@nfdi4plants/arctrl 1.0.7 → 1.2.0

package/ISA/ISA.Json/context/rocrate/isa_organization_context.js

@@ -0,0 +1,22 @@
+import { Record } from "../../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, string_type } from "../../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Json } from "../../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, Organization, name) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.Organization = Organization;
+        this.name = name;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.ISA.Json.ROCrateContext.Organization.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["Organization", string_type], ["name", string_type]]);
+}
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["Organization", new Json(0, ["sdo:Organization"])], ["name", new Json(0, ["sdo:name"])]]]);
+
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Organization\": \"sdo:Organization\",\r\n    \r\n    \"name\": \"sdo:name\"\r\n  }\r\n}\r\n    ";
+

package/ISA/ISA.Json/context/rocrate/isa_person_context.js

@@ -0,0 +1,31 @@
+import { Record } from "../../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, string_type } from "../../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Json } from "../../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, Person, firstName, lastName, midInitials, email, address, phone, fax, comments, roles, affiliation) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.Person = Person;
+        this.firstName = firstName;
+        this.lastName = lastName;
+        this.midInitials = midInitials;
+        this.email = email;
+        this.address = address;
+        this.phone = phone;
+        this.fax = fax;
+        this.comments = comments;
+        this.roles = roles;
+        this.affiliation = affiliation;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.ISA.Json.ROCrateContext.Person.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["Person", string_type], ["firstName", string_type], ["lastName", string_type], ["midInitials", string_type], ["email", string_type], ["address", string_type], ["phone", string_type], ["fax", string_type], ["comments", string_type], ["roles", string_type], ["affiliation", string_type]]);
+}
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["Person", new Json(0, ["sdo:Person"])], ["firstName", new Json(0, ["sdo:givenName"])], ["lastName", new Json(0, ["sdo:familyName"])], ["midInitials", new Json(0, ["sdo:additionalName"])], ["email", new Json(0, ["sdo:email"])], ["address", new Json(0, ["sdo:address"])], ["phone", new Json(0, ["sdo:telephone"])], ["fax", new Json(0, ["sdo:faxNumber"])], ["comments", new Json(0, ["sdo:disambiguatingDescription"])], ["roles", new Json(0, ["sdo:jobTitle"])], ["affiliation", new Json(0, ["sdo:affiliation"])]]]);
+
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Person\": \"sdo:Person\",\r\n    \r\n    \"firstName\": \"sdo:givenName\",\r\n    \"lastName\": \"sdo:familyName\",\r\n    \"midInitials\": \"sdo:additionalName\",\r\n    \"email\": \"sdo:email\",\r\n    \"address\": \"sdo:address\",\r\n    \"phone\": \"sdo:telephone\",\r\n    \"fax\": \"sdo:faxNumber\",\r\n    \"comments\": \"sdo:disambiguatingDescription\",\r\n    \"roles\": \"sdo:jobTitle\",\r\n    \"affiliation\": \"sdo:affiliation\"\r\n  }\r\n}\r\n    ";
+

