@nfdi4plants/arctrl 3.0.0-beta.9 → 3.0.0

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

@@ -0,0 +1,79 @@
+import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
+import { value, bind, defaultArg, unwrap, map } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { tryFromString, toString } from './DateTime.js';
+import { now } from '../../node_modules/@fable-org/fable-library-js/Date.js';
+import { Option_fromSeq, ResizeArray_map, ResizeArray_choose, ResizeArray_filter } from '../Core/Helper/Collections.js';
+import { ScholarlyArticleConversion_composeScholarlyArticle_D324A6D, ScholarlyArticleConversion_decomposeScholarlyArticle_Z6839B9E8 } from './ScholarlyArticle.js';
+import { PersonConversion_composePerson_Z64D846DC, PersonConversion_decomposePerson_Z6839B9E8 } from './Person.js';
+import { BaseTypes_composeComment_Z13201A7E, BaseTypes_decomposeComment_Z2F770004 } from './Basic.js';
+import { toList, delay, append } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+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 { LDDataset } from '../ROCrate/LDTypes/Dataset.js';
+
+class InvestigationConversion {
+  constructor() {
+  }
+}
+function InvestigationConversion_$reflection() {
+  return class_type("ARCtrl.Conversion.InvestigationConversion", void 0, InvestigationConversion);
+}
+function InvestigationConversion_composeInvestigation_Z284BC0AC(investigation, fs, ignoreBrokenWR) {
+  let collection;
+  let name;
+  const matchValue = investigation.Title;
+  if (matchValue == null) {
+    throw new Error("Investigation must have a title");
+  } else {
+    name = value(matchValue);
+  }
+  const dateCreated = bind(tryFromString, investigation.SubmissionDate);
+  const datePublished = defaultArg(bind(tryFromString, investigation.PublicReleaseDate), now());
+  const publications = Option_fromSeq(ResizeArray_map(ScholarlyArticleConversion_composeScholarlyArticle_D324A6D, investigation.Publications));
+  const creators = Option_fromSeq(ResizeArray_map(PersonConversion_composePerson_Z64D846DC, investigation.Contacts));
+  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_2) => StudyConversion_composeStudy_ZFE0E38E(s_2, unwrap(fs)), investigation.Studies), delay(() => append(ResizeArray_choose((w) => {
+    try {
+      return WorkflowConversion_composeWorkflow_42450E6E(w, unwrap(fs));
+    } catch (matchValue_1) {
+      if (ignoreBrokenWR != null && value(ignoreBrokenWR)) {
+        return void 0;
+      } else {
+        throw matchValue_1;
+      }
+    }
+  }, investigation.Workflows), delay(() => ResizeArray_choose((r) => {
+    try {
+      return RunConversion_composeRun_Z8CC08AC(r, unwrap(fs));
+    } catch (matchValue_2) {
+      if (ignoreBrokenWR != null && value(ignoreBrokenWR)) {
+        return void 0;
+      } else {
+        throw matchValue_2;
+      }
+    }
+  }, investigation.Runs))))))))), Array.from(collection)));
+  const mentions = Option_fromSeq([]);
+  return LDDataset.createInvestigation(investigation.Identifier, name, void 0, unwrap(creators), unwrap(dateCreated), datePublished, void 0, unwrap(investigation.Description), unwrap(hasParts), unwrap(publications), unwrap(comments), unwrap(mentions));
+}
+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);
+  const dateCreated = map(toString, LDDataset.tryGetDateCreatedAsDateTime(investigation, unwrap(context)));
+  const datePublished = map(toString, LDDataset.tryGetDatePublishedAsDateTime(investigation, unwrap(context)));
+  const publications = ResizeArray_map((p) => ScholarlyArticleConversion_decomposeScholarlyArticle_Z6839B9E8(p, unwrap(graph), unwrap(context)), LDDataset.getCitations(investigation, unwrap(graph), unwrap(context)));
+  const creators = ResizeArray_map((c) => PersonConversion_decomposePerson_Z6839B9E8(c, unwrap(graph), unwrap(context)), LDDataset.getCreators(investigation, unwrap(graph), unwrap(context)));
+  const datasets = LDDataset.getHasPartsAsDataset(investigation, unwrap(graph), unwrap(context));
+  const studies = ResizeArray_map((d_3) => StudyConversion_decomposeStudy_Z6839B9E8(d_3, unwrap(graph), unwrap(context)), ResizeArray_filter((d_2) => LDDataset.validateStudy(d_2, unwrap(context)), datasets));
+  const assays = ResizeArray_map((d_5) => AssayConversion_decomposeAssay_Z6839B9E8(d_5, unwrap(graph), unwrap(context)), ResizeArray_filter((d_4) => LDDataset.validateAssay(d_4, unwrap(context)), datasets));
+  const workflows = ResizeArray_map((d_7) => WorkflowConversion_decomposeWorkflow_Z6839B9E8(d_7, unwrap(graph), unwrap(context)), ResizeArray_filter((d_6) => LDDataset.validateARCWorkflow(d_6, unwrap(graph), unwrap(context)), datasets));
+  const runs = ResizeArray_map((d_9) => RunConversion_decomposeRun_Z6839B9E8(d_9, unwrap(graph), unwrap(context)), ResizeArray_filter((d_8) => LDDataset.validateARCRun(d_8, unwrap(context)), datasets));
+  const comments = ResizeArray_map((c_1) => BaseTypes_decomposeComment_Z2F770004(c_1, unwrap(context)), LDDataset.getComments(investigation, unwrap(graph), unwrap(context)));
+  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);
+}
+
+export { InvestigationConversion, InvestigationConversion_$reflection, InvestigationConversion_composeInvestigation_Z284BC0AC, InvestigationConversion_decomposeInvestigation_Z6839B9E8 };

