@nfdi4plants/arctrl 2.0.0-alpha.2 → 2.0.0-alpha.4

package/ARC.js

@@ -1,5 +1,6 @@
-import { concat, fold, map, exactlyOne, choose } from "./fable_modules/fable-library-js.4.16.0/Array.js";
+import { concat, fold, map, exactlyOne, tryPick, choose } from "./fable_modules/fable-library-js.4.16.0/Array.js";
 import { ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49, ARCtrl_ArcAssay__ArcAssay_ToDeleteContract, ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F } from "./Contract/ArcAssay.js";
+import { ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5, ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5, ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static, ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static } from "./Contract/Datamap.js";
 import { ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49, ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F } from "./Contract/ArcStudy.js";
 import { ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49, ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F } from "./Contract/ArcInvestigation.js";
 import { collect, empty, iterate, find, tryFind, map as map_1, singleton, append, delay, toList, toArray } from "./fable_modules/fable-library-js.4.16.0/Seq.js";
@@ -11,14 +12,16 @@ import { Contract } from "./Contract/Contract.js";
 import { ofArray } from "./fable_modules/fable-library-js.4.16.0/List.js";
 import { tryISAReadContractFromPath } from "./Contract/ARC.js";
 import { ArcTables } from "./Core/Table/ArcTables.js";
-import { comparePrimitives, safeHash } from "./fable_modules/fable-library-js.4.16.0/Util.js";
 import { addToDict } from "./fable_modules/fable-library-js.4.16.0/MapUtil.js";
 import { toFsWorkbook, toLightFsWorkbook } from "./Spreadsheet/ArcInvestigation.js";
 import { ArcInvestigation } from "./Core/ArcTypes.js";
-import { Assay_fileNameFromIdentifier, Study_fileNameFromIdentifier } from "./Core/Helper/Identifier.js";
+import { Assay_datamapFileNameFromIdentifier, Assay_fileNameFromIdentifier, Study_datamapFileNameFromIdentifier, Study_fileNameFromIdentifier } from "./Core/Helper/Identifier.js";
 import { ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_353D0DB7 } from "./Spreadsheet/ArcStudy.js";
-import { toFsWorkbook as toFsWorkbook_1 } from "./Spreadsheet/ArcAssay.js";
-import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.5.1.3/Cells/FsCellsCollection.fs.js";
+import { DataMap__get_StaticHash, DataMap__set_StaticHash_Z524259A4 } from "./Core/Table/DataMap.js";
+import { comparePrimitives, safeHash } from "./fable_modules/fable-library-js.4.16.0/Util.js";
+import { toFsWorkbook as toFsWorkbook_1 } from "./Spreadsheet/DataMap.js";
+import { toFsWorkbook as toFsWorkbook_2 } from "./Spreadsheet/ArcAssay.js";
+import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.6.1.2/Cells/FsCellsCollection.fs.js";
 import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitignoreContract, Init_createInitContract_6DFDD678 } from "./Contract/Git.js";
 import { FSharpSet__Contains, ofSeq, unionMany } from "./fable_modules/fable-library-js.4.16.0/Set.js";
 import { ofSeq as ofSeq_1 } from "./fable_modules/fable-library-js.4.16.0/Map.js";
@@ -33,10 +36,18 @@ export function ARCAux_getArcAssaysFromContracts(contracts) {
     return choose(ARCtrl_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, contracts);
 }
 
+export function ARCAux_getAssayDataMapFromContracts(assayIdentifier, contracts) {
+    return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static(assayIdentifier, c), contracts);
+}
+
 export function ARCAux_getArcStudiesFromContracts(contracts) {
     return choose(ARCtrl_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F, contracts);
 }
 