package/ISA/ISA.Json/context/rocrate/isa_process_context.js

@@ -0,0 +1,31 @@
+import { Record } from "../../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, string_type } from "../../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Json } from "../../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, Process, ArcProcess, name, executesProtocol, performer, date, previousProcess, nextProcess, input, output, comments) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.Process = Process;
+        this.ArcProcess = ArcProcess;
+        this.name = name;
+        this.executesProtocol = executesProtocol;
+        this.performer = performer;
+        this.date = date;
+        this.previousProcess = previousProcess;
+        this.nextProcess = nextProcess;
+        this.input = input;
+        this.output = output;
+        this.comments = comments;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.ISA.Json.ROCrateContext.Process.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["Process", string_type], ["ArcProcess", string_type], ["name", string_type], ["executesProtocol", string_type], ["performer", string_type], ["date", string_type], ["previousProcess", string_type], ["nextProcess", string_type], ["input", string_type], ["output", string_type], ["comments", string_type]]);
+}
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["Process", new Json(0, ["sdo:Thing"])], ["ArcProcess", new Json(0, ["arc:ARC#ARC_00000048"])], ["name", new Json(0, ["arc:ARC#ARC_00000019"])], ["executesProtocol", new Json(0, ["arc:ARC#ARC_00000086"])], ["performer", new Json(0, ["arc:ARC#ARC_00000089"])], ["date", new Json(0, ["arc:ARC#ARC_00000090"])], ["previousProcess", new Json(0, ["arc:ARC#ARC_00000091"])], ["nextProcess", new Json(0, ["arc:ARC#ARC_00000092"])], ["input", new Json(0, ["arc:ARC#ARC_00000095"])], ["output", new Json(0, ["arc:ARC#ARC_00000096"])], ["comments", new Json(0, ["sdo:disambiguatingDescription"])]]]);
+
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Process\": \"sdo:Thing\",\r\n    \"ArcProcess\": \"arc:ARC#ARC_00000048\",\r\n\r\n    \"name\": \"arc:ARC#ARC_00000019\",\r\n    \"executesProtocol\": \"arc:ARC#ARC_00000086\",\r\n    \"performer\": \"arc:ARC#ARC_00000089\",\r\n    \"date\": \"arc:ARC#ARC_00000090\",\r\n    \"previousProcess\": \"arc:ARC#ARC_00000091\",\r\n    \"nextProcess\": \"arc:ARC#ARC_00000092\",\r\n    \"input\": \"arc:ARC#ARC_00000095\",\r\n    \"output\": \"arc:ARC#ARC_00000096\",\r\n\r\n    \"comments\": \"sdo:disambiguatingDescription\"\r\n  }\r\n}\r\n    ";
+

package/ISA/ISA.Json/context/rocrate/isa_process_parameter_value_context.js

@@ -0,0 +1,25 @@
+import { Record } from "../../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, string_type } from "../../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Json } from "../../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, ProcessParameterValue, ArcProcessParameterValue, category, value, unit) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.ProcessParameterValue = ProcessParameterValue;
+        this.ArcProcessParameterValue = ArcProcessParameterValue;
+        this.category = category;
+        this.value = value;
+        this.unit = unit;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.ISA.Json.ROCrateContext.ProcessParameterValue.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["ProcessParameterValue", string_type], ["ArcProcessParameterValue", string_type], ["category", string_type], ["value", string_type], ["unit", string_type]]);
+}
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["ProcessParameterValue", new Json(0, ["sdo:PropertyValue"])], ["ArcProcessParameterValue", new Json(0, ["arc:ARC#ARC_00000088"])], ["category", new Json(0, ["arc:ARC#ARC_00000062"])], ["value", new Json(0, ["arc:ARC#ARC_00000087"])], ["unit", new Json(0, ["arc:ARC#ARC_00000106"])]]]);
+
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"ProcessParameterValue\": \"sdo:PropertyValue\",\r\n    \"ArcProcessParameterValue\": \"arc:ARC#ARC_00000088\",\r\n\r\n    \"category\": \"arc:ARC#ARC_00000062\",\r\n    \"value\": \"arc:ARC#ARC_00000087\",\r\n    \"unit\": \"arc:ARC#ARC_00000106\"\r\n  }\r\n}\r\n    ";
+

package/ISA/ISA.Json/context/rocrate/isa_protocol_context.js

@@ -0,0 +1,30 @@
+import { Record } from "../../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, string_type } from "../../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Json } from "../../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, Protocol, ArcProtocol, name, protocolType, description, version, components, parameters, uri, comments) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.Protocol = Protocol;
+        this.ArcProtocol = ArcProtocol;
+        this.name = name;
+        this.protocolType = protocolType;
+        this.description = description;
+        this.version = version;
+        this.components = components;
+        this.parameters = parameters;
+        this.uri = uri;
+        this.comments = comments;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.ISA.Json.ROCrateContext.Protocol.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["Protocol", string_type], ["ArcProtocol", string_type], ["name", string_type], ["protocolType", string_type], ["description", string_type], ["version", string_type], ["components", string_type], ["parameters", string_type], ["uri", string_type], ["comments", string_type]]);
+}
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["Protocol", new Json(0, ["sdo:Thing"])], ["ArcProtocol", new Json(0, ["arc:ARC#ARC_00000040"])], ["name", new Json(0, ["arc:ARC#ARC_00000019"])], ["protocolType", new Json(0, ["arc:ARC#ARC_00000060"])], ["description", new Json(0, ["arc:ARC#ARC_00000004"])], ["version", new Json(0, ["arc:ARC#ARC_00000020"])], ["components", new Json(0, ["arc:ARC#ARC_00000064"])], ["parameters", new Json(0, ["arc:ARC#ARC_00000062"])], ["uri", new Json(0, ["arc:ARC#ARC_00000061"])], ["comments", new Json(0, ["arc:ARC#ARC_00000016"])]]]);
+
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Protocol\": \"sdo:Thing\",\r\n    \"ArcProtocol\": \"arc:ARC#ARC_00000040\",\r\n\r\n    \"name\": \"arc:ARC#ARC_00000019\",\r\n    \"protocolType\": \"arc:ARC#ARC_00000060\",\r\n    \"description\": \"arc:ARC#ARC_00000004\",\r\n    \"version\": \"arc:ARC#ARC_00000020\",\r\n    \"components\": \"arc:ARC#ARC_00000064\",\r\n    \"parameters\": \"arc:ARC#ARC_00000062\",\r\n    \"uri\": \"arc:ARC#ARC_00000061\",\r\n    \"comments\": \"arc:ARC#ARC_00000016\"\r\n  }\r\n}\r\n    ";
+

