@nfdi4plants/arctrl 3.0.0-alpha.2 → 3.0.0-alpha.4

package/README.md

@@ -1,4 +1,4 @@
-
+
 ![logo](logos/ARCtrl_horizontal.png)
 
 # ARCtrl
@@ -68,11 +68,11 @@ On windows you can use the `setup.cmd` to run the following steps automatically!
     
     `py -m venv .venv`
 
-4. Install [Poetry](https://python-poetry.org/) and dependencies
+4. Install [uv](https://docs.astral.sh/uv/) and dependencies
 
    1. `.\.venv\Scripts\python.exe -m pip install -U pip setuptools`
-   2. `.\.venv\Scripts\python.exe -m pip install poetry`
-   3. `.\.venv\Scripts\python.exe -m poetry install --no-root`
+   2. `.\.venv\Scripts\python.exe -m pip install uv`
+   3. `.\.venv\Scripts\python.exe -m uv pip install -r pyproject.toml --group dev`
 
 Verify correct setup with `./build.cmd runtests` ✨
 
@@ -90,11 +90,11 @@ Measured on 13th Gen Intel(R) Core(TM) i7-13800H
 
 | Name | Description | FSharp Time (ms) | JavaScript Time (ms) | Python Time (ms) |
 | --- | --- | --- | --- | --- |
-| Table_GetHashCode | From a table with 1 column and 10000 rows, retrieve the Hash Code |  5 | 21 | 226 |
-| Table_AddRows | Add 10000 rows to a table with 4 columns. |  15 | 22 | 289 |
-| Table_fillMissingCells | For a table 6 columns and 20000 rows, where each row has one missing value, fill those values with default values. | 49 | 108 | 4813 |
-| Table_ToJson | Serialize a table with 5 columns and 10000 rows to json. |  1099 | 481 | 6833 |
-| Table_ToCompressedJson | Serialize a table with 5 columns and 10000 rows to compressed json. |  261 |  2266 | 717334 |
-| Assay_toJson | Parse an assay with one table with 10000 rows and 6 columns to json |  915 | 2459 | 28799 |
-| Study_FromWorkbook | Parse a workbook with one study with 10000 rows and 6 columns to an ArcStudy |  97 | 87 | 1249 |
-| Investigation_ToWorkbook_ManyStudies | Parse an investigation with 1500 studies to a workbook |  621 | 379 | 9974 |
+| Table_GetHashCode | From a table with 1 column and 10000 rows, retrieve the Hash Code |  2 ± 0 | 9 ± 7 | 133 ± 7 |
+| Table_AddRows | Add 10000 rows to a table with 4 columns. |  40 ± 9 | 20 ± 8 | 309 ± 26 |
+| Table_fillMissingCells | For a table 6 columns and 20000 rows, where each row has one missing value, fill those values with default values. | 55 ± 31 | 101 ± 11 | 3375 ± 221 |
+| Table_ToJson | Serialize a table with 5 columns and 10000 rows to json. |  1027 ± 200 | 293 ± 56 | 17990 ± 1482 |
+| Table_ToCompressedJson | Serialize a table with 5 columns and 10000 rows to compressed json. |  216 ± 19 |  4552 ± 326 | 6188 ± 839 |
+| Assay_toJson | Parse an assay with one table with 10000 rows and 6 columns to json |  856 ± 42 | 271 ± 55 | 19278 ± 1289 |
+| Study_FromWorkbook | Parse a workbook with one study with 10000 rows and 6 columns to an ArcStudy |  84 ± 29 | 96 ± 12 | 1787 ± 1410 |
+| Investigation_ToWorkbook_ManyStudies | Parse an investigation with 1500 studies to a workbook |  387 ± 71 | 442 ± 61 | 6305 ± 660 |

