
+ feedback: PropTypes.string
+};
+
+
+RepoReviewButtonBar.defaultProps = {
+ buttons: ['Decline', 'Comments', 'Review', 'Submit', 'Accept'],
+ buttonFunc: () => { },
+ reviewLevel: 0,
+ pubState: '',
+ comments: {},
+ summary: '',
+ feedback: ''
+};
+
+export default RepoReviewButtonBar;
diff --git a/app/assets/javascripts/libHome/RepoReviewCommon.js b/app/assets/javascripts/libHome/RepoReviewCommon.js
new file mode 100644
index 000000000..790e6324e
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoReviewCommon.js
@@ -0,0 +1,98 @@
+import React from 'react';
+import PropTypes from 'prop-types';
+import { Alert } from 'react-bootstrap';
+import { startsWith } from 'lodash';
+
+const AffiliationMap = (affiliationIds) => {
+ const aId = [].concat.apply([], affiliationIds);
+ const affiliationMap = {};
+ let aCount = 0;
+ aId.map((e) => {
+ if (!affiliationMap[e]) {
+ aCount += 1;
+ affiliationMap[e] = aCount;
+ }
+ });
+ return affiliationMap;
+};
+
+const CommentComponent = (comment, title, feedback, feedbackTitle) => {
+ const reviewer = (comment ?
+ (
+
+ {title}
+
+ {comment}
+
+ )
+ :
+
+ );
+ const submitter = (feedback ?
+ (
+
+ {feedbackTitle}
+
+ {feedback}
+
+ )
+ :
+
+ );
+ return (
+
+ {reviewer}
+ {submitter}
+
+ );
+};
+
+const CommentDisplay = ({ elReview, commentKey }) => {
+ let objectKey = commentKey;
+ if (startsWith(commentKey, 'Reaction_Analysis_')) {
+ objectKey = 'Reaction Analysis';
+ } else if (startsWith(commentKey, 'Product_Analysis_')) {
+ objectKey = 'Product Analysis';
+ } else if (startsWith(commentKey, 'Analysis_')) {
+ objectKey = 'Analysis';
+ }
+
+ if (elReview) {
+ switch (objectKey) {
+ case 'Summary':
+ return CommentComponent(elReview.summary, 'Review Summary', elReview.feedback, 'Submitter Summary');
+ case 'Reference':
+ case 'Reaction Table':
+ case 'Description':
+ case 'Additional information':
+ case 'Properties':
+ case 'TLC-Control':
+ case 'Reaction Analysis':
+ case 'Product Analysis':
+ case 'Analysis':
+ return (elReview.comments && elReview.comments[commentKey]) ?
+ CommentComponent(
+ elReview.comments[commentKey].comment, `Review Comment on ${commentKey}`,
+ elReview.comments[commentKey].feedback, `Feedback on ${commentKey}`
+ ) : ;
+ default:
+ return ;
+ }
+ }
+ return ;
+};
+
+CommentDisplay.propTypes = {
+ elReview: PropTypes.oneOfType([PropTypes.object, PropTypes.array]),
+ commentKey: PropTypes.string.isRequired
+};
+
+CommentDisplay.defaultProps = {
+ elReview: null
+};
+
+export {
+ AffiliationMap,
+ CommentComponent,
+ CommentDisplay
+};
diff --git a/app/assets/javascripts/libHome/RepoReviewDetails.js b/app/assets/javascripts/libHome/RepoReviewDetails.js
new file mode 100644
index 000000000..e50834c7c
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoReviewDetails.js
@@ -0,0 +1,76 @@
+import React, { Component } from 'react';
+import PublicStore from '../components/stores/PublicStore';
+import RepoReactionDetails from './RepoReactionDetails';
+import RepoSampleDetails from './RepoSampleDetails';
+
+export default class RepoReviewDetails extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ element: props.element,
+ commentInfo: {},
+ summaryInfo: '',
+ feedbackInfo: '',
+ pubState: '',
+ reviewLevel: 0,
+ submitter: '',
+ };
+
+ this.onStoreChange = this.onStoreChange.bind(this);
+ }
+
+ componentDidMount() {
+ PublicStore.listen(this.onStoreChange);
+ }
+
+ componentWillUnmount() {
+ PublicStore.unlisten(this.onStoreChange);
+ }
+
+ onStoreChange(state) {
+ this.setState(prevState => ({ ...prevState, ...state }));
+ }
+
+ switchTypeRender() {
+ const { currentElement, elementType } = this.state;
+
+ if (typeof (currentElement) === 'undefined' || !currentElement) {
+ return ;
+ }
+ switch (elementType) {
+ case 'reaction':
+ return (
+ );
+ case 'sample':
+ return (
+ );
+ default: return ;
+ }
+ }
+
+ render() {
+ return (
+
+ {this.switchTypeRender()}
+
+ );
+ }
+}
diff --git a/app/assets/javascripts/libHome/RepoSample.js b/app/assets/javascripts/libHome/RepoSample.js
new file mode 100644
index 000000000..68b13e86d
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoSample.js
@@ -0,0 +1,150 @@
+import React, { Component } from 'react';
+import PropTypes from 'prop-types';
+import { Button, Jumbotron, Panel } from 'react-bootstrap';
+import ArrayUtils from '../components/utils/ArrayUtils';
+import {
+ AffiliationList,
+ AnalysesTypeJoinLabel,
+ AuthorList,
+ ChemotionId,
+ CommentBtn,
+ ContributorInfo,
+ DateInfo,
+ Doi,
+ IconLicense,
+ IconToMyDB,
+ RenderPublishAnalysesPanel,
+ SidToPubChem,
+ ToggleIndicator,
+} from './RepoCommon';
+import { AffiliationMap } from './RepoReviewCommon';
+import { Citation, literatureContent, RefByUserInfo } from '../components/LiteratureCommon';
+
+export default class RepoSample extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ expandSA: true,
+ };
+ this.toggleSA = this.toggleSA.bind(this);
+ this.renderAnalyses = this.renderAnalyses.bind(this);
+ }
+
+ toggleSA() {
+ const { expandSA } = this.state;
+ this.setState({ expandSA: !expandSA });
+ }
+
+ renderAnalyses(analyses) {
+ const orderAnalyses = ArrayUtils.sortArrByIndex(analyses);
+ return orderAnalyses.map((analysis) => {
+ const kind = (analysis.extended_metadata['kind'] || '').split('|').pop().trim();
+ return (
+
+
+
+
+ );
+ });
+ }
+
+ render() {
+ const {
+ sample, pubData, tagData, isPublished,
+ canComment, handleCommentBtn, isLogin
+ } = this.props;
+ const { expandSA } = this.state;
+
+ const affiliationMap = AffiliationMap(sample.affiliation_ids);
+
+ const references = sample.literatures ? sample.literatures.map(lit => (
+
+
+
+
+ )) : [];
+
+ const refArray = [];
+ let referencesText = '';
+ if (canComment && sample.literatures) {
+ sample.literatures.forEach((lit) => {
+ const content = literatureContent(lit, true);
+ refArray.push(content);
+ });
+ referencesText = refArray.join('');
+ }
+
+ const iupacUserDefined = ((sample.showed_name == sample.molecule_iupac) || sample.showed_name == null)
+ ?
+ : Name: {sample.showed_name}
;
+
+ const analyses = (sample.analyses && sample.analyses.children && sample.analyses.children.length > 0 && sample.analyses.children[0].children) || [];
+ return (
+
+
+
+
+
+ {IconLicense(sample.license, (sample.author_ids.length > 1))}
+
+
+ {iupacUserDefined}
+
+
+ Author{sample.author_ids.length > 1 ? 's' : ''}:
+
+
+
+
+
+
+ {sample.reaction_ids.map(rid => (
+
+ ))}
+
+
+
+ Reference{references.length > 1 ? 's' : null}:
+
+
+
+
+ {AnalysesTypeJoinLabel(ArrayUtils.sortArrByIndex(analyses), 'Sample')}
+
+ { }}>
+
+
+ {this.renderAnalyses(analyses)}
+
+
+
+
+ );
+ }
+}
+
+RepoSample.propTypes = {
+ sample: PropTypes.object.isRequired,
+ pubData: PropTypes.object.isRequired,
+ tagData: PropTypes.object.isRequired,
+ isPublished: PropTypes.bool.isRequired,
+ canComment: PropTypes.bool,
+ handleCommentBtn: PropTypes.func,
+ isLogin: PropTypes.bool
+};
+
+RepoSample.defaultProps = {
+ canComment: false,
+ handleCommentBtn: () => {},
+ isLogin: false
+};
diff --git a/app/assets/javascripts/libHome/RepoSampleDetails.js b/app/assets/javascripts/libHome/RepoSampleDetails.js
new file mode 100644
index 000000000..00d1ec23b
--- /dev/null
+++ b/app/assets/javascripts/libHome/RepoSampleDetails.js
@@ -0,0 +1,236 @@
+import React, { Component } from 'react';
+import { Panel } from 'react-bootstrap';
+import PropTypes from 'prop-types';
+import {
+ ClosePanel,
+ MoleculeInfo,
+} from './RepoCommon';
+import LoadingActions from '../components/actions/LoadingActions';
+import PublicActions from '../components/actions/PublicActions';
+import RepoReviewButtonBar from './RepoReviewButtonBar';
+import RepoCommentModal from '../components/common/RepoCommentModal';
+import RepoReviewModal from '../components/common/RepoReviewModal';
+import RepoSample from './RepoSample';
+
+export default class RepoSampleDetails extends Component {
+ constructor(props) {
+ super(props);
+ this.state = {
+ showReviewModal: false,
+ btnAction: '',
+ showCommentModal: false,
+ commentField: '',
+ originInfo: '',
+ };
+ this.handleReviewBtn = this.handleReviewBtn.bind(this);
+ this.handleSubmitReview = this.handleSubmitReview.bind(this);
+ this.handleCommentBtn = this.handleCommentBtn.bind(this);
+ this.handleSubmitComment = this.handleSubmitComment.bind(this);
+ }
+
+ handleReviewBtn(showReviewModal, btnAction) {
+ this.setState({ showReviewModal, btnAction });
+ }
+
+ handleSubmitReview(elementId, comments, summary, feedback, action) {
+ LoadingActions.start();
+ PublicActions.reviewPublish(elementId, 'sample', comments, summary, feedback, action);
+ this.setState({ showReviewModal: false });
+ }
+
+ handleCommentBtn(show, field, orgInfo) {
+ this.setState({
+ showCommentModal: show,
+ commentField: field,
+ originInfo: orgInfo
+ });
+ }
+
+ handleSubmitComment(elementId, elementType, field, comment, origInfo) {
+ LoadingActions.start();
+ const cinfo = {};
+ if (typeof (cinfo[field]) === 'undefined') {
+ cinfo[field] = {};
+ }
+ const today = new Date();
+ const d = `${today.getDate()}-${today.getMonth() + 1}-${today.getFullYear()} `;
+ const t = `${today.getHours()}:${today.getMinutes() + 1}:${today.getSeconds()} `;
+ const dt = `${d} ${t}`;
+ if (this.props.reviewLevel === 2) {
+ cinfo[field].feedback = comment;
+ cinfo[field].origInfo = origInfo;
+ cinfo[field].feedback_time = dt;
+ } else {
+ cinfo[field].comment = comment;
+ cinfo[field].origInfo = origInfo;
+ cinfo[field].comment_time = dt;
+ }
+
+ PublicActions.updateComment(elementId, elementType, cinfo);
+ this.setState({ showCommentModal: false });
+ }
+
+ render() {
+ const {
+ element,
+ isPublished,
+ canComment,
+ reviewLevel,
+ submitter,
+ pubState,
+ comments,
+ summary,
+ feedback,
+ canClose,
+ buttons
+ } = this.props;
+
+ if (typeof (element) === 'undefined' || !element) {
+ return ;
+ }
+
+ const {
+ molecule, isLogin
+ } = element;
+
+ const idyLogin = typeof isLogin === 'undefined' ? true : isLogin;
+
+ let samples = [];
+ let pubData = {};
+ let tagData = {};
+ let { sample } = element;
+ if (isPublished) {
+ samples = element.published_samples;
+ sample = samples.find(x => x !== undefined);
+ sample.id = sample.sample_id;
+ } else {
+ samples.push(element.sample);
+ pubData = element.publication;
+ }
+
+ tagData = (pubData.taggable_data) || {};
+ const details = (samples || []).map((s) => {
+ if (isPublished) {
+ pubData = {
+ id: s.pub_id
+ };
+ tagData = {
+ published_at: s.published_at,
+ doi_reg_at: s.doi_reg_at
+ };
+ }
+ const el = {
+ id: s.id || s.sample_id,
+ sid: s.sid,
+ affiliation_ids: s.affiliation_ids || tagData.affiliation_ids,
+ affiliations: s.affiliations || tagData.affiliations,
+ literatures: s.literatures || element.literatures,
+ license: s.license || tagData.license || 'CC BY-SA',
+ author_ids: s.author_ids || tagData.author_ids || [],
+ contributors: s.contributors || tagData.contributors,
+ creators: s.creators || tagData.creators,
+ doi: s.doi || element.doi,
+ reaction_ids: s.reaction_ids || [],
+ showed_name: s.showed_name,
+ molecule_iupac: molecule.iupac_name || [],
+ analyses: s.analyses || element.analyses || []
+ };
+
+ return (
+
+ );
+ });
+
+ return (
+
+
+ {
+ canComment ?
+ : ''
+ }
+ {canClose ? : ''}
+
+
+ {details}
+
+ {
+ canComment ?
+
+ this.setState({ showCommentModal: false })}
+ />
+ this.setState({ showReviewModal: false })}
+ />
+
: ''
+ }
+
+
+
+ );
+ }
+}
+
+RepoSampleDetails.propTypes = {
+ element: PropTypes.object.isRequired,
+ isPublished: PropTypes.bool,
+ canComment: PropTypes.bool,
+ reviewLevel: PropTypes.number,
+ submitter: PropTypes.string,
+ pubState: PropTypes.string,
+ comments: PropTypes.object,
+ summary: PropTypes.string,
+ feedback: PropTypes.string,
+ canClose: PropTypes.bool,
+ buttons: PropTypes.arrayOf(PropTypes.string),
+};
+
+RepoSampleDetails.defaultProps = {
+ isPublished: false,
+ canComment: false,
+ reviewLevel: 0,
+ submitter: '',
+ pubState: '',
+ comments: {},
+ summary: '',
+ feedback: '',
+ canClose: true,
+ buttons: ['Decline', 'Comments', 'Review', 'Submit', 'Accept'],
+};
diff --git a/app/assets/javascripts/libHome/homeRoutes.js b/app/assets/javascripts/libHome/homeRoutes.js
new file mode 100644
index 000000000..2e73d3f61
--- /dev/null
+++ b/app/assets/javascripts/libHome/homeRoutes.js
@@ -0,0 +1,219 @@
+import PublicActions from '../components/actions/PublicActions'
+import PublicFetcher from '../components/fetchers/PublicFetcher'
+
+const routes = {
+ '/': 'root',
+ target: {
+ root: function(e) {
+ Aviator.navigate('/home/welcome')
+ }
+ },
+
+ '/welcome': {
+ target: {
+ show: function(e) {
+ PublicActions.openRepositoryPage("welcome")
+ },
+ },
+ '/': 'show'
+ },
+
+ '/home': {
+ target: {
+ show: function(e) {
+ PublicActions.openRepositoryPage("home")
+ },
+ },
+ '/': 'show'
+ },
+ '/publications': {
+ target: {
+ show: function(e) {
+ PublicActions.openRepositoryPage("publications")
+ },
+ },
+ '/': 'show'
+ },
+ '/review': {
+ target: {
+ show: function(e) {
+ PublicActions.openRepositoryPage("review")
+ },
+ },
+ '/': 'show'
+ },
+ '/about': {
+ target: {
+ show: function(e) {
+ PublicActions.openRepositoryPage("about")
+ },
+ },
+ '/': 'show'
+ },
+ '/contact': {
+ target: {
+ show: function(e) {
+ PublicActions.openRepositoryPage("contact")
+ },
+ },
+ '/': 'show'
+ },
+
+ '/newsroom': {
+ target: {
+ list: function (e) {
+ PublicActions.articles();
+ },
+ show: function (e) {
+ PublicActions.displayArticle(e.params.key)
+ },
+ },
+ '/': 'list',
+ '/:key': 'show'
+ },
+
+ '/newseditor': {
+ target: {
+ edit: function (e) {
+ PublicActions.editArticle(e.params.key)
+ },
+ show: function (e) {
+ PublicActions.editArticle('new')
+ },
+ },
+ '/show': 'show',
+ '/:key': 'edit'
+ },
+
+ '/howtoeditor': {
+ target: {
+ edit: function (e) {
+ PublicActions.editHowTo(e.params.key)
+ },
+ show: function (e) {
+ PublicActions.editHowTo('ein')
+ },
+ },
+ '/show': 'show',
+ '/:key': 'edit'
+ },
+
+ '/directive': {
+ target: {
+ show: function(e) {
+ PublicActions.openRepositoryPage("directive")
+ },
+ },
+ '/': 'show'
+ },
+
+ '/datasets': {
+ target: {
+ show: function(e) {
+ PublicActions.displayDataset(e.params.datasetId)
+ },
+ },
+ '/:datasetId': 'show'
+ },
+
+ '/molecules': {
+ target: {
+ show: function(e) {
+ PublicActions.displayMolecule(e.params.moleculeId)
+ },
+ },
+ '/:moleculeId': 'show'
+ },
+
+ '/reactions': {
+ target: {
+ show: function(e) {
+ PublicActions.displayReaction(e.params.reactionId)
+ },
+ },
+ '/:reactionId': 'show'
+ },
+
+ '/pid': {
+ target: {
+ show: function(e) {
+ PublicFetcher.queryPid({id: e.params.id})
+ }
+ },
+ '/:id': 'show'
+ },
+
+ '/inchikey': {
+ target: {
+ show: function(e) {
+ let url = e.uri.replace("/inchikey/", "")
+ let query = url.split(".")
+
+ if (query.length > 0) {
+ let version = query[1] || ""
+ let splitIndex = query[0].indexOf("/")
+ if (splitIndex < 0) splitIndex = query[0].length
+ let params = {
+ inchikey: query[0].substring(0, splitIndex),
+ type: query[0].substring(splitIndex + 1),
+ version: version
+ }
+
+ PublicFetcher.queryInchikey(params)
+ }
+
+ },
+ },
+ '/*': 'show'
+ },
+
+ '/review_reaction': {
+ target: {
+ show: function(e) {
+ PublicActions.displayReviewReaction(e.params.reactionId)
+ },
+ },
+ '/:reactionId': 'show'
+ },
+
+ '/review_sample': {
+ target: {
+ show: function(e) {
+ PublicActions.displayReviewSample(e.params.sampleId)
+ },
+ },
+ '/:sampleId': 'show'
+ },
+
+ '/embargo': {
+ target: {
+ list: function (e) {
+ PublicActions.openRepositoryPage("embargo");
+ },
+ show: function (e) {
+ PublicActions.displayReviewEmbargo(e.params.elementType, e.params.elementId)
+ },
+ },
+ '/': 'list',
+ '/:elementType/:elementId': 'show'
+ },
+
+ '/howto': {
+ target: {
+ list: function (e) {
+ PublicActions.howtos();
+ },
+ show: function (e) {
+ PublicActions.displayHowTo(e.params.key)
+ },
+ },
+ '/': 'list',
+ '/:key': 'show'
+ },
+}
+
+export default function() {
+ Aviator.root = '/home'
+ Aviator.pushStateEnabled = true
+ Aviator.setRoutes(routes)
+}
diff --git a/app/assets/stylesheets/application.scss.erb b/app/assets/stylesheets/application.scss.erb
index 767095c13..f0f499742 100644
--- a/app/assets/stylesheets/application.scss.erb
+++ b/app/assets/stylesheets/application.scss.erb
@@ -23,6 +23,63 @@
<%Bundler.load.current_dependencies.select{|dep| dep.groups.include?(:plugins)}.map(&:name).each do |plugin|%>
@import "<%=plugin%>";
<%end%>
+//////////////////////////
+ .main-image {
+ width: 100%;
+ margin-top: -10px;
+ position: relative;
+ display: inline-block;
+ background-color: #337ab7;
+}
+
+.main-image p {
+ margin-top: 10px;
+ font-size: 40px;
+ color: white;
+ text-align: center;
+ font-weight: 600;
+}
+
+.main-image img {
+ position: absolute;
+ overflow: visible;
+}
+
+.main-image img#book-image {
+ margin-top: -100px;
+ width: 300px;
+ opacity: 0%;
+}
+
+.main-image img#logo-image {
+ position: relative;
+}
+
+.main-image img#molecule-image {
+ right: 10px;
+ margin-top: -184px;
+}
+.main-image::before {
+ content: "";
+ top: 0;
+ left: 0;
+ position: absolute;
+ height: 100%;
+ width: 100%;
+}
+
+.dfg_logo img{
+ height: 25px;
+}
+.info-panel p {
+ margin: auto;
+}
+
+.info-panel ul {
+ padding-left: 40%;
+ text-align: left;
+}
+//////////////////////////
label.required:after {
content: " *";
@@ -30,12 +87,36 @@ label.required:after {
.navbar-custom {
border-radius: 0;
+ padding: 0px;
background-color: #EFEFEF;
+ // : none;
+ // background-image: -webkit-linear-gradient(left, #EFEFEF 0%, #0d47a1 100%);
+ // background-image: linear-gradient(to left, #EFEFEF 0%, #0d47a1 100%);
+
+ // background-repeat: repeat-x;
+
a.dropdown-toggle:hover {
color: black;
}
}
+
+// .white-nav-item {
+//
+// a {
+// color: white !important;
+//
+// &:hover {
+// color: grey !important;
+// text-decoration: none;
+// }
+//
+// &:focus {
+// color: black !important;
+// text-decoration: none;
+// }
+// }
+// }
.custom-modal {
width: 100%;
}
diff --git a/app/assets/stylesheets/collection_tree.css b/app/assets/stylesheets/collection_tree.css
index 4af907d3c..ac930bc6d 100644
--- a/app/assets/stylesheets/collection_tree.css
+++ b/app/assets/stylesheets/collection_tree.css
@@ -20,6 +20,10 @@
overflow: auto;
}
+.title-public {
+ background: Lavender;
+}
+
.tree-view li {
margin-left: -13px;
list-style-type: none;
diff --git a/app/assets/stylesheets/common.scss b/app/assets/stylesheets/common.scss
index cd4838e43..f3ada692b 100644
--- a/app/assets/stylesheets/common.scss
+++ b/app/assets/stylesheets/common.scss
@@ -1,3 +1,11 @@
+$color-chem-blue: #337ab7;
+$color-chem-logo-blue: #3a9fd3;
+$color-required: #d9534f;
+
+.field_required {
+ color: $color-required;
+}
+
// --- color ---
.c-text--grey {
color: grey;
@@ -55,7 +63,6 @@
line-height: 1;
}
-
.span-checkbox {
-webkit-border-radius: 0;
border-radius: 0;
@@ -201,6 +208,91 @@
overflow-y: scroll;
height: 85px;
}
+ }
+}
+
+.publish_tooltip {
+ .tooltip-inner {
+ text-align: left;
+ white-space: pre-wrap;
+ }
+}
+
+.review_element_label {
+ color: #333;
+ border-style: solid;
+ border-width: thin;
+ border-radius: 4px;
+ padding: 4px;
+
+ i {
+ font-size: 1.2em !important;
+ }
+}
+
+.list_focus_off {
+ cursor: pointer;
+ background-color: #F5F5F5;
+}
+.list_focus_on {
+ cursor: pointer;
+ background-color: #d4edda !important;
+}
+
+.feature {
+ display: flex;
+ .feature-block {
+ display: block;
+ position: relative;
+ padding: 16px 24px 32px 24px;
+ text-decoration: none;
+ z-index: 0;
+ overflow: hidden;
+ height: 100%;
+ &:before {
+ content: "";
+ position: absolute;
+ z-index: -1;
+ right: -16px;
+ background: unset;
+ height: 26px;
+ width: 100%;
+ transform: scale(1);
+ transform-origin: 50% 50%;
+ transition: transform 0.25s ease-out;
+ bottom: 50%;
+ }
+ &:hover:before {
+ transform: scale(8);
+ background: $color-chem-blue;
+ }
+ div {
+ padding: 8px;
+ display: inline-block;
+ }
+ h3 {
+ text-align: left;
+ }
+ i {
+ text-align: center;
+ display: inline-block;
+ color: $color-chem-blue;
+ position: relative;
+ }
+ }
+
+ .feature-block:hover {
+ p {
+ transition: all 0.3s ease-out;
+ color: #ffffff;
+ }
+ h3 {
+ transition: all 0.3s ease-out;
+ color: #ffffff;
+ }
+ i {
+ color: #ffffff;
+ }
}
}
@@ -209,4 +301,49 @@
border-color: #bfbfbf;
border-style: dashed;
border-width: thin;
-}
\ No newline at end of file
+}
+
+.home-title {
+ font-size: x-large;
+ font-weight: bolder;
+ text-align: center;
+ padding-top: 60px;
+ padding-bottom: 30px;
+ & > span {
+ position: relative;
+ padding: 0 5px;
+ &:before {
+ content: "";
+ display: block;
+ width: 100%;
+ height: 1px;
+ position: absolute;
+ top: 50%;
+ background-color: #777;
+ right: 100%;
+ }
+ &:after {
+ content: "";
+ display: block;
+ width: 100%;
+ height: 1px;
+ position: absolute;
+ top: 50%;
+ background-color: #777;
+ left: 100%;
+ }
+ }
+}
+
+.display-false {
+ display: none !important;
