@nfdi4plants/arctrl 1.0.0-beta.5 → 1.0.0-beta.7

package/ARC.js

@@ -1,22 +1,22 @@
-import { concat, fold, exactlyOne, choose, map } from "./fable_modules/fable-library.4.5.0/Array.js";
-import { toFsWorkbook as toFsWorkbook_1, fromFsWorkbook } from "./ISA/ISA.Spreadsheet/ArcAssay.js";
-import { tryFromContract } from "./Contracts/Contracts.ArcAssay.js";
-import { ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9, ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D } from "./ISA/ISA.Spreadsheet/ArcStudy.js";
-import { tryFromContract as tryFromContract_1 } from "./Contracts/Contracts.ArcStudy.js";
-import { toFsWorkbook, fromFsWorkbook as fromFsWorkbook_1 } from "./ISA/ISA.Spreadsheet/ArcInvestigation.js";
-import { tryFromContract as tryFromContract_2 } from "./Contracts/Contracts.ArcInvestigation.js";
-import { collect, toList, empty, singleton, append, delay, iterate, find, tryFind, toArray } from "./fable_modules/fable-library.4.5.0/Seq.js";
+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 { 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";
 import { FileSystem } from "./FileSystem/FileSystem.js";
-import { bind, map as map_1, value as value_2, defaultArg, unwrap } from "./fable_modules/fable-library.4.5.0/Option.js";
+import { bind, map as map_2, value as value_2, defaultArg, unwrap } from "./fable_modules/fable-library.4.5.0/Option.js";
+import { getStudyFolderPath, getAssayFolderPath } from "./Path.js";
+import { Contract } from "./Contract/Contract.js";
+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 { 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";
+import { toFsWorkbook as toFsWorkbook_1 } from "./ISA/ISA.Spreadsheet/ArcAssay.js";
 import { Dictionary_tryGet } from "./fable_modules/FsSpreadsheet.5.0.1/Cells/FsCellsCollection.fs.js";
-import { Contract } from "./Contract/Contract.js";
 import { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitignoreContract, Init_createInitContract_6DFDD678 } from "./Contracts/Contracts.Git.js";
 import { FSharpSet__Contains, ofSeq, unionMany } from "./fable_modules/fable-library.4.5.0/Set.js";
 import { comparePrimitives } from "./fable_modules/fable-library.4.5.0/Util.js";
@@ -24,15 +24,15 @@ import { ofSeq as ofSeq_1 } from "./fable_modules/fable-library.4.5.0/Map.js";
 import { class_type } from "./fable_modules/fable-library.4.5.0/Reflection.js";
 
 export function ARCAux_getArcAssaysFromContracts(contracts) {
-    return map(fromFsWorkbook, choose(tryFromContract, contracts));
+    return choose(ARCtrl_ISA_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F, contracts);
 }
 
 export function ARCAux_getArcStudiesFromContracts(contracts) {
-    return map(ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D, choose(tryFromContract_1, contracts));
+    return choose(ARCtrl_ISA_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F, contracts);
 }
 
 export function ARCAux_getArcInvestigationFromContracts(contracts) {
-    return fromFsWorkbook_1(exactlyOne(choose(tryFromContract_2, contracts)));
+    return exactlyOne(choose(ARCtrl_ISA_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F, contracts));
 }
 