+export function ARCAux_getStudyDataMapFromContracts(studyIdentifier, contracts) {
+    return tryPick((c) => ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static(studyIdentifier, c), contracts);
+}
+
 export function ARCAux_getArcInvestigationFromContracts(contracts) {
     return exactlyOne(choose(ARCtrl_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts));
 }
@@ -48,13 +59,17 @@ export function ARCAux_updateFSByISA(isa, fs) {
     }
     else {
         const inv = isa;
-        patternInput = [toArray(inv.StudyIdentifiers), toArray(inv.AssayIdentifiers)];
+        patternInput = [toArray(inv.Studies), toArray(inv.Assays)];
     }
-    const assays = FileSystemTree.createAssaysFolder(map((assayName) => FileSystemTree.createAssayFolder(assayName), patternInput[1]));
-    const studies = FileSystemTree.createStudiesFolder(map((studyName) => FileSystemTree.createStudyFolder(studyName), patternInput[0]));
+    let assaysFolder;
+    const assays_1 = map((a) => FileSystemTree.createAssayFolder(a.Identifier, a.DataMap != null), patternInput[1]);
+    assaysFolder = FileSystemTree.createAssaysFolder(assays_1);
+    let studiesFolder;
+    const studies_1 = map((s) => FileSystemTree.createStudyFolder(s.Identifier, s.DataMap != null), patternInput[0]);
+    studiesFolder = FileSystemTree.createStudiesFolder(studies_1);
     const investigation = FileSystemTree.createInvestigationFile();
     let tree_1;
-    const tree = FileSystemTree.createRootFolder([investigation, assays, studies]);
+    const tree = FileSystemTree.createRootFolder([investigation, assaysFolder, studiesFolder]);
     tree_1 = FileSystem.create({
         tree: tree,
     });
@@ -178,6 +193,8 @@ export class ARC {
                 const registeredStudy = registeredStudyOpt;
                 registeredStudy.UpdateReferenceByStudyFile(study, true);
             }
+            const datamap = ARCAux_getAssayDataMapFromContracts(study.Identifier, contracts);
+            study.DataMap = datamap;
             study.StaticHash = (study.GetLightHashCode() | 0);
         });
         assays.forEach((assay) => {
@@ -193,10 +210,12 @@ export class ARC {
             let updatedTables;
             const array_6 = assay_1.StudiesRegisteredIn;
             updatedTables = fold((tables, study_1) => ArcTables.updateReferenceTablesBySheets(new ArcTables(study_1.Tables), tables, false), new ArcTables(assay_1.Tables), array_6);
+            const datamap_1 = ARCAux_getAssayDataMapFromContracts(assay_1.Identifier, contracts);
+            assay_1.DataMap = datamap_1;
             assay_1.Tables = updatedTables.Tables;
         });
         iterate((a_3) => {
-            a_3.StaticHash = (safeHash(a_3) | 0);
+            a_3.StaticHash = (a_3.GetLightHashCode() | 0);
         }, investigation.Assays);
         iterate((s_2) => {
             s_2.StaticHash = (s_2.GetLightHashCode() | 0);
@@ -226,10 +245,20 @@ export class ARC {
             iterate((s) => {
                 s.StaticHash = (s.GetLightHashCode() | 0);
                 addToDict(workbooks, Study_fileNameFromIdentifier(s.Identifier), ["ISA_Study", ARCtrl_ArcStudy__ArcStudy_toFsWorkbook_Static_353D0DB7(s)]);
+                if (s.DataMap != null) {
+                    const dm = value_2(s.DataMap);
+                    DataMap__set_StaticHash_Z524259A4(dm, safeHash(dm));
+                    addToDict(workbooks, Study_datamapFileNameFromIdentifier(s.Identifier), ["ISA_Datamap", toFsWorkbook_1(dm)]);
+                }
             }, inv.Studies);
             iterate((a) => {
-                a.StaticHash = (safeHash(a) | 0);
-                addToDict(workbooks, Assay_fileNameFromIdentifier(a.Identifier), ["ISA_Assay", toFsWorkbook_1(a)]);
+                a.StaticHash = (a.GetLightHashCode() | 0);
+                addToDict(workbooks, Assay_fileNameFromIdentifier(a.Identifier), ["ISA_Assay", toFsWorkbook_2(a)]);
+                if (a.DataMap != null) {
+                    const dm_1 = value_2(a.DataMap);
+                    DataMap__set_StaticHash_Z524259A4(dm_1, safeHash(dm_1));
+                    addToDict(workbooks, Assay_datamapFileNameFromIdentifier(a.Identifier), ["ISA_Datamap", toFsWorkbook_1(dm_1)]);
+                }
             }, inv.Assays);
         }
         return map((fp) => {
@@ -256,14 +285,80 @@ export class ARC {
                 return append(collect((s) => {
                     const hash_1 = s.GetLightHashCode() | 0;
