{ navigator.clipboard.writeText(contentToText(content)); }}>
-
+
@@ -1980,11 +1956,11 @@ class PublishAnalysesTag extends Component {
:
Content:
-
Status: {status} {statusMsg}
}
-
+
@@ -2221,7 +2197,6 @@ export {
DownloadJsonBtn,
EditorTips,
ElementIcon,
- ElStateLabel,
ElAspect,
EmbargoCom,
IconToMyDB,
@@ -2230,7 +2205,6 @@ export {
isDatasetPass,
HomeFeature,
MoleculeInfo,
- NewsroomTemplate,
PublishAnalysesTag,
PublishTypeAs,
ReactionSchemeOnlyInfo,
@@ -2244,7 +2218,6 @@ export {
SchemeWord,
SidToPubChem,
OrcidIcon,
- SvgPath,
ToggleIndicator,
CollectionDesc
};
diff --git a/app/packs/src/repoHome/RepoEmbargo.js b/app/packs/src/repoHome/RepoEmbargo.js
index 71d468817..21353d28d 100644
--- a/app/packs/src/repoHome/RepoEmbargo.js
+++ b/app/packs/src/repoHome/RepoEmbargo.js
@@ -209,22 +209,29 @@ export default class RepoEmbargo extends Component {
handleEmbargoRelease() {
const { selectEmbargo, current_user } = this.state;
+ const isSubmitter =
+ current_user?.id === selectEmbargo?.published_by ||
+ (selectEmbargo?.review?.submitters || []).includes(current_user?.id);
if (selectEmbargo === null) {
alert('Please select an embargo first!');
- } else if (current_user.id !== selectEmbargo.published_by) {
+ } else if (!isSubmitter) {
alert('only the submitter can perform the release!');
} else {
EmbargoActions.releaseEmbargo(selectEmbargo.element_id);
- alert(`The embargo on [${selectEmbargo.taggable_data && selectEmbargo.taggable_data.label}] has been released!`);
+ alert(`The submission for the release of the embargo [${selectEmbargo.taggable_data && selectEmbargo.taggable_data.label}] has been completed!`);
}
}
handleEmbargoDelete(shouldPerform) {
if (shouldPerform) {
const { selectEmbargo, current_user } = this.state;
+ const isSubmitter =
+ current_user?.id === selectEmbargo?.published_by ||
+ (selectEmbargo?.review?.submitters || []).includes(current_user?.id);
+
if (selectEmbargo === null) {
alert('Please select an embargo first!');
- } else if (current_user?.is_reviewer === false && current_user.id !== selectEmbargo.published_by) {
+ } else if (!isSubmitter) {
alert('only the submitter can delete the release!');
} else {
EmbargoActions.deleteEmbargo(selectEmbargo.element_id);
@@ -242,7 +249,8 @@ export default class RepoEmbargo extends Component {
rendeActionBtn(bundles) {
const { selectEmbargo, elements, current_user } = this.state;
const acceptedEl = ((typeof (elements) !== 'undefined' && elements) || []).filter(e => e.state === 'accepted');
- const actionButtons = (!selectEmbargo || !current_user || (current_user?.is_reviewer == false && current_user.id !== selectEmbargo.published_by)) ? :
+ const is_submitter = current_user?.id === selectEmbargo?.published_by || (selectEmbargo?.review?.submitters || []).includes(current_user?.id);
+ const actionButtons = (!selectEmbargo || !current_user || (current_user?.is_reviewer == false && !is_submitter)) ? :
(
Content:
-
{
});
const viewDetailBtn =
- currentUser.is_reviewer || currentUser.is_submitter ? (
+ currentUser.is_reviewer ||
+ currentUser.is_submitter ||
+ (rec?.review?.submitters || []).includes(currentUser?.id) ||
+ currentUser?.type === RepoConst.U_TYPE.ANONYMOUS ? (
) : null;
- const viewComment = comment ? (
-
- {comment}
-
- ) : null;
+ const viewComment =
+ comment && (currentUser.is_reviewer || currentUser.is_submitter) ? (
+
+ {comment}
+
+ ) : null;
return (
+
- Chemotion-Repository unique ID}>
+
+ Chemotion-Repository unique ID
+
+ }
+ >
- an embargo bundle contains publications which have been published at the same time}>
+
+ an embargo bundle contains publications which have been published at
+ the same time
+
+ }
+ >
When the X-Vial icon available, a physical sample of this molecule was registered to the Molecule Archive of the Compound Platform and can be requested from there}>
+
+ When the X-Vial icon available, a physical sample of this molecule
+ was registered to the Molecule Archive of the Compound Platform and
+ can be requested from there
+
+ }
+ >
);
};
-const RepoMoleculeList = (props) => {
- const {
- molecule, currentElement, isPubElement, advFlag, advType, advValue
- } = props;
- const listClass = (currentElement && currentElement.molecule && currentElement.molecule.id === molecule.id) ? 'list_focus_on' : 'list_focus_off';
+function RepoMoleculeList(props) {
+ const { molecule, currentElement, isPubElement, advFlag, advType, advValue } =
+ props;
+ const listClass =
+ currentElement?.molecule?.id === molecule.id
+ ? 'list_focus_on'
+ : 'list_focus_off';
const svgPathSample = molecule.sample_svg_file
? `/images/samples/${molecule.sample_svg_file}`
: `/images/molecules/${molecule.molecule_svg_file}`;
const pubchemInfo = pubchemTag(molecule);
return (
-
- |
+
+
{molecule.iupac_name}
- {pubchemInfo ?
@@ -80,17 +132,17 @@ const RepoMoleculeList = (props) => {
);
-};
+}
RepoMoleculeList.propTypes = {
molecule: PropTypes.object.isRequired,
currentElement: PropTypes.object,
isPubElement: PropTypes.bool,
+ advFlag: PropTypes.bool.isRequired,
+ advType: PropTypes.string.isRequired,
+ advValue: PropTypes.array.isRequired,
};
-RepoMoleculeList.defaultProps = {
- isPubElement: false,
- currentElement: null
-};
+RepoMoleculeList.defaultProps = { isPubElement: false, currentElement: null };
export default RepoMoleculeList;
diff --git a/app/packs/src/repoHome/RepoNewsEditor.js b/app/packs/src/repoHome/RepoNewsEditor.js
index cb9c3331e..f7fc76d89 100644
--- a/app/packs/src/repoHome/RepoNewsEditor.js
+++ b/app/packs/src/repoHome/RepoNewsEditor.js
@@ -1,5 +1,16 @@
import React, { Component } from 'react';
-import { Alert, Jumbotron, Row, Col, Form, FormGroup, FormControl, ControlLabel, Button, InputGroup } from 'react-bootstrap';
+import {
+ Alert,
+ Button,
+ Col,
+ ControlLabel,
+ Form,
+ FormGroup,
+ FormControl,
+ InputGroup,
+ Jumbotron,
+ Row,
+} from 'react-bootstrap';
import Dropzone from 'react-dropzone';
import moment from 'moment';
import ArticleFetcher from 'src/repo/fetchers/ArticleFetcher';
@@ -7,11 +18,17 @@ import NewsPreviewModal from 'src/components/common/NewsPreviewModal';
import PublicStore from 'src/stores/alt/repo/stores/PublicStore';
import { ConfirmModal } from 'src/components/common/ConfirmModal';
import Attachment from 'src/models/Attachment';
-import { EditorTips, DateFormatDMYTime, NewsroomTemplate } from 'src/repoHome/RepoCommon';
+import { EditorTips, DateFormatDMYTime } from 'src/repoHome/RepoCommon';
import { contentToText } from 'src/utilities/quillFormat';
import { EditorBtn, EditorBaseBtn } from 'src/libHome/RepoHowTo/EditorBtn';
import EditorStelle from 'src/libHome/RepoHowTo/EditorStelle';
+const NewsroomTemplate = {
+ title: '',
+ content: {},
+ article: [],
+};
+
const extractIntro = (article) => {
const result = article.filter(a => a.art === 'txt');
if (result.length < 1) {
diff --git a/app/packs/src/repoHome/RepoNewsReader.js b/app/packs/src/repoHome/RepoNewsReader.js
index 16ef2764d..6ac6d0e25 100644
--- a/app/packs/src/repoHome/RepoNewsReader.js
+++ b/app/packs/src/repoHome/RepoNewsReader.js
@@ -2,7 +2,7 @@ import React, { Component } from 'react';
import { Panel, Row, Col } from 'react-bootstrap';
import uuid from 'uuid';
import PublicStore from 'src/stores/alt/repo/stores/PublicStore';
-import QuillViewer from 'src/components/QuillViewer';
+import Quill2Viewer from 'src/components/Quill2Viewer';
import { DateFormatYMDLong } from 'src/repoHome/RepoCommon';
export default class RepoNewsReader extends Component {
@@ -96,7 +96,7 @@ export default class RepoNewsReader extends Component {
news.article ?
news.article.map((s) => {
if (s.art === 'txt') {
- return ({
+ ...base,
+ height: '36px',
+ minHeight: '36px',
+ minWidth: '200px',
+ borderRadius: 'unset',
+ border: '1px solid #ccc',
+ }),
+ multiValue: styles => ({
+ ...styles,
+ backgroundColor: '#00b8d91a',
+ opacity: '0.8',
+ }),
+ multiValueLabel: styles => ({
+ ...styles,
+ color: '#0052CC',
+ }),
+ }}
+ />
+ );
+ }
return (
Advanced Search}>
diff --git a/app/packs/src/repoHome/RepoReactionDetails.js b/app/packs/src/repoHome/RepoReactionDetails.js
index 22374045d..cf362952e 100644
--- a/app/packs/src/repoHome/RepoReactionDetails.js
+++ b/app/packs/src/repoHome/RepoReactionDetails.js
@@ -1,3 +1,4 @@
+/* eslint-disable react/forbid-prop-types */
import React, { Component } from 'react';
import { Panel, Row, Col, Button, Jumbotron } from 'react-bootstrap';
import PropTypes from 'prop-types';
@@ -139,7 +140,17 @@ export default class RepoReactionDetails extends Component {
reactionInfo(reaction) {
const { showScheme, showRinchi, showProp, showTlc } = this.state;
- const { canComment, review_info, review, isPublished } = this.props;
+ const {
+ canComment: propsCanComment,
+ review_info,
+ review,
+ isPublished,
+ } = this.props;
+ const { currentUser } = UserStore.getState();
+ const canComment =
+ currentUser?.type === RepoConst.U_TYPE.ANONYMOUS
+ ? false
+ : propsCanComment;
const svgPath = `/images/reactions/${reaction.reaction_svg_file}`;
const content = reaction.description;
@@ -150,9 +161,9 @@ export default class RepoReactionDetails extends Component {
? content.ops[0].insert.trim()
: '';
let descQV = (
-
+
Description:
-
+
-
ID
{`CRS-${pubData}`}
+ ID
+ {`CRS-${pubData}`}
-
Embargo
{molecule.embargo}
+ Embargo
+ {molecule.embargo}
-
Author
{molecule.author_name}
+ Author
+ {molecule.author_name}
-
Published on
{getFormattedISODate(molecule.published_at)}
+ Published on
+
+ {getFormattedISODate(molecule.published_at)}
+
-
- Analyses
{molecule.ana_cnt || 0}
+ Analyses
+ {molecule.ana_cnt || 0}
-
X-Vial
{xvialTag(molecule)}
+ X-Vial
+ {xvialTag(molecule)}
@@ -528,37 +581,7 @@ export default class RepoPubl extends Component {
className="o-author"
/>
-
- ({
- ...base,
- height: '36px',
- minHeight: '36px',
- minWidth: '200px',
- borderRadius: 'unset',
- border: '1px solid #ccc',
- }),
- multiValue: styles => ({
- ...styles,
- backgroundColor: '#00b8d91a',
- opacity: '0.8',
- }),
- multiValueLabel: styles => ({
- ...styles,
- color: '#0052CC',
- }),
- }}
- />
-
+ {valSelect}
@@ -608,7 +625,7 @@ export default class RepoReactionDetails extends Component {
1
}
/>
-
{
const content = props.reaction.description;
const contentlength = (content && content.ops && content.ops.length > 0
&& content.ops[0].insert) ? content.ops[0].insert.trim().length : 0;
const descQV = contentlength > 0 ?
- (Description:
diff --git a/app/packs/src/repoHome/RepoReview.js b/app/packs/src/repoHome/RepoReview.js
index 30f23de0a..a5192df6c 100644
--- a/app/packs/src/repoHome/RepoReview.js
+++ b/app/packs/src/repoHome/RepoReview.js
@@ -12,7 +12,12 @@ import UserStore from 'src/stores/alt/stores/UserStore';
import RepositoryFetcher from 'src/repo/fetchers/RepositoryFetcher';
import LoadingActions from 'src/stores/alt/actions/LoadingActions';
import { getFormattedISODateTime } from 'src/components/chemrepo/date-utils';
-import { SvgPath, ElStateLabel, SchemeWord, ChecklistPanel } from 'src/repoHome/RepoCommon';
+import StateLabel from 'src/components/chemrepo/common/StateLabel';
+import SVGView from 'src/components/chemrepo/SVGViewPan';
+import { SchemeWord, ChecklistPanel } from 'src/repoHome/RepoCommon';
+import { ShowUserLabels, SearchUserLabels } from 'src/components/UserLabels';
+
+
// import RepoReviewModal from '../components/common/RepoReviewModal';
const renderElement = (e, currentElement, embargoBtn) => {
@@ -30,10 +35,13 @@ const renderElement = (e, currentElement, embargoBtn) => {
{schemeOnly ?
+function RepoReviewButtonBar(props) {
+ let authorModel = '';
+
+ if (props?.review_info?.groupleader !== true) {
+ authorModel = (
+
{
props.showComment === true && props.buttons.filter(b => b === 'Comments').map(b =>
showCommentButton(b, props.buttonFunc, (props.currComment)))
@@ -102,14 +116,16 @@ const RepoReviewButtonBar = props =>
elementId={props.element.id}
elementType={props.element.elementType.toLowerCase()}
/>
-
- );
+ {authorModel}
+ )
+};
RepoReviewButtonBar.propTypes = {
element: PropTypes.shape({
id: PropTypes.number,
- elementType: PropTypes.string
+ elementType: PropTypes.string,
+ user_labels: PropTypes.arrayOf(PropTypes.number)
}).isRequired,
buttons: PropTypes.arrayOf(PropTypes.string),
buttonFunc: PropTypes.func,
@@ -128,7 +144,7 @@ RepoReviewButtonBar.defaultProps = {
showComment: true,
schemeOnly: false,
currComment: {},
- taggData: {}
+ taggData: {},
};
export default RepoReviewButtonBar;
diff --git a/app/packs/src/repoHome/RepoSampleDetails.js b/app/packs/src/repoHome/RepoSampleDetails.js
index fe0754c6b..b820b2507 100644
--- a/app/packs/src/repoHome/RepoSampleDetails.js
+++ b/app/packs/src/repoHome/RepoSampleDetails.js
@@ -1,14 +1,13 @@
import React, { Component } from 'react';
import { Panel } from 'react-bootstrap';
import PropTypes from 'prop-types';
-import {
- ClosePanel,
- MoleculeInfo,
-} from 'src/repoHome/RepoCommon';
+import { ClosePanel, MoleculeInfo } from 'src/repoHome/RepoCommon';
+import UserStore from 'src/stores/alt/stores/UserStore';
import LoadingActions from 'src/stores/alt/actions/LoadingActions';
import ReviewActions from 'src/stores/alt/repo/actions/ReviewActions';
import RepoReviewButtonBar from 'src/repoHome/RepoReviewButtonBar';
import RepoSample from 'src/repoHome/RepoSample';
+import RepoConst from 'src/components/chemrepo/common/RepoConst';
export default class RepoSampleDetails extends Component {
constructor(props) {
@@ -44,12 +43,17 @@ export default class RepoSampleDetails extends Component {
const {
element,
isPublished,
- canComment,
+ canComment: propsCanComment,
review_info,
showComment,
review,
canClose,
} = this.props;
+ const { currentUser } = UserStore.getState();
+ const canComment =
+ currentUser?.type === RepoConst.U_TYPE.ANONYMOUS
+ ? false
+ : propsCanComment;
let { buttons } = this.props;
@@ -93,6 +97,12 @@ export default class RepoSampleDetails extends Component {
doi_reg_at: s.doi_reg_at
};
}
+
+ if (typeof s === 'undefined' || !s) {
+ console.log('Sample is undefined');
+ return null;
+ }
+
const el = {
id: s.id || s.sample_id,
decoupled: s.decoupled,
@@ -120,6 +130,8 @@ export default class RepoSampleDetails extends Component {
boiling_point: s.boiling_point || '',
melting_point: s.melting_point || '',
labels: (isPublished ? s.labels : labels) || [],
+ molecular_mass: s.molecular_mass || '',
+ sum_formula: s.sum_formula || '',
};
return (
@@ -142,17 +154,18 @@ export default class RepoSampleDetails extends Component {
{
canComment ?
+ {canClose ?
