@nfdi4plants/arctrl 2.0.0-alpha.4 → 2.0.0-alpha.5

package/ARC.js

@@ -3,11 +3,13 @@ import { ARCtrl_ArcAssay__ArcAssay_ToUpdateContract, ARCtrl_ArcAssay__ArcAssay_T
 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";
+import { collect, empty, iterate, find, tryFind, map as map_1, singleton, append, delay, toList, contains, toArray } from "./fable_modules/fable-library-js.4.16.0/Seq.js";
 import { FileSystemTree } from "./FileSystem/FileSystemTree.js";
 import { FileSystem } from "./FileSystem/FileSystem.js";
 import { bind, map as map_2, value as value_2, defaultArg, unwrap } from "./fable_modules/fable-library-js.4.16.0/Option.js";
+import { comparePrimitives, safeHash, stringHash } from "./fable_modules/fable-library-js.4.16.0/Util.js";
 import { getStudyFolderPath, getAssayFolderPath } from "./FileSystem/Path.js";
+import { printf, toText, replace } from "./fable_modules/fable-library-js.4.16.0/String.js";
 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";
@@ -18,16 +20,14 @@ import { ArcInvestigation } from "./Core/ArcTypes.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 { 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 { Clone_createCloneContract_5000466F, Init_createAddRemoteContract_Z721C83C5, gitignoreContract, gitattributesContract, 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";
 import { fromString } from "./fable_modules/Thoth.Json.JavaScript.0.1.0/Decode.fs.js";
 import { encoder, decoder as decoder_1 } from "./Json/ARC.js";
-import { printf, toText } from "./fable_modules/fable-library-js.4.16.0/String.js";
 import { toString } from "./fable_modules/Thoth.Json.JavaScript.0.1.0/Encode.fs.js";
 import { defaultSpaces } from "./Json/Encode.js";
 import { class_type } from "./fable_modules/fable-library-js.4.16.0/Reflection.js";
@@ -118,14 +118,22 @@ export class ARC {
         this$._fs = fs;
     }
     RemoveAssay(assayIdentifier) {
+        let i;
         const this$ = this;
         let isa;
         const matchValue = this$.ISA;
         if (matchValue == null) {
             throw new Error("Cannot remove assay from null ISA value.");
         }
+        else if ((i = matchValue, contains(assayIdentifier, i.AssayIdentifiers, {
+            Equals: (x, y) => (x === y),
+            GetHashCode: stringHash,
+        }))) {
+            const i_1 = matchValue;
+            isa = i_1;
+        }
         else {
-            isa = matchValue;
+            throw new Error("ARC does not contain assay with given name");
         }
         const assay = isa.GetAssay(assayIdentifier);
         const studies = assay.StudiesRegisteredIn;
@@ -137,6 +145,33 @@ export class ARC {
         const collection = toList(delay(() => append(singleton(ARCtrl_ArcAssay__ArcAssay_ToDeleteContract(assay)), delay(() => append(singleton(ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49(isa)), delay(() => map_1(ARCtrl_ArcStudy__ArcStudy_ToUpdateContract, studies)))))));
         return Array.from(collection);
     }
+    RenameAssay(oldAssayIdentifier, newAssayIdentifier) {
+        let i;
+        const this$ = this;
+        let isa;
+        const matchValue = this$.ISA;
+        if (matchValue == null) {
+            throw new Error("Cannot rename assay in null ISA value.");
+        }
+        else if ((i = matchValue, contains(oldAssayIdentifier, i.AssayIdentifiers, {
+            Equals: (x, y) => (x === y),
+            GetHashCode: stringHash,
+        }))) {
+            const i_1 = matchValue;
+            isa = i_1;
+        }
+        else {
+            throw new Error("ARC does not contain assay with given name");
+        }
+        isa.RenameAssay(oldAssayIdentifier, newAssayIdentifier);
+        const paths = this$.FileSystem.Tree.ToFilePaths();
+        const oldAssayFolderPath = getAssayFolderPath(oldAssayIdentifier);
