@nfdi4plants/arctrl 3.0.0-beta.3 → 3.0.0-beta.4

package/dist/ts/ts/Json/Study.js

@@ -0,0 +1,326 @@
+import { Option_fromValueWithDefault, ResizeArray_map } from '../Core/Helper/Collections.js';
+import { defaultArgWith, map, value, defaultArg, unwrap, bind } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { ofArray, map as map$1, empty, choose, singleton, tryFind } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { ArcStudy, ArcAssay } from '../Core/ArcTypes.js';
+import { tryInclude, tryIncludeSeq, tryIncludeList } from './Encode.js';
+import { ISAJson_decoder as ISAJson_decoder$2, decoder as decoder$1, ROCrate_decoder as ROCrate_decoder$2, encoder as encoder$1, ROCrate_encoder as ROCrate_encoder$1, ISAJson_encoder as ISAJson_encoder$2 } from './Publication.js';
+import { ISAJson_decoder as ISAJson_decoder$5, decoder as decoder$2, ROCrate_decoder as ROCrate_decoder$3, encoder as encoder$2, ROCrate_encoder as ROCrate_encoder$2, ISAJson_encoder as ISAJson_encoder$3 } from './Person.js';
+import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_decoder, OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_encoder, OntologyAnnotation_ROCrate_encoderDefinedTerm, OntologyAnnotation_ISAJson_encoder } from './OntologyAnnotation.js';
+import { decoder as decoder$3, decoderCompressed as decoderCompressed$1, encoder as encoder$3, encoderCompressed as encoderCompressed$1 } from './Table/ArcTable.js';
+import { decoder as decoder$4, decoderCompressed as decoderCompressed$2, encoder as encoder$4, encoderCompressed as encoderCompressed$2 } from './DataMap/DataMap.js';
+import { ISAJson_decoder as ISAJson_decoder$3, decoder as decoder$5, ROCrate_decoder as ROCrate_decoder$4, encoder as encoder$5, ROCrate_encoder as ROCrate_encoder$6, ISAJson_encoder as ISAJson_encoder$6 } from './Comment.js';
+import { isEmpty, map as map$2 } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { string, list, resizeArray, object } from '../fable_modules/Thoth.Json.Core.0.7.0/Decode.fs.js';
+import { getEnumerator, disposeSafe } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { replace } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { createMissingIdentifier, Study_tryIdentifierFromFileName, Study_tryFileNameFromIdentifier, Study_fileNameFromIdentifier } from '../Core/Helper/Identifier.js';
+import { ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D, Person_getSourceAssayIdentifiersFromComments, Person_removeSourceAssayComments, ARCtrl_ArcTables__ArcTables_GetProcesses, Person_setSourceAssayComment } from '../Core/Conversion.js';
+import { list as list$1 } from '../fable_modules/Thoth.Json.Core.0.7.0/Encode.fs.js';
+import { ISAJson_decoder as ISAJson_decoder$1, ROCrate_decoder as ROCrate_decoder$1, ROCrate_encoder as ROCrate_encoder$3, ISAJson_encoder as ISAJson_encoder$4 } from './Process/Process.js';
+import { ISAJson_decoder as ISAJson_decoder$4, ROCrate_decoder as ROCrate_decoder$5, ROCrate_encoder as ROCrate_encoder$4, ISAJson_encoder as ISAJson_encoder$5 } from './Assay.js';
+import { ROCrate_encoder as ROCrate_encoder$5 } from './Data.js';
+import { getData, getUnits, getFactors, getCharacteristics, getProtocols } from '../Core/Process/ProcessSequence.js';
+import { context_jsonvalue } from './context/rocrate/isa_study_context.js';
+import { encoder as encoder$6 } from './Process/Factor.js';
+import { encoder as encoder$7 } from './Process/MaterialAttribute.js';
+import { encoder as encoder$8 } from './Process/StudyMaterials.js';
+import { ISAJson_encoder as ISAJson_encoder$1 } from './Process/Protocol.js';
+import { encode } from './IDTable.js';
+import { Decode_objectNoAdditionalProperties } from './Decode.js';
+
+function Helper_getAssayInformation(assays, study) {
+  if (assays != null) {
+    return ResizeArray_map((assayId) => defaultArg(tryFind((a) => a.Identifier === assayId, value(assays)), ArcAssay.init(assayId)), study.RegisteredAssayIdentifiers);
+  } else {
+    return study.GetRegisteredAssaysOrIdentifier();
+  }
+}
+function encoder(study) {
+  let value;
+  const values_1 = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = study.Identifier, {
+    Encode(helpers) {
+      return helpers.encodeString(value);
+    }
+  })], tryInclude("Title", (value_1) => ({
+    Encode(helpers_1) {
+      return helpers_1.encodeString(value_1);
+    }
+  }), study.Title), tryInclude("Description", (value_3) => ({
+    Encode(helpers_2) {
+      return helpers_2.encodeString(value_3);
+    }
+  }), study.Description), tryInclude("SubmissionDate", (value_5) => ({
+    Encode(helpers_3) {
+      return helpers_3.encodeString(value_5);
+    }
+  }), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => ({
