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

package/dist/ts/ts/Json/Encode.js

@@ -0,0 +1,65 @@
+import { defaultArg, map, value } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { isEmpty, map as map$2, toArray } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { seq, list, tuple2 } from '../fable_modules/Thoth.Json.Core.0.7.0/Encode.fs.js';
+import { item } from '../../node_modules/@fable-org/fable-library-js/Array.js';
+import { isEmpty as isEmpty$1, map as map$1 } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { toString } from '../../node_modules/@fable-org/fable-library-js/Date.js';
+import { count } from '../../node_modules/@fable-org/fable-library-js/CollectionUtil.js';
+import { toFail, printf } from '../../node_modules/@fable-org/fable-library-js/String.js';
+
+function tryInclude(name, encoder, value) {
+  return [name, map(encoder, value)];
+}
+function tryIncludeSeq(name, encoder, value) {
+  return [name, isEmpty(value) ? void 0 : seq(map$2(encoder, value))];
+}
+function tryIncludeList(name, encoder, value) {
+  return [name, isEmpty$1(value) ? void 0 : list(map$1(encoder, value))];
+}
+function tryIncludeListOpt(name, encoder, value$1) {
+  let o;
+  return [name, value$1 != null ? (o = value(value$1), isEmpty$1(o) ? void 0 : list(map$1(encoder, o))) : void 0];
+}
+const DefaultSpaces = 0;
+function defaultSpaces(spaces) {
+  return defaultArg(spaces, DefaultSpaces);
+}
+function dateTime(d) {
+  const value = item(0, toString(d, "O").split("+"));
+  return {
+    Encode(helpers) {
+      return helpers.encodeString(value);
+    }
+  };
+}
+function resizeArrayOrSingleton(encoder, values) {
+  if (values.length === 1) {
+    return encoder(values[0]);
+  } else {
+    return seq(map$2(encoder, values));
+  }
+}
+function intDictionary(valueEncoder, values) {
+  if (count(values) === 0) {
+    return {
+      Encode(helpers) {
+        return helpers.encodeNull();
+      }
+    };
+  } else {
+    return seq(toArray(map$2((_arg) => {
+      const activePatternResult = _arg;
+      const k = activePatternResult[0] | 0;
+      if (k > 2147483647 ? true : k < -2147483648) {
+        toFail(printf("Key %d is out of bounds for Int32"))(k);
+      }
+      return tuple2((value) => ({
+        Encode(helpers_1) {
+          return helpers_1.encodeSignedIntegralNumber(value);
+        }
+      }), valueEncoder, k, activePatternResult[1]);
+    }, values)));
+  }
+}
+
+export { DefaultSpaces, dateTime, defaultSpaces, intDictionary, resizeArrayOrSingleton, tryInclude, tryIncludeList, tryIncludeListOpt, tryIncludeSeq };

package/dist/ts/ts/Json/IDTable.d.ts

@@ -1,4 +1,4 @@
-import { IEncodable } from '../fable_modules/Thoth.Json.Core.0.4.0/Types.fs.js';
+import { IEncodable } from '../fable_modules/Thoth.Json.Core.0.7.0/Types.fs.js';
 import { IMap } from '@fable-org/fable-library-js/Util.js';
 export declare function encodeID(id: string): IEncodable;
 export declare function encode<Value>(genID: ((arg0: Value) => string), encoder: ((arg0: Value) => IEncodable), value: Value, table: IMap<string, IEncodable>): IEncodable;

package/dist/ts/ts/Json/IDTable.js

@@ -0,0 +1,28 @@
+import { map } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { addToDict } from '../../node_modules/@fable-org/fable-library-js/MapUtil.js';
+
+function encodeID(id) {
+  const values_1 = [["@id", {
+    Encode(helpers) {
+      return helpers.encodeString(id);
+    }
+  }]];
+  return {
+    Encode(helpers_1) {
+      const arg = map((tupledArg) => [tupledArg[0], tupledArg[1].Encode(helpers_1)], values_1);
+      return helpers_1.encodeObject(arg);
+    }
+  };
+}
+function encode(genID, encoder, value, table) {
+  const id = genID(value);
+  if (table.has(id)) {
+    return encodeID(id);
+  } else {
+    const v = encoder(value);
+    addToDict(table, genID(value), v);
+    return v;
+  }
+}
+
+export { encode, encodeID };