+        const newAssayFolderPath = getAssayFolderPath(newAssayIdentifier);
+        const renamedPaths = map((p) => replace(p, oldAssayFolderPath, newAssayFolderPath), paths);
+        this$.SetFilePaths(renamedPaths);
+        const collection = toList(delay(() => append(singleton(Contract.createRename(oldAssayFolderPath, newAssayFolderPath)), delay(() => this$.GetUpdateContracts()))));
+        return Array.from(collection);
+    }
     RemoveStudy(studyIdentifier) {
         const this$ = this;
         let isa;
@@ -155,6 +190,33 @@ export class ARC {
         const collection = ofArray([Contract.createDelete(studyFolderPath), ARCtrl_ArcInvestigation__ArcInvestigation_ToUpdateContract_6FCE9E49(isa)]);
         return Array.from(collection);
     }
+    RenameStudy(oldStudyIdentifier, newStudyIdentifier) {
+        let i;
+        const this$ = this;
+        let isa;
+        const matchValue = this$.ISA;
+        if (matchValue == null) {
+            throw new Error("Cannot rename study in null ISA value.");
+        }
+        else if ((i = matchValue, contains(oldStudyIdentifier, i.StudyIdentifiers, {
+            Equals: (x, y) => (x === y),
+            GetHashCode: stringHash,
+        }))) {
+            const i_1 = matchValue;
+            isa = i_1;
+        }
+        else {
+            throw new Error("ARC does not contain study with given name");
+        }
+        isa.RenameStudy(oldStudyIdentifier, newStudyIdentifier);
+        const paths = this$.FileSystem.Tree.ToFilePaths();
+        const oldStudyFolderPath = getStudyFolderPath(oldStudyIdentifier);
+        const newStudyFolderPath = getStudyFolderPath(newStudyIdentifier);
+        const renamedPaths = map((p) => replace(p, oldStudyFolderPath, newStudyFolderPath), paths);
+        this$.SetFilePaths(renamedPaths);
+        const collection = toList(delay(() => append(singleton(Contract.createRename(oldStudyFolderPath, newStudyFolderPath)), delay(() => this$.GetUpdateContracts()))));
+        return Array.from(collection);
+    }
     static fromFilePaths(filePaths) {
         return new ARC(void 0, void 0, FileSystem.fromFilePaths(filePaths));
     }
@@ -366,7 +428,7 @@ export class ARC {
     }
     GetGitInitContracts(branch, repositoryAddress, defaultGitignore) {
         const defaultGitignore_1 = defaultArg(defaultGitignore, false);
-        return toArray(delay(() => append(singleton(Init_createInitContract_6DFDD678(unwrap(branch))), delay(() => append(defaultGitignore_1 ? singleton(gitignoreContract) : empty(), delay(() => ((repositoryAddress != null) ? singleton(Init_createAddRemoteContract_Z721C83C5(value_2(repositoryAddress))) : empty())))))));
+        return toArray(delay(() => append(singleton(Init_createInitContract_6DFDD678(unwrap(branch))), delay(() => append(singleton(gitattributesContract), delay(() => append(defaultGitignore_1 ? singleton(gitignoreContract) : empty(), delay(() => ((repositoryAddress != null) ? singleton(Init_createAddRemoteContract_Z721C83C5(value_2(repositoryAddress))) : empty())))))))));
     }
     static getCloneContract(remoteUrl, merge, branch, token, nolfs) {
         return Clone_createCloneContract_5000466F(remoteUrl, unwrap(merge), unwrap(branch), unwrap(token), unwrap(nolfs));
@@ -442,7 +504,7 @@ export class ARC {
         }, (tree = ((paths = ((array = FileSystemTree.toFilePaths()(this$._fs.Copy().Tree), array.filter((p) => !FSharpSet__Contains(registeredPayload, p)))), FileSystemTree.fromFilePaths(paths))), ignoreHidden ? FileSystemTree.filterFiles((n) => !(n.indexOf(".") === 0))(tree) : tree)), FileSystemTree.fromFilePaths([]));
     }
     static get DefaultContracts() {
-        return ofSeq_1([[".gitignore", gitignoreContract]], {
+        return ofSeq_1([[".gitignore", gitignoreContract], [".gitattributes", gitattributesContract]], {
             Compare: comparePrimitives,
         });
     }