+}
+
+.display-true {
+ .initial {
+ display: initial;
+ }
+ .inherit {
+ display: inherit;
+ }
+}
diff --git a/app/assets/stylesheets/elements_details.css b/app/assets/stylesheets/elements_details.css
index 1e3c7fca7..9e8f9cc7f 100644
--- a/app/assets/stylesheets/elements_details.css
+++ b/app/assets/stylesheets/elements_details.css
@@ -5,7 +5,6 @@
.button-right {
float: right;
right: 0px;
- z-index: 1;
margin-left: 2px;
}
@@ -128,3 +127,21 @@
width: 100%;
padding: 0 !important;
}
+
+.full-screen .element-panel-detail > .panel-body {
+ overflow-x: hidden;
+ overflow-y: hidden;
+ max-height: calc(100vh - 110px);
+}
+
+.normal-screen .element-panel-detail > .panel-body {
+ overflow-x: hidden;
+ overflow-y: scroll;
+ max-height: calc(100vh - 240px);
+}
+
+.element-panel-detail .full {
+ overflow-x: hidden;
+ overflow-y: scroll;
+ max-height: calc(100vh - 150px);
+}
diff --git a/app/assets/stylesheets/elements_table.scss b/app/assets/stylesheets/elements_table.scss
index ddb54ba11..f7e913a82 100644
--- a/app/assets/stylesheets/elements_table.scss
+++ b/app/assets/stylesheets/elements_table.scss
@@ -115,6 +115,11 @@ th.drag {
overflow-y: scroll;
}
+// .list-guest-elements {
+// @extend .list-elements;
+// max-height: calc(100vh - 170px);
+// }
+
.list-pagination {
margin: 5px 0 0 0;
}
@@ -153,10 +158,56 @@ th.drag {
border-top: 0
}
+.review-entries > tbody > tr > td {
+ border-top: 1
+}
+
+.public-element {
+ height: calc(100vh - 128px);
+ overflow-x: hidden;
+ overflow-y: scroll;
+}
+
+.public-list {
+ height: calc(100vh - 220px);
+ overflow-x: hidden;
+ overflow-y: scroll;
+}
+
+.public-list-adv {
+ height: calc(100vh - 300px);
+ overflow-x: hidden;
+ overflow-y: scroll;
+}
+
+.review-element {
+ height: calc(100vh - 110px);
+ overflow-x: hidden;
+ overflow-y: scroll;
+}
+
+.review-list {
+ height: calc(100vh - 214px);
+ overflow-x: hidden;
+ overflow-y: scroll;
+}
+
@media only screen and (max-width: 1500px) {
.list-elements {
- height: calc(100vh - 350px);
+ height: calc(100vh - 330px);
+ }
+
+ .public-element {
+ height: calc(100vh - 204px);
+ overflow-x: hidden;
+ overflow-y: scroll;
}
+ .public-list {
+ height: calc(100vh - 226px);
+ overflow-x: hidden;
+ overflow-y: scroll;
+ }
+
}
@-webkit-keyframes blink-1 {
@@ -229,4 +280,3 @@ th.drag {
-moz-animation: blink-3 4s infinite ; /* Fx 5+ */
animation: blink-3 4s infinite ; /* IE 10+, Fx 29+ */
}
-
diff --git a/app/assets/stylesheets/flexbox.css b/app/assets/stylesheets/flexbox.css
new file mode 100644
index 000000000..1f128871d
--- /dev/null
+++ b/app/assets/stylesheets/flexbox.css
@@ -0,0 +1,156 @@
+.cards_flex {
+ display: flex;
+ display: -webkit-flex;
+ -webkit-justify-content: center;
+ -webkit-align-items: center;
+ justify-content: center;
+ align-items: center;
+}
+
+.cards_ary {
+ width: 100%;
+ display: flex;
+ display: -webkit-flex;
+ justify-content: center;
+ -webkit-justify-content: center;
+ max-width: calc(95vw);
+}
+
+.card--1 .card__img, .card--1 .card__img--hover {
+ background-image: url('../images/spectraviewer.png');
+ object-fit: cover;
+}
+
+.card--2 .card__img, .card--2 .card__img--hover {
+ background-image: url('../images/chemeln.jpg');
+ object-fit: cover;
+}
+
+.card--3 .card__img, .card--3 .card__img--hover {
+ background-image: url('../images/chemrepo.png');
+ object-fit: cover;
+}
+
+.card--4 .card__img, .card--4 .card__img--hover {
+ background-image: url('../images/chemscanner.png');
+ object-fit: cover;
+}
+
+.card__like {
+ width: 40px;
+ float: right;
+}
+
+.card__clock {
+ width: 15px;
+ vertical-align: middle;
+ fill: #337ab7;
+}
+.card__time {
+ font-size: 18px;
+ font-weight: bold;
+ color: #337ab7;
+ vertical-align: middle;
+ margin-left: 5px;
+
+}
+
+.card__clock-info {
+ float: right;
+}
+
+.card__img {
+ visibility: hidden;
+ background-size: cover;
+ background-position: center;
+ background-repeat: no-repeat;
+ width: 100%;
+ height: 350px;
+ border-top-left-radius: 12px;
+ border-top-right-radius: 12px;
+ object-fit: cover;
+}
+
+.card__info-hover {
+ position: absolute;
+ padding: 16px;
+ width: 100%;
+ opacity: 0;
+ top: 0;
+ text-align: start;
+}
+
+.card__img--hover {
+ transition: 0.2s all ease-out;
+ background-size: cover;
+ background-position: center;
+ background-repeat: no-repeat;
+ width: 100%;
+ position: absolute;
+ height: 350px;
+ border-top-left-radius: 12px;
+ border-top-right-radius: 12px;
+ top: 0;
+ object-fit: cover;
+}
+.card_u {
+ margin-right: 50px;
+ transition: all .2s cubic-bezier(0.175, 0.885, 0, 1);
+ background-color: #fff;
+ width: 25%;
+ position: relative;
+ border-radius: 12px;
+ overflow: hidden;
+ box-shadow: 20px 20px 10px -8px rgba(0, 0, 0,0.1)
+}
+.card_u:hover {
+ box-shadow: 0px 30px 18px -8px rgba(0, 0, 0,0.1);
+ transform: scale(1.10, 1.10);
+}
+
+.card__info {
+ z-index: 2;
+ background-color: #fff;
+ border-bottom-left-radius: 12px;
+ border-bottom-right-radius: 12px;
+ padding: 16px 24px 24px 24px;
+}
+
+.card__title {
+ margin-top: 25px;
+ margin-bottom: 5px;
+}
+
+.card__desc {
+ margin-top: 10px;
+ font-weight: bolder !important;
+ color: #337ab7;
+ position: relative;
+ opacity: 1 !important;
+ height: 300px;
+ width: 100%;
+ font-size: 0.8vw;
+ vertical-align: middle;
+ display: table-cell;
+}
+
+.card__try {
+ position: relative;
+ z-index: 6;
+ display: flex;
+ display: -webkit-flex;
+}
+
+.card_u:hover .card__img--hover {
+ height: 100%;
+ opacity: 0.1;
+}
+
+.card_u:hover .card__info {
+ background-color: transparent;
+ position: relative;
+}
+
+.card_u:hover .card__info-hover {
+ opacity: 1;
+}
diff --git a/app/assets/stylesheets/home.scss b/app/assets/stylesheets/home.scss
index e69de29bb..ad3b7133f 100644
--- a/app/assets/stylesheets/home.scss
+++ b/app/assets/stylesheets/home.scss
@@ -0,0 +1,23 @@
+.div-table {
+ display: table;
+ border-spacing: 10px;
+
+ .span-row {
+ display: table-row;
+
+ span {
+ display: table-cell;
+ vertical-align: middle;
+ }
+ }
+}
+.small-p .ql-editor > p {
+ font-size: small;
+}
+
+iframe#home-tos {
+ width: 100%;
+ min-height: 80vh;
+ height: auto;
+ border: inherit;
+}
diff --git a/app/assets/stylesheets/howto.scss b/app/assets/stylesheets/howto.scss
new file mode 100644
index 000000000..bab44f000
--- /dev/null
+++ b/app/assets/stylesheets/howto.scss
@@ -0,0 +1,111 @@
+// .howto {
+.editor-stelle {
+ font-size: larger;
+ font-weight: bolder;
+ background-color: #eeeeee;
+}
+ .editor-btn {
+ float: left;
+ margin: 20px 0px 20px 0px;
+ button {
+ height: 30px;
+ width: 60px;
+ margin-right: 10px;
+ }
+ }
+ .editor-btn-right {
+ float: right;
+ margin-bottom: 20px;
+ button {
+ height: 30px;
+ width: 60px;
+ margin-left: 10px;
+ }
+ }
+ .editor-field {
+ padding: 0px 100px 70px 100px;
+ border: darkcyan medium dotted;
+ label {
+ margin-top: 5px;
+ }
+ .title {
+ font-size: 1.6em;
+ font-weight: bold;
+ }
+ .drag-source {
+ cursor: move;
+ float: right;
+ margin-top: 5px;
+ margin-right: 5px;
+ }
+ &.static {
+ margin-bottom: 20px;
+
+ .ql-editor {
+ padding: 0;
+ }
+
+ .ql-hidden {
+ display: none;
+ }
+ }
+
+ .image-container {
+ text-align: center;
+
+ img {
+ max-width: 100%;
+ }
+
+ p {
+ margin-bottom: 0;
+ }
+ }
+ }
+ .editor-field-drop-target {
+ height: 20px;
+ background-color: #eeeeee;
+
+ .indicator {
+ height: 10px;
+ }
+
+ &.can-drop {
+ .indicator {
+ border-bottom: 4px dashed lightgray;
+ }
+ }
+
+ &.is-over {
+ .indicator {
+ border-bottom: 4px dashed #31708f;
+ }
+ }
+ }
+
+ .editor-field-drop-add-field {
+ float: left;
+ margin-bottom: 20px;
+
+ button {
+ height: 30px;
+ width: 60px;
+ margin-right: 10px;
+ }
+ }
+ .dropzone {
+ min-height: 50px;
+ width: 100%;
+ border: 3px dashed lightgray;
+
+ .image-container {
+ margin: 15px;
+ }
+
+ p {
+ text-align: center;
+ padding-top: 12px;
+ color: grey;
+ }
+ }
+// }
diff --git a/app/assets/stylesheets/navigation.scss b/app/assets/stylesheets/navigation.scss
index fa53b3d6d..011923568 100644
--- a/app/assets/stylesheets/navigation.scss
+++ b/app/assets/stylesheets/navigation.scss
@@ -16,6 +16,13 @@
}
}
+.navig-smaller-font {
+ a.dropdown-toggle {
+ font-size: 70%;
+ }
+}
+
+
@media only screen and (min-width: 1366px) and (min-height: 500px) {
.card-navigation {
/* position: fixed;
@@ -78,3 +85,7 @@
border-top: 1px solid #ccc;
}
}
+
+.navbar-guest {
+ display: inline;
+}
diff --git a/app/assets/stylesheets/news.scss b/app/assets/stylesheets/news.scss
new file mode 100644
index 000000000..8e886aaa8
--- /dev/null
+++ b/app/assets/stylesheets/news.scss
@@ -0,0 +1,282 @@
+@import url('https://fonts.googleapis.com/css?family=EB+Garamond:400,700,700i,800,800i');
+@import url('https://fonts.googleapis.com/css?family=Spectral:400,700,700i');
+
+$timelinecolor: #5A5A5A; // #337ab7; // #0079bf;
+$boxbackgroundcolor: rgba(62,62,62, 0.1);
+
+.newseditor_review {
+ border: none;
+ font-family: 'Spectral', serif;
+ & .panel-heading {
+ background-color: white !important;
+ border: none;
+ font-weight: bolder;
+ & > span {
+ font-size: 2em;
+ font-weight: bolder;
+ }
+ }
+ & .panel-body {
+ background-color: white !important;
+ border: none;
+ max-height: 50vh;
+ overflow-Y: auto;
+ border-radius: 6px;
+ & > span {
+ font-size: 1.6em;
+ font-family: 'Spectral', serif;
+ }
+ & .ql-container .ql-editor > p > img {
+ max-width: 30vw;
+ }
+ }
+}
+
+.news_time_box {
+ margin:0 0 0 10%;
+ // height: 630px;
+ // overflow: hidden;
+ padding: 0px 0px 40px 120px;
+ & > ul {
+ list-style-type: none;
+ margin: 0;
+ padding: 0;
+ position: relative;
+ transition: all 0.5s linear;
+ top: unset;
+ &:last-of-type{
+ // top:80px
+ &:before {
+ top: unset;
+ }
+ }
+ &:before {
+ content: "";
+ display: block;
+ width: 0;
+ // height: 100%;
+ height: 80%;
+ border:1px dashed $timelinecolor;
+ position: absolute;
+ // top:0;
+ top: 100px;
+ left:30px
+ }
+ & > li {
+ margin: 20px 60px 60px;
+ position: relative;
+ padding: 10px 20px;
+ background-color: $boxbackgroundcolor;
+ // background:rgba(255, 255, 255, 0.3);
+ // color:#fff;
+ border-radius: 10px;
+ box-shadow: 1px 1px 2px 0px rgba(0,0,0,0.5);
+ line-height: 20px;
+ // width: 35%;
+ & > span {
+ content: "";
+ display: block;
+ width: 0;
+ height: 100%;
+ border: 1px solid $timelinecolor;
+ position: absolute;
+ top :0;
+ left: -30px;
+ &:before, &:after {
+ content: "";
+ display: block;
+ width: 30px;
+ height: 30px;
+ border-radius: 50%;
+ background: $timelinecolor;
+ border:2px solid #fff;
+ position: absolute;
+ left: -15px
+ }
+ &:before {
+ top: -10px;
+ }
+ &:after {
+ top: 95%;
+ background-color: #eee; // aliceblue;
+ border: 2px solid $timelinecolor;
+ }
+ }
+ & .title {
+ font-weight: bolder;
+ font-size: 2rem;
+ background-color: unset;
+ line-height: 1.6;
+ }
+ & .readedit {
+ font-weight: normal;
+ float: right;
+ }
+ }
+ }
+ & .content {
+ font-weight: normal;
+ }
+ & .author {
+ margin-top: 10px;
+ text-transform: capitalize;
+ font-style: italic;
+ // text-align: right;
+ margin-right: 20px
+ }
+ & .created_at span{
+ position: absolute;
+ left: -100px;
+ color: $timelinecolor; // #5A5A5A;
+ font-size:80%;
+ font-weight: bold;
+ }
+ & .created_at span:first-child{
+ top:-6px;
+ left: -220px;
+ font-size: large;
+ font-weight: normal;
+ }
+ & .created_at span:last-child{top:94%}
+
+}
+
+// @import 'https://fonts.googleapis.com/css?family=Open+Sans:300,400';
+.news-preview-dialog {
+ display: block;
+ padding-left: 0px;
+ top: 45% !important;
+ width: 60vw !important;
+}
+
+%reset { margin: 0; padding: 0; }
+%flex { display: flex; justify-content: center; align-items: center; }
+
+@mixin animated($timein: null, $delay: null) {
+ transition: all $timein ease-in-out;
+ transition-delay: $delay;
+}
+
+@mixin dimensions($width: null, $height: null) { width: $width; min-height: $height; }
+
+// $maincolor: #009688;
+$maincolor: #337ab7;
+// html{height: 100%;}
+// body{
+
+// @extend %flex;
+// font-family: 'Open Sans', sans-serif;
+// width: 100%;
+// min-height: 100%;
+// background: #009688;
+// font-size: 16px;
+// overflow: hidden;
+// }
+
+
+// *, *:before, *:after {
+// box-sizing: border-box;
+// }
+.news-content{
+ position: relative;
+ // animation: animatop 0.9s cubic-bezier(0.425, 1.140, 0.470, 1.125) forwards ;
+}
+
+.news-card{
+ @include dimensions( 580px, 100px);
+ padding: 20px;
+ border-radius: 3px;
+ background-color: white;
+ box-shadow: 0px 10px 20px rgba(0,0,0,0.2);
+ position: relative;
+ overflow: hidden;
+ &:after {
+ content: '';
+ display: block;
+ width: 190px;
+ height: 300px;
+ // background: cadetblue;
+ background: #337ab7;
+ position: absolute;
+ animation: rotatemagic 0.75s cubic-bezier(0.425, 1.040, 0.470, 1.105) 1s both;
+ }
+}
+
+.badgescard{
+ padding: 10px 20px;
+ border-radius: 3px;
+ background-color: #ECECEC;
+ width: 560px;
+ box-shadow: 0px 10px 20px rgba(0, 0, 0, 0.2);
+ position: relative;
+ z-index: -1;
+ left: 10px;
+ bottom: 10px;
+ margin-bottom: 50px;
+ justify-content: flex-end;
+ @extend %flex;
+ animation: animainfos 0.5s cubic-bezier(0.425, 1.040, 0.470, 1.105) 0.75s forwards;
+ span {
+ font-size: 1em;
+ margin: 0px 2px;
+ opacity: 0.6;
+ }
+}
+
+.firstinfo{
+ @extend %flex;
+ flex-direction: row;
+ z-index:2;
+ position: relative;
+ img{
+ // border-radius: 50%;
+ width: 120px;
+ height: 120px;
+ }
+ .profileinfo{
+ padding: 0px 20px;
+ width: 100vw;
+ // h1{ font-size: 1.8em;}
+ h1{ font-size: 1.6em; font-weight: bolder; }
+ h3{ font-size: 1.2em;
+ color: $maincolor;
+ font-style: italic;
+ }
+ p.bio{
+ padding: 10px 0px;
+ color: #5A5A5A;
+ line-height: 1.2;
+ font-style: initial;
+ }
+ }
+}
+
+@keyframes animatop{
+ 0%{
+ opacity: 0;
+ bottom: -500px;}
+ 100%{
+ opacity: 1;
+ bottom: 0px;}
+}
+
+@keyframes animainfos{
+ 0%{
+ bottom: 30px;}
+ 100%{
+ bottom: 0px;}
+}
+
+@keyframes rotatemagic{
+ 0%{
+ opacity: 0;
+ transform: rotate(-0deg);
+ top: -24px;
+ left: -253px;
+ }
+ 100%{
+ transform: rotate(-30deg);
+ top: -24px;
+ left: -78px;
+ }
+}
\ No newline at end of file
diff --git a/app/assets/stylesheets/newsroom.css b/app/assets/stylesheets/newsroom.css
new file mode 100644
index 000000000..0641ab1e8
--- /dev/null
+++ b/app/assets/stylesheets/newsroom.css
@@ -0,0 +1,607 @@
+@import url('https://fonts.googleapis.com/css?family=EB+Garamond:400,700,700i,800,800i');
+@import url('https://fonts.googleapis.com/css?family=Spectral:400,700,700i');
+
+.chemotion_news {
+ font-size: 5rem;
+ font-weight: bold;
+ text-align: center;
+ font-family: 'EB Garamond', serif;
+ /* font-style: italic; */
+ margin-bottom: 10px;
+ text-shadow: 4px 4px 4px #aaa;
+ border-top-color: black;
+ border-top-style: double;
+ border-bottom-color: black;
+ border-bottom-style: double;
+}
+
+.required_style {
+ display: inline;
+ font-weight: normal;
+ color: #d9534f;
+ padding-left: 8px;
+ font-size: 1.2em;
+}
+
+.newseditor, .required, .article_title, .article_content {
+ display: inline;
+ font-weight: normal;
+}
+
+.newseditor .required {
+ color: #d9534f;
+ padding-left: 8px;
+ font-size: 1.2em;
+}
+
+.newseditor .article_title {
+ font-size: 1.6em;
+ font-weight: bold;
+}
+
+.newseditor .article_content {
+ color: #777777;
+ padding-left: 8px;
+ font-size: 1.2em;
+}
+
+.newsreader_panel {
+ border: none;
+ font-family: 'Spectral', serif;
+}
+
+.newsreader_panel .panel-heading {
+ background-color: white !important;
+ border: none;
+ font-weight: bolder;
+ /* height: 26vh; */
+}
+
+.newsreader_panel .panel-heading > h2 {
+ font-size: 2.6em;
+ font-weight: bolder;
+}
+
+.newsreader_panel .panel-body {
+ background-color: white !important;
+ border: none;
+ /* height: calc(100vh - 390px); */
+ overflow-Y: auto;
+ border-radius: 6px;
+}
+
+.news_quillviewer {
+ display: flex;
+ flex-direction: column;
+}
+.news_quillviewer > span {
+ font-size: 1.6em;
+ font-family: 'Spectral', serif;
+}
+.news_quillviewer > div {
+ margin-left: auto;
+ margin-right: auto;
+}
+.news_quillviewer > div > img {
+ display: block;
+ max-height: 100%;
+ max-width: 100%;
+}
+
+.newsreader_panel .panel-body .ql-container .ql-editor > p > img {
+ max-width: 30vw;
+}
+
+.newsroom {
+ display: flex;
+ justify-content: center;
+ flex-direction: column;
+ max-width: 1000px;
+ margin: auto;
+}
+
+.news_latest_block {
+ /* position: relative; */
+ margin-bottom: 50px;
+ background-color: #FFF;
+ -webkit-box-shadow: 1px 1px 9px 0px rgba(0,0,0,0.75);
+ -moz-box-shadow: 1px 1px 9px 0px rgba(0,0,0,0.75);
+ box-shadow: 1px 1px 9px 0px rgba(0,0,0,0.75);
+ padding: 40px;
+ /* flex-grow: 2; */
+ display: -webkit-flex; /* Safari */
+ display: flex;
+ justify-content: flex-start;
+ -webkit-flex-direction: row; /* Safari 6.1+ */
+ flex-direction: row;
+}
+
+.news_latest {
+ position: relative;
+ height: 400px;
+ /* width: 900px; */
+ margin-bottom: 50px;
+ background-color: #FFF;
+ -webkit-box-shadow: 1px 1px 9px 0px rgba(0,0,0,0.75);
+ -moz-box-shadow: 1px 1px 9px 0px rgba(0,0,0,0.75);
+ box-shadow: 1px 1px 9px 0px rgba(0,0,0,0.75);
+ padding: 50px;
+ /* flex-grow: 2; */
+ display: -webkit-flex; /* Safari */
+ display: flex;
+ justify-content: flex-start;
+ -webkit-flex-direction: row; /* Safari 6.1+ */
+ flex-direction: row;
+}
+
+.news_latest .badge {
+ position: absolute;
+ right: 50px;
+ bottom: 360px;
+ box-sizing: border-box;
+ padding-top: 12px;
+ background-color: #f1c40f;
+ width: 80px;
+ height: 80px;
+ color: #4B4B4B;
+ text-align: center;
+ border-radius: 50%;
+ -webkit-box-shadow: 10px 10px 50px 0px rgba(0, 0, 0, 0.75);
+ -moz-box-shadow: 10px 10px 50px 0px rgba(0, 0, 0, 0.75);
+ box-shadow: 10px 10px 50px 0px rgba(0, 0, 0, 0.75);
+}
+
+.news_latest .badge_green {
+ position: absolute;
+ right: 50px;
+ bottom: 360px;
+ box-sizing: border-box;
+ padding-top: 12px;
+ background-color: #2ecc71;
+ width: 80px;
+ height: 80px;
+ color: #4B4B4B;
+ text-align: center;
+ border-radius: 50%;
+ -webkit-box-shadow: 10px 10px 50px 0px rgba(0, 0, 0, 0.75);
+ -moz-box-shadow: 10px 10px 50px 0px rgba(0, 0, 0, 0.75);
+ box-shadow: 10px 10px 50px 0px rgba(0, 0, 0, 0.75);
+}
+
+.news_latest .news_image {
+ width: 60%;
+ max-width: 100%;
+ /* background-image: url('../images/chemeln.jpg'); */
+ background-size: contain;
+ background-repeat: no-repeat;
+}
+
+.news_latest .news_image > svg {
+ width: 90px !important;
+ height: 90px !important;
+}
+
+.news_latest > img {
+ vertical-align: bottom;
+}
+
+.news_latest .news_title {
+ font-size: 3rem;
+ font-weight: bolder;
+ color: #0079bf;
+ word-break: break-word;
+}
+
+.news_author {
+ font-size: 1.4rem;
+ margin-top: 5px;
+ font-weight: normal;
+}
+
+.news_author > img {
+ /* padding-top: 2px; */
+ margin-left: 10px;
+ float: left;
+ height: 20px;
+ width: 20px;
+ border-radius: 50%;
+}
+
+.heading_separator {
+ margin-top: 10px;
+ border: 1px solid #C3C3C3;
+}
+
+.news_card {
+ border: none !important;
+ margin-right: 10px;
+ margin-bottom: 80px !important;
+ box-shadow: unset !important;
+}
+
+.news_header {
+ width: auto;
+ /* height: 150px; */
+ background-color: white !important;
+ /* text-align: center; */
+ padding: 10px !important;
+ margin-left: 30px;
+ margin-right: 30px;
+}
+
+.news_header > img {
+ height: 100px;
+ width: auto;
+}
+
+.news_body {
+ /* min-height: 150px; */
+ padding-right: 30px !important;
+ padding-left: 30px !important;
+}
+
+.news_title {
+ font-size: 2.2rem;
+ font-weight: bolder;
+ color: #0079bf;
+ /* color: #4B4B4B; */
+ word-break: break-word;
+}
+
+.news_content {
+ text-align: justify;
+ font-size: 1.5rem;
+ line-height: 150%;
+ color: #4B4B4B;
+ max-height: 146px;
+ text-overflow: clip;
+ overflow: hidden;
+ white-space: pre-line;
+}
+
+.news_content_card_s {
+ text-align: justify;
+ font-size: 1.5rem;
+ line-height: 150%;
+ color: #4B4B4B;
+ /* height: 100px; */
+ max-height: 146px;
+ text-overflow: clip;
+ overflow: hidden;
+ white-space: pre-line;
+}
+
+.news_card_content {
+ position: relative;
+}
+
+.news_card_content .news_card_s {
+ width: 70vw;
+ min-height: 200px;
+ padding: 20px;
+ border-radius: 3px;
+ background-color: white;
+ box-shadow: 0px 10px 10px rgba(0, 0, 0, 0.2);
+ position: relative;
+ overflow: hidden;
+}
+
+.news_card_content .news_card_s::before
+ {
+ content: '';
+ display: block;
+ width: 190px;
+ height: 300px;
+ background: #e0e0e0;
+ position: absolute;
+ transform: rotate(-30deg);
+ top: -24px;
+ left: -78px;
+}
+
+.card_info {
+ display: flex;
+ justify-content: center;
+ align-items: center;
+ flex-direction: row;
+ z-index: 2;
+ position: relative;
+}
+
+.card_info .info {
+ padding: 0px 20px;
+ width: 100vw;
+}
+
+.card_info .info > h1 {
+ font-size: 1.6em;
+ font-weight: bolder;
+ word-break: break-word;
+ margin-top: unset;
+ margin-bottom: unset;
+}
+
+.card_info .info > span {
+ font-size: 0.9em;
+ margin: 0px 1px;
+ opacity: 0.8;
+}
+
+.card_info .info .short_content {
+ max-height: 100px;
+}
+
+.card_info .info .short_content::before {
+ background: linear-gradient(hsla(0,0%,100%,0.6),#fff);
+ content: "";