package/dist/ts/ts/Json/Investigation.d.ts

@@ -1,6 +1,6 @@
 import { FSharpList } from '@fable-org/fable-library-js/List.js';
 import { Option } from '@fable-org/fable-library-js/Option.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 { ArcInvestigation } from '../Core/ArcTypes.js';
 import { IMap } from '@fable-org/fable-library-js/Util.js';
 import { int32 } from '@fable-org/fable-library-js/Int32.js';

package/dist/ts/ts/Json/Investigation.js

@@ -0,0 +1,229 @@
+import { ofArray, unzip, empty, choose } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { value, defaultArg, unwrap, map as map$1 } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { tryInclude, tryIncludeSeq } from './Encode.js';
+import { ISAJson_decoder as ISAJson_decoder$2, decoder as decoder$1, ROCrate_decoder as ROCrate_decoder$2, encoder as encoder$1, ISAJson_encoder as ISAJson_encoder$1, ROCrate_encoder as ROCrate_encoder$1 } from './OntologySourceReference.js';
+import { ISAJson_decoder as ISAJson_decoder$3, decoder as decoder$2, ROCrate_decoder as ROCrate_decoder$3, encoder as encoder$2, ISAJson_encoder as ISAJson_encoder$2, ROCrate_encoder as ROCrate_encoder$2 } from './Publication.js';
+import { ISAJson_decoder as ISAJson_decoder$4, decoder as decoder$3, ROCrate_decoder as ROCrate_decoder$4, encoder as encoder$3, ISAJson_encoder as ISAJson_encoder$3, ROCrate_encoder as ROCrate_encoder$3 } from './Person.js';
+import { decoder as decoder$4, decoderCompressed as decoderCompressed$1, encoder as encoder$4, encoderCompressed as encoderCompressed$1 } from './Assay.js';
+import { ArcInvestigation } from '../Core/ArcTypes.js';
+import { ISAJson_decoder as ISAJson_decoder$1, decoder as decoder$5, decoderCompressed as decoderCompressed$2, ROCrate_decoder as ROCrate_decoder$1, encoder as encoder$5, ISAJson_encoder as ISAJson_encoder$4, ROCrate_encoder as ROCrate_encoder$4, encoderCompressed as encoderCompressed$2 } from './Study.js';
+import { ISAJson_decoder as ISAJson_decoder$5, decoder as decoder$6, ROCrate_decoder as ROCrate_decoder$5, encoder as encoder$6, ISAJson_encoder as ISAJson_encoder$5, ROCrate_encoder as ROCrate_encoder$5 } from './Comment.js';
+import { concat, map } 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 { stringHash } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { toString, today } from '../../node_modules/@fable-org/fable-library-js/Date.js';
+import { context_jsonvalue } from './context/rocrate/isa_investigation_context.js';
+import { createMissingIdentifier } from '../Core/Helper/Identifier.js';
+import { distinctBy } from '../../node_modules/@fable-org/fable-library-js/Seq2.js';
+import { Decode_objectNoAdditionalProperties } from './Decode.js';
+
+function encoder(inv) {
+  let value;
+  const values_1 = choose((tupledArg) => map$1((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = inv.Identifier, {
+    Encode(helpers) {
+      return helpers.encodeString(value);
+    }
+  })], tryInclude("Title", (value_1) => ({
+    Encode(helpers_1) {
+      return helpers_1.encodeString(value_1);
+    }
+  }), inv.Title), tryInclude("Description", (value_3) => ({
+    Encode(helpers_2) {
+      return helpers_2.encodeString(value_3);
+    }
+  }), inv.Description), tryInclude("SubmissionDate", (value_5) => ({
+    Encode(helpers_3) {
+      return helpers_3.encodeString(value_5);
+    }
+  }), inv.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => ({
+    Encode(helpers_4) {
+      return helpers_4.encodeString(value_7);
+    }
+  }), inv.PublicReleaseDate), tryIncludeSeq("OntologySourceReferences", encoder$1, inv.OntologySourceReferences), tryIncludeSeq("Publications", encoder$2, inv.Publications), tryIncludeSeq("Contacts", encoder$3, inv.Contacts), tryIncludeSeq("Assays", encoder$4, inv.Assays), tryIncludeSeq("Studies", encoder$5, inv.Studies), tryIncludeSeq("RegisteredStudyIdentifiers", (value_9) => ({
+    Encode(helpers_5) {
+      return helpers_5.encodeString(value_9);
+    }