+    Encode(helpers_4) {
+      return helpers_4.encodeString(value_7);
+    }
+  }), study.PublicReleaseDate), tryIncludeSeq("Publications", encoder$1, study.Publications), tryIncludeSeq("Contacts", encoder$2, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", encoder$3, study.Tables), tryInclude("DataMap", encoder$4, study.DataMap), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => ({
+    Encode(helpers_5) {
+      return helpers_5.encodeString(value_9);
+    }
+  }), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", encoder$5, study.Comments)]));
+  return {
+    Encode(helpers_6) {
+      const arg = map$2((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_6)], values_1);
+      return helpers_6.encodeObject(arg);
+    }
+  };
+}
+const decoder = object((get$) => {
+  let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, objectArg_9, arg_21, objectArg_10, arg_23, objectArg_11;
+  return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = resizeArray(decoder$1), objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11))), unwrap((arg_13 = resizeArray(decoder$2), objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13))), unwrap((arg_15 = resizeArray(OntologyAnnotation_decoder), objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15))), unwrap((arg_17 = resizeArray(decoder$3), objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17))), unwrap((objectArg_9 = get$.Optional, objectArg_9.Field("DataMap", decoder$4))), unwrap((arg_21 = resizeArray(string), objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredAssayIdentifiers", arg_21))), unwrap((arg_23 = resizeArray(decoder$5), objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23))));
+});
+function encoderCompressed(stringTable, oaTable, cellTable, study) {
+  let value;
+  const values_1 = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = study.Identifier, {
+    Encode(helpers) {
+      return helpers.encodeString(value);
+    }
+  })], tryInclude("Title", (value_1) => ({
+    Encode(helpers_1) {
+      return helpers_1.encodeString(value_1);
+    }
+  }), study.Title), tryInclude("Description", (value_3) => ({
+    Encode(helpers_2) {
+      return helpers_2.encodeString(value_3);
+    }
+  }), study.Description), tryInclude("SubmissionDate", (value_5) => ({
+    Encode(helpers_3) {
+      return helpers_3.encodeString(value_5);
+    }
+  }), study.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => ({
+    Encode(helpers_4) {
+      return helpers_4.encodeString(value_7);
+    }
+  }), study.PublicReleaseDate), tryIncludeSeq("Publications", encoder$1, study.Publications), tryIncludeSeq("Contacts", encoder$2, study.Contacts), tryIncludeSeq("StudyDesignDescriptors", OntologyAnnotation_encoder, study.StudyDesignDescriptors), tryIncludeSeq("Tables", (table) => encoderCompressed$1(stringTable, oaTable, cellTable, table), study.Tables), tryInclude("DataMap", (dm) => encoderCompressed$2(stringTable, oaTable, cellTable, dm), study.DataMap), tryIncludeSeq("RegisteredAssayIdentifiers", (value_9) => ({
+    Encode(helpers_5) {
+      return helpers_5.encodeString(value_9);
+    }
+  }), study.RegisteredAssayIdentifiers), tryIncludeSeq("Comments", encoder$5, study.Comments)]));
+  return {
+    Encode(helpers_6) {
+      const arg = map$2((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_6)], values_1);
+      return helpers_6.encodeObject(arg);
+    }
+  };
+}
+function decoderCompressed(stringTable, oaTable, cellTable) {
+  return object((get$) => {
+    let objectArg, objectArg_1, objectArg_2, objectArg_3, objectArg_4, arg_11, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9, arg_21, objectArg_10, arg_23, objectArg_11;
+    return new ArcStudy((objectArg = get$.Required, objectArg.Field("Identifier", string)), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("Title", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("Description", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("SubmissionDate", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("PublicReleaseDate", string))), unwrap((arg_11 = resizeArray(decoder$1), objectArg_5 = get$.Optional, objectArg_5.Field("Publications", arg_11))), unwrap((arg_13 = resizeArray(decoder$2), objectArg_6 = get$.Optional, objectArg_6.Field("Contacts", arg_13))), unwrap((arg_15 = resizeArray(OntologyAnnotation_decoder), objectArg_7 = get$.Optional, objectArg_7.Field("StudyDesignDescriptors", arg_15))), unwrap((arg_17 = resizeArray(decoderCompressed$1(stringTable, oaTable, cellTable)), objectArg_8 = get$.Optional, objectArg_8.Field("Tables", arg_17))), unwrap((arg_19 = decoderCompressed$2(), objectArg_9 = get$.Optional, objectArg_9.Field("DataMap", arg_19))), unwrap((arg_21 = resizeArray(string), objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredAssayIdentifiers", arg_21))), unwrap((arg_23 = resizeArray(decoder$5), objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23))));