                     return append((s.StaticHash === 0) ? ARCtrl_ArcStudy__ArcStudy_ToCreateContract_6FCE9E49(s, true) : ((s.StaticHash !== hash_1) ? singleton(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract(s)) : empty()), delay(() => {
+                        let dm_1;
                         s.StaticHash = (hash_1 | 0);
-                        return empty();
+                        const matchValue_1 = s.DataMap;
+                        let matchResult, dm_2, dm_3;
+                        if (matchValue_1 != null) {
+                            if (DataMap__get_StaticHash(matchValue_1) === 0) {
+                                matchResult = 0;
+                                dm_2 = matchValue_1;
+                            }
+                            else if ((dm_1 = matchValue_1, DataMap__get_StaticHash(dm_1) !== safeHash(dm_1))) {
+                                matchResult = 1;
+                                dm_3 = matchValue_1;
+                            }
+                            else {
+                                matchResult = 2;
+                            }
+                        }
+                        else {
+                            matchResult = 2;
+                        }
+                        switch (matchResult) {
+                            case 0:
+                                return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5(dm_2, s.Identifier)), delay(() => {
+                                    DataMap__set_StaticHash_Z524259A4(dm_2, safeHash(dm_2));
+                                    return empty();
+                                }));
+                            case 1:
+                                return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(dm_3, s.Identifier)), delay(() => {
+                                    DataMap__set_StaticHash_Z524259A4(dm_3, safeHash(dm_3));
+                                    return empty();
+                                }));
+                            default: {
+                                return empty();
+                            }
+                        }
                     }));
                 }, inv_2.Studies), delay(() => collect((a) => {
-                    const hash_2 = safeHash(a) | 0;
+                    const hash_2 = a.GetLightHashCode() | 0;
                     return append((a.StaticHash === 0) ? ARCtrl_ArcAssay__ArcAssay_ToCreateContract_6FCE9E49(a, true) : ((a.StaticHash !== hash_2) ? singleton(ARCtrl_ArcAssay__ArcAssay_ToUpdateContract(a)) : empty()), delay(() => {
+                        let dm_5;
                         a.StaticHash = (hash_2 | 0);
-                        return empty();
+                        const matchValue_2 = a.DataMap;
+                        let matchResult_1, dm_6, dm_7;
+                        if (matchValue_2 != null) {
+                            if (DataMap__get_StaticHash(matchValue_2) === 0) {
+                                matchResult_1 = 0;
+                                dm_6 = matchValue_2;
+                            }
+                            else if ((dm_5 = matchValue_2, DataMap__get_StaticHash(dm_5) !== safeHash(dm_5))) {
+                                matchResult_1 = 1;
+                                dm_7 = matchValue_2;
+                            }
+                            else {
+                                matchResult_1 = 2;
+                            }
+                        }
+                        else {
+                            matchResult_1 = 2;
+                        }
+                        switch (matchResult_1) {
+                            case 0:
+                                return append(singleton(ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5(dm_6, a.Identifier)), delay(() => {
+                                    DataMap__set_StaticHash_Z524259A4(dm_6, safeHash(dm_6));
+                                    return empty();
+                                }));
+                            case 1:
+                                return append(singleton(ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5(dm_7, a.Identifier)), delay(() => {
+                                    DataMap__set_StaticHash_Z524259A4(dm_7, safeHash(dm_7));
+                                    return empty();
+                                }));
+                            default: {
+                                return empty();
+                            }
+                        }
                     }));
                 }, inv_2.Assays)));
             }));