+ height: 80px;
+ position: absolute;
+ left: 0px;
+ top: 240px;
+ width: 100%;
+}
+
+.news_card_content .news_card_s .read {
+ position: absolute;
+ /* bottom: 10px; */
+ /* right: 10px; */
+ z-index: 2;
+ padding: 0px 20px;
+}
+
+.news_card_badge_s {
+ padding: 10px 10px;
+ border-radius: 3px;
+ background-color: #ECECEC;
+ /* width: 240px; */
+ width: calc(70vw - 20px);
+ box-shadow: 0px 10px 10px rgba(0, 0, 0, 0.2);
+ position: relative;
+ z-index: -1;
+ left: 10px;
+ bottom: 0px;
+ margin-bottom: 50px;
+ justify-content: flex-end;
+ text-align: right;
+}
+
+.news_card_badge_s > span {
+ font-size: 0.9em;
+ margin: 0px 1px;
+ opacity: 0.6;
+ font-style: italic;
+}
+
+.news_card_badge_s > img {
+ /* padding-top: 3px;
+ float: left; */
+ height: auto;
+ width: 15px;
+}
+
+.news_column {
+ display: flex;
+ justify-content: center;
+}
+
+.news_badge {
+ position: relative;
+ width: 100px;
+ display: inline-block;
+ margin: 40px;
+}
+.news_badge .title {
+ font-weight: bold;
+ font-size: 0.8em;
+ position: absolute;
+ top: -28px;
+ border-radius: 8px 8px 0 0;
+ text-align: center;
+ width: 100%;
+ background: red;
+ padding: 10px 0;
+}
+.news_badge .subtitle {
+ position: absolute;
+ font-size: 0.8em;
+ width: 100%;
+ text-align: center;
+ color: white;
+ position: absolute;
+ top: 100px;
+}
+.news_badge .subtitle:after {
+ content: "★ ★ ★";
+ display: block;
+ font-size: .4em;
+ position: relative;
+ margin: 15px 0 0;
+ transition: all .3s;
+}
+.news_badge:hover .subtitle:after {
+ word-spacing: 30px;
+}
+
+.howto_page {
+ margin: auto;
+ height: calc(90vh);
+ overflow: auto;
+}
+
+.red .title {
+ background: #DC514E;
+}
+.red .subtitle:after {
+ color: #DC514E;
+}
+
+.green .title {
+ background: #2ecc71;
+}
+.green .subtitle:after {
+ color: #2ecc71;
+}
+
+.gray .title {
+ background: #95a5a6;
+}
+.gray .subtitle:after {
+ color: #95a5a6;
+}
+
+.yellow .title {
+ background: #f1c40f;
+}
+.yellow .subtitle:after {
+ color: #f1c40f;
+}
+
+.blue .title {
+ background: #3498db;
+}
+.blue .subtitle:after {
+ color: #3498db;
+}
+
+.news_pager {
+ /* position: absolute; */
+ right: 60px;
+ bottom: 60px;
+ box-sizing: border-box;
+ padding-top: 15px;
+ background-color: #DC514E;
+ width: 60px;
+ height: 60px;
+ color: white;
+ text-align: center;
+ border-radius: 50%;
+ -webkit-box-shadow: 0px 0px 5px 5px rgba(241, 147, 147, 0.75);
+ -moz-box-shadow: 0px 0px 5px 5px rgba(241, 147, 147, 0.75);
+ box-shadow: 0px 0px 5px 5px rgba(241, 147, 147, 0.75);
+}
+
+/* common */
+.ribbon {
+ width: 150px;
+ height: 150px;
+ overflow: hidden;
+ position: absolute;
+ z-index: 10;
+}
+.ribbon::before,
+.ribbon::after {
+ position: absolute;
+ z-index: -1;
+ content: '';
+ display: block;
+ border: 5px solid #2980b9;
+}
+.ribbon span {
+ position: absolute;
+ display: block;
+ width: 225px;
+ padding: 15px 0;
+ background-color: #3498db;
+ box-shadow: 0 5px 10px rgba(0,0,0,.1);
+ color: #fff;
+ font: 700 18px/1 'Lato', sans-serif;
+ text-shadow: 0 1px 1px rgba(0,0,0,.2);
+ text-transform: uppercase;
+ text-align: center;
+}
+
+/* top left*/
+.ribbon-top-left {
+ top: -10px;
+ left: -10px;
+}
+.ribbon-top-left::before,
+.ribbon-top-left::after {
+ border-top-color: transparent;
+ border-left-color: transparent;
+}
+.ribbon-top-left::before {
+ top: 0;
+ right: 0;
+}
+.ribbon-top-left::after {
+ bottom: 0;
+ left: 0;
+}
+.ribbon-top-left span {
+ right: -25px;
+ top: 30px;
+ transform: rotate(-45deg);
+}
+
+/* top right*/
+.ribbon-top-right {
+ top: -10px;
+ right: -10px;
+}
+.ribbon-top-right::before,
+.ribbon-top-right::after {
+ border-top-color: transparent;
+ border-right-color: transparent;
+}
+.ribbon-top-right::before {
+ top: 0;
+ left: 0;
+}
+.ribbon-top-right::after {
+ bottom: 0;
+ right: 0;
+}
+.ribbon-top-right span {
+ left: -25px;
+ top: 30px;
+ transform: rotate(45deg);
+}
+
+/* bottom left*/
+.ribbon-bottom-left {
+ bottom: -10px;
+ left: -10px;
+}
+.ribbon-bottom-left::before,
+.ribbon-bottom-left::after {
+ border-bottom-color: transparent;
+ border-left-color: transparent;
+}
+.ribbon-bottom-left::before {
+ bottom: 0;
+ right: 0;
+}
+.ribbon-bottom-left::after {
+ top: 0;
+ left: 0;
+}
+.ribbon-bottom-left span {
+ right: -25px;
+ bottom: 30px;
+ transform: rotate(225deg);
+}
+
+/* bottom right*/
+.ribbon-bottom-right {
+ bottom: -10px;
+ right: -10px;
+}
+.ribbon-bottom-right::before,
+.ribbon-bottom-right::after {
+ border-bottom-color: transparent;
+ border-right-color: transparent;
+}
+.ribbon-bottom-right::before {
+ bottom: 0;
+ left: 0;
+}
+.ribbon-bottom-right::after {
+ top: 0;
+ right: 0;
+}
+.ribbon-bottom-right span {
+ left: -25px;
+ bottom: 30px;
+ transform: rotate(-225deg);
+}
diff --git a/app/assets/stylesheets/quill_viewer.scss b/app/assets/stylesheets/quill_viewer.scss
index 3b0aa224a..1e059ca50 100644
--- a/app/assets/stylesheets/quill_viewer.scss
+++ b/app/assets/stylesheets/quill_viewer.scss
@@ -1,3 +1,10 @@
.quill-viewer .ql-tooltip {
height: 0px;
}
+
+.ql-disabled {
+ .ql-hidden {
+ display: none;
+ }
+}
+
diff --git a/app/assets/stylesheets/reaction.scss b/app/assets/stylesheets/reaction.scss
index 08efc4408..155f0d64d 100644
--- a/app/assets/stylesheets/reaction.scss
+++ b/app/assets/stylesheets/reaction.scss
@@ -222,3 +222,7 @@ table.reaction-scheme-solvent {
//from {top: 0px;}
from { background-color: aliceblue;}
}
+
+.publishReactionModal {
+ margin: unset !important;
+}
diff --git a/app/assets/stylesheets/repo_home.scss b/app/assets/stylesheets/repo_home.scss
new file mode 100644
index 000000000..28fa66c5b
--- /dev/null
+++ b/app/assets/stylesheets/repo_home.scss
@@ -0,0 +1,231 @@
+.repo-home {
+ display: block;
+ max-width: 1200px;
+ margin: auto;
+ // height: calc(100vh - 80px);
+ // overflow-y: scroll;
+}
+
+.card-well {
+ background-color: #f5f5f5;
+ border: 1px solid #e3e3e3;
+ border-radius: 6px;
+ height: 50vh;//auto; //calc(80vh - 190px);
+ // overflow-x: auto;
+ padding: 20px;
+
+}
+
+.card-well-competition {
+ @extend .card-well;
+ padding: 30px 15px;
+
+ .carl-spt{
+ background-color: white;
+ }
+
+ .carl-spt-item {
+ height: 360px;
+ text-align: center;
+ }
+
+ .carl-spt-item .caption {
+ left: 15%;
+ right: 15%;
+ padding-top: 0px;
+ bottom: 0px;
+ }
+
+ .carl-spt-item-s {
+ height: 220px;
+ text-align: center;
+ }
+
+ .carl-spt-item-s .caption {
+ left: 15%;
+ right: 15%;
+ padding-bottom: 0px;
+ bottom: 0px;
+ }
+
+ img {
+ width: 100%;
+ }
+
+ p {
+ bottom: -45px;
+ color: black;
+ position: relative;
+ text-align: justify;
+ text-shadow: none;
+ }
+
+ .carousel-control.left, .carousel-control.right {
+ background-image: none !important;
+ }
+
+ .italic-desc {
+ font-size: 1.4rem;
+ font-style: italic;
+ }
+}
+
+.thumbnail-spt img {
+ width: 25%;
+}
+
+.icon-chemotion {
+ margin: 30px;
+ width: 90%;
+}
+
+.repository-for {
+ margin: 30px;
+ line-height: 45px;
+}
+
+.visibility-impact {
+ left: 30px;
+ width: 300px !important;
+}
+
+.chem-finder {
+ left: 10%;
+ top: 10px;
+
+ img {
+ width: 90%;
+ }
+}
+
+.bot-navbar {
+ right: 0px;
+ left: 0px;
+ bottom: 0px;
+ z-index: 1030;
+ background-color: #efefef;
+}
+
+.card-partners {
+ background-color: #f5f5f5;
+ // height: calc(50vh - 134px);
+ .partner-heading {
+ background-color: #f5f5f5;
+ // border: 1px solid #e3e3e3;
+ border-radius: 6px;
+ // height: 80px;
+ margin: 20px 5px 0;
+ padding: 5px;
+ text-align: center;
+ }
+
+ .partner-row {
+ display: flex;
+ justify-content: center;
+ overflow-x: auto;
+ padding-top: 30px;
+ }
+
+ .partners-info {
+ height: 250px;
+ // height: auto;
+ // width: 250px;
+ position: relative;
+ display: table-cell;
+ // display: inline-flex;
+ margin: 5px;
+ border: 0px;
+ background-color: #f5f5f5;
+
+ img {
+ display: block;
+ margin: auto;
+ max-height: 90%;
+ max-width: 90%;
+ opacity: 1.0;
+ z-index: 1;
+ // position: absolute;
+ // top: 0%;
+ }
+
+ &:hover img {
+ opacity: 0.2;
+ }
+
+ &:hover {
+ border:2px solid #ddd;
+ }
+
+ &:hover .info {
+ opacity: 1.0;
+ }
+
+ .info {
+ top: 0%;
+ left: 0%;
+ opacity: 0.0;
+ position: absolute;
+ padding: 5px;
+ margin: 5px;
+ text-align: justify;
+ }
+ }
+}
+
+
+.repo-about {
+ display: block;
+ // height: calc(100vh - 80px);
+ // overflow-y: scroll;
+}
+
+.card-icons {
+ div {
+ height: 100px;
+ position:relative;
+ }
+
+ img {
+ max-height: 100%;
+ max-width: 100%;
+ position: absolute;
+ top: 0;
+ left: 0;
+ right: 0;
+ bottom: 0;
+ margin: auto;
+ }
+}
+
+.card-well-about {
+ background-color: #f5f5f5;
+ border: 1px solid #e3e3e3;
+ border-radius: 6px;
+ //overflow: auto;
+ padding: 30px;
+ text-align: center;
+ // height: 80vh;
+}
+
+.panel-analyses-public {
+ margin: 2px !important;
+}
+
+.carl-sample svg {
+ max-width: 100%;
+ max-height: 500px;
+ height: 300px;
+ width: 100%;
+}
+
+.reaction-scheme-word {
+ font-size: smaller;
+ color: #337ab7;
+}
+
+.move-embargo-dialog {
+ display: block;
+ padding-left: 0px;
+ top: 45% !important;
+ width: 40vw !important;
+}
diff --git a/app/assets/stylesheets/search.scss b/app/assets/stylesheets/search.scss
index 7d4dbd240..7acc1af7b 100644
--- a/app/assets/stylesheets/search.scss
+++ b/app/assets/stylesheets/search.scss
@@ -19,6 +19,10 @@
position: relative;
z-index: 2;
}
+
+ .button-caret {
+ border-radius: unset;
+ }
}
.list-group-item-wrap {
diff --git a/app/assets/stylesheets/switch.scss b/app/assets/stylesheets/switch.scss
index d3db4f3ec..d9ba6518d 100644
--- a/app/assets/stylesheets/switch.scss
+++ b/app/assets/stylesheets/switch.scss
@@ -85,6 +85,91 @@
}
}
+.switchb {
+ position: relative;
+ display: inline-block;
+ box-sizing: border-box;
+ width: 44px;
+ height: 22px;
+ line-height: 20px;
+ vertical-align: middle;
+ border-radius: 20px 20px;
+ border: 1px solid #ccc;
+ background-color: #5cb85c;
+ cursor: pointer;
+ transition-timing-function: ease;
+
+ &-inner {
+ color:#fff;
+ top:4px;
+ font-size: 14px;
+ position: absolute;
+ left: 25px;
+ }
+
+ &:after{
+ position: absolute;
+ width: 18px;
+ height: 18px;
+ left: 3%;
+ top:4px;
+ border-radius: 50% 50%;
+ background-color: #ffffff;
+ content: " ";
+ cursor: pointer;
+ transform: scale(1);
+ transition-timing-function: ease;
+ animation-duration: 0.3;
+ animation-name: switchOff;
+ }
+
+ &:hover:after{
+ transform: scale(1.1);
+ animation-name: switchOn;
+ }
+
+ &:focus {
+ outline: none;
+ }
+
+ &-checked{
+ background-color: #5bc0de;
+ .switchb-inner {
+ left: 10px;
+ }
+ &:after{
+ left: 77%;
+ }
+ }
+
+ &-disabled{
+ cursor: no-drop;
+ background: #ccc;
+ border-color:#ccc;
+
+ &:after{
+ background: #9e9e9e;
+ animation-name: none;
+ cursor: no-drop;
+ }
+
+ &:hover:after{
+ transform: scale(1);
+ animation-name: none;
+ }
+ }
+
+ &-label {
+ display: inline-block;
+ line-height: 20px;
+ font-size: 14px;
+ padding-left: 10px;
+ vertical-align: middle;
+ white-space: normal;
+ pointer-events: none;
+ user-select: text;
+ }
+}
@keyframes switchOn {
0% {
transform: scale(1);
diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index 779c5b692..a380a15cd 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -2,6 +2,7 @@ class ApplicationController < ActionController::Base
# Prevent CSRF attacks by raising an exception.
# For APIs, you may want to use :null_session instead.
protect_from_forgery with: :exception
+ # before_action :store_user_location!, if: :storable_location?
before_action :authenticate_user!
protect_from_forgery with: :null_session, if: Proc.new { |c| c.request.format == 'application/json' }
@@ -15,9 +16,16 @@ def configure_permitted_parameters
affiliations_attributes: [
:country,
:organization,
- :department,
- :group
+ :department
]
])
end
+
+ # def storable_location?
+ # request.get? && is_navigational_format? && !devise_controller? && !request.xhr?
+ # end
+
+ # def store_user_location!
+ # store_location_for(:user, )
+ # end
end
diff --git a/app/controllers/pages_controller.rb b/app/controllers/pages_controller.rb
index 3e5b13454..f77b5a1ea 100644
--- a/app/controllers/pages_controller.rb
+++ b/app/controllers/pages_controller.rb
@@ -1,6 +1,6 @@
class PagesController < ApplicationController
skip_before_action :authenticate_user!, only: [
- :home, :about, :chemscanner, :chemspectra, :chemspectra_editor
+ :home, :about, :directive, :root_page
]
before_action :fetch_affiliations, only: [:affiliations, :update_affiliations]
before_action :build_affiliation, only: [:affiliations, :update_affiliations]
@@ -11,17 +11,31 @@ def about; end
def docx; end
- def welcome; end
+ def mydb; end
def editor; end
+ def root_page
+ render layout: 'root_layout'
+ end
+
+ def directive; end
+
+ def settings; end
+
+ def tokens
+ @origin = params[:origin]
+ aks = AuthenticationKey.where(user_id: current_user, role: "gate in")
+ @fqdns = aks.pluck :fqdn
+ end
+
def update_user
@user = current_user
@user.counters['reactions'] = params[:reactions_count].to_i
@user.reaction_name_prefix = params[:reaction_name_prefix]
if @user.save
flash['success'] = 'User settings is successfully saved!'
- redirect_to root_path
+ redirect_to main_app.root_url
else
flash.now['danger'] = 'Not saved! Please check input fields.'
render 'user'
@@ -98,13 +112,13 @@ def fetch_affiliations
def affiliation_params
params.require(:affiliation).permit(
:id, :_destroy,
- :country, :organization, :department, :group,
+ :country, :organization, :department,
:from, :to, :from_month, :to_month
)
end
def sliced_affiliation_params
- affiliation_params.slice(:country, :organization, :department, :group)
+ affiliation_params.slice(:country, :organization, :department)
end
def affiliations_params
@@ -112,7 +126,7 @@ def affiliations_params
:utf8, :_method, :authenticity_token, :commit,
affiliations: [
:id, :_destroy,
- # :country, :organization, :department, :group,
+ # :country, :organization, :department,
:from, :to, :from_month, :to_month
]
)
diff --git a/app/controllers/users/registrations_controller.rb b/app/controllers/users/registrations_controller.rb
index 59c9d6716..e21df304e 100644
--- a/app/controllers/users/registrations_controller.rb
+++ b/app/controllers/users/registrations_controller.rb
@@ -9,7 +9,6 @@ class Users::RegistrationsController < Devise::RegistrationsController
def new
build_resource({})
-
@affiliation = resource.affiliations.build
set_minimum_password_length
diff --git a/app/jobs/chemotion_embargo_pubchem_job.rb b/app/jobs/chemotion_embargo_pubchem_job.rb
new file mode 100644
index 000000000..a73d92cb5
--- /dev/null
+++ b/app/jobs/chemotion_embargo_pubchem_job.rb
@@ -0,0 +1,111 @@
+class ChemotionEmbargoPubchemJob < ActiveJob::Base
+ attr_reader :embargo_collection, :publication, :element, :publications
+
+ def perform(embargo_col_id)
+ @embargo_collection = Collection.find(embargo_col_id)
+ @sync_emb_col = @embargo_collection.sync_collections_users&.first
+
+ pub_samples = Publication.where(ancestry: nil, element: @embargo_collection.samples).order(updated_at: :desc)
+ pub_reactions = Publication.where(ancestry: nil, element: @embargo_collection.reactions).order(updated_at: :desc)
+ @pub_list = pub_samples + pub_reactions
+ @pub_list.each do |embargo_pub|
+ @publication = Publication.find(embargo_pub.id)
+ @publications = [publication] + publication.descendants
+ @element = publication.element
+ publications.each do |pub|
+ pub.transition_from_start_to_metadata_uploading!
+ end
+ publications.each do |pub|
+ pub.transition_from_metadata_uploading_to_uploaded!
+ end
+ publications.each do |pub|
+ pub.transition_from_metadata_uploaded_to_doi_registering!
+ end
+ publications.each do |pub|
+ pub.transition_from_doi_registering_to_registered!
+ end
+ publications.reverse_each do |pub|
+ if pub.element_type == 'Sample'
+ pub.transition_from_doi_registered_to_pubchem_registering!
+ else
+ pub.transition_from_doi_registered_to_completing!
+ end
+ end
+ publications.each do |pub|
+ pub.transition_from_completing_to_completed!
+ end
+ end
+ send_pubchem
+ remove_publish_pending
+ send_email
+ end
+
+ def remove_publish_pending
+ @pub_list.each do |embargo_pub|
+ @publication = Publication.find(embargo_pub.id)
+ ot = @publication.original_element&.tag&.taggable_data&.delete('publish_pending')
+ @publication.original_element.tag.save! unless ot.nil?
+ if @publication.element_type == 'Reaction'
+ @publication.original_element&.samples.each do |s|
+ t = s.tag&.taggable_data&.delete('publish_pending')
+ s.tag.save! unless t.nil?
+ end
+ end
+ end
+ end
+
+ def send_pubchem
+ sdf = ""
+ pubchem_list = Publication.where(element: @embargo_collection.samples)
+ pubchem_list.each do |pub|
+ metadata_obj = OpenStruct.new(sample: pub.element)
+ metadata_file = ERB.new(File.read(
+ File.join(Rails.root,'app', 'publish', 'pubchem_metadata.sdf.erb')
+ ))
+ mt = metadata_file.result(metadata_obj.instance_eval { binding })
+ pub.element.update_publication_tag(pubchem_reg_at: DateTime.now)
+ pd = pub.taggable_data.merge(pubchem_reg_at: DateTime.now)
+ sdf += mt
+ end
+ message = "\n---Embargo MOLFILE START---"
+ #Publication.logger([message, sdf, "(Embargo Pubchem FTP upload #{Rails.env.production ? '' : 'NOT'} sent (mode: #{ENV['PUBLISH_MODE']})"])
+ publication_logger ||= Logger.new(File.join(Rails.root, 'log', 'publication.log'))
+ message = [message, sdf, "Embargo Pubchem FTP upload sdf"].flatten.join("\n")
+ publication_logger.info(
+ <<~INFO
+ ******** MODE #{ENV['PUBLISH_MODE']}********
+ Embargo Collection: #{@embargo_collection.id} - #{@embargo_collection.label} ( #{@embargo_collection.samples.map{ |s| s.id }} )
+ #{message}
+ ********************************************************************************
+ INFO
+ )
+
+ if Rails.env.production? && ENV['PUBLISH_MODE'] == 'production'
+ ftp = Net::FTP.new('ftp-private.ncbi.nlm.nih.gov')
+ ftp.passive = true
+ ftp.login(ENV['PUBCHEM_LOGIN'], ENV['PUBCHEM_PASSWORD'])
+ ftp.puttextcontent(sdf, @embargo_collection.id.to_s + '.sdf.in')
+ ftp.close
+ else
+ #file_path = Rails.public_path.join('pubchem_upload', "#{self.job_id}_#{@embargo_collection.id}.sdf.in")
+ #File.write(file_path, sdf)
+ end
+
+ pubchem_list.each do |pub|
+ pub.update_columns(state: 'completing')
+ pub.transition_from_completing_to_completed!
+ end
+ end
+
+ def send_email
+ if ENV['PUBLISH_MODE'] == 'production'
+ PublicationMailer.mail_publish_embargo_release(@embargo_collection.id).deliver_now
+ end
+ Message.create_msg_notification(
+ channel_subject: Channel::PUBLICATION_REVIEW,
+ message_from: @sync_emb_col.user_id,
+ data_args: {subject: "Congratulations! Embargo Collection #{@embargo_collection.label} released and published"}
+ )
+ end
+end
+
diff --git a/app/jobs/chemotion_repo_publishing_job.rb b/app/jobs/chemotion_repo_publishing_job.rb
new file mode 100644
index 000000000..dc2172dc4
--- /dev/null
+++ b/app/jobs/chemotion_repo_publishing_job.rb
@@ -0,0 +1,159 @@
+class ChemotionRepoPublishingJob < ActiveJob::Base
+ attr_reader :publication, :element, :publications
+ INVALID_STATE = "INVALID STATE"
+
+ def perform(id, action, current_user_id = 0)
+ @publication = Publication.find(id)
+ @publications = [publication] + publication.descendants
+ @publications.each { |d| d.update_columns(state: action) }
+
+ @element = publication.element
+ publication.logger("publication STARTS")
+
+ unless publication.state.present?
+ publication.logger(INVALID_STATE)
+ raise INVALID_STATE
+ end
+
+ send(publication.state)
+ end
+
+ private
+
+ def accepted
+ publications.each do |pub|
+ pub.transition_from_start_to_metadata_uploading!
+ end
+ transition_success?(
+ Publication::STATE_ACCEPTED,
+ Publication::STATE_DC_METADATA_UPLOADING
+ )
+ dc_metadata_uploading
+ end
+
+ def dc_metadata_uploading
+ publications.each do |pub|
+ pub.transition_from_metadata_uploading_to_uploaded!
+ end
+ transition_success?(
+ Publication::STATE_DC_METADATA_UPLOADING,
+ Publication::STATE_DC_METADATA_UPLOADED
+ )
+ dc_metadata_uploaded
+ end
+
+ def dc_metadata_uploaded
+ publications.each do |pub|
+ pub.transition_from_metadata_uploaded_to_doi_registering!
+ end
+ transition_success?(
+ Publication::STATE_DC_METADATA_UPLOADED,
+ Publication::STATE_DC_DOI_REGISTERING
+ )
+ dc_doi_registering
+ end
+
+ def dc_doi_registering
+ publications.each do |pub|
+ pub.transition_from_doi_registering_to_registered!
+ end
+ transition_success?(
+ Publication::STATE_DC_DOI_REGISTERING,
+ Publication::STATE_DC_DOI_REGISTERED
+ )
+ dc_doi_registered
+ end
+
+ def dc_doi_registered
+ publications.reverse_each do |pub|
+ if pub.element_type == 'Sample'
+ pub.transition_from_doi_registered_to_pubchem_registering!
+ else
+ pub.transition_from_doi_registered_to_completing!
+ end
+ end
+ transition_success?(
+ Publication::STATE_DC_DOI_REGISTERED,
+ [Publication::STATE_PUBCHEM_REGISTERING, Publication::STATE_COMPLETING]
+ )
+ pubchem_registering
+ end
+
+ def pubchem_registering
+ publications.each do |pub|
+ if pub.element_type == 'Sample'
+ pub.transition_from_doi_pubchem_registering_to_registered!
