@nfdi4plants/arctrl 3.2.3 → 3.3.1

package/dist/ts/ts/Conversion/ScholarlyArticle.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"ScholarlyArticle.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/ScholarlyArticle.ts"],"names":[],"mappings":"AACA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAKjF,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AASzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAOpD,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAErD,qBAAa,0BAA0B;;CAGtC;AAED,wBAAgB,sCAAsC,IAAI,QAAQ,CAEjE;AAED,wBAAgB,kDAAkD,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAezF;AAED,wBAAgB,iDAAiD,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAmCrF;AAED,wBAAgB,mDAAmD,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,EAAE,CAG7F;AAED,wBAAgB,oDAAoD,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAOhH;AAED,wBAAgB,oDAAoD,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAEnH;AAED,wBAAgB,0DAA0D,CAAC,WAAW,EAAE,WAAW,GAAG,MAAM,CAkB3G;AAED,wBAAgB,8DAA8D,CAAC,EAAE,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,WAAW,CAiB5I"}
+{"version":3,"file":"ScholarlyArticle.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/ScholarlyArticle.ts"],"names":[],"mappings":"AACA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAKjF,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AASzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAOpD,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAErD,qBAAa,0BAA0B;;CAGtC;AAED,wBAAgB,sCAAsC,IAAI,QAAQ,CAEjE;AAED,wBAAgB,kDAAkD,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAezF;AAED,wBAAgB,iDAAiD,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAmCrF;AAED,wBAAgB,mDAAmD,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,EAAE,CAG7F;AAED,wBAAgB,oDAAoD,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAOhH;AAED,wBAAgB,oDAAoD,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAEnH;AAED,wBAAgB,0DAA0D,CAAC,WAAW,EAAE,WAAW,GAAG,MAAM,CA8F3G;AAED,wBAAgB,8DAA8D,CAAC,EAAE,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,WAAW,CAiB5I"}

package/dist/ts/ts/Conversion/ScholarlyArticle.js

@@ -1,5 +1,5 @@
 import { class_type } from '../../node_modules/@fable-org/fable-library-ts/Reflection.js';
-import { toText, printf, concat, join } from '../../node_modules/@fable-org/fable-library-ts/String.js';
+import { toText, printf, concat, join, toConsole } from '../../node_modules/@fable-org/fable-library-ts/String.js';
 import { LDPerson } from '../ROCrate/LDTypes/Person.js';
 import { fromString } from '../fable_modules/Thoth.Json.JavaScript.0.5.0/Decode.fs.js';
 import { decoder, encoder } from '../Json/ROCrate/LDNode.js';
@@ -91,34 +91,100 @@ function ScholarlyArticleConversion_composeScholarlyArticle_D324A6D(publication)
   if (matchValue == null) {
     throw new Exception("Publication must have a title");
   } else {
-    title = value(matchValue);
+    title = matchValue;
   }
   let authors_1;
   const option_1 = publication.Authors;
-  authors_1 = option_1 != null ? ScholarlyArticleConversion_composeAuthors_Z721C83C5(value(option_1)) : void 0;
+  authors_1 = option_1 != null ? ScholarlyArticleConversion_composeAuthors_Z721C83C5(option_1) : void 0;
   const comments = Option_fromSeq(ResizeArray_map(BaseTypes_composeComment_Z13201A7E, publication.Comments));
   const identifiers = Array.from(toList(delay(() => append(publication.DOI != null && value(publication.DOI) !== "" ? singleton(LDPropertyValue.createDOI(value(publication.DOI))) : empty(), delay(() => publication.PubMedID != null && value(publication.PubMedID) !== "" ? singleton(LDPropertyValue.createPubMedID(value(publication.PubMedID))) : empty())))));