+  }), inv.RegisteredStudyIdentifiers), tryIncludeSeq("Comments", encoder$6, inv.Comments)]));
+  return {
+    Encode(helpers_6) {
+      const arg = map((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_6)], values_1);
+      return helpers_6.encodeObject(arg);
+    }
+  };
+}
+const decoder = object((get$) => {
+  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, arg_19, objectArg_9, arg_21, objectArg_10, arg_23, objectArg_11;
+  return new ArcInvestigation((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("OntologySourceReferences", arg_11))), unwrap((arg_13 = resizeArray(decoder$2), objectArg_6 = get$.Optional, objectArg_6.Field("Publications", arg_13))), unwrap((arg_15 = resizeArray(decoder$3), objectArg_7 = get$.Optional, objectArg_7.Field("Contacts", arg_15))), unwrap((arg_17 = resizeArray(decoder$4), objectArg_8 = get$.Optional, objectArg_8.Field("Assays", arg_17))), unwrap((arg_19 = resizeArray(decoder$5), objectArg_9 = get$.Optional, objectArg_9.Field("Studies", arg_19))), void 0, void 0, unwrap((arg_21 = resizeArray(string), objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredStudyIdentifiers", arg_21))), unwrap((arg_23 = resizeArray(decoder$6), objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23))));
+});
+function encoderCompressed(stringTable, oaTable, cellTable, inv) {
+  let value;
+  const values_1 = choose((tupledArg) => map$1((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["Identifier", (value = inv.Identifier, {
+    Encode(helpers) {
+      return helpers.encodeString(value);
+    }
+  })], tryInclude("Title", (value_1) => ({
+    Encode(helpers_1) {
+      return helpers_1.encodeString(value_1);
+    }
+  }), inv.Title), tryInclude("Description", (value_3) => ({
+    Encode(helpers_2) {
+      return helpers_2.encodeString(value_3);
+    }
+  }), inv.Description), tryInclude("SubmissionDate", (value_5) => ({
+    Encode(helpers_3) {
+      return helpers_3.encodeString(value_5);
+    }
+  }), inv.SubmissionDate), tryInclude("PublicReleaseDate", (value_7) => ({
+    Encode(helpers_4) {
+      return helpers_4.encodeString(value_7);
+    }
+  }), inv.PublicReleaseDate), tryIncludeSeq("OntologySourceReferences", encoder$1, inv.OntologySourceReferences), tryIncludeSeq("Publications", encoder$2, inv.Publications), tryIncludeSeq("Contacts", encoder$3, inv.Contacts), tryIncludeSeq("Assays", (assay) => encoderCompressed$1(stringTable, oaTable, cellTable, assay), inv.Assays), tryIncludeSeq("Studies", (study) => encoderCompressed$2(stringTable, oaTable, cellTable, study), inv.Studies), tryIncludeSeq("RegisteredStudyIdentifiers", (value_9) => ({
+    Encode(helpers_5) {
+      return helpers_5.encodeString(value_9);
+    }
+  }), inv.RegisteredStudyIdentifiers), tryIncludeSeq("Comments", encoder$6, inv.Comments)]));
+  return {
+    Encode(helpers_6) {
+      const arg = map((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_6)], values_1);
+      return helpers_6.encodeObject(arg);
+    }
+  };
+}
+function decoderCompressed(stringTable, oaTable, cellTable) {
+  return object((get$) => {
+    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 ArcInvestigation((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("OntologySourceReferences", arg_11))), unwrap((arg_13 = resizeArray(decoder$2), objectArg_6 = get$.Optional, objectArg_6.Field("Publications", arg_13))), unwrap((arg_15 = resizeArray(decoder$3), objectArg_7 = get$.Optional, objectArg_7.Field("Contacts", arg_15))), unwrap((arg_17 = resizeArray(decoderCompressed$1(stringTable, oaTable, cellTable)), objectArg_8 = get$.Optional, objectArg_8.Field("Assays", arg_17))), unwrap((arg_19 = resizeArray(decoderCompressed$2(stringTable, oaTable, cellTable)), objectArg_9 = get$.Optional, objectArg_9.Field("Studies", arg_19))), void 0, void 0, unwrap((arg_21 = resizeArray(string), objectArg_10 = get$.Optional, objectArg_10.Field("RegisteredStudyIdentifiers", arg_21))), unwrap((arg_23 = resizeArray(decoder$6), objectArg_11 = get$.Optional, objectArg_11.Field("Comments", arg_23))));
+  });