+
-
+
@@ -52,10 +60,13 @@ const renderElement = (e, currentElement, embargoBtn) => {
{e.title}
By {e.published_by} at
- {getFormattedISODateTime(e.submit_at)} {ElStateLabel(e.state)} {ElStateLabel(e.embargo)}
+ {getFormattedISODateTime(e.submit_at)} {StateLabel(e.state)} {StateLabel(e.embargo)}
{embargoBtn}
+
+
-
+
@@ -99,6 +110,7 @@ export default class RepoReview extends Component {
this.handleSubmitReview = this.handleSubmitReview.bind(this);
this.handleReviewUpdate = this.handleReviewUpdate.bind(this);
this.handleCommentUpdate = this.handleCommentUpdate.bind(this);
+ this.setUserLabel = this.setUserLabel.bind(this);
}
componentDidMount() {
@@ -141,22 +153,31 @@ export default class RepoReview extends Component {
ReviewActions.updateComment(elementId, elementType, cinfo);
}
+ setUserLabel(label) {
+ const { userLabel } = this.state;
+ this.setState({ userLabel: label });
+ if (userLabel !== label) ReviewActions.setUserLabel(label);
+
+ this.handleElementSelection('label', label);
+ }
+
+
onPerPageChange(e) {
const {
- page, selectType, selectState, searchType, searchValue
+ page, selectType, selectState, selectLabel, searchType, searchValue
} = this.state;
const perPage = e.target.value;
this.setState({ perPage });
- ReviewActions.getElements(selectType, selectState, searchType, searchValue, page, perPage);
+ ReviewActions.getElements(selectType, selectState, selectLabel, searchType, searchValue, page, perPage);
}
onPaginationSelect(eventKey) {
const {
- pages, perPage, selectType, selectState, searchType, searchValue
+ pages, perPage, selectType, selectState, selectLabel, searchType, searchValue
} = this.state;
if (eventKey > 0 && eventKey <= pages) {
ReviewActions.getElements(
- selectType, selectState, searchType, searchValue,
+ selectType, selectState, selectLabel, searchType, searchValue,
eventKey, perPage
);
}
@@ -231,18 +252,18 @@ export default class RepoReview extends Component {
}
handleSelectType(val) {
- const { selectType, selectState, perPage } = this.state;
+ const { selectType, selectState, perPage, selectLabel } = this.state;
if (val && (val === 'Submitter' || val === 'Embargo')) {
RepositoryFetcher.fetchReviewSearchOptions(val, selectType, selectState).then((res) => {
const options = res && res.result && res.result
.map(u => ({ value: u.key, name: u.name, label: u.label }));
this.setState({ listTypeOptions: options });
- ReviewActions.getElements(selectType, selectState, val, '', 1, perPage);
+ ReviewActions.getElements(selectType, selectState, selectLabel, val, '', 1, perPage);
}).catch((errorMessage) => {
console.log(errorMessage);
});
} else {
- ReviewActions.getElements(selectType, selectState, val, '', 1, perPage);
+ ReviewActions.getElements(selectType, selectState, selectLabel, val, '', 1, perPage);
}
}
@@ -255,32 +276,35 @@ export default class RepoReview extends Component {
handleSelectAdvValue(val) {
const {
- perPage, selectType, selectState, searchType
+ perPage, selectType, selectState, selectLabel, searchType
} = this.state;
if (val) {
this.setState({ page: 1, searchValue: val });
- ReviewActions.getElements(selectType, selectState, searchType, val, 1, perPage);
+ ReviewActions.getElements(selectType, selectState, selectLabel, searchType, val, 1, perPage);
}
}
handleElementSelection(t, event) {
- const { perPage, searchType, searchValue } = this.state;
+ const { perPage, searchType, selectLabel, searchValue } = this.state;
if (t === 'type') {
this.setState({ selectType: event });
- ReviewActions.getElements(event, this.state.selectState, searchType, searchValue, 1, perPage);
+ ReviewActions.getElements(event, this.state.selectState, selectLabel, searchType, searchValue, 1, perPage);
} else if (t === 'state') {
this.setState({ selectState: event });
- ReviewActions.getElements(this.state.selectType, event, searchType, searchValue, 1, perPage);
+ ReviewActions.getElements(this.state.selectType, event, selectLabel, searchType, searchValue, 1, perPage);
+ } else if (t === 'label') {
+ // this.setState({ selectState: event });
+ ReviewActions.getElements(this.state.selectType, this.state.selectState, event, searchType, searchValue, 1, perPage);
}
}
handleKeyDown(event) {
const {
- perPage, selectType, selectState, searchType, searchValue
+ perPage, selectType, selectState, selectLabel, searchType, searchValue
} = this.state;
switch (event.keyCode) {
case 13: // Enter
- ReviewActions.getElements(selectType, selectState, searchType, searchValue, 1, perPage);
+ ReviewActions.getElements(selectType, selectState, selectLabel, searchType, searchValue, 1, perPage);
event.preventDefault();
break;
default:
@@ -315,7 +339,7 @@ export default class RepoReview extends Component {
}
renderSearch() {
- const { searchType, searchValue, listTypeOptions } = this.state;
+ const { searchType, searchValue, listTypeOptions, userLabel } = this.state;
const customClass = '.btn-unified';
const optSearchType = ['All', 'Samples', 'Reactions'];
@@ -344,6 +368,7 @@ export default class RepoReview extends Component {
>
{this.renderMenuItems('state', optSearchState)}
+
{details}
diff --git a/app/packs/src/stores/alt/actions/UIActions.js b/app/packs/src/stores/alt/actions/UIActions.js
index 8acdf2b46..91bc65178 100644
--- a/app/packs/src/stores/alt/actions/UIActions.js
+++ b/app/packs/src/stores/alt/actions/UIActions.js
@@ -131,6 +131,10 @@ class UIActions {
return filterCreatedAt;
}
+ setUserLabel(label) {
+ return label;
+ }
+
setFromDate(date) {
return date;
}
diff --git a/app/packs/src/stores/alt/repo/actions/PublicActions.js b/app/packs/src/stores/alt/repo/actions/PublicActions.js
index e5e05c16d..bdce23fd3 100644
--- a/app/packs/src/stores/alt/repo/actions/PublicActions.js
+++ b/app/packs/src/stores/alt/repo/actions/PublicActions.js
@@ -298,8 +298,8 @@ class PublicActions {
}
}
- getElements(type='All', state='pending', searchType='All', searchValue='', page=1, perPage=10) {
- return (dispatch) => { RepositoryFetcher.fetchReviewElements(type, state, searchType, searchValue, page, perPage)
+ getElements(type='All', state='pending', label, searchType='All', searchValue='', page=1, perPage=10) {
+ return (dispatch) => { RepositoryFetcher.fetchReviewElements(type, state, label, searchType, searchValue, page, perPage)
.then((result) => {
dispatch(result)
}).catch((errorMessage) => {
@@ -351,6 +351,22 @@ class PublicActions {
setSearchParams(params) {
return params;
}
+
+ loadSpectraForNMRDisplayer(spcInfos) {
+ const idxs = spcInfos && spcInfos.map(si => si.idx);
+ if (idxs.length === 0) {
+ return null;
+ }
+
+ return (dispatch) => {
+ PublicFetcher.fetchFiles(idxs)
+ .then((fetchedFiles) => {
+ dispatch({ fetchedFiles, spcInfos });
+ }).catch((errorMessage) => {
+ console.log(errorMessage); // eslint-disable-line
+ });
+ };
+ }
}
export default alt.createActions(PublicActions);
diff --git a/app/packs/src/stores/alt/repo/actions/RepositoryActions.js b/app/packs/src/stores/alt/repo/actions/RepositoryActions.js
index ccdef7edc..52e30875e 100644
--- a/app/packs/src/stores/alt/repo/actions/RepositoryActions.js
+++ b/app/packs/src/stores/alt/repo/actions/RepositoryActions.js
@@ -1,13 +1,16 @@
/* eslint-disable class-methods-use-this */
import alt from 'src/stores/alt/alt';
import RepositoryFetcher from 'src/repo/fetchers/RepositoryFetcher';
+import LoadingActions from 'src/stores/alt/actions/LoadingActions';
class RepositoryActions {
publishSample(params, closeView = false) {
return (dispatch) => { RepositoryFetcher.publishSample(params)
.then((result) => {
if (result != null) {
- dispatch({ element: result, closeView })
+ dispatch(result)
+ } else {
+ LoadingActions.stop();
}
}).catch((errorMessage) => {
console.log(errorMessage);
@@ -20,6 +23,7 @@ class RepositoryActions {
dispatch({ element: result })
}).catch((errorMessage) => {
console.log(errorMessage);
+ dispatch({ element: element })
});};
}
@@ -40,6 +44,8 @@ class RepositoryActions {
.then((result) => {
if (result != null) {
dispatch({ element: result, closeView })
+ } else {
+ LoadingActions.stop();
}
}).catch((errorMessage) => {
console.log(errorMessage);
diff --git a/app/packs/src/stores/alt/repo/actions/ReviewActions.js b/app/packs/src/stores/alt/repo/actions/ReviewActions.js
index 55c25a619..29cf40b96 100644
--- a/app/packs/src/stores/alt/repo/actions/ReviewActions.js
+++ b/app/packs/src/stores/alt/repo/actions/ReviewActions.js
@@ -14,7 +14,7 @@ class ReviewActions {
}
fetchSample(id) {
- return (dispatch) => { RepositoryFetcher.fetchSample(id, false)
+ return (dispatch) => { RepositoryFetcher.fetchSample(id)
.then((result) => {
dispatch(result)
}).catch((errorMessage) => {
@@ -25,7 +25,7 @@ class ReviewActions {
}
displayReviewReaction(id) {
- return (dispatch) => { RepositoryFetcher.fetchReaction(id, false)
+ return (dispatch) => { RepositoryFetcher.fetchReaction(id)
.then((result) => {
dispatch({id, element: result})
}).catch((errorMessage) => {
@@ -35,7 +35,7 @@ class ReviewActions {
}
displayReviewSample(id) {
- return (dispatch) => { RepositoryFetcher.fetchSample(id, false)
+ return (dispatch) => { RepositoryFetcher.fetchSample(id)
.then((result) => {
dispatch({id, element: result})
}).catch((errorMessage) => {
@@ -54,8 +54,8 @@ class ReviewActions {
}
- getElements(type='All', state='pending', searchType='All', searchValue='', page=1, perPage=10) {
- return (dispatch) => { RepositoryFetcher.fetchReviewElements(type, state, searchType, searchValue, page, perPage)
+ getElements(type='All', state='pending', label=null, searchType='All', searchValue='', page=1, perPage=10) {
+ return (dispatch) => { RepositoryFetcher.fetchReviewElements(type, state, label, searchType, searchValue, page, perPage)
.then((result) => {
dispatch(result)
}).catch((errorMessage) => {
@@ -64,7 +64,6 @@ class ReviewActions {
}
}
-
updateComment(id, type, comments) {
return (dispatch) => {
RepositoryFetcher.updateComment(id, type, comments)
@@ -75,6 +74,26 @@ class ReviewActions {
});
};
}
+
+ saveReviewLabel(element, ids) {
+ return dispatch => {
+ RepositoryFetcher.saveReviewLabel({
+ elementId: element.id,
+ elementType: element.elementType,
+ user_labels: ids,
+ })
+ .then(() => {
+ dispatch(element);
+ })
+ .catch(errorMessage => {
+ console.log(errorMessage);
+ });
+ };
+ }
+
+ setUserLabel(label) {
+ return label;
+ }
}
export default alt.createActions(ReviewActions);
diff --git a/app/packs/src/stores/alt/repo/stores/EmbargoStore.js b/app/packs/src/stores/alt/repo/stores/EmbargoStore.js
index 67cf041b8..427563477 100644
--- a/app/packs/src/stores/alt/repo/stores/EmbargoStore.js
+++ b/app/packs/src/stores/alt/repo/stores/EmbargoStore.js
@@ -68,7 +68,7 @@ class EmbargoStore {
EmbargoActions.getEmbargoBundle();
// refresh element list
PublicActions.getElements(
- this.selectType, this.selectState, this.searchType,
+ this.selectType, this.selectState, null, this.searchType,
this.searchValue, this.page, this.perPage
);
}
diff --git a/app/packs/src/stores/alt/repo/stores/PublicStore.js b/app/packs/src/stores/alt/repo/stores/PublicStore.js
index 0265e4a41..e39d6d88d 100644
--- a/app/packs/src/stores/alt/repo/stores/PublicStore.js
+++ b/app/packs/src/stores/alt/repo/stores/PublicStore.js
@@ -29,6 +29,7 @@ class PublicStore {
this.showReviewModal = false;
this.showCommendModal = false;
this.reviewData = {};
+ this.u = {};
this.bindListeners({
handleInitialize: PublicActions.initialize,
diff --git a/app/packs/src/stores/alt/repo/stores/ReviewStore.js b/app/packs/src/stores/alt/repo/stores/ReviewStore.js
index 6cae15339..29fcc2f60 100644
--- a/app/packs/src/stores/alt/repo/stores/ReviewStore.js
+++ b/app/packs/src/stores/alt/repo/stores/ReviewStore.js
@@ -1,8 +1,10 @@
import Aviator from 'aviator';
import alt from 'src/stores/alt/alt';
+import UserStore from 'src/stores/alt/stores/UserStore';
import PublicActions from 'src/stores/alt/repo/actions/PublicActions';
import ReviewActions from 'src/stores/alt/repo/actions/ReviewActions';
import EmbargoActions from 'src/stores/alt/repo/actions/EmbargoActions';
+import RepoConst from 'src/components/chemrepo/common/RepoConst';
class ReviewStore {
constructor() {
@@ -15,6 +17,7 @@ class ReviewStore {
//this.bundles = [];
this.selectType;
this.selectState;
+ this.selectLabel;
this.searchType;
this.searchValue;
this.currentElement = null;
@@ -34,6 +37,8 @@ class ReviewStore {
handleClose: PublicActions.close,
handleRefreshEmbargoBundles: EmbargoActions.getEmbargoBundle,
handleEmbargoAssign: EmbargoActions.assignEmbargo,
+ handleSetUserLabel: ReviewActions.setUserLabel,
+ handleSaveReviewLabel: ReviewActions.saveReviewLabel,
});
}
@@ -52,7 +57,7 @@ class ReviewStore {
EmbargoActions.getEmbargoBundle();
// refresh element list
ReviewActions.getElements(
- this.selectType, this.selectState, this.searchType,
+ this.selectType, this.selectState, this.selectLabel, this.searchType,
this.searchValue, this.page, this.perPage
);
}
@@ -109,53 +114,104 @@ class ReviewStore {
this.setState({ review: result.review, showReviewModal: false, showCommentModal: false });
}
+ handleSaveReviewLabel(element) {
+ if (element.elementType === 'Reaction') {
+ ReviewActions.displayReviewReaction(element.id);
+ } else if (element.elementType === 'Sample') {
+ ReviewActions.displayReviewSample(element.id);
+ }
+ ReviewActions.getElements(
+ this.selectType || 'All',
+ this.selectState || 'pending',
+ this.selectLabel,
+ this.searchType || 'All',
+ this.searchValue || '',
+ this.page,
+ this.perPage
+ );
+ }
+
handelReviewPublish(results) {
// const { history, checklist, reviewComments } = results.review;
- this.setState({ review: results.review, showReviewModal: false, showCommentModal: false, review_info: results.review_info });
- ReviewActions.getElements(this.selectType || 'All', this.selectState || 'pending', this.searchType || 'All', this.searchValue || '', this.page, this.perPage);
+ this.setState({
+ review: results.review,
+ showReviewModal: false,
+ showCommentModal: false,
+ review_info: results.review_info,
+ });
+ ReviewActions.getElements(
+ this.selectType || 'All',
+ this.selectState || 'pending',
+ this.selectLabel,
+ this.searchType || 'All',
+ this.searchValue || '',
+ this.page,
+ this.perPage
+ );
}
handleDisplayReviewReaction(result) {
- const publication = (result.element && result.element.reaction && result.element.reaction.publication) || {};
- if (result.element?.review_info == null || result.element?.review_info?.review_level === 0) {
+ const publication = result.element?.reaction?.publication || {};
+ if (
+ result.element?.review_info == null ||
+ result.element?.review_info?.review_level === 0
+ ) {
//Aviator.navigate('/home');
} else {
- this.setState({
- guestPage: 'review',
- elementType: 'reaction',
- queryId: result?.id || 0,
- reaction: result?.element?.reaction || {},
- currentElement: result?.element || {},
- showReviewModal: false,
- showCommentModal: false,
- review: publication?.review || {},
- review_info: result?.element?.review_info || {},
- });
- Aviator.navigate(`/review/review_reaction/${result.id}`, { silent: true });
+ const currentUser =
+ (UserStore.getState() && UserStore.getState().currentUser) || {};
+ if (currentUser?.type === RepoConst.U_TYPE.ANONYMOUS) {
+ EmbargoActions.displayReviewEmbargo('reaction', result?.id);
+ } else {
+ this.setState({
+ guestPage: 'review',
+ elementType: 'reaction',
+ queryId: result?.id || 0,
+ reaction: result?.element?.reaction || {},
+ currentElement: result?.element || {},
+ showReviewModal: false,
+ showCommentModal: false,
+ review: publication?.review || {},
+ review_info: result?.element?.review_info || {},
+ });
+ Aviator.navigate(`/review/review_reaction/${result.id}`, {
+ silent: true,
+ });
+ }
}
}
handleDisplayReviewSample(result) {
const publication = result?.element?.publication || {};
-
- if (result.element?.review_info == null || result.element?.review_info?.review_level === 0) {
+ if (
+ result.element?.review_info == null ||
+ result.element?.review_info?.review_level === 0
+ ) {
//Aviator.navigate('/home');
} else {
- this.setState({
- guestPage: 'review',
- elementType: 'sample',
- queryId: result.id || 0,
- currentElement: result?.element || {},
- showReviewModal: false,
- showCommentModal: false,
- review: publication?.review || {},
- review_info: result?.element?.review_info || {},
- });
- Aviator.navigate(`/review/review_sample/${result.id}`, { silent: true });
+ const currentUser =
+ (UserStore.getState() && UserStore.getState().currentUser) || {};
+ if (currentUser?.type === RepoConst.U_TYPE.ANONYMOUS) {
+ EmbargoActions.displayReviewEmbargo('sample', result?.id);
+ } else {
+ this.setState({
+ guestPage: 'review',
+ elementType: 'sample',
+ queryId: result.id || 0,
+ currentElement: result?.element || {},
+ showReviewModal: false,
+ showCommentModal: false,
+ review: publication?.review || {},
+ review_info: result?.element?.review_info || {},
+ });
+ Aviator.navigate(`/review/review_sample/${result.id}`, { silent: true });
+ }
}
}
-
+ handleSetUserLabel(label) {
+ this.setState({ selectLabel: label });
+ }
};
