@nfdi4plants/arctrl 2.3.1 → 2.4.0

package/Core/Table/ArcTable.js

@@ -83,10 +83,16 @@ export class ArcTable {
         const this$ = this;
         return getColumnCount(this$.Headers) | 0;
     }
+    static columnCount(table) {
+        return table.ColumnCount;
+    }
     get RowCount() {
         const this$ = this;
         return getRowCount(this$.Values) | 0;
     }
+    static rowCount(table) {
+        return table.RowCount;
+    }
     get Columns() {
         const this$ = this;
         return toArray(delay(() => map((i) => this$.GetColumn(i), rangeDouble(0, 1, this$.ColumnCount - 1))));

package/Core/Table/CompositeHeader.js

@@ -490,6 +490,10 @@ export class CompositeHeader extends Union {
         const this$ = this;
         return (this$.tag === 3) ? (new CompositeHeader(3, [this$.fields[0].Copy()])) : ((this$.tag === 2) ? (new CompositeHeader(2, [this$.fields[0].Copy()])) : ((this$.tag === 1) ? (new CompositeHeader(1, [this$.fields[0].Copy()])) : ((this$.tag === 0) ? (new CompositeHeader(0, [this$.fields[0].Copy()])) : this$)));
     }
+    TryGetTerm() {
+        const this$ = this;
+        return (this$.tag === 3) ? this$.fields[0] : ((this$.tag === 2) ? this$.fields[0] : ((this$.tag === 1) ? this$.fields[0] : ((this$.tag === 0) ? this$.fields[0] : undefined)));
+    }
     static component(oa) {
         return new CompositeHeader(0, [oa]);
     }

package/Json/Assay.js

@@ -71,7 +71,7 @@ export function ROCrate_genID(a) {
         return "#EmptyAssay";
     }
     else {
-        return `#assay/${replace(matchValue, " ", "_")}`;
+        return `assays/${replace(matchValue, " ", "_")}/`;
     }
 }
 

package/Json/Investigation.js

@@ -10,6 +10,7 @@ import { ISAJson_decoder as ISAJson_decoder_5, ISAJson_encoder as ISAJson_encode
 import { concat, map as map_1 } from "../fable_modules/fable-library-js.4.24.0/Seq.js";
 import { list as list_1, resizeArray, string, object } from "../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
 import { ArcInvestigation } from "../Core/ArcTypes.js";
+import { toString, today } from "../fable_modules/fable-library-js.4.24.0/Date.js";
 import { context_jsonvalue } from "./context/rocrate/isa_investigation_context.js";
 import { createMissingIdentifier } from "../Core/Helper/Identifier.js";
 import { distinctBy } from "../fable_modules/fable-library-js.4.24.0/Seq2.js";
@@ -104,7 +105,7 @@ export function ROCrate_genID(i) {
 }
 
 export function ROCrate_encoder(oa) {
-    let value, value_3, value_4;
+    let value, value_3, value_4, value_12, copyOfStruct;
     const values = choose((tupledArg) => map((v_1) => [tupledArg[0], v_1], tupledArg[1]), ofArray([["@id", (value = ROCrate_genID(oa), {
         Encode(helpers) {
             return helpers.encodeString(value);
@@ -137,11 +138,11 @@ export function ROCrate_encoder(oa) {
         Encode(helpers_7) {
             return helpers_7.encodeString(value_9);
         },
-    }), oa.SubmissionDate), tryInclude("publicReleaseDate", (value_11) => ({
+    }), oa.SubmissionDate), ["publicReleaseDate", (value_12 = defaultArg(oa.PublicReleaseDate, (copyOfStruct = today(), toString(copyOfStruct, "yyyy-MM-dd"))), {
         Encode(helpers_8) {
-            return helpers_8.encodeString(value_11);
+            return helpers_8.encodeString(value_12);
         },
-    }), oa.PublicReleaseDate), tryIncludeSeq("ontologySourceReferences", ROCrate_encoder_1, oa.OntologySourceReferences), tryIncludeSeq("publications", ROCrate_encoder_2, oa.Publications), tryIncludeSeq("people", ROCrate_encoder_3, oa.Contacts), tryIncludeSeq("studies", (s) => ROCrate_encoder_4(undefined, s), oa.Studies), tryIncludeSeq("comments", ROCrate_encoder_5, oa.Comments), ["@context", context_jsonvalue]]));
+    })], tryIncludeSeq("ontologySourceReferences", ROCrate_encoder_1, oa.OntologySourceReferences), tryIncludeSeq("publications", ROCrate_encoder_2, oa.Publications), tryIncludeSeq("people", ROCrate_encoder_3, oa.Contacts), tryIncludeSeq("studies", (s) => ROCrate_encoder_4(undefined, s), oa.Studies), tryIncludeSeq("comments", ROCrate_encoder_5, oa.Comments), ["@context", context_jsonvalue]]));
     return {
         Encode(helpers_9) {
             const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_9)], values);

