Update to ARCtrl v2.0.0 #187

nfdi4plants · Jun 18, 2024 · 9ec2aab · 9ec2aab
1 parent 4b8db4b
commit 9ec2aab
Show file tree

Hide file tree

Showing 8 changed files with 19 additions and 24 deletions.
diff --git a/package.json b/package.json
@@ -27,9 +27,9 @@
     "typecheck": "npm run typecheck:main && npm run typecheck:preload && npm run typecheck:renderer"
   },
   "dependencies": {
-    "@fslab/fsspreadsheet": "^5.0.0",
+    "@fslab/fsspreadsheet": "^6.1.3",
     "@imengyu/vue3-context-menu": "^1.3.5",
-    "@nfdi4plants/arctrl": "^1.1.0",
+    "@nfdi4plants/arctrl": "^2.0.0-alpha.7",
     "@nfdi4plants/exceljs": "0.2.0",
     "@quasar/extras": "^1.16.9",
     "chokidar": "^3.5.3",

diff --git a/packages/renderer/src/ArcControlService.ts b/packages/renderer/src/ArcControlService.ts
@@ -2,11 +2,9 @@ import { reactive } from 'vue'
 
 import AppProperties from './AppProperties.ts';
 
-import { ARC } from "@nfdi4plants/arctrl/ARC.js";
-import { ArcInvestigation } from "@nfdi4plants/arctrl/ISA/ISA/ArcTypes/ArcTypes.js";
-import { gitignoreContract } from "@nfdi4plants/arctrl/Contracts/Contracts.Git.js";
+import { ARC, ArcInvestigation } from "@nfdi4plants/arctrl";
+import { gitignoreContract } from "@nfdi4plants/arctrl/Contract/Git";
 import { Xlsx } from '@fslab/fsspreadsheet/Xlsx.js';
-import {FileSystemTree} from '@nfdi4plants/arctrl/FileSystem/FileSystemTree.js'
 import {Contract} from '@nfdi4plants/arctrl/Contract/Contract.js'
 
 import pDebounce from 'p-debounce';

diff --git a/packages/renderer/src/Property.ts b/packages/renderer/src/Property.ts
@@ -1,6 +1,6 @@
 import { reactive, watch, ref } from 'vue';
 
-import {OntologyAnnotation} from '@nfdi4plants/arctrl/ISA/ISA/JsonTypes/OntologyAnnotation.js';
+import {OntologyAnnotation} from '@nfdi4plants/arctrl';
 
 const autoLabel = property => {
   let words = property
@@ -26,7 +26,7 @@ const Property = (model: any,property: string, config?: any)=>{
   // console.log(property, model[property]);
   config = config || {};
   if(config.type==='ontology' && !model[property])
-    model[property] = OntologyAnnotation.fromString('');
+    model[property] = new OntologyAnnotation('');
 
   const p = reactive({
     model: model,

diff --git a/packages/renderer/src/components/FormInput.vue b/packages/renderer/src/components/FormInput.vue
@@ -2,7 +2,7 @@
 
 import { date } from 'quasar'
 
-import {OntologyAnnotation} from '@nfdi4plants/arctrl/ISA/ISA/JsonTypes/OntologyAnnotation.js';
+import {OntologyAnnotation} from '@nfdi4plants/arctrl';
 
 export interface Props {
   property: Object
@@ -40,7 +40,7 @@ const isValidTerm = ()=>{
       :options="props.property.options"
       :option-id="'TermAccessionNumber'"
       :option-label="a=> a ? a.NameText : ''"
-      @input-value="v=>{if(props.property.model[props.property.property].NameText!==v){props.property.model[props.property.property] = OntologyAnnotation.fromString(v)}}"
+      @input-value="v=>{if(props.property.model[props.property.property].NameText!==v){props.property.model[props.property.property] = new OntologyAnnotation(v)}}"
       @filter="props.property.filter"
       :disable="props.property.disabled"
       options-dense
@@ -83,7 +83,7 @@ const isValidTerm = ()=>{
       :options="props.property.options"
       :option-id="'TermAccessionNumber'"
       :option-label="a=> a ? a.NameText : ''"
-      @input-value="v=>{if(props.property.model[props.property.property].NameText!==v){props.property.model[props.property.property] = OntologyAnnotation.fromString(v)}}"
+      @input-value="v=>{if(props.property.model[props.property.property].NameText!==v){props.property.model[props.property.property] = new OntologyAnnotation(v)}}"
       @filter="props.property.filter"
       :disable="props.property.disabled"
       options-dense

diff --git a/packages/renderer/src/dialogs/NewAssayDialog.vue b/packages/renderer/src/dialogs/NewAssayDialog.vue
@@ -3,7 +3,7 @@ import { useDialogPluginComponent } from 'quasar';
 import { reactive, onMounted, watch, ref } from 'vue';
 import ArcControlService from '../ArcControlService.ts';
 import {ArcStudy} from "@nfdi4plants/arctrl"
-import {checkValidCharacters} from '@nfdi4plants/arctrl/ISA/ISA/Identifier.js'
+import {checkValidCharacters} from '@nfdi4plants/arctrl/Core/Helper/Identifier.js'
 import * as internal from 'stream';
 