package/Contract/ARC.js

@@ -3,6 +3,7 @@ import { $007CInvestigationPath$007C_$007C } from "./ArcInvestigation.js";
 import { Contract } from "./Contract.js";
 import { $007CAssayPath$007C_$007C } from "./ArcAssay.js";
 import { $007CStudyPath$007C_$007C } from "./ArcStudy.js";
+import { $007CDatamapPath$007C_$007C } from "./Datamap.js";
 
 /**
  * Tries to create READ contract with DTOType = ISA_Assay, ISA_Study or ISA_Investigation from given path relative to ARC root.
@@ -27,7 +28,14 @@ export function tryISAReadContractFromPath(path) {
                 return Contract.createRead(p_2, "ISA_Study");
             }
             else {
-                return void 0;
+                const activePatternResult_3 = $007CDatamapPath$007C_$007C(split);
+                if (activePatternResult_3 != null) {
+                    const p_3 = activePatternResult_3;
+                    return Contract.createRead(p_3, "ISA_Datamap");
+                }
+                else {
+                    return void 0;
+                }
             }
         }
     }

package/Contract/Datamap.js

@@ -0,0 +1,180 @@
+import { equalsWith, item } from "../fable_modules/fable-library-js.4.16.0/Array.js";
+import { combineMany } from "../FileSystem/Path.js";
+import { safeHash, defaultOf } from "../fable_modules/fable-library-js.4.16.0/Util.js";
+import { Study_datamapFileNameFromIdentifier, Assay_datamapFileNameFromIdentifier } from "../Core/Helper/Identifier.js";
+import { Contract } from "./Contract.js";
+import { fromFsWorkbook, toFsWorkbook } from "../Spreadsheet/DataMap.js";
+import { DataMap__set_StaticHash_Z524259A4 } from "../Core/Table/DataMap.js";
+
+export function $007CDatamapPath$007C_$007C(input) {
+    let matchResult;
+    if (!equalsWith((x, y) => (x === y), input, defaultOf()) && (input.length === 3)) {
+        if (item(0, input) === "assays") {
+            if (item(2, input) === "isa.datamap.xlsx") {
+                matchResult = 0;
+            }
+            else {
+                matchResult = 2;
+            }
+        }
+        else if (item(0, input) === "studies") {
+            if (item(2, input) === "isa.datamap.xlsx") {
+                matchResult = 1;
+            }
+            else {
+                matchResult = 2;
+            }
+        }
+        else {
+            matchResult = 2;
+        }
+    }
+    else {
+        matchResult = 2;
+    }
+    switch (matchResult) {
+        case 0: {
+            const anyAssayName = item(1, input);
+            return combineMany(input);
+        }
+        case 1: {
+            const anyStudyName = item(1, input);
+            return combineMany(input);
+        }
+        default:
+            return void 0;
+    }
+}
+
+export function ARCtrl_DataMap__DataMap_ToCreateContractForAssay_Z721C83C5(this$, assayIdentifier) {
+    const path = Assay_datamapFileNameFromIdentifier(assayIdentifier);
+    return Contract.createCreate(path, "ISA_Datamap", toFsWorkbook(this$));
+}
+
+export function ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5(this$, assayIdentifier) {
+    const path = Assay_datamapFileNameFromIdentifier(assayIdentifier);
+    return Contract.createUpdate(path, "ISA_Datamap", toFsWorkbook(this$));
+}
+
+export function ARCtrl_DataMap__DataMap_ToDeleteContractForAssay_Z721C83C5(this$, assayIdentifier) {
+    const path = Assay_datamapFileNameFromIdentifier(assayIdentifier);
+    return Contract.createDelete(path);
+}
+
+export function ARCtrl_DataMap__DataMap_toDeleteContractForAssay_Static_Z721C83C5(assayIdentifier) {
+    return (dataMap) => ARCtrl_DataMap__DataMap_ToDeleteContractForAssay_Z721C83C5(dataMap, assayIdentifier);
+}
+
