@nfdi4plants/arctrl 1.0.0-beta.7 → 1.0.0-beta.9

package/ARC.js

@@ -1,5 +1,5 @@
 import { concat, fold, map, exactlyOne, choose } from "./fable_modules/fable-library.4.5.0/Array.js";
-import { ARCtrl_ISA_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract, ARCtrl_ISA_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ISA_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, ARCtrl_ISA_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F, ARCtrl_ISA_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from "./Contracts/Contracts.ArcTypes.js";
+import { ARCtrl_ISA_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49, ARCtrl_ISA_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ISA_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, ARCtrl_ISA_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F, ARCtrl_ISA_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from "./Contracts/Contracts.ArcTypes.js";
 import { collect, empty, iterate, find, tryFind, map as map_1, singleton, append, delay, toList, toArray } from "./fable_modules/fable-library.4.5.0/Seq.js";
 import { createRunsFolder, createWorkflowsFolder, createInvestigationFile, createStudyFolder, createStudiesFolder, createAssayFolder, createAssaysFolder } from "./FileSystemTree.js";
 import { FileSystemTree } from "./FileSystem/FileSystemTree.js";
@@ -11,7 +11,7 @@ import { ofArray } from "./fable_modules/fable-library.4.5.0/List.js";
 import { tryISAReadContractFromPath } from "./Contracts/Contracts.ARCtrl.js";
 import { ArcTables } from "./ISA/ISA/ArcTypes/ArcTables.js";
 import { addToDict } from "./fable_modules/fable-library.4.5.0/MapUtil.js";
-import { toFsWorkbook } from "./ISA/ISA.Spreadsheet/ArcInvestigation.js";
+import { toFsWorkbook, toLightFsWorkbook } from "./ISA/ISA.Spreadsheet/ArcInvestigation.js";
 import { ArcInvestigation } from "./ISA/ISA/ArcTypes/ArcTypes.js";
 import { Assay_fileNameFromIdentifier, Study_fileNameFromIdentifier } from "./ISA/ISA/Identifier.js";
 import { ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9 } from "./ISA/ISA.Spreadsheet/ArcStudy.js";
@@ -113,7 +113,7 @@ export class ARC {
         const assayFolderPath = getAssayFolderPath(assayIdentifier);
         const filteredPaths = paths.filter((p) => !(p.indexOf(assayFolderPath) === 0));
         this$.SetFilePaths(filteredPaths);
-        const collection = toList(delay(() => append(singleton(ARCtrl_ISA_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => append(singleton(ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract(isa)), delay(() => map_1(ARCtrl_ISA_ArcStudy__ArcStudy_ToUpdateContract, studies)))))));
+        const collection = toList(delay(() => append(singleton(ARCtrl_ISA_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => append(singleton(ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49(isa)), delay(() => map_1(ARCtrl_ISA_ArcStudy__ArcStudy_ToUpdateContract, studies)))))));
         return Array.from(collection);
     }
     RemoveStudy(studyIdentifier) {
@@ -131,7 +131,7 @@ export class ARC {
         const studyFolderPath = getStudyFolderPath(studyIdentifier);
         const filteredPaths = paths.filter((p) => !(p.indexOf(studyFolderPath) === 0));
         this$.SetFilePaths(filteredPaths);
-        const collection = ofArray([Contract.createDelete(studyFolderPath), ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract(isa)]);
+        const collection = ofArray([Contract.createDelete(studyFolderPath), ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49(isa)]);
         return Array.from(collection);
     }
     static fromFilePaths(filePaths) {
@@ -160,7 +160,7 @@ export class ARC {
         const array_4 = investigation.StudyIdentifiers;
         array_4.forEach((si) => {
             if (!studies.some((s) => (s.Identifier === si))) {
-                investigation.RemoveStudy(si);
+                investigation.DeleteStudy(si);
             }
         });
         studies.forEach((study) => {
@@ -197,16 +197,17 @@ export class ARC {
         newFS = ARCAux_updateFSByCWL(this$._cwl, fs);
         this$._fs = newFS;
     }
-    GetWriteContracts() {
+    GetWriteContracts(isLight) {
         const this$ = this;
+        const isLight_1 = defaultArg(isLight, true);
         const workbooks = new Map([]);
         const matchValue = this$.ISA;
         if (matchValue == null) {
-            addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", toFsWorkbook(ArcInvestigation.create("MISSING_IDENTIFIER_"))]);
+            addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", toLightFsWorkbook(ArcInvestigation.create("MISSING_IDENTIFIER_"))]);
         }
         else {
             const inv = matchValue;
-            addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", toFsWorkbook(inv)]);
+            addToDict(workbooks, "isa.investigation.xlsx", ["ISA_Investigation", (isLight_1 ? (toLightFsWorkbook) : (toFsWorkbook))(inv)]);
             iterate((s) => {
                 addToDict(workbooks, Study_fileNameFromIdentifier(s.Identifier), ["ISA_Study", ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9(s)]);
             }, inv.Studies);