+}
+function ROCrate_genID(i) {
+  return "./";
+}
+function ROCrate_encoder(oa) {
+  let value, value_3, value_4, value_12, copyOfStruct;
+  const values_1 = choose((tupledArg) => map$1((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value = ROCrate_genID(), {
+    Encode(helpers) {
+      return helpers.encodeString(value);
+    }
+  })], ["@type", {
+    Encode(helpers_1) {
+      return helpers_1.encodeString("Investigation");
+    }
+  }], ["additionalType", {
+    Encode(helpers_2) {
+      return helpers_2.encodeString("Investigation");
+    }
+  }], ["identifier", (value_3 = oa.Identifier, {
+    Encode(helpers_3) {
+      return helpers_3.encodeString(value_3);
+    }
+  })], ["filename", (value_4 = ArcInvestigation.FileName, {
+    Encode(helpers_4) {
+      return helpers_4.encodeString(value_4);
+    }
+  })], tryInclude("title", (value_5) => ({
+    Encode(helpers_5) {
+      return helpers_5.encodeString(value_5);
+    }
+  }), oa.Title), tryInclude("description", (value_7) => ({
+    Encode(helpers_6) {
+      return helpers_6.encodeString(value_7);
+    }
+  }), oa.Description), tryInclude("submissionDate", (value_9) => ({
+    Encode(helpers_7) {
+      return helpers_7.encodeString(value_9);
+    }
+  }), oa.SubmissionDate), ["publicReleaseDate", (value_12 = defaultArg(oa.PublicReleaseDate, (copyOfStruct = today(), toString(copyOfStruct, "yyyy-MM-dd"))), {
+    Encode(helpers_8) {
+      return helpers_8.encodeString(value_12);
+    }
+  })], tryIncludeSeq("ontologySourceReferences", ROCrate_encoder$1, oa.OntologySourceReferences), tryIncludeSeq("publications", ROCrate_encoder$2, oa.Publications), tryIncludeSeq("people", ROCrate_encoder$3, oa.Contacts), tryIncludeSeq("studies", (s) => ROCrate_encoder$4(void 0, s), oa.Studies), tryIncludeSeq("comments", ROCrate_encoder$5, oa.Comments), ["@context", context_jsonvalue]]));
+  return {
+    Encode(helpers_9) {
+      const arg = map((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_9)], values_1);
+      return helpers_9.encodeObject(arg);
+    }
+  };
+}
+const ROCrate_decoder = object((get$) => {
+  let arg_3, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9;
+  let identifier;
+  let matchValue;
+  const objectArg = get$.Optional;
+  matchValue = objectArg.Field("identifier", string);
+  identifier = matchValue == null ? createMissingIdentifier() : value(matchValue);
+  const patternInput = unzip(defaultArg((arg_3 = list(ROCrate_decoder$1), objectArg_1 = get$.Optional, objectArg_1.Field("studies", arg_3)), empty()));
+  const studiesRaw = patternInput[0];
+  let assays;
+  const collection = distinctBy((a) => a.Identifier, concat(patternInput[1]), {
+    Equals: (x, y) => x === y,
+    GetHashCode: stringHash
+  });
+  assays = Array.from(collection);
+  const studies = Array.from(studiesRaw);
+  let studyIdentifiers;
+  const collection_1 = map((a_1) => a_1.Identifier, studiesRaw);
+  studyIdentifiers = Array.from(collection_1);
+  return new ArcInvestigation(identifier, unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("title", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("description", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("submissionDate", string))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("publicReleaseDate", string))), unwrap((arg_13 = resizeArray(ROCrate_decoder$2), objectArg_6 = get$.Optional, objectArg_6.Field("ontologySourceReferences", arg_13))), unwrap((arg_15 = resizeArray(ROCrate_decoder$3), objectArg_7 = get$.Optional, objectArg_7.Field("publications", arg_15))), unwrap((arg_17 = resizeArray(ROCrate_decoder$4), objectArg_8 = get$.Optional, objectArg_8.Field("people", arg_17))), assays, studies, void 0, void 0, studyIdentifiers, unwrap((arg_19 = resizeArray(ROCrate_decoder$5), objectArg_9 = get$.Optional, objectArg_9.Field("comments", arg_19))));
+});
+const ISAJson_allowedFields = ofArray(["@id", "filename", "identifier", "title", "description", "submissionDate", "publicReleaseDate", "ontologySourceReferences", "publications", "people", "studies", "comments", "@type", "@context"]);