package/dist/ts/cjs/index.js

@@ -1,11 +1,13 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.WebController = exports.Contract = exports.Comment = exports.OntologyAnnotation = exports.Publication = exports.Person = exports.XlsxController = exports.JsonController = exports.Templates = exports.Organisation = exports.Template = exports.ArcTable = exports.CompositeColumn = exports.IOType = exports.CompositeHeader = exports.CompositeCell = exports.ArcInvestigation = exports.ArcStudy = exports.ArcAssay = exports.ARC = void 0;
+exports.ROCrate = exports.WebController = exports.Contract = exports.Comment = exports.OntologyAnnotation = exports.Publication = exports.Person = exports.XlsxController = exports.JsonController = exports.Templates = exports.Organisation = exports.Template = exports.ArcTable = exports.CompositeColumn = exports.IOType = exports.CompositeHeader = exports.CompositeCell = exports.ArcInvestigation = exports.ArcWorkflow = exports.ArcRun = exports.ArcStudy = exports.ArcAssay = exports.ARC = void 0;
 var ARC_js_1 = require("./ts/ARC.js");
 Object.defineProperty(exports, "ARC", { enumerable: true, get: function () { return ARC_js_1.ARC; } });
 var ArcTypes_js_1 = require("./ts/Core/ArcTypes.js");
 Object.defineProperty(exports, "ArcAssay", { enumerable: true, get: function () { return ArcTypes_js_1.ArcAssay; } });
 Object.defineProperty(exports, "ArcStudy", { enumerable: true, get: function () { return ArcTypes_js_1.ArcStudy; } });
+Object.defineProperty(exports, "ArcRun", { enumerable: true, get: function () { return ArcTypes_js_1.ArcRun; } });
+Object.defineProperty(exports, "ArcWorkflow", { enumerable: true, get: function () { return ArcTypes_js_1.ArcWorkflow; } });
 Object.defineProperty(exports, "ArcInvestigation", { enumerable: true, get: function () { return ArcTypes_js_1.ArcInvestigation; } });
 var CompositeCell_js_1 = require("./ts/Core/Table/CompositeCell.js");
 Object.defineProperty(exports, "CompositeCell", { enumerable: true, get: function () { return CompositeCell_js_1.CompositeCell; } });
@@ -37,3 +39,47 @@ var Contract_js_1 = require("./ts/Contract/Contract.js");
 Object.defineProperty(exports, "Contract", { enumerable: true, get: function () { return Contract_js_1.Contract; } });
 var Template_Web_js_1 = require("./ts/Template.Web.js");
 Object.defineProperty(exports, "WebController", { enumerable: true, get: function () { return Template_Web_js_1.WebController; } });
+/// RO-Crate
+const LDObject_js_1 = require("./ts/ROCrate/LDObject.js");
+const LDContext_js_1 = require("./ts/ROCrate/LDContext.js");
+const ROCrateContext_js_1 = require("./ts/ROCrate/ROCrateContext.js");
+const Comment_js_2 = require("./ts/ROCrate/Generic/Comment.js");
+const DefinedTerm_js_1 = require("./ts/ROCrate/Generic/DefinedTerm.js");
+const File_js_1 = require("./ts/ROCrate/Generic/File.js");
+const LabProcess_js_1 = require("./ts/ROCrate/Generic/LabProcess.js");
+const LabProtocol_js_1 = require("./ts/ROCrate/Generic/LabProtocol.js");
+const Organization_js_1 = require("./ts/ROCrate/Generic/Organization.js");
+const Person_js_2 = require("./ts/ROCrate/Generic/Person.js");
+const PostalAddress_js_1 = require("./ts/ROCrate/Generic/PostalAddress.js");
+const PropertyValue_js_1 = require("./ts/ROCrate/Generic/PropertyValue.js");
+const Sample_js_1 = require("./ts/ROCrate/Generic/Sample.js");
+const ScholarlyArticle_js_1 = require("./ts/ROCrate/Generic/ScholarlyArticle.js");
+const Dataset_js_1 = require("./ts/ROCrate/Generic/Dataset.js");
+const LDObject_js_2 = require("./ts/JsonIO/LDObject.js");
+const LDObject_js_3 = require("./ts/JsonIO/LDObject.js");
+const Conversion_js_1 = require("./ts/Conversion.js");
+exports.ROCrate = {
+    LDNode: LDObject_js_1.LDNode,
+    LDGraph: LDObject_js_1.LDGraph,
+    LDValue: LDObject_js_1.LDValue,
+    LDRef: LDObject_js_1.LDRef,
+    LDContext: LDContext_js_1.LDContext,
+    initV1_1: ROCrateContext_js_1.initV1_1,
+    initV1_2DRAFT: ROCrateContext_js_1.initV1_2DRAFT,
+    initBioschemasContext: ROCrateContext_js_1.initBioschemasContext,
+    LDComment: Comment_js_2.LDComment,
+    LDDefinedTerm: DefinedTerm_js_1.LDDefinedTerm,
+    LDFile: File_js_1.LDFile,
+    LDLabProcess: LabProcess_js_1.LDLabProcess,
+    LDLabProtocol: LabProtocol_js_1.LDLabProtocol,
+    LDOrganization: Organization_js_1.LDOrganization,
+    LDPerson: Person_js_2.LDPerson,
+    LDPostalAddress: PostalAddress_js_1.LDPostalAddress,
+    LDPropertyValue: PropertyValue_js_1.LDPropertyValue,
+    LDSample: Sample_js_1.LDSample,
+    LDScholarlyArticle: ScholarlyArticle_js_1.LDScholarlyArticle,
+    LDDataset: Dataset_js_1.LDDataset,
+    LDGraphIO: LDObject_js_2.LDGraphExtensions_PyJsInterop,
+    LDNodeIO: LDObject_js_3.LDNodeExtensions_PyJsInterop,
+    Conversion: Conversion_js_1.TypeExtensions_Conversion
+};