package/Contracts/Contracts.ArcTypes.js

@@ -1,8 +1,9 @@
 import { combineMany } from "../FileSystem/Path.js";
 import { equalsWith } from "../fable_modules/fable-library.4.5.0/Array.js";
 import { defaultOf } from "../fable_modules/fable-library.4.5.0/Util.js";
+import { unwrap, defaultArg } from "../fable_modules/fable-library.4.5.0/Option.js";
+import { fromFsWorkbook, toFsWorkbook, toLightFsWorkbook } from "../ISA/ISA.Spreadsheet/ArcInvestigation.js";
 import { Contract } from "../Contract/Contract.js";
-import { fromFsWorkbook, toFsWorkbook } from "../ISA/ISA.Spreadsheet/ArcInvestigation.js";
 import { Assay_fileNameFromIdentifier, Study_fileNameFromIdentifier } from "../ISA/ISA/Identifier.js";
 import { ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D, ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9 } from "../ISA/ISA.Spreadsheet/ArcStudy.js";
 import { getAssayFolderPath, getStudyFolderPath } from "../Path.js";
@@ -85,20 +86,22 @@ export function $007CInvestigationPath$007C_$007C(input) {
     }
 }
 
-export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToCreateContract(this$) {
-    return Contract.createCreate("isa.investigation.xlsx", "ISA_Investigation", toFsWorkbook(this$));
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToCreateContract_6FCE9E49(this$, isLight) {
+    const converter = defaultArg(isLight, true) ? (toLightFsWorkbook) : (toFsWorkbook);
+    return Contract.createCreate("isa.investigation.xlsx", "ISA_Investigation", converter(this$));
 }
 
-export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$) {
-    return Contract.createUpdate("isa.investigation.xlsx", "ISA_Investigation", toFsWorkbook(this$));
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49(this$, isLight) {
+    const converter = defaultArg(isLight, true) ? (toLightFsWorkbook) : (toFsWorkbook);
+    return Contract.createUpdate("isa.investigation.xlsx", "ISA_Investigation", converter(this$));
 }
 
-export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_toCreateContract_Static_Z4D87C88C(inv) {
-    return ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToCreateContract(inv);
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_toCreateContract_Static_6EB1BBBD(inv, isLight) {
+    return ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToCreateContract_6FCE9E49(inv, unwrap(isLight));
 }
 
-export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_toUpdateContract_Static_Z4D87C88C(inv) {
-    return ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract(inv);
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_toUpdateContract_Static_6EB1BBBD(inv, isLight) {
+    return ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49(inv, unwrap(isLight));
 }
 