+function ISAJson_encoder(idMap, inv) {
+  let value, value_1, value_2;
+  const values_1 = choose((tupledArg) => map$1((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value = ROCrate_genID(), {
+    Encode(helpers) {
+      return helpers.encodeString(value);
+    }
+  })], ["filename", (value_1 = ArcInvestigation.FileName, {
+    Encode(helpers_1) {
+      return helpers_1.encodeString(value_1);
+    }
+  })], ["identifier", (value_2 = inv.Identifier, {
+    Encode(helpers_2) {
+      return helpers_2.encodeString(value_2);
+    }
+  })], tryInclude("title", (value_3) => ({
+    Encode(helpers_3) {
+      return helpers_3.encodeString(value_3);
+    }
+  }), inv.Title), tryInclude("description", (value_5) => ({
+    Encode(helpers_4) {
+      return helpers_4.encodeString(value_5);
+    }
+  }), inv.Description), tryInclude("submissionDate", (value_7) => ({
+    Encode(helpers_5) {
+      return helpers_5.encodeString(value_7);
+    }
+  }), inv.SubmissionDate), tryInclude("publicReleaseDate", (value_9) => ({
+    Encode(helpers_6) {
+      return helpers_6.encodeString(value_9);
+    }
+  }), inv.PublicReleaseDate), tryIncludeSeq("ontologySourceReferences", (osr) => ISAJson_encoder$1(idMap, osr), inv.OntologySourceReferences), tryIncludeSeq("publications", (oa) => ISAJson_encoder$2(idMap, oa), inv.Publications), tryIncludeSeq("people", (person) => ISAJson_encoder$3(idMap, person), inv.Contacts), tryIncludeSeq("studies", (s) => ISAJson_encoder$4(idMap, void 0, s), inv.Studies), tryIncludeSeq("comments", (comment) => ISAJson_encoder$5(idMap, comment), inv.Comments)]));
+  return {
+    Encode(helpers_7) {
+      const arg = map((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_7)], values_1);
+      return helpers_7.encodeObject(arg);
+    }
+  };
+}
+const ISAJson_decoder = Decode_objectNoAdditionalProperties(ISAJson_allowedFields, (get$) => {
+  let arg_3, objectArg_1, objectArg_2, objectArg_3, objectArg_4, objectArg_5, arg_13, objectArg_6, arg_15, objectArg_7, arg_17, objectArg_8, arg_19, objectArg_9;
+  let identifer;
+  let matchValue;
+  const objectArg = get$.Optional;
+  matchValue = objectArg.Field("identifier", string);
+  identifer = matchValue == null ? createMissingIdentifier() : value(matchValue);
+  const patternInput = unzip(defaultArg((arg_3 = list(ISAJson_decoder$1), objectArg_1 = get$.Optional, objectArg_1.Field("studies", arg_3)), empty()));
+  const studiesRaw = patternInput[0];
+  let assays;
+  const collection = distinctBy((a) => a.Identifier, concat(patternInput[1]), {
+    Equals: (x, y) => x === y,
+    GetHashCode: stringHash
+  });
+  assays = Array.from(collection);
+  const studies = Array.from(studiesRaw);
+  let studyIdentifiers;
+  const collection_1 = map((a_1) => a_1.Identifier, studiesRaw);
+  studyIdentifiers = Array.from(collection_1);
+  return new ArcInvestigation(identifer, unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("title", string))), unwrap((objectArg_3 = get$.Optional, objectArg_3.Field("description", string))), unwrap((objectArg_4 = get$.Optional, objectArg_4.Field("submissionDate", string))), unwrap((objectArg_5 = get$.Optional, objectArg_5.Field("publicReleaseDate", string))), unwrap((arg_13 = resizeArray(ISAJson_decoder$2), objectArg_6 = get$.Optional, objectArg_6.Field("ontologySourceReferences", arg_13))), unwrap((arg_15 = resizeArray(ISAJson_decoder$3), objectArg_7 = get$.Optional, objectArg_7.Field("publications", arg_15))), unwrap((arg_17 = resizeArray(ISAJson_decoder$4), objectArg_8 = get$.Optional, objectArg_8.Field("people", arg_17))), assays, studies, void 0, void 0, studyIdentifiers, unwrap((arg_19 = resizeArray(ISAJson_decoder$5), objectArg_9 = get$.Optional, objectArg_9.Field("comments", arg_19))));
+});
+
+export { ISAJson_allowedFields, ISAJson_decoder, ISAJson_encoder, ROCrate_decoder, ROCrate_encoder, ROCrate_genID, decoder, decoderCompressed, encoder, encoderCompressed };