diff --git a/app/packs/src/stores/alt/stores/ElementStore.js b/app/packs/src/stores/alt/stores/ElementStore.js
index e2d504498..fa19c9a98 100644
--- a/app/packs/src/stores/alt/stores/ElementStore.js
+++ b/app/packs/src/stores/alt/stores/ElementStore.js
@@ -607,7 +607,7 @@ class ElementStore {
const { profile } = UserStore.getState();
if (profile && profile.data && profile.data.layout) {
const { layout } = profile.data;
-
+
if (layout.sample && layout.sample > 0) { this.handleRefreshElements('sample'); }
if (layout.reaction && layout.reaction > 0) { this.handleRefreshElements('reaction'); }
if (layout.wellplate && layout.wellplate > 0) { this.handleRefreshElements('wellplate'); }
@@ -1112,8 +1112,8 @@ class ElementStore {
this.handleRefreshElementsForSearchById(type, uiState, currentSearchByID);
} else {
const per_page = uiState.number_of_results;
- const { fromDate, toDate, productOnly } = uiState;
- const params = { page, per_page, fromDate, toDate, productOnly, name: type };
+ const { fromDate, toDate, userLabel, productOnly } = uiState;
+ const params = { page, per_page, fromDate, userLabel, toDate, productOnly, name: type };
const fnName = type.split('_').map(x => x[0].toUpperCase() + x.slice(1)).join("") + 's';
let fn = `fetch${fnName}ByCollectionId`;
const allowedActions = [
@@ -1133,8 +1133,8 @@ class ElementStore {
}
MessagesFetcher.fetchSpectraMessages(0).then((result) => {
- result.messages.sort((a, b) => (a.id - b.id));
- const messages = result.messages;
+ result?.messages.sort((a, b) => (a.id - b.id));
+ const messages = result?.messages;
if (messages && messages.length > 0) {
const lastMsg = messages[0]
this.setState({ spectraMsg: lastMsg })
@@ -1144,18 +1144,19 @@ class ElementStore {
handleRefreshElementsForSearchById(type, uiState, currentSearchByID) {
currentSearchByID.page_size = uiState.number_of_results;
- const { filterCreatedAt, fromDate, toDate, productOnly } = uiState;
+ const { filterCreatedAt, fromDate, toDate, userLabel, productOnly } = uiState;
const { moleculeSort } = this.state;
const { page } = uiState[type];
let filterParams = {};
const elnElements = ['sample', 'reaction', 'screen', 'wellplate', 'research_plan'];
let modelName = !elnElements.includes(type) ? 'element' : type;
- if (fromDate || toDate || productOnly) {
+ if (fromDate || toDate || userLabel || productOnly) {
filterParams = {
filter_created_at: filterCreatedAt,
from_date: fromDate,
to_date: toDate,
+ user_label: userLabel,
product_only: productOnly,
}
}
diff --git a/app/packs/src/stores/alt/stores/SpectraStore.js b/app/packs/src/stores/alt/stores/SpectraStore.js
index 5399d4a6c..9f8e81dbd 100644
--- a/app/packs/src/stores/alt/stores/SpectraStore.js
+++ b/app/packs/src/stores/alt/stores/SpectraStore.js
@@ -38,7 +38,10 @@ class SpectraStore {
handleAddOthers: SpectraActions.AddOthers,
handleRegenerateEdited: SpectraActions.RegenerateEdited,
handleToggleModalNMRDisplayer: SpectraActions.ToggleModalNMRDisplayer,
- handleLoadSpectraForNMRDisplayer: SpectraActions.LoadSpectraForNMRDisplayer,
+ handleLoadSpectraForNMRDisplayer: [
+ SpectraActions.LoadSpectraForNMRDisplayer,
+ PublicActions.loadSpectraForNMRDisplayer,
+ ],
});
}
diff --git a/app/packs/src/stores/alt/stores/UIStore.js b/app/packs/src/stores/alt/stores/UIStore.js
index d23f9b949..a6794de65 100644
--- a/app/packs/src/stores/alt/stores/UIStore.js
+++ b/app/packs/src/stores/alt/stores/UIStore.js
@@ -65,6 +65,7 @@ class UIStore {
filterCreatedAt: true,
fromDate: null,
toDate: null,
+ userLabel: null,
productOnly: false,
number_of_results: 15,
currentCollection: null,
@@ -114,6 +115,7 @@ class UIStore {
handleShowModalChange: UIActions.updateModalProps,
handleHideModal: UIActions.hideModal,
handleSetFilterCreatedAt: UIActions.setFilterCreatedAt,
+ handleSetUserLabel: UIActions.setUserLabel,
handleSetFromDate: UIActions.setFromDate,
handleSetToDate: UIActions.setToDate,
handleSetProductOnly: UIActions.setProductOnly,
@@ -301,7 +303,7 @@ class UIStore {
handleSelectCollection(collection, hasChanged = false) {
const state = this.state;
const isSync = collection && collection.is_sync_to_me ? true : false;
- const { filterCreatedAt, fromDate, toDate, productOnly } = state;
+ const { filterCreatedAt, fromDate, toDate, userLabel, productOnly } = state;
if (!hasChanged) {
hasChanged = !state.currentCollection;
@@ -321,7 +323,7 @@ class UIStore {
this.state.isSync = isSync;
this.state.currentCollection = collection;
const per_page = state.number_of_results;
- const params = { per_page, filterCreatedAt, fromDate, toDate, productOnly };
+ const params = { per_page, filterCreatedAt, fromDate, toDate, userLabel, productOnly };
const { profile } = UserStore.getState();
if (profile && profile.data && profile.data.layout) {
@@ -387,7 +389,7 @@ class UIStore {
const state = this.state;
const isSync = state.isSync;
const searchResult = { ...state.currentSearchByID };
- const { filterCreatedAt, fromDate, toDate, productOnly } = state;
+ const { filterCreatedAt, fromDate, toDate, userLabel, productOnly } = state;
const { moleculeSort } = ElementStore.getState();
const per_page = state.number_of_results;
@@ -398,11 +400,12 @@ class UIStore {
const elnElements = ['sample', 'reaction', 'screen', 'wellplate', 'research_plan'];
let modelName = !elnElements.includes(key.slice(0, -1)) ? 'element' : key.slice(0, -1);
- if (fromDate || toDate || productOnly) {
+ if (fromDate || toDate || productOnly || userLabel) {
filterParams = {
filter_created_at: filterCreatedAt,
from_date: fromDate,
to_date: toDate,
+ user_label: userLabel,
product_only: productOnly,
}
}
@@ -491,6 +494,11 @@ class UIStore {
}
}
+ handleSetUserLabel(label) {
+ this.state.userLabel = label;
+ this.handleSelectCollection(this.state.currentCollection, true);
+ }
+
handleSetFromDate(fromDate) {
this.state.fromDate = fromDate;
this.handleSelectCollection(this.state.currentCollection, true);
diff --git a/app/packs/src/utilities/ElementUtils.js b/app/packs/src/utilities/ElementUtils.js
index 127bbd8aa..d99d62a61 100644
--- a/app/packs/src/utilities/ElementUtils.js
+++ b/app/packs/src/utilities/ElementUtils.js
@@ -182,7 +182,7 @@ const isEmwInMargin = (diff) => {
};
const emwInStr = (emw, msStr) => {
- const peaks = msStr.split(/,|:|;|=/).map((s) => {
+ const peaks = msStr.split(/,|:|;|\+|=/).map((s) => {
const t = s.replace('found', '')
.replace(/[\(\[\{](.*?)[\)\]\}]/g, '')
.replace(/\s/g, '');
diff --git a/app/packs/src/utilities/routesUtils.js b/app/packs/src/utilities/routesUtils.js
index 098cc9568..3690fa80f 100644
--- a/app/packs/src/utilities/routesUtils.js
+++ b/app/packs/src/utilities/routesUtils.js
@@ -11,6 +11,7 @@ import { elementNames } from 'src/apps/generic/Utils';
const collectionShow = (e) => {
UIActions.showElements.defer();
UserActions.fetchCurrentUser();
+ UserActions.fetchUserLabels();
const { profile } = UserStore.getState();
if (!profile) {
UserActions.fetchProfile();
@@ -60,6 +61,7 @@ const collectionShowCollectionManagement = () => {
const scollectionShow = (e) => {
UIActions.showElements();
UserActions.fetchCurrentUser();
+ UserActions.fetchUserLabels();
const { profile } = UserStore.getState();
if (!profile) {
UserActions.fetchProfile();
@@ -123,7 +125,7 @@ const sampleShowOrNew = (e) => {
// UIActions.selectTab(1);
};
-const cellLineShowOrNew = (e) => {
+const cellLineShowOrNew = (e) => {
if(e.params.new_cellLine||(e.params.new_cellLine===undefined&&e.params.cell_lineID==="new")){
ElementActions.generateEmptyCellLine(e.params.collectionID,e.params.cell_line_template);
}else{
@@ -258,7 +260,7 @@ const genericElShowOrNew = (e, type) => {
} else if (genericElID === 'copy') {
//
} else {
-
+
ElementActions.fetchGenericElById(genericElID, itype);
}
};
diff --git a/app/uploaders/attachment_uploader.rb b/app/uploaders/attachment_uploader.rb
index b3c0b8098..e9737abb0 100644
--- a/app/uploaders/attachment_uploader.rb
+++ b/app/uploaders/attachment_uploader.rb
@@ -43,7 +43,7 @@ def generate_location(io, context = {}) # rubocop:disable Metrics/AbcSize,Metric
Attacher.derivatives do |original|
file_extension = ".#{record.attachment.mime_type.split('/').last}" unless record.attachment.mime_type.nil?
- #
+ #
file_extension = '.svg' if file_extension == '.svg+xml'
file_extension = '.jpg' if file_extension == '.jpeg'
@@ -81,7 +81,21 @@ def self.create_derivatives(file_extension, file_path, original, attachment_id,
file_path.to_s, original, attachment_id, result, record
)
end
-
+ result
+ rescue StandardError => e
+ Rails.logger.error <<~TXT
+ --------- #{self.class.name} create_derivatives ------------
+ file_extension: #{file_extension}
+ file_path: #{file_path&.to_s}
+ original: #{original&.path}
+ attachment_id: #{attachment_id}
+ filename: #{record&.filename}
+ attachable_id: #{record&.attachable_id}
+
+ Error Message: #{e.message}
+ Error: #{e.backtrace.join("\n")}
+ --------------------------------------------------------------------
+ TXT
result
end
diff --git a/app/usecases/attachments/annotation/annotation_loader.rb b/app/usecases/attachments/annotation/annotation_loader.rb
index 7444b8af0..5f24b6ba9 100644
--- a/app/usecases/attachments/annotation/annotation_loader.rb
+++ b/app/usecases/attachments/annotation/annotation_loader.rb
@@ -21,7 +21,8 @@ def get_annotation_of_attachment(attachment_id)
--------- #{self.class.name} get_annotation_of_attachment ------------
attachment_id: #{attachment_id}
- Error Message: #{e.backtrace.join("\n")}
+ Error Message: #{e.message}
+ Error: #{e.backtrace.join("\n")}
--------------------------------------------------------------------
TXT
end
diff --git a/app/usecases/attachments/annotation/annotation_updater.rb b/app/usecases/attachments/annotation/annotation_updater.rb
index a18beef06..145104d3d 100644
--- a/app/usecases/attachments/annotation/annotation_updater.rb
+++ b/app/usecases/attachments/annotation/annotation_updater.rb
@@ -60,7 +60,8 @@ def update_thumbnail(attachment, svg_string)
AttachmentID: #{attachment&.id}
svg_string: #{svg_string}
- Error Message: #{e.backtrace.join("\n")}
+ Error Message: #{e.message}
+ Error: #{e.backtrace.join("\n")}
--------------------------------------------------------------------
TXT
end
diff --git a/app/usecases/attachments/copy.rb b/app/usecases/attachments/copy.rb
index 45b56d53a..255e873a1 100644
--- a/app/usecases/attachments/copy.rb
+++ b/app/usecases/attachments/copy.rb
@@ -22,6 +22,7 @@ def self.execute!(attachments, element, current_user_id)
attachable_id: element.id,
attachable_type: element.class.name,
aasm_state: original_attach.aasm_state,
+ con_state: original_attach.con_state,
created_by: current_user_id,
created_for: current_user_id,
filename: original_attach.filename,
@@ -56,7 +57,8 @@ def self.update_annotation(original_attach_id, copy_attach_id)
original_attach_id: #{original_attach_id}
copy_attach_id: #{copy_attach_id}
- Error Message: #{e.backtrace.join("\n")}
+ Error Message: #{e.message}
+ Error: #{e.backtrace.join("\n")}
--------------------------------------------------------------------
TXT
end
diff --git a/app/usecases/attachments/derivative_builder_factory.rb b/app/usecases/attachments/derivative_builder_factory.rb
index c74086fe4..5d0bd2856 100644
--- a/app/usecases/attachments/derivative_builder_factory.rb
+++ b/app/usecases/attachments/derivative_builder_factory.rb
@@ -21,6 +21,13 @@ def create_derivative_builders(data_type_in)
builders.append(creator.constantize.new) if @supported_formats_map[creator].include? data_type
end
+ builders
+ rescue StandardError => e
+ Rails.logger.error <<~TXT
+ --------- #{self.class.name} create_derivative_builders ------------
+ data_type_in: #{data_type_in}
+ --------------------------------------------------------------------
+ TXT
builders
end
diff --git a/config/initializers/ui_extensions.rb b/config/initializers/ui_extensions.rb
new file mode 100644
index 000000000..9ccffc21e
--- /dev/null
+++ b/config/initializers/ui_extensions.rb
@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+begin
+ ui_extensions_config = Rails.application.config_for(:ui_extensions)
+ Rails.application.configure do
+ config.u = ui_extensions_config
+ end
+rescue StandardError => e
+ Rails.logger.error "Could not load ui configuration. Error: #{e.message}"
+ Rails.application.configure do
+ config.u = {}.freeze
+ end
+end
diff --git a/config/initializers/variable_measured.rb b/config/initializers/variable_measured.rb
new file mode 100644
index 000000000..6e3917ef3
--- /dev/null
+++ b/config/initializers/variable_measured.rb
@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+begin
+ variable_measured_config = Rails.application.config_for(:variable_measured)
+ Rails.application.configure do
+ config.m = variable_measured_config
+ end
+rescue StandardError => e
+ Rails.logger.error "Could not load variable measured. Error: #{e.message}"
+ Rails.application.configure do
+ config.m = {}.freeze
+ end
+end
diff --git a/config/routes.rb b/config/routes.rb
index 655dface2..648b42c59 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -88,7 +88,6 @@
get 'welcome', to: 'pages#home'
get 'home', to: 'pages#home'
# get 'home', to: 'pages#home'
- get 'jsmol', to: 'pages#jsmol'
get 'directive', to: 'pages#directive'
get 'welcome', to: 'pages#home'
get 'about', to: 'pages#about'
diff --git a/config/ui_extensions.yml.example b/config/ui_extensions.yml.example
new file mode 100644
index 000000000..281a97fbb
--- /dev/null
+++ b/config/ui_extensions.yml.example
@@ -0,0 +1,18 @@
+development:
+ collection_icons:
+ - label: COLLECTION_LABEL_1
+ icons:
+ - filename: image1.png
+ title: image1_title
+ info: additional information
+ - filename: image2.png
+ title: image2_title
+ info: additional information
+ - label: COLLECTION_LABEL_2
+ icons:
+ - filename: image3.png
+ title: image3_title
+ info: additional information
+ - filename: image4.png
+ title: image4_title
+ info: additional information
diff --git a/config/variable_measured.yml.example b/config/variable_measured.yml.example
new file mode 100644
index 000000000..3bc4c6edb
--- /dev/null
+++ b/config/variable_measured.yml.example
@@ -0,0 +1,27 @@
+development:
+ dataset:
+ - ols_term: CHMO:0000593
+ desc: 1H nuclear magnetic resonance spectroscopy (1H NMR)
+ layers:
+ - identifier: set
+ fields:
+ - identifier: PULPROG
+ - identifier: temperature
+ - identifier: ph
+ - identifier: ns
+ - identifier: nucone
+ - identifier: general
+ fields:
+ - identifier: title
+ - identifier: creator
+ - ols_term: CHMO:0000595
+ desc: 13C nuclear magnetic resonance spectroscopy (13C NMR)
+ layers:
+ - identifier: layerAAA
+ fields:
+ - identifier: bbbb
+ - identifier: cccc
+ - identifier: layerBBB
+ fields:
+ - identifier: bbbb
+ - identifier: cccc
diff --git a/config/webpack/custom.js b/config/webpack/custom.js
index 72ab8c7ec..f3a05f728 100644
--- a/config/webpack/custom.js
+++ b/config/webpack/custom.js
@@ -16,7 +16,6 @@ module.exports = {
plugins: [
new webpack.DefinePlugin({
'process.version': JSON.stringify(process.version),
- 'process.env.MATOMO_URL': JSON.stringify(process.env.MATOMO_URL),
'process.env.SENTRY_FRONTEND_DSN': JSON.stringify(
process.env.SENTRY_FRONTEND_DSN
),
diff --git a/db/migrate/20200827144816_matrice_user_label.rb b/db/migrate/20200827144816_matrice_user_label.rb
deleted file mode 100644
index e49cf50c9..000000000
--- a/db/migrate/20200827144816_matrice_user_label.rb
+++ /dev/null
@@ -1,11 +0,0 @@
-class MatriceUserLabel < ActiveRecord::Migration[4.2]
- def change
- Matrice.create(
- name: 'userLabel',
- enabled: false,
- label: 'userLabel',
- include_ids: [],
- exclude_ids: []
- )
- end
-end
diff --git a/db/migrate/20230630140647_fill_new_plain_text_description_fields.rb b/db/migrate/20230630140647_fill_new_plain_text_description_fields.rb
index 36e7d81d6..02190e138 100644
--- a/db/migrate/20230630140647_fill_new_plain_text_description_fields.rb
+++ b/db/migrate/20230630140647_fill_new_plain_text_description_fields.rb
@@ -12,7 +12,7 @@ def up
# force gc of node processes
ObjectSpace.garbage_collect
rescue Exception => e
- byebug
+ # byebug
end
end
Screen.where.not(description: nil).find_each do |screen|
diff --git a/db/migrate/20230814121455_fill_new_plain_text_content_field_at_containers.rb b/db/migrate/20230814121455_fill_new_plain_text_content_field_at_containers.rb
index a21dbfdb0..4a63a602b 100644
--- a/db/migrate/20230814121455_fill_new_plain_text_content_field_at_containers.rb
+++ b/db/migrate/20230814121455_fill_new_plain_text_content_field_at_containers.rb
@@ -24,12 +24,12 @@ def up
container.update_columns(plain_text_content: content)
rescue Exception => e
- byebug
+ ## byebug
end
end
rescue Exception => e
- byebug
+ ## byebug
end
def down
diff --git a/db/migrate/20240530000001_remove_user_labels_from_matrix.rb b/db/migrate/20240530000001_remove_user_labels_from_matrix.rb
new file mode 100644
index 000000000..0c5ce1d25
--- /dev/null
+++ b/db/migrate/20240530000001_remove_user_labels_from_matrix.rb
@@ -0,0 +1,7 @@
+class RemoveUserLabelsFromMatrix < ActiveRecord::Migration[6.1]
+ def change
+ Matrice.find_by(name: 'userLabel')&.destroy!
