@nfdi4plants/arctrl 3.0.0-beta.7 → 3.0.0-beta.9
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/ts/ts/ARC.d.ts +17 -7
- package/dist/ts/ts/ARC.d.ts.map +1 -1
- package/dist/ts/ts/ARC.js +217 -92
- package/dist/ts/ts/Contract/ArcWorkflow.d.ts +1 -1
- package/dist/ts/ts/Contract/ArcWorkflow.d.ts.map +1 -1
- package/dist/ts/ts/Contract/ArcWorkflow.js +4 -5
- package/dist/ts/ts/Contract/Datamap.d.ts.map +1 -1
- package/dist/ts/ts/Contract/Datamap.js +27 -8
- package/dist/ts/ts/Conversion.d.ts.map +1 -1
- package/dist/ts/ts/Conversion.js +5 -5
- package/dist/ts/ts/Core/ArcTypes.d.ts +57 -92
- package/dist/ts/ts/Core/ArcTypes.d.ts.map +1 -1
- package/dist/ts/ts/Core/ArcTypes.js +425 -311
- package/dist/ts/ts/Core/DataMap.d.ts +18 -17
- package/dist/ts/ts/Core/DataMap.d.ts.map +1 -1
- package/dist/ts/ts/Core/DataMap.js +82 -64
- package/dist/ts/ts/Core/IdentifierSetters.d.ts.map +1 -1
- package/dist/ts/ts/Core/IdentifierSetters.js +1 -2
- package/dist/ts/ts/Json/DataMap/DataMap.d.ts.map +1 -1
- package/dist/ts/ts/Json/DataMap/DataMap.js +3 -3
- package/dist/ts/ts/Json/Workflow.d.ts +1 -1
- package/dist/ts/ts/Json/Workflow.d.ts.map +1 -1
- package/dist/ts/ts/Json/Workflow.js +17 -17
- package/dist/ts/ts/Spreadsheet/ArcWorkflow.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/ArcWorkflow.js +7 -6
- package/dist/ts/ts/Spreadsheet/DataMap.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/DataMap.js +2 -2
- package/dist/ts/ts/Spreadsheet/DataMapTable/DataMapTable.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/DataMapTable/DataMapTable.js +4 -4
- package/dist/ts/ts/Spreadsheet/Metadata/Workflow.d.ts.map +1 -1
- package/dist/ts/ts/Spreadsheet/Metadata/Workflow.js +23 -13
- package/package.json +1 -1
package/dist/ts/ts/ARC.js
CHANGED
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@@ -1,25 +1,25 @@
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import { FileSystem } from './FileSystem/FileSystem.js';
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import { unwrap, defaultArg, value, map as map$
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import { unwrap, defaultArg, value, map as map$1, bind, defaultArgWith } from '../node_modules/@fable-org/fable-library-js/Option.js';
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import { License } from './License.js';
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import { ArcInvestigation,
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import { ArcInvestigation, ArcInvestigation_$reflection } from './Core/ArcTypes.js';
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import { fullFillContractBatchAsync } from './ContractIO/ContractIO.js';
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import { FSharpResult$2_Error, FSharpResult$2_Ok } from '../node_modules/@fable-org/fable-library-js/Result.js';
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import { Contract } from './Contract/Contract.js';
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import { PromiseBuilder__Run_212F1D4B, PromiseBuilder__Delay_62FBFDE1 } from './fable_modules/Fable.Promise.3.2.0/Promise.fs.js';
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import { promise } from './fable_modules/Fable.Promise.3.2.0/PromiseImpl.fs.js';
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import { getAllFilePathsAsync } from './ContractIO/FileSystemHelper.js';
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import { toArray, contains, delay, append, singleton,
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import { toArray, contains, delay, append, singleton, iterate, tryFind, find, empty, collect, toList } from '../node_modules/@fable-org/fable-library-js/Seq.js';
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import { defaultOf, stringHash, comparePrimitives, curry2, safeHash, getEnumerator, disposeSafe, equals } from '../node_modules/@fable-org/fable-library-js/Util.js';
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import { getAssayFolderPath, getStudyFolderPath } from './FileSystem/Path.js';
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import { getAssayFolderPath, getRunFolderPath, getWorkflowFolderPath, getStudyFolderPath } from './FileSystem/Path.js';
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import { ARCtrl_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from './Contract/ArcAssay.js';
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import { ARCtrl_ArcRun__ArcRun_ToDeleteContract, ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F } from './Contract/ArcRun.js';
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import { ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract, ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F } from './Contract/ArcWorkflow.js';
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import { join, toFail, printf, replace, toText } from '../node_modules/@fable-org/fable-library-js/String.js';
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import { map, choose, fold, concat, contains as contains$2, append as append$1, tryPick, equalsWith, item } from '../node_modules/@fable-org/fable-library-js/Array.js';
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import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from './Contract/ArcInvestigation.js';
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import { ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F } from './Contract/ArcStudy.js';
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import { map as map$1, choose, fold, concat, contains as contains$2, append as append$1, tryPick, equalsWith, item } from '../node_modules/@fable-org/fable-library-js/Array.js';
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import { replace, join, toFail, printf, toText } from '../node_modules/@fable-org/fable-library-js/String.js';
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import { createMissingIdentifier, Study_fileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Assay_datamapFileNameFromIdentifier, Workflow_fileNameFromIdentifier, Workflow_datamapFileNameFromIdentifier, Run_fileNameFromIdentifier, Run_datamapFileNameFromIdentifier } from './Core/Helper/Identifier.js';