package/dist/ts/cjs/ts/Conversion.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.InvestigationConversion = exports.StudyConversion = exports.AssayConversion = exports.ScholarlyArticleConversion = exports.PersonConversion = exports.DatamapConversion = exports.ProcessConversion = exports.BaseTypes = exports.ColumnIndex_orderName = void 0;
+exports.TypeExtensions_Conversion = exports.InvestigationConversion = exports.StudyConversion = exports.AssayConversion = exports.ScholarlyArticleConversion = exports.PersonConversion = exports.DatamapConversion = exports.ProcessConversion = exports.BaseTypes = exports.ColumnIndex_orderName = void 0;
 exports.DateTime_tryFromString = DateTime_tryFromString;
 exports.DateTime_toString = DateTime_toString;
 exports.ColumnIndex_tryGetIndex = ColumnIndex_tryGetIndex;
@@ -63,9 +63,9 @@ exports.ProcessConversion_processToRows_Z6839B9E8 = ProcessConversion_processToR
 exports.CompositeRow_toProtocol = CompositeRow_toProtocol;
 exports.ARCtrl_ArcTable__ArcTable_fromProtocol_Static_Z6839B9E8 = ARCtrl_ArcTable__ArcTable_fromProtocol_Static_Z6839B9E8;
 exports.ARCtrl_ArcTable__ArcTable_GetProtocols = ARCtrl_ArcTable__ArcTable_GetProtocols;
-exports.ARCtrl_ArcTable__ArcTable_GetProcesses = ARCtrl_ArcTable__ArcTable_GetProcesses;
+exports.ARCtrl_ArcTable__ArcTable_GetProcesses_40457300 = ARCtrl_ArcTable__ArcTable_GetProcesses_40457300;
 exports.ARCtrl_ArcTable__ArcTable_fromProcesses_Static_Z3575FB5F = ARCtrl_ArcTable__ArcTable_fromProcesses_Static_Z3575FB5F;
-exports.ARCtrl_ArcTables__ArcTables_GetProcesses = ARCtrl_ArcTables__ArcTables_GetProcesses;
+exports.ARCtrl_ArcTables__ArcTables_GetProcesses_40457300 = ARCtrl_ArcTables__ArcTables_GetProcesses_40457300;
 exports.ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586 = ARCtrl_ArcTables__ArcTables_fromProcesses_Static_Z27F0B586;
 exports.DatamapConversion_$reflection = DatamapConversion_$reflection;
 exports.DatamapConversion_composeFragmentDescriptors_Z8923FA3 = DatamapConversion_composeFragmentDescriptors_Z8923FA3;
@@ -102,6 +102,7 @@ exports.ARCtrl_ArcStudy__ArcStudy_ToROCrateStudy = ARCtrl_ArcStudy__ArcStudy_ToR
 exports.ARCtrl_ArcStudy__ArcStudy_fromROCrateStudy_Static_Z6839B9E8 = ARCtrl_ArcStudy__ArcStudy_fromROCrateStudy_Static_Z6839B9E8;
 exports.ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation = ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation;
 exports.ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8 = ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8;
+exports.TypeExtensions_Conversion_$reflection = TypeExtensions_Conversion_$reflection;
 exports.ARCtrl_ROCrate_Dataset__Dataset_toArcAssay_Static_Z6839B9E8 = ARCtrl_ROCrate_Dataset__Dataset_toArcAssay_Static_Z6839B9E8;
 exports.ARCtrl_ROCrate_Dataset__Dataset_fromArcAssay_Static_1501C0F8 = ARCtrl_ROCrate_Dataset__Dataset_fromArcAssay_Static_1501C0F8;
 exports.ARCtrl_ROCrate_Dataset__Dataset_toArcStudy_Static_Z6839B9E8 = ARCtrl_ROCrate_Dataset__Dataset_toArcStudy_Static_Z6839B9E8;
@@ -879,7 +880,7 @@ function ProcessConversion_tryGetPerformerGetter(generalI, header) {
 /**
  * Given the header sequence of an ArcTable, returns a function for parsing each row of the table to a process
  */
-function ProcessConversion_getProcessGetter(processNameRoot, headers) {
+function ProcessConversion_getProcessGetter(assayName, studyName, processNameRoot, headers) {
     const headers_1 = (0, Seq_js_1.indexed)(headers);
     const valueHeaders = (0, Seq_js_1.toList)((0, Seq_js_1.indexed)((0, Seq_js_1.filter)((arg) => arg[1].IsCvParamColumn, headers_1)));
     const charGetters = (0, List_js_1.choose)((tupledArg) => {
@@ -958,6 +959,7 @@ function ProcessConversion_getProcessGetter(processNameRoot, headers) {
         const paramvalues = (0, Option_js_1.map)((collection_4) => Array.from(collection_4), (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_4) => f_4(matrix_6)(i_6), parameterValueGetters)));
         const comments = (0, Option_js_1.map)((collection_5) => Array.from(collection_5), (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_5) => f_5(matrix_6)(i_6), commentGetters)));
         const components = (0, Option_js_1.map)((collection_6) => Array.from(collection_6), (0, Collections_js_1.Option_fromValueWithDefault)((0, List_js_1.empty)(), (0, List_js_1.map)((f_6) => f_6(matrix_6)(i_6), componentGetters)));
+        const id = LabProcess_js_1.LDLabProcess.genId(processNameRoot, (0, Option_js_1.unwrap)(assayName), (0, Option_js_1.unwrap)(studyName)) + (`_${i_6}`);
         let protocol;
         const name = (0, Option_js_1.map)((f_7) => f_7(matrix_6)(i_6), protocolREFGetter);
         const protocolId = LabProtocol_js_1.LDLabProtocol.genId((0, Option_js_1.unwrap)(name), processNameRoot);
@@ -965,7 +967,7 @@ function ProcessConversion_getProcessGetter(processNameRoot, headers) {
         const matchValue_2 = inputGetter_1(matrix_6)(i_6);
         const matchValue_3 = outputGetter_1(matrix_6)(i_6);
         const agent = (0, Option_js_1.map)((f_12) => f_12(matrix_6)(i_6), performerGetter);
-        return LabProcess_js_1.LDLabProcess.create(pn, matchValue_2, matchValue_3, undefined, (0, Option_js_1.unwrap)(agent), (0, Option_js_1.unwrap)(protocol), (0, Option_js_1.unwrap)(paramvalues), undefined, (0, Option_js_1.unwrap)(comments));
+        return LabProcess_js_1.LDLabProcess.create(pn, matchValue_2, matchValue_3, id, (0, Option_js_1.unwrap)(agent), (0, Option_js_1.unwrap)(protocol), (0, Option_js_1.unwrap)(paramvalues), undefined, (0, Option_js_1.unwrap)(comments));
     });
 }
 /**
@@ -1291,12 +1293,12 @@ function ARCtrl_ArcTable__ArcTable_GetProtocols(this$) {
 /**
  * Returns the list of processes specidified in this ArcTable
  */
-function ARCtrl_ArcTable__ArcTable_GetProcesses(this$) {
+function ARCtrl_ArcTable__ArcTable_GetProcesses_40457300(this$, assayName, studyName) {
     if (this$.RowCount === 0) {
         return (0, List_js_1.singleton)(LabProcess_js_1.LDLabProcess.create(this$.Name));