package/dist/ts/ts/Conversion/Person.d.ts

@@ -0,0 +1,16 @@
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { LDGraph, LDNode } from '../ROCrate/LDObject.js';
+import { LDContext } from '../ROCrate/LDContext.js';
+import { Person } from '../Core/Person.js';
+export declare class PersonConversion {
+    constructor();
+}
+export declare function PersonConversion_$reflection(): TypeInfo;
+export declare function PersonConversion_get_orcidKey(): string;
+export declare function PersonConversion_composeAffiliation_Z721C83C5(affiliation: string): LDNode;
+export declare function PersonConversion_decomposeAffiliation_Z2F770004(affiliation: LDNode, context?: LDContext): string;
+export declare function PersonConversion_composeAddress_Z721C83C5(address: string): any;
+export declare function PersonConversion_decomposeAddress_4E60E31B(address: any): string;
+export declare function PersonConversion_composePerson_Z64D846DC(person: Person): LDNode;
+export declare function PersonConversion_decomposePerson_Z6839B9E8(person: LDNode, graph?: LDGraph, context?: LDContext): Person;
+//# sourceMappingURL=Person.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"Person.d.ts","sourceRoot":"","sources":["../../../../src/ARCtrl/ts/Conversion/Person.ts"],"names":[],"mappings":"AAAA,OAAO,EAAc,QAAQ,EAAE,MAAM,2CAA2C,CAAC;AAIjF,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAC;AAMzD,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AAOpD,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAG3C,qBAAa,gBAAgB;;CAG5B;AAED,wBAAgB,4BAA4B,IAAI,QAAQ,CAEvD;AAED,wBAAgB,6BAA6B,IAAI,MAAM,CAEtD;AAED,wBAAgB,6CAA6C,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,CAczF;AAED,wBAAgB,+CAA+C,CAAC,WAAW,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAOhH;AAED,wBAAgB,yCAAyC,CAAC,OAAO,EAAE,MAAM,GAAG,GAAG,CAW9E;AAED,wBAAgB,0CAA0C,CAAC,OAAO,EAAE,GAAG,GAAG,MAAM,CAU/E;AAED,wBAAgB,wCAAwC,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAc/E;AAED,wBAAgB,0CAA0C,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,SAAS,GAAG,MAAM,CAevH"}