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import { ofSeq, contains as contains$1, unionMany, FSharpSet__Contains } from '../node_modules/@fable-org/fable-library-js/Set.js';
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import { ResizeArray_iter, ResizeArray_map } from './Core/Helper/Collections.js';
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import { DataMap__get_DataContexts, DataMap__set_StaticHash_Z524259A4, DataMap__get_StaticHash } from './Core/DataMap.js';
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import { FileSystemTree_Folder, FileSystemTree, FileSystemTree_File } from './FileSystem/FileSystemTree.js';
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import { tryISAReadContractFromPath } from './Contract/ARC.js';
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import { setInvestigationIdentifier } from './Core/IdentifierSetters.js';
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@@ -32,9 +32,8 @@ import { ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F } from './Sprea
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import { ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E } from './Spreadsheet/ArcWorkflow.js';
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import { ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8 } from './Spreadsheet/ArcRun.js';
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import { Dictionary_tryGet } from './fable_modules/FsSpreadsheet.7.0.0-alpha.1/Cells/FsCellsCollection.fs.js';
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import { ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F } from './Contract/ArcStudy.js';
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import { ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5, ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForWorkflow_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForRun_Static } from './Contract/Datamap.js';
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import { ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49, ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract, ARCtrl_ArcWorkflow__ArcWorkflow_tryFromReadContract_Static_7570923F } from './Contract/ArcWorkflow.js';
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import { ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49, ARCtrl_ArcRun__ArcRun_ToUpdateContract, ARCtrl_ArcRun__ArcRun_tryFromReadContract_Static_7570923F } from './Contract/ArcRun.js';
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import { Init_createInitContract_6DFDD678, gitignoreContract, gitattributesContract, Init_createAddRemoteContract_Z721C83C5, Clone_createCloneContract_5000466F } from './Contract/Git.js';
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import { ofSeq as ofSeq$1 } from '../node_modules/@fable-org/fable-library-js/Map.js';
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import { fromString } from './fable_modules/Thoth.Json.JavaScript.0.4.1/Decode.fs.js';
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@@ -46,17 +45,16 @@ import { FSharpRef } from '../node_modules/@fable-org/fable-library-js/Types.js'
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import { class_type } from '../node_modules/@fable-org/fable-library-js/Reflection.js';
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class ARC extends ArcInvestigation {
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constructor(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks,
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constructor(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, fs, license) {
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super(identifier, unwrap(title), unwrap(description), unwrap(submissionDate), unwrap(publicReleaseDate), unwrap(ontologySourceReferences), unwrap(publications), unwrap(contacts), unwrap(assays), unwrap(studies), unwrap(workflows), unwrap(runs), unwrap(registeredStudyIdentifiers), unwrap(comments), unwrap(remarks));
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let fs_1;
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const this$ = new FSharpRef(defaultOf());
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this$.contents = this;
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this._cwl = cwl;
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this._license = license;
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this._fs = (fs_1 = defaultArg(fs, FileSystem.create({
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tree: FileSystemTree_Folder("", [])
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})), ARCAux_updateFSByARC(this$.contents, license, fs_1));
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this["init@
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this["init@96"] = 1;
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}
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get FileSystem() {
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const this$ = this;
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const this$ = this;
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this$._license = license;
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}
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static fromArcInvestigation(isa,
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return new ARC(isa.Identifier, unwrap(isa.Title), unwrap(isa.Description), unwrap(isa.SubmissionDate), unwrap(isa.PublicReleaseDate), isa.OntologySourceReferences, isa.Publications, isa.Contacts, isa.Assays, isa.Studies, isa.Workflows, isa.Runs, isa.RegisteredStudyIdentifiers, isa.Comments, isa.Remarks,
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static fromArcInvestigation(isa, fs, license) {
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return new ARC(isa.Identifier, unwrap(isa.Title), unwrap(isa.Description), unwrap(isa.SubmissionDate), unwrap(isa.PublicReleaseDate), isa.OntologySourceReferences, isa.Publications, isa.Contacts, isa.Assays, isa.Studies, isa.Workflows, isa.Runs, isa.RegisteredStudyIdentifiers, isa.Comments, isa.Remarks, unwrap(fs), unwrap(license));
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}