package/dist/ts/ts/Json/OntologyAnnotation.d.ts

@@ -1,6 +1,6 @@
 import { IMap } from '@fable-org/fable-library-js/Util.js';
 import { int32 } from '@fable-org/fable-library-js/Int32.js';
-import { IEncodable, Decoder$1 } from '../fable_modules/Thoth.Json.Core.0.4.0/Types.fs.js';
+import { IEncodable, Decoder$1 } from '../fable_modules/Thoth.Json.Core.0.7.0/Types.fs.js';
 import { Option } from '@fable-org/fable-library-js/Option.js';
 import { OntologyAnnotation } from '../Core/OntologyAnnotation.js';
 export declare const AnnotationValue_decoder: Decoder$1<string>;

package/dist/ts/ts/Json/OntologyAnnotation.js

@@ -0,0 +1,194 @@
+import { oneOf, map, string, int, float, object, resizeArray } from '../fable_modules/Thoth.Json.Core.0.7.0/Decode.fs.js';
+import { int32ToString } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { ofArray, choose } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { unwrap, map as map$1, value } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { tryInclude, tryIncludeSeq } from './Encode.js';
+import { decoder, ROCrate_decoderDisambiguatingDescription, encoder, ROCrate_encoderDisambiguatingDescription } from './Comment.js';
+import { map as map$2, filter } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { OntologyAnnotation } from '../Core/OntologyAnnotation.js';
+import { decodeString, encodeString } from './StringTable.js';
+import { replace } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { URIModule_toString } from '../Core/URI.js';
+import { context_jsonvalue } from './context/rocrate/isa_ontology_annotation_context.js';
+import { context_jsonvalue as context_jsonvalue$1 } from './context/rocrate/property_value_context.js';
+import { orderName } from '../Core/Process/ColumnIndex.js';
+import { encode } from './IDTable.js';
+
+const AnnotationValue_decoder = oneOf(ofArray([map(int32ToString, int), map((value_1) => value_1.toString(), float), string]));
+function OntologyAnnotation_encoder(oa) {
+  const values_1 = choose((tupledArg) => map$1((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([tryInclude("annotationValue", (value) => ({
+    Encode(helpers) {
+      return helpers.encodeString(value);
+    }
+  }), oa.Name), tryInclude("termSource", (value_2) => ({
+    Encode(helpers_1) {
+      return helpers_1.encodeString(value_2);
+    }
+  }), oa.TermSourceREF), tryInclude("termAccession", (value_4) => ({
+    Encode(helpers_2) {
+      return helpers_2.encodeString(value_4);
+    }
+  }), oa.TermAccessionNumber), tryIncludeSeq("comments", encoder, oa.Comments)]));
+  return {
+    Encode(helpers_3) {
+      const arg = map$2((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_3)], values_1);
+      return helpers_3.encodeObject(arg);
+    }
+  };
+}
+const OntologyAnnotation_decoder = object((get$) => {
+  let objectArg, objectArg_1, objectArg_2, arg_7, objectArg_3;
+  return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("annotationValue", AnnotationValue_decoder))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("termSource", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("termAccession", string))), unwrap((arg_7 = resizeArray(decoder), objectArg_3 = get$.Optional, objectArg_3.Field("comments", arg_7))));
+});
+function OntologyAnnotation_compressedEncoder(stringTable, oa) {
+  const values_1 = choose((tupledArg) => map$1((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([tryInclude("a", (s) => encodeString(stringTable, s), oa.Name), tryInclude("ts", (s_1) => encodeString(stringTable, s_1), oa.TermSourceREF), tryInclude("ta", (s_2) => encodeString(stringTable, s_2), oa.TermAccessionNumber), tryIncludeSeq("comments", encoder, oa.Comments)]));