+ else
+ pub.transition_from_doi_registered_to_completing!
+ end
+ end
+ transition_success?(
+ Publication::STATE_PUBCHEM_REGISTERING,
+ [Publication::STATE_PUBCHEM_REGISTERED, Publication::STATE_COMPLETING]
+ )
+ pubchem_registered
+ end
+
+ def pubchem_registered
+ publications.each do |pub|
+ if pub.element_type == 'Sample'
+ pub.transition_from_pubchem_registered_to_completing!
+ else
+ pub.transition_from_doi_registered_to_completing!
+ end
+ end
+ transition_success?(
+ Publication::STATE_PUBCHEM_REGISTERED,
+ Publication::STATE_COMPLETING
+ )
+ completing
+ end
+
+ def completing
+ publications.each do |pub|
+ pub.transition_from_completing_to_completed!
+ end
+ transition_success?(
+ Publication::STATE_COMPLETING,
+ Publication::STATE_COMPLETED
+ )
+ completed
+ end
+
+ def completed
+ remove_publish_pending
+ if ENV['PUBLISH_MODE'] == 'production'
+ PublicationMailer.mail_publish_approval(@publication.id).deliver_now
+ end
+ Message.create_msg_notification(
+ channel_subject: Channel::PUBLICATION_REVIEW,
+ message_from: @publication.published_by || @publication.taggable_data['creators']&.first&.dig('id'),
+ data_args: {subject: "Congratulations! Chemotion Repository: #{@publication.doi.suffix} published"}
+ )
+ end
+
+ def published
+ end
+
+ def remove_publish_pending
+ ot = @publication.original_element&.tag&.taggable_data&.delete('publish_pending')
+ @publication.original_element.tag.save! unless ot.nil?
+ if @publication.element_type == 'Reaction'
+ @publication.original_element&.samples.each do |s|
+ t = s.tag&.taggable_data&.delete('publish_pending')
+ s.tag.save! unless t.nil?
+ end
+ end
+ end
+
+ def transition_success?(from_state, to_state)
+ failed = publications.select{|pub| !([to_state].flatten.include?(pub.state))}
+ .map{|pub| [pub.id, pub.state]}
+ if failed.present?
+ message = "TRANSITION FROM #{from_state} to #{to_state}, FAILED\n failed for publications: #{failed}"
+ publication.logger(message)
+ raise message
+ end
+ true
+ end
+end
diff --git a/app/jobs/chemotion_repo_reviewing_job.rb b/app/jobs/chemotion_repo_reviewing_job.rb
new file mode 100644
index 000000000..ad8a0085b
--- /dev/null
+++ b/app/jobs/chemotion_repo_reviewing_job.rb
@@ -0,0 +1,114 @@
+class ChemotionRepoReviewingJob < ActiveJob::Base
+ attr_reader :publication, :publications
+ INVALID_STATE = "INVALID STATE"
+
+ def perform(id, action, current_user_id = 0)
+ @publication = Publication.find(id)
+ @publications = [publication] + publication.descendants
+ @publications.each { |d| d.update_columns(state: action) }
+ @current_user_id = current_user_id
+ # @element = publication.element
+ publication.logger("publication STARTS")
+
+ unless publication.state.present?
+ publication.logger(INVALID_STATE)
+ raise INVALID_STATE
+ end
+
+ # process_element
+ notify_users
+ mail_users
+ end
+
+ private
+
+ # NB: Moved to model
+ # def process_element
+ # case publication.state
+ # when Publication::STATE_PENDING
+ # publication.move_to_pending_collection
+ # when Publication::STATE_REVIEWED
+ # publication.move_to_review_collection
+ # when Publication::STATE_ACCEPTED
+ # publication.move_to_accepted_collection
+ # when Publication::STATE_DECLINED
+ # publication.declined_reverse_original_element
+ # publication.declined_move_collections
+ # end
+ # end
+
+ def notify_users
+ args = {
+ channel_subject: Channel::PUBLICATION_REVIEW,
+ message_from: publication.published_by || publication.taggable_data['creators']&.first&.dig('id')
+ }
+
+ case publication.state
+ when Publication::STATE_PENDING
+ args[:message_to] = User.reviewer_ids
+ args[:data_args] = {
+ subject: "Chemotion Repository: Review Request for #{publication.doi.suffix}"
+ }
+ when Publication::STATE_REVIEWED
+ args[:data_args] = {
+ subject: "Chemotion Repository: Modification request for #{publication.doi.suffix} \n Please check the reviewer's comments and request for modification. \n Once done with the revision, you can then resubmit your publication."
+ }
+ when Publication::STATE_ACCEPTED
+ args[:data_args] = {
+ subject: "Chemotion Repository: Publication Accepted. for #{publication.doi.suffix} \n Once the embargo is released, this submission will be published."
+ }
+ when Publication::STATE_DECLINED
+ title = publication.published_by == @current_user_id ? 'withdrawn' : 'rejected'
+ args[:data_args] = {
+ subject: "Chemotion Repository: Publication #{title}. for #{publication.doi.suffix}."
+ }
+ # when Publication::STATE_RETRACTED
+ else
+ return
+ end
+ Message.create_msg_notification(args)
+ end
+
+ def mail_users
+ return unless ENV['PUBLISH_MODE'] == 'production'
+
+ case publication.state
+ when Publication::STATE_PENDING
+ PublicationMailer.mail_reviewing_request(publication.id).deliver_now
+ when Publication::STATE_REVIEWED
+ PublicationMailer.mail_reviewed_request(publication.id).deliver_now
+ when Publication::STATE_ACCEPTED
+ PublicationMailer.mail_accepted_request(publication.id).deliver_now
+ when Publication::STATE_DECLINED
+ PublicationMailer.mail_declined_request(publication.id, @current_user_id).deliver_now unless @current_user_id.zero?
+ else
+ return
+ end
+ end
+
+ # NB: NOT USED?
+ # NB: Moved to model
+ # def release_original_element
+ # ot = publication.original_element&.tag&.taggable_data&.delete("publish_#{publication.element_type.downcase}")
+ # publication.original_element.tag.save! unless ot.nil?
+ #
+ # case publication.element_type
+ # when 'Sample'
+ # clear_orig_analyses(publication.original_element)
+ # when 'Reaction'
+ # clear_orig_analyses(publication.original_element)
+ # publication.original_element&.samples&.each do |s|
+ # t = s.tag&.taggable_data&.delete('publish_sample')
+ # s.tag.save! unless t.nil?
+ # clear_orig_analyses(s)
+ # end
+ # end
+ # end
+
+ # def clear_orig_analyses(element)
+ # element&.analyses&.each do |a|
+ # t = a.tag&.taggable_data&.delete('publish_analysis')
+ # a.tag.save! unless t.nil?
+ # end
+ # end
+end
diff --git a/app/jobs/pubchem_sid_job.rb b/app/jobs/pubchem_sid_job.rb
new file mode 100644
index 000000000..8ffb7b31a
--- /dev/null
+++ b/app/jobs/pubchem_sid_job.rb
@@ -0,0 +1,16 @@
+# Job to update publication SID by using DOI
+class PubchemSidJob < ActiveJob::Base
+ queue_as :pubchem_sid
+
+ # NB: PC has request restriction policy and timeout , hence the sleep_time params
+ # see http://pubchemdocs.ncbi.nlm.nih.gov/programmatic-access$_RequestVolumeLimitations
+ def perform(sleep_time: 10)
+ Publication.where(element_type: 'Sample')
+ .where("taggable_data->>'sid' isnull and taggable_data->>'doi' IS NOT NULL and state = 'completed'")
+ .order("id asc").each do |pub|
+ sid_info = Chemotion::PubchemService.sid_from_doi(pub.taggable_data["doi"])
+ pub.update!(taggable_data: pub.taggable_data.merge(sid: sid_info)) unless sid_info.nil?
+ sleep sleep_time
+ end
+ end
+ end
diff --git a/app/mailers/publication_mailer.rb b/app/mailers/publication_mailer.rb
new file mode 100644
index 000000000..6b9c009cd
--- /dev/null
+++ b/app/mailers/publication_mailer.rb
@@ -0,0 +1,246 @@
+class PublicationMailer < ActionMailer::Base
+ default from: ENV['DEVISE_SENDER'] || 'eln'
+
+ def external_review_content
+ <<~TXT
+ #{ENV['PUBLISH_MODE'] == 'staging' ? "TESTING MODE" : ""}
+
+ A temporary account for #{@embargo_collection} has been created!
+ Account: #{@external_acct}
+ Password: #{@external_pwd}
+
+ You can use this account/password to access:
+ #{@proto + @host}/home/embargo
+ TXT
+ end
+
+ def reviewing_content
+ <<~TXT
+ #{ENV['PUBLISH_MODE'] == 'staging' ? "TESTING MODE" : ""}
+ Creator: #{@creator&.name}
+ #{@publication.element_type} ##{@publication.element_id} is pending for publication.
+ Please help reviewing it at:
+ #{@proto + @host}/home/review/review_#{@publication.element_type.underscore}/#{@publication.element_id}
+ TXT
+ end
+
+ def reviewed_content
+ <<~TXT
+ #{ENV['PUBLISH_MODE'] == 'staging' ? "TESTING MODE" : ""}
+ Dear #{@creator&.name}
+
+ #{@publication.element_type} ##{@publication.element_id} has been reviewed.
+
+ Please check the reviewer's comments and request for modification:
+ #{@proto + @host}/home/review/review_#{@publication.element_type.underscore}/#{@publication.element_id}
+
+ You can also see the comments and edit your publication directly from your [Reviewing] collection at:
+ #{@proto + @host}/mydb/scollection/#{@creator_reviewing_scol_id}/#{@publication.element_type.underscore}/#{@publication.element_id}
+
+ Once done with the revision, you can then resubmit your publication.
+ TXT
+ end
+
+ def accepted_content
+ <<~TXT
+ #{ENV['PUBLISH_MODE'] == 'staging' ? "TESTING MODE" : ""}
+ Dear #{@creator&.name}
+
+ #{@publication.element_type} ##{@publication.element_id} has been accepted.
+
+ Once the embargo is released, this publication will be published.
+ TXT
+ end
+
+ def approved_content
+ <<~TXT
+ #{ENV['PUBLISH_MODE'] == 'staging' ? "TESTING MODE" : ""}
+ Congratulations!
+ Your #{@publication.element_type} ##{@publication.element_id} has been published.
+
+ See it at:
+ #{@proto + @host}/inchikey/#{@doi.suffix}
+ TXT
+ end
+
+
+ def embargo_released_content
+ <<~TXT
+ #{ENV['PUBLISH_MODE'] == 'staging' ? "TESTING MODE" : ""}
+ Congratulations!
+ Your embargo #{@embargo_collection} has been released.
+
+ See it at:
+ #{@proto + @host}/mydb/scollection/#{@sync_emb_col.id}
+ TXT
+ end
+
+ def declined_content
+ <<~TXT
+ #{ENV['PUBLISH_MODE'] == 'staging' ? "TESTING MODE" : ""}
+ Congratulations!
+ Your #{@publication.element_type} ##{@publication.element_id} has been declined.
+
+ See it at:
+ #{@proto + @host}/mydb/collection/all/#{@publication.element_type.underscore}/#{@publication.element_id.to_s}
+ TXT
+ end
+
+ def subject(prefix)
+ "Chemotion Repository: #{prefix} for #{@doi.suffix}"
+ end
+
+ def reviewers
+ # Person.where(id: User.reviewer_ids).pluck :email
+ []
+ end
+
+ def init_params(publication_id,current_user_id=0)
+ @publication = Publication.find(publication_id)
+ @doi = @publication.doi
+ # @publications = [@publication] + @publication.descendants
+ # @element = @publication.element
+ @is_submitter = @publication.published_by == current_user_id || false
+ @creator_id = @publication.published_by || @publication.taggable_data['creators']&.first&.dig('id')
+ @creator = User.find(@creator_id) unless @creator_id.nil?
+ @creator_reviewing_scol_id = @creator.reviewing_collection&.sync_collections_users&.first&.id if @publication.state === 'reviewed'
+
+ case ENV['PUBLISH_MODE']
+ when 'production'
+ if Rails.env.production?
+ @proto = "https://"
+ @host = "www.chemotion-repository.net"
+ end
+ when 'staging'
+ @proto = "http://"
+ @host = ENV['HOST'] || "localhost:3000"
+ end
+ end
+
+ def init_external_params(current_user, collection_label, email, pwd)
+ @creator = current_user
+ @embargo_collection = collection_label
+ @external_acct = email
+ @external_pwd = pwd
+
+ case ENV['PUBLISH_MODE']
+ when 'production'
+ if Rails.env.production?
+ @proto = "https://"
+ @host = "www.chemotion-repository.net"
+ end
+ when 'staging'
+ @proto = "http://"
+ @host = ENV['HOST'] || "localhost:3000"
+ end
+ end
+
+ def mail_reviewed_request(publication_id)
+ init_params(publication_id)
+ #reviewed_notify
+ mail(
+ to: @creator.email,
+ bcc: reviewers,
+ subject: subject('Publication Reviewed'),
+ ) do |format|
+ format.html
+ format.text { render plain: reviewed_content }
+ end
+ end
+
+ def mail_reviewing_request(publication_id)
+ init_params(publication_id)
+ #reviewing_notify
+ return unless reviewers.present?
+
+ mail(
+ to: reviewers,
+ subject: subject('Pending for publication. Review Request')
+ ) do |format|
+ format.html
+ format.text { render plain: reviewing_content }
+ end
+ end
+
+ def mail_accepted_request(publication_id)
+ init_params(publication_id)
+ #accepted_notify
+ mail(
+ to: @creator.email,
+ bcc: reviewers,
+ subject: subject('Publication Accepted')
+ ) do |format|
+ format.html
+ format.text { render plain: accepted_content }
+ end
+ end
+
+ def mail_publish_approval(publication_id)
+ init_params(publication_id)
+ #approved_notify
+ mail(
+ to: @creator.email,
+ bcc: reviewers,
+ subject: subject('Publication Approved'),
+ ) do |format|
+ format.html
+ format.text { render plain: approved_content }
+ end
+ end
+
+ def mail_publish_embargo_release(embargo_col_id)
+ @embargo_collection = Collection.find(embargo_col_id)
+ @sync_emb_col = @embargo_collection.sync_collections_users&.first
+ @creator = User.find(@sync_emb_col.user_id)
+
+ case ENV['PUBLISH_MODE']
+ when 'production'
+ if Rails.env.production?
+ @proto = "https://"
+ @host = "www.chemotion-repository.net"
+ end
+ when 'staging'
+ @proto = "http://"
+ @host = ENV['HOST'] || "localhost:3000"
+ end
+
+ #approved_notify
+ mail(
+ to: @creator.email,
+ bcc: reviewers,
+ subject: "Chemotion Repository: Embargo collection: #{@embargo_collection.label} released",
+ ) do |format|
+ format.html
+ format.text { render plain: embargo_released_content }
+ end
+ end
+
+ def mail_declined_request(publication_id, current_user_id)
+ init_params(publication_id,current_user_id)
+ @action_title = @is_submitter ? 'withdrawn' : 'rejected'
+
+ #rejected_notify
+ mail(
+ to: @creator.email,
+ bcc: reviewers,
+ subject: subject('Publication '+@action_title),
+ ) do |format|
+ format.html
+ format.text { render plain: approved_content }
+ end
+ end
+
+ def mail_external_review(current_user, collection_label, email, pwd)
+ init_external_params(current_user, collection_label, email, pwd)
+ #anonymous_notify
+ mail(
+ to: @creator.email,
+ bcc: reviewers,
+ subject: "Chemotion Repository: A temporary account for ["+ @embargo_collection +"] has been created",
+ ) do |format|
+ format.html
+ format.text { render plain: external_review_content }
+ end
+ end
+
+end
diff --git a/app/models/affiliation.rb b/app/models/affiliation.rb
index 9f0cd63da..1778ba21a 100644
--- a/app/models/affiliation.rb
+++ b/app/models/affiliation.rb
@@ -28,13 +28,18 @@ class Affiliation < ActiveRecord::Base
has_many :users, through: :user_affiliations
def output_array_full
- [group, department, organization, country]
+ [department, organization, country]
end
def output_full
output_array_full.map{|e| !e.blank? && e || nil}.compact.join(', ')
end
+ # def output_dep_org_country
+ # output_array_full[1..-1].map{|e| !e.blank? && e || nil}.compact.join(', ')
+ # end
+
+
private
def from_to
diff --git a/app/models/anonymous.rb b/app/models/anonymous.rb
new file mode 100644
index 000000000..e1aa78add
--- /dev/null
+++ b/app/models/anonymous.rb
@@ -0,0 +1,50 @@
+# == Schema Information
+#
+# Table name: users
+#
+# id :integer not null, primary key
+# email :string default(""), not null
+# encrypted_password :string default(""), not null
+# reset_password_token :string
+# reset_password_sent_at :datetime
+# remember_created_at :datetime
+# sign_in_count :integer default(0), not null
+# current_sign_in_at :datetime
+# last_sign_in_at :datetime
+# current_sign_in_ip :inet
+# last_sign_in_ip :inet
+# created_at :datetime not null
+# updated_at :datetime not null
+# name :string
+# first_name :string not null
+# last_name :string not null
+# deleted_at :datetime
+# counters :hstore not null
+# name_abbreviation :string(5)
+# type :string default("Person")
+# reaction_name_prefix :string(3) default("R")
+# layout :hstore not null
+# confirmation_token :string
+# confirmed_at :datetime
+# confirmation_sent_at :datetime
+# unconfirmed_email :string
+# selected_device_id :integer
+# failed_attempts :integer default(0), not null
+# unlock_token :string
+# locked_at :datetime
+# account_active :boolean
+#
+# Indexes
+#
+# index_users_on_confirmation_token (confirmation_token) UNIQUE
+# index_users_on_deleted_at (deleted_at)
+# index_users_on_email (email) UNIQUE
+# index_users_on_reset_password_token (reset_password_token) UNIQUE
+# index_users_on_unlock_token (unlock_token) UNIQUE
+#
+
+class Anonymous < User
+ def send_on_create_confirmation_instructions
+
+ end
+end
diff --git a/app/models/attachment.rb b/app/models/attachment.rb
index daaaad6f1..5bfbbc370 100644
--- a/app/models/attachment.rb
+++ b/app/models/attachment.rb
@@ -208,6 +208,12 @@ def store_file_and_thumbnail_for_dup
else
self.thumb_data = store.read_thumb
end
+ #TODO check for path collision:
+ # depending on storage, key needs to be changed
+ if self.storage == 'tmp'
+ self.key = nil
+ generate_key
+ end
stored = store.store_file
self.thumb = store.store_thumb if stored
self.save if stored
diff --git a/app/models/channel.rb b/app/models/channel.rb
index 24d0d1563..40390f7e9 100644
--- a/app/models/channel.rb
+++ b/app/models/channel.rb
@@ -31,6 +31,9 @@ class Channel < ActiveRecord::Base
EDITOR_CALLBACK = 'EditorCallback'
COLLECTION_ZIP = 'Collection Import and Export'
COLLECTION_ZIP_FAIL = 'Collection Import and Export Failure'
+ # REPOSITORY ONLY
+ PUBLICATION_REVIEW = 'Publication Review'
+ PUBLICATION_PUBLISHED = 'Publication Published'
class << self
def build_message(**args)
diff --git a/app/models/collaborator.rb b/app/models/collaborator.rb
new file mode 100644
index 000000000..84888db07
--- /dev/null
+++ b/app/models/collaborator.rb
@@ -0,0 +1,52 @@
+# == Schema Information
+#
+# Table name: users
+#
+# id :integer not null, primary key
+# email :string default(""), not null
+# encrypted_password :string default(""), not null
+# reset_password_token :string
+# reset_password_sent_at :datetime
+# remember_created_at :datetime
+# sign_in_count :integer default(0), not null
+# current_sign_in_at :datetime
+# last_sign_in_at :datetime
+# current_sign_in_ip :inet
+# last_sign_in_ip :inet
+# created_at :datetime not null
+# updated_at :datetime not null
+# name :string
+# first_name :string not null
+# last_name :string not null
+# deleted_at :datetime
+# counters :hstore not null
+# name_abbreviation :string(5)
+# type :string default("Person")
+# reaction_name_prefix :string(3) default("R")
+# layout :hstore not null
+# confirmation_token :string
+# confirmed_at :datetime
+# confirmation_sent_at :datetime
+# unconfirmed_email :string
+# selected_device_id :integer
+# failed_attempts :integer default(0), not null
+# unlock_token :string
+# locked_at :datetime
+# account_active :boolean
+#
+# Indexes
+#
+# index_users_on_confirmation_token (confirmation_token) UNIQUE
+# index_users_on_deleted_at (deleted_at)
+# index_users_on_email (email) UNIQUE
+# index_users_on_reset_password_token (reset_password_token) UNIQUE
+# index_users_on_unlock_token (unlock_token) UNIQUE
+#
+
+class Collaborator < User
+ def send_on_create_confirmation_instructions
+
+ end
+ end
+
+
diff --git a/app/models/collection.rb b/app/models/collection.rb
index 8ac37dc8b..0e617ea3a 100644
--- a/app/models/collection.rb
+++ b/app/models/collection.rb
@@ -69,6 +69,47 @@ class Collection < ActiveRecord::Base
default_scope { ordered }
+ def self.public_collection_id
+ ENV['PUBLIC_COLL_ID']&.to_i
+ end
+
+ def self.public_collection
+ find_by(id: ENV['PUBLIC_COLL_ID']) || find_by(
+ user_id: User.chemotion_user.id,
+ label: ENV['PUBLIC_COLL']
+ )
+ end
+
+ def self.scheme_only_reactions_collection
+ find_by(id: ENV['SCHEME_ONLY_REACTIONS_COLL_ID']) || find_by(
+ user_id: User.chemotion_user.id,
+ label: ENV['SCHEME_ONLY_REACTIONS_COLL']
+ ) || find_by(
+ user_id: User.chemotion_user.id,
+ label: 'Scheme-only reactions'
+ )
+ end
+
+ def self.scheme_only_reactions_collection_id
+ ENV['SCHEME_ONLY_REACTIONS_COLL_ID']&.to_i
+ end
+
+ def self.element_to_review_collection
+ where(
+ user_id: User.chemotion_user.id,
+ label: 'Element To Review',
+ is_synchronized: true
+ )
+ end
+
+ def self.reviewed_collection
+ where(
+ user_id: User.chemotion_user.id,
+ label: 'Reviewed',
+ is_synchronized: true
+ )
+ end
+
def self.get_all_collection_for_user(user_id)
find_by(user_id: user_id, label: 'All', is_locked: true)
end
diff --git a/app/models/concerns/publishing.rb b/app/models/concerns/publishing.rb
new file mode 100644
index 000000000..71f11bc50
--- /dev/null
+++ b/app/models/concerns/publishing.rb
@@ -0,0 +1,228 @@
+module Publishing
+ class Net::FTP
+ def puttextcontent(content, remotefile, &block)
+ f = StringIO.new(content)
+ begin
+ storlines('STOR ' + remotefile, f, &block)
+ ensure
+ f.close
+ end
+ end
+ end
+
+ extend ActiveSupport::Concern
+
+ included do
+
+ has_one :publication, as: :element
+ has_one :publication_as_source, as: :original_element
+
+ def publication_tag
+ self.tag.taggable_data['publication']
+ end
+
+ def reserve_suffix
+ return Doi.create_for_element!(self) unless (d = self.doi)
+
+ if self.is_a?(Sample) && d.inchikey != self.molecule.inchikey
+ d.update!(doiable: nil)
+ return Doi.create_for_element!(self)
+ elsif self.is_a?(Reaction) && (d.inchikey.tr('reaction/','') != self.products_short_rinchikey_trimmed)
+ d.update!(doiable: nil)
+ return Doi.create_for_element!(self)
+ end
+ d
+ end
+
+ def reserve_suffix_analyses(as = Container.none)
+ ids = as.map(&:id)
+ if self.is_a?(Sample)
+ ik = self.molecule.inchikey
+ analysis_set = self.analyses.where(id: ids)
+ elsif self.is_a?(Reaction)
+ ik = self.products_short_rinchikey_trimmed
+ analysis_set = self.analyses.where(id: ids) |
+ Container.where(id: (self.samples.map(&:analyses).flatten.map(&:id) & ids))
+ end
+
+ analysis_set.each do |analysis|
+ if (doi = analysis.doi)
+ type = analysis.extended_metadata['kind'].delete(' ')
+ if (doi&.inchikey != ik) || (type != doi&.analysis_type)
+ doi.update!(doiable: nil)
+ doi d = analysis.doi= Doi.create_for_analysis!(analysis)
+ end
+ else
+ doi = Doi.create_for_analysis!(analysis)
+ end
+ end
+ end
+
+ def full_doi
+ return nil unless (d = Doi.find_by(doiable: self))
+ d.full_doi
+ end
+
+ def generate_doi(version)
+ version_str = version.to_i.zero? ? '' : '.' + version.to_s
+ inchikey_version = self.molecule.inchikey + version_str
+ "#{Datacite::Mds.new.doi_prefix}/#{inchikey_version}"
+ end
+
+ def create_publication_tag(contributor, author_ids, license)
+ authors = User.where(id: author_ids, type: %w(Person Collaborator))
+ .includes(:affiliations)
+ .order("position(users.id::text in '#{author_ids}')")
+ affiliations = authors.map(&:current_affiliations)
+ affiliations_output = {}
+ affiliations.flatten.each do |aff|
+ affiliations_output[aff.id] = aff.output_full
+ end
+ publication = {
+ published_by: author_ids[0],
+ author_ids: author_ids,
+ creators: authors.map { |author|
+ {
+ 'givenName' => author.first_name,
+ 'familyName' => author.last_name,
+ 'name' => author.name,
+ 'ORCID' => author.orcid,
+ 'affiliationIds' => author.current_affiliations.map(&:id),
+ 'id' => author.id
+ }
+ },
+ contributors: {
+ 'givenName' => contributor.first_name,
+ 'familyName' => contributor.last_name,
+ 'name' => contributor.name,
+ 'ORCID' => contributor.orcid,
+ 'affiliations' => contributor.current_affiliations.map{ |aff| aff.output_full },
+ 'id' => contributor.id
+ },
+ affiliations: affiliations_output,
+ affiliation_ids: affiliations.map { |as| as.map(&:id) },
+ queued_at: DateTime.now,
+ license: license
+ }
+ et = self.tag
+ et.update!(
+ taggable_data: (et.taggable_data || {}).merge(publication: publication)
+ )
+ end
+
+ ##
+ # Update the tag['publication'] for a (being) published public sample
+
+ def update_publication_tag(**args)
+ data = args.slice(
+ :doi_reg_at, :pubchem_reg_at, :published_at, :sample_version, :doi, :chem_first
+ )
+ et = self.tag
+ td = et.taggable_data
+ td['publication'].merge!(data)
+
+ ## update molecule tag
+ if self.is_a?(Sample)
+ mt = self.molecule.tag
+ mt_data = mt.taggable_data || {}
+ # chemotion_first unless already chemotion_first
+ mt_data['chemotion'] ||= {}
+
+ if args[:chem_first] && mt_data['chemotion']['chemotion_first'].blank?