 export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F(c) {

package/ISA/ISA/ArcTypes/ArcTable.js

@@ -9,14 +9,14 @@ import { sortBy, indexed, mapIndexed, singleton as singleton_1, initialize, sort
 import { append, collect as collect_1, initialize as initialize_1, singleton as singleton_2, empty as empty_1, iterate, isEmpty } from "../../../fable_modules/fable-library.4.5.0/List.js";
 import { StringBuilder__AppendLine_Z721C83C5, StringBuilder_$ctor } from "../../../fable_modules/fable-library.4.5.0/System.Text.js";
 import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
-import { join, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { join, toConsole, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
 import { CompositeCell } from "./CompositeCell.js";
 import { CompositeHeader } from "./CompositeHeader.js";
 import { createMissingIdentifier } from "../Identifier.js";
 import { ARCtrl_ISA_Component__Component_TryGetColumnIndex, ARCtrl_ISA_ProtocolParameter__ProtocolParameter_TryGetColumnIndex } from "../JsonTypes/ColumnIndex.js";
 import { Protocol_create_Z7DFD6E67, Protocol_addComponent, Protocol_addParameter, Protocol_setName, Protocol_setDescription, Protocol_setUri, Protocol_setVersion, Protocol_setProtocolType } from "../JsonTypes/Protocol.js";
 import { OntologyAnnotation } from "../JsonTypes/OntologyAnnotation.js";
-import { ProtocolParameter_create_Z6C54B221 } from "../JsonTypes/ProtocolParameter.js";
+import { ProtocolParameter } from "../JsonTypes/ProtocolParameter.js";
 import { Component_create_61502994 } from "../JsonTypes/Component.js";
 import { Array_groupBy, List_distinct } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
 import { toProtocol } from "./CompositeRow.js";
@@ -27,33 +27,33 @@ import { class_type } from "../../../fable_modules/fable-library.4.5.0/Reflectio
 
 export class ArcTable {
     constructor(name, headers, values) {
-        this._name = name;
-        this["Headers@"] = headers;
-        this["Values@"] = values;
+        this["name@20"] = name;
+        this["headers@21"] = headers;
+        this["values@22"] = values;
     }
     get Headers() {
-        const __ = this;
-        return __["Headers@"];
+        const this$ = this;
+        return this$["headers@21"];
     }
-    set Headers(v) {
-        const __ = this;
-        __["Headers@"] = v;
+    set Headers(newHeaders) {
+        const this$ = this;
+        this$["headers@21"] = newHeaders;
     }
     get Values() {
-        const __ = this;
-        return __["Values@"];
+        const this$ = this;
+        return this$["values@22"];
     }
-    set Values(v) {
-        const __ = this;
-        __["Values@"] = v;
+    set Values(newValues) {
+        const this$ = this;
+        this$["values@22"] = newValues;
     }
     get Name() {
         const this$ = this;
-        return this$._name;
+        return this$["name@20"];
     }
     set Name(newName) {
         const this$ = this;
-        this$._name = newName;
+        this$["name@20"] = newName;
     }
     static create(name, headers, values) {
         return new ArcTable(name, headers, values);
@@ -720,7 +720,7 @@ export class ArcTable {
                 case 8:
                     return Protocol_setName(p, "");
                 case 3:
-                    return Protocol_addParameter(ProtocolParameter_create_Z6C54B221(void 0, h.fields[0]), p);
+                    return Protocol_addParameter(ProtocolParameter.create(void 0, h.fields[0]), p);
                 case 0:
                     return Protocol_addComponent(Component_create_61502994(void 0, void 0, void 0, h.fields[0]), p);
                 default:
@@ -739,15 +739,18 @@ export class ArcTable {
     GetProcesses() {
         const this$ = this;
         if (this$.RowCount === 0) {
+            toConsole(printf("GetProcesses xddd"));
             return singleton_2(Process_create_Z42860F3E(void 0, this$.Name));
         }
         else {
+            toConsole(printf("GetProcesses rofl"));
             let getter;
             const clo = ProcessParsing_getProcessGetter(this$.Name, this$.Headers);
             getter = ((arg) => {
                 const clo_1 = clo(arg);
                 return clo_1;
             });
+            toConsole(printf("GetProcesses roflcopter"));
             return ProcessParsing_mergeIdenticalProcesses(toList(delay(() => map((i) => getter(this$.Values)(i), rangeDouble(0, 1, this$.RowCount - 1)))));
         }
     }