+ rescue StandardError => e
+ Rails.logger.error "Error changing channel msg: #{e.message}"
+ end
+end
diff --git a/db/migrate/20240531000003_user_labels_publication.rb b/db/migrate/20240531000003_user_labels_publication.rb
new file mode 100644
index 000000000..bcfea7508
--- /dev/null
+++ b/db/migrate/20240531000003_user_labels_publication.rb
@@ -0,0 +1,9 @@
+class UserLabelsPublication < ActiveRecord::Migration[6.1]
+ def change
+ Publication.where(element_type: 'Sample').each do |pub|
+ pub.publish_user_labels
+ end
+ rescue StandardError => e
+ Rails.logger.error "Error changing channel msg: #{e.message}"
+ end
+end
diff --git a/db/migrate/20240607000000_add_submission_notification.rb b/db/migrate/20240607000000_add_submission_notification.rb
new file mode 100644
index 000000000..b346cccb0
--- /dev/null
+++ b/db/migrate/20240607000000_add_submission_notification.rb
@@ -0,0 +1,14 @@
+class AddSubmissionNotification < ActiveRecord::Migration[6.1]
+ def change
+ channel = Channel.find_by(subject: Channel::SUBMITTING)
+ return unless channel.nil?
+ attributes = {
+ subject: Channel::SUBMITTING,
+ channel_type: 8,
+ msg_template: '{"data": "The submission has been submitted!",
+ "action":"Submission"
+ }'
+ }
+ Channel.create(attributes)
+ end
+end
diff --git a/lib/chemotion/open_babel_service.rb b/lib/chemotion/open_babel_service.rb
index 5096c804e..1d9d456f0 100644
--- a/lib/chemotion/open_babel_service.rb
+++ b/lib/chemotion/open_babel_service.rb
@@ -412,6 +412,8 @@ def self.molfile_clear_hydrogens molfile, options={}
end
def self.svg_from_molfile molfile, options={}
+ return nil if molfile.blank?
+
c = OpenBabel::OBConversion.new
c.set_in_format 'mol'
c.set_out_format 'svg'
@@ -428,6 +430,9 @@ def self.svg_from_molfile molfile, options={}
#m.do_transformations c.get_options(OpenBabel::OBConversion::GENOPTIONS), c
c.write_string(m, false)
+ rescue StandardError => e
+ Rails.logger.error e
+ nil
end
# Return an array of 32
diff --git a/lib/chemotion/orcid_service.rb b/lib/chemotion/orcid_service.rb
index a05d7d16c..68521dfd5 100644
--- a/lib/chemotion/orcid_service.rb
+++ b/lib/chemotion/orcid_service.rb
@@ -10,10 +10,14 @@ def self.record_person(orcid)
record = Nokogiri::XML(record).to_xml
record = Hash.from_xml(record).as_json
+ emails = record.dig('person', 'emails', 'email')
+ email = email['email'] if emails.is_a?(Hash)
+ email = email = emails.first['email'] if emails.is_a?(Array)
+
person = OpenStruct.new(
given_names: record.dig('person', 'name', 'given_names'),
family_name: record.dig('person', 'name', 'family_name'),
- email: record.dig('person', 'emails', 'email', 'email')
+ email: email
)
result = OpenStruct.new(person: person)
result
diff --git a/lib/import/import_collections.rb b/lib/import/import_collections.rb
index e811467b3..b07252fe4 100644
--- a/lib/import/import_collections.rb
+++ b/lib/import/import_collections.rb
@@ -147,10 +147,8 @@ def import_collections
# collection = Collection.find(@col_id)
collection = Collection.find_or_create_by(user_id: @current_user_id, label: 'Imported Data', is_locked: true, position: 3)
- @uuid = nil
-
@data.fetch('Collection', {}).each do |uuid, fields|
- @uuid = uuid
+ update_instances!(uuid, collection)
end
# @data.fetch('Collection', {}).each do |uuid, fields|
@@ -171,16 +169,13 @@ def import_collections
# add collection to @instances map
# update_instances!(uuid, collection)
# end
- update_instances!(@uuid, collection)
end
def gate_collection
collection = Collection.find(@col_id)
- @uuid = nil
@data.fetch('Collection', {}).each do |uuid, _fields|
- @uuid = uuid
+ update_instances!(uuid, collection)
end
- update_instances!(@uuid, collection)
end
def fetch_bound(value)
@@ -656,7 +651,8 @@ def import_literals
literal = Literal.create!(
fields.slice(
'element_type',
- 'category'
+ 'category',
+ 'litype',
).merge(
user_id: @current_user_id,
element: element,
diff --git a/lib/repo/embargo_handler.rb b/lib/repo/embargo_handler.rb
new file mode 100644
index 000000000..6eed0b102
--- /dev/null
+++ b/lib/repo/embargo_handler.rb
@@ -0,0 +1,144 @@
+module Repo
+ class EmbargoHandler
+ def self.find_or_create_embargo(cid, current_user)
+ if (cid == 0)
+ chemotion_user = User.chemotion_user
+ new_col_label = current_user.initials + '_' + Time.now.strftime('%Y-%m-%d')
+ col_check = Collection.where([' label like ? ', new_col_label + '%'])
+ new_col_label = new_col_label << '_' << (col_check&.length + 1)&.to_s if col_check&.length.positive?
+ new_embargo_col = Collection.create!(user: chemotion_user, label: new_col_label, ancestry: current_user.publication_embargo_collection.id)
+ SyncCollectionsUser.find_or_create_by(user: current_user, shared_by_id: chemotion_user.id, collection_id: new_embargo_col.id,
+ permission_level: 0, sample_detail_level: 10, reaction_detail_level: 10,
+ fake_ancestry: current_user.publication_embargo_collection.sync_collections_users.first.id.to_s)
+ #embargo = Embargo.create!(name: new_embargo_col.label, collection_id: new_embargo_col.id, created_by: current_user.id)
+ d = Doi.create_for_element!(new_embargo_col)
+
+ Publication.create!(
+ state: Publication::STATE_PENDING,
+ element: new_embargo_col,
+ published_by: current_user.id,
+ doi: d,
+ taggable_data: { label: new_embargo_col.label, col_doi: d.full_doi }
+ )
+ new_embargo_col
+ else
+ Collection.find(cid)
+ end
+ rescue StandardError => e
+ Repo::EmbargoHandler.logger.error ["[find_or_create_embargo] cid: #{cid}, current_user: #{current_user&.id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+ end
+
+ def self.release_embargo(embargo_collection_id, user_id)
+ embargo_collection = Collection.find(embargo_collection_id)
+ return { error: 'Embargo collection not found' } if embargo_collection.nil?
+
+ current_user = User.find(user_id)
+ return { error: 'User not found' } if current_user.nil?
+
+ col_pub = embargo_collection.publication
+ is_submitter = col_pub&.review&.dig('submitters')&.include?(current_user.id) || col_pub&.published_by == current_user.id
+ return { error: "only the owner of embargo #{embargo_collection.label} can perform the release."} if col_pub.nil? || !is_submitter
+
+ col_pub.update(accepted_at: Time.now.utc)
+ col_pub.refresh_embargo_metadata
+ 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
+
+ check_state = pub_list.select { |pub| pub.state != Publication::STATE_ACCEPTED }
+ return { error: "Embargo #{embargo_collection.label} release failed, because not all elements have been 'accepted'."} if check_state.present?
+
+ scheme_only_list = pub_list.select { |pub| pub.taggable_data['scheme_only'] == true }
+ if pub_list.flatten.length == scheme_only_list.flatten.length
+ col_pub.update(state: 'scheme_only')
+ else
+ col_pub.update(state: 'accepted')
+ end
+
+ pub_list.each do |pub|
+ params = { id: pub.element_id, type: pub.element_type }
+ Repo::ReviewProcess.new(params, current_user.id, 'release').element_submit(pub)
+ end
+ Repo::EmbargoHandler.remove_anonymous(embargo_collection)
+ Repo::EmbargoHandler.handle_embargo_collections(embargo_collection, current_user)
+ case ENV['PUBLISH_MODE']
+ when 'production'
+ if Rails.env.production?
+ ChemotionEmbargoPubchemJob.set(queue: "publishing_embargo_#{embargo_collection.id}").perform_later(embargo_collection.id)
+ end
+ when 'staging'
+ ChemotionEmbargoPubchemJob.perform_now(embargo_collection.id)
+ else 'development'
+ end
+ { message: "Embargo #{embargo_collection.label} has been released" }
+ rescue StandardError => e
+ Repo::EmbargoHandler.logger.error ["[release_embargo] embargo_collection_id: #{embargo_collection_id}, user_id: #{user_id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+ Message.create_msg_notification(
+ channel_id: Channel.find_by(subject: Channel::SUBMITTING)&.id,
+ message_from: User.find_by(name_abbreviation: 'CHI')&.id,
+ autoDismiss: 5,
+ message_content: { 'data': "release_embargo exception, User: [#{user_id}], embargo_collection_id: [#{embargo_collection_id}], got error, #{e.message}" },
+ )
+ { error: e.message }
+ end
+
+ def self.delete(embargo_collection_id, user_id)
+ embargo_collection = Collection.find(embargo_collection_id)
+ return { error: 'Embargo collection not found' } if embargo_collection.nil?
+
+ current_user = User.find(user_id)
+ return { error: 'User not found' } if current_user.nil?
+
+ element_cnt = embargo_collection.samples.count + embargo_collection.reactions.count
+ if element_cnt.positive?
+ { error: "Delete Embargo #{embargo_collection.label} deletion failed: the collection is not empty. Please refresh your page."}
+ else
+ Repo::EmbargoHandler.remove_anonymous(embargo_collection)
+ Repo::EmbargoHandler.remove_embargo_collection(embargo_collection)
+ { message: "Embargo #{embargo_collection.label} has been deleted" }
+ end
+ rescue StandardError => e
+ Repo::EmbargoHandler.logger.error ["[delete embargo] embargo_collection_id: #{embargo_collection_id}, user_id: #{user_id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+ { error: e.message }
+ end
+
+ ### private methods
+
+ def self.remove_anonymous(col)
+ anonymous_ids = col.sync_collections_users.joins("INNER JOIN users on sync_collections_users.user_id = users.id")
+ .where("users.type='Anonymous'").pluck(:user_id)
+ anonymous_ids.each do |anonymous_id|
+ anonymous = Anonymous.find(anonymous_id)
+ anonymous.sync_in_collections_users.destroy_all
+ anonymous.collections.each { |c| c.really_destroy! }
+ anonymous.really_destroy!
+ end
+ rescue StandardError => e
+ Repo::EmbargoHandler.logger.error ["[remove_anonymous] col_id: #{col&.id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+ end
+
+ def self.remove_embargo_collection(col)
+ col&.publication.really_destroy!
+ col.sync_collections_users.destroy_all
+ col.really_destroy!
+ end
+
+ def self.handle_embargo_collections(col, current_user)
+ col.update_columns(ancestry: current_user.published_collection.id)
+ sync_emb_col = col.sync_collections_users.where(user_id: current_user.id)&.first
+ sync_published_col = SyncCollectionsUser.joins("INNER JOIN collections ON collections.id = sync_collections_users.collection_id ")
+ .where("collections.label='Published Elements'")
+ .where("sync_collections_users.user_id = #{current_user.id}").first
+ sync_emb_col.update_columns(fake_ancestry: sync_published_col.id)
+ rescue StandardError => e
+ Repo::EmbargoHandler.logger.error ["[handle_embargo_collections] col_id: #{col&.id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
+ raise e
+ end
+
+ def self.logger
+ @@embargo_logger ||= Logger.new(Rails.root.join('log/embargo.log')) # rubocop:disable Style/ClassVars
+ end
+
+ end
+end
+
diff --git a/lib/repo/fetch_handler.rb b/lib/repo/fetch_handler.rb
new file mode 100644
index 000000000..5c152ccb5
--- /dev/null
+++ b/lib/repo/fetch_handler.rb
@@ -0,0 +1,152 @@
+# frozen_string_literal: true
+
+# A helper for fetching data from the repository
+# It includes the following methods:
+# 1. find_embargo_collection: Find the embargo collection of a publication
+# 2. repo_review_info: Get the review information of a publication
+# 3. repo_review_level: Get the review level of a publication
+# 4. literatures_by_cat: Fetch literatures by category
+# 5. get_reaction_table: Fetch the reaction table
+
+module Repo
+ class FetchHandler
+
+ def self.find_embargo_collection(root_publication)
+ has_embargo_col = root_publication.element&.collections&.select { |c| c['ancestry'].to_i == User.with_deleted.find(root_publication.published_by).publication_embargo_collection.id }
+ has_embargo_col && has_embargo_col.length > 0 ? has_embargo_col.first : OpenStruct.new(label: '')
+ rescue StandardError => e
+ Rails.logger.error(e.message)
+ Rails.logger.error(e.backtrace.join("\n"))
+ raise e
+ end
+
+ def self.repo_review_info(root_publication, user_id)
+ {
+ submitter: root_publication&.published_by == user_id || root_publication&.review&.dig('submitters')&.include?(user_id) || false,
+ reviewer: User.reviewer_ids&.include?(user_id) || false,
+ groupleader: root_publication&.review&.dig('reviewers')&.include?(user_id),
+ leaders: User.where(id: root_publication&.review&.dig('reviewers'))&.map{ |u| { name: u.name, id: u.id, type: u.type } },
+ preapproved: root_publication&.review&.dig('checklist', 'glr', 'status') == true,
+ review_level: Repo::FetchHandler.repo_review_level(root_publication, user_id)
+ }
+ rescue StandardError => e
+ Rails.logger.error(e.message)
+ Rails.logger.error(e.backtrace.join("\n"))
+ raise e
+ end
+
+ def self.repo_review_level(root_publication, user_id)
+ return 3 if User.reviewer_ids&.include? user_id
+ return 0 if root_publication.nil?