package/Contract/Contract.js

@@ -87,6 +87,9 @@ export class Contract extends Record {
     static createExecute(dto, path) {
         return new Contract("EXECUTE", defaultArg(path, ""), "Cli", dto);
     }
+    static createRename(oldPath, newPath) {
+        return new Contract("RENAME", oldPath, void 0, newPath);
+    }
 }
 
 export function Contract_$reflection() {

package/Contract/Git.js

@@ -1,5 +1,6 @@
 import { Contract, CLITool } from "./Contract.js";
 import { dgi } from "../FileSystem/DefaultGitignore.js";
+import { dga } from "../FileSystem/DefaultGitattributes.js";
 import { class_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
 import { value, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { replace } from "../fable_modules/fable-library-js.4.16.0/String.js";
@@ -19,6 +20,8 @@ export function createGitContract(arguments$) {
 
 export const gitignoreContract = Contract.createCreate(".gitignore", "PlainText", dgi);
 
+export const gitattributesContract = Contract.createCreate(".gitattributes", "PlainText", dga);
+
 export class Init {
     constructor() {
     }

package/Core/ArcTypes.js

@@ -1,5 +1,5 @@
 import { value as value_4, defaultArg, map, unwrap } from "../fable_modules/fable-library-js.4.16.0/Option.js";
-import { collect, append as append_3, tryFind, removeAt, tryFindIndex, exists, choose, item, map as map_1, delay, toList, fold, length, forAll, contains, filter, toArray } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
+import { collect, append as append_3, tryFind, removeAt, iterateIndexed, iterate, tryFindIndex, exists, choose, item, map as map_1, delay, toList, fold, length, forAll, contains, filter, toArray } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { defaultOf, safeHash, equals, disposeSafe, getEnumerator, stringHash } from "../fable_modules/fable-library-js.4.16.0/Util.js";
 import { ResizeArray_choose, ResizeArray_filter, ResizeArray_map } from "./Helper/Collections.js";
 import { DataMap__Copy } from "./Table/DataMap.js";
@@ -1576,6 +1576,28 @@ export class ArcInvestigation {
             return newInv;
         };
     }
+    RenameAssay(oldIdentifier, newIdentifier) {
+        const this$ = this;
+        iterate((a) => {
+            if (a.Identifier === oldIdentifier) {
+                a.Identifier = newIdentifier;
+            }
+        }, this$.Assays);
+        iterate((s) => {
+            iterateIndexed((i, ai) => {
+                if (ai === oldIdentifier) {
+                    s.RegisteredAssayIdentifiers[i] = newIdentifier;
+                }
+            }, s.RegisteredAssayIdentifiers);
+        }, this$.Studies);
+    }
+    static renameAssay(oldIdentifier, newIdentifier) {
+        return (inv) => {
+            const newInv = inv.Copy();
+            newInv.RenameAssay(oldIdentifier, newIdentifier);
+            return newInv;
+        };
+    }
     SetAssayAt(index, assay) {
         const this$ = this;
         const assayIdent = assay.Identifier;
@@ -1810,6 +1832,26 @@ export class ArcInvestigation {
             return copy;
         };
     }
+    RenameStudy(oldIdentifier, newIdentifier) {
+        const this$ = this;
+        iterate((s) => {
+            if (s.Identifier === oldIdentifier) {
+                s.Identifier = newIdentifier;
+            }
+        }, this$.Studies);
+        iterateIndexed((i, si) => {
+            if (si === oldIdentifier) {
+                this$.RegisteredStudyIdentifiers[i] = newIdentifier;
+            }
+        }, this$.RegisteredStudyIdentifiers);
+    }
+    static renameStudy(oldIdentifier, newIdentifier) {
+        return (inv) => {
+            const newInv = inv.Copy();
+            newInv.RenameStudy(oldIdentifier, newIdentifier);
+            return newInv;
+        };
+    }
     SetStudyAt(index, study) {
         const this$ = this;
         const study_1 = study;

package/Core/Conversion.js

@@ -1,7 +1,7 @@
 import { remove, toFail, endsWith, printf, toText } from "../fable_modules/fable-library-js.4.16.0/String.js";
 import { Comment$ } from "./Comment.js";
 import { zip as zip_1, fold, empty as empty_1, singleton as singleton_1, append, delay, map as map_1, filter, toList, indexed, tryPick, choose } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
-import { unwrap, value as value_9, map, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
+import { unwrap, value as value_10, map, defaultArg } from "../fable_modules/fable-library-js.4.16.0/Option.js";
 import { Option_fromValueWithDefault, ResizeArray_filter } from "./Helper/Collections.js";
 import { Value as Value_2 } from "./Process/Value.js";
 import { Component_create_4208F9FC } from "./Process/Component.js";
@@ -68,7 +68,7 @@ export function Person_getSourceAssayIdentifiersFromComments(person) {
 export function Person_removeSourceAssayComments(person) {
     return ResizeArray_filter((c) => {
         if (c.Name != null) {
-            return !(value_9(c.Name).indexOf(Person_AssayIdentifierPrefix) === 0);
+            return !(value_10(c.Name).indexOf(Person_AssayIdentifierPrefix) === 0);
         }
         else {
             return false;
@@ -80,7 +80,7 @@ export function Person_setOrcidFromComments(person) {
     const person_1 = person.Copy();
     const isOrcidComment = (c) => {
         if (c.Name != null) {
-            return endsWith(value_9(c.Name).toLocaleUpperCase(), Person_orcidKey);
+            return endsWith(value_10(c.Name).toLocaleUpperCase(), Person_orcidKey);
         }
         else {
             return false;
@@ -341,28 +341,28 @@ export function JsonTypes_cellOfValue(value, unit) {
  * Convert an ISA Component to a CompositeHeader and Cell tuple
  */
 export function JsonTypes_decomposeComponent(c) {
-    return [new CompositeHeader(0, [value_9(c.ComponentType)]), JsonTypes_cellOfValue(c.ComponentValue, c.ComponentUnit)];
+    return [new CompositeHeader(0, [value_10(c.ComponentType)]), JsonTypes_cellOfValue(c.ComponentValue, c.ComponentUnit)];
 }
 