 export function ARCAux_updateFSByISA(isa, fs) {
@@ -92,9 +92,56 @@ export class ARC {
         const this$ = this;
         return this$._fs;
     }
+    set FileSystem(fs) {
+        const this$ = this;
+        this$._fs = fs;
+    }
+    RemoveAssay(assayIdentifier) {
+        const this$ = this;
+        let isa;
+        const matchValue = this$.ISA;
+        if (matchValue == null) {
+            throw new Error("Cannot remove assay from null ISA value.");
+        }
+        else {
+            isa = matchValue;
+        }
+        const assay = isa.GetAssay(assayIdentifier);
+        const studies = assay.StudiesRegisteredIn;
+        isa.RemoveAssay(assayIdentifier);
+        const paths = this$.FileSystem.Tree.ToFilePaths();
+        const assayFolderPath = getAssayFolderPath(assayIdentifier);
+        const filteredPaths = paths.filter((p) => !(p.indexOf(assayFolderPath) === 0));
+        this$.SetFilePaths(filteredPaths);
+        const collection = toList(delay(() => append(singleton(ARCtrl_ISA_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => append(singleton(ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract(isa)), delay(() => map_1(ARCtrl_ISA_ArcStudy__ArcStudy_ToUpdateContract, studies)))))));
+        return Array.from(collection);
+    }
+    RemoveStudy(studyIdentifier) {
+        const this$ = this;
+        let isa;
+        const matchValue = this$.ISA;
+        if (matchValue == null) {
+            throw new Error("Cannot remove study from null ISA value.");
+        }
+        else {
+            isa = matchValue;
+        }
+        isa.RemoveStudy(studyIdentifier);
+        const paths = this$.FileSystem.Tree.ToFilePaths();
+        const studyFolderPath = getStudyFolderPath(studyIdentifier);
+        const filteredPaths = paths.filter((p) => !(p.indexOf(studyFolderPath) === 0));
+        this$.SetFilePaths(filteredPaths);
+        const collection = ofArray([Contract.createDelete(studyFolderPath), ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract(isa)]);
+        return Array.from(collection);
+    }
     static fromFilePaths(filePaths) {
         return new ARC(void 0, void 0, FileSystem.fromFilePaths(filePaths));
     }
+    SetFilePaths(filePaths) {
+        const this$ = this;
+        const tree = FileSystemTree.fromFilePaths(filePaths);
+        this$._fs = (new FileSystem(tree, this$._fs.History));
+    }
     GetReadContracts() {
         const this$ = this;
         return choose(tryISAReadContractFromPath, this$._fs.Tree.ToFilePaths());
@@ -104,8 +151,20 @@ export class ARC {
         const investigation = ARCAux_getArcInvestigationFromContracts(contracts);
         const studies = map((tuple) => tuple[0], ARCAux_getArcStudiesFromContracts(contracts));
         const assays = ARCAux_getArcAssaysFromContracts(contracts);
+        const array_2 = investigation.AssayIdentifiers;
+        array_2.forEach((ai) => {
+            if (!assays.some((a) => (a.Identifier === ai))) {
+                investigation.DeleteAssay(ai);
+            }
+        });
+        const array_4 = investigation.StudyIdentifiers;
+        array_4.forEach((si) => {
+            if (!studies.some((s) => (s.Identifier === si))) {
+                investigation.RemoveStudy(si);
+            }
+        });
         studies.forEach((study) => {
-            const registeredStudyOpt = tryFind((s) => (s.Identifier === study.Identifier), investigation.Studies);
+            const registeredStudyOpt = tryFind((s_1) => (s_1.Identifier === study.Identifier), investigation.Studies);
             if (registeredStudyOpt == null) {
                 investigation.AddStudy(study);
             }
@@ -115,7 +174,7 @@ export class ARC {
             }
         });
         assays.forEach((assay) => {
-            const registeredAssayOpt = tryFind((a) => (a.Identifier === assay.Identifier), investigation.Assays);
+            const registeredAssayOpt = tryFind((a_1) => (a_1.Identifier === assay.Identifier), investigation.Assays);
             if (registeredAssayOpt == null) {
                 investigation.AddAssay(assay);
             }
@@ -123,10 +182,10 @@ export class ARC {
                 const registeredAssay = registeredAssayOpt;
                 registeredAssay.UpdateReferenceByAssayFile(assay, true);
             }
-            const assay_1 = find((a_1) => (a_1.Identifier === assay.Identifier), investigation.Assays);
+            const assay_1 = find((a_2) => (a_2.Identifier === assay.Identifier), investigation.Assays);
             let updatedTables;
-            const array_2 = assay_1.StudiesRegisteredIn;
-            updatedTables = fold((tables, study_1) => ArcTables.updateReferenceTablesBySheets(new ArcTables(study_1.Tables), tables, false), new ArcTables(assay_1.Tables), array_2);
+            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);
             assay_1.Tables = updatedTables.Tables;
         });
         this$.ISA = investigation;
@@ -176,14 +235,14 @@ export class ARC {
     }
     Copy() {
         const this$ = this;
-        const isaCopy = map_1((i) => i.Copy(), this$._isa);
+        const isaCopy = map_2((i) => i.Copy(), this$._isa);
         const fsCopy = this$._fs.Copy();
         return new ARC(unwrap(isaCopy), this$._cwl, fsCopy);
     }
     GetRegisteredPayload(IgnoreHidden) {
         let tree, paths, array_3;
         const this$ = this;
-        const registeredStudies = defaultArg(map_1((isa) => isa.Studies.slice(), map_1((i) => i.Copy(), this$._isa)), []);
+        const registeredStudies = defaultArg(map_2((isa) => isa.Studies.slice(), map_2((i) => i.Copy(), this$._isa)), []);
         const registeredAssays = concat(map((s) => s.RegisteredAssays.slice(), registeredStudies));
         const includeFiles = unionMany([ofSeq(["isa.investigation.xlsx", "README.md"], {
             Compare: comparePrimitives,