     }
     else {
-        const getter = ProcessConversion_getProcessGetter(this$.Name, this$.Headers);
+        const getter = ProcessConversion_getProcessGetter(assayName, studyName, this$.Name, this$.Headers);
         return (0, Seq_js_1.toList)((0, Seq_js_1.delay)(() => (0, Seq_js_1.map)((i) => getter(this$.Values)(i), (0, Range_js_1.rangeDouble)(0, 1, this$.RowCount - 1))));
     }
 }
@@ -1314,8 +1316,8 @@ function ARCtrl_ArcTable__ArcTable_fromProcesses_Static_Z3575FB5F(name, ps, grap
 /**
  * Return a list of all the processes in all the tables.
  */
-function ARCtrl_ArcTables__ArcTables_GetProcesses(this$) {
-    return (0, List_js_1.collect)(ARCtrl_ArcTable__ArcTable_GetProcesses, (0, Seq_js_1.toList)(this$.Tables));
+function ARCtrl_ArcTables__ArcTables_GetProcesses_40457300(this$, assayName, studyName) {
+    return (0, List_js_1.collect)((t) => ARCtrl_ArcTable__ArcTable_GetProcesses_40457300(t, (0, Option_js_1.unwrap)(assayName), (0, Option_js_1.unwrap)(studyName)), (0, Seq_js_1.toList)(this$.Tables));
 }
 /**
  * Create a collection of tables from a list of processes.
@@ -1569,7 +1571,7 @@ function AssayConversion_composeAssay_1501C0F8(assay) {
     const measurementTechnique = (0, Option_js_1.map)(BaseTypes_composeDefinedTerm_ZDED3A0F, assay.TechnologyPlatform);
     const variableMeasured = (0, Option_js_1.map)(BaseTypes_composePropertyValueFromOA_ZDED3A0F, assay.MeasurementType);
     const creators = (0, Collections_js_1.Option_fromSeq)((0, Collections_js_1.ResizeArray_map)(PersonConversion_composePerson_Z64D846DC, assay.Performers));
-    const processSequence = (0, Collections_js_1.Option_fromSeq)((collection = ARCtrl_ArcTables__ArcTables_GetProcesses(new ArcTables_js_1.ArcTables(assay.Tables)), Array.from(collection)));
+    const processSequence = (0, Collections_js_1.Option_fromSeq)((collection = ARCtrl_ArcTables__ArcTables_GetProcesses_40457300(new ArcTables_js_1.ArcTables(assay.Tables), assay.Identifier), Array.from(collection)));
     const fragmentDescriptors = (0, Option_js_1.map)(DatamapConversion_composeFragmentDescriptors_Z8923FA3, assay.DataMap);
     const dataFiles = (0, Option_js_1.map)((ps) => AssayConversion_getDataFilesFromProcesses_6BABD1B0(ps, (0, Option_js_1.unwrap)(fragmentDescriptors)), processSequence);
     const variableMeasureds = (variableMeasured == null) ? ((fragmentDescriptors == null) ? undefined : ((fds_1 = (0, Option_js_1.value)(fragmentDescriptors), fds_1))) : ((fragmentDescriptors == null) ? ((vm_1 = (0, Option_js_1.value)(variableMeasured), (0, Collections_js_1.ResizeArray_singleton)(vm_1))) : ((fds = (0, Option_js_1.value)(fragmentDescriptors), (vm = (0, Option_js_1.value)(variableMeasured), (0, Collections_js_1.ResizeArray_appendSingleton)(vm, fds)))));
@@ -1603,7 +1605,7 @@ function StudyConversion_composeStudy_1680536E(study) {
     const dateModified = (0, Date_js_1.now)();
     const publications = (0, Collections_js_1.Option_fromSeq)((0, Collections_js_1.ResizeArray_map)(ScholarlyArticleConversion_composeScholarlyArticle_D324A6D, study.Publications));
     const creators = (0, Collections_js_1.Option_fromSeq)((0, Collections_js_1.ResizeArray_map)(PersonConversion_composePerson_Z64D846DC, study.Contacts));
-    const processSequence = (0, Collections_js_1.Option_fromSeq)((collection = ARCtrl_ArcTables__ArcTables_GetProcesses(new ArcTables_js_1.ArcTables(study.Tables)), Array.from(collection)));
+    const processSequence = (0, Collections_js_1.Option_fromSeq)((collection = ARCtrl_ArcTables__ArcTables_GetProcesses_40457300(new ArcTables_js_1.ArcTables(study.Tables), undefined, study.Identifier), Array.from(collection)));
     const fragmentDescriptors = (0, Option_js_1.map)(DatamapConversion_composeFragmentDescriptors_Z8923FA3, study.DataMap);
     const dataFiles = (0, Option_js_1.map)((ps) => AssayConversion_getDataFilesFromProcesses_6BABD1B0(ps, (0, Option_js_1.unwrap)(fragmentDescriptors)), processSequence);
     const comments = (0, Collections_js_1.Option_fromSeq)((0, Collections_js_1.ResizeArray_map)(BaseTypes_composeComment_Z13201A7E, study.Comments));
@@ -1680,6 +1682,32 @@ function ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation(this$)
 function ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(a, graph, context) {
     return InvestigationConversion_decomposeInvestigation_Z6839B9E8(a, (0, Option_js_1.unwrap)(graph), (0, Option_js_1.unwrap)(context));
 }
+class TypeExtensions_Conversion {
+    constructor() {
+    }
+    static arcAssayToDataset(a) {
+        return ARCtrl_ArcAssay__ArcAssay_ToROCrateAssay(a);
+    }
+    static datasetToArcAssay(a, graph, context) {
+        return ARCtrl_ArcAssay__ArcAssay_fromROCrateAssay_Static_Z6839B9E8(a, (0, Option_js_1.unwrap)(graph), (0, Option_js_1.unwrap)(context));
+    }
+    static arcStudyToDataset(a) {
+        return ARCtrl_ArcStudy__ArcStudy_ToROCrateStudy(a);
+    }
+    static datasetToArcStudy(a, graph, context) {
+        return ARCtrl_ArcStudy__ArcStudy_fromROCrateStudy_Static_Z6839B9E8(a, (0, Option_js_1.unwrap)(graph), (0, Option_js_1.unwrap)(context));
+    }
+    static arcInvestigationToDataset(a) {
+        return ARCtrl_ArcInvestigation__ArcInvestigation_ToROCrateInvestigation(a);
+    }
+    static datasetToArcInvestigation(a, graph, context) {
+        return ARCtrl_ArcInvestigation__ArcInvestigation_fromROCrateInvestigation_Static_Z6839B9E8(a, (0, Option_js_1.unwrap)(graph), (0, Option_js_1.unwrap)(context));
+    }
+}
+exports.TypeExtensions_Conversion = TypeExtensions_Conversion;
+function TypeExtensions_Conversion_$reflection() {
+    return (0, Reflection_js_1.class_type)("ARCtrl.Conversion.TypeExtensions.Conversion", undefined, TypeExtensions_Conversion);
+}
 function ARCtrl_ROCrate_Dataset__Dataset_toArcAssay_Static_Z6839B9E8(a, graph, context) {
     return AssayConversion_decomposeAssay_Z6839B9E8(a, (0, Option_js_1.unwrap)(graph), (0, Option_js_1.unwrap)(context));
 }