   let status;
   const option_3 = publication.Status;
-  status = option_3 != null ? BaseTypes_composeDefinedTerm_ZDED3A0F(value(option_3)) : void 0;
-  return LDScholarlyArticle.create(title, identifiers, void 0, unwrap(authors_1), void 0, unwrap(status), unwrap(comments));
+  status = option_3 != null ? BaseTypes_composeDefinedTerm_ZDED3A0F(option_3) : void 0;
+  const isUrl = (s) => {
+    if (s.startsWith("http://")) {
+      return true;
+    } else {
+      return s.startsWith("https://");
+    }
+  };
+  let id;
+  const matchValue_1 = publication.DOI;
+  const matchValue_2 = publication.PubMedID;
+  let matchResult = void 0, doi_2 = void 0, doi_3 = void 0, pubMedID_4 = void 0, pubMedID_5 = void 0;
+  if (matchValue_1 != null) {
+    if (isUrl(matchValue_1)) {
+      matchResult = 0;
+      doi_2 = matchValue_1;
+    } else if (matchValue_1 !== "") {
+      matchResult = 1;
+      doi_3 = matchValue_1;
+    } else if (matchValue_2 != null) {
+      if (isUrl(matchValue_2)) {
+        matchResult = 2;
+        pubMedID_4 = matchValue_2;
+      } else if (matchValue_2 !== "") {
+        matchResult = 3;
+        pubMedID_5 = matchValue_2;
+      } else {
+        matchResult = 4;
+      }
+    } else {
+      matchResult = 4;
+    }
+  } else if (matchValue_2 != null) {
+    if (isUrl(matchValue_2)) {
+      matchResult = 2;
+      pubMedID_4 = matchValue_2;
+    } else if (matchValue_2 !== "") {
+      matchResult = 3;
+      pubMedID_5 = matchValue_2;
+    } else {
+      matchResult = 4;
+    }
+  } else {
+    matchResult = 4;
+  }
+  switch (matchResult) {
+    case 0: {
+      id = doi_2;
+      break;
+    }
+    case 1: {
+      id = concat("https://doi.org/", doi_3);
+      break;
+    }
+    case 2: {
+      id = pubMedID_4;
+      break;
+    }
+    case 3: {
+      id = concat("https://pubmed.ncbi.nlm.nih.gov/", pubMedID_5, "/");
+      break;
+    }
+    default: {
+      toConsole(printf('Warning: Publication "%s" has neither a DOI nor a PubMed ID, so it cannot be given an absolute URL as @id as required by RO-Crate.'))(title);
+      id = void 0;
+    }
+  }
+  return LDScholarlyArticle.create(title, identifiers, unwrap(id), unwrap(authors_1), void 0, unwrap(status), unwrap(comments));
 }
 function ScholarlyArticleConversion_decomposeScholarlyArticle_Z6839B9E8(sa, graph, context) {
   const title = LDScholarlyArticle.getHeadlineAsString(sa, unwrap(context));
   let authors;
   const option_1 = Option_fromSeq(LDScholarlyArticle.getAuthors(sa, unwrap(graph), unwrap(context)));
-  authors = option_1 != null ? ScholarlyArticleConversion_decomposeAuthors_1AAAE9A5(value(option_1), unwrap(context)) : void 0;
+  authors = option_1 != null ? ScholarlyArticleConversion_decomposeAuthors_1AAAE9A5(option_1, unwrap(context)) : void 0;
   const comments = ResizeArray_map((c) => BaseTypes_decomposeComment_Z2F770004(c, unwrap(context)), LDScholarlyArticle.getComments(sa, unwrap(graph), unwrap(context)));
   let status;
   const option_3 = LDScholarlyArticle.tryGetCreativeWorkStatus(sa, unwrap(graph), unwrap(context));
-  status = option_3 != null ? BaseTypes_decomposeDefinedTerm_Z2F770004(value(option_3), unwrap(context)) : void 0;
+  status = option_3 != null ? BaseTypes_decomposeDefinedTerm_Z2F770004(option_3, unwrap(context)) : void 0;
   const identifiers = LDScholarlyArticle.getIdentifiersAsPropertyValue(sa, unwrap(graph), unwrap(context));
   let doi;
   const _arg = ResizeArray_tryPick((i) => LDPropertyValue.tryGetAsDOI(i, unwrap(context)), identifiers);
-  doi = _arg == null ? LDScholarlyArticle.tryGetSameAsAsString(sa, unwrap(context)) : value(_arg);