 /**
  * Convert an ISA ProcessParameterValue to a CompositeHeader and Cell tuple
  */
 export function JsonTypes_decomposeParameterValue(ppv) {
-    return [new CompositeHeader(3, [value_9(value_9(ppv.Category).ParameterName)]), JsonTypes_cellOfValue(ppv.Value, ppv.Unit)];
+    return [new CompositeHeader(3, [value_10(value_10(ppv.Category).ParameterName)]), JsonTypes_cellOfValue(ppv.Value, ppv.Unit)];
 }
 
 /**
  * Convert an ISA FactorValue to a CompositeHeader and Cell tuple
  */
 export function JsonTypes_decomposeFactorValue(fv) {
-    return [new CompositeHeader(2, [value_9(value_9(fv.Category).FactorType)]), JsonTypes_cellOfValue(fv.Value, fv.Unit)];
+    return [new CompositeHeader(2, [value_10(value_10(fv.Category).FactorType)]), JsonTypes_cellOfValue(fv.Value, fv.Unit)];
 }
 
 /**
  * Convert an ISA MaterialAttributeValue to a CompositeHeader and Cell tuple
  */
 export function JsonTypes_decomposeCharacteristicValue(cv) {
-    return [new CompositeHeader(1, [value_9(value_9(cv.Category).CharacteristicType)]), JsonTypes_cellOfValue(cv.Value, cv.Unit)];
+    return [new CompositeHeader(1, [value_10(value_10(cv.Category).CharacteristicType)]), JsonTypes_cellOfValue(cv.Value, cv.Unit)];
 }
 
 /**
@@ -376,7 +376,7 @@ export function JsonTypes_decomposeProcessInput(pi) {
             return [new CompositeHeader(11, [new IOType(3, [])]), new CompositeCell(1, [defaultArg(pi.fields[0].Name, "")])];
         case 2: {
             const d = pi.fields[0];
-            const dataType = value_9(d.DataType);
+            const dataType = value_10(d.DataType);
             switch (dataType.tag) {
                 case 0:
                     return [new CompositeHeader(11, [new IOType(2, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
@@ -400,7 +400,7 @@ export function JsonTypes_decomposeProcessOutput(po) {
             return [new CompositeHeader(12, [new IOType(3, [])]), new CompositeCell(1, [defaultArg(po.fields[0].Name, "")])];
         case 1: {
             const d = po.fields[0];
-            const dataType = value_9(d.DataType);
+            const dataType = value_10(d.DataType);
             switch (dataType.tag) {
                 case 0:
                     return [new CompositeHeader(12, [new IOType(2, [])]), new CompositeCell(1, [defaultArg(d.Name, "")])];
@@ -455,7 +455,7 @@ export function JsonTypes_decomposeTechnologyPlatform(name) {
 }
 
 /**
- * If the headers of a node depict a component, returns a function for parsing the values of the matrix to the values of this component
+ * If the given headers depict a component, returns a function for parsing the values of the matrix to the values of this component
  */
 export function ProcessParsing_tryComponentGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === 0) {
@@ -469,7 +469,7 @@ export function ProcessParsing_tryComponentGetter(generalI, valueI, valueHeader)
 }
 
 /**
- * If the headers of a node depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
+ * If the given headers depict a parameter, returns a function for parsing the values of the matrix to the values of this type
  */
 export function ProcessParsing_tryParameterGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === 3) {
@@ -481,6 +481,9 @@ export function ProcessParsing_tryParameterGetter(generalI, valueI, valueHeader)
     }
 }
 
+/**
+ * If the given headers depict a factor, returns a function for parsing the values of the matrix to the values of this type
+ */
 export function ProcessParsing_tryFactorGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === 2) {
         const cat = new CompositeHeader(2, [ARCtrl_OntologyAnnotation__OntologyAnnotation_setColumnIndex_Static(valueI, valueHeader.fields[0])]);
@@ -491,6 +494,9 @@ export function ProcessParsing_tryFactorGetter(generalI, valueI, valueHeader) {
     }
 }
 
+/**
+ * If the given headers depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
+ */
 export function ProcessParsing_tryCharacteristicGetter(generalI, valueI, valueHeader) {
     if (valueHeader.tag === 1) {
         const cat = new CompositeHeader(1, [ARCtrl_OntologyAnnotation__OntologyAnnotation_setColumnIndex_Static(valueI, valueHeader.fields[0])]);
@@ -502,7 +508,7 @@ export function ProcessParsing_tryCharacteristicGetter(generalI, valueI, valueHe
 }
 