package/ISA/ISA.Json/context/rocrate/isa_protocol_parameter_context.js

@@ -0,0 +1,23 @@
+import { Record } from "../../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, string_type } from "../../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Json } from "../../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, ProtocolParamter, ArcProtocolParameter, parameterName) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.ProtocolParamter = ProtocolParamter;
+        this.ArcProtocolParameter = ArcProtocolParameter;
+        this.parameterName = parameterName;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.ISA.Json.ROCrateContext.ProtocolParameter.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["ProtocolParamter", string_type], ["ArcProtocolParameter", string_type], ["parameterName", string_type]]);
+}
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["ProtocolParameter", new Json(0, ["sdo:Thing"])], ["ArcProtocolParameter", new Json(0, ["arc:ARC#ARC_00000063"])], ["parameterName", new Json(0, ["arc:ARC#ARC_00000100"])]]]);
+
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"ProtocolParameter\": \"sdo:Thing\",\r\n    \"ArcProtocolParameter\": \"arc:ARC#ARC_00000063\",\r\n\r\n    \"parameterName\": \"arc:ARC#ARC_00000100\"\r\n  }\r\n}\r\n    ";
+

package/ISA/ISA.Json/context/rocrate/isa_publication_context.js

@@ -0,0 +1,27 @@
+import { Record } from "../../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, string_type } from "../../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Json } from "../../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, Publication, pubMedID, doi, title, status, authorList, comments) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.Publication = Publication;
+        this.pubMedID = pubMedID;
+        this.doi = doi;
+        this.title = title;
+        this.status = status;
+        this.authorList = authorList;
+        this.comments = comments;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.ISA.Json.ROCrateContext.Publication.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["Publication", string_type], ["pubMedID", string_type], ["doi", string_type], ["title", string_type], ["status", string_type], ["authorList", string_type], ["comments", string_type]]);
+}
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["Publication", new Json(0, ["sdo:ScholarlyArticle"])], ["pubMedID", new Json(0, ["sdo:url"])], ["doi", new Json(0, ["sdo:sameAs"])], ["title", new Json(0, ["sdo:headline"])], ["status", new Json(0, ["sdo:creativeWorkStatus"])], ["authorList", new Json(0, ["sdo:author"])], ["comments", new Json(0, ["sdo:disambiguatingDescription"])]]]);
+
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Publication\": \"sdo:ScholarlyArticle\",\r\n    \r\n    \"pubMedID\": \"sdo:url\",\r\n    \"doi\": \"sdo:sameAs\",\r\n    \"title\": \"sdo:headline\",\r\n    \"status\": \"sdo:creativeWorkStatus\",\r\n    \"authorList\": \"sdo:author\",\r\n    \"comments\": \"sdo:disambiguatingDescription\"\r\n  }\r\n}\r\n    ";
+