package/Json/Study.js

@@ -8,7 +8,7 @@ import { ISAJson_decoder as ISAJson_decoder_3, ISAJson_encoder as ISAJson_encode
 import { OntologyAnnotation_ISAJson_decoder, OntologyAnnotation_ISAJson_encoder, OntologyAnnotation_ROCrate_decoderDefinedTerm, OntologyAnnotation_ROCrate_encoderDefinedTerm, OntologyAnnotation_decoder, OntologyAnnotation_encoder } from "./OntologyAnnotation.js";
 import { decoderCompressed as decoderCompressed_1, encoderCompressed as encoderCompressed_1, decoder as decoder_4, encoder as encoder_7 } from "./Table/ArcTable.js";
 import { decoderCompressed as decoderCompressed_2, encoderCompressed as encoderCompressed_2, decoder as decoder_5, encoder as encoder_8 } from "./DataMap/DataMap.js";
-import { ISAJson_decoder as ISAJson_decoder_5, ISAJson_encoder as ISAJson_encoder_6, ROCrate_decoder as ROCrate_decoder_5, ROCrate_encoder as ROCrate_encoder_5, decoder as decoder_6, encoder as encoder_9 } from "./Comment.js";
+import { ISAJson_decoder as ISAJson_decoder_5, ISAJson_encoder as ISAJson_encoder_6, ROCrate_decoder as ROCrate_decoder_5, ROCrate_encoder as ROCrate_encoder_6, decoder as decoder_6, encoder as encoder_9 } from "./Comment.js";
 import { isEmpty, map as map_1 } from "../fable_modules/fable-library-js.4.24.0/Seq.js";
 import { list as list_2, resizeArray, string, object } from "../fable_modules/Thoth.Json.Core.0.4.0/Decode.fs.js";
 import { replace } from "../fable_modules/fable-library-js.4.24.0/String.js";
@@ -17,9 +17,10 @@ import { Person_removeSourceAssayComments, Person_getSourceAssayIdentifiersFromC
 import { list as list_1 } from "../fable_modules/Thoth.Json.Core.0.4.0/Encode.fs.js";
 import { ISAJson_decoder as ISAJson_decoder_1, ISAJson_encoder as ISAJson_encoder_4, ROCrate_decoder as ROCrate_decoder_2, ROCrate_encoder as ROCrate_encoder_3 } from "./Process/Process.js";
 import { ISAJson_decoder as ISAJson_decoder_2, ISAJson_encoder as ISAJson_encoder_5, ROCrate_decoder as ROCrate_decoder_1, ROCrate_encoder as ROCrate_encoder_4 } from "./Assay.js";
+import { ROCrate_encoder as ROCrate_encoder_5 } from "./Data.js";
+import { getProtocols, getCharacteristics, getFactors, getUnits, getData } from "../Core/Process/ProcessSequence.js";
 import { context_jsonvalue } from "./context/rocrate/isa_study_context.js";
 import { disposeSafe, getEnumerator } from "../fable_modules/fable-library-js.4.24.0/Util.js";
-import { getProtocols, getCharacteristics, getFactors, getUnits } from "../Core/Process/ProcessSequence.js";
 import { encoder as encoder_10 } from "./Process/Factor.js";
 import { encoder as encoder_11 } from "./Process/MaterialAttribute.js";
 import { encoder as encoder_12 } from "./Process/StudyMaterials.js";
@@ -127,7 +128,7 @@ export function ROCrate_genID(a) {
         return "#EmptyStudy";
     }
     else {
-        return `#study/${replace(matchValue, " ", "_")}`;
+        return `studies/${replace(matchValue, " ", "_")}/`;
     }
 }
 
