@nfdi4plants/arctrl 3.2.2 → 3.3.0

package/dist/ts/ts/Conversion/ColumnIndex.js

@@ -5,10 +5,8 @@ import { int32ToString } from '../../node_modules/@fable-org/fable-library-ts/Ut
 
 function tryInt(str) {
   let matchValue;
-  let outArg = 0;
-  matchValue = [tryParse(str, 511, false, 32, new FSharpRef(() => outArg | 0, (v) => {
-    outArg = v | 0;
-  })), outArg];
+  const cell = new FSharpRef(0);
+  matchValue = [tryParse(str, 511, false, 32, cell), cell.contents];
   if (matchValue[0]) {
     return matchValue[1];
   } else {

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

@@ -1 +1 @@
-{"version":3,"file":"DateTime.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/DateTime.ts"],"names":[],"mappings":"AAOA,OAAO,EAAoB,MAAM,EAAE,MAAM,uCAAuC,CAAC;AAIjF,eAAO,MAAM,eAAe,iBAAiB,CAAC;AAE9C,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,CAWrD;AAED,wBAAgB,QAAQ,CAAC,CAAC,EAAE,IAAI,GAAG,MAAM,CAExC;AAED,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,GAAG,CAQtC;AAED,wBAAgB,YAAY,CAAC,CAAC,EAAE,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,CAUnD"}
+{"version":3,"file":"DateTime.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/DateTime.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,MAAM,EAAE,MAAM,uCAAuC,CAAC;AAI/D,eAAO,MAAM,eAAe,iBAAiB,CAAC;AAE9C,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,CAWrD;AAED,wBAAgB,QAAQ,CAAC,CAAC,EAAE,IAAI,GAAG,MAAM,CAExC;AAED,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,GAAG,CAQtC;AAED,wBAAgB,YAAY,CAAC,CAAC,EAAE,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,CAUnD"}

package/dist/ts/ts/Conversion/DateTime.js

@@ -2,7 +2,6 @@ import { fromString } from '../fable_modules/Thoth.Json.JavaScript.0.5.0/Decode.
 import { Decode_datetime } from '../Json/Decode.js';
 import { Exception } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
 import { toText, printf } from '../../node_modules/@fable-org/fable-library-ts/String.js';
-import { value } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
 import { toString as toString$1 } from '../fable_modules/Thoth.Json.JavaScript.0.5.0/Encode.fs.js';
 import { dateTime } from '../Json/Encode.js';
 
@@ -27,7 +26,7 @@ function compose(s) {
   if (matchValue == null) {
     return s;
   } else {
-    return value(matchValue);
+    return matchValue;
   }
 }
 function tryDecompose(d) {

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

@@ -1 +1 @@
-{"version":3,"file":"Investigation.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Investigation.ts"],"names":[],"mappings":"AACA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAUjF,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAKzD,OAAO,EAAE,gBAAgB,EAA2C,MAAM,qBAAqB,CAAC;AAMhG,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AACzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAEpD,qBAAa,uBAAuB;;CAGnC;AAED,wBAAgB,mCAAmC,IAAI,QAAQ,CAE9D;AAED,wBAAgB,sDAAsD,CAAC,aAAa,EAAE,gBAAgB,EAAE,EAAE,CAAC,EAAE,UAAU,EAAE,cAAc,CAAC,EAAE,OAAO,GAAG,MAAM,CA6DzJ;AAED,wBAAgB,wDAAwD,CAAC,aAAa,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,gBAAgB,CAwBtJ"}
+{"version":3,"file":"Investigation.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Investigation.ts"],"names":[],"mappings":"AACA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAUjF,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAKzD,OAAO,EAAE,gBAAgB,EAA2C,MAAM,qBAAqB,CAAC;AAMhG,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AACzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAEpD,qBAAa,uBAAuB;;CAGnC;AAED,wBAAgB,mCAAmC,IAAI,QAAQ,CAE9D;AAED,wBAAgB,sDAAsD,CAAC,aAAa,EAAE,gBAAgB,EAAE,EAAE,CAAC,EAAE,UAAU,EAAE,cAAc,CAAC,EAAE,OAAO,GAAG,MAAM,CA6DzJ;AAED,wBAAgB,wDAAwD,CAAC,aAAa,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,gBAAgB,CAyBtJ"}