package/dist/ts/cjs/ts/Core/Helper/Collections.js

@@ -9,6 +9,9 @@ exports.Dictionary_addOrUpdate = Dictionary_addOrUpdate;
 exports.Dictionary_ofSeq = Dictionary_ofSeq;
 exports.Dictionary_tryFind = Dictionary_tryFind;
 exports.Dictionary_ofSeqWithMerge = Dictionary_ofSeqWithMerge;
+exports.Dictionary_init = Dictionary_init;
+exports.Dictionary_items = Dictionary_items;
+exports.StringDictionary_ofSeq = StringDictionary_ofSeq;
 exports.ResizeArray_create = ResizeArray_create;
 exports.ResizeArray_singleton = ResizeArray_singleton;
 exports.ResizeArray_map = ResizeArray_map;
@@ -152,6 +155,18 @@ function Dictionary_ofSeqWithMerge(merge, s) {
     }, s);
     return dict;
 }
+function Dictionary_init() {
+    return new MutableMap_js_1.Dictionary([], {
+        Equals: Util_js_1.equals,
+        GetHashCode: Util_js_1.structuralHash,
+    });
+}
+function Dictionary_items(dict) {
+    return dict;
+}
+function StringDictionary_ofSeq(s) {
+    return new Map(s);
+}
 function ResizeArray_create(i, v) {
     const a = [];
     if (i > 0) {