+  doi = _arg == null ? LDScholarlyArticle.tryGetSameAsAsString(sa, unwrap(context)) : _arg;
   let pubMedID;
   const _arg_1 = ResizeArray_tryPick((i_1) => LDPropertyValue.tryGetAsPubMedID(i_1, unwrap(context)), identifiers);
-  pubMedID = _arg_1 == null ? LDScholarlyArticle.tryGetUrlAsString(sa, unwrap(context)) : value(_arg_1);
+  pubMedID = _arg_1 == null ? LDScholarlyArticle.tryGetUrlAsString(sa, unwrap(context)) : _arg_1;
   return Publication.create(unwrap(pubMedID), unwrap(doi), unwrap(authors), title, unwrap(status), comments);
 }
 

package/dist/ts/ts/Conversion/Study.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"Study.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Study.ts"],"names":[],"mappings":"AACA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAQjF,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAEzD,OAAO,EAAE,QAAQ,EAAoB,MAAM,qBAAqB,CAAC;AAUjE,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AACzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAEpD,qBAAa,eAAe;;CAG3B;AAED,wBAAgB,2BAA2B,IAAI,QAAQ,CAEtD;AAED,wBAAgB,qCAAqC,CAAC,KAAK,EAAE,QAAQ,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,CAuC9F;AAED,wBAAgB,wCAAwC,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,QAAQ,CAoBtH"}
+{"version":3,"file":"Study.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Study.ts"],"names":[],"mappings":"AACA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AASjF,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAEzD,OAAO,EAAE,QAAQ,EAAoB,MAAM,qBAAqB,CAAC;AASjE,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AACzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAEpD,qBAAa,eAAe;;CAG3B;AAED,wBAAgB,2BAA2B,IAAI,QAAQ,CAEtD;AAED,wBAAgB,qCAAqC,CAAC,KAAK,EAAE,QAAQ,EAAE,EAAE,CAAC,EAAE,UAAU,GAAG,MAAM,CAkD9F;AAED,wBAAgB,wCAAwC,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,QAAQ,CAqBtH"}

package/dist/ts/ts/Conversion/Study.js

@@ -1,9 +1,10 @@
 import { class_type } from '../../node_modules/@fable-org/fable-library-ts/Reflection.js';
-import { some, value, unwrap } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
+import { BaseTypes_warnIfTitleEmpty_Z2FC25A28, BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
+import { some, value, unwrap, defaultArg } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
 import { compose, dateModifiedKey, tryDecompose } from './DateTime.js';
 import { tryFind } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
 import { Comment$ } from '../Core/Comment.js';
-import { Option_fromSeq, ResizeArray_map, Option_fromValueWithDefault, ResizeArray_append } from '../Core/Helper/Collections.js';
+import { Option_fromSeq, ResizeArray_map, ResizeArray_filter, ResizeArray_append, Option_fromValueWithDefault } from '../Core/Helper/Collections.js';
 import { ScholarlyArticleConversion_composeScholarlyArticle_D324A6D, ScholarlyArticleConversion_decomposeScholarlyArticle_Z6839B9E8 } from './ScholarlyArticle.js';
 import { ArcStudy } from '../Core/ArcTypes.js';
 import { PersonConversion_composePerson_2B0BECCC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
@@ -12,7 +13,6 @@ import { ArcTables } from '../Core/Table/ArcTables.js';
 import { Datamap } from '../Core/Datamap.js';
 import { DatamapConversion_composeFragmentDescriptors_Z892BFC3, DatamapConversion_decomposeFragmentDescriptors_Z6E59645F } from './Datamap.js';
 import { AssayConversion_getDataFilesFromProcesses_6BABD1B0 } from './Assay.js';
-import { BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
 import { LDDataset } from '../ROCrate/LDTypes/Dataset.js';
 import { ofSeq } from '../../node_modules/@fable-org/fable-library-ts/List.js';
 
@@ -25,12 +25,13 @@ function StudyConversion_$reflection() {