package/dist/ts/ts/Conversion/Investigation.js

@@ -1,9 +1,9 @@
 import { class_type } from '../../node_modules/@fable-org/fable-library-ts/Reflection.js';
-import { value, some, defaultArg, unwrap } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
-import { Exception } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
+import { some, defaultArg, value, unwrap } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
+import { Exception, equals } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
 import { compose, dateModifiedKey, tryDecompose } from './DateTime.js';
 import { now } from '../../node_modules/@fable-org/fable-library-ts/Date.js';
-import { tryFind, toList, delay, append } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
+import { tryFind, toList, delay, append, exists } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
 import { Comment$ } from '../Core/Comment.js';
 import { Option_fromSeq, ResizeArray_map, ResizeArray_choose, ResizeArray_filter, ResizeArray_append } from '../Core/Helper/Collections.js';
 import { ScholarlyArticleConversion_composeScholarlyArticle_D324A6D, ScholarlyArticleConversion_decomposeScholarlyArticle_Z6839B9E8 } from './ScholarlyArticle.js';
@@ -12,8 +12,8 @@ import { BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeComment_Z2F77000
 import { AssayConversion_composeAssay_Z5C53FD5C, AssayConversion_decomposeAssay_Z6839B9E8 } from './Assay.js';
 import { ArcInvestigation } from '../Core/ArcTypes.js';
 import { StudyConversion_composeStudy_ZFE0E38E, StudyConversion_decomposeStudy_Z6839B9E8 } from './Study.js';
-import { WorkflowConversion_composeWorkflow_42450E6E, WorkflowConversion_decomposeWorkflow_Z6839B9E8 } from './Workflow.js';
-import { RunConversion_composeRun_Z8CC08AC, RunConversion_decomposeRun_Z6839B9E8 } from './Run.js';
+import { WorkflowConversion_composeWorkflow_38B68F62, WorkflowConversion_decomposeWorkflow_Z6839B9E8 } from './Workflow.js';
+import { RunConversion_composeRun_3F79BD1, RunConversion_decomposeRun_Z6839B9E8 } from './Run.js';
 import { LDDataset } from '../ROCrate/LDTypes/Dataset.js';
 