 /**
- * If the headers of a node depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
+ * If the given headers depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
  */
 export function ProcessParsing_tryGetProtocolTypeGetter(generalI, header) {
     if (header.tag === 4) {
@@ -513,6 +519,9 @@ export function ProcessParsing_tryGetProtocolTypeGetter(generalI, header) {
     }
 }
 
+/**
+ * If the given headers depict a protocolREF, returns a function for parsing the values of the matrix to the values of this type
+ */
 export function ProcessParsing_tryGetProtocolREFGetter(generalI, header) {
     if (header.tag === 8) {
         return (matrix) => ((i) => getItemFromDict(matrix, [generalI, i]).AsFreeText);
@@ -522,6 +531,9 @@ export function ProcessParsing_tryGetProtocolREFGetter(generalI, header) {
     }
 }
 
+/**
+ * If the given headers depict a protocolDescription, returns a function for parsing the values of the matrix to the values of this type
+ */
 export function ProcessParsing_tryGetProtocolDescriptionGetter(generalI, header) {
     if (header.tag === 5) {
         return (matrix) => ((i) => getItemFromDict(matrix, [generalI, i]).AsFreeText);
@@ -531,6 +543,9 @@ export function ProcessParsing_tryGetProtocolDescriptionGetter(generalI, header)
     }
 }
 
+/**
+ * If the given headers depict a protocolURI, returns a function for parsing the values of the matrix to the values of this type
+ */
 export function ProcessParsing_tryGetProtocolURIGetter(generalI, header) {
     if (header.tag === 6) {
         return (matrix) => ((i) => getItemFromDict(matrix, [generalI, i]).AsFreeText);
@@ -540,6 +555,9 @@ export function ProcessParsing_tryGetProtocolURIGetter(generalI, header) {
     }
 }
 
+/**
+ * If the given headers depict a protocolVersion, returns a function for parsing the values of the matrix to the values of this type
+ */
 export function ProcessParsing_tryGetProtocolVersionGetter(generalI, header) {
     if (header.tag === 7) {
         return (matrix) => ((i) => getItemFromDict(matrix, [generalI, i]).AsFreeText);
@@ -549,6 +567,9 @@ export function ProcessParsing_tryGetProtocolVersionGetter(generalI, header) {
     }
 }
 
+/**
+ * If the given headers depict an input, returns a function for parsing the values of the matrix to the values of this type
+ */
 export function ProcessParsing_tryGetInputGetter(generalI, header) {
     if (header.tag === 11) {
         return (matrix) => ((i) => JsonTypes_composeProcessInput(header, getItemFromDict(matrix, [generalI, i])));
@@ -558,6 +579,9 @@ export function ProcessParsing_tryGetInputGetter(generalI, header) {
     }
 }
 
+/**
+ * If the given headers depict an output, returns a function for parsing the values of the matrix to the values of this type
+ */
 export function ProcessParsing_tryGetOutputGetter(generalI, header) {
     if (header.tag === 12) {
         return (matrix) => ((i) => JsonTypes_composeProcessOutput(header, getItemFromDict(matrix, [generalI, i])));
@@ -567,6 +591,18 @@ export function ProcessParsing_tryGetOutputGetter(generalI, header) {
     }
 }
 