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

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+import { class_type } from '../../node_modules/@fable-org/fable-library-js/Reflection.js';
+import { LDOrganization } from '../ROCrate/LDTypes/Organization.js';
+import { fromString } from '../fable_modules/Thoth.Json.JavaScript.0.4.1/Decode.fs.js';
+import { decoder, encoder } from '../Json/ROCrate/LDNode.js';
+import { LDNode } from '../ROCrate/LDObject.js';
+import { toText, printf } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { isEmpty, filter } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { unwrap, value, map } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { toString } from '../fable_modules/Thoth.Json.JavaScript.0.4.1/Encode.fs.js';
+import { Option_fromSeq, ResizeArray_map } from '../Core/Helper/Collections.js';
+import { BaseTypes_composeDefinedTerm_ZDED3A0F, BaseTypes_decomposeDefinedTerm_Z2F770004 } from './Basic.js';
+import { toString as toString$1 } from '../../node_modules/@fable-org/fable-library-js/Types.js';
+import { Comment$ } from '../Core/Comment.js';
+import { LDPerson } from '../ROCrate/LDTypes/Person.js';
+import { Person } from '../Core/Person.js';
+import { tryGetOrcidNumber } from '../Core/Helper/ORCID.js';
+
+class PersonConversion {
+  constructor() {
+  }
+}
+function PersonConversion_$reflection() {
+  return class_type("ARCtrl.Conversion.PersonConversion", void 0, PersonConversion);
+}
+function PersonConversion_get_orcidKey() {
+  return "ORCID";
+}
+function PersonConversion_composeAffiliation_Z721C83C5(affiliation) {
+  let arg;
+  try {
+    const matchValue = fromString(decoder, affiliation);
+    if (matchValue.tag === /* Error */
+    1) {
+      throw new Error((arg = matchValue.fields[0], toText(printf("Error decoding string: %O"))(arg)));
+    } else {
+      return matchValue.fields[0];
+    }
+  } catch (matchValue_1) {
+    return LDOrganization.create(affiliation);
+  }
+}
+function PersonConversion_decomposeAffiliation_Z2F770004(affiliation, context) {
+  if (isEmpty(filter((n) => n !== LDOrganization.name, affiliation.GetPropertyNames(unwrap(context))))) {
+    return LDOrganization.getNameAsString(affiliation, unwrap(context));
+  } else {
+    return toString(0, encoder(affiliation));
+  }
+}
+function PersonConversion_composeAddress_Z721C83C5(address) {
+  let matchValue;
+  try {
+    return matchValue = fromString(decoder, address), matchValue.tag === /* Error */
+    1 ? (() => {
+      let arg;
+      throw new Error((arg = matchValue.fields[0], toText(printf("Error decoding string: %O"))(arg)));
+    })() : matchValue.fields[0];
+  } catch (matchValue_1) {
+    return address;
+  }
+}
+function PersonConversion_decomposeAddress_4E60E31B(address) {
+  if (typeof address === "string") {
+    return address;
+  } else if (address instanceof LDNode) {
+    return toString(0, encoder(address));
+  } else {
+    throw new Error("Address must be a string or a Json.LDNode");
+  }
+}
+function PersonConversion_composePerson_Z64D846DC(person) {
+  let givenName;
+  const matchValue = person.FirstName;
+  if (matchValue == null) {
+    throw new Error("Person must have a given name");
+  } else {
+    givenName = value(matchValue);
+  }
+  const jobTitles = Option_fromSeq(ResizeArray_map(BaseTypes_composeDefinedTerm_ZDED3A0F, person.Roles));
+  const disambiguatingDescriptions = Option_fromSeq(ResizeArray_map(toString$1, person.Comments));
+  const address_1 = map(PersonConversion_composeAddress_Z721C83C5, person.Address);
+  const affiliation_1 = map(PersonConversion_composeAffiliation_Z721C83C5, person.Affiliation);
+  return LDPerson.create(givenName, unwrap(person.ORCID), void 0, unwrap(affiliation_1), unwrap(person.EMail), unwrap(person.LastName), void 0, unwrap(jobTitles), unwrap(person.MidInitials), address_1, unwrap(disambiguatingDescriptions), unwrap(person.Fax), unwrap(person.Phone));
+}
+function PersonConversion_decomposePerson_Z6839B9E8(person, graph, context) {
+  const orcid = tryGetOrcidNumber(person.Id);
+  let address;
+  const matchValue = LDPerson.tryGetAddressAsString(person, unwrap(context));
+  if (matchValue == null) {
+    const matchValue_1 = LDPerson.tryGetAddressAsPostalAddress(person, unwrap(graph), unwrap(context));
+    address = matchValue_1 == null ? void 0 : PersonConversion_decomposeAddress_4E60E31B(value(matchValue_1));
+  } else {
+    address = value(matchValue);
+  }
+  const roles = ResizeArray_map((r) => BaseTypes_decomposeDefinedTerm_Z2F770004(r, unwrap(context)), LDPerson.getJobTitlesAsDefinedTerm(person, unwrap(graph), unwrap(context)));
+  const comments = ResizeArray_map((s_1) => Comment$.fromString(s_1), LDPerson.getDisambiguatingDescriptionsAsString(person, unwrap(context)));
+  const affiliation = map((a_3) => PersonConversion_decomposeAffiliation_Z2F770004(a_3, unwrap(context)), LDPerson.tryGetAffiliation(person, unwrap(graph), unwrap(context)));
+  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);
+}
+
+export { PersonConversion, PersonConversion_$reflection, PersonConversion_composeAddress_Z721C83C5, PersonConversion_composeAffiliation_Z721C83C5, PersonConversion_composePerson_Z64D846DC, PersonConversion_decomposeAddress_4E60E31B, PersonConversion_decomposeAffiliation_Z2F770004, PersonConversion_decomposePerson_Z6839B9E8, PersonConversion_get_orcidKey };