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TryWriteAsync(arcPath) {
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const this$ = this;
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@@ -136,12 +134,116 @@ class ARC extends ArcInvestigation {
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const assayFolderPath = getAssayFolderPath(assayIdentifier);
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const filteredPaths = paths.filter((p) => !p.startsWith(assayFolderPath));
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this$.SetFilePaths(filteredPaths);
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return toArray(delay(() => append(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() =>
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return toArray(delay(() => append(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => this$.GetUpdateContracts()))));
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}
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GetRunRemoveContracts(runIdentifier) {
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const this$ = this;
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if (!contains(runIdentifier, this$.RunIdentifiers, {
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Equals: (x, y) => x === y,
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GetHashCode: stringHash
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})) {
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throw new Error("ARC does not contain run with given name");
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}
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const run = this$.GetRun(runIdentifier);
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this$.DeleteRun(runIdentifier);
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const paths = this$.FileSystem.Tree.ToFilePaths();
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const runFolderPath = getRunFolderPath(runIdentifier);
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const filteredPaths = paths.filter((p) => !p.startsWith(runFolderPath));
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this$.SetFilePaths(filteredPaths);
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return toArray(delay(() => append(singleton(ARCtrl_ArcRun__ArcRun_ToDeleteContract(run)), delay(() => this$.GetUpdateContracts()))));
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}
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GetWorkflowRemoveContracts(workflowIdentifier) {
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const this$ = this;
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if (!contains(workflowIdentifier, this$.WorkflowIdentifiers, {
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Equals: (x, y) => x === y,
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GetHashCode: stringHash
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})) {
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throw new Error("ARC does not contain workflow with given name");
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}
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const workflow = this$.GetWorkflow(workflowIdentifier);
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this$.DeleteWorkflow(workflowIdentifier);
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const paths = this$.FileSystem.Tree.ToFilePaths();
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const workflowFolderPath = getWorkflowFolderPath(workflowIdentifier);
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const filteredPaths = paths.filter((p) => !p.startsWith(workflowFolderPath));
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this$.SetFilePaths(filteredPaths);
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return toArray(delay(() => append(singleton(ARCtrl_ArcWorkflow__ArcWorkflow_ToDeleteContract(workflow)), delay(() => this$.GetUpdateContracts()))));
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}
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TryRemoveAssayAsync(arcPath, assayIdentifier) {
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const this$ = this;
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return fullFillContractBatchAsync(arcPath, this$.GetAssayRemoveContracts(assayIdentifier));
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}
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TryRemoveRunAsync(arcPath, runIdentifier) {
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const this$ = this;
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return fullFillContractBatchAsync(arcPath, this$.GetRunRemoveContracts(runIdentifier));
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}
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TryRemoveWorkflowAsync(arcPath, workflowIdentifier) {
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const this$ = this;
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return fullFillContractBatchAsync(arcPath, this$.GetWorkflowRemoveContracts(workflowIdentifier));
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}
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RemoveRunAsync(arcPath, runIdentifier) {
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const this$ = this;
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return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => this$.TryRemoveRunAsync(arcPath, runIdentifier).then((_arg) => {
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const result = _arg;
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if (result.tag === /* Error */
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1) {
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const appended = join("\n", map((e) => e, result.fields[0]));
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toFail(printf("Could not remove run, failed with the following errors %s"))(appended);
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return Promise.resolve();
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} else {
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return Promise.resolve();