+ return 2 if root_publication.published_by === user_id || root_publication&.review&.dig('submitters')&.include?(user_id)
+ sync_cols = root_publication.element.sync_collections_users.where(user_id: user_id)
+ return 1 if (sync_cols&.length > 0)
+ return 0
+ rescue StandardError => e
+ Rails.logger.error(e.message)
+ Rails.logger.error(e.backtrace.join("\n"))
+ raise e
+ end
+
+ def self.literatures_by_cat(id, type, cat='public')
+ literatures = Literature.by_element_attributes_and_cat(id, type.classify, cat)
+ .joins("inner join users on literals.user_id = users.id")
+ .select(
+ <<~SQL
+ literatures.* , literals.element_type, literals.element_id,
+ json_object_agg(literals.id, literals.litype) as litype,
+ json_object_agg(literals.id, users.first_name || chr(32) || users.last_name) as ref_added_by
+ SQL
+ ).group('literatures.id, literals.element_type, literals.element_id').as_json
+ literatures
+ end
+
+ def self.get_reaction_table(id)
+ schemeAll = ReactionsSample.where('reaction_id = ? and type != ?', id, 'ReactionsPurificationSolventSample')
+ .joins(:sample)
+ .joins("inner join molecules on samples.molecule_id = molecules.id")
+ .select(
+ <<~SQL
+ reactions_samples.id,
+ (select name from molecule_names mn where mn.id = samples.molecule_name_id) as molecule_iupac_name,
+ molecules.iupac_name, molecules.sum_formular,
+ molecules.molecular_weight, samples.name, samples.short_label,
+ samples.real_amount_value, samples.real_amount_unit,
+ samples.target_amount_value, samples.target_amount_unit,
+ samples.purity, samples.density, samples.external_label,
+ samples.molarity_value, samples.molarity_unit,
+ reactions_samples.equivalent,reactions_samples.scheme_yield,
+ reactions_samples."position" as rs_position,
+ case when reactions_samples."type" = 'ReactionsStartingMaterialSample' then 'starting_materials'
+ when reactions_samples."type" = 'ReactionsReactantSample' then 'reactants'
+ when reactions_samples."type" = 'ReactionsProductSample' then 'products'
+ when reactions_samples."type" = 'ReactionsSolventSample' then 'solvents'
+ when reactions_samples."type" = 'ReactionsPurificationSolventSample' then 'purification_solvents'
+ else reactions_samples."type"
+ end mat_group,
+ case when reactions_samples."type" = 'ReactionsStartingMaterialSample' then 1
+ when reactions_samples."type" = 'ReactionsReactantSample' then 2
+ when reactions_samples."type" = 'ReactionsProductSample' then 3
+ when reactions_samples."type" = 'ReactionsSolventSample' then 4
+ when reactions_samples."type" = 'ReactionsPurificationSolventSample' then 5
+ else 6
+ end type_seq
+ SQL
+ ).order('reactions_samples.position ASC').as_json
+
+ schemeSorted = schemeAll.sort_by {|o| o['type_seq']}
+ solvents_sum = schemeAll.select{ |d| d['mat_group'] === 'solvents'}.sum { |r|
+ value = (r['real_amount_value'].nil? || r['real_amount_value'].zero?) ? r['target_amount_value'].to_f : r['real_amount_value'].to_f
+ unit = (r['real_amount_value'].nil? || r['real_amount_value'].zero?) ? r['target_amount_unit'] : r['real_amount_unit']
+
+ has_molarity = !r['molarity_value'].nil? && r['molarity_value'] > 0.0 && (r['density'] === 0.0) || false
+ has_density = !r['density'].nil? && r['density'] > 0.0 && (r['molarity_value'] === 0.0) || false
+
+ molarity = r['molarity_value'] && r['molarity_value'].to_f || 1.0
+ density = r['density'] && r['density'].to_f || 1.0
+ purity = r['purity'] && r['purity'].to_f || 1.0
+ molecular_weight = r['molecular_weight'] && r['molecular_weight'].to_f || 1.0
+
+ r['amount_g'] = unit === 'g'? value : unit === 'mg'? value.to_f / 1000.0 : unit === 'mol' ? (value / purity) * molecular_weight : unit === 'l' && !has_molarity && !has_density ? 0 : has_molarity ? value * molarity * molecular_weight : value * density * 1000
+ r['amount_l'] = unit === 'l'? value : !has_molarity && !has_density ? 0 : has_molarity ? (r['amount_g'].to_f * purity) / (molarity * molecular_weight) : has_density ? r['amount_g'].to_f / (density * 1000) : 0
+ r['amount_l'].nil? ? 0 : r['amount_l'].to_f
+ }
+
+ schemeList = []
+ schemeList = schemeSorted.map do |r|
+ scheme = {}
+ value = (r['real_amount_value'].nil? || r['real_amount_value'].zero?) ? r['target_amount_value'].to_f : r['real_amount_value'].to_f
+ unit = (r['real_amount_value'].nil? || r['real_amount_value'].zero?) ? r['target_amount_unit'] : r['real_amount_unit']
+ has_molarity = !r['molarity_value'].nil? && r['molarity_value'] > 0.0 && (r['density'] === 0.0) || false
+ has_density = !r['density'].nil? && r['density'] > 0.0 && (r['molarity_value'] === 0.0) || false
+
+ molarity = r['molarity_value'] && r['molarity_value'].to_f || 1.0
+ density = r['density'] && r['density'].to_f || 1.0
+ purity = r['purity'] && r['purity'].to_f || 1.0
+ molecular_weight = r['molecular_weight'] && r['molecular_weight'].to_f || 1.0
+ r['amount_g'] = unit === 'g'? value : unit === 'mg'? value.to_f / 1000.0 : unit === 'mol' ? (value / purity) * molecular_weight : unit === 'l' && !has_molarity && !has_density ? 0 : has_molarity ? value * molarity * molecular_weight : value * density * 1000
+ r['amount_l'] = unit === 'l'? value : !has_molarity && !has_density ? 0 : has_molarity ? (r['amount_g'].to_f * purity) / (molarity * molecular_weight) : has_density ? r['amount_g'].to_f / (density * 1000) : 0
+
+ if r['mat_group'] === 'solvents'
+ r['equivalent'] = r['amount_l'] / solvents_sum
+ else
+ r['amount_mol'] = unit === 'mol'? value : has_molarity ? r['amount_l'] * molarity : r['amount_g'].to_f * purity / molecular_weight
+ r['dmv'] = !has_molarity && !has_density ? '- / -' : has_density ? + density.to_s + ' / - ' : ' - / ' + molarity.to_s + r['molarity_unit']
+ end
+
+ r.delete('real_amount_value');
+ r.delete('real_amount_unit');
+ r.delete('target_amount_value');
+ r.delete('target_amount_unit');
+ r.delete('molarity_value');
+ r.delete('molarity_unit');
+ r.delete('purity');
+ r.delete('molecular_weight');
+ r.delete('rs_position');
+ r.delete('density');
+ r
+ end
+ schemeList
+ end
+ end
+end
diff --git a/lib/repo/review_process.rb b/lib/repo/review_process.rb
new file mode 100644
index 000000000..e34df6b49
--- /dev/null
+++ b/lib/repo/review_process.rb
@@ -0,0 +1,391 @@
+module Repo
+ class ReviewProcess
+ def initialize(args, user_id, action = nil)
+ @user_id = user_id ## required
+ @type = args[:type] ## required
+ @id = args[:id] ## required
+ @action = action
+ @comment = args[:comment]
+ @comments = args[:comments]
+ @checklist = args[:checklist]
+ @reviewComments = args[:reviewComments]
+ @step = 0
+ init_data
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def process
+ return unless ['reaction', 'sample', 'collection'].include?(@type)
+ return unless ['comment', 'comments', 'reviewed', 'submit', 'approved', 'accepted', 'declined'].include?(@action)
+
+ logger(next_step, 'save_comments')
+ save_comments(action_name, @action != 'comments') unless @action == 'comment' || @action == 'approved'
+ logger(next_step, "process_#{@action} started")
+ @publication = send("process_#{@action}")
+ logger(next_step, "process_#{@action} completed")
+ refresh_embargo
+ @publication
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def element_submit(root)
+ logger(next_step, "element_submit(#{root.id})")
+ root.descendants.each { |np| np.destroy! if np.element.nil? }
+ root.element.reserve_suffix
+ root.element.reserve_suffix_analyses(root.element.analyses) if root.element.analyses&.length > 0
+ root.element.analyses&.each do |a|
+ accept_new_analysis(root, a, Publication.find_by(element: a).nil?)
+ end
+ case root.element_type
+ when 'Sample'
+ analyses_ids = root.element.analyses.pluck(:id)
+ root.update!(taggable_data: root.taggable_data.merge(analysis_ids: analyses_ids))
+ root.element.analyses.each do |sa|
+ accept_new_analysis(root, sa, Publication.find_by(element: sa).nil?)
+ end
+
+ when 'Reaction'
+ root.element.products.each do |pd|
+ Publication.find_by(element_type: 'Sample', element_id: pd.id)&.destroy! if pd.analyses&.length == 0
+ next if pd.analyses&.length == 0
+ pd.reserve_suffix
+ pd.reserve_suffix_analyses(pd.analyses)
+ pd.reload
+ prod_pub = Publication.find_by(element: pd)
+ if prod_pub.nil?
+ accept_new_sample(root, pd)
+ else
+ pd.analyses.each do |rpa|
+ accept_new_analysis(prod_pub, rpa, Publication.find_by(element: rpa).nil?)
+ end
+ end
+ end
+ end
+ root.reload
+ root.update_columns(doi_id: root.element.doi.id) unless root.doi_id == root.element.doi.id
+ root.descendants.each { |pub_a|
+ next if pub_a.element.nil?
+ pub_a.update_columns(doi_id: pub_a.element.doi.id) unless pub_a.doi_id == pub_a.element&.doi&.id
+ }
+ begin
+ logger(next_step, "update_tag_doi(#{root.element.id})")
+ Repo::SubmissionApis.update_tag_doi(root.element)
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ end
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ private
+
+ def refresh_embargo
+ return if @type == 'collection'
+
+ embargo = Repo::FetchHandler.find_embargo_collection(@root_publication)
+ embargo_pub = embargo.publication if embargo.present?
+ embargo_pub&.refresh_embargo_metadata
+ end
+
+ def process_review_info
+ logger(next_step, "process_review_info")
+ element_class = Object.const_get("Entities::#{@type.capitalize}Entity")
+ element = element_class.represent(@root_publication.element)
+ review_info = Repo::FetchHandler.repo_review_info(@root_publication, @user_id)
+ his = @root_publication.review&.slice('history') unless User.reviewer_ids.include?(@user_id) || @root_publication.review.dig('reviewers')&.include?(@user_id)
+ { "#{@type}": element, review: his || @root_publication.review, review_info: review_info }
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ ### TODO: add description for each method
+ def process_comment
+ save_comment(@comments)
+ his = @root_publication.review&.slice('history') unless User.reviewer_ids.include?(@user_id)
+ { review: his || @root_publication.review }
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def process_comments
+ process_review_info
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def process_reviewed
+ element_submit(@root_publication)
+ pub_update_state(Publication::STATE_REVIEWED)
+ process_review_info
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def process_submit
+ element_submit(@root_publication)
+ pub_update_state(Publication::STATE_PENDING)
+ process_review_info
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def process_approved ## group leader only
+ approve_comments
+ process_review_info
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def process_accepted
+ element_submit(@root_publication)
+ public_literature
+ pub_update_state(Publication::STATE_ACCEPTED)
+ process_review_info
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def process_declined
+ pub_update_state(Publication::STATE_DECLINED)
+ ## TO BE HANDLED - remove from embargo collection
+ process_review_info
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def pub_update_state(state)
+ logger(next_step, "pub_update_state(#{state})")
+
+ @root_publication.update_state(state)
+ @root_publication.process_new_state_job(state)
+ # @embargo_pub&.refresh_embargo_metadata
+ ##################### CHI to check
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def init_data
+ logger(@step, 'init_data', show_params, :info)
+ @current_user = User.find_by(id: @user_id)
+ # @embargo_collection = EmbargoHandler.find_or_create_embargo(@embargo_id, @current_user) if @embargo_id.present? && @embargo_id >= 0
+ @root_publication = Publication.find_by(element_type: @type.classify, element_id: @id).root
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def show_params
+ { action: @action, root_pub_id: @root_publication&.id, user_id: @user_id, type: @type, element_id: @id, comment: @comment, comments: @comments, checklist: @checklist, reviewComments: @reviewComments}
+ end
+
+ ### Save detail comment to the current review history
+ def save_comment(comment)
+ return if comment.nil? || comment.keys&.empty?
+
+ review = @root_publication.review || {}
+ review_history = review['history'] || []
+ current = review_history.last
+ comments = current['comments'] || {}
+ comment[comment.keys[0]]['timestamp'] = Time.now.strftime('%d-%m-%Y %H:%M:%S') unless comment.keys.empty?
+ comment[comment.keys[0]]['username'] = @current_user.name
+ comment[comment.keys[0]]['userid'] = @current_user.id
+
+ current['comments'] = comments.deep_merge(comment || {})
+ review['history'] = review_history
+ @root_publication.update!(review: review)
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def save_comments(action, his = true)
+ review = @root_publication.review || {}
+ review_history = review['history'] || []
+ current = review_history.last || {}
+ current['state'] = %w[accepted declined].include?(action) ? action : @root_publication.state
+ current['action'] = action unless action.nil?
+ current['username'] = @current_user.name
+ current['userid'] = @current_user.id
+ current['comment'] = @comment unless @comment.nil?
+ current['type'] = @root_publication.state == Publication::STATE_PENDING ? 'reviewed' : 'submit'
+ current['timestamp'] = Time.now.strftime('%d-%m-%Y %H:%M:%S')
+
+ if review_history.length == 0
+ review_history[0] = current
+ else
+ review_history[review_history.length - 1] = current
+ end
+ if his ## add next_node
+ next_node = { action: 'revising', type: 'submit', state: 'reviewed' } if @root_publication.state == Publication::STATE_PENDING
+ next_node = { action: 'reviewing', type: 'reviewed', state: 'pending' } if @root_publication.state == Publication::STATE_REVIEWED
+ review_history << next_node
+ review['history'] = review_history
+ else
+
+ # is_leader = review.dig('reviewers')&.include?(current_user&.id)
+ if @root_publication.state == Publication::STATE_PENDING && (action.nil? || action == Publication::STATE_REVIEWED)
+ next_node = { action: 'reviewing', type: 'reviewed', state: 'pending' }
+ review_history << next_node
+ review['history'] = review_history
+ end
+ end
+ if @checklist&.length&.positive?
+ revst = review['checklist'] || {}
+ @checklist.each do |k, v|
+ revst[k] = v['status'] == true ? { status: v['status'], user: @current_user.name, updated_at: Time.now.strftime('%d-%m-%Y %H:%M:%S') } : { status: false } unless revst[k] && revst[k]['status'] == v['status']
+ end
+ review['checklist'] = revst
+ end
+ review['reviewComments'] = @reviewComments if @reviewComments.present?
+ @root_publication.update!(review: review)
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def approve_comments
+ review = @root_publication.review || {}
+ review_history = review['history'] || []
+ current = review_history.last
+ current['username'] = @current_user.name
+ current['userid'] = @current_user.id
+ current['action'] = 'pre-approved'
+ current['comment'] = @comment unless @comment.nil?
+ current['timestamp'] = Time.now.strftime('%d-%m-%Y %H:%M:%S')
+ review_history[review_history.length - 1] = current
+ next_node = { action: 'reviewing', type: 'reviewed', state: 'pending' }
+ review_history << next_node
+ review['history'] = review_history
+ revst = review['checklist'] || {}
+ revst['glr'] = { status: true, user: @current_user.name, updated_at: Time.now.strftime('%d-%m-%Y %H:%M:%S') }
+ review['checklist'] = revst
+ @root_publication.update!(review: review)
+ end
+
+ def accept_new_sample(root, sample)
+ pub_s = Publication.create!(
+ state: Publication::STATE_PENDING,
+ element: sample,
+ doi: sample&.doi,
+ published_by: root.published_by,
+ parent: root,
+ taggable_data: root.taggable_data
+ )
+ sample.analyses.each do |sa|
+ accept_new_analysis(pub_s, sa)
+ end
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def accept_new_analysis(root, analysis, nil_analysis = true)
+ if nil_analysis
+ ap = Publication.create!(
+ state: Publication::STATE_PENDING,
+ element: analysis,
+ doi: analysis.doi,
+ published_by: root.published_by,
+ parent: root,
+ taggable_data: root.taggable_data
+ )
+ atag = ap.taggable_data
+ aids = atag&.delete('analysis_ids')
+ aoids = atag&.delete('original_analysis_ids')
+ ap.save! if aids || aoids
+ end
+ begin
+ analysis.children.where(container_type: 'dataset').each do |ds|
+ ds.attachments.each do |att|
+ if MimeMagic.by_path(att.filename)&.type&.start_with?('image')
+ file_path = File.join('public/images/publications/', att.id.to_s, '/', att.filename)
+ public_path = File.join('public/images/publications/', att.id.to_s)
+ FileUtils.mkdir_p(public_path)
+ File.write(file_path, att.read_file.force_encoding("utf-8"))
+ end
+ end
+ end
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ Attachment.logger.error <<~TXT
+ --------- #{self.class.name} accept_new_analysis ------------
+ root.id: #{root.id}
+ analysis: #{analysis.id}
+ nil_analysis: #{nil_analysis}
+
+ Error Message: #{e.message}
+ Error: #{e.backtrace.join("\n")}
+ --------------------------------------------------------------------
+ TXT
+ end
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+
+ def public_literature
+ publications = [@root_publication] + @root_publication.descendants
+ publications.each do |pub|
+ next unless pub.element_type == 'Reaction' || pub.element_type == 'Sample'
+ literals = Literal.where(element_type: pub.element_type, element_id: pub.element_id)
+ literals&.each { |l| l.update_columns(category: 'public') } unless literals.nil?
+ end
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+ def action_name
+ return nil if @action == 'comments'
+ return 'review' if @action == 'reviewed'
+ return 'revision' if @action == 'submit'
+ return 'approved' if @action == 'approved'
+ return 'accepted' if @action == 'accepted'
+ return 'declined' if @action == 'declined'
+ end
+
+ def next_step
+ @step += 1
+ end
+
+ def logger(step, msg, options = {}, log_level = :debug)
+ review_logger.send(log_level, "step: [#{step}], message: [#{msg}]\n ")
+ review_logger.send(log_level, "options [#{options}]\n ") if options.present?
+ end
+
+ def log_exception(exception, options = {})
+ review_logger.error(self.class.name);
+ review_logger.error("options [#{options}] \n ")
+ review_logger.error(show_params);
+ review_logger.error("exception: #{exception.message}")
+ review_logger.error(exception.backtrace.join("\n"))
+
+ # send email to admin
+ Message.create_msg_notification(
+ channel_id: Channel.find_by(subject: Channel::SUBMITTING)&.id,
+ message_from: User.find_by(name_abbreviation: 'CHI')&.id,
+ autoDismiss: 5,
+ message_content: { 'data': "Exception, User: [#{@user_id}], the original submission [#{@type}: #{@id}], got error, #{exception.message}" },
+ )
+ end
+
+ def review_logger
+ @@review_logger ||= Logger.new(Rails.root.join('log/reviewing.log'))
+ end
+ end
+end
\ No newline at end of file
diff --git a/lib/repo/submission.rb b/lib/repo/submission.rb
new file mode 100644
index 000000000..3216b8365
--- /dev/null
+++ b/lib/repo/submission.rb
@@ -0,0 +1,532 @@
+module Repo
+ class Submission
+ def initialize(args)
+ @user_id = args[:user_id]
+ @type = args[:type]
+ @id = args[:id]
+ @author_ids = args[:author_ids]
+ @group_reviewers = args[:group_leaders]
+ @analyses_ids = args[:analyses_ids]
+ @literal_ids = args[:refs]
+ @license = args[:license]
+ @embargo_id = args[:embargo]
+ @scheme_only = args[:scheme_only] || false
+ @scheme_params = args[:scheme_params] || []
+ @step = 0
+ init_data
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def next_step
+ @step += 1
+ end
+
+ def submitting
+ logger(next_step, __method__)
+ return unless @type == 'Sample' || @type == 'Reaction'
+
+ @element = @type.constantize.find_by(id: @id)
+
+ scheme_only_handling if @type == 'Reaction' && @scheme_only == true
+ @analyses = @element&.analyses&.where(id: @analyses_ids)
+ @analysis_set = @analyses | Container.where(id: @element.samples.flat_map { |s| s.analyses.ids } & @analyses_ids) if @type == 'Reaction' && @analyses_ids.present?