 class InvestigationConversion {
@@ -30,12 +30,12 @@ function InvestigationConversion_composeInvestigation_Z284BC0AC(investigation, f
   if (matchValue == null) {
     throw new Exception("Investigation must have a title");
   } else {
-    name = value(matchValue);
+    name = matchValue;
   }
   let dateCreated;
   const option_1 = investigation.SubmissionDate;
-  dateCreated = option_1 != null ? some(compose(value(option_1))) : void 0;
-  const datePublished = defaultArg((option_3 = investigation.PublicReleaseDate, option_3 != null ? some(compose(value(option_3))) : void 0), now());
+  dateCreated = option_1 != null ? some(compose(option_1)) : void 0;
+  const datePublished = defaultArg((option_3 = investigation.PublicReleaseDate, option_3 != null ? some(compose(option_3)) : void 0), now());
   let dateModified;
   const option_8 = tryFind((c) => {
     if (c.Name != null) {
@@ -45,9 +45,9 @@ function InvestigationConversion_composeInvestigation_Z284BC0AC(investigation, f
     }
   }, investigation.Comments);
   if (option_8 != null) {
-    const c_1 = value(option_8);
+    const c_1 = option_8;
     const option_6 = c_1.Value;
-    dateModified = option_6 != null ? some(compose(value(option_6))) : void 0;
+    dateModified = option_6 != null ? some(compose(option_6)) : void 0;
   } else {
     dateModified = void 0;
   }
@@ -56,7 +56,7 @@ function InvestigationConversion_composeInvestigation_Z284BC0AC(investigation, f
   const comments = Option_fromSeq(ResizeArray_map(BaseTypes_composeComment_Z13201A7E, investigation.Comments));
   const hasParts = Option_fromSeq((collection = toList(delay(() => append(ResizeArray_map((a_3) => AssayConversion_composeAssay_Z5C53FD5C(a_3, unwrap(fs)), investigation.Assays), delay(() => append(ResizeArray_map((s_3) => StudyConversion_composeStudy_ZFE0E38E(s_3, unwrap(fs)), investigation.Studies), delay(() => append(ResizeArray_choose((w) => {
     try {
-      return WorkflowConversion_composeWorkflow_42450E6E(w, unwrap(fs));
+      return WorkflowConversion_composeWorkflow_38B68F62(w, unwrap(fs));
     } catch (matchValue_1) {
       if (ignoreBrokenWR != null && value(ignoreBrokenWR)) {
         return void 0;
@@ -66,7 +66,7 @@ function InvestigationConversion_composeInvestigation_Z284BC0AC(investigation, f
     }
   }, investigation.Workflows), delay(() => ResizeArray_choose((r) => {
     try {
-      return RunConversion_composeRun_Z8CC08AC(r, unwrap(fs));
+      return RunConversion_composeRun_3F79BD1(r, unwrap(fs));
     } catch (matchValue_2) {
       if (ignoreBrokenWR != null && value(ignoreBrokenWR)) {
         return void 0;
@@ -81,7 +81,7 @@ function InvestigationConversion_composeInvestigation_Z284BC0AC(investigation, f
 function InvestigationConversion_decomposeInvestigation_Z6839B9E8(investigation, graph, context) {
   let title;
   const matchValue = LDDataset.tryGetNameAsString(investigation, unwrap(context));
-  title = matchValue == null ? LDDataset.tryGetHeadlineAsString(investigation, unwrap(context)) : value(matchValue);
+  title = matchValue == null ? LDDataset.tryGetHeadlineAsString(investigation, unwrap(context)) : matchValue;
   let dateCreated;
   const option_1 = LDDataset.tryGetDateCreated(investigation, unwrap(context));
   dateCreated = option_1 != null ? tryDecompose(value(option_1)) : void 0;
@@ -100,7 +100,8 @@ function InvestigationConversion_decomposeInvestigation_Z6839B9E8(investigation,
   const runs = ResizeArray_map((d_10) => RunConversion_decomposeRun_Z6839B9E8(d_10, unwrap(graph), unwrap(context)), ResizeArray_filter((d_9) => LDDataset.validateARCRun(d_9, unwrap(context)), datasets));
   let comments;
   const c_2 = ResizeArray_map((c_1) => BaseTypes_decomposeComment_Z2F770004(c_1, unwrap(context)), LDDataset.getComments(investigation, unwrap(graph), unwrap(context)));
-  comments = dateModified != null ? ResizeArray_append(c_2, [new Comment$(dateModifiedKey, value(dateModified))]) : c_2;
+  const hasDateModifiedComment = exists((c_3) => equals(c_3.Name, dateModifiedKey), c_2);
+  comments = dateModified != null && !hasDateModifiedComment ? ResizeArray_append(c_2, [new Comment$(dateModifiedKey, value(dateModified))]) : c_2;
   return ArcInvestigation.create(LDDataset.getIdentifierAsString(investigation, unwrap(context)), unwrap(title), unwrap(LDDataset.tryGetDescriptionAsString(investigation, unwrap(context))), unwrap(dateCreated), unwrap(datePublished), void 0, publications, creators, assays, studies, workflows, runs, void 0, comments);
 }
 