package/ISA/ISA.Json/context/rocrate/isa_sample_context.js

@@ -0,0 +1,26 @@
+import { Record } from "../../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, string_type } from "../../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Json } from "../../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, Sample, ArcSample, name, characteristics, factorValues, derivesFrom) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.Sample = Sample;
+        this.ArcSample = ArcSample;
+        this.name = name;
+        this.characteristics = characteristics;
+        this.factorValues = factorValues;
+        this.derivesFrom = derivesFrom;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.ISA.Json.ROCrateContext.Sample.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["Sample", string_type], ["ArcSample", string_type], ["name", string_type], ["characteristics", string_type], ["factorValues", string_type], ["derivesFrom", string_type]]);
+}
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["Sample", new Json(0, ["sdo:Thing"])], ["ArcSample", new Json(0, ["arc:ARC#ARC_00000070"])], ["name", new Json(0, ["arc:name"])], ["characteristics", new Json(0, ["arc:ARC#ARC_00000080"])], ["factorValues", new Json(0, ["arc:ARC#ARC_00000083"])], ["derivesFrom", new Json(0, ["arc:ARC#ARC_00000082"])]]]);
+
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Sample\": \"sdo:Thing\",\r\n    \"ArcSample\": \"arc:ARC#ARC_00000070\",\r\n\r\n    \"name\": \"arc:name\",\r\n    \"characteristics\": \"arc:ARC#ARC_00000080\",\r\n    \"factorValues\": \"arc:ARC#ARC_00000083\",\r\n    \"derivesFrom\": \"arc:ARC#ARC_00000082\"\r\n  }\r\n}\r\n    ";
+

package/ISA/ISA.Json/context/rocrate/isa_source_context.js

@@ -0,0 +1,25 @@
+import { Record } from "../../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, string_type } from "../../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Json } from "../../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, Source, ArcSource, identifier, characteristics, name) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.Source = Source;
+        this.ArcSource = ArcSource;
+        this.identifier = identifier;
+        this.characteristics = characteristics;
+        this.name = name;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.ISA.Json.ROCrateContext.Source.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["Source", string_type], ["ArcSource", string_type], ["identifier", string_type], ["characteristics", string_type], ["name", string_type]]);
+}
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["Source", new Json(0, ["sdo:Thing"])], ["ArcSource", new Json(0, ["arc:ARC#ARC_00000071"])], ["identifier", new Json(0, ["sdo:identifier"])], ["name", new Json(0, ["arc:ARC#ARC_00000019"])], ["characteristics", new Json(0, ["arc:ARC#ARC_00000080"])]]]);
+
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Source\": \"sdo:Thing\",\r\n    \"ArcSource\": \"arc:ARC#ARC_00000071\",\r\n\r\n    \"identifier\": \"sdo:identifier\",\r\n\r\n    \"name\": \"arc:ARC#ARC_00000019\",\r\n    \"characteristics\": \"arc:ARC#ARC_00000080\"\r\n  }\r\n}\r\n    ";
+