+ @analysis_set_ids = @analysis_set&.map(&:id) if @type == 'Reaction' && @analysis_set && @analysis_set.length > 0
+
+ logger(next_step, 'create_publication_tag')
+ @publication_tag = create_publication_tag
+
+ logger(next_step, 'reviewer_collections')
+ reviewer_collections
+
+ logger(next_step, "prepare_#{@type.downcase}_data")
+ @publication = send("prepare_#{@type.downcase}_data")
+
+ logger(next_step, 'process_element')
+ @publication.process_element
+
+ logger(next_step, 'update_tag_doi')
+
+ begin
+ Repo::SubmissionApis.update_tag_doi(@publication.element)
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ end
+
+ if col_pub = @embargo_collection&.publication
+ logger(next_step, 'refresh_embargo_metadata')
+ col_pub.refresh_embargo_metadata
+ end
+ logger(next_step, 'process_new_state_job')
+ @publication.process_new_state_job
+
+ send_message_to_user
+
+ logger(next_step, "#{__method__} completed, submmited element [#{@new_root&.id&.to_s}]\n ", {}, :info)
+
+ rescue StandardError => e
+ log_exception(e, { step: @step, method: __method__ })
+ raise e
+ end
+
+
+ private
+
+ def show_params
+ { user_id: @user_id, type: @type, id: @id, author_ids: @author_ids, group_leaders: @group_reviewers, analyses_ids: @analyses_ids, refs: @literal_ids, license: @license, embargo: @embargo_id }
+ end
+
+ def init_data
+ logger(@step, 'init_data', show_params, :info)
+ @current_user = User.find_by(id: @user_id)
+ @literals = Literal.where(id: @literal_ids) if @literal_ids.present?
+ @embargo_collection = EmbargoHandler.find_or_create_embargo(@embargo_id, @current_user) if @embargo_id.present? && @embargo_id >= 0
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def create_publication_tag
+ authors = User.where(type: %w[Person Collaborator], id: @author_ids)
+ .includes(:affiliations)
+ .order(Arel.sql("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
+ {
+ published_by: @author_ids[0],
+ author_ids: @author_ids,
+ creators: authors.map do |author|
+ {
+ 'givenName' => author.first_name,
+ 'familyName' => author.last_name,
+ 'name' => author.name,
+ 'ORCID' => author.orcid,
+ 'affiliationIds' => author.current_affiliations.map(&:id),
+ 'id' => author.id
+ }
+ end,
+ contributors: {
+ 'givenName' => @current_user.first_name,
+ 'familyName' => @current_user.last_name,
+ 'name' => @current_user.name,
+ 'ORCID' => @current_user.orcid,
+ 'affiliations' => @current_user.current_affiliations.map(&:output_full),
+ 'id' => @current_user.id
+ },
+ affiliations: affiliations_output,
+ affiliation_ids: affiliations.map { |as| as.map(&:id) },
+ queued_at: DateTime.now,
+ license: @license,
+ scheme_only: @scheme_only
+ }
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+
+ def prepare_reaction_data
+ @reaction_analysis_set = @element.analyses.where(id: @analysis_set_ids)
+ @new_root = duplicate_reaction
+ @element.tag_as_published(@new_root, @reaction_analysis_set)
+ @new_root.create_publication_tag(@current_user, @author_ids, @license)
+ @new_root.samples.each do |new_sample|
+ new_sample.create_publication_tag(@current_user, @author_ids, @license)
+ end
+ @new_publication = Publication.find_by(element: @new_root)
+ add_submission_history(@new_publication)
+ @new_publication
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def prepare_sample_data
+ @new_root = duplicate_sample(@element, @analyses)
+ @element.tag_as_published(@new_root, @analyses)
+ @new_root.create_publication_tag(@current_user, @author_ids, @license)
+ @element.untag_reserved_suffix
+ @new_publication = Publication.find_by(element: @new_root)
+ add_submission_history(@new_publication)
+ @new_publication
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+
+ def add_submission_history(root)
+ init_node = {
+ state: 'submission',
+ action: 'submission',
+ timestamp: Time.now.strftime('%d-%m-%Y %H:%M:%S'),
+ username: @current_user.name,
+ user_id: @current_user.id,
+ type: 'submit'
+ }
+ review = root.review || {}
+ history = review['history'] || []
+ history << init_node
+
+ current_node = {
+ action: 'reviewing',
+ type: 'reviewed',
+ state: 'pending'
+ }
+ history << current_node
+ review['history'] = history
+ review['reviewers'] = @group_reviewers if @group_reviewers.present?
+ root.update!(review: review)
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def reviewer_collections
+ c = @current_user.pending_collection
+ User.reviewer_ids.each do |rev_id|
+ SyncCollectionsUser.find_or_create_by(
+ collection_id: c.id,
+ user_id: rev_id,
+ shared_by_id: c.user_id,
+ permission_level: 3,
+ sample_detail_level: 10,
+ reaction_detail_level: 10,
+ label: 'REVIEWING'
+ )
+ end
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def duplicate_reaction
+ new_reaction = @element.dup
+ princhi_string, princhi_long_key, princhi_short_key, princhi_web_key = @element.products_rinchis
+
+ new_reaction.collections << @current_user.pending_collection
+ new_reaction.collections << Collection.element_to_review_collection
+ new_reaction.collections << @embargo_collection unless @embargo_collection.nil?
+
+ dir = File.join(Rails.root, 'public', 'images', 'reactions')
+ rsf = @element.reaction_svg_file
+ path = File.join(dir, rsf)
+ new_rsf = "#{Time.now.to_i}-#{rsf}"
+ dest = File.join(dir, new_rsf)
+
+ new_reaction.save!
+ new_reaction.copy_segments(segments: @element.segments, current_user_id: @user_id)
+ unless @literals.nil?
+ lits = @literals&.select { |lit| lit['element_type'] == 'Reaction' && lit['element_id'] == @element.id }
+ duplicate_literals(new_reaction, lits)
+ end
+ if File.exists? path
+ FileUtils.cp(path, dest)
+ new_reaction.update_columns(reaction_svg_file: new_rsf)
+ end
+ # new_reaction.save!
+ et = new_reaction.tag
+ data = et.taggable_data || {}
+ # data[:products_rinchi] = {
+ # rinchi_string: princhi_string,
+ # rinchi_long_key: princhi_long_key,
+ # rinchi_short_key: princhi_short_key,
+ # rinchi_web_key: princhi_web_key
+ # }
+ et.update!(taggable_data: data)
+
+ if (d = @element.doi)
+ d.update!(doiable: new_reaction)
+ else
+ # NB: the reaction has still no sample, so it cannot get a proper rinchi needed for the doi
+ # => use the one from original reaction
+ d = Doi.create_for_element!(new_reaction, 'reaction/' + @element.products_short_rinchikey_trimmed)
+ end
+
+ pub = Publication.create!(
+ state: Publication::STATE_PENDING,
+ element: new_reaction,
+ original_element: @element,
+ published_by: @user_id,
+ doi: d,
+ taggable_data: @publication_tag.merge(
+ author_ids: @author_ids,
+ original_analysis_ids: @analysis_set_ids,
+ products_rinchi: {
+ rinchi_string: princhi_string,
+ rinchi_long_key: princhi_long_key,
+ rinchi_short_key: princhi_short_key,
+ rinchi_web_key: princhi_web_key
+ }
+ )
+ )
+
+ duplicate_analyses(new_reaction, @reaction_analysis_set, 'reaction/' + @element.products_short_rinchikey_trimmed)
+ @element.reactions_samples.each do |rs|
+ new_rs = rs.dup
+ sample = @current_user.samples.find_by(id: rs.sample_id)
+ if @scheme_only == true
+ sample.target_amount_value = 0.0
+ sample.real_amount_value = nil
+ end
+ sample_analysis_set = sample.analyses.where(id: @analysis_set_ids)
+ new_sample = duplicate_sample(sample, sample_analysis_set, pub.id)
+ sample.tag_as_published(new_sample, sample_analysis_set)
+ new_rs.sample_id = new_sample
+ new_rs.reaction_id = new_reaction.id
+ new_rs.sample_id = new_sample.id
+ new_rs.reaction_id = new_reaction.id
+ new_rs.save!
+ end
+
+ new_reaction.update_svg_file!
+ new_reaction.reload
+ new_reaction.save!
+ new_reaction.reload
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def duplicate_sample(sample = @sample, analyses = @analyses, parent_publication_id = nil)
+ new_sample = sample.dup
+ new_sample.reprocess_svg if new_sample.sample_svg_file.blank?
+ new_sample.collections << @current_user.pending_collection
+ new_sample.collections << Collection.element_to_review_collection
+ new_sample.collections << @embargo_collection unless @embargo_collection.nil?
+ new_sample.save!
+ new_sample.copy_segments(segments: sample.segments, current_user_id: @current_user.id) if sample.segments
+ duplicate_residues(new_sample, sample) if sample.residues
+ duplicate_elemental_compositions(new_sample, sample) if sample.elemental_compositions
+ duplicate_user_labels(new_sample, sample, @current_user&.id)
+ unless @literals.nil?
+ lits = @literals&.select { |lit| lit['element_type'] == 'Sample' && lit['element_id'] == sample.id }
+ duplicate_literals(new_sample, lits)
+ end
+ duplicate_analyses(new_sample, analyses, new_sample.molecule.inchikey)
+ has_analysis = new_sample.analyses.present?
+ if (has_analysis = new_sample.analyses.present?)
+ if (d = sample.doi)
+ d.update!(doiable: new_sample)
+ else
+ d = Doi.create_for_element!(new_sample)
+ end
+ pub = Publication.create!(
+ state: Publication::STATE_PENDING,
+ element: new_sample,
+ original_element: sample,
+ published_by: @current_user.id,
+ doi: d,
+ parent_id: parent_publication_id,
+ taggable_data: @publication_tag.merge(
+ author_ids: @author_ids,
+ user_labels: sample.tag.taggable_data['user_labels'],
+ original_analysis_ids: analyses.pluck(:id),
+ analysis_ids: new_sample.analyses.pluck(:id)
+ )
+ )
+ end
+ new_sample.analyses.each do |ana|
+ Publication.find_by(element: ana).update(parent: pub)
+ end
+ new_sample
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def duplicate_residues(newSample, originalSample)
+ originalSample&.residues&.each do |res|
+ newRes = Residue.find_or_create_by(sample_id: newSample.id, residue_type: res.residue_type)
+ newRes.update_columns(custom_info: res.custom_info)
+ end
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def duplicate_elemental_compositions(newSample, originalSample)
+ originalSample&.elemental_compositions&.each do |ec|
+ newComposition = ElementalComposition.find_or_create_by(sample_id: newSample.id, composition_type: ec.composition_type)
+ newComposition.update_columns(data: ec.data, loading: ec.loading)
+ end
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def duplicate_user_labels(new_element, original_element, current_user_id)
+ user_labels = original_element.tag&.taggable_data&.dig('user_labels')
+ return if user_labels.nil?
+
+ tag = new_element.tag
+ taggable_data = tag.taggable_data || {}
+ taggable_data['user_labels'] = user_labels
+ tag.update!(taggable_data: taggable_data)
+
+ if new_element.respond_to?(:publication) && pub = new_element.publication
+ pub.update_user_labels(data['user_labels'], current_user_id) if pub.present?
+ end
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def duplicate_literals(element, literals)
+ literals&.each do |lit|
+ attributes = {
+ literature_id: lit.literature_id,
+ element_id: element.id,
+ element_type: lit.element_type,
+ category: 'detail',
+ user_id: lit.user_id,
+ litype: lit.litype
+ }
+ Literal.create(attributes)
+ end
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ def duplicate_analyses(new_element, analyses_arr, ik = nil)
+ unless new_element.container
+ Container.create_root_container(containable: new_element)
+ new_element.reload
+ end
+ analyses = Container.analyses_container(new_element.container.id).first
+ parent_publication = new_element.publication
+ analyses_arr&.each do |ana|
+ new_ana = analyses.children.create(
+ name: ana.name,
+ container_type: ana.container_type,
+ description: ana.description
+ )
+ new_ana.extended_metadata = ana.extended_metadata
+ new_ana.save!
+
+ # move reserved doi
+ if (d = ana.doi)
+ d.update(doiable: new_ana)
+ else
+ d = Doi.create_for_analysis!(new_ana, ik)
+ end
+ Publication.create!(
+ state: Publication::STATE_PENDING,
+ element: new_ana,
+ original_element: ana,
+ published_by: @current_user.id,
+ doi: d,
+ parent: new_element.publication,
+ taggable_data: @publication_tag.merge(
+ author_ids: @author_ids
+ )
+ )
+ # duplicate datasets and copy attachments
+ ana.children.where(container_type: 'dataset').each do |ds|
+ new_dataset = new_ana.children.create(container_type: 'dataset')
+ new_dataset.name = ds.name
+ new_dataset.extended_metadata = ds.extended_metadata
+ new_dataset.save!
+ new_dataset.copy_dataset(ds)
+ clone_attachs = ds.attachments
+ Usecases::Attachments::Copy.execute!(clone_attachs, new_dataset, @current_user.id) if clone_attachs.present?
+ end
+ end
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ raise e
+ end
+
+ # def update_tag_doi(element)
+ # unless element.nil? || element&.doi.nil? || element&.tag.nil?
+ # mds = Datacite::Mds.new
+ # et = element.tag
+ # tag_data = (et.taggable_data && et.taggable_data['publication']) || {}
+ # tag_data['doi'] = "#{mds.doi_prefix}/#{element&.doi.suffix}"
+ # et.update!(
+ # taggable_data: (et.taggable_data || {}).merge(publication: tag_data)
+ # )
+ # if element&.class&.name == 'Reaction'
+ # element&.publication.children.each do |child|
+ # next unless child&.element&.class&.name == 'Sample'
+
+ # update_tag_doi(child.element)
+ # end
+ # end
+ # end
+ # rescue StandardError => e
+ # log_exception(e, method: __method__)
+ # raise e
+ # end
+
+ def scheme_only_handling
+ return unless @type == 'Reaction' && @scheme_only == true
+
+ @element.reactions_samples.select { |rs| rs.type == 'ReactionsProductSample' }.map do |p|
+ py = @scheme_params[:scheme_yield].select { |o| o['id'] == p.sample_id }
+ p.equivalent = py[0]['_equivalent'] if py && !py.empty?
+ p.scheme_yield = py[0]['_equivalent'] if py && !py.empty?
+ end
+
+ @element.reactions_samples.select{ |rs| rs.type != 'ReactionsProductSample' }.map do |p|
+ p.equivalent = 0
+ end
+ @element.name = ''
+ @element.purification = '{}'
+ @element.dangerous_products = '{}'
+ @element.description = { 'ops' => [{ 'insert' => '' }] } unless @scheme_params[:schemeDesc]
+ @element.observation = { 'ops' => [{ 'insert' => '' }] }
+ @element.tlc_solvents = ''
+ @element.tlc_description = ''
+ @element.rf_value = 0
+ @element.rxno = nil
+ @element.role = ''
+ @element.temperature = @scheme_params[:temperature]
+ @element.duration = "#{@scheme_params[:duration][:dispValue]} #{@scheme_params[:duration][:dispUnit]}" unless @scheme_params[:duration].nil?
+ end
+
+ def send_message_to_user
+ is_scheme_ony = @scheme_only == true ? 'scheme-only ' : ''
+ Message.create_msg_notification(
+ channel_id: Channel.find_by(subject: Channel::SUBMITTING)&.id,
+ message_from: @user_id,
+ autoDismiss: 5,
+ message_content: { 'data': "The submission [#{is_scheme_ony}#{@type}: #{@new_root.short_label}] has been generated from the original submission [#{@type}: #{@element.short_label}]" },
+ )
+ rescue StandardError => e
+ log_exception(e, method: __method__)
+ end
+
+ def logger(step, msg, options = {}, log_level = :debug)
+ submit_logger.send(log_level, "step: [#{step}], message: [#{msg}]\n ")
+ submit_logger.send(log_level, "options [#{options}]\n ") if options.present?
+ end
+
+ def log_exception(exception, options = {})
+ submit_logger.error(self.class.name);
+ submit_logger.error("options [#{options}] \n ")
+ submit_logger.error(show_params);
+ submit_logger.error("exception: #{exception.message}")
+ submit_logger.error(exception.backtrace.join("\n"))
+
+ # send message to admin
+ Message.create_msg_notification(
+ channel_id: Channel.find_by(subject: Channel::SUBMITTING)&.id,
+ message_from: User.find_by(name_abbreviation: 'CHI')&.id,
+ autoDismiss: 5,
+ message_content: { 'data': "Exception, User: [#{@user_id}], the original submission [#{@type}: #{@id}], new submission [#{@new_root&.id}] #{@new_root&.short_label}] got error, #{exception.message}" },
+ )
+
+ end
+
+ def submit_logger
+ @@submit_logger ||= Logger.new(Rails.root.join('log/submission.log'))
+ end
+
+ end
+end
\ No newline at end of file
diff --git a/lib/repo/submission_apis.rb b/lib/repo/submission_apis.rb
new file mode 100644
index 000000000..53abfb68b
--- /dev/null
+++ b/lib/repo/submission_apis.rb
@@ -0,0 +1,26 @@
+module Repo
+ class SubmissionApis
+ def self.update_tag_doi(element)
+ unless element.nil? || element&.doi.nil? || element&.tag.nil?