 }
 function StudyConversion_composeStudy_ZFE0E38E(study, fs) {
   let i = void 0, collection = void 0;
+  BaseTypes_warnIfTitleEmpty_Z2FC25A28("Study", study.Identifier, study.Title);
   let dateCreated;
   const option_1 = study.SubmissionDate;
-  dateCreated = option_1 != null ? some(compose(value(option_1))) : void 0;
+  dateCreated = option_1 != null ? some(compose(option_1)) : void 0;
   let datePublished;
   const option_3 = study.PublicReleaseDate;
-  datePublished = option_3 != null ? some(compose(value(option_3))) : void 0;
+  datePublished = option_3 != null ? some(compose(option_3)) : void 0;
   let dateModified;
   const option_7 = tryFind((c) => {
     if (c.Name != null) {
@@ -40,26 +41,35 @@ function StudyConversion_composeStudy_ZFE0E38E(study, fs) {
     }
   }, study.Comments);
   if (option_7 != null) {
-    const c_1 = value(option_7);
+    const c_1 = option_7;
     const option_5 = c_1.Value;
-    dateModified = option_5 != null ? some(compose(value(option_5))) : void 0;
+    dateModified = option_5 != null ? some(compose(option_5)) : void 0;
   } else {
     dateModified = void 0;
   }
   const publications = Option_fromSeq(ResizeArray_map(ScholarlyArticleConversion_composeScholarlyArticle_D324A6D, study.Publications));
   let persons;
   const option_9 = study.Investigation;
-  persons = option_9 != null ? (i = value(option_9), i.GetAllPersons()) : void 0;
+  persons = option_9 != null ? (i = option_9, i.GetAllPersons()) : void 0;
   const creators = Option_fromSeq(ResizeArray_map((c_2) => PersonConversion_composePerson_2B0BECCC(c_2, unwrap(persons)), study.Contacts));
   const processSequence = Option_fromSeq((collection = ARCtrl_ArcTables__ArcTables_GetProcesses_5E660E5C(new ArcTables(study.Tables), void 0, study.Identifier, unwrap(fs)), Array.from(collection)));
   let fragmentDescriptors;
   const option_11 = study.Datamap;
-  fragmentDescriptors = option_11 != null ? DatamapConversion_composeFragmentDescriptors_Z892BFC3(value(option_11)) : void 0;
+  fragmentDescriptors = option_11 != null ? DatamapConversion_composeFragmentDescriptors_Z892BFC3(option_11) : void 0;
   let dataFiles;
   const option_13 = processSequence;
-  dataFiles = option_13 != null ? AssayConversion_getDataFilesFromProcesses_6BABD1B0(value(option_13), unwrap(fragmentDescriptors)) : void 0;
+  dataFiles = option_13 != null ? AssayConversion_getDataFilesFromProcesses_6BABD1B0(option_13, unwrap(fragmentDescriptors)) : void 0;
+  let registeredAssays;
+  const matchValue = study.Investigation;
+  if (matchValue == null) {
+    registeredAssays = [];
+  } else {
+    const inv = matchValue;
+    registeredAssays = ResizeArray_map((a_3) => LDDataset.createAssay(a_3), ResizeArray_filter((assayIdentifier) => inv.ContainsAssay(assayIdentifier), study.RegisteredAssayIdentifiers));
+  }
+  const hasParts = Option_fromSeq(ResizeArray_append(defaultArg(dataFiles, []), registeredAssays));
   const comments = Option_fromSeq(ResizeArray_map(BaseTypes_composeComment_Z13201A7E, study.Comments));
-  return LDDataset.createStudy(study.Identifier, void 0, unwrap(creators), dateCreated, datePublished, dateModified, unwrap(study.Description), unwrap(dataFiles), unwrap(study.Title), unwrap(publications), unwrap(fragmentDescriptors), unwrap(comments), void 0, unwrap(processSequence));
+  return LDDataset.createStudy(study.Identifier, void 0, unwrap(creators), dateCreated, datePublished, dateModified, unwrap(study.Description), unwrap(hasParts), unwrap(study.Title), unwrap(publications), unwrap(fragmentDescriptors), unwrap(comments), void 0, unwrap(processSequence));
 }
 function StudyConversion_decomposeStudy_Z6839B9E8(study, graph, context) {