package/dist/ts/ts/Conversion/Person.js

@@ -6,7 +6,7 @@ import { LDNode } from '../ROCrate/LDObject.js';
 import { Exception, equals } from '../../node_modules/@fable-org/fable-library-ts/Util.js';
 import { toText, printf, toFail } from '../../node_modules/@fable-org/fable-library-ts/String.js';
 import { isEmpty, filter, tryFind } from '../../node_modules/@fable-org/fable-library-ts/Seq.js';
-import { unwrap, value, some } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
+import { unwrap, some } from '../../node_modules/@fable-org/fable-library-ts/Option.js';
 import { toString } from '../fable_modules/Thoth.Json.JavaScript.0.5.0/Encode.fs.js';
 import { Person } from '../Core/Person.js';
 import { tryGetOrcidNumber } from '../Core/Helper/ORCID.js';
@@ -81,34 +81,34 @@ function PersonConversion_composePerson_2B0BECCC(person, persons) {
         } else {
           return false;
         }
-      }, value(persons));
+      }, persons);
       if (option_1 != null) {
-        const p_1 = value(option_1);
+        const p_1 = option_1;
         orcid = p_1.ORCID;
       } else {
         orcid = void 0;
       }
     }
   } else {
-    const o = value(matchValue);
+    const o = matchValue;
     const matchValue_1 = tryGetOrcidNumber(o);
-    orcid = matchValue_1 == null ? toFail(printf("Invalid ORCID: %s"))(o) : value(matchValue_1);
+    orcid = matchValue_1 == null ? toFail(printf("Invalid ORCID: %s"))(o) : matchValue_1;
   }
   let givenName;
   const matchValue_2 = person.FirstName;
   if (matchValue_2 == null) {
     throw new Exception("Person must have a given name");
   } else {
-    givenName = value(matchValue_2);
+    givenName = matchValue_2;
   }
   const jobTitles = Option_fromSeq(ResizeArray_map(BaseTypes_composeDefinedTerm_ZDED3A0F, person.Roles));
   const disambiguatingDescriptions = Option_fromSeq(ResizeArray_map(toString$1, person.Comments));
   let address_1;
   const option_3 = person.Address;
-  address_1 = option_3 != null ? some(PersonConversion_composeAddress_Z721C83C5(value(option_3))) : void 0;
+  address_1 = option_3 != null ? some(PersonConversion_composeAddress_Z721C83C5(option_3)) : void 0;
   let affiliation_1;
   const option_5 = person.Affiliation;
-  affiliation_1 = option_5 != null ? PersonConversion_composeAffiliation_Z721C83C5(value(option_5)) : void 0;
+  affiliation_1 = option_5 != null ? PersonConversion_composeAffiliation_Z721C83C5(option_5) : void 0;
   return LDPerson.create(givenName, unwrap(orcid), void 0, unwrap(affiliation_1), unwrap(person.EMail), unwrap(person.LastName), void 0, unwrap(jobTitles), unwrap(person.MidInitials), address_1, unwrap(disambiguatingDescriptions), unwrap(person.Fax), unwrap(person.Phone));
 }
 function PersonConversion_decomposePerson_Z6839B9E8(person, graph, context) {
@@ -117,15 +117,15 @@ function PersonConversion_decomposePerson_Z6839B9E8(person, graph, context) {
   const matchValue = LDPerson.tryGetAddressAsString(person, unwrap(context));
   if (matchValue == null) {
     const matchValue_1 = LDPerson.tryGetAddressAsPostalAddress(person, unwrap(graph), unwrap(context));
-    address = matchValue_1 == null ? void 0 : PersonConversion_decomposeAddress_4E60E31B(value(matchValue_1));
+    address = matchValue_1 == null ? void 0 : PersonConversion_decomposeAddress_4E60E31B(matchValue_1);
   } else {
-    address = value(matchValue);
+    address = matchValue;
   }
   const roles = ResizeArray_map((r) => BaseTypes_decomposeDefinedTerm_Z2F770004(r, unwrap(context)), LDPerson.getJobTitlesAsDefinedTerm(person, unwrap(graph), unwrap(context)));
   const comments = ResizeArray_map((s_1) => Comment$.fromString(s_1), LDPerson.getDisambiguatingDescriptionsAsString(person, unwrap(context)));
   let affiliation;
   const option_1 = LDPerson.tryGetAffiliation(person, unwrap(graph), unwrap(context));
-  affiliation = option_1 != null ? PersonConversion_decomposeAffiliation_Z2F770004(value(option_1), unwrap(context)) : void 0;
+  affiliation = option_1 != null ? PersonConversion_decomposeAffiliation_Z2F770004(option_1, unwrap(context)) : void 0;
   return Person.create(unwrap(orcid), unwrap(LDPerson.tryGetFamilyNameAsString(person, unwrap(context))), LDPerson.getGivenNameAsString(person, unwrap(context)), unwrap(LDPerson.tryGetAdditionalNameAsString(person, unwrap(context))), unwrap(LDPerson.tryGetEmailAsString(person, unwrap(context))), unwrap(LDPerson.tryGetTelephoneAsString(person, unwrap(context))), unwrap(LDPerson.tryGetFaxNumberAsString(person, unwrap(context))), unwrap(address), unwrap(affiliation), roles, comments);
 }
 

package/dist/ts/ts/Conversion/Process.d.ts

@@ -75,9 +75,11 @@ export declare function ProcessConversion_getProcessGetter(assayName: Option<str
 /**
  * Groups processes by their name, or by the name of the protocol they execute
  *
- * Process names are taken from the Worksheet name and numbered: SheetName_1, SheetName_2, etc.
+ * Process names are taken from the Worksheet name and numbered from 0: SheetName_0, SheetName_1, etc. Every row has a suffix.
  *
- * This function decomposes this name into a root name and a number, and groups processes by root name.
+ * This function decomposes the name into a root name and a number, and groups processes by root name.
+ * A name without a number that fits in an Int32 is the group key as it is, if it is not blank.
+ * Otherwise the key is the protocol name, then a blank name, then the protocol @id, then a new missing identifier.
  */
 export declare function ProcessConversion_groupProcesses_Z27F0B586(processes: FSharpList<LDNode>, graph?: LDGraph, context?: LDContext): FSharpList<[string, FSharpList<LDNode>]>;
 /**

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

@@ -1 +1 @@
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