package/dist/ts/cjs/ts/Core/Table/ArcTableAux.js

@@ -1,5 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.CellDictionary_addOrUpdate = CellDictionary_addOrUpdate;
+exports.CellDictionary_ofSeq = CellDictionary_ofSeq;
+exports.CellDictionary_tryFind = CellDictionary_tryFind;
 exports.getColumnCount = getColumnCount;
 exports.getRowCount = getRowCount;
 exports.boxHashValues = boxHashValues;
@@ -29,22 +32,50 @@ exports.Unchecked_compositeHeaderMainColumnEqual = Unchecked_compositeHeaderMain
 exports.Unchecked_moveColumnTo = Unchecked_moveColumnTo;
 exports.Unchecked_alignByHeaders = Unchecked_alignByHeaders;
 const Int32_js_1 = require("@fable-org/fable-library-js/Int32.js");
-const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
-const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
-const CompositeCell_js_1 = require("./CompositeCell.js");
 const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
+const CompositeCell_js_1 = require("./CompositeCell.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
+const MutableMap_js_1 = require("@fable-org/fable-library-js/MutableMap.js");
+const Types_js_1 = require("@fable-org/fable-library-js/Types.js");
 const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
 const List_js_1 = require("@fable-org/fable-library-js/List.js");
 const String_js_1 = require("@fable-org/fable-library-js/String.js");
-const Collections_js_1 = require("../Helper/Collections.js");
 const Double_js_1 = require("@fable-org/fable-library-js/Double.js");
 const Array_js_1 = require("@fable-org/fable-library-js/Array.js");
 const Map_js_1 = require("@fable-org/fable-library-js/Map.js");
 const Seq2_js_1 = require("@fable-org/fable-library-js/Seq2.js");
 const Set_js_1 = require("@fable-org/fable-library-js/Set.js");
-const Types_js_1 = require("@fable-org/fable-library-js/Types.js");
 const Range_js_1 = require("@fable-org/fable-library-js/Range.js");
-const MutableMap_js_1 = require("@fable-org/fable-library-js/MutableMap.js");
+const Collections_js_1 = require("../Helper/Collections.js");
+function CellDictionary_addOrUpdate(key_, key__1, value, dict) {
+    const key = [key_, key__1];
+    if (dict.has(key)) {
+        dict.set(key, value);
+    }
+    else {
+        (0, MapUtil_js_1.addToDict)(dict, key, value);
+    }
+}
+function CellDictionary_ofSeq(s) {
+    return new MutableMap_js_1.Dictionary(s, {
+        Equals: Util_js_1.equalArrays,
+        GetHashCode: Util_js_1.arrayHash,
+    });
+}
+function CellDictionary_tryFind(key_, key__1, dict) {
+    let patternInput;
+    let outArg = (0, Util_js_1.defaultOf)();
+    patternInput = [(0, MapUtil_js_1.tryGetValue)(dict, [key_, key__1], new Types_js_1.FSharpRef(() => outArg, (v) => {
+            outArg = v;
+        })), outArg];
+    if (patternInput[0]) {
+        return patternInput[1];
+    }
+    else {
+        return undefined;
+    }
+}
 function getColumnCount(headers) {
     return headers.length;
 }
@@ -206,7 +237,7 @@ function SanityChecks_validate(headers, values, raiseException) {
     return isValid;
 }
 function Unchecked_tryGetCellAt(column, row, cells) {
-    return (0, Collections_js_1.Dictionary_tryFind)([column, row], cells);
+    return CellDictionary_tryFind(column, row, cells);
 }
 /**
  * Add or update a cell in the dictionary.
@@ -221,7 +252,7 @@ function Unchecked_addCellAt(columnIndex, rowIndex, c, cells) {
     (0, MapUtil_js_1.addToDict)(cells, [columnIndex, rowIndex], c);
 }
 function Unchecked_moveCellTo(fromCol, fromRow, toCol, toRow, cells) {
-    const matchValue = (0, Collections_js_1.Dictionary_tryFind)([fromCol, fromRow], cells);
+    const matchValue = CellDictionary_tryFind(fromCol, fromRow, cells);
     if (matchValue == null) {
     }
     else {

package/dist/ts/cjs/ts/Json/StringTable.js

@@ -7,10 +7,11 @@ exports.encodeString = encodeString;
 exports.decodeString = decodeString;
 const Array_js_1 = require("@fable-org/fable-library-js/Array.js");
 const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
 const Decode_fs_js_1 = require("../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
-const Collections_js_1 = require("../Core/Helper/Collections.js");
 const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
 const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
+const Types_js_1 = require("@fable-org/fable-library-js/Types.js");
 const Result_js_1 = require("@fable-org/fable-library-js/Result.js");
 function arrayFromMap(otm) {
     const a = (0, Array_js_1.fill)(new Array(otm.size), 0, otm.size, "");
@@ -34,7 +35,13 @@ function encoder(ot) {
 }
 exports.decoder = (0, Decode_fs_js_1.array)(Decode_fs_js_1.string);
 function encodeString(otm, s) {
-    const matchValue = (0, Collections_js_1.Dictionary_tryFind)(s, otm);
+    let matchValue;
+    let patternInput;
+    let outArg = (0, Util_js_1.defaultOf)();
+    patternInput = [(0, MapUtil_js_1.tryGetValue)(otm, s, new Types_js_1.FSharpRef(() => outArg, (v) => {
+            outArg = (v | 0);
+        })), outArg];
+    matchValue = (patternInput[0] ? patternInput[1] : undefined);
     if (matchValue == null) {
         const i_1 = otm.size | 0;
         (0, MapUtil_js_1.addToDict)(otm, s, i_1);

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

@@ -6,15 +6,15 @@ exports.decoder = decoder;
 exports.encodeCell = encodeCell;
 exports.decodeCell = decodeCell;
 const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Collections_js_1 = require("../../Core/Helper/Collections.js");
 const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
 const Array_js_1 = require("@fable-org/fable-library-js/Array.js");
 const CompositeCell_js_1 = require("./CompositeCell.js");
 const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
-const Collections_js_1 = require("../../Core/Helper/Collections.js");
 const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
 const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
 function arrayFromMap(otm) {
-    return (0, Seq_js_1.toArray)((0, Seq_js_1.map)((kv_1) => kv_1[0], (0, Seq_js_1.sortBy)((kv) => kv[1], otm, {
+    return (0, Seq_js_1.toArray)((0, Seq_js_1.map)((kv_1) => kv_1[0], (0, Seq_js_1.sortBy)((kv) => kv[1], (0, Collections_js_1.Dictionary_items)(otm), {
         Compare: Util_js_1.comparePrimitives,
     })));
 }

package/dist/ts/cjs/ts/Json/Table/OATable.js

@@ -6,15 +6,15 @@ exports.decoder = decoder;
 exports.encodeOA = encodeOA;
 exports.decodeOA = decodeOA;
 const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
+const Collections_js_1 = require("../../Core/Helper/Collections.js");
 const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
 const Array_js_1 = require("@fable-org/fable-library-js/Array.js");
 const OntologyAnnotation_js_1 = require("../OntologyAnnotation.js");
 const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
-const Collections_js_1 = require("../../Core/Helper/Collections.js");
 const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
 const MapUtil_js_1 = require("@fable-org/fable-library-js/MapUtil.js");
 function arrayFromMap(otm) {
-    return (0, Seq_js_1.toArray)((0, Seq_js_1.map)((kv_1) => kv_1[0], (0, Seq_js_1.sortBy)((kv) => kv[1], otm, {
+    return (0, Seq_js_1.toArray)((0, Seq_js_1.map)((kv_1) => kv_1[0], (0, Seq_js_1.sortBy)((kv) => kv[1], (0, Collections_js_1.Dictionary_items)(otm), {
         Compare: Util_js_1.comparePrimitives,
     })));
 }