@@ -172,7 +173,7 @@ export function ROCrate_encoder(assays, s) {
         Encode(helpers_8) {
             return helpers_8.encodeString(value_12);
         },
-    }), s.PublicReleaseDate), tryIncludeSeq("publications", ROCrate_encoder_1, s.Publications), tryIncludeSeq("people", ROCrate_encoder_2, s.Contacts), tryIncludeList("processSequence", (studyName = s.Identifier, (oa_3) => ROCrate_encoder_3(studyName, undefined, oa_3)), processes), tryIncludeSeq("assays", (studyName_1 = s.Identifier, (a_1) => ROCrate_encoder_4(studyName_1, a_1)), assays_1), tryIncludeSeq("comments", ROCrate_encoder_5, s.Comments), ["@context", context_jsonvalue]]));
+    }), s.PublicReleaseDate), tryIncludeSeq("publications", ROCrate_encoder_1, s.Publications), tryIncludeSeq("people", ROCrate_encoder_2, s.Contacts), tryIncludeList("processSequence", (studyName = s.Identifier, (oa_3) => ROCrate_encoder_3(studyName, undefined, oa_3)), processes), tryIncludeSeq("assays", (studyName_1 = s.Identifier, (a_1) => ROCrate_encoder_4(studyName_1, a_1)), assays_1), tryIncludeList("dataFiles", ROCrate_encoder_5, getData(processes)), tryIncludeSeq("comments", ROCrate_encoder_6, s.Comments), ["@context", context_jsonvalue]]));
     return {
         Encode(helpers_9) {
             const arg = map_1((tupledArg_1) => [tupledArg_1[0], tupledArg_1[1].Encode(helpers_9)], values);

package/Json/context/rocrate/isa_investigation_context.js

@@ -42,7 +42,7 @@ export const context_jsonvalue = (() => {
         },
     }], ["title", {
         Encode(helpers_3) {
-            return helpers_3.encodeString("sdo:headline");
+            return helpers_3.encodeString("sdo:name");
         },
     }], ["additionalType", {
         Encode(helpers_4) {
@@ -93,5 +93,5 @@ export const context_jsonvalue = (() => {
     };
 })();
 
-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    \"Investigation\": \"sdo:Dataset\",\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    \"studies\": \"sdo:hasPart\",\r\n    \"ontologySourceReferences\": \"sdo:mentions\",\r\n    \"comments\": \"sdo:disambiguatingDescription\",\r\n\r\n    \"publications?\": \"sdo:SubjectOf?\",\r\n    \"filename\": \"sdo:alternateName\"\r\n  }\r\n}\r\n    ";
+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    \"Investigation\": \"sdo:Dataset\",\r\n\r\n    \"identifier\" : \"sdo:identifier\",\r\n    \"title\": \"sdo:name\",\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    \"studies\": \"sdo:hasPart\",\r\n    \"ontologySourceReferences\": \"sdo:mentions\",\r\n    \"comments\": \"sdo:disambiguatingDescription\",\r\n\r\n    \"publications?\": \"sdo:SubjectOf?\",\r\n    \"filename\": \"sdo:alternateName\"\r\n  }\r\n}\r\n    ";
 

package/Json/context/rocrate/isa_study_context.js

@@ -81,27 +81,31 @@ export const context_jsonvalue = (() => {
         Encode(helpers_10) {
             return helpers_10.encodeString("sdo:hasPart");
         },
-    }], ["filename", {
+    }], ["dataFiles", {
         Encode(helpers_11) {
-            return helpers_11.encodeString("sdo:alternateName");
+            return helpers_11.encodeString("sdo:hasPart");
         },
-    }], ["comments", {
+    }], ["filename", {
         Encode(helpers_12) {
-            return helpers_12.encodeString("sdo:comment");
+            return helpers_12.encodeString("sdo:alternateName");
         },
-    }], ["processSequence", {
+    }], ["comments", {
         Encode(helpers_13) {
-            return helpers_13.encodeString("sdo:about");
+            return helpers_13.encodeString("sdo:comment");
         },
-    }], ["studyDesignDescriptors", {
+    }], ["processSequence", {
         Encode(helpers_14) {
-            return helpers_14.encodeString("arc:ARC#ARC_00000037");
+            return helpers_14.encodeString("sdo:about");
+        },
+    }], ["studyDesignDescriptors", {
+        Encode(helpers_15) {
+            return helpers_15.encodeString("arc:ARC#ARC_00000037");
         },
     }]];
     return {
-        Encode(helpers_15) {
-            const arg = map((tupledArg) => [tupledArg[0], tupledArg[1].Encode(helpers_15)], values);
-            return helpers_15.encodeObject(arg);
+        Encode(helpers_16) {
+            const arg = map((tupledArg) => [tupledArg[0], tupledArg[1].Encode(helpers_16)], values);
+            return helpers_16.encodeObject(arg);
         },
     };
 })();