+ mds = Datacite::Mds.new
+ et = element.tag
+ tag_data = (et.taggable_data && et.taggable_data['publication']) || {}
+ tag_data['doi'] = "#{mds.doi_prefix}/#{element&.doi.suffix}"
+ et.update!(
+ taggable_data: (et.taggable_data || {}).merge(publication: tag_data)
+ )
+ if element&.class&.name == 'Reaction'
+ element&.publication.children.each do |child|
+ next unless child&.element&.class&.name == 'Sample'
+
+ Repo::SubmissionApis.update_tag_doi(child.element)
+ end
+ end
+ end
+ rescue StandardError => e
+ Rails.logger.error(e)
+ raise e
+ end
+
+ end
+end
\ No newline at end of file
diff --git a/package.json b/package.json
index 6ddeb7238..0169c910e 100644
--- a/package.json
+++ b/package.json
@@ -28,7 +28,7 @@
"aviator": "v0.6.1",
"base-64": "^0.1.0",
"chem-generic-ui": "^1.4.0-rc1",
- "chem-generic-ui-viewer": "^1.3.0",
+ "chem-generic-ui-viewer": "^1.3.3",
"chemotion-converter-client": "0.5.0",
"citation-js": "0.6.8",
"classnames": "^2.2.5",
@@ -66,6 +66,7 @@
"quill-delta": "3.4.3",
"quill-delta-to-html": "0.8.2",
"quill-delta-to-plaintext": "^1.0.0",
+ "quill2": "npm:quill@^2.0.2",
"raw-loader": "^4.0.2",
"react": "^17.0.2",
"react-async-script-loader": "0.3.0",
@@ -92,7 +93,7 @@
"react-json-editor-ajrm": "^2.5.10",
"react-markdown": "^6.0.2",
"react-modal-resizable-draggable": "^0.1.6",
- "react-molviewer": "^1.0.0",
+ "react-molviewer": "^1.1.3",
"react-notification-system": "^0.2.7",
"react-papaparse": "^3.17.2",
"react-pdf": "^7.7.3",
@@ -113,7 +114,7 @@
"redux": "^4.1.0",
"redux-immutable": "^4.0.0",
"redux-thunk": "^2.0.0",
- "repo-review-ui": "^0.0.14",
+ "repo-review-ui": "^0.0.17",
"sha256": "^0.2.0",
"spark-md5": "^3.0.1",
"svgedit": "^7.3.0",
diff --git a/yarn.lock b/yarn.lock
index 698f2b64f..3c01f118b 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -1869,6 +1869,11 @@
resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-common-types/-/fontawesome-common-types-6.4.0.tgz#88da2b70d6ca18aaa6ed3687832e11f39e80624b"
integrity sha512-HNii132xfomg5QVZw0HwXXpN22s7VBHQBv9CeOu9tfJnhsWQNd2lmTNi8CSrnw5B+5YOmzu1UoPAyxaXsJ6RgQ==
+"@fortawesome/fontawesome-common-types@6.6.0":
+ version "6.6.0"
+ resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-common-types/-/fontawesome-common-types-6.6.0.tgz#31ab07ca6a06358c5de4d295d4711b675006163f"
+ integrity sha512-xyX0X9mc0kyz9plIyryrRbl7ngsA9jz77mCZJsUkLl+ZKs0KWObgaEBoSgQiYWAsSmjz/yjl0F++Got0Mdp4Rw==
+
"@fortawesome/fontawesome-svg-core@^6.1.2":
version "6.4.0"
resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-svg-core/-/fontawesome-svg-core-6.4.0.tgz#3727552eff9179506e9203d72feb5b1063c11a21"
@@ -1876,6 +1881,13 @@
dependencies:
"@fortawesome/fontawesome-common-types" "6.4.0"
+"@fortawesome/fontawesome-svg-core@^6.5.2":
+ version "6.6.0"
+ resolved "https://registry.yarnpkg.com/@fortawesome/fontawesome-svg-core/-/fontawesome-svg-core-6.6.0.tgz#2a24c32ef92136e98eae2ff334a27145188295ff"
+ integrity sha512-KHwPkCk6oRT4HADE7smhfsKudt9N/9lm6EJ5BVg0tD1yPA5hht837fB87F8pn15D8JfTqQOjhKTktwmLMiD7Kg==
+ dependencies:
+ "@fortawesome/fontawesome-common-types" "6.6.0"
+
"@fortawesome/free-regular-svg-icons@^6.1.2":
version "6.4.0"
resolved "https://registry.yarnpkg.com/@fortawesome/free-regular-svg-icons/-/free-regular-svg-icons-6.4.0.tgz#cacc53bd8d832d46feead412d9ea9ce80a55e13a"
@@ -1883,6 +1895,13 @@
dependencies:
"@fortawesome/fontawesome-common-types" "6.4.0"
+"@fortawesome/free-regular-svg-icons@^6.5.2":
+ version "6.6.0"
+ resolved "https://registry.yarnpkg.com/@fortawesome/free-regular-svg-icons/-/free-regular-svg-icons-6.6.0.tgz#fc49a947ac8dfd20403c9ea5f37f0919425bdf04"
+ integrity sha512-Yv9hDzL4aI73BEwSEh20clrY8q/uLxawaQ98lekBx6t9dQKDHcDzzV1p2YtBGTtolYtNqcWdniOnhzB+JPnQEQ==
+ dependencies:
+ "@fortawesome/fontawesome-common-types" "6.6.0"
+
"@fortawesome/free-solid-svg-icons@^6.1.2":
version "6.4.0"
resolved "https://registry.yarnpkg.com/@fortawesome/free-solid-svg-icons/-/free-solid-svg-icons-6.4.0.tgz#48c0e790847fa56299e2f26b82b39663b8ad7119"
@@ -1890,6 +1909,13 @@
dependencies:
"@fortawesome/fontawesome-common-types" "6.4.0"
+"@fortawesome/free-solid-svg-icons@^6.5.2":
+ version "6.6.0"
+ resolved "https://registry.yarnpkg.com/@fortawesome/free-solid-svg-icons/-/free-solid-svg-icons-6.6.0.tgz#061751ca43be4c4d814f0adbda8f006164ec9f3b"
+ integrity sha512-IYv/2skhEDFc2WGUcqvFJkeK39Q+HyPf5GHUrT/l2pKbtgEIv1al1TKd6qStR5OIwQdN1GZP54ci3y4mroJWjA==
+ dependencies:
+ "@fortawesome/fontawesome-common-types" "6.6.0"
+
"@fortawesome/react-fontawesome@^0.2.0":
version "0.2.0"
resolved "https://registry.yarnpkg.com/@fortawesome/react-fontawesome/-/react-fontawesome-0.2.0.tgz#d90dd8a9211830b4e3c08e94b63a0ba7291ddcf4"
@@ -1897,6 +1923,13 @@
dependencies:
prop-types "^15.8.1"
+"@fortawesome/react-fontawesome@^0.2.1":
+ version "0.2.2"
+ resolved "https://registry.yarnpkg.com/@fortawesome/react-fontawesome/-/react-fontawesome-0.2.2.tgz#68b058f9132b46c8599875f6a636dad231af78d4"
+ integrity sha512-EnkrprPNqI6SXJl//m29hpaNzOp1bruISWaOiRtkMi/xSvHJlzc2j2JAYS7egxt/EbjSNV/k6Xy0AQI6vB2+1g==
+ dependencies:
+ prop-types "^15.8.1"
+
"@gar/promisify@^1.0.1":
version "1.1.2"
resolved "https://registry.npmjs.org/@gar/promisify/-/promisify-1.1.2.tgz"
@@ -2742,11 +2775,6 @@
resolved "https://registry.npmjs.org/@redux-saga/types/-/types-1.1.0.tgz"
integrity sha512-afmTuJrylUU/0OtqzaRkbyYFFNgCF73Bvel/sw90pvGrWIZ+vyoIJqA6eMSoA6+nb443kTmulmBtC9NerXboNg==
-"@remix-run/router@1.13.0":
- version "1.13.0"
- resolved "https://registry.yarnpkg.com/@remix-run/router/-/router-1.13.0.tgz#7e29c4ee85176d9c08cb0f4456bff74d092c5065"
- integrity sha512-5dMOnVnefRsl4uRnAdoWjtVTdh8e6aZqgM4puy9nmEADH72ck+uXwzpJLEKE9Q6F8ZljNewLgmTfkxUrBdv4WA==
-
"@restart/hooks@^0.4.7":
version "0.4.9"
resolved "https://registry.yarnpkg.com/@restart/hooks/-/hooks-0.4.9.tgz#ad858fb39d99e252cccce19416adc18fc3f18fcb"
@@ -3809,11 +3837,6 @@ adler-32@~1.3.0:
dependencies:
printj "~1.2.2"
-ag-grid-community@^27.3.0:
- version "27.3.0"
- resolved "https://registry.yarnpkg.com/ag-grid-community/-/ag-grid-community-27.3.0.tgz#b1e94a58026aaf2f0cd7920e35833325b5e762c7"
- integrity sha512-R5oZMXEHXnOLrmhn91J8lR0bv6IAnRcU6maO+wKLMJxffRWaAYFAuw1jt7bdmcKCv8c65F6LEBx4ykSOALa9vA==
-
ag-grid-community@^28.2.1:
version "28.2.1"
resolved "https://registry.yarnpkg.com/ag-grid-community/-/ag-grid-community-28.2.1.tgz#50778cb2254ee79497222781909d8364007dd91e"
@@ -3824,13 +3847,6 @@ ag-grid-community@^31.0.0, ag-grid-community@~31.0.3:
resolved "https://registry.yarnpkg.com/ag-grid-community/-/ag-grid-community-31.0.3.tgz#80870881a3be03aa5df890b4a70409ef5d781e7f"
integrity sha512-k81YmLaOQOab9BavYD+Pw2smZSl6TXOJqj9hRuf70XQl3EknOHCGcra7joJxZRJLMKE/HdR+u33TNyX4TCuWfg==
-ag-grid-react@^27.3.0:
- version "27.3.0"
- resolved "https://registry.yarnpkg.com/ag-grid-react/-/ag-grid-react-27.3.0.tgz#fe06647653f8b0b349b8e613aab8ea2e07915562"
- integrity sha512-2bs9YfJ/shvBZQLLjny4NFvht+ic6VtpTPO0r3bHHOhlL3Fjx2rGvS6AHSwfvu+kJacHCta30PjaEbX8T3UDyw==
- dependencies:
- prop-types "^15.8.1"
-
ag-grid-react@^28.2.1:
version "28.2.1"
resolved "https://registry.yarnpkg.com/ag-grid-react/-/ag-grid-react-28.2.1.tgz#c38585b8f165a5cf9343eab6994c06855f5b2caf"
@@ -4483,24 +4499,6 @@ bluebird@^3.7.2:
resolved "https://registry.yarnpkg.com/bluebird/-/bluebird-3.7.2.tgz#9f229c15be272454ffa973ace0dbee79a1b0c36f"
integrity sha512-XpNj6GDQzdfW+r2Wnn7xiSAd7TM3jzkxGXBGTtWKuSXv1xUV+azxAm8jdWZN06QTQk+2N2XB9jRDkvbmQmcRtg==
-body-parser@1.20.1:
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- resolved "https://registry.yarnpkg.com/body-parser/-/body-parser-1.20.1.tgz#b1812a8912c195cd371a3ee5e66faa2338a5c668"
- integrity sha512-jWi7abTbYwajOytWCQc37VulmWiRae5RyTpaCyDcS5/lMdtwSz5lOpDE67srw/HYe35f1z3fDQw+3txg7gNtWw==
- dependencies:
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- content-type "~1.0.4"
- debug "2.6.9"
- depd "2.0.0"
- destroy "1.2.0"
- http-errors "2.0.0"
- iconv-lite "0.4.24"
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- unpipe "1.0.0"
-
body-parser@1.20.2:
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resolved "https://registry.yarnpkg.com/body-parser/-/body-parser-1.20.2.tgz#6feb0e21c4724d06de7ff38da36dad4f57a747fd"
@@ -4519,24 +4517,6 @@ body-parser@1.20.2:
type-is "~1.6.18"
unpipe "1.0.0"
-body-parser@1.20.1:
- version "1.20.1"
- resolved "https://registry.yarnpkg.com/body-parser/-/body-parser-1.20.1.tgz#b1812a8912c195cd371a3ee5e66faa2338a5c668"
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- dependencies:
- bytes "3.1.2"
- content-type "~1.0.4"
- debug "2.6.9"
- depd "2.0.0"
- destroy "1.2.0"
- http-errors "2.0.0"
- iconv-lite "0.4.24"
- on-finished "2.4.1"
- qs "6.11.0"
- raw-body "2.5.1"
- type-is "~1.6.18"
- unpipe "1.0.0"
-
bonjour-service@^1.0.11:
version "1.0.11"
resolved "https://registry.yarnpkg.com/bonjour-service/-/bonjour-service-1.0.11.tgz#5418e5c1ac91c89a406f853a942e7892829c0d89"
@@ -4885,22 +4865,22 @@ cheerio@^1.0.0-rc.3:
parse5-htmlparser2-tree-adapter "^6.0.1"
tslib "^2.2.0"
-chem-generic-ui-viewer@^1.3.0:
- version "1.3.0"
- resolved "https://registry.yarnpkg.com/chem-generic-ui-viewer/-/chem-generic-ui-viewer-1.3.0.tgz#27cac2f0b6c58435b0980535c1c403b6783ce973"
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+chem-generic-ui-viewer@^1.3.3:
+ version "1.3.3"
+ resolved "https://registry.yarnpkg.com/chem-generic-ui-viewer/-/chem-generic-ui-viewer-1.3.3.tgz#dc54e26622fb004a85d58139f2c24ec6e68be1a3"
+ integrity sha512-l3o60Lf+oDJGcEyC9W6cX8pJdnmMqpUeF4wsE9jM9kc7Kpqs7DLcEGei+dPsG/6+mQQKPqdZkNWWKZDJK0/A5g==
dependencies:
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- "@fortawesome/free-regular-svg-icons" "^6.1.2"
- "@fortawesome/free-solid-svg-icons" "^6.1.2"
- "@fortawesome/react-fontawesome" "^0.2.0"
+ "@fortawesome/fontawesome-svg-core" "^6.5.2"
+ "@fortawesome/free-regular-svg-icons" "^6.5.2"
+ "@fortawesome/free-solid-svg-icons" "^6.5.2"
+ "@fortawesome/react-fontawesome" "^0.2.1"
chem-units "^1.1.0"
+ generic-ui-core "^1.4.6"
lodash "^4.17.21"
numeral "^2.0.6"
prop-types "^15.8.1"
react "^17.0.2"
react-dom "^17.0.2"
- react-select "5.2.2"
uuid "^8.3.2"
chem-generic-ui@^1.4.0-rc1:
@@ -4936,6 +4916,11 @@ chem-units@^1.1.0:
resolved "https://registry.yarnpkg.com/chem-units/-/chem-units-1.1.0.tgz#65d93db9686a50bb59430e34732f497aa2804be8"
integrity sha512-A3jY/B2aEb5s9bmg2lk77QYUl4xCTTCeeKQPbKfwvcD7DseuL40UF6o5Veusfkip8NOcdQ3X6m2hNLMdJKXHbg==
+chem-units@^1.2.0:
+ version "1.2.0"
+ resolved "https://registry.yarnpkg.com/chem-units/-/chem-units-1.2.0.tgz#370b89ba225a84112ca1d201adb3343d9cddb9fd"
+ integrity sha512-Yzz6Re1ZSvEwZc0aINCj2yVvsZrdPms+RcF4EPdHLDdJK8ElHG73pFJM+3cIW1sLn9cddDSnqST7Qnltcy+n/w==
+
chemotion-converter-client@0.5.0:
version "0.5.0"
resolved "https://registry.yarnpkg.com/chemotion-converter-client/-/chemotion-converter-client-0.5.0.tgz#a5c99b1f7bb215f86a7ebd2d78d5c7c6c92eb1b2"
@@ -5401,21 +5386,11 @@ cookie-signature@1.0.6:
resolved "https://registry.npmjs.org/cookie-signature/-/cookie-signature-1.0.6.tgz"
integrity sha1-4wOogrNCzD7oylE6eZmXNNqzriw=
-cookie@0.5.0:
- version "0.5.0"
- resolved "https://registry.yarnpkg.com/cookie/-/cookie-0.5.0.tgz#d1f5d71adec6558c58f389987c366aa47e994f8b"
- integrity sha512-YZ3GUyn/o8gfKJlnlX7g7xq4gyO6OSuhGPKaaGssGB2qgDUS0gPgtTvoyZLTt9Ab6dC4hfc9dV5arkvc/OCmrw==
-
cookie@0.6.0:
version "0.6.0"
resolved "https://registry.yarnpkg.com/cookie/-/cookie-0.6.0.tgz#2798b04b071b0ecbff0dbb62a505a8efa4e19051"
integrity sha512-U71cyTamuh1CRNCfpGY6to28lxvNwPG4Guz/EVjgf3Jmzv0vlDp1atT9eS5dDjMYHucpHbWns6Lwf3BKz6svdw==
-cookie@0.5.0:
- version "0.5.0"
- resolved "https://registry.yarnpkg.com/cookie/-/cookie-0.5.0.tgz#d1f5d71adec6558c58f389987c366aa47e994f8b"
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-
cookie@^0.3.1:
version "0.3.1"
resolved "https://registry.npmjs.org/cookie/-/cookie-0.3.1.tgz"
@@ -7255,6 +7230,11 @@ eventemitter3@^4.0.0:
resolved "https://registry.npmjs.org/eventemitter3/-/eventemitter3-4.0.7.tgz"
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+eventemitter3@^5.0.1:
+ version "5.0.1"