+ mt_data['chemotion']['chemotion_first'] = args[:chem_first]
+ end
+
+ mt_data['chemotion']['doi'] = args[:doi] unless mt_data['chemotion']['doi'].present?
+ mt_data['chemotion']['last_published_at'] = args[:published_at]
+
+ mt.update!(taggable_data: mt_data)
+ end
+ et.save!
+ end
+
+ ##
+ # Update the tag of the original sample (and of its analysis) used for publication
+
+ def tag_as_published(pub_sample, ori_analyses)
+ et = self.tag
+ if (pub_sample.is_a? Reaction)
+ et.update!(
+ taggable_data: (et.taggable_data || {}).merge(public_reaction: pub_sample.id, publish_pending: true)
+ )
+ else
+ et.update!(
+ taggable_data: (et.taggable_data || {}).merge(public_sample: pub_sample.id, publish_pending: true)
+ )
+ end
+
+ ori_analyses.each do |analysis|
+ analysis.reload
+ aid = pub_sample.analyses.select { |a| a.extended_metadata == analysis.extended_metadata }&.first&.id || true
+ at = analysis.tag
+ at.update!(
+ taggable_data: (at.taggable_data || {}).merge(public_analysis: aid)
+ )
+ xm = analysis.extended_metadata
+ xm.delete('publish')
+ xm['public_analysis'] = aid
+ analysis.update!(extended_metadata: xm)
+ end
+ end
+
+ def tag_reserved_suffix(ori_analyses)
+ et = self.tag
+ et.update!(
+ taggable_data: (et.taggable_data || {}).merge(reserved_doi: self.doi.full_doi)
+ )
+ ori_analyses.each do |analysis|
+ at = analysis.tag
+ d = analysis.doi.full_doi
+ at.update!(
+ taggable_data: (at.taggable_data || {}).merge(reserved_doi: d)
+ )
+ xm = analysis.extended_metadata
+ xm['reserved_doi'] = d
+ xm['publish'] = true
+ analysis.update!(extended_metadata: xm)
+ end
+ end
+
+ def untag_reserved_suffix()
+ et = self.tag
+ taggable_data = et.taggable_data || {}
+ taggable_data.delete('reserved_doi')
+ et.update!(taggable_data: taggable_data)
+
+ self.analyses.each do |analysis|
+ at = analysis.tag
+ td = at.taggable_data
+ td.delete('reserved_doi')
+ at.update!(taggable_data: td)
+
+ xm = analysis.extended_metadata
+ xm.delete('reserved_doi')
+ analysis.update!(extended_metadata: xm)
+ end
+ end
+
+ # remove doi link if molecule changes
+ def check_doi
+ d = self.doi
+ return true unless d
+ if self.is_a?(Sample) && molecule_id_changed?
+ d.update!(doiable: nil)
+ self.untag_reserved_suffix
+
+ elsif self.is_a?(Reaction) && (d.inchikey.tr('reaction/', '') != self.products_short_rinchikey_trimmed)
+ d.update!(doiable: nil)
+ self.untag_reserved_suffix
+ self.products.each do |s|
+ sd = s.doi
+ sd.update!(doiable: nil) unless sd.nil?
+ s.untag_reserved_suffix
+ end
+ end
+ true
+ end
+ end
+end
diff --git a/app/models/concerns/reaction_rinchi.rb b/app/models/concerns/reaction_rinchi.rb
index 75f47bd20..4452da863 100644
--- a/app/models/concerns/reaction_rinchi.rb
+++ b/app/models/concerns/reaction_rinchi.rb
@@ -45,11 +45,33 @@ def retrieve_molfiles
def no_structure
<<~MOLFILE
-
+
ACCLDraw04191619342D
-
+
0 0 0 0 0 0 0 0 0 0999 V2000
M END
MOLFILE
end
+
+ def products_rinchis
+ mols_rcts, mols_prds, mols_agts = self.retrieve_molfiles
+ rcts = Rinchi::MolVect.new
+ # mols_rcts.each do |rct| rcts.push(rct) end
+ [].each do |rct| rcts.push(rct) end
+ prds = Rinchi::MolVect.new
+ mols_prds.each do |prd| prds.push(prd) end
+ agts = Rinchi::MolVect.new
+ # mols_agts.each do |agt| agts.push(agt) end
+ [].each do |agt| agts.push(agt) end
+ Rinchi.convert(rcts, prds, agts)
+ end
+
+ def products_short_rinchikey
+ _, _, result, _ = products_rinchis
+ result
+ end
+
+ def products_short_rinchikey_trimmed
+ products_short_rinchikey.sub(/Short-RInChIKey=/, '')
+ end
end
diff --git a/app/models/concerns/taggable.rb b/app/models/concerns/taggable.rb
index 74bcf9f8d..3f0cd7de1 100644
--- a/app/models/concerns/taggable.rb
+++ b/app/models/concerns/taggable.rb
@@ -59,7 +59,7 @@ def collection_tag
cols = []
send(klass).each do |cc|
next unless c = cc.collection
- next if c.label == 'All' && c.is_locked
+ next if (c.label == 'All' && c.is_locked) || (c.id == Collection.public_collection_id)
cols.push({
name: c.label, is_shared: c.is_shared, user_id: c.user_id,
id: c.id, shared_by_id: c.shared_by_id,
diff --git a/app/models/container.rb b/app/models/container.rb
index fe98d0c37..cfc613a8d 100644
--- a/app/models/container.rb
+++ b/app/models/container.rb
@@ -23,9 +23,13 @@ class Container < ActiveRecord::Base
include ElementCodes
belongs_to :containable, polymorphic: true
has_many :attachments, as: :attachable
+ has_one :publication, as: :element
+ include Taggable
+
+ has_one :doi, as: :doiable
# TODO: dependent destroy for attachments should be implemented when attachment get paranoidized instead of this DJ
before_destroy :delete_attachment
- has_closure_tree
+ has_closure_tree order: "extended_metadata->'index' asc"
scope :analyses_for_root, ->(root_id) {
where(container_type: 'analysis').joins(
@@ -33,6 +37,18 @@ class Container < ActiveRecord::Base
)
}
+ scope :analyses_container, ->(id) {
+ where(container_type: 'analyses').joins(
+ <<~SQL
+ inner join container_hierarchies ch
+ on (ch.ancestor_id = #{id} and ch.descendant_id = containers.id)
+ or (ch.descendant_id = #{id} and ch.ancestor_id = containers.id)
+ SQL
+ )
+ }
+
+ before_save :check_doi
+
def analyses
Container.analyses_for_root(self.id)
end
@@ -47,8 +63,6 @@ def self.create_root_container(**args)
root_con
end
- private
-
def delete_attachment
if Rails.env.production?
attachments.each { |attachment|
@@ -58,4 +72,41 @@ def delete_attachment
attachments.each(&:destroy!)
end
end
+
+ def generate_doi version
+ type = self.extended_metadata['kind'].delete(' ') if self.extended_metadata['kind']
+ version_str = version.to_i == 0 ? "" : "." + version.to_s
+ term_id = (type || '').split('|').first.sub!(':','')
+ if self.root.containable.respond_to? :molecule
+ ds_version = self.root.containable.molecule.inchikey + "/" + term_id + version_str
+ elsif self.root.containable.respond_to? :products_short_rinchikey_trimmed
+ ds_version = "reaction/" + self.root.containable.products_short_rinchikey_trimmed+ "/" + term_id + version_str
+ else
+ ds_version = term_id + version_str
+ end
+ "#{Datacite::Mds.new.doi_prefix}/#{ds_version}"
+ end
+
+ def full_doi
+ return nil unless (d = Doi.find_by(doiable: self))
+ d.full_doi
+ end
+
+ def unassociate_doi(d = self.doi)
+ d.update(doiable: nil) unless d.nil?
+ self.extended_metadata.delete('reserved_doi')
+ at = self.tag
+ at.taggable_data.delete('reserved_doi')
+ at.save
+ end
+
+ def check_doi
+ # unassoicate doi if type has changed
+ if (d = self.doi) && self.container_type == 'analysis'
+ if self.extended_metadata['kind']&.delete(' ') != d.analysis_type
+ unassociate_doi(d)
+ end
+ end
+ true
+ end
end
diff --git a/app/models/doi.rb b/app/models/doi.rb
new file mode 100644
index 000000000..2717cb4c9
--- /dev/null
+++ b/app/models/doi.rb
@@ -0,0 +1,172 @@
+# == Schema Information
+#
+# Table name: dois
+#
+# id :integer not null, primary key
+# molecule_id :integer
+# inchikey :string
+# molecule_count :integer
+# analysis_id :integer
+# analysis_type :string
+# analysis_count :integer
+# metadata :jsonb
+# minted :boolean default(FALSE)
+# minted_at :datetime
+# created_at :datetime not null
+# updated_at :datetime not null
+# doiable_id :integer
+# doiable_type :string
+# suffix :string
+#
+# Indexes
+#
+# index_dois_on_suffix (suffix) UNIQUE
+# index_on_dois (inchikey,molecule_count,analysis_type,analysis_count) UNIQUE
+#
+# Foreign Keys
+#
+# fk_rails_... (molecule_id => molecules.id)
+#
+
+class Doi < ActiveRecord::Base
+
+ belongs_to :doiable, polymorphic: true
+ belongs_to :molecule
+ belongs_to :analysis, class_name: 'Container'
+
+
+ before_save :align_suffix
+
+ def build_suffix
+ s = "#{inchikey}"
+ s += ".#{molecule_count}" if molecule_count.to_i > 0
+ if analysis_type.present?
+ term_id = analysis_type.split('|').first.sub!(':','')
+ s += "/#{term_id}"
+ s += ".#{analysis_count}" if analysis_count.to_i > 0
+ end
+ s
+ end
+
+ def generate_doi
+ "#{Datacite::Mds.new.doi_prefix}/#{suffix}"
+ end
+
+ def full_doi
+ "#{Datacite::Mds.new.doi_prefix}/#{suffix}"
+ end
+
+ def self.find_by_doi(doi)
+ d = split_doi(doi)
+ find_by(suffix: d[:suffix])
+ end
+
+ def self.find_by_split_suffix(suffix)
+ split_suffix = split_suffix(suffix)
+ find_by(split_suffix)
+ end
+
+ def self.create_for_analysis!(analysis, ik = nil)
+ if !ik
+ rt = analysis.root_element
+ ik = (rt.is_a?(Sample) && rt.molecule.inchikey) ||
+ (rt.is_a?(Reaction) && rt.products_short_rinchikey_trimmed)
+ raise "only works with sample/reaction analysis" unless ik
+ end
+ type = analysis.extended_metadata['kind'].delete(' ')
+ type = type.presence || 'nd'
+ ds = Doi.select("*, coalesce(analysis_count, 0) as real_count")
+ .where(inchikey: ik, analysis_type: type)
+ .order('real_count desc')
+ if ds.blank?
+ ac = 0
+ version = ''
+ else
+ ac = ds.first.analysis_count.to_i.next
+ version = ".#{ac}"
+ end
+ term_id = type.split('|').first.sub!(':','')
+ suffix = "#{ik}/#{term_id}#{version}"
+ Doi.create!(
+ inchikey: ik,
+ doiable_id: analysis.id,
+ doiable_type: analysis.class.name,
+ analysis_count: ac,
+ suffix: suffix,
+ analysis_type: type
+ )
+ end
+
+ def self.create_for_element!(element, ik = nil)
+ klass = element.class.name
+ ik ||= case klass
+ when 'Sample'
+ element.molecule.inchikey
+ when 'Reaction'
+ "reaction/" + element.products_short_rinchikey_trimmed
+ end
+
+ ds = Doi.select("*, coalesce(molecule_count, 0) as real_count")
+ .where(inchikey: ik)
+ .order('real_count desc')
+ if ds.blank?
+ mc = 0
+ version = ''
+ else
+ mc = ds.first.molecule_count.to_i.next
+ version = ".#{mc}"
+ end
+ suffix = "#{ik}#{version}"
+ d = Doi.create!(
+ inchikey: ik,
+ doiable_id: element.id,
+ doiable_type: klass,
+ molecule_count: mc,
+ suffix: suffix
+ )
+ end
+
+ private
+
+ def self.extract_suffix(doi)
+ if doi.match(/(10\..+?)\//)
+ $'
+ end
+ end
+
+ def self.split_doi(doi)
+ if doi.match(/(10\..+?)\//)
+ { prefix: $1, suffix: $', split_suffix: split_suffix($') }
+ else
+ {}
+ end
+ end
+
+ def self.split_suffix(suffix)
+ if suffix.match(/([\w-]+)(?:\.(\d+))?(?:\/((?:.+62\.5)|(?:[^.]+))?(?:\.(\d+))?)?\z/)
+ {
+ inchikey: $1,
+ molecule_count: $2,
+ analysis_type: $3,
+ analysis_count: $4,
+ }
+ else
+ {}
+ end
+ end
+
+ def align_suffix
+ if suffix_changed? && !inchikey_changed? && !analysis_type_changed?
+ s = self.class.split_suffix(suffix)
+ self.inchikey = s[:inchikey]
+ self.molecule_count = s[:molecule_count]
+ self.analysis_type = s[:analysis_type]
+ self.analysis_count = s[:analysis_count]
+ else !suffix_changed? && inchikey_changed?
+ self.suffix = build_suffix
+ end
+ # throw(:abort) unless suffix == build_suffix
+ suffix == build_suffix
+ end
+
+end
diff --git a/app/models/literature.rb b/app/models/literature.rb
index 0cfb1e56e..59b0a4160 100644
--- a/app/models/literature.rb
+++ b/app/models/literature.rb
@@ -33,7 +33,8 @@ class Literature < ActiveRecord::Base
scope :add_user_info, -> {
joins("inner join users on users.id = literals.user_id")
- .select("literatures.*, literals.id as literal_id, literals.user_id, (users.first_name || chr(32) || users.last_name) as user_name")
+ .select("literatures.*, literals.id as literal_id, literals.element_type, literals.user_id,
+ (users.first_name || chr(32) || users.last_name) as user_name")
}
scope :add_element_and_user_info, -> {
diff --git a/app/models/publication.rb b/app/models/publication.rb
new file mode 100644
index 000000000..095c452a0
--- /dev/null
+++ b/app/models/publication.rb
@@ -0,0 +1,597 @@
+# == Schema Information
+#
+# Table name: publications
+#
+# id :integer not null, primary key
+# state :string
+# metadata :jsonb
+# taggable_data :jsonb
+# dois :jsonb
+# element_type :string
+# element_id :integer
+# doi_id :integer
+# created_at :datetime
+# updated_at :datetime
+# deleted_at :datetime
+# original_element_type :string
+# original_element_id :integer
+# ancestry :string
+# metadata_xml :text
+# published_by :integer
+# published_at :datetime
+# review :jsonb
+#
+# Indexes
+#
+# index_publications_on_ancestry (ancestry)
+#
+
+class Publication < ActiveRecord::Base
+ class Net::FTP
+ def puttextcontent(content, remotefile, &block)
+ f = StringIO.new(content)
+ begin
+ storlines('STOR ' + remotefile, f, &block)
+ ensure
+ f.close
+ end
+ end
+ end
+
+ acts_as_paranoid
+ has_ancestry
+ belongs_to :element, polymorphic: true
+ belongs_to :original_element, polymorphic: true
+ belongs_to :doi
+
+ STATE_START = 'start'
+
+ STATE_DC_METADATA_UPLOADING = 'dc_metadata_uploading'
+ STATE_DC_METADATA_UPLOADED = 'dc_metadata_uploaded'
+
+ # STATE_DC_METADATA_ANALYSES_UPLOADING = 'dc_metadata_analyses_uploading'
+ # STATE_DC_METADATA_ANALYSES_UPLOADED = 'dc_metadata_analyses_uploaded'
+
+ STATE_DC_DOI_REGISTERING = 'dc_doi_registering'
+ STATE_DC_DOI_REGISTERED = 'dc_doi_registered'
+
+ STATE_PUBCHEM_REGISTERING = 'pubchem_registering'
+ STATE_PUBCHEM_REGISTERED = 'pubchem_registered'
+
+ # STATE_DC_DOI_MINT_ANALYSES_START = 'dc_doi_mint_analyses_start'
+ # STATE_DC_DOI_MINT_ANALYSES_DONE = 'dc_doi_mint_analyses_done'
+
+ STATE_COMPLETING = 'completing'
+ STATE_COMPLETED = 'completed'
+ STATE_PUBLISHED = 'published'
+
+ STATE_ACCEPTED = 'accepted'
+ STATE_PENDING = 'pending'
+ STATE_DECLINED = 'declined'
+ STATE_REVIEWED = 'reviewed'
+ STATE_RETRACTED = 'retracted'
+
+ def embargoed?(root_publication = root)
+ cid = User.find(root_publication.published_by).publication_embargo_collection.id
+ embargo_col = root_publication.element.collections.select { |c| c['ancestry'].to_i == cid }
+ embargo_col.present? ? true : false
+ end
+
+ # Moving publication element to collections according to publication state
+
+ def update_state(new_state)
+ update_columns(state: new_state)
+ descendants.each { |d| d.update_columns(state: new_state) }
+ process_element(new_state)
+ end
+
+ def process_element(new_state = state)
+ case new_state
+ when Publication::STATE_PENDING
+ move_to_pending_collection
+ when Publication::STATE_REVIEWED
+ move_to_review_collection
+ when Publication::STATE_ACCEPTED
+ move_to_accepted_collection
+ when Publication::STATE_DECLINED
+ declined_reverse_original_element
+ declined_move_collections
+ end
+ end
+
+ # WARNING: for STATE_ACCEPTED the method does more than just notify users (see ChemotionRepoPublishingJob)
+ # TODO: separate publishing responsability
+ def inform_users(new_state = state, current_user_id = 0)
+ method = if ENV['PUBLISH_MODE'] == 'production' && Rails.env.production?
+ :perform_later
+ elsif ENV['PUBLISH_MODE'] == 'staging'
+ :perform_now
+ end
+ return unless method
+
+ queue_name = new_state.to_s
+ klass = if new_state == Publication::STATE_ACCEPTED && !embargoed?
+ queue_name = 'publishing'
+ ChemotionRepoPublishingJob
+ else
+ ChemotionRepoReviewingJob
+ end
+ klass.set(queue: "#{queue_name} #{id}").send(method, id, new_state, current_user_id)
+ end
+
+ # remove publication element from editable collections
+ def move_to_accepted_collection
+ pub_user = User.find(published_by)
+ return false unless pub_user && element
+ return true unless embargoed?
+
+ ## do not move if in reviewing, but why ???
+ # reviewing_col = element.collections.where(id: pub_user.reviewing_collection.id).pluck(:id)
+ # return false if reviewing_col.present?
+
+ case element_type
+ when 'Sample'
+ CollectionsSample
+ when 'Reaction'
+ CollectionsReaction
+ end.remove_in_collection(
+ element.id,
+ element.collections.where(
+ id: [pub_user.pending_collection.id, pub_user.reviewing_collection.id]
+ ).pluck(:id) + Collection.element_to_review_collection.pluck(:id)
+ )
+ end
+
+ # move publication element from reviewer editable collection to submitter editable collection
+ # move publication element from submitter readable collection to reviewer readable collection
+ def move_to_review_collection
+ pub_user = User.find(published_by)
+ return false unless pub_user && element
+
+ case element_type
+ when 'Sample'
+ CollectionsSample
+ when 'Reaction'
+ CollectionsReaction
+ end.move_to_collection(
+ element.id,
+ [pub_user.pending_collection.id] + Collection.element_to_review_collection.pluck(:id),
+ [pub_user.reviewing_collection.id] + Collection.reviewed_collection.pluck(:id)
+ )
+ end
+
+ def move_to_pending_collection
+ pub_user = User.find(published_by)
+ return false unless pub_user && element
+
+ case element_type
+ when 'Sample'
+ CollectionsSample
+ when 'Reaction'
+ CollectionsReaction
+ end.move_to_collection(
+ element.id,
+ [pub_user.reviewing_collection.id] + Collection.reviewed_collection.pluck(:id),
+ [pub_user.pending_collection.id] + Collection.element_to_review_collection.pluck(:id)
+ )
+ end
+
+ def declined_reverse_original_element
+ oet = original_element&.tag
+ oet&.taggable_data&.delete('publish_pending')
+ oet&.taggable_data&.delete('public_reaction') if element_type == 'Reaction'
+ oet&.taggable_data&.delete('public_sample') if element_type == 'Sample'
+ oet&.save!
+ original_element&.analyses&.each do |a|
+ a.reload
+ a.tag&.taggable_data&.delete('public_analysis') && a.tag.save!
+ a.extended_metadata&.delete('public_analysis') && a.save!
+ end
+ declined_reverse_original_reaction_elements
+ end
+
+ def declined_reverse_original_reaction_elements
+ element_type == 'Reaction' && original_element&.samples&.each do |s|
+ spp = s.tag&.taggable_data&.delete('publish_pending')
+ sps = s.tag&.taggable_data&.delete('public_sample')
+ s.tag&.save! unless spp.nil? && sps.nil?
+ original_element&.analyses&.each do |a|
+ a.reload
+ a.tag&.taggable_data&.delete('public_analysis') && a.tag.save!
+ a.extended_metadata&.delete('public_analysis') && a.save!
+ end
+ end
+ end
+
+ def declined_move_collections
+ all_col_id = User.find(published_by).all_collection&.id
+ return unless element && all_col_id
+
+ col_ids = element&.collections&.pluck(:id)
+ et = element.tag
+ et.taggable_data = et.taggable_data.merge(decline: true)
+ tag_pub = et.taggable_data&.delete('publication')
+ et.save!
+ case element_type
+ when 'Reaction'
+ CollectionsReaction
+ when 'Sample'
+ CollectionsSample
+ end.move_to_collection(element_id, col_ids, all_col_id)
+ end
+
+ # NB: ?NOT USED? Was it meant for declining/rejecting publication
+ # NB: was Moved to model from ChemotionRepoReviewingJob
+ # TODO: move this to publising concern ?
+ # def release_original_element
+ # ot = original_element&.tag&.taggable_data&.delete("publish_#{element_type.downcase}")
+ # original_element.tag.save! unless ot.nil?
+ #
+ # case element_type
+ # when 'Sample'
+ # clear_orig_analyses(original_element)
+ # when 'Reaction'
+ # clear_orig_analyses(original_element)
+ # original_element&.samples&.each do |s|
+ # t = s.tag&.taggable_data&.delete('publish_sample')
+ # s.tag.save! unless t.nil?
+ # clear_orig_analyses(s)
+ # end
+ # end
+ # end
+
+ # TODO: mv this to publishing concern ??
+ # def clear_orig_analyses(el = element)
+ # el&.analyses&.each do |a|
+ # t = a.tag&.taggable_data&.delete('publish_analysis')
+ # a.tag.save! unless t.nil?
+ # end
+ # end
+
+ def publication_logger
+ @@publication_logger ||= Logger.new(File.join(Rails.root, 'log', 'publication.log'))
+ end
+
+ def doi_bag
+ d = doi
+ case element_type
+ when 'Sample'
+ dois = {
+ sample: {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ inchikey: d.inchikey,
+ count: d.molecule_count
+ },
+ analyses_dois: {}
+ }
+ children.each do |a|
+ d = a.doi
+ dois[:analyses_dois][a.element_id.to_s] = {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ type: d.analysis_type,
+ count: d.analysis_count
+ }
+ end
+ when 'Reaction'
+ dois = {
+ reaction: {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ inchikey: d.inchikey,
+ count: d.molecule_count
+ },
+ analyses_dois: {}
+ }
+ children.where(element_type: 'Container').each do |a|
+ d = a.doi
+ dois[:analyses_dois][a.element_id.to_s] = {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ type: d.analysis_type,
+ count: d.analysis_count
+ }
+ end
+ dois['samples'] = {}
+ children.where(element_type: 'Sample').each do |new_sample|
+ d = new_sample.doi
+ if d
+ dois['samples'][new_sample.element_id.to_s] = {
+ sample: {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ inchikey: d.inchikey,
+ count: d.molecule_count
+ },
+ analyses_dois: {}
+ }
+ end
+ end
+ when 'Container'
+ parent_doi = parent.doi
+ dois = {
+ analysis: {
+ DOI: d.full_doi,
+ suffix: d.suffix,
+ inchikey: d.inchikey,
+ count: d.molecule_count
+ },
+ parent_element: {
+ DOI: parent_doi.full_doi,
+ suffix: parent_doi.suffix,
+ inchikey: parent_doi.inchikey,
+ count: parent_doi.molecule_count
+ }
+ }
+ end
+ return dois
+ end
+
+ def scheme_only
+ taggable_data && taggable_data['scheme_only'] == true ? true : false
+ end
+
+ def rights_data
+ rights = {
+ schemeURI: 'https://spdx.org/licenses/',
+ rightsIdentifierScheme: 'SPDX',
+ rightsIdentifier: 'CC-BY-SA-4.0',
+ rightsURI: 'http://creativecommons.org/licenses/by-sa/4.0/',
+ rightsName: 'Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)'
+ }
+ if taggable_data && taggable_data['license'].present?