package/Contracts/Contracts.ARCtrl.js

@@ -1,8 +1,6 @@
 import { split as split_1 } from "../FileSystem/Path.js";
-import { $007CInvestigationPath$007C_$007C } from "./Contracts.ArcInvestigation.js";
+import { $007CStudyPath$007C_$007C, $007CAssayPath$007C_$007C, $007CInvestigationPath$007C_$007C } from "./Contracts.ArcTypes.js";
 import { Contract } from "../Contract/Contract.js";
-import { $007CAssayPath$007C_$007C } from "./Contracts.ArcAssay.js";
-import { $007CStudyPath$007C_$007C } from "./Contracts.ArcStudy.js";
 
 /**
  * Tries to create READ contract with DTOType = ISA_Assay, ISA_Study or ISA_Investigation from given path relative to ARC root.

package/Contracts/Contracts.ArcTypes.js

@@ -0,0 +1,253 @@
+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 { 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";
+import { fromFsWorkbook as fromFsWorkbook_1, toFsWorkbook as toFsWorkbook_1 } from "../ISA/ISA.Spreadsheet/ArcAssay.js";
+
+export function $007CStudyPath$007C_$007C(input) {
+    let matchResult;
+    if (!equalsWith((x, y) => (x === y), input, defaultOf()) && (input.length === 3)) {
+        if (input[0] === "studies") {
+            if (input[2] === "isa.study.xlsx") {
+                matchResult = 0;
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+        else {
+            matchResult = 1;
+        }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0: {
+            const anyStudyName = input[1];
+            return combineMany(input);
+        }
+        default:
+            return void 0;
+    }
+}
+
+export function $007CAssayPath$007C_$007C(input) {
+    let matchResult;
+    if (!equalsWith((x, y) => (x === y), input, defaultOf()) && (input.length === 3)) {
+        if (input[0] === "assays") {
+            if (input[2] === "isa.assay.xlsx") {
+                matchResult = 0;
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+        else {
+            matchResult = 1;
+        }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0: {
+            const anyAssayName = input[1];
+            return combineMany(input);
+        }
+        default:
+            return void 0;
+    }
+}
+
+export function $007CInvestigationPath$007C_$007C(input) {
+    let matchResult;
+    if (!equalsWith((x, y) => (x === y), input, defaultOf()) && (input.length === 1)) {
+        if (input[0] === "isa.investigation.xlsx") {
+            matchResult = 0;
+        }
+        else {
+            matchResult = 1;
+        }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0:
+            return combineMany(input);
+        default:
+            return void 0;
+    }
+}
+
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToCreateContract(this$) {
+    return Contract.createCreate("isa.investigation.xlsx", "ISA_Investigation", toFsWorkbook(this$));
+}
+
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract(this$) {
+    return Contract.createUpdate("isa.investigation.xlsx", "ISA_Investigation", toFsWorkbook(this$));
+}
+
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_toCreateContract_Static_Z4D87C88C(inv) {
+    return ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToCreateContract(inv);
+}
+
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_toUpdateContract_Static_Z4D87C88C(inv) {
+    return ARCtrl_ISA_ArcInvestigation__ArcInvestigation_ToUpdateContract(inv);
+}
+
+export function ARCtrl_ISA_ArcInvestigation__ArcInvestigation_tryFromReadContract_Static_7570923F(c) {
+    let matchResult, fsworkbook;
+    if (c.Operation === "READ") {
+        if (c.DTOType != null) {
+            if (c.DTOType === "ISA_Investigation") {
+                if (c.DTO != null) {
+                    matchResult = 0;
+                    fsworkbook = c.DTO;
+                }
+                else {
+                    matchResult = 1;
+                }
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+        else {
+            matchResult = 1;