package/Json/context/rocrate/rocrate_context.js

@@ -50,7 +50,7 @@ export const context_jsonvalue = (() => {
         },
     }], ["conformsTo", {
         Encode(helpers_4) {
-            return helpers_4.encodeString("sdo:conformsTo");
+            return helpers_4.encodeString("http://purl.org/dc/terms/conformsTo");
         },
     }]];
     return {

package/README.md

@@ -1,3 +1,6 @@
+
+![logo](logos/ARCtrl_horizontal.png)
+
 # ARCtrl
 
 > **ARCtrl** the easy way to read, manipulate and write ARCs in __.NET__, __JavaScript__ and __Python__! ❤️
@@ -34,9 +37,7 @@ pip install arctrl
 
 ## Docs
 
-Currently we provide some documentation in form of markdown files in the `/docs` folder of this repository!
-
-[Check it out!](/docs)
+Documentation can be found [here](https://nfdi4plants.github.io/nfdi4plants.knowledgebase/arctrl/)
 
 ## Development
 
@@ -75,6 +76,14 @@ On windows you can use the `setup.cmd` to run the following steps automatically!
 
 Verify correct setup with `./build.cmd runtests` ✨
 
+## Branding
+
+Feel free to reference `ARCtrl` on slides or elsewhere using our logos:
+
+|Square | Horizontal | Vertical |
+| - | - | - |
+| ![square](logos/ARCtrl_square.png) | ![horizontal](logos/ARCtrl_horizontal.png) |  ![vertical](logos/ARCtrl_vertical.png) |
+
 ## Performance
 
 Measured on 13th Gen Intel(R) Core(TM) i7-13800H

package/Spreadsheet/DataMap.js

@@ -1,6 +1,8 @@
 import { printf, toFail } from "../fable_modules/fable-library-js.4.24.0/String.js";
-import { tryPick } from "../fable_modules/fable-library-js.4.24.0/Seq.js";
+import { forAll, tryPick } from "../fable_modules/fable-library-js.4.24.0/Seq.js";
 import { toFsWorksheet, tryFromFsWorksheet } from "./DataMapTable/DataMapTable.js";
+import { FsCellsCollection__get_Count } from "../fable_modules/FsSpreadsheet.6.3.1/Cells/FsCellsCollection.fs.js";
+import { DataMap_init } from "../Core/DataMap.js";
 import { FsWorkbook } from "../fable_modules/FsSpreadsheet.6.3.1/FsWorkbook.fs.js";
 
 /**
@@ -8,9 +10,15 @@ import { FsWorkbook } from "../fable_modules/FsSpreadsheet.6.3.1/FsWorkbook.fs.j
  */
 export function fromFsWorkbook(doc) {
     try {
-        const dataMapTable = tryPick(tryFromFsWorksheet, doc.GetWorksheets());
+        const worksheets = doc.GetWorksheets();
+        const dataMapTable = tryPick(tryFromFsWorksheet, worksheets);
         if (dataMapTable == null) {
-            throw new Error("No DataMapTable found in workbook");
+            if (forAll((sheet) => (FsCellsCollection__get_Count(sheet.CellCollection) === 0), worksheets)) {
+                return DataMap_init();
+            }
+            else {
+                throw new Error("No DataMapTable was found in any of the sheets of the workbook");
+            }
         }
         else {
             return dataMapTable;