+/**
+ * If the given headers depict a comment, returns a function for parsing the values of the matrix to the values of this type
+ */
+export function ProcessParsing_tryGetCommentGetter(generalI, header) {
+    if (header.tag === 14) {
+        return (matrix) => ((i) => (new Comment$(header.fields[0], getItemFromDict(matrix, [generalI, i]).AsFreeText)));
+    }
+    else {
+        return void 0;
+    }
+}
+
 /**
  * Given the header sequence of an ArcTable, returns a function for parsing each row of the table to a process
  */
@@ -594,8 +630,9 @@ export function ProcessParsing_getProcessGetter(processNameRoot, headers) {
     const protocolDescriptionGetter = tryPick((tupledArg_6) => ProcessParsing_tryGetProtocolDescriptionGetter(tupledArg_6[0], tupledArg_6[1]), headers_1);
     const protocolURIGetter = tryPick((tupledArg_7) => ProcessParsing_tryGetProtocolURIGetter(tupledArg_7[0], tupledArg_7[1]), headers_1);
     const protocolVersionGetter = tryPick((tupledArg_8) => ProcessParsing_tryGetProtocolVersionGetter(tupledArg_8[0], tupledArg_8[1]), headers_1);
+    const commentGetters = toList(choose((tupledArg_9) => ProcessParsing_tryGetCommentGetter(tupledArg_9[0], tupledArg_9[1]), headers_1));
     let inputGetter_1;
-    const matchValue = tryPick((tupledArg_9) => ProcessParsing_tryGetInputGetter(tupledArg_9[0], tupledArg_9[1]), headers_1);
+    const matchValue = tryPick((tupledArg_10) => ProcessParsing_tryGetInputGetter(tupledArg_10[0], tupledArg_10[1]), headers_1);
     if (matchValue == null) {
         inputGetter_1 = ((matrix_1) => ((i_1) => singleton(new ProcessInput(0, [Source_create_Z5CA08497(void 0, `${processNameRoot}_Input_${i_1}`, toList(map_1((f_1) => f_1(matrix_1)(i_1), charGetters)))]))));
     }
@@ -608,7 +645,7 @@ export function ProcessParsing_getProcessGetter(processNameRoot, headers) {
         }));
     }
     let outputGetter_1;
-    const matchValue_1 = tryPick((tupledArg_10) => ProcessParsing_tryGetOutputGetter(tupledArg_10[0], tupledArg_10[1]), headers_1);
+    const matchValue_1 = tryPick((tupledArg_11) => ProcessParsing_tryGetOutputGetter(tupledArg_11[0], tupledArg_11[1]), headers_1);
     if (matchValue_1 == null) {
         outputGetter_1 = ((matrix_3) => ((i_3) => singleton(new ProcessOutput(0, [Sample_create_62424AD2(void 0, `${processNameRoot}_Output_${i_3}`, void 0, toList(map_1((f_3) => f_3(matrix_3)(i_3), factorValueGetters)))]))));
     }
@@ -623,9 +660,10 @@ export function ProcessParsing_getProcessGetter(processNameRoot, headers) {
     return (matrix_4) => ((i_4) => {
         const pn = map((p) => Process_composeName(p, i_4), Option_fromValueWithDefault("", processNameRoot));
         const paramvalues = Option_fromValueWithDefault(empty(), map_2((f_4) => f_4(matrix_4)(i_4), parameterValueGetters));
-        const parameters = map((list_5) => map_2((pv) => value_9(pv.Category), list_5), paramvalues);
+        const parameters = map((list_5) => map_2((pv) => value_10(pv.Category), list_5), paramvalues);
+        const comments = Option_fromValueWithDefault(empty(), map_2((f_5) => f_5(matrix_4)(i_4), commentGetters));
         let protocol;
-        const p_1 = Protocol_make(void 0, map((f_5) => f_5(matrix_4)(i_4), protocolREFGetter), map((f_6) => f_6(matrix_4)(i_4), protocolTypeGetter), map((f_7) => f_7(matrix_4)(i_4), protocolDescriptionGetter), map((f_8) => f_8(matrix_4)(i_4), protocolURIGetter), map((f_9) => f_9(matrix_4)(i_4), protocolVersionGetter), parameters, Option_fromValueWithDefault(empty(), map_2((f_10) => f_10(matrix_4)(i_4), componentGetters)), void 0);
+        const p_1 = Protocol_make(void 0, map((f_6) => f_6(matrix_4)(i_4), protocolREFGetter), map((f_7) => f_7(matrix_4)(i_4), protocolTypeGetter), map((f_8) => f_8(matrix_4)(i_4), protocolDescriptionGetter), map((f_9) => f_9(matrix_4)(i_4), protocolURIGetter), map((f_10) => f_10(matrix_4)(i_4), protocolVersionGetter), parameters, Option_fromValueWithDefault(empty(), map_2((f_11) => f_11(matrix_4)(i_4), componentGetters)), void 0);
         let matchResult;
         if (p_1.Name == null) {
             if (p_1.ProtocolType == null) {
@@ -670,7 +708,7 @@ export function ProcessParsing_getProcessGetter(processNameRoot, headers) {
         const inputs = inputGetter_1(matrix_4)(i_4);
         const outputs = outputGetter_1(matrix_4)(i_4);
         patternInput = (((length(inputs) === 1) && (length(outputs) === 2)) ? [ofArray([item(0, inputs), item(0, inputs)]), outputs] : (((length(inputs) === 2) && (length(outputs) === 1)) ? [inputs, ofArray([item(0, outputs), item(0, outputs)])] : [inputs, outputs]));
-        return Process_make(void 0, pn, protocol, paramvalues, void 0, void 0, void 0, void 0, patternInput[0], patternInput[1], void 0);
+        return Process_make(void 0, pn, protocol, paramvalues, void 0, void 0, void 0, void 0, patternInput[0], patternInput[1], comments);
     });
 }
 