   let dateCreated;
@@ -77,10 +87,11 @@ function StudyConversion_decomposeStudy_Z6839B9E8(study, graph, context) {
   const v = DatamapConversion_decomposeFragmentDescriptors_Z6E59645F(LDDataset.getVariableMeasuredAsFragmentDescriptors(study, unwrap(graph), unwrap(context)), unwrap(graph), unwrap(context));
   datamap = Option_fromValueWithDefault(Datamap.init(), v);
   const tables = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586(ofSeq(LDDataset.getAboutsAsLabProcess(study, unwrap(graph), unwrap(context))), unwrap(graph), unwrap(context));
+  const registeredAssayIdentifiers = ResizeArray_map((d_5) => LDDataset.getIdentifierAsString(d_5, unwrap(context)), ResizeArray_filter((d_4) => LDDataset.validateAssay(d_4, unwrap(context)), LDDataset.getHasPartsAsDataset(study, unwrap(graph), unwrap(context))));
   let comments;
   const c_2 = ResizeArray_map((c_1) => BaseTypes_decomposeComment_Z2F770004(c_1, unwrap(context)), LDDataset.getComments(study, unwrap(graph), unwrap(context)));
   comments = dateModified != null ? ResizeArray_append(c_2, [new Comment$(dateModifiedKey, value(dateModified))]) : c_2;
-  return ArcStudy.create(LDDataset.getIdentifierAsString(study, unwrap(context)), unwrap(LDDataset.tryGetNameAsString(study, unwrap(context))), unwrap(LDDataset.tryGetDescriptionAsString(study, unwrap(context))), unwrap(dateCreated), unwrap(datePublished), publications, creators, void 0, tables.Tables, unwrap(datamap), void 0, comments);
+  return ArcStudy.create(LDDataset.getIdentifierAsString(study, unwrap(context)), unwrap(LDDataset.tryGetNameAsString(study, unwrap(context))), unwrap(LDDataset.tryGetDescriptionAsString(study, unwrap(context))), unwrap(dateCreated), unwrap(datePublished), publications, creators, void 0, tables.Tables, unwrap(datamap), registeredAssayIdentifiers, comments);
 }
 
 export { StudyConversion, StudyConversion_$reflection, StudyConversion_composeStudy_ZFE0E38E, StudyConversion_decomposeStudy_Z6839B9E8 };

package/dist/ts/ts/Conversion/Table.js

@@ -2,7 +2,7 @@ import { fold, zip, toList, delay, map } from '../../node_modules/@fable-org/fab
 import { LDLabProtocol } from '../ROCrate/LDTypes/LabProtocol.js';
 import { BaseTypes_composeComponent, BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_decomposeComponent_Z2F770004 } from './Basic.js';
 import { ResizeArray_appendSingleton, ResizeArray_singleton } from '../Core/Helper/Collections.js';
-import { unwrap, some, value } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
+import { unwrap, some } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
 import { ArcTable } from '../Core/Table/ArcTable.js';
 import { getEnumerator, disposeSafe, safeHash, equals } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
 import { ARCtrl_ROCrate_LDNode__LDNode_TryGetColumnIndex } from './ColumnIndex.js';
@@ -137,10 +137,10 @@ function ARCtrl_ArcTable__ArcTable_fromProtocol_Static_Z6839B9E8(p, graph, conte
   } finally {
     disposeSafe(enumerator);
   }
-  option_1 = LDLabProtocol.tryGetDescriptionAsString(p, unwrap(context)), option_1 != null ? some((d = value(option_1), t.AddProtocolDescriptionColumn(ResizeArray_singleton(d)))) : void 0;
-  option_3 = LDLabProtocol.tryGetVersionAsString(p, unwrap(context)), option_3 != null ? some((d_1 = value(option_3), t.AddProtocolVersionColumn(ResizeArray_singleton(d_1)))) : void 0;
-  option_5 = ProcessConversion_tryGetProtocolType_Z6839B9E8(p, void 0, unwrap(context)), option_5 != null ? some((d_2 = value(option_5), t.AddProtocolTypeColumn(ResizeArray_singleton(d_2)))) : void 0;
-  option_7 = LDLabProtocol.tryGetUrl(p, unwrap(context)), option_7 != null ? some((d_3 = value(option_7), t.AddProtocolUriColumn(ResizeArray_singleton(d_3)))) : void 0;