+        }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0:
+            return fromFsWorkbook(fsworkbook);
+        default:
+            return void 0;
+    }
+}
+
+export function ARCtrl_ISA_ArcStudy__ArcStudy_ToCreateContract(this$) {
+    const path = Study_fileNameFromIdentifier(this$.Identifier);
+    return Contract.createCreate(path, "ISA_Study", ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9(this$));
+}
+
+export function ARCtrl_ISA_ArcStudy__ArcStudy_ToUpdateContract(this$) {
+    const path = Study_fileNameFromIdentifier(this$.Identifier);
+    return Contract.createUpdate(path, "ISA_Study", ARCtrl_ISA_ArcStudy__ArcStudy_toFsWorkbook_Static_Z2A9662E9(this$));
+}
+
+export function ARCtrl_ISA_ArcStudy__ArcStudy_ToDeleteContract(this$) {
+    const path = getStudyFolderPath(this$.Identifier);
+    return Contract.createDelete(path);
+}
+
+export function ARCtrl_ISA_ArcStudy__ArcStudy_toDeleteContract_Static_1B3D5E9B(study) {
+    return ARCtrl_ISA_ArcStudy__ArcStudy_ToDeleteContract(study);
+}
+
+export function ARCtrl_ISA_ArcStudy__ArcStudy_toCreateContract_Static_1B3D5E9B(study) {
+    return ARCtrl_ISA_ArcStudy__ArcStudy_ToCreateContract(study);
+}
+
+export function ARCtrl_ISA_ArcStudy__ArcStudy_toUpdateContract_Static_1B3D5E9B(study) {
+    return ARCtrl_ISA_ArcStudy__ArcStudy_ToUpdateContract(study);
+}
+
+export function ARCtrl_ISA_ArcStudy__ArcStudy_tryFromReadContract_Static_7570923F(c) {
+    let matchResult, fsworkbook;
+    if (c.Operation === "READ") {
+        if (c.DTOType != null) {
+            if (c.DTOType === "ISA_Study") {
+                if (c.DTO != null) {
+                    matchResult = 0;
+                    fsworkbook = c.DTO;
+                }
+                else {
+                    matchResult = 1;
+                }
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+        else {
+            matchResult = 1;
+        }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0:
+            return ARCtrl_ISA_ArcStudy__ArcStudy_fromFsWorkbook_Static_32154C9D(fsworkbook);
+        default:
+            return void 0;
+    }
+}
+
+export function ARCtrl_ISA_ArcAssay__ArcAssay_ToCreateContract(this$) {
+    const path = Assay_fileNameFromIdentifier(this$.Identifier);
+    return Contract.createCreate(path, "ISA_Assay", toFsWorkbook_1(this$));
+}
+
+export function ARCtrl_ISA_ArcAssay__ArcAssay_ToUpdateContract(this$) {
+    const path = Assay_fileNameFromIdentifier(this$.Identifier);
+    return Contract.createUpdate(path, "ISA_Assay", toFsWorkbook_1(this$));
+}
+
+export function ARCtrl_ISA_ArcAssay__ArcAssay_ToDeleteContract(this$) {
+    const path = getAssayFolderPath(this$.Identifier);
+    return Contract.createDelete(path);
+}
+
+export function ARCtrl_ISA_ArcAssay__ArcAssay_toDeleteContract_Static_1C75D08D(assay) {
+    return ARCtrl_ISA_ArcAssay__ArcAssay_ToDeleteContract(assay);
+}
+
+export function ARCtrl_ISA_ArcAssay__ArcAssay_toCreateContract_Static_1C75D08D(assay) {
+    return ARCtrl_ISA_ArcAssay__ArcAssay_ToCreateContract(assay);
+}
+
+export function ARCtrl_ISA_ArcAssay__ArcAssay_toUpdateContract_Static_1C75D08D(assay) {
+    return ARCtrl_ISA_ArcAssay__ArcAssay_ToUpdateContract(assay);
+}
+
+export function ARCtrl_ISA_ArcAssay__ArcAssay_tryFromReadContract_Static_7570923F(c) {
+    let matchResult, fsworkbook;
+    if (c.Operation === "READ") {
+        if (c.DTOType != null) {
+            if (c.DTOType === "ISA_Assay") {
+                if (c.DTO != null) {
+                    matchResult = 0;
+                    fsworkbook = c.DTO;
+                }
+                else {
+                    matchResult = 1;
+                }
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+        else {
+            matchResult = 1;
+        }
+    }
+    else {
+        matchResult = 1;
+    }
+    switch (matchResult) {
+        case 0:
+            return fromFsWorkbook_1(fsworkbook);
+        default:
+            return void 0;
+    }
+}
+