 export type NewAssayInformation = {

diff --git a/packages/renderer/src/dialogs/NewStudyDialog.vue b/packages/renderer/src/dialogs/NewStudyDialog.vue
@@ -3,7 +3,7 @@ import { useDialogPluginComponent } from 'quasar';
 import { reactive, onMounted, watch, ref } from 'vue';
 
 import ArcControlService from '../ArcControlService';
-import {checkValidCharacters} from '@nfdi4plants/arctrl/ISA/ISA/Identifier.js'
+import {checkValidCharacters} from '@nfdi4plants/arctrl/Core/Helper/Identifier.js'
 
 
 const iProps : {

diff --git a/packages/renderer/src/views/ArcTreeView.vue b/packages/renderer/src/views/ArcTreeView.vue
@@ -10,7 +10,7 @@ import AddProtocolDialog from '../dialogs/AddProtocolDialog.vue';
 import NewAssayDialog from '../dialogs/NewAssayDialog.vue';
 import { NewAssayInformation } from '../dialogs/NewAssayDialog.vue';
 import { useQuasar } from 'quasar'
-import {ArcStudy, ArcAssay} from '@nfdi4plants/arctrl/ISA/ISA/ArcTypes/ArcTypes.js';
+import {ArcStudy, ArcAssay} from '@nfdi4plants/arctrl';
 import NewStudyDialog from '../dialogs/NewStudyDialog.vue';
 
 const Image = 'image';

diff --git a/packages/renderer/src/views/SwateView.vue b/packages/renderer/src/views/SwateView.vue
@@ -3,10 +3,7 @@ import { onMounted, onUnmounted, ref, watch, reactive } from 'vue';
 import ArcControlService from '../ArcControlService.ts';
 import AppProperties from '../AppProperties.ts';
 import SwateControlService from '../SwateControlService.ts';
-import { ArcInvestigation, ArcAssay, ArcStudy } from '@nfdi4plants/arctrl';
-import { ArcAssay_fromArcJsonString, ArcAssay_toArcJsonString } from '@nfdi4plants/arctrl/ISA/ISA.Json/ArcTypes/ArcAssay.js'
-import { ArcStudy_fromArcJsonString, ArcStudy_toArcJsonString } from '@nfdi4plants/arctrl/ISA/ISA.Json/ArcTypes/ArcStudy.js'
-import { ArcInvestigation_fromArcJsonString, ArcInvestigation_toArcJsonString } from '@nfdi4plants/arctrl/ISA/ISA.Json/ArcTypes/ArcInvestigation.js'
+import { ArcInvestigation, ArcAssay, ArcStudy, JsonController } from '@nfdi4plants/arctrl';
 
 let iframe: any | HTMLElement = ref({})
 
@@ -44,19 +41,19 @@ const send = (msg: Msg, data: any = null): void => {
   switch (msg) {
     case Msg.InvestigationToSwate:
       if (data instanceof ArcInvestigation) {
-        const jsonString = ArcInvestigation_toArcJsonString(data);
+        const jsonString = JsonController.Investigation.toJsonString(data,0)
         toSwate({ ArcInvestigationJsonString: jsonString });
       } else return console.error('Invalid data type for Msg.InvestigationToSwate');
       break;
     case Msg.AssayToSwate:
       if (data instanceof ArcAssay) {
-        const jsonString = ArcAssay_toArcJsonString(data);
+        const jsonString = JsonController.Assay.toJsonString(data,0)
         toSwate({ ArcAssayJsonString: jsonString });
       } else return console.error('Invalid data type for Msg.AssayToSwate');
       break;
     case Msg.StudyToSwate:
       if (data instanceof ArcStudy) {
-        const jsonString = ArcStudy_toArcJsonString(data);
+        const jsonString = JsonController.Study.toJsonString(data,0);
         toSwate({ ArcStudyJsonString: jsonString });
       } else return console.error('Invalid data type for Msg.AssayToSwate');
       break;
@@ -103,17 +100,17 @@ const SwateAPI: SwateAPI = {
     send(Msg.PathsToSwate, selection)
   },
   InvestigationToARCitect: (investigationJsonString: string) => {
-    let investigation = ArcInvestigation_fromArcJsonString(investigationJsonString);
+    let investigation = JsonController.Investigation.fromJsonString(investigationJsonString);
     ArcControlService.props.arc.ISA = investigation;
   },
   AssayToARCitect: (assayJsonString: string) => {
-    let assay = ArcAssay_fromArcJsonString(assayJsonString);
+    let assay = JsonController.Assay.fromJsonString(assayJsonString);
     ArcControlService.props.arc.ISA.SetAssay(assay.Identifier, assay);
   },
   StudyToARCitect: (studyJsonString: string) => {
     /// ignore assays, I am actually not sure why this must be create, but it will be empty. Must talk to Lukas Weil about this.
     /// ~Kevin F. 12.01.2024
-    let study = ArcStudy_fromArcJsonString(studyJsonString);
+    let study = JsonController.Study.fromJsonString(studyJsonString);
     ArcControlService.props.arc.ISA.SetStudy(study.Identifier, study);
   },
   Error: (e) => {