+  });
+}
+function ROCrate_genID(a) {
+  const matchValue = a.Identifier;
+  if (matchValue === "") {
+    return "#EmptyStudy";
+  } else {
+    return `studies/${replace(matchValue, " ", "_")}/`;
+  }
+}
+function ROCrate_encoder(assays, s) {
+  let value, value_3, studyName, studyName_1;
+  const fileName = Study_tryFileNameFromIdentifier(s.Identifier);
+  const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(s);
+  const assays_1 = Helper_getAssayInformation(assays, s);
+  const values_1 = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value = ROCrate_genID(s), {
+    Encode(helpers) {
+      return helpers.encodeString(value);
+    }
+  })], ["@type", list$1(singleton({
+    Encode(helpers_1) {
+      return helpers_1.encodeString("Study");
+    }
+  }))], ["additionalType", {
+    Encode(helpers_2) {
+      return helpers_2.encodeString("Study");
+    }
+  }], ["identifier", (value_3 = s.Identifier, {
+    Encode(helpers_3) {
+      return helpers_3.encodeString(value_3);
+    }
+  })], tryInclude("filename", (value_4) => ({
+    Encode(helpers_4) {
+      return helpers_4.encodeString(value_4);
+    }
+  }), fileName), tryInclude("title", (value_6) => ({
+    Encode(helpers_5) {
+      return helpers_5.encodeString(value_6);
+    }
+  }), s.Title), tryInclude("description", (value_8) => ({
+    Encode(helpers_6) {
+      return helpers_6.encodeString(value_8);
+    }
+  }), s.Description), tryIncludeSeq("studyDesignDescriptors", OntologyAnnotation_ROCrate_encoderDefinedTerm, s.StudyDesignDescriptors), tryInclude("submissionDate", (value_10) => ({
+    Encode(helpers_7) {
+      return helpers_7.encodeString(value_10);
+    }
+  }), s.SubmissionDate), tryInclude("publicReleaseDate", (value_12) => ({
+    Encode(helpers_8) {
+      return helpers_8.encodeString(value_12);
+    }
+  }), s.PublicReleaseDate), tryIncludeSeq("publications", ROCrate_encoder$1, s.Publications), tryIncludeSeq("people", ROCrate_encoder$2, s.Contacts), tryIncludeList("processSequence", (studyName = s.Identifier, (oa_3) => ROCrate_encoder$3(studyName, void 0, oa_3)), processes), tryIncludeSeq("assays", (studyName_1 = s.Identifier, (a_1) => ROCrate_encoder$4(studyName_1, a_1)), assays_1), tryIncludeList("dataFiles", ROCrate_encoder$5, getData(processes)), tryIncludeSeq("comments", ROCrate_encoder$6, s.Comments), ["@context", context_jsonvalue]]));
+  return {
+    Encode(helpers_9) {
+      const arg = map$2((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_9)], values_1);
+      return helpers_9.encodeObject(arg);
+    }
+  };
+}
+const ROCrate_decoder = object((get$) => {
+  let objectArg, arg_6, objectArg_2, objectArg_3, objectArg_4, objectArg_5, objectArg_6, arg_16, objectArg_7, arg_18, objectArg_8, arg_20, objectArg_9, arg_22, objectArg_10;
+  const identifier = defaultArg(bind(Study_tryIdentifierFromFileName, (objectArg = get$.Optional, objectArg.Field("filename", string))), createMissingIdentifier());
+  let assays;
+  const arg_3 = list(ROCrate_decoder$5);
+  const objectArg_1 = get$.Optional;
+  assays = objectArg_1.Field("assays", arg_3);
+  const assayIdentifiers = map((arg_4) => {
+    const collection = map$1((a) => a.Identifier, arg_4);
+    return Array.from(collection);
+  }, assays);
+  const tables = map((ps) => ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(ps).Tables, (arg_6 = list(ROCrate_decoder$1), objectArg_2 = get$.Optional, objectArg_2.Field("processSequence", arg_6)));
+  return [new ArcStudy(identifier, unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("title", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("description", string))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("submissionDate", string))), unwrap((objectArg_6 = get$.Optional, objectArg_6.Field("publicReleaseDate", string))), unwrap((arg_16 = resizeArray(ROCrate_decoder$2), objectArg_7 = get$.Optional, objectArg_7.Field("publications", arg_16))), unwrap((arg_18 = resizeArray(ROCrate_decoder$3), objectArg_8 = get$.Optional, objectArg_8.Field("people", arg_18))), unwrap((arg_20 = resizeArray(OntologyAnnotation_ROCrate_decoderDefinedTerm), objectArg_9 = get$.Optional, objectArg_9.Field("studyDesignDescriptors", arg_20))), unwrap(tables), void 0, unwrap(assayIdentifiers), unwrap((arg_22 = resizeArray(ROCrate_decoder$4), objectArg_10 = get$.Optional, objectArg_10.Field("comments", arg_22)))), defaultArg(assays, empty())];