package/ISA/ISA.Json/context/rocrate/isa_study_context.js

@@ -0,0 +1,42 @@
+import { Record } from "../../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, string_type } from "../../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Json } from "../../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, Study, ArcStudy, identifier, title, description, submissionDate, publicReleaseDate, publications, people, assays, filename, comments, protocols, materials, otherMaterials, sources, samples, processSequence, factors, characteristicCategories, unitCategories, studyDesignDescriptors) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.Study = Study;
+        this.ArcStudy = ArcStudy;
+        this.identifier = identifier;
+        this.title = title;
+        this.description = description;
+        this.submissionDate = submissionDate;
+        this.publicReleaseDate = publicReleaseDate;
+        this.publications = publications;
+        this.people = people;
+        this.assays = assays;
+        this.filename = filename;
+        this.comments = comments;
+        this.protocols = protocols;
+        this.materials = materials;
+        this.otherMaterials = otherMaterials;
+        this.sources = sources;
+        this.samples = samples;
+        this.processSequence = processSequence;
+        this.factors = factors;
+        this.characteristicCategories = characteristicCategories;
+        this.unitCategories = unitCategories;
+        this.studyDesignDescriptors = studyDesignDescriptors;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.ISA.Json.ROCrateContext.Study.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["Study", string_type], ["ArcStudy", string_type], ["identifier", string_type], ["title", string_type], ["description", string_type], ["submissionDate", string_type], ["publicReleaseDate", string_type], ["publications", string_type], ["people", string_type], ["assays", string_type], ["filename", string_type], ["comments", string_type], ["protocols", string_type], ["materials", string_type], ["otherMaterials", string_type], ["sources", string_type], ["samples", string_type], ["processSequence", string_type], ["factors", string_type], ["characteristicCategories", string_type], ["unitCategories", string_type], ["studyDesignDescriptors", string_type]]);
+}
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["Study", new Json(0, ["sdo:Dataset"])], ["ArcStudy", new Json(0, ["arc:ARC#ARC_00000014"])], ["identifier", new Json(0, ["sdo:identifier"])], ["title", new Json(0, ["sdo:headline"])], ["description", new Json(0, ["sdo:description"])], ["submissionDate", new Json(0, ["sdo:dateCreated"])], ["publicReleaseDate", new Json(0, ["sdo:datePublished"])], ["publications", new Json(0, ["sdo:citation"])], ["people", new Json(0, ["sdo:creator"])], ["assays", new Json(0, ["sdo:hasPart"])], ["filename", new Json(0, ["sdo:description"])], ["comments", new Json(0, ["sdo:disambiguatingDescription"])], ["protocols", new Json(0, ["arc:ARC#ARC_00000039"])], ["materials", new Json(0, ["arc:ARC#ARC_00000045"])], ["otherMaterials", new Json(0, ["arc:ARC#ARC_00000045"])], ["sources", new Json(0, ["arc:ARC#ARC_00000045"])], ["samples", new Json(0, ["arc:ARC#ARC_00000045"])], ["processSequence", new Json(0, ["arc:ARC#ARC_00000047"])], ["factors", new Json(0, ["arc:ARC#ARC_00000043"])], ["characteristicCategories", new Json(0, ["arc:ARC#ARC_00000049"])], ["unitCategories", new Json(0, ["arc:ARC#ARC_00000051"])], ["studyDesignDescriptors", new Json(0, ["arc:ARC#ARC_00000037"])]]]);
+
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n\r\n    \"Study\": \"sdo:Dataset\",\r\n    \"ArcStudy\": \"arc:ARC#ARC_00000014\",\r\n\r\n    \"identifier\": \"sdo:identifier\",\r\n    \"title\": \"sdo:headline\",\r\n    \"description\": \"sdo:description\",\r\n    \"submissionDate\": \"sdo:dateCreated\",\r\n    \"publicReleaseDate\": \"sdo:datePublished\",\r\n    \"publications\": \"sdo:citation\",\r\n    \"people\": \"sdo:creator\",\r\n    \"assays\": \"sdo:hasPart\",\r\n    \"filename\": \"sdo:description\",\r\n    \"comments\": \"sdo:disambiguatingDescription\",\r\n\r\n    \"protocols\": \"arc:ARC#ARC_00000039\",\r\n    \"materials\": \"arc:ARC#ARC_00000045\",\r\n    \"otherMaterials\": \"arc:ARC#ARC_00000045\",\r\n    \"sources\": \"arc:ARC#ARC_00000045\",\r\n    \"samples\": \"arc:ARC#ARC_00000045\",\r\n    \"processSequence\": \"arc:ARC#ARC_00000047\",\r\n    \"factors\": \"arc:ARC#ARC_00000043\",\r\n    \"characteristicCategories\": \"arc:ARC#ARC_00000049\",\r\n    \"unitCategories\": \"arc:ARC#ARC_00000051\",\r\n    \"studyDesignDescriptors\": \"arc:ARC#ARC_00000037\"\r\n  }\r\n}\r\n    ";
+

package/ISA/ISA.Json/context/rocrate/rocrate_context.js

@@ -0,0 +1,25 @@
+import { Record } from "../../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { record_type, string_type } from "../../../../fable_modules/fable-library-js.4.13.0/Reflection.js";
+import { Json } from "../../../../fable_modules/Thoth.Json.Core.0.2.1/Types.fs.js";
+
+export class IContext extends Record {
+    constructor(sdo, arc, CreativeWork, about, conformsTo) {
+        super();
+        this.sdo = sdo;
+        this.arc = arc;
+        this.CreativeWork = CreativeWork;
+        this.about = about;
+        this.conformsTo = conformsTo;
+    }
+}
+
+export function IContext_$reflection() {
+    return record_type("ARCtrl.ISA.Json.ROCrateContext.ROCrate.IContext", [], IContext, () => [["sdo", string_type], ["arc", string_type], ["CreativeWork", string_type], ["about", string_type], ["conformsTo", string_type]]);
+}
+
+export const conformsTo_jsonvalue = new Json(5, [[["@id", new Json(0, ["https://w3id.org/ro/crate/1.1"])]]]);
+
+export const context_jsonvalue = new Json(5, [[["sdo", new Json(0, ["http://schema.org/"])], ["arc", new Json(0, ["http://purl.org/nfdi4plants/ontology/"])], ["CreativeWork", new Json(0, ["sdo:CreativeWork"])], ["about", new Json(0, ["sdo:about"])], ["conformsTo", new Json(0, ["sdo:conformsTo"])]]]);
+
+export const context_str = "\r\n{\r\n  \"@context\": {\r\n    \"sdo\": \"http://schema.org/\",\r\n    \"arc\": \"http://purl.org/nfdi4plants/ontology/\",\r\n    \r\n    \"CreativeWork\": \"sdo:CreativeWork\",\r\n\r\n    \"about\": \"sdo:about\",\r\n    \"conformsTo\": \"sdo:conformsTo\"\r\n  }\r\n}\r\n    ";
+