+  option_1 = LDLabProtocol.tryGetDescriptionAsString(p, unwrap(context)), option_1 != null ? some((d = option_1, t.AddProtocolDescriptionColumn(ResizeArray_singleton(d)))) : void 0;
+  option_3 = LDLabProtocol.tryGetVersionAsString(p, unwrap(context)), option_3 != null ? some((d_1 = option_3, t.AddProtocolVersionColumn(ResizeArray_singleton(d_1)))) : void 0;
+  option_5 = ProcessConversion_tryGetProtocolType_Z6839B9E8(p, void 0, unwrap(context)), option_5 != null ? some((d_2 = option_5, t.AddProtocolTypeColumn(ResizeArray_singleton(d_2)))) : void 0;
+  option_7 = LDLabProtocol.tryGetUrl(p, unwrap(context)), option_7 != null ? some((d_3 = option_7, t.AddProtocolUriColumn(ResizeArray_singleton(d_3)))) : void 0;
   t.AddProtocolNameColumn(ResizeArray_singleton(name));
   return t;
 }

package/dist/ts/ts/Conversion/Workflow.d.ts

@@ -5,16 +5,16 @@ import { Option } from '@fable-org/fable-library-ts/Option.ts';
 import { LDGraph, LDNode } from '../ROCrate/LDObject.ts';
 import { CWLInput, InputBinding } from '../CWL/Inputs.ts';
 import { LDContext } from '../ROCrate/LDContext.ts';
-import { CWLOutput, OutputBinding } from '../CWL/Outputs.ts';
+import { CWLOutput, OutputBinding, OutputGlob_$union } from '../CWL/Outputs.ts';
 import { Component } from '../Core/Process/Component.ts';
 import { CWLProcessingUnit_$union } from '../CWL/CWLProcessingUnit.ts';
 import { WorkflowStep, WorkflowStepRun_$union } from '../CWL/WorkflowSteps.ts';
+import { CWLWorkflowDescription } from '../CWL/WorkflowDescription.ts';
+import { FileSystem } from '../FileSystem/FileSystem.ts';
 import { CWLToolDescription } from '../CWL/ToolDescription.ts';
 import { CWLExpressionToolDescription } from '../CWL/ExpressionToolDescription.ts';
 import { CWLOperationDescription } from '../CWL/OperationDescription.ts';
-import { CWLWorkflowDescription } from '../CWL/WorkflowDescription.ts';
 import { ArcWorkflow } from '../Core/ArcTypes.ts';
-import { FileSystem } from '../FileSystem/FileSystem.ts';
 export declare class WorkflowConversion {
     constructor();
 }
@@ -25,7 +25,7 @@ export declare function WorkflowConversion_composeFormalParamInputIdentifiers(pr
 export declare function WorkflowConversion_composeFormalParameterFromInput_Z7A02DED7(inp: CWLInput, workflowName?: string, runName?: string): LDNode;
 export declare function WorkflowConversion_decomposeInputBindings_1AAAE9A5(identifiers: LDNode[], context?: LDContext): Option<InputBinding>;
 export declare function WorkflowConversion_decomposeInputFromFormalParameter_2664C4B8(inp: LDNode, context?: LDContext, graph?: LDGraph): CWLInput;
-export declare function WorkflowConversion_composeFormalParameterOutputIdentifiers_6DFDD678(glob: Option<string>): Option<LDNode[]>;
+export declare function WorkflowConversion_composeFormalParameterOutputIdentifiers_A254C9D(glob: Option<OutputGlob_$union>): Option<LDNode[]>;
 export declare function WorkflowConversion_composeFormalParameterFromOutput_Z25C7EC80(out: CWLOutput, workflowName?: string, runName?: string): LDNode;
 export declare function WorkflowConversion_decomposeOutputBindings_1AAAE9A5(identifiers: LDNode[], context?: LDContext): OutputBinding;
 export declare function WorkflowConversion_decomposeOutputFromFormalParameter_2664C4B8(outp: LDNode, context?: LDContext, graph?: LDGraph): CWLOutput;
@@ -42,14 +42,38 @@ export declare function WorkflowConversion_get_expressionToolDescriptionTypeName
 export declare function WorkflowConversion_get_operationDescriptionTypeName(): string;
 /**
  * Converts a workflow step run payload to a storable dataset identifier.