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}
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})));
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}
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RemoveWorkflowAsync(arcPath, workflowIdentifier) {
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const this$ = this;
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return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => this$.TryRemoveWorkflowAsync(arcPath, workflowIdentifier).then((_arg) => {
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const result = _arg;
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if (result.tag === /* Error */
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1) {
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const appended = join("\n", map((e) => e, result.fields[0]));
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toFail(printf("Could not remove workflow, failed with the following errors %s"))(appended);
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return Promise.resolve();
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} else {
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return Promise.resolve();
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}
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})));
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}
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TryRenameRunAsync(arcPath, oldRunIdentifier, newRunIdentifier) {
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const this$ = this;
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return fullFillContractBatchAsync(arcPath, this$.GetRunRenameContracts(oldRunIdentifier, newRunIdentifier));
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}
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TryRenameWorkflowAsync(arcPath, oldWorkflowIdentifier, newWorkflowIdentifier) {
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const this$ = this;
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return fullFillContractBatchAsync(arcPath, this$.GetWorkflowRenameContracts(oldWorkflowIdentifier, newWorkflowIdentifier));
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}
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RenameRunAsync(arcPath, oldRunIdentifier, newRunIdentifier) {
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const this$ = this;
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return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => this$.TryRenameRunAsync(arcPath, oldRunIdentifier, newRunIdentifier).then((_arg) => {
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const result = _arg;
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if (result.tag === /* Error */
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1) {
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const appended = join("\n", map((e) => e, result.fields[0]));
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toFail(printf("Could not rename run, failed with the following errors %s"))(appended);
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return Promise.resolve();
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} else {
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return Promise.resolve();
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}
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})));
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}
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RenameWorkflowAsync(arcPath, oldWorkflowIdentifier, newWorkflowIdentifier) {
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const this$ = this;
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return PromiseBuilder__Run_212F1D4B(promise, PromiseBuilder__Delay_62FBFDE1(promise, () => this$.TryRenameWorkflowAsync(arcPath, oldWorkflowIdentifier, newWorkflowIdentifier).then((_arg) => {
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const result = _arg;
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if (result.tag === /* Error */
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1) {
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const appended = join("\n", map((e) => e, result.fields[0]));
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toFail(printf("Could not rename workflow, failed with the following errors %s"))(appended);
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return Promise.resolve();
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} else {
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return Promise.resolve();
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}
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})));
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}
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GetAssayRenameContracts(oldAssayIdentifier, newAssayIdentifier) {
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const this$ = this;
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if (!contains(oldAssayIdentifier, this$.AssayIdentifiers, {
|
|
@@ -154,10 +256,42 @@ class ARC extends ArcInvestigation {
|
|
|
154
256
|
const paths = this$.FileSystem.Tree.ToFilePaths();
|
|
155
257
|
const oldAssayFolderPath = getAssayFolderPath(oldAssayIdentifier);
|
|
156
258
|
const newAssayFolderPath = getAssayFolderPath(newAssayIdentifier);
|
|
157
|
-
const renamedPaths = map
|
|
259
|
+
const renamedPaths = map((p) => replace(p, oldAssayFolderPath, newAssayFolderPath), paths);
|
|
158
260
|
this$.SetFilePaths(renamedPaths);
|
|
159
261
|
return toArray(delay(() => append(singleton(Contract.createRename(oldAssayFolderPath, newAssayFolderPath)), delay(() => this$.GetUpdateContracts()))));
|
|
160
262
|
}
|
|
263
|
+
GetRunRenameContracts(oldRunIdentifier, newRunIdentifier) {
|
|
264
|
+
const this$ = this;
|
|
265
|
+
if (!contains(oldRunIdentifier, this$.RunIdentifiers, {
|
|
266
|
+
Equals: (x, y) => x === y,
|
|
267
|
+
GetHashCode: stringHash
|
|
268
|
+
})) {
|
|
269
|
+
throw new Error("ARC does not contain run with given name");
|
|
270
|
+
}
|
|
271
|
+
super.RenameRun(oldRunIdentifier, newRunIdentifier);
|
|
272
|
+
const paths = this$.FileSystem.Tree.ToFilePaths();