+  return {
+    Encode(helpers) {
+      const arg = map$2((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers)], values_1);
+      return helpers.encodeObject(arg);
+    }
+  };
+}
+function OntologyAnnotation_compressedDecoder(stringTable) {
+  return object((get$) => {
+    let arg_1, objectArg, arg_3, objectArg_1, arg_5, objectArg_2, arg_7, objectArg_3;
+    return new OntologyAnnotation(unwrap((arg_1 = decodeString(stringTable), objectArg = get$.Optional, objectArg.Field("a", arg_1))), unwrap((arg_3 = decodeString(stringTable), objectArg_1 = get$.Optional, objectArg_1.Field("ts", arg_3))), unwrap((arg_5 = decodeString(stringTable), objectArg_2 = get$.Optional, objectArg_2.Field("ta", arg_5))), unwrap((arg_7 = resizeArray(decoder), objectArg_3 = get$.Optional, objectArg_3.Field("comments", arg_7))));
+  });
+}
+function OntologyAnnotation_ROCrate_genID(o) {
+  const matchValue = o.TermAccessionNumber;
+  if (matchValue == null) {
+    const matchValue_1 = o.TermSourceREF;
+    if (matchValue_1 == null) {
+      const matchValue_2 = o.Name;
+      if (matchValue_2 == null) {
+        return "#DummyOntologyAnnotation";
+      } else {
+        return "#UserTerm_" + replace(value(matchValue_2), " ", "_");
+      }
+    } else {
+      return "#" + replace(value(matchValue_1), " ", "_");
+    }
+  } else {
+    return URIModule_toString(value(matchValue));
+  }
+}
+function OntologyAnnotation_ROCrate_encoderDefinedTerm(oa) {
+  let value;
+  const values_1 = choose((tupledArg) => map$1((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value = OntologyAnnotation_ROCrate_genID(oa), {
+    Encode(helpers) {
+      return helpers.encodeString(value);
+    }
+  })], ["@type", {
+    Encode(helpers_1) {
+      return helpers_1.encodeString("OntologyAnnotation");
+    }
+  }], tryInclude("annotationValue", (value_2) => ({
+    Encode(helpers_2) {
+      return helpers_2.encodeString(value_2);
+    }
+  }), oa.Name), tryInclude("termSource", (value_4) => ({
+    Encode(helpers_3) {
+      return helpers_3.encodeString(value_4);
+    }
+  }), oa.TermSourceREF), tryInclude("termAccession", (value_6) => ({
+    Encode(helpers_4) {
+      return helpers_4.encodeString(value_6);
+    }
+  }), oa.TermAccessionNumber), tryIncludeSeq("comments", ROCrate_encoderDisambiguatingDescription, oa.Comments), ["@context", context_jsonvalue]]));
+  return {
+    Encode(helpers_5) {
+      const arg = map$2((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_5)], values_1);
+      return helpers_5.encodeObject(arg);
+    }
+  };
+}
+const OntologyAnnotation_ROCrate_decoderDefinedTerm = object((get$) => {
+  let objectArg, objectArg_1, objectArg_2, arg_7, objectArg_3;
+  return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("annotationValue", AnnotationValue_decoder))), unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("termSource", string))), unwrap((objectArg_2 = get$.Optional, objectArg_2.Field("termAccession", string))), unwrap((arg_7 = resizeArray(ROCrate_decoderDisambiguatingDescription), objectArg_3 = get$.Optional, objectArg_3.Field("comments", arg_7))));
+});
+function OntologyAnnotation_ROCrate_encoderPropertyValue(oa) {
+  let value;
+  const values_1 = choose((tupledArg) => map$1((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value = OntologyAnnotation_ROCrate_genID(oa), {
+    Encode(helpers) {
+      return helpers.encodeString(value);
+    }
+  })], ["@type", {
+    Encode(helpers_1) {
+      return helpers_1.encodeString("PropertyValue");
+    }
+  }], tryInclude("category", (value_2) => ({