@@ -683,21 +721,21 @@ export function ProcessParsing_getProcessGetter(processNameRoot, headers) {
  */
 export function ProcessParsing_groupProcesses(ps) {
     return List_groupBy((x) => {
-        if ((x.Name != null) && (Process_decomposeName_Z721C83C5(value_9(x.Name))[1] != null)) {
-            return Process_decomposeName_Z721C83C5(value_9(x.Name))[0];
+        if ((x.Name != null) && (Process_decomposeName_Z721C83C5(value_10(x.Name))[1] != null)) {
+            return Process_decomposeName_Z721C83C5(value_10(x.Name))[0];
         }
-        else if ((x.ExecutesProtocol != null) && (value_9(x.ExecutesProtocol).Name != null)) {
-            return value_9(value_9(x.ExecutesProtocol).Name);
+        else if ((x.ExecutesProtocol != null) && (value_10(x.ExecutesProtocol).Name != null)) {
+            return value_10(value_10(x.ExecutesProtocol).Name);
         }
-        else if ((x.Name != null) && (value_9(x.Name).indexOf("_") >= 0)) {
-            const lastUnderScoreIndex = value_9(x.Name).lastIndexOf("_") | 0;
-            return remove(value_9(x.Name), lastUnderScoreIndex);
+        else if ((x.Name != null) && (value_10(x.Name).indexOf("_") >= 0)) {
+            const lastUnderScoreIndex = value_10(x.Name).lastIndexOf("_") | 0;
+            return remove(value_10(x.Name), lastUnderScoreIndex);
         }
         else if (x.Name != null) {
-            return value_9(x.Name);
+            return value_10(x.Name);
         }
-        else if ((x.ExecutesProtocol != null) && (value_9(x.ExecutesProtocol).ID != null)) {
-            return value_9(value_9(x.ExecutesProtocol).ID);
+        else if ((x.ExecutesProtocol != null) && (value_10(x.ExecutesProtocol).ID != null)) {
+            return value_10(value_10(x.ExecutesProtocol).ID);
         }
         else {
             return createMissingIdentifier();
@@ -713,14 +751,14 @@ export function ProcessParsing_groupProcesses(ps) {
  */
 export function ProcessParsing_mergeIdenticalProcesses(processes) {
     const l = List_groupBy((x) => {
-        if ((x.Name != null) && (Process_decomposeName_Z721C83C5(value_9(x.Name))[1] != null)) {
-            return [Process_decomposeName_Z721C83C5(value_9(x.Name))[0], boxHashOption(x.ExecutesProtocol), map(boxHashSeq, x.ParameterValues)];
+        if ((x.Name != null) && (Process_decomposeName_Z721C83C5(value_10(x.Name))[1] != null)) {
+            return [Process_decomposeName_Z721C83C5(value_10(x.Name))[0], boxHashOption(x.ExecutesProtocol), map(boxHashSeq, x.ParameterValues), map(boxHashSeq, x.Comments)];
         }
-        else if ((x.ExecutesProtocol != null) && (value_9(x.ExecutesProtocol).Name != null)) {
-            return [value_9(value_9(x.ExecutesProtocol).Name), boxHashOption(x.ExecutesProtocol), map(boxHashSeq, x.ParameterValues)];
+        else if ((x.ExecutesProtocol != null) && (value_10(x.ExecutesProtocol).Name != null)) {
+            return [value_10(value_10(x.ExecutesProtocol).Name), boxHashOption(x.ExecutesProtocol), map(boxHashSeq, x.ParameterValues), map(boxHashSeq, x.Comments)];
         }
         else {
-            return [createMissingIdentifier(), boxHashOption(x.ExecutesProtocol), map(boxHashSeq, x.ParameterValues)];
+            return [createMissingIdentifier(), boxHashOption(x.ExecutesProtocol), map(boxHashSeq, x.ParameterValues), map(boxHashSeq, x.Comments)];
         }
     }, processes, {
         Equals: equalArrays,
@@ -732,12 +770,12 @@ export function ProcessParsing_mergeIdenticalProcesses(processes) {
         const pVs = item(0, processes_1).ParameterValues;
         const inputs = Option_fromValueWithDefault(empty(), collect((p) => defaultArg(p.Inputs, empty()), processes_1));
         const outputs = Option_fromValueWithDefault(empty(), collect((p_1) => defaultArg(p_1.Outputs, empty()), processes_1));
-        return Process_create_Z7C1F7FA9(void 0, (length(l) > 1) ? Process_composeName(n, i) : n, item(0, processes_1).ExecutesProtocol, pVs, void 0, void 0, void 0, void 0, inputs, outputs);
+        return Process_create_Z7C1F7FA9(void 0, (length(l) > 1) ? Process_composeName(n, i) : n, unwrap(item(0, processes_1).ExecutesProtocol), unwrap(pVs), void 0, void 0, void 0, void 0, unwrap(inputs), unwrap(outputs), unwrap(item(0, processes_1).Comments));
     }, l);
 }
 