+});
+function ISAJson_encoder(idMap, assays, s) {
+  const f = (s_1) => {
+    let studyName, value_6, value_8, studyName_1, studyName_2;
+    const study = s_1.Copy(true);
+    const fileName = Study_fileNameFromIdentifier(study.Identifier);
+    let assays_1;
+    const n = [];
+    let enumerator = getEnumerator(Helper_getAssayInformation(assays, study));
+    try {
+      while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+        const a = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+        const assay = a.Copy();
+        let enumerator_1 = getEnumerator(assay.Performers);
+        try {
+          while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
+            const person_1 = Person_setSourceAssayComment(enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"](), assay.Identifier);
+            void study.Contacts.push(person_1);
+          }
+        } finally {
+          disposeSafe(enumerator_1);
+        }
+        assay.Performers = [];
+        void n.push(assay);
+      }
+    } finally {
+      disposeSafe(enumerator);
+    }
+    assays_1 = n;
+    const processes = ARCtrl_ArcTables__ArcTables_GetProcesses(study);
+    const encodedUnits = tryIncludeList("unitCategories", (oa) => OntologyAnnotation_ISAJson_encoder(idMap, oa), getUnits(processes));
+    const encodedFactors = tryIncludeList("factors", (value_1) => encoder$6(idMap, value_1), getFactors(processes));
+    const encodedCharacteristics = tryIncludeList("characteristicCategories", (value_3) => encoder$7(idMap, value_3), getCharacteristics(processes));
+    const encodedMaterials = tryInclude("materials", (ps) => encoder$8(idMap, ps), Option_fromValueWithDefault(empty(), processes));
+    let encodedProtocols;
+    const value_5 = getProtocols(processes);
+    encodedProtocols = tryIncludeList("protocols", (studyName = s_1.Identifier, (oa_1) => ISAJson_encoder$1(studyName, void 0, void 0, idMap, oa_1)), value_5);
+    const values_1 = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value_6 = ROCrate_genID(study), {
+      Encode(helpers) {
+        return helpers.encodeString(value_6);
+      }
+    })], ["filename", {
+      Encode(helpers_1) {
+        return helpers_1.encodeString(fileName);
+      }
+    }], ["identifier", (value_8 = study.Identifier, {
+      Encode(helpers_2) {
+        return helpers_2.encodeString(value_8);
+      }
+    })], tryInclude("title", (value_9) => ({
+      Encode(helpers_3) {
+        return helpers_3.encodeString(value_9);
+      }
+    }), study.Title), tryInclude("description", (value_11) => ({
+      Encode(helpers_4) {
+        return helpers_4.encodeString(value_11);
+      }
+    }), study.Description), tryInclude("submissionDate", (value_13) => ({
+      Encode(helpers_5) {
+        return helpers_5.encodeString(value_13);
+      }
+    }), study.SubmissionDate), tryInclude("publicReleaseDate", (value_15) => ({
+      Encode(helpers_6) {
+        return helpers_6.encodeString(value_15);
+      }
+    }), study.PublicReleaseDate), tryIncludeSeq("publications", (oa_2) => ISAJson_encoder$2(idMap, oa_2), study.Publications), tryIncludeSeq("people", (person_2) => ISAJson_encoder$3(idMap, person_2), study.Contacts), tryIncludeSeq("studyDesignDescriptors", (oa_3) => OntologyAnnotation_ISAJson_encoder(idMap, oa_3), study.StudyDesignDescriptors), encodedProtocols, encodedMaterials, tryIncludeList("processSequence", (studyName_1 = s_1.Identifier, (oa_4) => ISAJson_encoder$4(studyName_1, void 0, idMap, oa_4)), processes), tryIncludeSeq("assays", (studyName_2 = s_1.Identifier, (a_2) => ISAJson_encoder$5(studyName_2, idMap, a_2)), assays_1), encodedFactors, encodedCharacteristics, encodedUnits, tryIncludeSeq("comments", (comment) => ISAJson_encoder$6(idMap, comment), study.Comments)]));
+    return {
+      Encode(helpers_7) {
+        const arg = map$2((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_7)], values_1);
+        return helpers_7.encodeObject(arg);
+      }
+    };
+  };
+  if (idMap != null) {
+    return encode(ROCrate_genID, f, s, value(idMap));
+  } else {
+    return f(s);
+  }
+}
+const ISAJson_allowedFields = ofArray(["@id", "filename", "identifier", "title", "description", "submissionDate", "publicReleaseDate", "publications", "people", "studyDesignDescriptors", "protocols", "materials", "assays", "factors", "characteristicCategories", "unitCategories", "processSequence", "comments", "@type", "@context"]);
+const ISAJson_decoder = Decode_objectNoAdditionalProperties(ISAJson_allowedFields, (get$) => {
+  let objectArg, arg_5, objectArg_2, objectArg_5, objectArg_6, objectArg_7, objectArg_8, arg_21, objectArg_9, arg_23, objectArg_10, arg_25, objectArg_11;