package/ISA/ISA/ArcTypes/ArcTableAux.js

@@ -7,24 +7,24 @@ import { CompositeCell } from "./CompositeCell.js";
 import { max } from "../../../fable_modules/fable-library.4.5.0/Double.js";
 import { iterateIndexed } from "../../../fable_modules/fable-library.4.5.0/Array.js";
 import { FSharpSet__get_MinimumElement, FSharpSet__get_IsEmpty, difference, ofSeq as ofSeq_1 } from "../../../fable_modules/fable-library.4.5.0/Set.js";
-import { Value_fromString_Z721C83C5, Value as Value_1 } from "../JsonTypes/Value.js";
+import { Value as Value_1 } from "../JsonTypes/Value.js";
 import { Component_fromOptions } from "../JsonTypes/Component.js";
-import { ProcessParameterValue_create_569825F3 } from "../JsonTypes/ProcessParameterValue.js";
-import { ProtocolParameter_create_Z6C54B221 } from "../JsonTypes/ProtocolParameter.js";
+import { ProtocolParameter } from "../JsonTypes/ProtocolParameter.js";
+import { ProcessParameterValue } from "../JsonTypes/ProcessParameterValue.js";
 import { FactorValue_create_18335379 } from "../JsonTypes/FactorValue.js";
 import { Factor } from "../JsonTypes/Factor.js";
 import { toString } from "../../../fable_modules/fable-library.4.5.0/Types.js";
 import { MaterialAttributeValue_create_7F714043 } from "../JsonTypes/MaterialAttributeValue.js";
 import { MaterialAttribute_create_Z6C54B221 } from "../JsonTypes/MaterialAttribute.js";
 import { ProcessInput_getCharacteristicValues_102B6859, ProcessInput__isMaterial, ProcessInput__isData, ProcessInput_setCharacteristicValues, ProcessInput__get_Name, ProcessInput__isSource, ProcessInput__isSample, ProcessInput, ProcessInput_createDerivedData_Z721C83C5, ProcessInput_createRawData_Z721C83C5, ProcessInput_createImageFile_Z721C83C5, ProcessInput_createMaterial_2363974C, ProcessInput_createSample_Z6DF16D07, ProcessInput_createSource_7888CE42 } from "../JsonTypes/ProcessInput.js";
-import { remove, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
+import { toConsole, remove, printf, toFail } from "../../../fable_modules/fable-library.4.5.0/String.js";
 import { ProcessOutput_getFactorValues_11830B70, ProcessOutput__isMaterial, ProcessOutput__isData, ProcessOutput_setFactorValues, ProcessOutput__get_Name, ProcessOutput__isSample, ProcessOutput, ProcessOutput_createDerivedData_Z721C83C5, ProcessOutput_createRawData_Z721C83C5, ProcessOutput_createImageFile_Z721C83C5, ProcessOutput_createMaterial_2363974C, ProcessOutput_createSample_Z6DF16D07 } from "../JsonTypes/ProcessOutput.js";
 import { IOType, CompositeHeader } from "./CompositeHeader.js";
 import { tryGetFactorColumnIndex, tryGetCharacteristicColumnIndex, tryGetComponentIndex, tryGetParameterColumnIndex, ARCtrl_ISA_OntologyAnnotation__OntologyAnnotation_SetColumnIndex_Z524259A4 } from "../JsonTypes/ColumnIndex.js";
 import { Source_create_7A281ED9 } from "../JsonTypes/Source.js";
 import { Sample_create_E50ED22 } from "../JsonTypes/Sample.js";
 import { Process_create_Z42860F3E, Process_decomposeName_Z721C83C5, Process_make, Process_composeName } from "../JsonTypes/Process.js";
-import { List_tryPickAndRemove, Option_fromValueWithDefault } from "../Helper.js";
+import { List_tryPickAndRemove, HashCodes_boxHashSeq, Option_fromValueWithDefault } from "../Helper.js";
 import { Protocol_make } from "../JsonTypes/Protocol.js";
 import { List_groupBy } from "../../../fable_modules/fable-library.4.5.0/Seq2.js";
 import { createMissingIdentifier } from "../Identifier.js";
@@ -420,9 +420,9 @@ export function JsonTypes_valueOfCell(value) {
         case 0:
             return [new Value_1(0, [value.fields[0]]), void 0];
         case 2:
-            return [Value_fromString_Z721C83C5(value.fields[0]), value.fields[1]];
+            return [Value_1.fromString(value.fields[0]), value.fields[1]];
         default:
-            return [Value_fromString_Z721C83C5(value.fields[0]), void 0];
+            return [Value_1.fromString(value.fields[0]), void 0];
     }
 }
 