- * String runs preserve the path, while inline runs are mapped to stable inline markers.
+ * A run that names a file in a folder of the ARC is resolved against the folder of the CWL file and written as a path
+ * from the root of the crate with a leading "./", like the ids of the files in the crate. Any other run that names a
+ * file is written as it is. Inline runs are mapped to stable inline markers. A process whose class is a directive has
+ * no path and no marker, so it has no identifier.
  */
-export declare function WorkflowConversion_runToIdentifier_Z4EBA8CB1(run: WorkflowStepRun_$union): string;
+export declare function WorkflowConversion_runToIdentifier_Z4E98F2C(cwlFilePath: string, run: WorkflowStepRun_$union): Option<string>;
+/**
+ * Converts the identifier of a workflow step back to its run as the CWL file writes it. An identifier that is a path
+ * from the root of the crate into a folder of the ARC becomes the path relative to the folder of the CWL file. Any
+ * other identifier stays as it is: an inline marker, or a run as written, which is what older crates hold.
+ */
+export declare function WorkflowConversion_identifierToRun_Z384F8060(cwlFilePath: string, identifier: string): string;
 /**
  * Attempts to decode a CWL processing unit from an LDGraph node addressed by a resolved run path.
  * Supports direct WorkflowProtocol nodes and ARC Workflow/Run datasets that reference a main workflow protocol.
  */
 export declare function WorkflowConversion_tryDecodeProcessingUnitFromGraph_Z5AC69418(resolvedRunPath: string, graph?: LDGraph, context?: LDContext): Option<CWLProcessingUnit_$union>;
+/**
+ * Returns the local files that a CWL file needs, as paths from the root of the ARC. These are the run of every step
+ * that names a file, the target of every $import, $include and $mixin directive and the location or path of every
+ * File literal, each resolved against the folder of the CWL file that holds it. A Directory literal adds every file
+ * under its directory. A file that a step runs adds the files that it needs in turn, when the step holds the process
+ * that its run resolved to. References with a URI scheme, absolute paths, paths outside the ARC and paths that are
+ * not in the file system are left out. Each CWL file is visited once, so a cycle of references ends.
+ */
+export declare function WorkflowConversion_getReferencedFilePaths_589B7F6(cwlFilePath: string, processingUnit: CWLProcessingUnit_$union, fs: FileSystem): string[];
+/**
+ * The File entities of the local files that a CWL file needs, which the dataset of its workflow or run holds as
+ * parts. A file that is one of the given parts of the dataset is left out, so it stays one part. The files come in
+ * the order of getReferencedFilePaths.