package/dist/ts/cjs/ts/JsonIO/LDObject.js

@@ -0,0 +1,107 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.LDGraphExtensions_PyJsInterop = exports.LDNodeExtensions_PyJsInterop = void 0;
+exports.ARCtrl_ROCrate_LDNode__LDNode_fromROCrateJsonString_Static_Z721C83C5 = ARCtrl_ROCrate_LDNode__LDNode_fromROCrateJsonString_Static_Z721C83C5;
+exports.ARCtrl_ROCrate_LDNode__LDNode_toROCrateJsonString_Static_71136F3F = ARCtrl_ROCrate_LDNode__LDNode_toROCrateJsonString_Static_71136F3F;
+exports.ARCtrl_ROCrate_LDNode__LDNode_ToROCrateJsonString_71136F3F = ARCtrl_ROCrate_LDNode__LDNode_ToROCrateJsonString_71136F3F;
+exports.LDNodeExtensions_PyJsInterop_$reflection = LDNodeExtensions_PyJsInterop_$reflection;
+exports.ARCtrl_ROCrate_LDGraph__LDGraph_fromROCrateJsonString_Static_Z721C83C5 = ARCtrl_ROCrate_LDGraph__LDGraph_fromROCrateJsonString_Static_Z721C83C5;
+exports.ARCtrl_ROCrate_LDGraph__LDGraph_toROCrateJsonString_Static_71136F3F = ARCtrl_ROCrate_LDGraph__LDGraph_toROCrateJsonString_Static_71136F3F;
+exports.ARCtrl_ROCrate_LDGraph__LDGraph_ToROCrateJsonString_71136F3F = ARCtrl_ROCrate_LDGraph__LDGraph_ToROCrateJsonString_71136F3F;
+exports.LDGraphExtensions_PyJsInterop_$reflection = LDGraphExtensions_PyJsInterop_$reflection;
+const Decode_fs_js_1 = require("../fable_modules/Thoth.Json.JavaScript.0.3.0/Decode.fs.js");
+const LDNode_js_1 = require("../Json/ROCrate/LDNode.js");
+const String_js_1 = require("@fable-org/fable-library-js/String.js");
+const Encode_fs_js_1 = require("../fable_modules/Thoth.Json.JavaScript.0.3.0/Encode.fs.js");
+const Encode_js_1 = require("../Json/Encode.js");
+const Option_js_1 = require("@fable-org/fable-library-js/Option.js");
+const Reflection_js_1 = require("@fable-org/fable-library-js/Reflection.js");
+const LDGraph_js_1 = require("../Json/ROCrate/LDGraph.js");
+function ARCtrl_ROCrate_LDNode__LDNode_fromROCrateJsonString_Static_Z721C83C5(s) {
+    let arg;
+    const matchValue = (0, Decode_fs_js_1.fromString)(LDNode_js_1.decoder, s);
+    if (matchValue.tag === /* Error */ 1) {
+        throw new Error((arg = matchValue.fields[0], (0, String_js_1.toText)((0, String_js_1.printf)("Error decoding string: %O"))(arg)));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+/**
+ * exports in json-ld format
+ */
+function ARCtrl_ROCrate_LDNode__LDNode_toROCrateJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = (0, LDNode_js_1.encoder)(obj);
+        return (0, Encode_fs_js_1.toString)((0, Encode_js_1.defaultSpaces)(spaces), value);
+    };
+}
+function ARCtrl_ROCrate_LDNode__LDNode_ToROCrateJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ROCrate_LDNode__LDNode_toROCrateJsonString_Static_71136F3F((0, Option_js_1.unwrap)(spaces))(this$);
+}
+class LDNodeExtensions_PyJsInterop {
+    constructor() {
+    }
+    static fromROCrateJsonString(s) {
+        let arg;
+        const matchValue = (0, Decode_fs_js_1.fromString)(LDNode_js_1.decoder, s);
+        if (matchValue.tag === /* Error */ 1) {
+            throw new Error((arg = matchValue.fields[0], (0, String_js_1.toText)((0, String_js_1.printf)("Error decoding string: %O"))(arg)));
+        }
+        else {
+            return matchValue.fields[0];
+        }
+    }
+    static toROCrateJsonString(node, spaces) {
+        const value = (0, LDNode_js_1.encoder)(node);
+        return (0, Encode_fs_js_1.toString)((0, Encode_js_1.defaultSpaces)(spaces), value);
+    }
+}
+exports.LDNodeExtensions_PyJsInterop = LDNodeExtensions_PyJsInterop;
+function LDNodeExtensions_PyJsInterop_$reflection() {
+    return (0, Reflection_js_1.class_type)("ARCtrl.Json.LDNodeExtensions.PyJsInterop", undefined, LDNodeExtensions_PyJsInterop);
+}
+function ARCtrl_ROCrate_LDGraph__LDGraph_fromROCrateJsonString_Static_Z721C83C5(s) {
+    let arg;
+    const matchValue = (0, Decode_fs_js_1.fromString)(LDGraph_js_1.decoder, s);
+    if (matchValue.tag === /* Error */ 1) {
+        throw new Error((arg = matchValue.fields[0], (0, String_js_1.toText)((0, String_js_1.printf)("Error decoding string: %O"))(arg)));
+    }
+    else {
+        return matchValue.fields[0];
+    }
+}
+/**
+ * exports in json-ld format
+ */
+function ARCtrl_ROCrate_LDGraph__LDGraph_toROCrateJsonString_Static_71136F3F(spaces) {
+    return (obj) => {
+        const value = (0, LDGraph_js_1.encoder)(obj);
+        return (0, Encode_fs_js_1.toString)((0, Encode_js_1.defaultSpaces)(spaces), value);
+    };
+}
+function ARCtrl_ROCrate_LDGraph__LDGraph_ToROCrateJsonString_71136F3F(this$, spaces) {
+    return ARCtrl_ROCrate_LDGraph__LDGraph_toROCrateJsonString_Static_71136F3F((0, Option_js_1.unwrap)(spaces))(this$);
+}
+class LDGraphExtensions_PyJsInterop {
+    constructor() {
+    }
+    static fromROCrateJsonString(s) {
+        let arg;
+        const matchValue = (0, Decode_fs_js_1.fromString)(LDGraph_js_1.decoder, s);
+        if (matchValue.tag === /* Error */ 1) {
+            throw new Error((arg = matchValue.fields[0], (0, String_js_1.toText)((0, String_js_1.printf)("Error decoding string: %O"))(arg)));
+        }
+        else {
+            return matchValue.fields[0];
+        }
+    }
+    static toROCrateJsonString(graph, spaces) {
+        const value = (0, LDGraph_js_1.encoder)(graph);
+        return (0, Encode_fs_js_1.toString)((0, Encode_js_1.defaultSpaces)(spaces), value);
+    }
+}
+exports.LDGraphExtensions_PyJsInterop = LDGraphExtensions_PyJsInterop;
+function LDGraphExtensions_PyJsInterop_$reflection() {
+    return (0, Reflection_js_1.class_type)("ARCtrl.Json.LDGraphExtensions.PyJsInterop", undefined, LDGraphExtensions_PyJsInterop);
+}