+ case taggable_data['license']
+ when 'CC BY'
+ rights[:rightsIdentifier] = 'CC-BY-4.0'
+ rights[:rightsURI] = 'http://creativecommons.org/licenses/by/4.0/'
+ rights[:rightsName] = 'Attribution 4.0 International (CC BY 4.0)'
+ when 'CC0'
+ rights[:rightsIdentifier] = 'CC0-1.0'
+ rights[:rightsURI] = 'http://creativecommons.org/publicdomain/zero/1.0/'
+ rights[:rightsName] = 'CC0 1.0 Universal'
+ end
+ end
+ rights
+ end
+
+ def datacite_metadata_xml
+ parent_element = parent&.element
+
+ metadata_obj = OpenStruct.new(element: element, pub_tag: taggable_data, dois: doi_bag, parent_element: parent_element.presence, rights: rights_data)
+ erb_file = if element_type == 'Container'
+ "app/publish/datacite_metadata_#{parent_element.class.name.downcase}_#{element_type.downcase}.html.erb"
+ else
+ "app/publish/datacite_metadata_#{element_type.downcase}.html.erb"
+ end
+ metadata_file = ERB.new(File.read(File.join(
+ Rails.root,
+ erb_file
+ )))
+ metadata_file.result(metadata_obj.instance_eval { binding })
+ end
+
+ def persit_datacite_metadata_xml!
+ mt = datacite_metadata_xml
+ self.update!(metadata_xml: mt)
+ mt
+ end
+
+ def transition_from_start_to_metadata_uploading!
+ return unless valid_transition(STATE_DC_METADATA_UPLOADING)
+ mt = datacite_metadata_xml
+ self.update!(metadata_xml: mt, state: STATE_DC_METADATA_UPLOADING)
+ end
+
+ def transition_from_metadata_uploading_to_uploaded!
+ return unless valid_transition(STATE_DC_METADATA_UPLOADED)
+ if (ENV['DATACITE_MODE'] == 'test' || ENV['PUBLISH_MODE'] == 'production') && scheme_only == false
+ resp = Datacite::Mds.new.upload_metadata(metadata_xml)
+ success = resp.is_a?(Net::HTTPSuccess)
+ message = "#{resp.inspect}: metadata upload#{"ing fail" if !success}ed"
+ else
+ success = true
+ message = "metadata not uploaded in mode #{ENV['PUBLISH_MODE']}"
+ end
+ logger([message, metadata])
+ raise "#{message}" unless success
+ self.update!(state: STATE_DC_METADATA_UPLOADED)
+ end
+
+ def transition_from_metadata_uploaded_to_doi_registering!
+ return unless valid_transition(STATE_DC_DOI_REGISTERING)
+ self.update!(state: STATE_DC_DOI_REGISTERING)
+ end
+
+ def transition_from_doi_registering_to_registered!
+ return unless valid_transition(STATE_DC_DOI_REGISTERED)
+ mds = Datacite::Mds.new
+ suffix = doi.suffix
+ short_doi = "#{mds.doi_prefix}/#{suffix}"
+ url = "https://#{mds.doi_domain}/inchikey/#{suffix}"
+ if (ENV['DATACITE_MODE'] == 'test' || ENV['PUBLISH_MODE'] == 'production') && scheme_only == false
+ resp = mds.mint(short_doi, url)
+ success = resp.is_a?(Net::HTTPSuccess)
+ message = "#{resp.inspect}: DOI mint#{'ing fail' unless success}ed"
+ else
+ success = true
+ message = "DOI not minted in mode #{ENV['PUBLISH_MODE']}"
+ end
+ logger([message, "doi: #{short_doi}", "url: #{url}"])
+ raise "#{message}:\n #{short_doi} <-> #{url}" unless success
+ doi_date = DateTime.now
+ case element_type
+ when 'Sample'
+ chem_first = element.pubchem_cid.blank?
+ tag_data = {
+ doi_reg_at: doi_date,
+ sample_version: doi.molecule_count,
+ doi: short_doi
+ }
+ tag_data[:chem_first] = doi_date if chem_first
+ element.update_publication_tag(tag_data)
+ when 'Container'
+ et = ElementTag.find_or_create_by(
+ taggable_type: 'Container', taggable_id: element_id
+ )
+ tag_data = parent.element.publication_tag.merge({
+ published_at: doi_date,
+ dataset_version: doi.analysis_count,
+ analysis_doi: short_doi
+ })
+ et.update!(
+ taggable_data: (et.taggable_data || {}).merge(publication: tag_data)
+ )
+ when 'Reaction'
+ tag_data = {
+ doi_reg_at: doi_date,
+ reaction_version: doi.molecule_count,
+ doi: short_doi
+ }
+ element.update_publication_tag(tag_data)
+ end
+
+ pd = taggable_data.merge(tag_data)
+ self.update!(state: STATE_DC_DOI_REGISTERED,taggable_data: taggable_data.merge(pd))
+ end
+
+ def transition_from_doi_registered_to_pubchem_registering!
+ return unless valid_transition(STATE_PUBCHEM_REGISTERING)
+ self.update!(state: STATE_PUBCHEM_REGISTERING)
+ end
+
+ def transition_from_doi_pubchem_registering_to_registered!
+ return unless valid_transition(STATE_PUBCHEM_REGISTERED)
+ if element_type == 'Sample'
+ metadata_obj = OpenStruct.new(sample: element)
+ metadata_file = ERB.new(File.read(
+ File.join(Rails.root,'app', 'publish', 'pubchem_metadata.sdf.erb')
+ ))
+ mt = metadata_file.result(metadata_obj.instance_eval { binding })
+ if (production = Rails.env.production? && ENV['PUBLISH_MODE'] == 'production') && scheme_only == false
+ ftp = Net::FTP.new('ftp-private.ncbi.nlm.nih.gov')
+ ftp.passive = true
+ ftp.login(ENV['PUBCHEM_LOGIN'], ENV['PUBCHEM_PASSWORD'])
+ ftp.puttextcontent(mt, doi.suffix + '.sdf.in')
+ ftp.close
+ end
+ message = "\n---MOLFILE START---"
+ element.update_publication_tag(pubchem_reg_at: DateTime.now)
+ pd = taggable_data.merge(pubchem_reg_at: DateTime.now)
+ logger([message, mt, "Pubchem FTP upload #{production ? '' : 'NOT'} sent (mode: #{ENV['PUBLISH_MODE']})"])
+ end
+ self.update!(state: STATE_PUBCHEM_REGISTERED, taggable_data: taggable_data.merge(pd))
+ end
+
+ def transition_from_pubchem_registered_to_completing!
+ return unless valid_transition(STATE_COMPLETING)
+ self.update!(state: STATE_COMPLETING)
+ end
+
+ def transition_from_doi_registered_to_completing!
+ return unless valid_transition(STATE_COMPLETING)
+ self.update!(state: STATE_COMPLETING)
+ end
+
+ def transition_from_completing_to_completed!
+ return unless valid_transition(STATE_COMPLETED)
+ pd = {}
+ if element_type != 'Container'
+ creator_ids = taggable_data['author_ids']
+ su_id = User.chemotion_user.id
+
+ pending_collection_ids = Collection.joins(
+ "INNER JOIN sync_collections_users ON sync_collections_users.collection_id = collections.id"
+ ).where("sync_collections_users.shared_by_id = ?", su_id)
+ .where("sync_collections_users.user_id in (?)", creator_ids)
+ .where("collections.label = 'Pending Publications'").pluck(:id)
+
+ my_published_collection_ids = Collection.joins(
+ "INNER JOIN sync_collections_users ON sync_collections_users.collection_id = collections.id"
+ ).where("sync_collections_users.shared_by_id = ?", User.chemotion_user.id)
+ .where("sync_collections_users.user_id in (?)", creator_ids)
+ .where("collections.label = 'Published Elements'")
+ .pluck(:id)
+
+
+ if element_type == 'Reaction' && scheme_only
+ published_collection_ids = my_published_collection_ids + [Collection.scheme_only_reactions_collection.id]
+ else
+ published_collection_ids = my_published_collection_ids + [Collection.public_collection_id]
+ end
+
+
+ collections_klass = "Collections#{element_type}".constantize
+ collections_klass.remove_in_collection([element_id], pending_collection_ids)
+ collections_klass.remove_in_collection([element_id], Collection.element_to_review_collection.pluck(:id))
+ collections_klass.create_in_collection([element_id], published_collection_ids)
+
+ time = DateTime.now
+ element.update_publication_tag(published_at: time)
+ pd = taggable_data.merge(published_at: time)
+ logger(['moved to collections'])
+ end
+ self.update!(state: STATE_COMPLETED, taggable_data: taggable_data.merge(pd), published_at: time)
+ end
+
+ def default_line
+ @default_line ||= "#{element_type} #{element_id}: "
+ end
+
+ def valid_transition(to_state)
+ case to_state
+ when STATE_START
+ valid = [STATE_START].include?(state)
+
+ when STATE_ACCEPTED
+ valid = [STATE_ACCEPTED].include?(state)
+
+ when STATE_DC_METADATA_UPLOADING
+ valid = [STATE_ACCEPTED].include?(state)
+
+ when STATE_DC_METADATA_UPLOADED
+ valid = [STATE_DC_METADATA_UPLOADING].include?(state)
+
+ when STATE_DC_DOI_REGISTERING
+ valid = [STATE_DC_METADATA_UPLOADED].include?(state)
+
+ when STATE_DC_DOI_REGISTERED
+ valid = [STATE_DC_DOI_REGISTERING].include?(state)
+
+ when STATE_PUBCHEM_REGISTERING
+ valid = (element_type == 'Sample') && [STATE_DC_DOI_REGISTERED].include?(state)
+
+ when STATE_PUBCHEM_REGISTERED
+ valid = [STATE_PUBCHEM_REGISTERING].include?(state)
+
+ when STATE_COMPLETING
+ valid = if element_type == 'Sample'
+ [STATE_PUBCHEM_REGISTERED].include?(state)
+ else
+ [STATE_DC_DOI_REGISTERED, STATE_COMPLETING].include?(state)
+ end
+
+ when STATE_COMPLETED
+ valid = [STATE_COMPLETING].include?(state)
+ end
+
+ log_invalid_transition(to_state) unless valid
+ valid
+ end
+
+ def log_invalid_transition(to_state)
+ logger("CANNOT TRANSITION from #{state} to #{to_state}")
+ end
+
+ def logger(message_arr)
+ message = [message_arr].flatten.join("\n")
+ publication_logger.info(
+ <<~INFO
+ ******** MODE #{ENV['PUBLISH_MODE']}********
+ Publication #{id}. STATE: #{state}: #{default_line}
+ #{message}
+ ********************************************************************************
+ INFO
+ )
+ end
+end
diff --git a/app/models/publication_authors.rb b/app/models/publication_authors.rb
new file mode 100644
index 000000000..9f0c840a0
--- /dev/null
+++ b/app/models/publication_authors.rb
@@ -0,0 +1,14 @@
+# == Schema Information
+#
+# Table name: publication_authors
+#
+# author_id :text
+# element_id :integer
+# element_type :string
+# state :string
+# doi_id :integer
+# ancestry :string
+#
+
+class PublicationAuthors < ActiveRecord::Base
+end
diff --git a/app/models/publication_ontologies.rb b/app/models/publication_ontologies.rb
new file mode 100644
index 000000000..c11f0c176
--- /dev/null
+++ b/app/models/publication_ontologies.rb
@@ -0,0 +1,15 @@
+# == Schema Information
+#
+# Table name: publication_ontologies
+#
+# element_type :string
+# element_id :integer
+# container_id :integer
+# published_at :datetime
+# ontologies :text
+# term_id :text
+# label :text
+#
+
+class PublicationOntologies < ActiveRecord::Base
+end
diff --git a/app/models/reaction.rb b/app/models/reaction.rb
index cfbe76073..d0b4afd6b 100644
--- a/app/models/reaction.rb
+++ b/app/models/reaction.rb
@@ -50,6 +50,7 @@ class Reaction < ActiveRecord::Base
include ElementCodes
include Taggable
include ReactionRinchi
+ include Publishing
serialize :description, Hash
serialize :observation, Hash
@@ -133,14 +134,18 @@ class Reaction < ActiveRecord::Base
has_many :sync_collections_users, through: :collections
+ has_one :doi, as: :doiable
+
belongs_to :creator, foreign_key: :created_by, class_name: 'User'
validates :creator, presence: true
before_save :update_svg_file!
before_save :cleanup_array_fields
before_save :auto_format_temperature!
+ before_save :check_doi
before_create :auto_set_short_label
+
after_create :update_counter
has_one :container, :as => :containable
@@ -202,7 +207,6 @@ def update_svg_file!
svg_file.close
self.reaction_svg_file = svg_file_name
- # end
else
paths = {}
%i(starting_materials reactants products).each do |prop|
@@ -230,7 +234,8 @@ def svg_path(sample_svg, molecule_svg)
end
def yield_amount(sample_id)
- ReactionsProductSample.find_by(reaction_id: self.id, sample_id: sample_id).try(:equivalent)
+ rps = ReactionsProductSample.find_by(reaction_id: self.id, sample_id: sample_id)
+ rps.scheme_yield || rps.equivalent
end
def solvents_in_svg
diff --git a/app/models/reactions_product_sample.rb b/app/models/reactions_product_sample.rb
index f2cdeab0b..c7c060442 100644
--- a/app/models/reactions_product_sample.rb
+++ b/app/models/reactions_product_sample.rb
@@ -2,16 +2,17 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
#
# Indexes
#
diff --git a/app/models/reactions_purification_solvent_sample.rb b/app/models/reactions_purification_solvent_sample.rb
index b19861710..b459d8cf2 100644
--- a/app/models/reactions_purification_solvent_sample.rb
+++ b/app/models/reactions_purification_solvent_sample.rb
@@ -2,16 +2,17 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
#
# Indexes
#
diff --git a/app/models/reactions_reactant_sample.rb b/app/models/reactions_reactant_sample.rb
index a63c1c729..0d97f8ac4 100644
--- a/app/models/reactions_reactant_sample.rb
+++ b/app/models/reactions_reactant_sample.rb
@@ -2,16 +2,17 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
#
# Indexes
#
diff --git a/app/models/reactions_sample.rb b/app/models/reactions_sample.rb
index bb7eba51f..a9ca24ad1 100644
--- a/app/models/reactions_sample.rb
+++ b/app/models/reactions_sample.rb
@@ -2,16 +2,17 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
#
# Indexes
#
diff --git a/app/models/reactions_solvent_sample.rb b/app/models/reactions_solvent_sample.rb
index 7aaea0583..38567eace 100644
--- a/app/models/reactions_solvent_sample.rb
+++ b/app/models/reactions_solvent_sample.rb
@@ -2,16 +2,17 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
#
# Indexes
#
diff --git a/app/models/reactions_starting_material_sample.rb b/app/models/reactions_starting_material_sample.rb
index 5b68fe827..c5c7c5ea7 100644
--- a/app/models/reactions_starting_material_sample.rb
+++ b/app/models/reactions_starting_material_sample.rb
@@ -2,16 +2,17 @@
#
# Table name: reactions_samples
#
-# id :integer not null, primary key
-# reaction_id :integer
-# sample_id :integer
-# reference :boolean
-# equivalent :float
-# position :integer
-# type :string
-# deleted_at :datetime
-# waste :boolean default(FALSE)
-# coefficient :float default(1.0)
+# id :integer not null, primary key
+# reaction_id :integer
+# sample_id :integer
+# reference :boolean
+# equivalent :float
+# position :integer
+# type :string
+# deleted_at :datetime
+# waste :boolean default(FALSE)
+# coefficient :float default(1.0)
+# scheme_yield :float
#
# Indexes
#
diff --git a/app/models/report.rb b/app/models/report.rb
index 854b12f40..52aaec8cc 100644
--- a/app/models/report.rb
+++ b/app/models/report.rb
@@ -71,6 +71,10 @@ def create_docx
Reporter::WorkerRxnList.new(
report: self, template_path: tpl_path, ext: 'html'
).process
+ when 'doi_list_xlsx'
+ Reporter::WorkerDoiList.new(
+ report: self, ext: 'xlsx'
+ ).process
else
Reporter::Worker.new(
report: self, template_path: tpl_path
diff --git a/app/models/sample.rb b/app/models/sample.rb
index 4071d6f28..5a4f72f04 100644
--- a/app/models/sample.rb
+++ b/app/models/sample.rb
@@ -37,7 +37,6 @@
# molecule_name_id :integer
# molfile_version :string(20)
# stereo :jsonb
-# mol_rdkit :string
# metrics :string default("mmm")
#
# Indexes
@@ -50,6 +49,12 @@
#
class Sample < ActiveRecord::Base
+
+
+ require 'net/ftp'
+ require 'erb'
+ require 'ostruct'
+
acts_as_paranoid
include ElementUIStateScopes
include PgSearch
@@ -58,6 +63,7 @@ class Sample < ActiveRecord::Base
include AnalysisCodes
include UnitConvertable
include Taggable
+ include Publishing
STEREO_ABS = ['any', 'rac', 'meso', '(S)', '(R)', '(Sp)', '(Rp)', '(Sa)'].freeze
STEREO_REL = ['any', 'syn', 'anti', 'p-geminal', 'p-ortho', 'p-meta', 'p-para', 'cis', 'trans', 'fac', 'mer'].freeze
@@ -150,6 +156,7 @@ class Sample < ActiveRecord::Base
before_save :attach_svg, :init_elemental_compositions,
:set_loading_from_ea
before_save :auto_set_short_label
+ before_save :check_doi
before_create :check_molecule_name
after_save :update_counter
after_create :create_root_container
@@ -192,6 +199,8 @@ class Sample < ActiveRecord::Base
belongs_to :creator, foreign_key: :created_by, class_name: 'User'
belongs_to :molecule
+ has_one :doi, as: :doiable
+
accepts_nested_attributes_for :molecule_name
accepts_nested_attributes_for :collections_samples
accepts_nested_attributes_for :molecule, update_only: true
@@ -205,6 +214,14 @@ class Sample < ActiveRecord::Base
delegate :computed_props, to: :molecule, prefix: true
delegate :inchikey, to: :molecule, prefix: true, allow_nil: true
+ def molfile_pubchem
+ version = Chemotion::OpenBabelService.molfile_version(self.molfile)
+ mf = Chemotion::OpenBabelService.mofile_clear_coord_bonds(self.molfile, version)
+ mf = molfile unless mf
+ mf&.split(/^\$\$\$\$/).first
+ end
+
+
def molecule_sum_formular
self.molecule ? self.molecule.sum_formular : ''
end
@@ -229,6 +246,18 @@ def analyses
self.container ? self.container.analyses : Container.none
end
+ #TODO move to molecule (chemotion_ELN)
+ def pubchem_cid
+ mol = self.molecule
+ cid = mol.tag && mol.tag.taggable_data && mol.tag.taggable_data['pubchem_cid']
+ if cid
+ cid
+ else
+ mol.update_tag!(pubchem_tag: true)
+ mol.tag.taggable_data['pubchem_cid']
+ end
+ end
+
def self.associated_by_user_id_and_reaction_ids(user_id, reaction_ids)