+export function ARCtrl_DataMap__DataMap_toUpdateContractForAssay_Static_Z721C83C5(assayIdentifier) {
+    return (dataMap) => ARCtrl_DataMap__DataMap_ToUpdateContractForAssay_Z721C83C5(dataMap, assayIdentifier);
+}
+
+export function ARCtrl_DataMap__DataMap_tryFromReadContractForAssay_Static(assayIdentifier, c) {
+    let fsworkbook;
+    const path = Assay_datamapFileNameFromIdentifier(assayIdentifier);
+    let matchResult, fsworkbook_1, p_1;
+    if (c.Operation === "READ") {
+        if (c.DTOType != null) {
+            if (c.DTOType === "ISA_Datamap") {
+                if (c.DTO != null) {
+                    if ((fsworkbook = c.DTO, c.Path === path)) {
+                        matchResult = 0;
+                        fsworkbook_1 = c.DTO;
+                        p_1 = c.Path;
+                    }
+                    else {
+                        matchResult = 1;
+                    }
+                }
+                else {
+                    matchResult = 1;
+                }
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+        else {
+            matchResult = 1;
+        }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0: {
+            const dm = fromFsWorkbook(fsworkbook_1);
+            DataMap__set_StaticHash_Z524259A4(dm, safeHash(dm));
+            return dm;
+        }
+        default:
+            return void 0;
+    }
+}
+
+export function ARCtrl_DataMap__DataMap_ToCreateContractForStudy_Z721C83C5(this$, studyIdentifier) {
+    const path = Study_datamapFileNameFromIdentifier(studyIdentifier);
+    return Contract.createCreate(path, "ISA_Datamap", toFsWorkbook(this$));
+}
+
+export function ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(this$, studyIdentifier) {
+    const path = Study_datamapFileNameFromIdentifier(studyIdentifier);
+    return Contract.createUpdate(path, "ISA_Datamap", toFsWorkbook(this$));
+}
+
+export function ARCtrl_DataMap__DataMap_ToDeleteContractForStudy_Z721C83C5(this$, studyIdentifier) {
+    const path = Study_datamapFileNameFromIdentifier(studyIdentifier);
+    return Contract.createDelete(path);
+}
+
+export function ARCtrl_DataMap__DataMap_toDeleteContractForStudy_Static_Z721C83C5(studyIdentifier) {
+    return (dataMap) => ARCtrl_DataMap__DataMap_ToDeleteContractForStudy_Z721C83C5(dataMap, studyIdentifier);
+}
+
+export function ARCtrl_DataMap__DataMap_toUpdateContractForStudy_Static_Z721C83C5(studyIdentifier) {
+    return (dataMap) => ARCtrl_DataMap__DataMap_ToUpdateContractForStudy_Z721C83C5(dataMap, studyIdentifier);
+}
+
+export function ARCtrl_DataMap__DataMap_tryFromReadContractForStudy_Static(studyIdentifier, c) {
+    let fsworkbook;
+    const path = Study_datamapFileNameFromIdentifier(studyIdentifier);
+    let matchResult, fsworkbook_1, p_1;
+    if (c.Operation === "READ") {
+        if (c.DTOType != null) {
+            if (c.DTOType === "ISA_Datamap") {
+                if (c.DTO != null) {
+                    if ((fsworkbook = c.DTO, c.Path === path)) {
+                        matchResult = 0;
+                        fsworkbook_1 = c.DTO;
+                        p_1 = c.Path;
+                    }
+                    else {
+                        matchResult = 1;
+                    }
+                }
+                else {
+                    matchResult = 1;
+                }
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+        else {
+            matchResult = 1;
+        }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0: {
+            const dm = fromFsWorkbook(fsworkbook_1);
+            DataMap__set_StaticHash_Z524259A4(dm, safeHash(dm));
+            return dm;
+        }
+        default:
+            return void 0;
+    }
+}
+