package/dist/ts/cjs/ts/JsonIO/Table/Compression.js

@@ -2,8 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.encode = encode;
 exports.decode = decode;
-const Util_js_1 = require("@fable-org/fable-library-js/Util.js");
-const MutableMap_js_1 = require("@fable-org/fable-library-js/MutableMap.js");
+const Collections_js_1 = require("../../Core/Helper/Collections.js");
 const Encode_fs_js_1 = require("../../fable_modules/Thoth.Json.JavaScript.0.3.0/Encode.fs.js");
 const CellTable_js_1 = require("../../Json/Table/CellTable.js");
 const OATable_js_1 = require("../../Json/Table/OATable.js");
@@ -11,15 +10,9 @@ const StringTable_js_1 = require("../../Json/StringTable.js");
 const Seq_js_1 = require("@fable-org/fable-library-js/Seq.js");
 const Decode_fs_js_1 = require("../../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js");
 function encode(encoder, obj) {
-    const stringTable = new Map([]);
-    const oaTable = new MutableMap_js_1.Dictionary([], {
-        Equals: Util_js_1.equals,
-        GetHashCode: Util_js_1.safeHash,
-    });
-    const cellTable = new MutableMap_js_1.Dictionary([], {
-        Equals: Util_js_1.equals,
-        GetHashCode: Util_js_1.safeHash,
-    });
+    const stringTable = (0, Collections_js_1.Dictionary_init)();
+    const oaTable = (0, Collections_js_1.Dictionary_init)();
+    const cellTable = (0, Collections_js_1.Dictionary_init)();
     const object = encoder(stringTable, oaTable, cellTable, obj);
     (0, Encode_fs_js_1.toString)(0, object);
     const values = [["cellTable", (0, CellTable_js_1.encoder)(stringTable, oaTable, (0, CellTable_js_1.arrayFromMap)(cellTable))], ["oaTable", (0, OATable_js_1.encoder)(stringTable, (0, OATable_js_1.arrayFromMap)(oaTable))], ["stringTable", (0, StringTable_js_1.encoder)((0, StringTable_js_1.arrayFromMap)(stringTable))], ["object", object]];

package/dist/ts/cjs/ts/ROCrate/Generic/LabProcess.js

@@ -216,7 +216,7 @@ class LDLabProcess {
     }
     static genId(name, assayName, studyName) {
         let study_1, assay_1, assay, study;
-        return (0, Helper_js_1.clean)((assayName == null) ? ((studyName != null) ? ((study_1 = (0, Option_js_1.value)(studyName), `#Process_${study_1}_${name}`)) : (`#Process_${name}`)) : ((studyName == null) ? ((assay_1 = (0, Option_js_1.value)(assayName), `#Process_${assay_1}_${name}`)) : ((assay = (0, Option_js_1.value)(assayName), (study = (0, Option_js_1.value)(studyName), `#Process_${study}_${assay}_${name}`)))));
+        return (0, Helper_js_1.clean)((assayName == null) ? ((studyName != null) ? ((study_1 = (0, Option_js_1.value)(studyName), `#Process_S_${study_1}_${name}`)) : (`#Process_${name}`)) : ((studyName == null) ? ((assay_1 = (0, Option_js_1.value)(assayName), `#Process_A_${assay_1}_${name}`)) : ((assay = (0, Option_js_1.value)(assayName), (study = (0, Option_js_1.value)(studyName), `#Process_S_${study}_A_${assay}_${name}`)))));
     }
     static create(name, objects, results, id, agent, executesLabProtocol, parameterValues, endTime, disambiguatingDescriptions, context) {
         const id_1 = (id == null) ? LDLabProcess.genId(name) : (0, Option_js_1.value)(id);