|
|
273
|
+
const oldPath = getRunFolderPath(oldRunIdentifier);
|
|
274
|
+
const newPath = getRunFolderPath(newRunIdentifier);
|
|
275
|
+
const renamedPaths = map((p) => replace(p, oldPath, newPath), paths);
|
|
276
|
+
this$.SetFilePaths(renamedPaths);
|
|
277
|
+
return toArray(delay(() => append(singleton(Contract.createRename(oldPath, newPath)), delay(() => this$.GetUpdateContracts()))));
|
|
278
|
+
}
|
|
279
|
+
GetWorkflowRenameContracts(oldWorkflowIdentifier, newWorkflowIdentifier) {
|
|
280
|
+
const this$ = this;
|
|
281
|
+
if (!contains(oldWorkflowIdentifier, this$.WorkflowIdentifiers, {
|
|
282
|
+
Equals: (x, y) => x === y,
|
|
283
|
+
GetHashCode: stringHash
|
|
284
|
+
})) {
|
|
285
|
+
throw new Error("ARC does not contain workflow with given name");
|
|
286
|
+
}
|
|
287
|
+
super.RenameWorkflow(oldWorkflowIdentifier, newWorkflowIdentifier);
|
|
288
|
+
const paths = this$.FileSystem.Tree.ToFilePaths();
|
|
289
|
+
const oldPath = getWorkflowFolderPath(oldWorkflowIdentifier);
|
|
290
|
+
const newPath = getWorkflowFolderPath(newWorkflowIdentifier);
|
|
291
|
+
const renamedPaths = map((p) => replace(p, oldPath, newPath), paths);
|
|
292
|
+
this$.SetFilePaths(renamedPaths);
|
|
293
|
+
return toArray(delay(() => append(singleton(Contract.createRename(oldPath, newPath)), delay(() => this$.GetUpdateContracts()))));
|
|
294
|
+
}
|
|
161
295
|
TryRenameAssayAsync(arcPath, oldAssayIdentifier, newAssayIdentifier) {
|
|
162
296
|
const this$ = this;
|
|
163
297
|
return fullFillContractBatchAsync(arcPath, this$.GetAssayRenameContracts(oldAssayIdentifier, newAssayIdentifier));
|
|
@@ -187,7 +321,7 @@ class ARC extends ArcInvestigation {
|
|
|
187
321
|
const paths = this$.FileSystem.Tree.ToFilePaths();
|
|
188
322
|
const oldStudyFolderPath = getStudyFolderPath(oldStudyIdentifier);
|
|
189
323
|
const newStudyFolderPath = getStudyFolderPath(newStudyIdentifier);
|
|
190
|
-
const renamedPaths = map
|
|
324
|
+
const renamedPaths = map((p) => replace(p, oldStudyFolderPath, newStudyFolderPath), paths);
|
|
191
325
|
this$.SetFilePaths(renamedPaths);
|
|
192
326
|
return toArray(delay(() => append(singleton(Contract.createRename(oldStudyFolderPath, newStudyFolderPath)), delay(() => this$.GetUpdateContracts()))));
|
|
193
327
|
}
|
|
@@ -201,7 +335,7 @@ class ARC extends ArcInvestigation {
|
|
|
201
335
|
const result = _arg;
|
|
202
336
|
if (result.tag === /* Error */
|
|
203
337
|
1) {
|
|
204
|
-
const appended = join("\n", map
|
|
338
|
+
const appended = join("\n", map((e) => e, result.fields[0]));
|
|
205
339
|
toFail(printf("Could not write ARC, failed with the following errors %s"))(appended);
|
|
206
340
|
return Promise.resolve();
|
|
207
341
|
} else {
|
|
@@ -215,7 +349,7 @@ class ARC extends ArcInvestigation {
|
|
|
215
349
|
const result = _arg;
|
|
216
350
|
if (result.tag === /* Error */
|
|
217
351
|
1) {
|
|
218
|
-
const appended = join("\n", map
|
|
352
|
+
const appended = join("\n", map((e) => e, result.fields[0]));
|
|
219
353
|
toFail(printf("Could not update ARC, failed with the following errors %s"))(appended);
|
|
220
354
|
return Promise.resolve();
|
|
221
355
|
} else {
|
|
@@ -229,7 +363,7 @@ class ARC extends ArcInvestigation {
|
|
|
229
363
|
const result = _arg;
|
|
230
364
|
if (result.tag === /* Error */
|
|
231
365
|
1) {
|
|
232
|
-
const appended = join("\n", map
|
|
366
|
+
const appended = join("\n", map((e) => e, result.fields[0]));
|
|
233
367
|
toFail(printf("Could not remove assay, failed with the following errors %s"))(appended);
|
|
234
368
|
return Promise.resolve();
|
|
235
369
|
} else {
|
|
@@ -243,7 +377,7 @@ class ARC extends ArcInvestigation {
|
|
|
243
377
|
const result = _arg;
|
|
244
378
|
if (result.tag === /* Error */
|
|
245
379
|
1) {
|
|
246
|
-
const appended = join("\n", map
|
|
380
|
+
const appended = join("\n", map((e) => e, result.fields[0]));
|
|
247
381
|
toFail(printf("Could not rename assay, failed with the following errors %s"))(appended);
|
|
248
382
|
return Promise.resolve();
|
|
249
383
|
} else {
|
|
@@ -257,7 +391,7 @@ class ARC extends ArcInvestigation {
|
|
|
257
391
|
const result = _arg;
|
|
258
392
|
if (result.tag === /* Error */
|
|
259
393
|
1) {
|
|
260
|
-
const appended = join("\n", map
|
|
394
|
+
const appended = join("\n", map((e) => e, result.fields[0]));
|
|
261
395
|
toFail(printf("Could not remove study, failed with the following errors %s"))(appended);
|
|
262
396
|
return Promise.resolve();
|
|
263
397
|
} else {
|
|
@@ -271,7 +405,7 @@ class ARC extends ArcInvestigation {
|
|
|
271
405
|
const result = _arg;
|
|
272
406
|
if (result.tag === /* Error */
|
|
273
407
|
1) {
|
|
274
|
-
const appended = join("\n", map
|
|
408
|
+
const appended = join("\n", map((e) => e, result.fields[0]));
|
|
275
409
|
toFail(printf("Could not rename study, failed with the following errors %s"))(appended);
|
|
276
410
|
return Promise.resolve();
|
|
277
411
|
} else {
|
|
@@ -284,7 +418,7 @@ class ARC extends ArcInvestigation {
|
|
|
284
418
|
const result = _arg;
|
|
285
419
|
if (result.tag === /* Error */
|
|
286
420
|
1) {
|
|
287
|
-
const appended = join("\n", map
|
|
421
|
+
const appended = join("\n", map((e) => e, result.fields[0]));
|
|
288
422
|
toFail(printf("Could not load ARC, failed with the following errors %s"))(appended);
|
|
289
423
|
return Promise.resolve(new ARC(createMissingIdentifier()));
|
|
290
424
|
} else {
|
|
@@ -337,7 +471,7 @@ class ARC extends ArcInvestigation {
|
|
|
337
471
|
const newFilePath_1 = dataNameFunction_2(c_1);
|
|
338
472
|
c_1.FilePath = newFilePath_1;
|
|
339
473
|
}
|
|
340
|
-
},
|
|
474
|
+
}, dm.DataContexts);
|
|
341
475
|
};
|
|
342
476
|
iterate((s) => {
|
|
343
477
|
const f_1 = (d) => d.GetAbsolutePathForStudy(s.Identifier, checkExistenceFromRoot);
|
|
@@ -358,7 +492,7 @@ class ARC extends ArcInvestigation {
|
|
|
358
492
|
}
|
|
359
493
|
static fromFilePaths(filePaths) {
|
|
360
494
|
const fs = FileSystem.fromFilePaths(filePaths);
|
|
361
|
-
return new ARC(createMissingIdentifier(), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0,
|
|
495
|
+
return new ARC(createMissingIdentifier(), void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, void 0, fs);