package/ISA/ISA.Spreadsheet/AnnotationTable/ArcTable.js

@@ -1,15 +1,16 @@
-import { iterateIndexed, length, ofArray, sortBy, collect, toArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { iterateIndexed, length, ofArray, sortBy, collect, toArray, empty, tail, head, isEmpty, cons, singleton, fold, map, reverse } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
 import { tryParseReferenceColumnHeader } from "../../ISA/Regex.js";
-import { map as map_1, toList, tryFind } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { map as map_1, toList, tryFind } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
 import { toFsColumns, fixDeprecatedIOHeader, fromFsColumns } from "./CompositeColumn.js";
+import { printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
 import { ArcTable } from "../../ISA/ArcTypes/ArcTable.js";
-import { FsWorksheet } from "../../../fable_modules/FsSpreadsheet.5.1.2/FsWorksheet.fs.js";
-import { comparePrimitives } from "../../../fable_modules/fable-library.4.5.0/Util.js";
-import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.1.2/Ranges/FsRangeAddress.fs.js";
-import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.1.2/FsAddress.fs.js";
-import { Dictionary_tryGet } from "../../../fable_modules/FsSpreadsheet.5.1.2/Cells/FsCellsCollection.fs.js";
-import { addToDict } from "../../../fable_modules/fable-library.4.5.0/MapUtil.js";
-import { FsRangeBase__Cell_Z3407A44B } from "../../../fable_modules/FsSpreadsheet.5.1.2/Ranges/FsRangeBase.fs.js";
+import { FsWorksheet } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsWorksheet.fs.js";
+import { comparePrimitives } from "../../../fable_modules/fable-library-js.4.13.0/Util.js";
+import { FsRangeAddress_$ctor_7E77A4A0 } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
+import { FsAddress_$ctor_Z37302880 } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
+import { Dictionary_tryGet } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCellsCollection.fs.js";
+import { addToDict } from "../../../fable_modules/fable-library-js.4.13.0/MapUtil.js";
+import { FsRangeBase__Cell_Z3407A44B } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeBase.fs.js";
 
 /**
  * Iterates over elements of the input list and groups adjacent elements.
@@ -91,49 +92,61 @@ export function composeColumns(columns) {
  * Returns the protocol described by the headers and a function for parsing the values of the matrix to the processes of this protocol
  */
 export function tryFromFsWorksheet(sheet) {
-    const matchValue = tryAnnotationTable(sheet);
-    if (matchValue == null) {
-        return void 0;
+    try {
+        const matchValue = tryAnnotationTable(sheet);
+        if (matchValue == null) {
+            return void 0;
+        }
+        else {
+            const t = matchValue;
+            const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, t.GetColumns(sheet.CellCollection)));
+            return ArcTable.addColumns(compositeColumns, void 0, true)(ArcTable.init(sheet.Name));
+        }
     }
-    else {
-        const t = matchValue;
-        const compositeColumns = composeColumns(map_1(fixDeprecatedIOHeader, t.GetColumns(sheet.CellCollection)));
-        return ArcTable.addColumns(compositeColumns, void 0, true)(ArcTable.init(sheet.Name));
+    catch (err) {
+        const arg = sheet.Name;
+        const arg_1 = err.message;
+        return toFail(printf("Could not parse table with name \"%s\":\n%s"))(arg)(arg_1);
     }
 }
 