+  const identifier = defaultArgWith((objectArg = get$.Optional, objectArg.Field("identifier", string)), () => {
+    let objectArg_1;
+    return defaultArg(bind(Study_tryIdentifierFromFileName, (objectArg_1 = get$.Optional, objectArg_1.Field("filename", string))), createMissingIdentifier());
+  });
+  const tables = map((arg_6) => {
+    const a = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(arg_6);
+    return a.Tables;
+  }, (arg_5 = list(ISAJson_decoder$1), objectArg_2 = get$.Optional, objectArg_2.Field("processSequence", arg_5)));
+  let assays;
+  const arg_8 = list(ISAJson_decoder$4);
+  const objectArg_3 = get$.Optional;
+  assays = objectArg_3.Field("assays", arg_8);
+  let personsRaw;
+  const arg_10 = resizeArray(ISAJson_decoder$5);
+  const objectArg_4 = get$.Optional;
+  personsRaw = objectArg_4.Field("people", arg_10);
+  const persons = [];
+  if (personsRaw != null) {
+    let enumerator = getEnumerator(value(personsRaw));
+    try {
+      while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+        const person = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+        const sourceAssays = Person_getSourceAssayIdentifiersFromComments(person);
+        const enumerator_1 = getEnumerator(sourceAssays);
+        try {
+          while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
+            const assayIdentifier = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
+            const enumerator_2 = getEnumerator(value(assays));
+            try {
+              while (enumerator_2["System.Collections.IEnumerator.MoveNext"]()) {
+                const assay = enumerator_2["System.Collections.Generic.IEnumerator`1.get_Current"]();
+                if (assay.Identifier === assayIdentifier) {
+                  void assay.Performers.push(person);
+                }
+              }
+            } finally {
+              disposeSafe(enumerator_2);
+            }
+          }
+        } finally {
+          disposeSafe(enumerator_1);
+        }
+        person.Comments = Person_removeSourceAssayComments(person);
+        if (isEmpty(sourceAssays)) {
+          void persons.push(person);
+        }
+      }
+    } finally {
+      disposeSafe(enumerator);
+    }
+  }
+  const assayIdentifiers = map((arg_11) => {
+    const collection = map$1((a_1) => a_1.Identifier, arg_11);
+    return Array.from(collection);
+  }, assays);
+  return [new ArcStudy(identifier, unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("title", string))), unwrap((objectArg_6 = get$.Optional, objectArg_6.Field("description", string))), unwrap((objectArg_7 = get$.Optional, objectArg_7.Field("submissionDate", string))), unwrap((objectArg_8 = get$.Optional, objectArg_8.Field("publicReleaseDate", string))), unwrap((arg_21 = resizeArray(ISAJson_decoder$2), objectArg_9 = get$.Optional, objectArg_9.Field("publications", arg_21))), unwrap(persons.length === 0 ? void 0 : persons), unwrap((arg_23 = resizeArray(OntologyAnnotation_ISAJson_decoder), objectArg_10 = get$.Optional, objectArg_10.Field("studyDesignDescriptors", arg_23))), unwrap(tables), void 0, unwrap(assayIdentifiers), unwrap((arg_25 = resizeArray(ISAJson_decoder$3), objectArg_11 = get$.Optional, objectArg_11.Field("comments", arg_25)))), defaultArg(assays, empty())];
+});
+
+export { Helper_getAssayInformation, ISAJson_allowedFields, ISAJson_decoder, ISAJson_encoder, ROCrate_decoder, ROCrate_encoder, ROCrate_genID, decoder, decoderCompressed, encoder, encoderCompressed };

package/dist/ts/ts/Json/Table/ArcTable.d.ts

@@ -1,7 +1,7 @@
 import { IMap } from '@fable-org/fable-library-js/Util.js';
 import { int32 } from '@fable-org/fable-library-js/Int32.js';
 import { CompositeCell_$union } from '../../Core/Table/CompositeCell.js';
-import { Decoder$1, IEncodable } from '../../fable_modules/Thoth.Json.Core.0.4.0/Types.fs.js';
+import { Decoder$1, IEncodable } from '../../fable_modules/Thoth.Json.Core.0.7.0/Types.fs.js';
 import { ArcTable } from '../../Core/Table/ArcTable.js';
 import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
 export declare function encoder(table: ArcTable): IEncodable;

package/dist/ts/ts/Json/Table/ArcTable.js

@@ -0,0 +1,210 @@
+import { arrayHash, equalArrays, getEnumerator, disposeSafe, int32ToString, compareArrays } from '../../../node_modules/@fable-org/fable-library-js/Util.js';
+import { decoder as decoder$1, encoder as encoder$2 } from './CompositeCell.js';
+import { getItemFromDict } from '../../../node_modules/@fable-org/fable-library-js/MapUtil.js';
+import { ErrorReason$1_BadPrimitive } from '../../fable_modules/Thoth.Json.Core.0.7.0/Types.fs.js';