(for_user(user_id).by_reaction_ids(reaction_ids)).uniq
end
diff --git a/app/models/user.rb b/app/models/user.rb
index 8f0f10aa8..f4b2005bb 100644
--- a/app/models/user.rb
+++ b/app/models/user.rb
@@ -86,7 +86,7 @@ class User < ActiveRecord::Base
message: "can be alphanumeric, middle '_' and '-' are allowed,"+
" but leading digit, or trailing '-' and '_' are not."}
validate :name_abbreviation_length
-# validate :academic_email
+ # validate :academic_email
validate :mail_checker
# NB: only Persons and Admins can get a confirmation email and confirm their email.
@@ -117,6 +117,12 @@ def name_abbreviation_length
elsif type == 'Device'
na.blank? || !na.length.between?(2, 6) && errors.add(:name_abbreviation,
"has to be 2 to 6 characters long")
+ elsif type == 'Anonymous'
+ na.blank? || !na.length.between?(2, 5) && errors.add(:name_abbreviation,
+ "has to be 2 to 5 characters long")
+ elsif type == 'Collaborator'
+ na.blank? || !na.length.between?(2, 5) && errors.add(:name_abbreviation,
+ "has to be 2 to 5 characters long")
else
na.blank? || !na.length.between?(2, 3) && errors.add(:name_abbreviation,
"has to be 2 to 3 characters long")
@@ -135,6 +141,10 @@ def mail_checker
)
end
+ def orcid
+ profile.data&.fetch('ORCID', nil)
+ end
+
def owns_collections?(collections)
collections.pluck(:user_id).uniq == [id]
end
@@ -211,6 +221,68 @@ def all_sync_in_collections_users
SyncCollectionsUser.where("user_id IN (?) ", [self.id]+self.groups.pluck(:id))
end
+ def self.is_public
+ self.find_by(email: ENV['SYS_EMAIL'])
+ end
+
+ # TODO: mv to initializers
+ def self.reviewer_ids
+ (ENV['REVIEWERS'] || '').split(',').map(&:to_i)
+ end
+
+ def is_article_editor
+ (ENV['NEWSROOM_EDITOR'] || "").split(",").include?(self.id.to_s)
+ end
+
+ def is_howto_editor
+ (ENV['HOWTO_EDITOR'] || "").split(",").include?(self.id.to_s)
+ end
+
+ def pending_collection
+ su_id = User.chemotion_user.id
+ Collection.joins(
+ "INNER JOIN sync_collections_users ON " +
+ "sync_collections_users.collection_id = collections.id")
+ .where("sync_collections_users.shared_by_id = #{su_id}")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.label = 'Pending Publications'").first
+ end
+
+ def reviewing_collection
+ su_id = User.chemotion_user.id
+ Collection.joins(
+ "INNER JOIN sync_collections_users ON " +
+ "sync_collections_users.collection_id = collections.id")
+ .where("sync_collections_users.shared_by_id = #{su_id}")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.label = 'Reviewing'").first
+ end
+
+ def published_collection
+ su_id = User.chemotion_user.id
+ Collection.joins("INNER JOIN sync_collections_users ON sync_collections_users.collection_id = collections.id")
+ .where("sync_collections_users.shared_by_id = #{su_id}")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.label = 'Published Elements'").first
+ end
+
+ def publication_embargo_collection
+ su_id = User.chemotion_user.id
+ Collection.joins("INNER JOIN sync_collections_users ON sync_collections_users.collection_id = collections.id")
+ .where("sync_collections_users.shared_by_id = #{su_id}")
+ .where("sync_collections_users.user_id = #{self.id}")
+ .where("collections.label = 'Embargoed Publications'").first
+ end
+
+ def all_collection
+ Collection.where(user: self, label: 'All', is_locked: true, position: 0)&.first
+
+ end
+
+ def self.chemotion_user
+ find_by(email: ENV['SYS_EMAIL'])
+ end
+
def current_affiliations
Affiliation.joins(
"INNER JOIN user_affiliations ua ON ua.affiliation_id = affiliations.id"
@@ -236,12 +308,43 @@ def molecule_editor
# - add subcollections
# - delete it
def create_all_collection
+ return if self.type == 'Anonymous'
Collection.create(user: self, label: 'All', is_locked: true, position: 0)
end
def create_chemotion_public_collection
return unless self.type == 'Person'
- Collection.create(user: self, label: 'chemotion.net', is_locked: true, position: 1)
+ chemotion_user = User.chemotion_user
+ # Collection.create(user: self, label: 'chemotion.net', is_locked: true, position: 1)
+ Collection.find_or_create_by(user: self, label: 'ELN Gate', is_locked: true, position: 1)
+ Collection.find_or_create_by(user: self, label: 'My Data', is_locked: true, position: 2)
+
+ sys_published_by = Collection.find_or_create_by(user_id: chemotion_user, label: 'Published by')
+ sys_pending_from = Collection.find_or_create_by(user_id: chemotion_user, label: 'Pending Publication from')
+ sys_reviewing_from = Collection.find_or_create_by(user_id: chemotion_user, label: 'Reviewing Publication from')
+ sys_ready_publish_from = Collection.find_or_create_by(user_id: chemotion_user, label: 'Embargoed Publications from')
+
+ sys_reviewing_collection = self.reviewing_collection || Collection.create(user: chemotion_user, label: 'Reviewing', ancestry: "#{sys_reviewing_from.id}")
+ sys_pending_collection = self.pending_collection || Collection.create(user: chemotion_user, label: 'Pending Publications', ancestry: "#{sys_pending_from.id}")
+ sys_published_collection = self.published_collection || Collection.create(user: chemotion_user, label: 'Published Elements', ancestry: "#{sys_published_by.id}")
+ sys_publication_embargo_collection = self.publication_embargo_collection || Collection.create(user: chemotion_user, label: 'Embargoed Publications', ancestry: "#{sys_ready_publish_from.id}")
+
+ root_label = "with %s" %chemotion_user.name_abbreviation
+ root_collection_attributes = {
+ label: root_label,
+ user: self,
+ shared_by_id: chemotion_user.id,
+ is_locked: true,
+ is_shared: true
+ }
+ rc = Collection.find_or_create_by(root_collection_attributes)
+
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: Collection.public_collection_id, permission_level: 0, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: Collection.scheme_only_reactions_collection.id, permission_level: 0, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: sys_published_collection.id, permission_level: 0, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: sys_pending_collection.id, permission_level: 0, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: sys_reviewing_collection.id, permission_level: 3, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
+ SyncCollectionsUser.find_or_create_by(user: self, shared_by_id: chemotion_user.id, collection_id: sys_publication_embargo_collection.id, permission_level: 0, sample_detail_level: 10, reaction_detail_level: 10, fake_ancestry: rc.id.to_s)
end
def set_account_active
diff --git a/app/models/users_collaborator.rb b/app/models/users_collaborator.rb
new file mode 100644
index 000000000..5179992d6
--- /dev/null
+++ b/app/models/users_collaborator.rb
@@ -0,0 +1,11 @@
+# == Schema Information
+#
+# Table name: users_collaborators
+#
+# id :integer not null, primary key
+# user_id :integer
+# collaborator_id :integer
+#
+
+class UsersCollaborator < ActiveRecord::Base
+end
diff --git a/app/publish/datacite_metadata_analysis.html.erb b/app/publish/datacite_metadata_analysis.html.erb
new file mode 100644
index 000000000..1b2f0285a
--- /dev/null
+++ b/app/publish/datacite_metadata_analysis.html.erb
@@ -0,0 +1,67 @@
+
+
+ <%= "#{dois[:analysis][:DOI]}"%>
+
+ <% pub_tag['creators'].each do |creator| %>
+
+ <%= creator['familyName'] %>, <%= creator['givenName'] %>
+ <%= creator['givenName'] %>
+ <%= creator['familyName'] %>
+ <% if creator['ORCID'].present? %>
+ <%=creator['ORCID']%>
+ <% end %>
+ <% if (aff_ids = creator['affiliationIds']).present? then aff_ids.each do |aff_id| %>
+ <%=pub_tag['affiliations'][aff_id.to_s]%>
+ <% end %>
+ <% end %>
+
+ <% end %>
+
+
+ <%= (element.extended_metadata['kind'] || '').split('|').pop %> (<%= parent_element.molecule.iupac_name %>)
+ <%= parent_element.molecule.inchistring %>
+
+ chemotion.net
+ <%= Time.now.strftime("%Y") %>
+ <% if pub_tag['contributors'].present? %>
+
+
+ <%= pub_tag['contributors']['familyName'] %>, <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['familyName'] %>
+ <% if pub_tag['contributors']['ORCID'].present? %>
+ <%=pub_tag['contributors']['ORCID']%>
+ <% end %>
+ <% if pub_tag['contributors'] && pub_tag['contributors']['affiliations'].present? then pub_tag['contributors']['affiliations'].each do |aff| %>
+ <%= aff %>
+ <% end %>
+ <% end %>
+
+
+ <% end %>
+
+ Chemistry
+
+ en
+
+ Dataset
+ 1
+
+ <%= rights[:rightsName] %>
+
+
+
+ dataset for <%= (element.extended_metadata['kind'] || '').split('|').pop %>
+ <%= element.extended_metadata['description'] %>
+ <%= Chemotion::QuillToHtml.new.convert(element.extended_metadata['content']) %>
+
+
+
+
+ <%# <% publication.sample.citations.each do |c| %1> %>
+ <%# <%= c.doi %1> %>
+ <%# <% end %1> %>
+ <%= "#{dois[:parent_element][:DOI]}" %>
+
+
+
diff --git a/app/publish/datacite_metadata_container.html.erb b/app/publish/datacite_metadata_container.html.erb
new file mode 100644
index 000000000..8750ea045
--- /dev/null
+++ b/app/publish/datacite_metadata_container.html.erb
@@ -0,0 +1,64 @@
+
+
+ <%= "#{dois[:analysis][:DOI]}"%>
+
+ <% pub_tag['creators'].each do |creator| %>
+
+ <%= creator['familyName'] %>, <%= creator['givenName'] %>
+ <%= creator['givenName'] %>
+ <%= creator['familyName'] %>
+ <% if creator['ORCID'].present? %>
+ <%=creator['ORCID']%>
+ <% end %>
+ <% if (aff_ids = creator['affiliationIds']).present? then aff_ids.each do |aff_id| %>
+ <%=pub_tag['affiliations'][aff_id.to_s]%>
+ <% end %>
+ <% end %>
+
+ <% end %>
+
+
+ <%= (element.extended_metadata['kind'] || '').split('|').pop %> (<%= parent_element.molecule.iupac_name %>)
+ <%= parent_element.molecule.inchistring %>)
+
+ chemotion.net
+ <%= Time.now.strftime("%Y") %>
+ <% if pub_tag['contributors'].present? %>
+
+
+ <%= pub_tag['contributors']['familyName'] %>, <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['familyName'] %>
+ <% if pub_tag['contributors']['ORCID'].present? %>
+ <%=pub_tag['contributors']['ORCID']%>
+ <% end %>
+ <% if pub_tag['contributors'] && pub_tag['contributors']['affiliations'].present? then pub_tag['contributors']['affiliations'].each do |aff| %>
+ <%= aff %>
+ <% end %>
+ <% end %>
+
+
+ <% end %>
+
+ Chemistry
+
+ en
+ Dataset
+ 1
+
+ <%= rights[:rightsName] %>
+
+
+
+ dataset for <%= (element.extended_metadata['kind'] || '').split('|').pop %>
+ <%= element.extended_metadata['description'] %>
+ <%= Nokogiri::HTML( Chemotion::QuillToHtml.new.convert(element.extended_metadata['content'])).text %>
+
+
+
+ <%# <% publication.sample.citations.each do |c| %1> %>
+ <%# <%= c.doi %1> %>
+ <%# <% end %1> %>
+ <%= "#{dois[:parent_element][:DOI]}" %>
+
+
diff --git a/app/publish/datacite_metadata_reaction.html.erb b/app/publish/datacite_metadata_reaction.html.erb
new file mode 100644
index 000000000..efb305dac
--- /dev/null
+++ b/app/publish/datacite_metadata_reaction.html.erb
@@ -0,0 +1,70 @@
+
+
+ <%= "#{dois[:reaction][:DOI]}" %>
+
+ <% pub_tag['creators'].each do |creator| %>
+
+ <%= creator['familyName'] %>, <%= creator['givenName'] %>
+ <%= creator['givenName'] %>
+ <%= creator['familyName'] %>
+ <% if creator['ORCID'].present? %>
+ <%=creator['ORCID']%>
+ <% end %>
+ <% if (aff_ids = creator['affiliationIds']).present? then aff_ids.each do |aff_id| %>
+ <%=pub_tag['affiliations'][aff_id.to_s]%>
+ <% end %>
+ <% end %>
+
+ <% end %>
+
+
+ <%= element.products_short_rinchikey %>
+ <%= element.rinchi_short_key %>
+
+ chemotion.net
+ <%= element.created_at.strftime("%Y") %>
+ <% if pub_tag['contributors'].present? %>
+
+
+ <%= pub_tag['contributors']['familyName'] %>, <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['familyName'] %>
+ <% if pub_tag['contributors']['ORCID'].present? %>
+ <%=pub_tag['contributors']['ORCID']%>
+ <% end %>
+ <% if pub_tag['contributors'] && pub_tag['contributors']['affiliations'].present? then pub_tag['contributors']['affiliations'].each do |aff| %>
+ <%= aff %>
+ <% end %>
+ <% end %>
+
+
+ <% end %>
+
+ <%= element.created_at %>
+
+
+
+ chemical reaction: structures conditions
+
+ en
+
+ reaction conditions
+ 1
+
+ <%= rights[:rightsName] %>
+
+
+
+ <%= REXML::Text.new(Nokogiri::HTML( Chemotion::QuillToHtml.new.convert(element.description.to_json)).text, false, nil, false).to_s %>
+
+
+
+
+ <% dois[:analyses_dois].each do |_, ds| %>
+ <%= "#{ds[:DOI]}" %>
+ <% end %>
+ <% dois['samples'].each do |sid, doi| %>
+ <%= "#{doi[:sample][:DOI]}" %>
+ <% end %>
+
+
diff --git a/app/publish/datacite_metadata_reaction_container.html.erb b/app/publish/datacite_metadata_reaction_container.html.erb
new file mode 100644
index 000000000..647d74f2f
--- /dev/null
+++ b/app/publish/datacite_metadata_reaction_container.html.erb
@@ -0,0 +1,64 @@
+
+
+ <%= "#{dois[:analysis][:DOI]}"%>
+
+ <% pub_tag['creators'].each do |creator| %>
+
+ <%= creator['familyName'] %>, <%= creator['givenName'] %>
+ <%= creator['givenName'] %>
+ <%= creator['familyName'] %>
+ <% if creator['ORCID'].present? %>
+ <%=creator['ORCID']%>
+ <% end %>
+ <% if (aff_ids = creator['affiliationIds']).present? then aff_ids.each do |aff_id| %>
+ <%=pub_tag['affiliations'][aff_id.to_s]%>
+ <% end %>
+ <% end %>
+
+ <% end %>
+
+
+ <%= (element.extended_metadata['kind'] || '').split('|').pop %>
+ <%= parent_element.doi.inchikey %>
+
+ chemotion.net
+ <%= Time.now.strftime("%Y") %>
+ <% if pub_tag['contributors'].present? %>
+
+
+ <%= pub_tag['contributors']['familyName'] %>, <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['familyName'] %>
+ <% if pub_tag['contributors']['ORCID'].present? %>
+ <%=pub_tag['contributors']['ORCID']%>
+ <% end %>
+ <% if pub_tag['contributors'] && pub_tag['contributors']['affiliations'].present? then pub_tag['contributors']['affiliations'].each do |aff| %>
+ <%= aff %>
+ <% end %>
+ <% end %>
+
+
+ <% end %>
+
+ Chemistry
+
+ en
+ Dataset
+ 1
+
+ <%= rights[:rightsName] %>
+
+
+
+ dataset for <%= (element.extended_metadata['kind'] || '').split('|').pop %>
+ <%= element.extended_metadata['description'] %>
+ <%= Nokogiri::HTML( Chemotion::QuillToHtml.new.convert(element.extended_metadata['content'])).text %>
+
+
+
+ <%# <% publication.sample.citations.each do |c| %1> %>
+ <%# <%= c.doi %1> %>
+ <%# <% end %1> %>
+ <%= "#{dois[:parent_element][:DOI]}" %>
+
+
diff --git a/app/publish/datacite_metadata_sample.html.erb b/app/publish/datacite_metadata_sample.html.erb
new file mode 100644
index 000000000..aa3acf1cc
--- /dev/null
+++ b/app/publish/datacite_metadata_sample.html.erb
@@ -0,0 +1,71 @@
+
+
+ <%= "#{dois[:sample][:DOI]}" %>
+
+ <% pub_tag['creators'].each do |creator| %>
+
+ <%= creator['familyName'] %>, <%= creator['givenName'] %>
+ <%= creator['givenName'] %>
+ <%= creator['familyName'] %>
+ <% if creator['ORCID'].present? %>
+ <%=creator['ORCID']%>
+ <% end %>
+ <% if (aff_ids = creator['affiliationIds']).present? then aff_ids.each do |aff_id| %>
+ <%=pub_tag['affiliations'][aff_id.to_s]%>
+ <% end %>
+ <% end %>
+
+ <% end %>
+
+
+ <%= element.molecule_name.name %>
+ <%= element.molecule.inchistring %>
+
+ chemotion.net
+ <%= element.created_at.strftime("%Y") %>
+ <% if pub_tag['contributors'].present? %>
+
+
+ <%= pub_tag['contributors']['familyName'] %>, <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['familyName'] %>
+ <% if pub_tag['contributors']['ORCID'].present? %>
+ <%=pub_tag['contributors']['ORCID']%>
+ <% end %>
+ <% if pub_tag['contributors'] && pub_tag['contributors']['affiliations'].present? then pub_tag['contributors']['affiliations'].each do |aff| %>
+ <%= aff %>
+ <% end %>
+ <% end %>
+
+
+ <% end %>
+
+ <%= element.created_at %>
+
+
+
+ Chemistry
+
+ en
+
+ Molecule
+ 1
+
+
+ This dataset contains experimental data from a sample (<%= element.molecule.iupac_name.present? ? "#{element.molecule.iupac_name}, " : '' %><%= element.molecule.inchistring %>).
+ The datasets from the following experiments are available:
+ <% element.analyses.each do |analysis| %>
+ <%= (analysis.extended_metadata['kind'] || '').split('|').pop %>
+ <% end %>
+
+
+
+
+ <% dois[:analyses_dois].each do |_, ds| %>
+ <%= "#{ds[:DOI]}" %>
+ <% end %>
+ <% if parent_element.presence %>
+ <%= "#{parent_element.full_doi}" %>
+ <% end %>
+
+
diff --git a/app/publish/datacite_metadata_sample_container.html.erb b/app/publish/datacite_metadata_sample_container.html.erb
new file mode 100644
index 000000000..8435fee2c
--- /dev/null
+++ b/app/publish/datacite_metadata_sample_container.html.erb
@@ -0,0 +1,64 @@
+
+
+ <%= "#{dois[:analysis][:DOI]}"%>
+
+ <% pub_tag['creators'].each do |creator| %>
+
+ <%= creator['familyName'] %>, <%= creator['givenName'] %>
+ <%= creator['givenName'] %>
+ <%= creator['familyName'] %>
+ <% if creator['ORCID'].present? %>
+ <%=creator['ORCID']%>
+ <% end %>
+ <% if (aff_ids = creator['affiliationIds']).present? then aff_ids.each do |aff_id| %>
+ <%=pub_tag['affiliations'][aff_id.to_s]%>
+ <% end %>
+ <% end %>
+
+ <% end %>
+
+
+ <%= (element.extended_metadata['kind'] || '').split('|').pop %> (<%= parent_element.molecule.iupac_name %>)
+ <%= parent_element.molecule.inchistring %>
+
+ chemotion.net
+ <%= Time.now.strftime("%Y") %>
+ <% if pub_tag['contributors'].present? %>
+
+
+ <%= pub_tag['contributors']['familyName'] %>, <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['givenName'] %>
+ <%= pub_tag['contributors']['familyName'] %>
+ <% if pub_tag['contributors']['ORCID'].present? %>
+ <%=pub_tag['contributors']['ORCID']%>
+ <% end %>
+ <% if pub_tag['contributors'] && pub_tag['contributors']['affiliations'].present? then pub_tag['contributors']['affiliations'].each do |aff| %>
+ <%= aff %>
+ <% end %>
+ <% end %>
+
+
+ <% end %>
+
+ Chemistry
+
+ en
+ Dataset
+ 1
+
+ <%= rights[:rightsName] %>
+
+
+
+ dataset for <%= (element.extended_metadata['kind'] || '').split('|').pop %>
+ <%= element.extended_metadata['description'] %>
+ <%= Nokogiri::HTML( Chemotion::QuillToHtml.new.convert(element.extended_metadata['content'])).text %>
+
+
+
+ <%# <% publication.sample.citations.each do |c| %1> %>
+ <%# <%= c.doi %1> %>
+ <%# <% end %1> %>
+ <%= "#{dois[:parent_element][:DOI]}" %>
+
+
diff --git a/app/publish/pubchem_metadata.sdf.erb b/app/publish/pubchem_metadata.sdf.erb
new file mode 100644
index 000000000..d42b0c753
--- /dev/null
+++ b/app/publish/pubchem_metadata.sdf.erb
@@ -0,0 +1,17 @@
+<%= sample.molfile_pubchem %>
+>
+<%= sample.molecule.inchikey %>
+
+>
+doi:<%= sample.full_doi %>
+
+>
+http://www.chemotion.net
+
+>
+https://dx.doi.org/<%= sample.full_doi %>
+
+>
+<%= sample.full_doi %>
+
+$$$$
diff --git a/app/search/all_element_search.rb b/app/search/all_element_search.rb
index 5269c2cd6..63df18ba1 100644
--- a/app/search/all_element_search.rb
+++ b/app/search/all_element_search.rb
@@ -1,5 +1,5 @@
class AllElementSearch
- PG_ELEMENTS = %w[Sample Reaction Screen Wellplate]
+ PG_ELEMENTS = %w[Sample Reaction] # Screen Wellplate]
def initialize(term)
@term = term
@@ -26,20 +26,50 @@ def empty?
def by_collection_id(id, current_user)
types = if (prof = current_user&.profile&.data)
- (prof.fetch('layout', {}).keys.map(&:capitalize)) & PG_ELEMENTS
+ (prof.fetch('layout', {'sample' => 1, 'reaction' => 2}).keys.map(&:capitalize)) & PG_ELEMENTS
else
PG_ELEMENTS
end
+ sample_filter =
+ # <<~SQL
+ " searchable_id in ( " \
+ " SELECT samples.id FROM samples " \
+ " INNER JOIN collections_samples cs on cs.collection_id = #{id} and cs.sample_id = samples.id and cs.deleted_at ISNULL " \
+ " EXCEPT " \
+ " SELECT samples.id FROM samples " \
+ " INNER JOIN reactions_samples rs on rs.sample_id = samples.id and rs.type not in ('ReactionsProductSample') " \
+ " WHERE rs.deleted_at ISNULL " \
+ " )"
+ # SQL
+ reaction_filter =
+ # <<~SQL
+ " searchable_id in ( " \
+ " SELECT reactions.id FROM reactions " \
+ " INNER JOIN collections_reactions cr on cr.collection_id = #{id} and cr.reaction_id = reactions.id and cr.deleted_at ISNULL " \
+ " INNER JOIN reactions_samples rs on rs.reaction_id = reactions.id and rs.type in ('ReactionsProductSample') and rs.deleted_at ISNULL " \
+ " )"
+ # SQL
first_type = types.first
query = "(searchable_type = '#{first_type}' AND searchable_id IN (" \
"SELECT #{first_type}_id FROM collections_#{first_type}s "\
"WHERE collection_id = #{id} AND deleted_at IS NULL))"
+
+ query = "(searchable_type = '#{first_type}' AND #{sample_filter} )" if (first_type === 'Sample')
+ query = "(searchable_type = '#{first_type}' AND #{reaction_filter} )" if (first_type === 'Reaction')
+
if (types.count > 1)
types[1..-1].each { |type|
- query = query +
- " OR (searchable_type = '#{type}' AND searchable_id IN (" \
- "SELECT #{type}_id FROM collections_#{type}s "\
- "WHERE collection_id = #{id} AND deleted_at IS NULL))"
+ case type
+ when 'Sample'
+ query = query + " OR (searchable_type = '#{type}' AND #{sample_filter} )"
+ when 'Reaction'
+ query = query + " OR (searchable_type = '#{type}' AND #{reaction_filter} )"
+ else
+ query = query +
+ " OR (searchable_type = '#{type}' AND searchable_id IN (" \
+ "SELECT #{type}_id FROM collections_#{type}s "\
+ "WHERE collection_id = #{id} AND deleted_at IS NULL))"
+ end
}
end
diff --git a/app/serializers/container_serializer.rb b/app/serializers/container_serializer.rb
index bf8db0dc8..78cfcca22 100644
--- a/app/serializers/container_serializer.rb
+++ b/app/serializers/container_serializer.rb
@@ -59,15 +59,21 @@ def get_extended_metadata(container)
end
def preview_img(container = object)
- first_child = container&.children&.first
- has_dataset = first_child && first_child.container_type == 'dataset'
- return 'not available' unless has_dataset
-
- attachment = first_child.attachments.find do |att|
- att.thumb && att.content_type&.match(Regexp.union(%w[jpg jpeg png tiff]))
+ dataset_ids = (container && container.children.map { |ds| ds.container_type == 'dataset' && ds.id }) || {}
+ return 'not available' if dataset_ids.empty?
+ attachments = Attachment.where_container(dataset_ids).to_a
+ attachments = attachments.select do |a|
+ a.thumb == true && a.attachable_type == 'Container' && dataset_ids.include?(a.attachable_id)
+ end
+ image_atts = attachments.select do |a_img|
+ a_img&.content_type&.match(Regexp.union(%w[jpg jpeg png tiff]))
end
- attachment ||= first_child.attachments.find(&:thumb)
+
+ attachment = image_atts.find(&:non_jcamp?).presence || image_atts[0]
+ attachment ||= attachments.find(&:non_jcamp?).presence || attachments[0]
+
preview = attachment.read_thumbnail if attachment
preview && Base64.encode64(preview) || 'not available'
+
end
end
diff --git a/app/serializers/molecule_guest_list_serializer.rb b/app/serializers/molecule_guest_list_serializer.rb
new file mode 100644
index 000000000..a0595d472
--- /dev/null
+++ b/app/serializers/molecule_guest_list_serializer.rb
@@ -0,0 +1,4 @@
+class MoleculeGuestListSerializer < ActiveModel::Serializer
+ attributes :id, :iupac_name, :inchikey, :inchistring, :sum_formular,
+ :molecule_svg_file, :tag, :sample_svg_file
+end
diff --git a/app/serializers/molecule_guest_serializer.rb b/app/serializers/molecule_guest_serializer.rb
new file mode 100644
index 000000000..981e8430c
--- /dev/null
+++ b/app/serializers/molecule_guest_serializer.rb
@@ -0,0 +1,4 @@
+class MoleculeGuestSerializer < ActiveModel::Serializer
+ attributes :id, :iupac_name, :inchikey, :inchistring, :sum_formular,
+ :molecule_svg_file, :molecular_weight, :cano_smiles, :tag, :exact_molecular_weight
+end
diff --git a/app/serializers/reaction_guest_list_serializer.rb b/app/serializers/reaction_guest_list_serializer.rb
new file mode 100644
index 000000000..11b861ad2
--- /dev/null
+++ b/app/serializers/reaction_guest_list_serializer.rb
@@ -0,0 +1,3 @@
+class ReactionGuestListSerializer < ActiveModel::Serializer
+ attributes :id, :name, :reaction_svg_file, :tag
+end
diff --git a/app/serializers/sample_policy_serializable.rb b/app/serializers/sample_policy_serializable.rb
index 87a002755..de59530f3 100644
--- a/app/serializers/sample_policy_serializable.rb
+++ b/app/serializers/sample_policy_serializable.rb
@@ -6,6 +6,7 @@ module SamplePolicySerializable
def initialize(element, options={})
original_initialize(element)
+ @element = element
@policy = options.class == Hash && options[:policy]
end
@@ -14,7 +15,13 @@ def can_update
end
def can_publish
- @policy && @policy.try(:destroy?)
+ cp = @policy && @policy.try(:destroy?)
+ # return false if !%w[Sample Reaction].include?(@element.class.name) ####
+ # || (@element.class.name == 'Sample' && @element.reactions&.length > 0) ####
+
+ pub = Publication.find_by(element: @element)
+ return cp if pub.nil? || pub&.state == 'reviewed'
+ false
end
end
end
diff --git a/app/serializers/sync_collection_remote_serializer.rb b/app/serializers/sync_collection_remote_serializer.rb
index e7bac5ea6..97b06cebd 100644
--- a/app/serializers/sync_collection_remote_serializer.rb
+++ b/app/serializers/sync_collection_remote_serializer.rb
@@ -2,6 +2,7 @@ class SyncCollectionRemoteSerializer < ActiveModel::Serializer
attributes :id, :label, :is_shared, :shared_by_id, :is_locked,
:permission_level, :sample_detail_level, :reaction_detail_level,
:wellplate_detail_level, :screen_detail_level, :shared_by, :shared_to
+ attributes :is_public
has_many :children
@@ -10,8 +11,7 @@ def children
end
def shared_by
- sharing_user = User.find_by(id: object.shared_by_id) || User.new
- UserSimpleSerializer.new(sharing_user).serializable_hash.deep_symbolize_keys
+ UserSimpleSerializer.new(sharer).serializable_hash.deep_symbolize_keys
end
def shared_to
@@ -19,4 +19,12 @@ def shared_to
UserSimpleSerializer.new(object.user).serializable_hash.deep_symbolize_keys
end
end
+
+ def is_public
+ !sharer.email.blank? && sharer.email == ENV['SYS_EMAIL']
+ end
+
+ def sharer
+ @sharer ||= User.find_by(id: object.shared_by_id) || User.new
+ end
end
diff --git a/app/views/devise/sessions/new.html.haml b/app/views/devise/sessions/new.html.haml
index f2c207204..c710d98aa 100644
--- a/app/views/devise/sessions/new.html.haml
+++ b/app/views/devise/sessions/new.html.haml
@@ -19,4 +19,4 @@
= f.submit "Log in", class: 'btn btn-primary'
= render "devise/shared/links"
- = link_to "Back", root_path
+ = link_to "Back", home_path
diff --git a/app/views/devise/shared/_affiliations.html.haml b/app/views/devise/shared/_affiliations.html.haml
index 2d30c1ec7..e034a5877 100644
--- a/app/views/devise/shared/_affiliations.html.haml
+++ b/app/views/devise/shared/_affiliations.html.haml
@@ -1,21 +1,17 @@
%script{:src => asset_path('affiliations.js')}
.form-group.field
- = f.label "Country"
+ = f.label "Country", class: "required"
%br/
= f.text_field :country, autofocus: true, class: 'form-control',
- id: 'country-select'
+ id: 'country-select', required: true
.form-group.field
= f.label "Organization", class: "required"
%br/
= f.text_field :organization, autofocus: true, class: 'form-control',
- id: 'organization-select', required: true, disabled: disabled
+ id: 'organization-select', required: true, readonly: disabled
.form-group.field
= f.label "Department"
%br/
= f.text_field :department, autofocus: true, class: 'form-control',
id: 'department-select'
-.form-group.field
- = f.label "Group"
%br/
- = f.text_field :group, autofocus: true, class: 'form-control',
- id: 'group-select'
diff --git a/app/views/devise/shared/_pn_and_tos.html.haml b/app/views/devise/shared/_pn_and_tos.html.haml
index e69de29bb..ff23e43f6 100644
--- a/app/views/devise/shared/_pn_and_tos.html.haml
+++ b/app/views/devise/shared/_pn_and_tos.html.haml
@@ -0,0 +1,7 @@
+.panel.panel-primary
+ .panel-heading
+ %fieldset
+ %input{ type:"checkbox", required: true}
+ %label I have read and I accept the directive to use the service
+ .panel-body{style: 'height: 300px; overflow-y: scroll; '}
+ = render file: "#{Rails.public_path}/directives/directives.html", layout: false
diff --git a/app/views/layouts/root_layout.haml b/app/views/layouts/root_layout.haml
new file mode 100644
index 000000000..5fd972334
--- /dev/null
+++ b/app/views/layouts/root_layout.haml
@@ -0,0 +1,12 @@
+!!!
+%html
+ %head
+ %meta{:content => "text/html; charset=UTF-8", "http-equiv" => "Content-Type"}/
+ %title Chemotion
+ = stylesheet_link_tag 'application', media: 'all', 'data-turbolinks-track' => true
+ = javascript_include_tag 'application', 'data-turbolinks-track' => true
+ = csrf_meta_tags
+ %body
+ = favicon_link_tag
+ .fluid-container
+ = yield
diff --git a/app/views/pages/_privacy_notice_and_terms_of_service.html b/app/views/pages/_privacy_notice_and_terms_of_service.html
new file mode 100644
index 000000000..2570e3afb
--- /dev/null
+++ b/app/views/pages/_privacy_notice_and_terms_of_service.html
@@ -0,0 +1,226 @@
+Directive to use the service chemotion-repository
+(last edited: 2019-11-04)
+
+By using the chemotion-website and the service of the chemotion-repository,
+you accept the following terms and conditions in full.