 export function toFsWorksheet(table) {
     const stringCount = new Map([]);
     const ws = new FsWorksheet(table.Name);
-    const columns = collect(toFsColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
-        Compare: comparePrimitives,
-    }));
-    const maxRow = length(head(columns)) | 0;
-    const maxCol = length(columns) | 0;
-    const fsTable = ws.Table("annotationTable", FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
-    iterateIndexed((colI, col) => {
-        iterateIndexed((rowI, cell) => {
-            let value;
-            const v = cell.ValueAsString();
-            if (rowI === 0) {
-                const matchValue = Dictionary_tryGet(v, stringCount);
-                if (matchValue == null) {
-                    addToDict(stringCount, cell.ValueAsString(), "");
-                    value = v;
+    if (table.Columns.length === 0) {
+        return ws;
+    }
+    else {
+        const columns = collect(toFsColumns, sortBy(classifyColumnOrder, ofArray(table.Columns), {
+            Compare: comparePrimitives,
+        }));
+        const maxRow = length(head(columns)) | 0;
+        const maxCol = length(columns) | 0;
+        const fsTable = ws.Table("annotationTable", FsRangeAddress_$ctor_7E77A4A0(FsAddress_$ctor_Z37302880(1, 1), FsAddress_$ctor_Z37302880(maxRow, maxCol)));
+        iterateIndexed((colI, col) => {
+            iterateIndexed((rowI, cell) => {
+                let value;
+                const v = cell.ValueAsString();
+                if (rowI === 0) {
+                    const matchValue = Dictionary_tryGet(v, stringCount);
+                    if (matchValue == null) {
+                        addToDict(stringCount, cell.ValueAsString(), "");
+                        value = v;
+                    }
+                    else {
+                        const spaces = matchValue;
+                        stringCount.set(v, spaces + " ");
+                        value = ((v + " ") + spaces);
+                    }
                 }
                 else {
-                    const spaces = matchValue;
-                    stringCount.set(v, spaces + " ");
-                    value = ((v + " ") + spaces);
+                    value = v;
                 }
-            }
-            else {
-                value = v;
-            }
-            const address = FsAddress_$ctor_Z37302880(rowI + 1, colI + 1);
-            FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);
-        }, col);
-    }, columns);
-    return ws;
+                const address = FsAddress_$ctor_Z37302880(rowI + 1, colI + 1);
+                FsRangeBase__Cell_Z3407A44B(fsTable, address, ws.CellCollection).SetValueAs(value);
+            }, col);
+        }, columns);
+        return ws;
+    }
 }
 

package/ISA/ISA.Spreadsheet/AnnotationTable/CompositeCell.js

@@ -1,7 +1,7 @@
-import { singleton, ofArray, head, tail, isEmpty, map } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { singleton, ofArray, head, tail, isEmpty, map } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
 import { CompositeCell } from "../../ISA/ArcTypes/CompositeCell.js";
-import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
-import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.2/Cells/FsCell.fs.js";
+import { printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
+import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
 
 export function fromFsCells(cells) {
     const cellValues = map((c) => c.ValueAsString(), cells);

package/ISA/ISA.Spreadsheet/AnnotationTable/CompositeColumn.js

@@ -1,15 +1,15 @@
 import { CompositeHeader, IOType } from "../../ISA/ArcTypes/CompositeHeader.js";
-import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
+import { toString } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
 import { toFsCells, fromFsCells } from "./CompositeHeader.js";
-import { singleton as singleton_1, ofArray, item, map } from "../../../fable_modules/fable-library.4.5.0/List.js";
-import { FsAddress__get_RowNumber } from "../../../fable_modules/FsSpreadsheet.5.1.2/FsAddress.fs.js";
-import { FsRangeAddress__get_LastAddress } from "../../../fable_modules/FsSpreadsheet.5.1.2/Ranges/FsRangeAddress.fs.js";
-import { FsRangeBase__get_RangeAddress } from "../../../fable_modules/FsSpreadsheet.5.1.2/Ranges/FsRangeBase.fs.js";
-import { singleton, append, toList, exists, map as map_1, delay, toArray } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { singleton as singleton_1, ofArray, item, map } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
+import { FsAddress__get_RowNumber } from "../../../fable_modules/FsSpreadsheet.5.1.3/FsAddress.fs.js";
+import { FsRangeAddress__get_LastAddress } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeAddress.fs.js";
+import { FsRangeBase__get_RangeAddress } from "../../../fable_modules/FsSpreadsheet.5.1.3/Ranges/FsRangeBase.fs.js";
+import { singleton, append, toList, exists, map as map_1, delay, toArray } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
 import { toFsCells as toFsCells_1, fromFsCells as fromFsCells_1 } from "./CompositeCell.js";
-import { rangeDouble } from "../../../fable_modules/fable-library.4.5.0/Range.js";
+import { rangeDouble } from "../../../fable_modules/fable-library-js.4.13.0/Range.js";
 import { CompositeColumn } from "../../ISA/ArcTypes/CompositeColumn.js";
-import { map as map_2 } from "../../../fable_modules/fable-library.4.5.0/Array.js";
+import { item as item_1, map as map_2 } from "../../../fable_modules/fable-library-js.4.13.0/Array.js";
 