package/Xlsx.js

@@ -1,9 +1,10 @@
 import { toFsWorkbook, fromFsWorkbook } from "./Spreadsheet/DataMap.js";
-import { FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static } from "./fable_modules/FsSpreadsheet.Js.6.3.1/FsExtensions.fs.js";
+import { map } from "./CrossAsync.js";
+import { FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static, FsSpreadsheet_FsWorkbook__FsWorkbook_fromXlsxFile_Static_Z721C83C5 } from "./fable_modules/FsSpreadsheet.Js.6.3.1/FsExtensions.fs.js";
 import { class_type } from "./fable_modules/fable-library-js.4.24.0/Reflection.js";
 import { ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F, ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D } from "./Spreadsheet/ArcAssay.js";
 import { ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522, ARCtrl_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D } from "./Spreadsheet/ArcStudy.js";
-import { map, unwrap } from "./fable_modules/fable-library-js.4.24.0/Option.js";
+import { map as map_1, unwrap } from "./fable_modules/fable-library-js.4.24.0/Option.js";
 import { ofSeq } from "./fable_modules/fable-library-js.4.24.0/List.js";
 import { ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF, ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D } from "./Spreadsheet/ArcInvestigation.js";
 
@@ -16,7 +17,10 @@ export class XlsxHelper_DatamapXlsx {
     toFsWorkbook(datamap) {
         return toFsWorkbook(datamap);
     }
-    toXlsxFile(path, datamap) {
+    fromXlsxFileAsync(path) {
+        return map(fromFsWorkbook, FsSpreadsheet_FsWorkbook__FsWorkbook_fromXlsxFile_Static_Z721C83C5(path));
+    }
+    toXlsxFileAsync(path, datamap) {
         return FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static(path, toFsWorkbook(datamap));
     }
 }
@@ -38,7 +42,10 @@ export class XlsxHelper_AssayXlsx {
     toFsWorkbook(assay) {
         return ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(assay);
     }
-    toXlsxFile(path, assay) {
+    fromXlsxFileAsync(path) {
+        return map(ARCtrl_ArcAssay__ArcAssay_fromFsWorkbook_Static_32154C9D, FsSpreadsheet_FsWorkbook__FsWorkbook_fromXlsxFile_Static_Z721C83C5(path));
+    }
+    toXlsxFileAsync(path, assay) {
         return FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static(path, ARCtrl_ArcAssay__ArcAssay_toFsWorkbook_Static_Z2508BE4F(assay));
     }
 }
@@ -58,10 +65,13 @@ export class XlsxHelper_StudyXlsx {
         return ARCtrl_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(fswb);
     }
     toFsWorkbook(study, assays) {
-        return ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(study, unwrap(map(ofSeq, assays)));
+        return ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(study, unwrap(map_1(ofSeq, assays)));
     }
-    toXlsxFile(path, study, assays) {
-        return FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static(path, ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(study, unwrap(map(ofSeq, assays))));
+    fromXlsxFileAsync(path) {
+        return map(ARCtrl_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D, FsSpreadsheet_FsWorkbook__FsWorkbook_fromXlsxFile_Static_Z721C83C5(path));
+    }
+    toXlsxFileAsync(path, study, assays) {
+        return FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static(path, ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_Z4CEFA522(study, unwrap(map_1(ofSeq, assays))));
     }
 }
 
@@ -82,7 +92,10 @@ export class XlsxHelper_InvestigationXlsx {
     toFsWorkbook(investigation) {
         return ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(investigation);
     }
-    toXlsxFile(path, investigation) {
+    fromXlsxFileAsync(path) {
+        return map(ARCtrl_ArcInvestigation__ArcInvestigation_fromFsWorkbook_Static_32154C9D, FsSpreadsheet_FsWorkbook__FsWorkbook_fromXlsxFile_Static_Z721C83C5(path));
+    }
+    toXlsxFileAsync(path, investigation) {
         return FsSpreadsheet_FsWorkbook__FsWorkbook_toXlsxFile_Static(path, ARCtrl_ArcInvestigation__ArcInvestigation_toFsWorkbook_Static_Z720BD3FF(investigation));
     }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@nfdi4plants/arctrl",
-  "version": "2.3.1",
+  "version": "2.4.0",
   "description": "Top level ARC DataModel and API function descriptions.",
   "type": "module",
   "main": "index.js",