+import { toList, delay, map as map$1, append, singleton, empty as empty$2 } from '../../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { list as list$1 } from '../../fable_modules/Thoth.Json.Core.0.7.0/Encode.fs.js';
+import { decoder as decoder$2, encoder as encoder$1 } from './CompositeHeader.js';
+import { intDictionary } from '../Encode.js';
+import { ColumnValueRefs_Constant, ColumnValueRefs_Sparse, ensureCellHashInValueMap, ArcTableValues, Unchecked_setCellAt } from '../../Core/Table/ArcTableAux.js';
+import { ArcTable } from '../../Core/Table/ArcTable.js';
+import { map, object, list, map$0027, string, resizeArray, int, Helpers_prependPath, tuple2, array } from '../../fable_modules/Thoth.Json.Core.0.7.0/Decode.fs.js';
+import { defaultArg } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { ofArray, empty } from '../../../node_modules/@fable-org/fable-library-js/List.js';
+import { Dictionary } from '../../../node_modules/@fable-org/fable-library-js/MutableMap.js';
+import { empty as empty$1 } from '../../../node_modules/@fable-org/fable-library-js/Map.js';
+import { Decode_tryOneOf, Decode_intDictionary, Decode_dictionary } from '../Decode.js';
+import { FSharpResult$2_Ok, FSharpResult$2_Error } from '../../../node_modules/@fable-org/fable-library-js/Result.js';
+import { decodeCell, encodeCell } from './CellTable.js';
+import { item, fold, fill, setItem, iterateIndexed } from '../../../node_modules/@fable-org/fable-library-js/Array.js';
+import { decodeString, encodeString } from '../StringTable.js';
+
+function encoder(table) {
+  const valueMap = table.Values.ValueMap;
+  const cellEncoder = (hash) => encoder$2(getItemFromDict(valueMap, hash));
+  const values = toList(delay(() => {
+    let value;
+    return append(singleton(["name", (value = table.Name, {
+      Encode(helpers) {
+        return helpers.encodeString(value);
+      }
+    })]), delay(() => append(table.Headers.length !== 0 ? singleton(["headers", list$1(toList(delay(() => map$1(encoder$1, table.Headers))))]) : empty$2(), delay(() => table.Values.RowCount !== 0 ? append(singleton(["columns", intDictionary((col) => {
+      if (col.tag === /* Sparse */
+      1) {
+        return intDictionary(cellEncoder, col.fields[0]);
+      } else {
+        return cellEncoder(col.fields[0]);
+      }
+    }, table.Values.Columns)]), delay(() => {
+      let value_1;
+      return singleton(["rowCount", (value_1 = table.RowCount | 0, {
+        Encode(helpers_1) {
+          return helpers_1.encodeSignedIntegralNumber(value_1);
+        }
+      })]);
+    })) : empty$2()))));
+  }));
+  return {
+    Encode(helpers_2) {
+      const arg = map$1((tupledArg) => [tupledArg[0], tupledArg[1].Encode(helpers_2)], values);
+      return helpers_2.encodeObject(arg);
+    }
+  };
+}
+const decoderV2Deprecated = object((get$) => {
+  let arg_1, objectArg, arg_3, objectArg_1, objectArg_2;
+  let decodedHeader;
+  const collection = defaultArg((arg_1 = list(decoder$2), objectArg = get$.Optional, objectArg.Field("header", arg_1)), empty());
+  decodedHeader = Array.from(collection);
+  const decodedValues = new Dictionary(defaultArg((arg_3 = map$0027(tuple2(int, int), decoder$1), objectArg_1 = get$.Optional, objectArg_1.Field("values", arg_3)), empty$1({
+    Compare: compareArrays
+  })), {
+    Equals: equalArrays,
+    GetHashCode: arrayHash
+  });
+  const t = ArcTable.create((objectArg_2 = get$.Required, objectArg_2.Field("name", string)), decodedHeader, []);
+  let enumerator = getEnumerator(decodedValues);
+  try {
+    while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
+      const activePatternResult = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
+      t.SetCellAt(activePatternResult[0][0], activePatternResult[0][1], activePatternResult[1]);
+    }
+  } finally {
+    disposeSafe(enumerator);
+  }
+  return t;
+});
+const decoder = (() => {
+  const valueMap = /* @__PURE__ */ new Map([]);
+  const cellDecoder = map((cell) => ensureCellHashInValueMap(cell, valueMap), decoder$1);
+  const columnDecoder = Decode_tryOneOf(ofArray([map(ColumnValueRefs_Constant, cellDecoder), map(ColumnValueRefs_Sparse, Decode_intDictionary(cellDecoder))]));
+  const decoder_1 = object((get$) => {
+    let arg_1, objectArg, arg_3, objectArg_1, objectArg_2, objectArg_3;
+    const decodedHeader = defaultArg((arg_1 = resizeArray(decoder$2), objectArg = get$.Optional, objectArg.Field("headers", arg_1)), []);
+    const values = new ArcTableValues(defaultArg((arg_3 = Decode_dictionary(int, columnDecoder), objectArg_1 = get$.Optional, objectArg_1.Field("columns", arg_3)), /* @__PURE__ */ new Map([])), valueMap, defaultArg((objectArg_2 = get$.Optional, objectArg_2.Field("rowCount", int)), 0));