|
|
362
496
|
}
|
|
363
497
|
SetFilePaths(filePaths) {
|
|
364
498
|
const this$ = this;
|
|
@@ -383,7 +517,7 @@ class ARC extends ArcInvestigation {
|
|
|
383
517
|
this$.Comments = investigation.Comments;
|
|
384
518
|
this$.Remarks = investigation.Remarks;
|
|
385
519
|
this$.RegisteredStudyIdentifiers = investigation.RegisteredStudyIdentifiers;
|
|
386
|
-
const studies = map
|
|
520
|
+
const studies = map((tuple) => tuple[0], ARCAux_getArcStudiesFromContracts(contracts));
|
|
387
521
|
const assays = ARCAux_getArcAssaysFromContracts(contracts);
|
|
388
522
|
const workflows = ARCAux_getArcWorkflowsFromContracts(contracts);
|
|
389
523
|
const runs = ARCAux_getArcRunsFromContracts(contracts);
|
|
@@ -433,12 +567,12 @@ class ARC extends ArcInvestigation {
|
|
|
433
567
|
assay_1.Tables = updatedTables.Tables;
|
|
434
568
|
});
|
|
435
569
|
workflows.forEach((workflow) => {
|
|
436
|
-
const datamap_2 = ARCAux_getWorkflowDataMapFromContracts(
|
|
437
|
-
if (
|
|
438
|
-
|
|
570
|
+
const datamap_2 = ARCAux_getWorkflowDataMapFromContracts(workflow.Identifier, contracts);
|
|
571
|
+
if (workflow.DataMap == null) {
|
|
572
|
+
workflow.DataMap = datamap_2;
|
|
439
573
|
}
|
|
440
574
|
this$.AddWorkflow(workflow);
|
|
441
|
-
|
|
575
|
+
workflow.StaticHash = workflow.GetLightHashCode() | 0;
|
|
442
576
|
});
|
|
443
577
|
runs.forEach((run) => {
|
|
444
578
|
const datamap_3 = ARCAux_getRunDataMapFromContracts(run.Identifier, contracts);
|
|
@@ -475,7 +609,7 @@ class ARC extends ArcInvestigation {
|
|
|
475
609
|
addToDict(filemap, Study_fileNameFromIdentifier(s.Identifier), ["ISA_Study", ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(s)]);
|
|
476
610
|
if (s.DataMap != null) {
|
|
477
611
|
const dm = value(s.DataMap);
|
|
478
|
-
|
|
612
|
+
dm.StaticHash = safeHash(dm) | 0;
|
|
479
613
|
addToDict(filemap, Study_datamapFileNameFromIdentifier(s.Identifier), ["ISA_Datamap", toFsWorkbook(dm)]);
|
|
480
614
|
}
|
|
481
615
|
}, this$.Studies);
|
|
@@ -484,17 +618,17 @@ class ARC extends ArcInvestigation {
|
|
|
484
618
|
addToDict(filemap, Assay_fileNameFromIdentifier(a.Identifier), ["ISA_Assay", ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(a)]);
|
|
485
619
|
if (a.DataMap != null) {
|
|
486
620
|
const dm_1 = value(a.DataMap);
|
|
487
|
-
|
|
621
|
+
dm_1.StaticHash = safeHash(dm_1) | 0;
|
|
488
622
|
addToDict(filemap, Assay_datamapFileNameFromIdentifier(a.Identifier), ["ISA_Datamap", toFsWorkbook(dm_1)]);
|
|
489
623
|
}
|
|
490
624
|
}, this$.Assays);
|
|
491
625
|
iterate((w) => {
|
|
492
|
-
|
|
493
|
-
addToDict(filemap, Workflow_fileNameFromIdentifier(
|
|
494
|
-
if (
|
|
495
|
-
const dm_2 = value(
|
|
496
|
-
|
|
497
|
-
addToDict(filemap, Workflow_datamapFileNameFromIdentifier(
|
|
626
|
+
w.StaticHash = w.GetLightHashCode() | 0;
|
|
627
|
+
addToDict(filemap, Workflow_fileNameFromIdentifier(w.Identifier), ["ISA_Workflow", ARCtrl_ArcWorkflow__ArcWorkflow_toFsWorkbook_Static_Z1C75CB0E(w)]);
|
|
628
|
+
if (w.DataMap != null) {
|
|
629
|
+
const dm_2 = value(w.DataMap);
|
|
630
|
+
dm_2.StaticHash = safeHash(dm_2) | 0;
|
|
631
|
+
addToDict(filemap, Workflow_datamapFileNameFromIdentifier(w.Identifier), ["ISA_Datamap", toFsWorkbook(dm_2)]);
|
|
498
632
|
}
|
|
499
633
|
}, this$.Workflows);
|
|
500
634
|
iterate((r) => {
|
|
@@ -502,7 +636,7 @@ class ARC extends ArcInvestigation {
|
|
|
502
636
|
addToDict(filemap, Run_fileNameFromIdentifier(r.Identifier), ["ISA_Run", ARCtrl_ArcRun__ArcRun_toFsWorkbook_Static_Z3EFAF6F8(r)]);
|
|
503
637
|
if (r.DataMap != null) {
|
|
504
638
|
const dm_3 = value(r.DataMap);
|
|
505
|
-
|
|
639
|
+
dm_3.StaticHash = safeHash(dm_3) | 0;
|
|
506
640
|
addToDict(filemap, Run_datamapFileNameFromIdentifier(r.Identifier), ["ISA_Datamap", toFsWorkbook(dm_3)]);
|
|
507
641
|
}
|
|
508
642
|
}, this$.Runs);
|
|
@@ -514,7 +648,7 @@ class ARC extends ArcInvestigation {
|
|
|
514
648
|
l.StaticHash = safeHash(l) | 0;
|
|
515
649
|
addToDict(filemap, l.Path, ["PlainText", l.Content]);
|
|
516
650
|
}
|
|
517
|
-
return map
|
|
651
|
+
return map((fp) => {
|
|
518
652
|
const matchValue_2 = Dictionary_tryGet(fp, filemap);
|
|
519
653
|
if (matchValue_2 == null) {
|
|
520
654
|
return Contract.createCreate(fp, "PlainText");
|
|
@@ -538,15 +672,15 @@ class ARC extends ArcInvestigation {
|
|
|
538
672
|
return append(collect((s) => {
|
|
539
673
|
const hash_1 = s.GetLightHashCode() | 0;
|
|
540
674
|
return append(s.StaticHash === 0 ? ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(s, true) : s.StaticHash !== hash_1 ? singleton(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract(s)) : empty(), delay(() => {
|
|
541
|
-
let dm_1;
|
|
675
|
+
let dm, dm_1;
|
|
542
676
|
s.StaticHash = hash_1 | 0;
|
|
543
677
|
const matchValue = s.DataMap;
|
|
544
678
|
let matchResult, dm_2, dm_3;
|
|
545
679
|
if (matchValue != null) {
|
|
546
|
-
if (
|
|
680
|
+
if (dm = value(matchValue), dm.StaticHash === 0) {
|
|
547
681
|
matchResult = 0;
|
|
548
682
|
dm_2 = value(matchValue);
|
|
549
|
-
} else if (dm_1 = value(matchValue),
|
|
683
|
+
} else if (dm_1 = value(matchValue), dm_1.StaticHash !== safeHash(dm_1)) {
|
|
550
684
|
matchResult = 1;
|
|
551
685
|
dm_3 = value(matchValue);
|
|
552
686
|
} else {
|
|
@@ -558,12 +692,12 @@ class ARC extends ArcInvestigation {
|
|
|
558
692
|
switch (matchResult) {
|
|
559
693
|
case 0:
|
|
560
694
|
return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
|
|
561
|
-
|
|
695
|
+
dm_2.StaticHash = safeHash(dm_2) | 0;
|
|
562
696
|
return empty();
|
|
563
697
|
}));
|
|
564
698
|
case 1:
|
|
565
699
|
return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
|
|
566
|
-
|
|
700
|
+
dm_3.StaticHash = safeHash(dm_3) | 0;
|
|
567
701
|
return empty();
|
|
568
702
|
}));
|
|
569
703
|
default: {
|
|
@@ -574,15 +708,15 @@ class ARC extends ArcInvestigation {
|
|
|
574
708
|
}, this$.Studies), delay(() => append(collect((a) => {
|
|
575
709
|
const hash_2 = a.GetLightHashCode() | 0;
|
|
576
710
|
return append(a.StaticHash === 0 ? ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(a, true) : a.StaticHash !== hash_2 ? singleton(ARCtrl_ArcAssay__ArcAssay_ToUpdateContract(a)) : empty(), delay(() => {
|
|
577
|
-