@@ -439,7 +439,8 @@ export function JsonTypes_composeComponent(header, value) {
  */
 export function JsonTypes_composeParameterValue(header, value) {
     const patternInput = JsonTypes_valueOfCell(value);
-    return ProcessParameterValue_create_569825F3(ProtocolParameter_create_Z6C54B221(void 0, header.ToTerm()), patternInput[0], unwrap(patternInput[1]));
+    const p = ProtocolParameter.create(void 0, header.ToTerm());
+    return ProcessParameterValue.create(p, patternInput[0], unwrap(patternInput[1]));
 }
 
 /**
@@ -939,27 +940,30 @@ export function ProcessParsing_groupProcesses(ps) {
  * Merges processes with the same name, protocol and param values
  */
 export function ProcessParsing_mergeIdenticalProcesses(processes) {
+    toConsole(printf("Merging identical processes aaaaaa"));
     const l = List_groupBy((x) => {
         if ((x.Name != null) && (Process_decomposeName_Z721C83C5(value_9(x.Name))[1] != null)) {
-            return [Process_decomposeName_Z721C83C5(value_9(x.Name))[0], x.ExecutesProtocol, x.ParameterValues];
+            return [Process_decomposeName_Z721C83C5(value_9(x.Name))[0], x.ExecutesProtocol, map_1(HashCodes_boxHashSeq, x.ParameterValues)];
         }
         else if ((x.ExecutesProtocol != null) && (value_9(x.ExecutesProtocol).Name != null)) {
-            return [value_9(value_9(x.ExecutesProtocol).Name), x.ExecutesProtocol, x.ParameterValues];
+            return [value_9(value_9(x.ExecutesProtocol).Name), x.ExecutesProtocol, map_1(HashCodes_boxHashSeq, x.ParameterValues)];
         }
         else {
-            return [createMissingIdentifier(), x.ExecutesProtocol, x.ParameterValues];
+            return [createMissingIdentifier(), x.ExecutesProtocol, map_1(HashCodes_boxHashSeq, x.ParameterValues)];
         }
     }, processes, {
         Equals: equalArrays,
         GetHashCode: arrayHash,
     });
+    toConsole(printf("Merging identical processes adwwdadawwda"));
     return mapIndexed((i, tupledArg) => {
         const _arg = tupledArg[0];
         const processes_1 = tupledArg[1];
         const n = _arg[0];
+        const pVs = item(0, processes_1).ParameterValues;
         const inputs = Option_fromValueWithDefault(empty_1(), collect((p) => defaultArg(p.Inputs, empty_1()), processes_1));
         const outputs = Option_fromValueWithDefault(empty_1(), collect((p_1) => defaultArg(p_1.Outputs, empty_1()), processes_1));
-        return Process_create_Z42860F3E(void 0, (length(l) > 1) ? Process_composeName(n, i) : n, _arg[1], _arg[2], void 0, void 0, void 0, void 0, inputs, outputs);
+        return Process_create_Z42860F3E(void 0, (length(l) > 1) ? Process_composeName(n, i) : n, _arg[1], pVs, void 0, void 0, void 0, void 0, inputs, outputs);
     }, l);
 }
 

package/ISA/ISA/ArcTypes/ArcTables.js

@@ -200,15 +200,15 @@ export function ArcTablesAux_SanityChecks_validateNewNamesUnique(newNames, exist
 
 export class ArcTables {
     constructor(initTables) {
-        this["Tables@"] = initTables;
+        this.tables = initTables;
     }
     get Tables() {
-        const __ = this;
-        return __["Tables@"];
+        const this$ = this;
+        return this$.tables;
     }
-    set Tables(v) {
-        const __ = this;
-        __["Tables@"] = v;
+    set Tables(newTables) {
+        const this$ = this;
+        this$.tables = newTables;
     }
     get_Item(index) {
         const this$ = this;