+    return ArcTable.fromArcTableValues((objectArg_3 = get$.Required, objectArg_3.Field("name", string)), decodedHeader, values);
+  });
+  return {
+    Decode(helper, column) {
+      return helper.hasProperty("values", column) ? decoderV2Deprecated.Decode(helper, column) : decoder_1.Decode(helper, column);
+    }
+  };
+})();
+function decoderCompressedColumn(cellTable, table, columnIndex) {
+  return {
+    Decode(helper, column) {
+      const matchValue = array(decodeCell(cellTable)).Decode(helper, column);
+      if (matchValue.tag === /* Error */
+      1) {
+        matchValue.fields[0];
+        const rangeDecoder = object((get$) => {
+          let from;
+          const objectArg = get$.Required;
+          from = objectArg.Field("f", int);
+          let to_;
+          const objectArg_1 = get$.Required;
+          to_ = objectArg_1.Field("t", int);
+          let value;
+          const arg_5 = decodeCell(cellTable);
+          const objectArg_2 = get$.Required;
+          value = objectArg_2.Field("v", arg_5);
+          for (let i = from; i <= to_; i++) {
+            Unchecked_setCellAt(columnIndex, i, value, table.Values);
+          }
+        });
+        const matchValue_1 = array(rangeDecoder).Decode(helper, column);
+        return matchValue_1.tag === /* Error */
+        1 ? FSharpResult$2_Error(matchValue_1.fields[0]) : FSharpResult$2_Ok(void 0);
+      } else {
+        iterateIndexed((r, cell) => {
+          Unchecked_setCellAt(columnIndex, r, cell, table.Values);
+        }, matchValue.fields[0]);
+        return FSharpResult$2_Ok(void 0);
+      }
+    }
+  };
+}
+function arrayi(decoderi) {
+  return {
+    Decode(helpers, value) {
+      if (helpers.isArray(value)) {
+        let i = -1;
+        const tokens = helpers.asArray(value);
+        return fold((acc, value_1) => {
+          let tupledArg;
+          i = i + 1 | 0;
+          if (acc.tag === /* Ok */
+          0) {
+            const acc_1 = acc.fields[0];
+            const matchValue = decoderi(i).Decode(helpers, value_1);
+            if (matchValue.tag === /* Ok */
+            0) {
+              const value_2 = matchValue.fields[0];
+              setItem(acc_1, i, value_2);
+              return FSharpResult$2_Ok(acc_1);
+            } else {
+              return FSharpResult$2_Error((tupledArg = matchValue.fields[0], Helpers_prependPath(".[" + int32ToString(i) + "]", tupledArg[0], tupledArg[1])));
+            }
+          } else {
+            return acc;
+          }
+        }, FSharpResult$2_Ok(fill(new Array(tokens.length), 0, tokens.length, null)), tokens);
+      } else {
+        return FSharpResult$2_Error(["", ErrorReason$1_BadPrimitive("an array", value)]);
+      }
+    }
+  };
+}
+function encoderCompressed(stringTable, oaTable, cellTable, table) {
+  const cellEncoder = (hash) => encodeCell(cellTable, getItemFromDict(table.Values.ValueMap, hash));
+  const values = toList(delay(() => append(singleton(["n", encodeString(stringTable, table.Name)]), delay(() => append(table.Headers.length !== 0 ? singleton(["h", list$1(toList(delay(() => map$1(encoder$1, table.Headers))))]) : empty$2(), delay(() => table.Values.RowCount !== 0 ? append(singleton(["c", intDictionary((col) => {
+    if (col.tag === /* Sparse */
+    1) {
+      return intDictionary(cellEncoder, col.fields[0]);
+    } else {
+      return cellEncoder(col.fields[0]);
+    }
+  }, table.Values.Columns)]), delay(() => {
+    let value;
+    return singleton(["r", (value = table.RowCount | 0, {
+      Encode(helpers) {
+        return helpers.encodeSignedIntegralNumber(value);
+      }
+    })]);
+  })) : empty$2()))))));
+  return {
+    Encode(helpers_1) {
+      const arg = map$1((tupledArg) => [tupledArg[0], tupledArg[1].Encode(helpers_1)], values);
+      return helpers_1.encodeObject(arg);
+    }
+  };
+}
+function decoderCompressedV2Deprecated(stringTable, oaTable, cellTable) {
+  return object((get$) => {
+    let arg_1, objectArg, arg_3, objectArg_1, arg_5, objectArg_2;
+    let decodedHeader;
+    const collection = defaultArg((arg_1 = list(decoder$2), objectArg = get$.Optional, objectArg.Field("h", arg_1)), empty());
+    decodedHeader = Array.from(collection);
+    const table = ArcTable.create((arg_3 = decodeString(stringTable), objectArg_1 = get$.Required, objectArg_1.Field("n", arg_3)), decodedHeader, []);
+    arg_5 = arrayi((columnIndex) => decoderCompressedColumn(cellTable, table, columnIndex)), objectArg_2 = get$.Optional, objectArg_2.Field("c", arg_5);
+    return table;
+  });
+}
+function decoderCompressed(stringTable, oaTable, cellTable) {