+ resolved "https://registry.yarnpkg.com/eventemitter3/-/eventemitter3-5.0.1.tgz#53f5ffd0a492ac800721bb42c66b841de96423c4"
+ integrity sha512-GWkBvjiSZK87ELrYOSESUYeVIc9mvLLf/nXalMOS5dYrgZq9o5OVkbZAVM06CVxYsCwH9BDZFPlQTlPA1j4ahA==
+
eventlistener@0.0.1:
version "0.0.1"
resolved "https://registry.npmjs.org/eventlistener/-/eventlistener-0.0.1.tgz"
@@ -7380,80 +7360,6 @@ express@^4.17.3:
utils-merge "1.0.1"
vary "~1.1.2"
-express@^4.18.2:
- version "4.18.2"
- resolved "https://registry.yarnpkg.com/express/-/express-4.18.2.tgz#3fabe08296e930c796c19e3c516979386ba9fd59"
- integrity sha512-5/PsL6iGPdfQ/lKM1UuielYgv3BUoJfz1aUwU9vHZ+J7gyvwdQXFEBIEIaxeGf0GIcreATNyBExtalisDbuMqQ==
- dependencies:
- accepts "~1.3.8"
- array-flatten "1.1.1"
- body-parser "1.20.1"
- content-disposition "0.5.4"
- content-type "~1.0.4"
- cookie "0.5.0"
- cookie-signature "1.0.6"
- debug "2.6.9"
- depd "2.0.0"
- encodeurl "~1.0.2"
- escape-html "~1.0.3"
- etag "~1.8.1"
- finalhandler "1.2.0"
- fresh "0.5.2"
- http-errors "2.0.0"
- merge-descriptors "1.0.1"
- methods "~1.1.2"
- on-finished "2.4.1"
- parseurl "~1.3.3"
- path-to-regexp "0.1.7"
- proxy-addr "~2.0.7"
- qs "6.11.0"
- range-parser "~1.2.1"
- safe-buffer "5.2.1"
- send "0.18.0"
- serve-static "1.15.0"
- setprototypeof "1.2.0"
- statuses "2.0.1"
- type-is "~1.6.18"
- utils-merge "1.0.1"
- vary "~1.1.2"
-
-express@^4.18.2:
- version "4.18.2"
- resolved "https://registry.yarnpkg.com/express/-/express-4.18.2.tgz#3fabe08296e930c796c19e3c516979386ba9fd59"
- integrity sha512-5/PsL6iGPdfQ/lKM1UuielYgv3BUoJfz1aUwU9vHZ+J7gyvwdQXFEBIEIaxeGf0GIcreATNyBExtalisDbuMqQ==
- dependencies:
- accepts "~1.3.8"
- array-flatten "1.1.1"
- body-parser "1.20.1"
- content-disposition "0.5.4"
- content-type "~1.0.4"
- cookie "0.5.0"
- cookie-signature "1.0.6"
- debug "2.6.9"
- depd "2.0.0"
- encodeurl "~1.0.2"
- escape-html "~1.0.3"
- etag "~1.8.1"
- finalhandler "1.2.0"
- fresh "0.5.2"
- http-errors "2.0.0"
- merge-descriptors "1.0.1"
- methods "~1.1.2"
- on-finished "2.4.1"
- parseurl "~1.3.3"
- path-to-regexp "0.1.7"
- proxy-addr "~2.0.7"
- qs "6.11.0"
- range-parser "~1.2.1"
- safe-buffer "5.2.1"
- send "0.18.0"
- serve-static "1.15.0"
- setprototypeof "1.2.0"
- statuses "2.0.1"
- type-is "~1.6.18"
- utils-merge "1.0.1"
- vary "~1.1.2"
-
extend-shallow@^2.0.1:
version "2.0.1"
resolved "https://registry.npmjs.org/extend-shallow/-/extend-shallow-2.0.1.tgz"
@@ -7537,7 +7443,7 @@ fast-diff@1.1.2:
resolved "https://registry.npmjs.org/fast-diff/-/fast-diff-1.1.2.tgz"
integrity sha512-KaJUt+M9t1qaIteSvjc6P3RbMdXsNhK61GRftR6SNxqmhthcd9MGIi4T+o0jD8LUSpSnSKXE20nLtJ3fOHxQig==
-fast-diff@^1.1.2:
+fast-diff@^1.1.2, fast-diff@^1.3.0:
version "1.3.0"
resolved "https://registry.yarnpkg.com/fast-diff/-/fast-diff-1.3.0.tgz#ece407fa550a64d638536cd727e129c61616e0f0"
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@@ -7915,6 +7821,14 @@ generic-ui-core@^1.3.0:
chem-units "^1.1.0"
lodash "^4.17.21"
+generic-ui-core@^1.4.6:
+ version "1.5.0"
+ resolved "https://registry.yarnpkg.com/generic-ui-core/-/generic-ui-core-1.5.0.tgz#2ed2d11901f90c1df2b946de1e82e56101e27728"
+ integrity sha512-MkoNSd2KompcjgfoSa+sGH2OAs2vowMJv13Pfas6nzJVDwSCmRTYFxMIKFjzJIhXd70QwAR4DcJ5T2UbwUyjmg==
+ dependencies:
+ chem-units "^1.2.0"
+ lodash "^4.17.21"
+
gensync@^1.0.0-beta.2:
version "1.0.0-beta.2"
resolved "https://registry.npmjs.org/gensync/-/gensync-1.0.0-beta.2.tgz"
@@ -8383,17 +8297,6 @@ http-errors@2.0.0:
statuses "2.0.1"
toidentifier "1.0.1"
-http-errors@2.0.0:
- version "2.0.0"
- resolved "https://registry.yarnpkg.com/http-errors/-/http-errors-2.0.0.tgz#b7774a1486ef73cf7667ac9ae0858c012c57b9d3"
- integrity sha512-FtwrG/euBzaEjYeRqOgly7G0qviiXoJWnvEH2Z1plBdXgbyjv34pHTSb9zoeHMyDy33+DWy5Wt9Wo+TURtOYSQ==
- dependencies:
- depd "2.0.0"
- inherits "2.0.4"
- setprototypeof "1.2.0"
- statuses "2.0.1"
- toidentifier "1.0.1"
-
http-errors@~1.6.2:
version "1.6.3"
resolved "https://registry.npmjs.org/http-errors/-/http-errors-1.6.3.tgz"
@@ -9848,6 +9751,11 @@ lodash.camelcase@^4.3.0:
resolved "https://registry.yarnpkg.com/lodash.camelcase/-/lodash.camelcase-4.3.0.tgz#b28aa6288a2b9fc651035c7711f65ab6190331a6"
integrity sha512-TwuEnCnxbc3rAvhf/LbG7tJUDzhqXyFnv3dtzLOPgCG/hODL7WFnsbwktkD7yUV0RrreP/l1PALq/YSg6VvjlA==
+lodash.clonedeep@^4.5.0:
+ version "4.5.0"
+ resolved "https://registry.yarnpkg.com/lodash.clonedeep/-/lodash.clonedeep-4.5.0.tgz#e23f3f9c4f8fbdde872529c1071857a086e5ccef"
+ integrity sha512-H5ZhCF25riFd9uB5UCkVKo61m3S/xZk1x4wA6yp/L3RFP6Z/eHH1ymQcGLo7J3GMPfm0V/7m1tryHuGVxpqEBQ==
+
lodash.debounce@^4.0.0, lodash.debounce@^4.0.8:
version "4.0.8"
resolved "https://registry.npmjs.org/lodash.debounce/-/lodash.debounce-4.0.8.tgz"
@@ -11229,6 +11137,11 @@ parchment@^1.1.2, parchment@^1.1.4:
resolved "https://registry.npmjs.org/parchment/-/parchment-1.1.4.tgz"
integrity sha512-J5FBQt/pM2inLzg4hEWmzQx/8h8D0CiDxaG3vyp9rKrQRSDgBlhjdP5jQGgosEajXPSQouXGHOmVdgo7QmJuOg==
+parchment@^3.0.0:
+ version "3.0.0"
+ resolved "https://registry.yarnpkg.com/parchment/-/parchment-3.0.0.tgz#2e3a4ada454e1206ae76ea7afcb50e9fb517e7d6"
+ integrity sha512-HUrJFQ/StvgmXRcQ1ftY6VEZUq3jA2t9ncFN4F84J/vN0/FPpQF+8FKXb3l6fLces6q0uOHj6NJn+2xvZnxO6A==
+
parent-module@^1.0.0:
version "1.0.1"
resolved "https://registry.npmjs.org/parent-module/-/parent-module-1.0.1.tgz"
@@ -11380,11 +11293,6 @@ pend@~1.2.0:
resolved "https://registry.yarnpkg.com/pend/-/pend-1.2.0.tgz#7a57eb550a6783f9115331fcf4663d5c8e007a50"
integrity sha1-elfrVQpng/kRUzH89GY9XI4AelA=
-pend@~1.2.0:
- version "1.2.0"
- resolved "https://registry.yarnpkg.com/pend/-/pend-1.2.0.tgz#7a57eb550a6783f9115331fcf4663d5c8e007a50"
- integrity sha1-elfrVQpng/kRUzH89GY9XI4AelA=
-
performance-now@^0.2.0:
version "0.2.0"
resolved "https://registry.npmjs.org/performance-now/-/performance-now-0.2.0.tgz"
@@ -11770,6 +11678,25 @@ quill-delta@^3.6.2:
extend "^3.0.2"
fast-diff "1.1.2"
+quill-delta@^5.1.0:
+ version "5.1.0"
+ resolved "https://registry.yarnpkg.com/quill-delta/-/quill-delta-5.1.0.tgz#1c4bc08f7c8e5cc4bdc88a15a1a70c1cc72d2b48"
+ integrity sha512-X74oCeRI4/p0ucjb5Ma8adTXd9Scumz367kkMK5V/IatcX6A0vlgLgKbzXWy5nZmCGeNJm2oQX0d2Eqj+ZIlCA==
+ dependencies:
+ fast-diff "^1.3.0"
+ lodash.clonedeep "^4.5.0"
+ lodash.isequal "^4.5.0"
+
+"quill2@npm:quill@^2.0.2":
+ version "2.0.2"
+ resolved "https://registry.yarnpkg.com/quill/-/quill-2.0.2.tgz#5b26bc10a74e9f7fdcfdb5156b3133a3ebf0a814"
+ integrity sha512-QfazNrhMakEdRG57IoYFwffUIr04LWJxbS/ZkidRFXYCQt63c1gK6Z7IHUXMx/Vh25WgPBU42oBaNzQ0K1R/xw==
+ dependencies:
+ eventemitter3 "^5.0.1"
+ lodash-es "^4.17.21"
+ parchment "^3.0.0"
+ quill-delta "^5.1.0"
+
quill@^1.3.7:
version "1.3.7"
resolved "https://registry.npmjs.org/quill/-/quill-1.3.7.tgz"
@@ -11819,16 +11746,6 @@ range-parser@^1.2.1, range-parser@~1.2.1:
resolved "https://registry.npmjs.org/range-parser/-/range-parser-1.2.1.tgz"
integrity sha512-Hrgsx+orqoygnmhFbKaHE6c296J+HTAQXoxEF6gNupROmmGJRoyzfG3ccAveqCBrwr/2yxQ5BVd/GTl5agOwSg==
-raw-body@2.5.1:
- version "2.5.1"
- resolved "https://registry.yarnpkg.com/raw-body/-/raw-body-2.5.1.tgz#fe1b1628b181b700215e5fd42389f98b71392857"
- integrity sha512-qqJBtEyVgS0ZmPGdCFPWJ3FreoqvG4MVQln/kCgF7Olq95IbOp0/BWyMwbdtn4VTvkM8Y7khCQ2Xgk/tcrCXig==
- dependencies:
- bytes "3.1.2"
- http-errors "2.0.0"
- iconv-lite "0.4.24"
- unpipe "1.0.0"
-
raw-body@2.5.2:
version "2.5.2"
resolved "https://registry.yarnpkg.com/raw-body/-/raw-body-2.5.2.tgz#99febd83b90e08975087e8f1f9419a149366b68a"
@@ -11839,16 +11756,6 @@ raw-body@2.5.2:
iconv-lite "0.4.24"
unpipe "1.0.0"
-raw-body@2.5.1:
- version "2.5.1"
- resolved "https://registry.yarnpkg.com/raw-body/-/raw-body-2.5.1.tgz#fe1b1628b181b700215e5fd42389f98b71392857"
- integrity sha512-qqJBtEyVgS0ZmPGdCFPWJ3FreoqvG4MVQln/kCgF7Olq95IbOp0/BWyMwbdtn4VTvkM8Y7khCQ2Xgk/tcrCXig==
- dependencies:
- bytes "3.1.2"
- http-errors "2.0.0"
- iconv-lite "0.4.24"
- unpipe "1.0.0"
-
raw-loader@^4.0.2:
version "4.0.2"
resolved "https://registry.npmjs.org/raw-loader/-/raw-loader-4.0.2.tgz"
@@ -12674,18 +12581,13 @@ react-modal-resizable-draggable@^0.1.6:
react-motion "^0.5.2"
react-transition-group "^4.4.1"
-react-molviewer@^1.0.0:
- version "1.0.0"
- resolved "https://registry.yarnpkg.com/react-molviewer/-/react-molviewer-1.0.0.tgz#08e1ae5919849541cb4c5e61d3886c9fefd6eccc"
- integrity sha512-sHWjtTm//nOf5nUtGJz4JL7heyYg1Cbwf8ittbpTCHruysQb6FTAfCNpPKp//6czg7KJK134QkZNal33MZQ9Dg==
+react-molviewer@^1.1.3:
+ version "1.1.3"
+ resolved "https://registry.yarnpkg.com/react-molviewer/-/react-molviewer-1.1.3.tgz#80183af3904d0ab6560762f2980d27c069fade59"
+ integrity sha512-muxVRJTEr+y2iOuztrQW3UtZh7ge5zhwskuo2h+w6GjEg1A4qva6NvOVRr95RiNP/PJtxgnO7NOowzUx9wzjJQ==
dependencies:
- express "^4.18.2"
- numeral "^2.0.6"
prop-types "^15.8.1"
react "^17.0.2"
- react-dom "^17.0.2"
- react-router-dom "^6.14.1"
- uuid "^9.0.0"
react-motion@^0.5.2:
version "0.5.2"
@@ -12839,21 +12741,6 @@ react-resizable-box@^2.0.4:
resolved "https://registry.yarnpkg.com/react-resizable-box/-/react-resizable-box-2.1.0.tgz#8bba081b5adbe2af0be4768c4f1de6a84a423aad"
integrity sha512-0U3kQfVyKnxCPdu/QWC4n/W8DvJmy+EGdq2lBSq2KvEnzhC1E0d/whZCz7PQ/Lq20RdPbHvn5/A2BtQgwcyCFg==
-react-router-dom@^6.14.1:
- version "6.20.0"
- resolved "https://registry.yarnpkg.com/react-router-dom/-/react-router-dom-6.20.0.tgz#7b9527a1e29c7fb90736a5f89d54ca01f40e264b"
- integrity sha512-CbcKjEyiSVpA6UtCHOIYLUYn/UJfwzp55va4yEfpk7JBN3GPqWfHrdLkAvNCcpXr8QoihcDMuk0dzWZxtlB/mQ==
- dependencies:
- "@remix-run/router" "1.13.0"
- react-router "6.20.0"
-
-react-router@6.20.0:
- version "6.20.0"
- resolved "https://registry.yarnpkg.com/react-router/-/react-router-6.20.0.tgz#4275a3567ecc55f7703073158048db10096bb539"
- integrity sha512-pVvzsSsgUxxtuNfTHC4IxjATs10UaAtvLGVSA1tbUE4GDaOSU1Esu2xF5nWLz7KPiMuW8BJWuPFdlGYJ7/rW0w==
- dependencies:
- "@remix-run/router" "1.13.0"
-
"react-select3@npm:react-select@^3.1.1":
version "3.2.0"
resolved "https://registry.npmjs.org/react-select/-/react-select-3.2.0.tgz"
@@ -13396,10 +13283,10 @@ replace-in-file@^6.3.5:
glob "^7.2.0"
yargs "^17.2.1"
-repo-review-ui@^0.0.14:
- version "0.0.14"
- resolved "https://registry.yarnpkg.com/repo-review-ui/-/repo-review-ui-0.0.14.tgz#88c432d632e5d4bc92db5f23a0c2c4df61c5de9d"
- integrity sha512-lt6NtIiJYgdwFYjOGuQ0ITcxXdc6FqmlKGRc/+MYlIGDfsuACaYko7rJ5GuA4oNTv4PtcjTa4JpFiUewLd0yPg==
+repo-review-ui@^0.0.17:
+ version "0.0.17"
+ resolved "https://registry.yarnpkg.com/repo-review-ui/-/repo-review-ui-0.0.17.tgz#c79f6ba6910f762cc779641c4fda020f8c82b538"
+ integrity sha512-kinVu0DbJ9q1aymsWWTze58arzCNVK7S+f2minxBHxnClLmYyDQp59zTIRnAr8zM1nCZpQ+9kz77PJF6wYWZxw==
dependencies:
"@fortawesome/fontawesome-svg-core" "^6.1.2"
"@fortawesome/free-regular-svg-icons" "^6.1.2"
@@ -13754,25 +13641,6 @@ send@0.18.0:
range-parser "~1.2.1"
statuses "2.0.1"
-send@0.18.0:
- version "0.18.0"
- resolved "https://registry.yarnpkg.com/send/-/send-0.18.0.tgz#670167cc654b05f5aa4a767f9113bb371bc706be"
- integrity sha512-qqWzuOjSFOuqPjFe4NOsMLafToQQwBSOEpS+FwEt3A2V3vKubTquT3vmLTQpFgMXp8AlFWFuP1qKaJZOtPpVXg==
- dependencies:
- debug "2.6.9"
- depd "2.0.0"
- destroy "1.2.0"
- encodeurl "~1.0.2"
- escape-html "~1.0.3"
- etag "~1.8.1"
- fresh "0.5.2"
- http-errors "2.0.0"
- mime "1.6.0"
- ms "2.1.3"
- on-finished "2.4.1"
- range-parser "~1.2.1"
- statuses "2.0.1"
-
serialize-javascript@6.0.0, serialize-javascript@^6.0.0:
version "6.0.0"
resolved "https://registry.npmjs.org/serialize-javascript/-/serialize-javascript-6.0.0.tgz"
@@ -13803,16 +13671,6 @@ serve-static@1.15.0:
parseurl "~1.3.3"
send "0.18.0"
-serve-static@1.15.0:
- version "1.15.0"
- resolved "https://registry.yarnpkg.com/serve-static/-/serve-static-1.15.0.tgz#faaef08cffe0a1a62f60cad0c4e513cff0ac9540"
- integrity sha512-XGuRDNjXUijsUL0vl6nSD7cwURuzEgglbOaFuZM9g3kwDXOWVTck0jLzjPzGD+TazWbboZYu52/9/XPdUgne9g==
- dependencies:
- encodeurl "~1.0.2"
- escape-html "~1.0.3"
- parseurl "~1.3.3"
- send "0.18.0"
-
set-blocking@^2.0.0:
version "2.0.0"
resolved "https://registry.npmjs.org/set-blocking/-/set-blocking-2.0.0.tgz"