+If you disagree with these terms and conditions or any part of these terms and conditions,
+you must not use this website.
+Some parts of this website may be subject to additional terms and conditions which will be
+made available to you as appropriate.
+Parts of this website may use strictly necessary and session cookies.
+By using this website and agreeing to these terms
+and conditions, you consent to our use of cookies in accordance with the terms of
+chemotion's Privacy Policy.
+
+The service chemotion-repository offers technical infrastructure to collect and
+share research data for chemical sciences.
+The data storage is accomplished by the service and all data are stored on servers of the
+KIT.
+The service allows a qualified realization of the recommendations of the German research
+foundation for the storage of research data.
+
+Service provider is the Institute of Organic Chemistry (IOC) in collaboration with the
+Steinbuchs Centre for Computing (SCC) and the Library at the KIT in Karlsruhe.
+
+
+ 1. General
+
+ 1.1 Authorization, registration and log-off
+
+Academic institutions are automatically recognized through the domain part of the email
+the user entered for registration. The users may use the service after their
+registration and confirmation of their email address. If the user's
+academic institution has not been properly recognized, the user shall communicate
+the error to the chemotion-repository. An email will also be sent to
+confirm the validity of the email address every time the user updates its email
+address on the portal and once a year. The administration of the individual
+authorization to use the service is carried out by the Institute of Organic
+Chemistry (KIT). The service providers will consider their right to check the
+correctness of the given data with respect to the affiliation and data of the
+user's registration. The log in and log off to the service is available
+via the website: chemotion-repository website.
+
+1.2 Readability and availability of the stored data
+
+Research data are stored at the Steinbuch Centre for Computing (SCC) guaranteed
+until 2028. The chemotion-repository intends to prolong this period
+successively by additional contracts with the SCC but the decision on any
+prolongation and the duration will be made solely by the two partners
+chemotion-repository and the SCC.
+The SCC makes every effort to ensure the best possible technical prerequisites
+for a long life of the data (best effort) with the available resources.
+These include, inter alia, adequate air conditioning, uninterrupted power supply,
+ and building protection.
+
+1.3 Admission
+
+The user accesses the chemotion-repository after registering on the website
+and successfully logging on. When registering, the operator checks the data
+and the agreement to use the service with the respective home institution.
+The user can access his data at any time as long as he has a valid access.
+
+1.4. Protocols
+
+HTTPS is enforced at all time.
+
+1.5 Deletion of files and content by users
+
+Files (content unpublished) that are stored in the repository in general can
+be deleted or changed by the user at any time.
+Files and data which are published (content published) cannot be deleted or changed anymore.
+The user agrees that those data (which are selected by the user individually) will be registered at DataCite (with retrieval of a DOI) and Pubchem (Pubchem substance SID).
+Authors should contact the repository curator at chemotion@ioc.kit.edu if they need to retract or amend published content.
+1.6 Maximum of data storage
+
+The data size per user is limited up to date to 10 GB. The operator will adapt
+allowed data size if this will be necessary in future.
+
+1.7 Costs and fees
+
+There are no fees or costs for the users
+
+1.8 Support via chemotion
+
+The provider will offer service for the use of the repository as long as the
+resources allow the support. The user is expected to familiarize with the given
+website and its applications. Support is available via the email address: chemotion@ioc.kit.edu.
+
+
+
+2. Data content
+
+2.1 Responsibility for data contents
+
+There are two types of contributed contents, unpublished and published contributed contents.
+User contributed content (unpublished): the user may upload user data which are not visible for other users, this content is visible only if the user is logged in or if he/she shares the content with other users.
+User contributed content (published): If the user selects single items or item groups to publish, the content will become available as open access for other users. The contents will be visible for the public and registered users will be able to download the content including the provided files.
+All uploaded contents are stored by the user in person. The data stored by him/her are always linked to the user's account data in the database of the storage system. Even if the account of a user is deleted, the connection of the stored data to the user's username (as defined with the registration) will be conserved.
+
+ - The user of the service is solely responsible for the contents of the contributed content of any type.
+ - The user is obligated to observe the legal regulations when storing sensitive and personal data.
+ - The uploaded user content must not be illegal or unlawful, must not infringe any third party's
+ legal rights, and must not be capable of giving rise to legal action whether against you
+ or chemotion-repository or a third party (in each case under any applicable law).
+
+ - You must not submit any user content to the website that is or has ever been the subject of any threatened or actual legal proceedings or other similar complaint.
+
+
+chemotion-repository reserves the right to edit or remove any material submitted to this website, or stored on chemotion-repository servers, or hosted or published upon this website.
+
+2.2 User contributed content (unpublished)
+
+User contributed content that is not published by the user is considered to be
+private unless the user shares the content which means that the user allows
+selected other users to view, edit, copy and store the users data.
+The user adapts the sharing options according to these actions and accepts
+that a sharing of content means always the disclosure of confidential content to others.
+
+2.3 User contributed content (published)
+
+In these terms and conditions, 'your published user content' means
+material (including without limitation text, images, audio material, video
+material and audio-visual material) that you submit to this website by using
+the function 'publish'. You grant to chemotion-repository,
+a worldwide, irrevocable, non-exclusive, royalty-free license to use, reproduce,
+adapt, publish, translate and distribute your user content in any existing or
+future media. You also grant to chemotion-repository
+the right to sub-license these rights, and the right to bring an action
+for infringement of these rights.
+
+
+3. Use of the repository
+Unless otherwise stated, chemotion-repository and/or its contributors own
+the intellectual property rights in the website and material on the website.
+Subject to the license below, all these intellectual property rights are reserved.
+
+Each content contributed and published by a user is made available under one of
+the following licenses that the contributing user has chosen during the publication process:
+
+
+You must not
+
+ - use material other than the DOIs from this website for any publication without
+ attribution or republish material from this website (including republication on another website)
+ without attribution (e.g. 'reused from Chemotion-Repository KIT') unless the material has been released under CC0
+
+
+ ;
+
+ - sublicense material other than allowed under the original license (
+
+ CC no sublicensing
+
+ ).
+
+
+
+3.1 Acceptable use
+
+You must not use this website in any way that causes, or may cause, damage to the website or impairment of the availability or accessibility of the website, or in any way which is unlawful, illegal, fraudulent or harmful, or in connection with any unlawful, illegal, fraudulent or harmful purpose or activity.
+You must not use this website to copy, store, host, transmit, send, use, publish or distribute any material which consists of (or is linked to) any spyware, computer virus, Trojan horse, worm, keystroke logger, rootkit or other malicious computer software.
+You must not conduct any systematic or automated data collection activities (including without limitation scraping, data mining, data extraction and data harvesting) on or in relation to this website without chemotion-repository's express written consent.
+
+3.2 Restricted access
+
+Access to certain areas of this website may be restricted. chemotion-repository reserves the right to restrict access to areas of this website, or indeed this entire website, at chemotion-repository's discretion.
+If chemotion-repository provides you with a user ID and password to enable you to access restricted areas of this website or other content or services, you must ensure that the user ID and password are kept confidential.
+
Chemotion-repository may disable your user ID and password in chemotion-repository sole discretion without notice or explanation.
+
+3.3 Copyright
+
+The content and works published on chemotion-repository's website, are governed by the copyright laws of Germany. Any duplication, processing, distribution or any form of utilization beyond the scope of copyright law shall require the prior written consent of the author or authors in question.
+
+3.4 DOI Ownership
+
+Chemotion-repository asserts no claims of ownership to Digital Object Identifiers (DOIs) acquired through the use of the chemotion-repository. Individual DOIs may be incorporated into the user's content and systems.
+
+3.5 No warranties
+
+This website is provided 'as is' without any representations or warranties, express or implied. Chemotion-repository makes no representations or warranties in relation to this website or the information and materials provided on this website.
+Without prejudice to the generality of the foregoing paragraph, chemotion-repository does not warrant that:
+
+ - this website will be constantly available, or available at all; or
+
- the information on this website is complete, true, accurate or non-misleading.
+
+Nothing on this website constitutes, or is meant to constitute, advice of any kind.
+
+3.6 Limitations of liability
+
+Chemotion-repository will not be liable to you (whether under the law of contact, the law of torts or otherwise) in relation to the contents of, or use of, or otherwise in connection with, this website:
+
+ - for any direct loss;
+ - for any indirect, special or consequential loss; or
+ - for any business losses, loss of revenue, income, profits or anticipated savings, loss of contracts or business relationships, loss of reputation or goodwill, or loss or corruption of information or data.
+
+3.7 Limitation of liability for internal content
+Chemotion-repository does not assume liability for the completeness or accuracy of any of the website. Chemotion-repository, as service provider, is liable for our own content on these pages in accordance with general laws. Chemotion-repository is not under obligation to monitor external information provided or stored on our website. Once aware of a specific infringement of the law, chemotion-repository will immediately remove the content in question. Any liability concerning this matter can only be assumed from the point in time at which the infringement becomes known to us.
+3.8 Limitation of liability for external links
+Our website contains links to the websites of third parties ('external links'). As the content of these websites is not under our control, we cannot assume any liability for such external content. In all cases, the provider of information of the linked websites is liable for the content and accuracy of the information provided. At the point in time when the links were placed, no infringements of the law were recognisable to us. As soon as an infringement of the law becomes known to us, we will immediately remove the link in question.
+These limitations of liability apply even if you have been expressly advised of the potential loss.
+3.9 Indemnity
+You hereby indemnify chemotion-repository and undertake to keep chemotion-repository indemnified against any losses, damages, costs, liabilities and expenses (including without limitation legal expenses and any amounts paid by chemotion-repository to a third party in settlement of a claim or dispute arising out of any breach by you of any provision of these terms and conditions.
+3.10 Assignment
+chemotion-repository may transfer, sub-contract or otherwise deal with chemotion-repository's rights and/or obligations under these terms and conditions without notifying you or obtaining your consent. You may not transfer, sub-contract or otherwise deal with your rights and/or obligations under these terms and conditions.
+3.11 Breaches of these terms and conditions
+Without prejudice to chemotion-repository's other rights under these terms and conditions, if you breach these terms and conditions in any way, chemotion-repository may take such action as chemotion-repository deems appropriate to deal with the breach.
+3.12 Law and jurisdiction
+Use of this website and the interpretation of this Disclaimer shall be governed by and construed in accordance with the laws of Germany, without regard to conflict of law provisions. Any dispute arising out of this Agreement shall be resolved in the courts in Germany. Through your continued use of this website, you agree to submit to the personal jurisdiction of the courts of Germany. Chemotion-repository may change this Disclaimer at any time without notice to you and without liability to you or any other party. It is your responsibility to periodically check this Disclaimer for changes. If you do not agree to any changes made to the Disclaimer, you should cease use of this website. Continued use of this website signifies acceptance of any changes made to the Disclaimer.
diff --git a/app/views/pages/affiliations.haml b/app/views/pages/affiliations.haml
index f1fcff101..6f83f9075 100644
--- a/app/views/pages/affiliations.haml
+++ b/app/views/pages/affiliations.haml
@@ -25,7 +25,6 @@
%th.col-xs-1 Country
%th.col-xs-3 Organization
%th.col-xs-2 Department
- %th.col-xs-2 Group
%th.col-xs-1 from
%th.col-xs-1 to
%th.col-xs-1
@@ -35,7 +34,6 @@
%td= aff.affiliation.country
%td= aff.affiliation.organization
%td= aff.affiliation.department
- %td= aff.affiliation.group
%td{id: "aff_#{aff.id}_from", class: 'affiliation_from'}= aff.from.strftime("%b-%Y") if aff.from
%td{id: "aff_#{aff.id}_to", class: 'affiliation_to' }= aff.to.strftime("%b-%Y") if aff.to
%td
diff --git a/app/views/pages/directive.html.haml b/app/views/pages/directive.html.haml
new file mode 100644
index 000000000..ce70498c4
--- /dev/null
+++ b/app/views/pages/directive.html.haml
@@ -0,0 +1,5 @@
+.panel.panel-primary
+ .panel-heading
+ Directive to use the service
+ .panel-body{style: 'height: auto; '}
+ = render 'pages/privacy_notice_and_terms_of_service'
diff --git a/app/views/pages/welcome.haml b/app/views/pages/mydb.haml
similarity index 97%
rename from app/views/pages/welcome.haml
rename to app/views/pages/mydb.haml
index f929129dd..f04a2a03f 100644
--- a/app/views/pages/welcome.haml
+++ b/app/views/pages/mydb.haml
@@ -1,4 +1,3 @@
#chemdrawjs-container
#app
#modal
-
diff --git a/app/views/pages/profiles.haml b/app/views/pages/profiles.haml
index 4ace4ae05..73fe409ac 100644
--- a/app/views/pages/profiles.haml
+++ b/app/views/pages/profiles.haml
@@ -20,4 +20,4 @@
%br/
%br/
- = link_to "Back", root_path
+ = link_to "Back", "/pages"
diff --git a/app/views/pages/root_page.html.erb b/app/views/pages/root_page.html.erb
new file mode 100644
index 000000000..b49304cbd
--- /dev/null
+++ b/app/views/pages/root_page.html.erb
@@ -0,0 +1,184 @@
+
+
+
+
+
+ <%= image_tag "logo.png", id: 'logo-image' %> CHEMOTION
+
+
+ Electronic Laboratory Notebook &
+ Repository for Research Data
+
+ <%= image_tag "molecule.png", id: 'molecule-image' %>
+
+
+
+
+
+
+
+
+
+
View, edit, and export spectra
from jcamp files
+
+
+
+
ChemSpectra
+
+
+
+ - Save your reactions and samples
+ - Make calculations
+ - Generate reports
+ - Import your data with ChemScanner
+
+
+
+
+
Electronic Lab Notebook
+
+
+
Repository for molecules, reactions and research data
+
+ - Publish your structures, attach your characterization data, and make them citable via DOI
+ - Automated registration at various scientific data providers
+ - Long-term archival - from scientists for scientists
+
+
+
+
+
Chemotion Repository
+
+
+
Extract chemical information from cdx, cdxml, or cdx(ml) containing doc and docx files
+
+
+
+
ChemScanner
+
+
+
+
+
+
+
+
+
+
Electronic Lab Notebook: Introduction Videos
+
+
+
+
+
+
+
+
+
+
+
Directive to use the service chemotion-repository
+(last edited: 2019-11-04)
+
+By using the chemotion-website and the service of the chemotion-repository,
+you accept the following terms and conditions in full.
+If you disagree with these terms and conditions or any part of these terms and conditions,
+you must not use this website.
+Some parts of this website may be subject to additional terms and conditions which will be
+made available to you as appropriate.
+Parts of this website may use strictly necessary and session cookies.
+By using this website and agreeing to these terms
+and conditions, you consent to our use of cookies in accordance with the terms of
+chemotion's Privacy Policy.
+
+The service chemotion-repository offers technical infrastructure to collect and
+share research data for chemical sciences.
+The data storage is accomplished by the service and all data are stored on servers of the
+KIT.
+The service allows a qualified realization of the recommendations of the German research
+foundation for the storage of research data.
+
+Service provider is the Institute of Organic Chemistry (IOC) in collaboration with the
+Steinbuchs Centre for Computing (SCC) and the Library at the KIT in Karlsruhe.
+
+
+ 1. General
+
+ 1.1 Authorization, registration and log-off
+
+Academic institutions are automatically recognized through the domain part of the email
+the user entered for registration. The users may use the service after their
+registration and confirmation of their email address. If the user's
+academic institution has not been properly recognized, the user shall communicate
+the error to the chemotion-repository. An email will also be sent to
+confirm the validity of the email address every time the user updates its email
+address on the portal and once a year. The administration of the individual
+authorization to use the service is carried out by the Institute of Organic
+Chemistry (KIT). The service providers will consider their right to check the
+correctness of the given data with respect to the affiliation and data of the
+user's registration. The log in and log off to the service is available
+via the website: chemotion-repository website.
+
+1.2 Readability and availability of the stored data
+
+Research data are stored at the Steinbuch Centre for Computing (SCC) guaranteed
+until 2028. The chemotion-repository intends to prolong this period
+successively by additional contracts with the SCC but the decision on any
+prolongation and the duration will be made solely by the two partners
+chemotion-repository and the SCC.
+The SCC makes every effort to ensure the best possible technical prerequisites
+for a long life of the data (best effort) with the available resources.
+These include, inter alia, adequate air conditioning, uninterrupted power supply,
+ and building protection.
+
+1.3 Admission
+
+The user accesses the chemotion-repository after registering on the website
+and successfully logging on. When registering, the operator checks the data
+and the agreement to use the service with the respective home institution.
+The user can access his data at any time as long as he has a valid access.
+
+1.4. Protocols
+
+HTTPS is enforced at all time.
+
+1.5 Deletion of files and content by users
+
+Files (content unpublished) that are stored in the repository in general can
+be deleted or changed by the user at any time.
+Files and data which are published (content published) cannot be deleted or changed anymore.
+The user agrees that those data (which are selected by the user individually) will be registered at DataCite (with retrieval of a DOI) and Pubchem (Pubchem substance SID).
+Authors should contact the repository curator at chemotion@ioc.kit.edu if they need to retract or amend published content.
+1.6 Maximum of data storage
+
+The data size per user is limited up to date to 10 GB. The operator will adapt
+allowed data size if this will be necessary in future.
+
+1.7 Costs and fees
+
+There are no fees or costs for the users
+
+1.8 Support via chemotion
+
+The provider will offer service for the use of the repository as long as the
+resources allow the support. The user is expected to familiarize with the given
+website and its applications. Support is available via the email address: chemotion@ioc.kit.edu.
+
+
+
+2. Data content
+
+2.1 Responsibility for data contents
+
+There are two types of contributed contents, unpublished and published contributed contents.
+User contributed content (unpublished): the user may upload user data which are not visible for other users, this content is visible only if the user is logged in or if he/she shares the content with other users.
+User contributed content (published): If the user selects single items or item groups to publish, the content will become available as open access for other users. The contents will be visible for the public and registered users will be able to download the content including the provided files.
+All uploaded contents are stored by the user in person. The data stored by him/her are always linked to the user's account data in the database of the storage system. Even if the account of a user is deleted, the connection of the stored data to the user's username (as defined with the registration) will be conserved.
+
+ - The user of the service is solely responsible for the contents of the contributed content of any type.
+ - The user is obligated to observe the legal regulations when storing sensitive and personal data.
+ - The uploaded user content must not be illegal or unlawful, must not infringe any third party's
+ legal rights, and must not be capable of giving rise to legal action whether against you
+ or chemotion-repository or a third party (in each case under any applicable law).
+
+ - You must not submit any user content to the website that is or has ever been the subject of any threatened or actual legal proceedings or other similar complaint.
+
+
+chemotion-repository reserves the right to edit or remove any material submitted to this website, or stored on chemotion-repository servers, or hosted or published upon this website.
+
+2.2 User contributed content (unpublished)
+
+User contributed content that is not published by the user is considered to be
+private unless the user shares the content which means that the user allows
+selected other users to view, edit, copy and store the users data.
+The user adapts the sharing options according to these actions and accepts
+that a sharing of content means always the disclosure of confidential content to others.
+
+2.3 User contributed content (published)
+
+In these terms and conditions, 'your published user content' means
+material (including without limitation text, images, audio material, video
+material and audio-visual material) that you submit to this website by using
+the function 'publish'. You grant to chemotion-repository,
+a worldwide, irrevocable, non-exclusive, royalty-free license to use, reproduce,
+adapt, publish, translate and distribute your user content in any existing or
+future media. You also grant to chemotion-repository
+the right to sub-license these rights, and the right to bring an action
+for infringement of these rights.
+
+
+3. Use of the repository
+Unless otherwise stated, chemotion-repository and/or its contributors own
+the intellectual property rights in the website and material on the website.
+Subject to the license below, all these intellectual property rights are reserved.
+
+Each content contributed and published by a user is made available under one of
+the following licenses that the contributing user has chosen during the publication process:
+
+
+You must not
+
+ - use material other than the DOIs from this website for any publication without
+ attribution or republish material from this website (including republication on another website)
+ without attribution (e.g. 'reused from Chemotion-Repository KIT') unless the material has been released under CC0
+
+
+ ;
+
+ - sublicense material other than allowed under the original license (
+
+ CC no sublicensing
+
+ ).
+
+
+
+3.1 Acceptable use
+
+You must not use this website in any way that causes, or may cause, damage to the website or impairment of the availability or accessibility of the website, or in any way which is unlawful, illegal, fraudulent or harmful, or in connection with any unlawful, illegal, fraudulent or harmful purpose or activity.
+You must not use this website to copy, store, host, transmit, send, use, publish or distribute any material which consists of (or is linked to) any spyware, computer virus, Trojan horse, worm, keystroke logger, rootkit or other malicious computer software.
+You must not conduct any systematic or automated data collection activities (including without limitation scraping, data mining, data extraction and data harvesting) on or in relation to this website without chemotion-repository's express written consent.
+
+3.2 Restricted access
+
+Access to certain areas of this website may be restricted. chemotion-repository reserves the right to restrict access to areas of this website, or indeed this entire website, at chemotion-repository's discretion.
+If chemotion-repository provides you with a user ID and password to enable you to access restricted areas of this website or other content or services, you must ensure that the user ID and password are kept confidential.
+
Chemotion-repository may disable your user ID and password in chemotion-repository sole discretion without notice or explanation.
+
+3.3 Copyright
+
+The content and works published on chemotion-repository's website, are governed by the copyright laws of Germany. Any duplication, processing, distribution or any form of utilization beyond the scope of copyright law shall require the prior written consent of the author or authors in question.
+
+3.4 DOI Ownership
+
+Chemotion-repository asserts no claims of ownership to Digital Object Identifiers (DOIs) acquired through the use of the chemotion-repository. Individual DOIs may be incorporated into the user's content and systems.
+
+3.5 No warranties
+
+This website is provided 'as is' without any representations or warranties, express or implied. Chemotion-repository makes no representations or warranties in relation to this website or the information and materials provided on this website.
+Without prejudice to the generality of the foregoing paragraph, chemotion-repository does not warrant that:
+
+ - this website will be constantly available, or available at all; or
+
- the information on this website is complete, true, accurate or non-misleading.
+
+Nothing on this website constitutes, or is meant to constitute, advice of any kind.
+
+3.6 Limitations of liability
+
+Chemotion-repository will not be liable to you (whether under the law of contact, the law of torts or otherwise) in relation to the contents of, or use of, or otherwise in connection with, this website:
+
+ - for any direct loss;
+ - for any indirect, special or consequential loss; or
+ - for any business losses, loss of revenue, income, profits or anticipated savings, loss of contracts or business relationships, loss of reputation or goodwill, or loss or corruption of information or data.
+
+3.7 Limitation of liability for internal content
+Chemotion-repository does not assume liability for the completeness or accuracy of any of the website. Chemotion-repository, as service provider, is liable for our own content on these pages in accordance with general laws. Chemotion-repository is not under obligation to monitor external information provided or stored on our website. Once aware of a specific infringement of the law, chemotion-repository will immediately remove the content in question. Any liability concerning this matter can only be assumed from the point in time at which the infringement becomes known to us.
+3.8 Limitation of liability for external links
+Our website contains links to the websites of third parties ('external links'). As the content of these websites is not under our control, we cannot assume any liability for such external content. In all cases, the provider of information of the linked websites is liable for the content and accuracy of the information provided. At the point in time when the links were placed, no infringements of the law were recognisable to us. As soon as an infringement of the law becomes known to us, we will immediately remove the link in question.
+These limitations of liability apply even if you have been expressly advised of the potential loss.
+3.9 Indemnity
+You hereby indemnify chemotion-repository and undertake to keep chemotion-repository indemnified against any losses, damages, costs, liabilities and expenses (including without limitation legal expenses and any amounts paid by chemotion-repository to a third party in settlement of a claim or dispute arising out of any breach by you of any provision of these terms and conditions.
+3.10 Assignment
+chemotion-repository may transfer, sub-contract or otherwise deal with chemotion-repository's rights and/or obligations under these terms and conditions without notifying you or obtaining your consent. You may not transfer, sub-contract or otherwise deal with your rights and/or obligations under these terms and conditions.
+3.11 Breaches of these terms and conditions
+Without prejudice to chemotion-repository's other rights under these terms and conditions, if you breach these terms and conditions in any way, chemotion-repository may take such action as chemotion-repository deems appropriate to deal with the breach.
+3.12 Law and jurisdiction
+Use of this website and the interpretation of this Disclaimer shall be governed by and construed in accordance with the laws of Germany, without regard to conflict of law provisions. Any dispute arising out of this Agreement shall be resolved in the courts in Germany. Through your continued use of this website, you agree to submit to the personal jurisdiction of the courts of Germany. Chemotion-repository may change this Disclaimer at any time without notice to you and without liability to you or any other party. It is your responsibility to periodically check this Disclaimer for changes. If you do not agree to any changes made to the Disclaimer, you should cease use of this website. Continued use of this website signifies acceptance of any changes made to the Disclaimer.
diff --git a/public/howto/.keep b/public/howto/.keep
new file mode 100644
index 000000000..e69de29bb
diff --git a/public/images/creative_common/cc-by-sa.svg b/public/images/creative_common/cc-by-sa.svg
new file mode 100644
index 000000000..f8502975c
--- /dev/null
+++ b/public/images/creative_common/cc-by-sa.svg
@@ -0,0 +1,199 @@
+
+
+
diff --git a/public/images/creative_common/cc-by.svg b/public/images/creative_common/cc-by.svg
new file mode 100644
index 000000000..e44c25f0a
--- /dev/null
+++ b/public/images/creative_common/cc-by.svg
@@ -0,0 +1,155 @@
+
+
+
diff --git a/public/images/creative_common/cc-zero.svg b/public/images/creative_common/cc-zero.svg
new file mode 100644
index 000000000..195592b7b
--- /dev/null
+++ b/public/images/creative_common/cc-zero.svg
@@ -0,0 +1,98 @@
+
+
+
+
diff --git a/public/images/wild_card/pubchem_sid.svg b/public/images/wild_card/pubchem_sid.svg
new file mode 100644
index 000000000..ac0d9f626
--- /dev/null
+++ b/public/images/wild_card/pubchem_sid.svg
@@ -0,0 +1,73 @@
+
+
+
+
diff --git a/public/newsroom/.keep b/public/newsroom/.keep
new file mode 100644
index 000000000..e69de29bb