+  const valueMap = /* @__PURE__ */ new Map([]);
+  const cellDecoder = map((i) => ensureCellHashInValueMap(item(i, cellTable), valueMap), int);
+  const columnDecoder = Decode_tryOneOf(ofArray([map(ColumnValueRefs_Constant, cellDecoder), map(ColumnValueRefs_Sparse, Decode_intDictionary(cellDecoder))]));
+  const decoder_1 = object((get$) => {
+    let arg_1, objectArg, arg_3, objectArg_1, objectArg_2, arg_7, objectArg_3;
+    const decodedHeader = defaultArg((arg_1 = resizeArray(decoder$2), objectArg = get$.Optional, objectArg.Field("h", arg_1)), []);
+    const values = new ArcTableValues(defaultArg((arg_3 = Decode_dictionary(int, columnDecoder), objectArg_1 = get$.Optional, objectArg_1.Field("c", arg_3)), /* @__PURE__ */ new Map([])), valueMap, defaultArg((objectArg_2 = get$.Optional, objectArg_2.Field("r", int)), 0));
+    return ArcTable.fromArcTableValues((arg_7 = decodeString(stringTable), objectArg_3 = get$.Required, objectArg_3.Field("n", arg_7)), decodedHeader, values);
+  });
+  return {
+    Decode(helper, column) {
+      return !helper.hasProperty("r", column) ? decoderCompressedV2Deprecated(stringTable, oaTable, cellTable).Decode(helper, column) : decoder_1.Decode(helper, column);
+    }
+  };
+}
+
+export { arrayi, decoder, decoderCompressed, decoderCompressedColumn, decoderCompressedV2Deprecated, decoderV2Deprecated, encoder, encoderCompressed };

package/dist/ts/ts/Json/Table/CellTable.d.ts

@@ -1,7 +1,7 @@
 import { CompositeCell_$union } from '../../Core/Table/CompositeCell.js';
 import { int32 } from '@fable-org/fable-library-js/Int32.js';
 import { IMap } from '@fable-org/fable-library-js/Util.js';
-import { Decoder$1, IEncodable } from '../../fable_modules/Thoth.Json.Core.0.4.0/Types.fs.js';
+import { Decoder$1, IEncodable } from '../../fable_modules/Thoth.Json.Core.0.7.0/Types.fs.js';
 import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
 export declare function arrayFromMap(otm: IMap<CompositeCell_$union, int32>): CompositeCell_$union[];
 export declare function encoder(stringTable: IMap<string, int32>, oaTable: IMap<OntologyAnnotation, int32>, ot: CompositeCell_$union[]): IEncodable;

package/dist/ts/ts/Json/Table/CellTable.js

@@ -0,0 +1,53 @@
+import { toArray, map as map$1, sortBy } from '../../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { Dictionary_items, Dictionary_tryFind } from '../../Core/Helper/Collections.js';
+import { comparePrimitives } from '../../../node_modules/@fable-org/fable-library-js/Util.js';
+import { map, item } from '../../../node_modules/@fable-org/fable-library-js/Array.js';
+import { decoderCompressed, encoderCompressed } from './CompositeCell.js';
+import { array, object, int } from '../../fable_modules/Thoth.Json.Core.0.7.0/Decode.fs.js';
+import { value } from '../../../node_modules/@fable-org/fable-library-js/Option.js';
+import { addToDict } from '../../../node_modules/@fable-org/fable-library-js/MapUtil.js';
+
+function arrayFromMap(otm) {
+  return toArray(map$1((kv_1) => kv_1[0], sortBy((kv) => kv[1], Dictionary_items(otm), {
+    Compare: comparePrimitives
+  })));
+}
+function encoder(stringTable, oaTable, ot) {
+  const values = map((cc) => encoderCompressed(stringTable, oaTable, cc), ot);
+  return {
+    Encode(helpers) {
+      const arg = map((v) => v.Encode(helpers), values);
+      return helpers.encodeArray(arg);
+    }
+  };
+}
+function decoder(stringTable, oaTable) {
+  return array(decoderCompressed(stringTable, oaTable));
+}
+function encodeCell(otm, cc) {
+  const matchValue = Dictionary_tryFind(cc, otm);
+  if (matchValue == null) {
+    const i_1 = otm.size | 0;
+    addToDict(otm, cc, i_1);
+    return {
+      Encode(helpers_1) {
+        return helpers_1.encodeSignedIntegralNumber(i_1);
+      }
+    };
+  } else {
+    const i = value(matchValue) | 0;
+    return {
+      Encode(helpers) {
+        return helpers.encodeSignedIntegralNumber(i);
+      }
+    };
+  }
+}
+function decodeCell(ot) {
+  return object((get$) => {
+    const i = get$.Required.Raw(int) | 0;
+    return item(i, ot).Copy();
+  });
+}
+
+export { arrayFromMap, decodeCell, decoder, encodeCell, encoder };

package/dist/ts/ts/Json/Table/CompositeCell.d.ts

@@ -1,5 +1,5 @@
 import { OntologyAnnotation } from '../../Core/OntologyAnnotation.js';
-import { Decoder$1, IEncodable } from '../../fable_modules/Thoth.Json.Core.0.4.0/Types.fs.js';
+import { Decoder$1, IEncodable } from '../../fable_modules/Thoth.Json.Core.0.7.0/Types.fs.js';
 import { CompositeCell_$union } from '../../Core/Table/CompositeCell.js';
 import { IMap } from '@fable-org/fable-library-js/Util.js';
 import { int32 } from '@fable-org/fable-library-js/Int32.js';