+    Encode(helpers_2) {
+      return helpers_2.encodeString(value_2);
+    }
+  }), oa.Name), tryInclude("categoryCode", (value_4) => ({
+    Encode(helpers_3) {
+      return helpers_3.encodeString(value_4);
+    }
+  }), oa.TermAccessionNumber), tryIncludeSeq("comments", ROCrate_encoderDisambiguatingDescription, oa.Comments), ["@context", context_jsonvalue$1]]));
+  return {
+    Encode(helpers_4) {
+      const arg = map$2((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_4)], values_1);
+      return helpers_4.encodeObject(arg);
+    }
+  };
+}
+const OntologyAnnotation_ROCrate_decoderPropertyValue = object((get$) => {
+  let objectArg, objectArg_1, arg_5, objectArg_2;
+  return OntologyAnnotation.create(unwrap((objectArg = get$.Optional, objectArg.Field("category", string))), void 0, unwrap((objectArg_1 = get$.Optional, objectArg_1.Field("categoryCode", string))), unwrap((arg_5 = resizeArray(ROCrate_decoderDisambiguatingDescription), objectArg_2 = get$.Optional, objectArg_2.Field("comments", arg_5))));
+});
+function OntologyAnnotation_ISAJson_encoder(idMap, oa) {
+  const f = (oa_1) => {
+    const comments = filter((c) => {
+      const matchValue = c.Name;
+      let matchResult;
+      if (matchValue != null) {
+        if (value(matchValue) === orderName) {
+          matchResult = 0;
+          value(matchValue);
+        } else {
+          matchResult = 1;
+        }
+      } else {
+        matchResult = 1;
+      }
+      switch (matchResult) {
+        case 0:
+          return false;
+        default:
+          return true;
+      }
+    }, oa_1.Comments);
+    const values_1 = choose((tupledArg) => map$1((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([tryInclude("@id", (value) => ({
+      Encode(helpers) {
+        return helpers.encodeString(value);
+      }
+    }), OntologyAnnotation_ROCrate_genID(oa_1)), tryInclude("annotationValue", (value_2) => ({
+      Encode(helpers_1) {
+        return helpers_1.encodeString(value_2);
+      }
+    }), oa_1.Name), tryInclude("termSource", (value_4) => ({
+      Encode(helpers_2) {
+        return helpers_2.encodeString(value_4);
+      }
+    }), oa_1.TermSourceREF), tryInclude("termAccession", (value_6) => ({
+      Encode(helpers_3) {
+        return helpers_3.encodeString(value_6);
+      }
+    }), oa_1.TermAccessionNumber), tryIncludeSeq("comments", encoder, comments)]));
+    return {
+      Encode(helpers_4) {
+        const arg = map$2((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_4)], values_1);
+        return helpers_4.encodeObject(arg);
+      }
+    };
+  };
+  if (idMap != null) {
+    return encode(OntologyAnnotation_ROCrate_genID, f, oa, value(idMap));
+  } else {
+    return f(oa);
+  }
+}
+const OntologyAnnotation_ISAJson_decoder = OntologyAnnotation_decoder;
+
+export { AnnotationValue_decoder, OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder, OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ROCrate_decoderPropertyValue, OntologyAnnotation_ROCrate_encoderDefinedTerm, OntologyAnnotation_ROCrate_encoderPropertyValue, OntologyAnnotation_ROCrate_genID, OntologyAnnotation_compressedDecoder, OntologyAnnotation_compressedEncoder, OntologyAnnotation_decoder, OntologyAnnotation_encoder };

package/dist/ts/ts/Json/OntologySourceReference.d.ts

@@ -1,5 +1,5 @@
 import { Option } from '@fable-org/fable-library-js/Option.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 { OntologySourceReference } from '../Core/OntologySourceReference.js';
 import { IMap } from '@fable-org/fable-library-js/Util.js';
 export declare function encoder(osr: OntologySourceReference): IEncodable;