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

@@ -0,0 +1,84 @@
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { LDGraph, LDNode } from '../ROCrate/LDObject.js';
+import { OntologyAnnotation } from '../Core/OntologyAnnotation.js';
+import { LDContext } from '../ROCrate/LDContext.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { CompositeCell_$union } from '../Core/Table/CompositeCell.js';
+import { ArcTable } from '../Core/Table/ArcTable.js';
+import { CompositeHeader_$union } from '../Core/Table/CompositeHeader.js';
+import { FileSystem } from '../FileSystem/FileSystem.js';
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+export declare class ProcessConversion {
+    constructor();
+}
+export declare function ProcessConversion_$reflection(): TypeInfo;
+export declare function ProcessConversion_tryGetProtocolType_Z6839B9E8(pv: LDNode, graph?: LDGraph, context?: LDContext): Option<OntologyAnnotation>;
+export declare function ProcessConversion_composeProcessName(processNameRoot: string, i: int32): string;
+export declare function ProcessConversion_decomposeProcessName_Z721C83C5(name: string): [string, Option<int32>];
+/**
+ * If the given headers depict a component, returns a function for parsing the values of the matrix to the values of this component
+ */
+export declare function ProcessConversion_tryComponentGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
+/**
+ * If the given headers depict a parameter, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessConversion_tryParameterGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
+/**
+ * If the given headers depict a factor, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessConversion_tryFactorGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
+/**
+ * If the given headers depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessConversion_tryCharacteristicGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
+/**
+ * If the given headers depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessConversion_tryGetProtocolTypeGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
+/**
+ * If the given headers depict a protocolREF, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessConversion_tryGetProtocolREFGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
+/**
+ * If the given headers depict a protocolDescription, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessConversion_tryGetProtocolDescriptionGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
+/**
+ * If the given headers depict a protocolURI, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessConversion_tryGetProtocolURIGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
+/**
+ * If the given headers depict a protocolVersion, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessConversion_tryGetProtocolVersionGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
+/**
+ * If the given headers depict an input, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessConversion_tryGetInputGetter(generalI: int32, header: CompositeHeader_$union, fs: Option<FileSystem>): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
+/**
+ * If the given headers depict an output, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessConversion_tryGetOutputGetter(generalI: int32, header: CompositeHeader_$union, fs: Option<FileSystem>): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
+/**
+ * If the given headers depict a comment, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessConversion_tryGetCommentGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
+export declare function ProcessConversion_tryGetPerformerGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => LDNode))>;
+/**
+ * Given the header sequence of an ArcTable, returns a function for parsing each row of the table to a process
+ */
+export declare function ProcessConversion_getProcessGetter(assayName: Option<string>, studyName: Option<string>, processNameRoot: string, headers: Iterable<CompositeHeader_$union>, fs: Option<FileSystem>): ((arg0: ArcTable) => ((arg0: int32) => LDNode));
+/**
+ * Groups processes by their name, or by the name of the protocol they execute
+ *
+ * Process names are taken from the Worksheet name and numbered: SheetName_1, SheetName_2, etc.
+ *
+ * This function decomposes this name into a root name and a number, and groups processes by root name.
+ */
+export declare function ProcessConversion_groupProcesses_Z27F0B586(processes: FSharpList<LDNode>, graph?: LDGraph, context?: LDContext): FSharpList<[string, FSharpList<LDNode>]>;
+/**
+ * Merges processes with the same name, protocol and param values
+ */
+export declare function ProcessConversion_processToRows_Z6839B9E8(p: LDNode, graph?: LDGraph, context?: LDContext): FSharpList<[CompositeHeader_$union, CompositeCell_$union]>[];
+//# sourceMappingURL=Process.d.ts.map

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

@@ -0,0 +1 @@
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