+ */
+export declare function WorkflowConversion_composeReferencedFiles_Z7F3BB4EE(cwlFilePath: string, processingUnit: CWLProcessingUnit_$union, fs: FileSystem, parts: Iterable<LDNode>): LDNode[];
 export declare function WorkflowConversion_composeWorkflowProtocolFromToolDescription_7B8357DA(filePath: string, workflow: CWLToolDescription, workflowName?: string, runName?: string): LDNode;
 export declare function WorkflowConversion_decomposeWorkflowProtocolToToolDescription_2664C4B8(protocol: LDNode, context?: LDContext, graph?: LDGraph): CWLToolDescription;
 /**
@@ -64,11 +88,17 @@ export declare function WorkflowConversion_composeWorkflowProtocolFromExpression
 export declare function WorkflowConversion_decomposeWorkflowProtocolToExpressionToolDescription_2664C4B8(protocol: LDNode, context?: LDContext, graph?: LDGraph): CWLExpressionToolDescription;
 export declare function WorkflowConversion_composeWorkflowProtocolFromOperationDescription_Z75DE0D49(filePath: string, operation: CWLOperationDescription, workflowName?: string, runName?: string): LDNode;
 export declare function WorkflowConversion_decomposeWorkflowProtocolToOperationDescription_2664C4B8(protocol: LDNode, context?: LDContext, graph?: LDGraph): CWLOperationDescription;
-export declare function WorkflowConversion_composeWorkflowStep_Z35AB9E5D<$a>(step: WorkflowStep, workflowID: $a): LDNode;
+/**
+ * A step with an id is named by it. A step without an id has no name in the crate and gets an identifier from its
+ * position, which names the node in the crate only and never becomes an id of the step. The file path is the path of
+ * the CWL file that holds the step, from the root of the ARC.
+ */
+export declare function WorkflowConversion_composeWorkflowStep_4F8B7302(step: WorkflowStep, filePath: string, position?: int32): LDNode;
 export declare function WorkflowConversion_composeWorkflowProtocolFromWorkflow_Z6FBB852F(filePath: string, workflow: CWLWorkflowDescription, workflowName?: string, runName?: string): LDNode;
 /**
  * Converts a workflow-step LD node into a CWL WorkflowStep.
- * Can optionally resolve run string references into inline CWL processing units via the graph.
+ * Can optionally resolve the run reference of the step via the graph. The step keeps the reference as its run and
+ * holds the resolved process in its ResolvedRun.
  */
 export declare function WorkflowConversion_decomposeWorkflowStep_77DD0449(step: LDNode, workflowFilePath?: string, resolveRunReferences?: boolean, context?: LDContext, graph?: LDGraph): WorkflowStep;
 /**
@@ -86,6 +116,15 @@ export declare function WorkflowConversion_composeWorkflowProtocolFromProcessing
  * Uses <c>additionalType</c> to discriminate Workflow, ExpressionTool, and Operation descriptions.
  */
 export declare function WorkflowConversion_decomposeWorkflowProtocolToProcessingUnit_ZB11202F(protocol: LDNode, resolveRunReferences?: boolean, context?: LDContext, graph?: LDGraph): CWLProcessingUnit_$union;
-export declare function WorkflowConversion_composeWorkflow_42450E6E(workflow: ArcWorkflow, fs?: FileSystem): LDNode;
+/**
+ * The dataset of a workflow. Its workflow is created at the given time, in UTC, and now when none is given. A time of
+ * kind Unspecified counts as local time, as in .NET. With a file system, the local files that the CWL file of the
+ * workflow needs are parts of the dataset.
+ */
+export declare function WorkflowConversion_composeWorkflow_38B68F62(workflow: ArcWorkflow, fs?: FileSystem, dateCreated?: Date): LDNode;
+/**
+ * Reads a workflow from its dataset. The crate does not hold the CWL file of the workflow, so the workflow comes
+ * back with no CWL description.
+ */
 export declare function WorkflowConversion_decomposeWorkflow_Z6839B9E8(workflow: LDNode, graph?: LDGraph, context?: LDContext): ArcWorkflow;
 //# sourceMappingURL=Workflow.d.ts.map

package/dist/ts/ts/Conversion/Workflow.d.ts.map

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