let dm_5;
|
|
711
|
+
let dm_4, dm_5;
|
|
578
712
|
a.StaticHash = hash_2 | 0;
|
|
579
713
|
const matchValue_1 = a.DataMap;
|
|
580
714
|
let matchResult_1, dm_6, dm_7;
|
|
581
715
|
if (matchValue_1 != null) {
|
|
582
|
-
if (
|
|
716
|
+
if (dm_4 = value(matchValue_1), dm_4.StaticHash === 0) {
|
|
583
717
|
matchResult_1 = 0;
|
|
584
718
|
dm_6 = value(matchValue_1);
|
|
585
|
-
} else if (dm_5 = value(matchValue_1),
|
|
719
|
+
} else if (dm_5 = value(matchValue_1), dm_5.StaticHash !== safeHash(dm_5)) {
|
|
586
720
|
matchResult_1 = 1;
|
|
587
721
|
dm_7 = value(matchValue_1);
|
|
588
722
|
} else {
|
|
@@ -594,12 +728,12 @@ class ARC extends ArcInvestigation {
|
|
|
594
728
|
switch (matchResult_1) {
|
|
595
729
|
case 0:
|
|
596
730
|
return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5(dm_6, a.Identifier)), delay(() => {
|
|
597
|
-
|
|
731
|
+
dm_6.StaticHash = safeHash(dm_6) | 0;
|
|
598
732
|
return empty();
|
|
599
733
|
}));
|
|
600
734
|
case 1:
|
|
601
735
|
return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5(dm_7, a.Identifier)), delay(() => {
|
|
602
|
-
|
|
736
|
+
dm_7.StaticHash = safeHash(dm_7) | 0;
|
|
603
737
|
return empty();
|
|
604
738
|
}));
|
|
605
739
|
default: {
|
|
@@ -608,17 +742,17 @@ class ARC extends ArcInvestigation {
|
|
|
608
742
|
}
|
|
609
743
|
}));
|
|
610
744
|
}, this$.Assays), delay(() => append(collect((w) => {
|
|
611
|
-
const hash_3 =
|
|
612
|
-
return append(
|
|
613
|
-
let dm_9;
|
|
614
|
-
|
|
615
|
-
const matchValue_2 =
|
|
745
|
+
const hash_3 = w.GetLightHashCode() | 0;
|
|
746
|
+
return append(w.StaticHash === 0 ? ARCtrl_ArcWorkflow__ArcWorkflow_ToCreateContract_6FCE9E49(w, true) : w.StaticHash !== hash_3 ? singleton(ARCtrl_ArcWorkflow__ArcWorkflow_ToUpdateContract(w)) : empty(), delay(() => {
|
|
747
|
+
let dm_8, dm_9;
|
|
748
|
+
w.StaticHash = hash_3 | 0;
|
|
749
|
+
const matchValue_2 = w.DataMap;
|
|
616
750
|
let matchResult_2, dm_10, dm_11;
|
|
617
751
|
if (matchValue_2 != null) {
|
|
618
|
-
if (
|
|
752
|
+
if (dm_8 = value(matchValue_2), dm_8.StaticHash === 0) {
|
|
619
753
|
matchResult_2 = 0;
|
|
620
754
|
dm_10 = value(matchValue_2);
|
|
621
|
-
} else if (dm_9 = value(matchValue_2),
|
|
755
|
+
} else if (dm_9 = value(matchValue_2), dm_9.StaticHash !== safeHash(dm_9)) {
|
|
622
756
|
matchResult_2 = 1;
|
|
623
757
|
dm_11 = value(matchValue_2);
|
|
624
758
|
} else {
|
|
@@ -629,13 +763,13 @@ class ARC extends ArcInvestigation {
|
|
|
629
763
|
}
|
|
630
764
|
switch (matchResult_2) {
|
|
631
765
|
case 0:
|
|
632
|
-
return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5(dm_10,
|
|
633
|
-
|
|
766
|
+
return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForWorkflow_Z721C83C5(dm_10, w.Identifier)), delay(() => {
|
|
767
|
+
dm_10.StaticHash = safeHash(dm_10) | 0;
|
|
634
768
|
return empty();
|
|
635
769
|
}));
|
|
636
770
|
case 1:
|
|
637
|
-
return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5(dm_11,
|
|
638
|
-
|
|
771
|
+
return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForWorkflow_Z721C83C5(dm_11, w.Identifier)), delay(() => {
|
|
772
|
+
dm_11.StaticHash = safeHash(dm_11) | 0;
|
|
639
773
|
return empty();
|
|
640
774
|
}));
|
|
641
775
|
default: {
|
|
@@ -646,15 +780,15 @@ class ARC extends ArcInvestigation {
|
|
|
646
780
|
}, this$.Workflows), delay(() => append(collect((r) => {
|
|
647
781
|
const hash_4 = r.GetLightHashCode() | 0;
|
|
648
782
|
return append(r.StaticHash === 0 ? ARCtrl_ArcRun__ArcRun_ToCreateContract_6FCE9E49(r, true) : r.StaticHash !== hash_4 ? singleton(ARCtrl_ArcRun__ArcRun_ToUpdateContract(r)) : empty(), delay(() => {
|
|
649
|
-
let dm_13;
|
|
783
|
+
let dm_12, dm_13;
|
|
650
784
|
r.StaticHash = hash_4 | 0;
|
|
651
785
|
const matchValue_3 = r.DataMap;
|
|
652
786
|
let matchResult_3, dm_14, dm_15;
|
|
653
787
|
if (matchValue_3 != null) {
|
|
654
|
-
if (
|
|
788
|
+
if (dm_12 = value(matchValue_3), dm_12.StaticHash === 0) {
|
|
655
789
|
matchResult_3 = 0;
|
|
656
790
|
dm_14 = value(matchValue_3);
|
|
657
|
-
} else if (dm_13 = value(matchValue_3),
|
|
791
|
+
} else if (dm_13 = value(matchValue_3), dm_13.StaticHash !== safeHash(dm_13)) {
|
|
658
792
|
matchResult_3 = 1;
|
|
659
793
|
dm_15 = value(matchValue_3);
|
|
660
794
|
} else {
|
|
@@ -666,12 +800,12 @@ class ARC extends ArcInvestigation {
|
|
|
666
800
|
switch (matchResult_3) {
|
|
667
801
|
case 0:
|
|
668
802
|
return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForRun_Z721C83C5(dm_14, r.Identifier)), delay(() => {
|
|
669
|
-
|
|
803
|
+
dm_14.StaticHash = safeHash(dm_14) | 0;
|
|
670
804
|
return empty();
|
|
671
805
|
}));
|
|
672
806
|
case 1:
|
|
673
807
|
return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForRun_Z721C83C5(dm_15, r.Identifier)), delay(() => {
|
|
674
|
-
|
|
808
|
+
dm_15.StaticHash = safeHash(dm_15) | 0;
|
|
675
809
|
return empty();
|
|
676
810
|
}));
|
|
677
811
|
default: {
|
|
@@ -734,7 +868,8 @@ class ARC extends ArcInvestigation {
|
|
|
734
868
|
try {
|
|
735
869
|
while (enumerator_2["System.Collections.IEnumerator.MoveNext"]()) {
|
|
736
870
|
const workflow = enumerator_2["System.Collections.Generic.IEnumerator`1.get_Current"]();
|
|
737
|
-
|
|
871
|
+
const copy_2 = workflow.Copy();
|
|
872
|
+
void nextWorkflows.push(copy_2);
|
|
738
873
|
}
|
|
739
874
|
} finally {
|
|
740
875
|
disposeSafe(enumerator_2);
|
|
@@ -755,19 +890,19 @@ class ARC extends ArcInvestigation {
|
|
|
755
890
|
const nextPublications = ResizeArray_map((c_3) => c_3.Copy(), this$.Publications);
|
|
756
891
|
const nextOntologySourceReferences = ResizeArray_map((c_4) => c_4.Copy(), this$.OntologySourceReferences);
|
|
757
892
|
const nextStudyIdentifiers = Array.from(this$.RegisteredStudyIdentifiers);
|
|
758
|
-
const nextLicense = map$
|
|
893
|
+
const nextLicense = map$1((_arg) => _arg.Copy(), this$.License);
|
|
759
894
|
const fsCopy = this$._fs.Copy();
|
|
760
|
-
return new ARC(this$.Identifier, unwrap(this$.Title), unwrap(this$.Description), unwrap(this$.SubmissionDate), unwrap(this$.PublicReleaseDate), nextOntologySourceReferences, nextPublications, nextContacts, nextAssays, nextStudies, nextWorkflows, nextRuns, nextStudyIdentifiers, nextComments, nextRemarks,
|
|
895