 /**
  * Checks if the column header is a deprecated IO Header. If so, fixes it.
@@ -47,13 +47,13 @@ export function toFsColumns(column) {
     const header = toFsCells(hasUnit, column.Header);
     const cells = map_2((cell) => toFsCells_1(isTerm, hasUnit, cell), column.Cells);
     if (hasUnit) {
-        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i) => item(0, cells[i]), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_1) => item(1, cells[i_1]), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_2) => item(2, cells[i_2]), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(3, header)), delay(() => map_1((i_3) => item(3, cells[i_3]), rangeDouble(0, 1, column.Cells.length - 1))))))]);
+        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i) => item(0, item_1(i, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_1) => item(1, item_1(i_1, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_2) => item(2, item_1(i_2, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(3, header)), delay(() => map_1((i_3) => item(3, item_1(i_3, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))]);
     }
     else if (isTerm) {
-        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_4) => item(0, cells[i_4]), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_5) => item(1, cells[i_5]), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_6) => item(2, cells[i_6]), rangeDouble(0, 1, column.Cells.length - 1))))))]);
+        return ofArray([toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_4) => item(0, item_1(i_4, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(1, header)), delay(() => map_1((i_5) => item(1, item_1(i_5, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))), toList(delay(() => append(singleton(item(2, header)), delay(() => map_1((i_6) => item(2, item_1(i_6, cells)), rangeDouble(0, 1, column.Cells.length - 1))))))]);
     }
     else {
-        return singleton_1(toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_7) => item(0, cells[i_7]), rangeDouble(0, 1, column.Cells.length - 1)))))));
+        return singleton_1(toList(delay(() => append(singleton(item(0, header)), delay(() => map_1((i_7) => item(0, item_1(i_7, cells)), rangeDouble(0, 1, column.Cells.length - 1)))))));
     }
 }
 

package/ISA/ISA.Spreadsheet/AnnotationTable/CompositeHeader.js

@@ -1,11 +1,11 @@
-import { printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
-import { singleton, tail, head, isEmpty, map } from "../../../fable_modules/fable-library.4.5.0/List.js";
+import { printf, toFail } from "../../../fable_modules/fable-library-js.4.13.0/String.js";
+import { singleton, tail, head, isEmpty, map } from "../../../fable_modules/fable-library-js.4.13.0/List.js";
 import { OntologyAnnotation } from "../../ISA/JsonTypes/OntologyAnnotation.js";
 import { ActivePatterns_$007COutputColumnHeader$007C_$007C, ActivePatterns_$007CInputColumnHeader$007C_$007C, tryParseComponentColumnHeader, tryParseCharacteristicColumnHeader, tryParseFactorColumnHeader, tryParseParameterColumnHeader, ActivePatterns_$007CUnitColumnHeader$007C_$007C, ActivePatterns_$007CTANColumnHeader$007C_$007C, ActivePatterns_$007CTSRColumnHeader$007C_$007C } from "../../ISA/Regex.js";
 import { IOType, CompositeHeader } from "../../ISA/ArcTypes/CompositeHeader.js";
-import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.2/Cells/FsCell.fs.js";
-import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
-import { empty, singleton as singleton_1, append, delay, toList } from "../../../fable_modules/fable-library.4.5.0/Seq.js";
+import { FsCell } from "../../../fable_modules/FsSpreadsheet.5.1.3/Cells/FsCell.fs.js";
+import { toString } from "../../../fable_modules/fable-library-js.4.13.0/Types.js";
+import { empty, singleton as singleton_1, append, delay, toList } from "../../../fable_modules/fable-library-js.4.13.0/Seq.js";
 
 export function ActivePattern_mergeIDInfo(idSpace1, localID1, idSpace2, localID2) {
     if (idSpace1 !== idSpace2) {