|
+
return new ARC(this$.Identifier, unwrap(this$.Title), unwrap(this$.Description), unwrap(this$.SubmissionDate), unwrap(this$.PublicReleaseDate), nextOntologySourceReferences, nextPublications, nextContacts, nextAssays, nextStudies, nextWorkflows, nextRuns, nextStudyIdentifiers, nextComments, nextRemarks, fsCopy, unwrap(nextLicense));
|
|
761
896
|
}
|
|
762
897
|
GetRegisteredPayload(IgnoreHidden) {
|
|
763
898
|
let tree, paths, array_3;
|
|
764
899
|
const this$ = this;
|
|
765
900
|
const copy = this$.Copy();
|
|
766
901
|
const registeredStudies = copy.Studies.slice();
|
|
767
|
-
const registeredAssays = concat(map
|
|
902
|
+
const registeredAssays = concat(map((s) => s.RegisteredAssays.slice(), registeredStudies));
|
|
768
903
|
const includeFiles = unionMany([ofSeq(toList(delay(() => append(singleton("isa.investigation.xlsx"), delay(() => append(singleton("README.md"), delay(() => this$.License != null ? singleton(value(this$.License).Path) : empty())))))), {
|
|
769
904
|
Compare: comparePrimitives
|
|
770
|
-
}), unionMany(map
|
|
905
|
+
}), unionMany(map((s_1) => {
|
|
771
906
|
const studyFoldername = `${"studies"}/${s_1.Identifier}`;
|
|
772
907
|
return ofSeq(toList(delay(() => append(singleton(`${studyFoldername}/${"isa.study.xlsx"}`), delay(() => append(singleton(`${studyFoldername}/${"README.md"}`), delay(() => collect((table) => collect((kv) => {
|
|
773
908
|
const textValue = kv[1].ToFreeTextCell().AsFreeText;
|
|
@@ -777,7 +912,7 @@ class ARC extends ArcInvestigation {
|
|
|
777
912
|
});
|
|
778
913
|
}, registeredStudies), {
|
|
779
914
|
Compare: comparePrimitives
|
|
780
|
-
}), unionMany(map
|
|
915
|
+
}), unionMany(map((a) => {
|
|
781
916
|
const assayFoldername = `${"assays"}/${a.Identifier}`;
|
|
782
917
|
return ofSeq(toList(delay(() => append(singleton(`${assayFoldername}/${"isa.assay.xlsx"}`), delay(() => append(singleton(`${assayFoldername}/${"README.md"}`), delay(() => collect((table_1) => collect((kv_1) => {
|
|
783
918
|
const textValue_1 = kv_1[1].ToFreeTextCell().AsFreeText;
|
|
@@ -858,7 +993,7 @@ class ARC extends ArcInvestigation {
|
|
|
858
993
|
let fileSystem;
|
|
859
994
|
const paths = Array.from(patternInput[1]);
|
|
860
995
|
fileSystem = FileSystem.fromFilePaths(paths);
|
|
861
|
-
return ARC.fromArcInvestigation(patternInput[0],
|
|
996
|
+
return ARC.fromArcInvestigation(patternInput[0], fileSystem, unwrap(patternInput[2]));
|
|
862
997
|
} catch (ex) {
|
|
863
998
|
const arg_1 = ex.message;
|
|
864
999
|
return toFail(printf("Could not parse ARC-RO-Crate metadata: \n%s"))(arg_1);
|
|
@@ -919,8 +1054,8 @@ class ARC extends ArcInvestigation {
|
|
|
919
1054
|
function ARC_$reflection() {
|
|
920
1055
|
return class_type("ARCtrl.ARC", void 0, ARC, ArcInvestigation_$reflection());
|
|
921
1056
|
}
|
|
922
|
-
function ARC_$
|
|
923
|
-
return new ARC(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks,
|
|
1057
|
+
function ARC_$ctor_Z443FB9BF(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, fs, license) {
|
|
1058
|
+
return new ARC(identifier, title, description, submissionDate, publicReleaseDate, ontologySourceReferences, publications, contacts, assays, studies, workflows, runs, registeredStudyIdentifiers, comments, remarks, fs, license);
|
|
924
1059
|
}
|
|
925
1060
|
function ARCAux_getArcAssaysFromContracts(contracts) {
|
|
926
1061
|
return choose(ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, contracts);
|
|
@@ -960,16 +1095,16 @@ function ARCAux_getLicenseFromContracts(contracts) {
|
|
|
960
1095
|
}
|
|
961
1096
|
function ARCAux_updateFSByARC(isa, license, fs) {
|
|
962
1097
|
let assaysFolder;
|
|
963
|
-
const assays = map
|
|
1098
|
+
const assays = map((a) => FileSystemTree.createAssayFolder(a.Identifier, a.DataMap != null), toArray(isa.Assays));
|
|
964
1099
|
assaysFolder = FileSystemTree.createAssaysFolder(assays);
|
|
965
1100
|
let studiesFolder;
|
|
966
|
-
const studies = map
|
|
1101
|
+
const studies = map((s) => FileSystemTree.createStudyFolder(s.Identifier, s.DataMap != null), toArray(isa.Studies));
|
|
967
1102
|
studiesFolder = FileSystemTree.createStudiesFolder(studies);
|
|
968
1103
|
let workflowsFolder;
|
|
969
|
-
const workflows = map
|
|
1104
|
+
const workflows = map((w) => FileSystemTree.createWorkflowFolder(w.Identifier, w.DataMap != null), toArray(isa.Workflows));
|
|
970
1105
|
workflowsFolder = FileSystemTree.createWorkflowsFolder(workflows);
|
|
971
1106
|
let runsFolder;
|
|
972
|
-
const runs = map
|
|
1107
|
+
const runs = map((r) => FileSystemTree.createRunFolder(r.Identifier, r.DataMap != null), toArray(isa.Runs));
|
|
973
1108
|
runsFolder = FileSystemTree.createRunsFolder(runs);
|
|
974
1109
|
const investigation = FileSystemTree.createInvestigationFile();
|
|
975
1110
|
let tree_1;
|
|
@@ -979,15 +1114,5 @@ function ARCAux_updateFSByARC(isa, license, fs) {
|
|
|
979
1114
|
});
|
|
980
1115
|
return fs.Union(tree_1);
|
|
981
1116
|
}
|
|
982
|
-
function ARCAux_updateFSByCWL(cwl, fs) {
|
|
983
|
-
const workflows = FileSystemTree.createWorkflowsFolder([]);
|
|
984
|
-
const runs = FileSystemTree.createRunsFolder([]);
|
|
985
|
-
let tree_1;
|
|
986
|
-
const tree = FileSystemTree.createRootFolder([workflows, runs]);
|
|
987
|
-
tree_1 = FileSystem.create({
|
|
988
|
-
tree
|
|
989
|
-
});
|
|
990
|
-
return fs.Union(tree_1);
|
|
991
|
-
}
|
|
992
1117
|
|
|
993
|
-
export { ARC, ARCAux_getArcAssaysFromContracts, ARCAux_getArcInvestigationFromContracts, ARCAux_getArcRunsFromContracts, ARCAux_getArcStudiesFromContracts, ARCAux_getArcWorkflowsFromContracts, ARCAux_getAssayDataMapFromContracts, ARCAux_getLicenseFromContracts, ARCAux_getRunDataMapFromContracts, ARCAux_getStudyDataMapFromContracts, ARCAux_getWorkflowDataMapFromContracts, ARCAux_updateFSByARC,
|
|
1118
|
+
export { ARC, ARCAux_getArcAssaysFromContracts, ARCAux_getArcInvestigationFromContracts, ARCAux_getArcRunsFromContracts, ARCAux_getArcStudiesFromContracts, ARCAux_getArcWorkflowsFromContracts, ARCAux_getAssayDataMapFromContracts, ARCAux_getLicenseFromContracts, ARCAux_getRunDataMapFromContracts, ARCAux_getStudyDataMapFromContracts, ARCAux_getWorkflowDataMapFromContracts, ARCAux_updateFSByARC, ARC_$ctor_Z443FB9BF, ARC_$reflection };
|