 export function ProcessParsing_processToRows(p) {
-    let list_3;
+    let list_4;
     const pvs = map_2((ppv) => [JsonTypes_decomposeParameterValue(ppv), tryGetParameterColumnIndex(ppv)], defaultArg(p.ParameterValues, empty()));
     let components;
     const matchValue = p.ExecutesProtocol;
@@ -749,8 +787,9 @@ export function ProcessParsing_processToRows(p) {
     }
     else {
         const prot_1 = matchValue_1;
-        protVals = toList(delay(() => append((prot_1.Name != null) ? singleton_1([new CompositeHeader(8, []), new CompositeCell(1, [value_9(prot_1.Name)])]) : empty_1(), delay(() => append((prot_1.ProtocolType != null) ? singleton_1([new CompositeHeader(4, []), new CompositeCell(0, [value_9(prot_1.ProtocolType)])]) : empty_1(), delay(() => append((prot_1.Description != null) ? singleton_1([new CompositeHeader(5, []), new CompositeCell(1, [value_9(prot_1.Description)])]) : empty_1(), delay(() => append((prot_1.Uri != null) ? singleton_1([new CompositeHeader(6, []), new CompositeCell(1, [value_9(prot_1.Uri)])]) : empty_1(), delay(() => ((prot_1.Version != null) ? singleton_1([new CompositeHeader(7, []), new CompositeCell(1, [value_9(prot_1.Version)])]) : empty_1())))))))))));
+        protVals = toList(delay(() => append((prot_1.Name != null) ? singleton_1([new CompositeHeader(8, []), new CompositeCell(1, [value_10(prot_1.Name)])]) : empty_1(), delay(() => append((prot_1.ProtocolType != null) ? singleton_1([new CompositeHeader(4, []), new CompositeCell(0, [value_10(prot_1.ProtocolType)])]) : empty_1(), delay(() => append((prot_1.Description != null) ? singleton_1([new CompositeHeader(5, []), new CompositeCell(1, [value_10(prot_1.Description)])]) : empty_1(), delay(() => append((prot_1.Uri != null) ? singleton_1([new CompositeHeader(6, []), new CompositeCell(1, [value_10(prot_1.Uri)])]) : empty_1(), delay(() => ((prot_1.Version != null) ? singleton_1([new CompositeHeader(7, []), new CompositeCell(1, [value_10(prot_1.Version)])]) : empty_1())))))))))));
     }
+    const comments = map_2((c) => [new CompositeHeader(14, [defaultArg(c.Name, "")]), new CompositeCell(1, [defaultArg(c.Value, "")])], defaultArg(p.Comments, empty()));
     return map_2((tupledArg_1) => {
         const ios = tupledArg_1[1];
         const inputForCharas = defaultArg(tryPick_1((tupledArg_2) => {
@@ -793,8 +832,8 @@ export function ProcessParsing_processToRows(p) {
         const vals = map_2((tuple_5) => tuple_5[0], sortBy((arg) => defaultArg(arg[1], 10000), append_1(chars, append_1(components, append_1(pvs, map_2((fv) => [JsonTypes_decomposeFactorValue(fv), tryGetFactorColumnIndex(fv)], ProcessOutput_getFactorValues_Z42C11600(outputForFactors))))), {
             Compare: comparePrimitives,
         }));
-        return toList(delay(() => append(singleton_1(JsonTypes_decomposeProcessInput(inputForType)), delay(() => append(protVals, delay(() => append(vals, delay(() => singleton_1(JsonTypes_decomposeProcessOutput(outputForType))))))))));
-    }, List_groupBy((tupledArg) => [ProcessInput__get_Name(tupledArg[0]), ProcessOutput__get_Name(tupledArg[1])], (list_3 = defaultArg(p.Outputs, empty()), zip(defaultArg(p.Inputs, empty()), list_3)), {
+        return toList(delay(() => append(singleton_1(JsonTypes_decomposeProcessInput(inputForType)), delay(() => append(protVals, delay(() => append(vals, delay(() => append(comments, delay(() => singleton_1(JsonTypes_decomposeProcessOutput(outputForType))))))))))));
+    }, List_groupBy((tupledArg) => [ProcessInput__get_Name(tupledArg[0]), ProcessOutput__get_Name(tupledArg[1])], (list_4 = defaultArg(p.Outputs, empty()), zip(defaultArg(p.Inputs, empty()), list_4)), {
         Equals: equalArrays,
         GetHashCode: arrayHash,
     }));
@@ -959,7 +998,7 @@ export function ARCtrl_ArcTable__ArcTable_fromProtocol_Static_3BF20962(p) {
     try {
         while (enumerator["System.Collections.IEnumerator.MoveNext"]()) {
             const pp = enumerator["System.Collections.Generic.IEnumerator`1.get_Current"]();
-            t.AddColumn(new CompositeHeader(3, [value_9(pp.ParameterName)]), void 0, ARCtrl_Process_ProtocolParameter__ProtocolParameter_TryGetColumnIndex(pp));
+            t.AddColumn(new CompositeHeader(3, [value_10(pp.ParameterName)]), void 0, ARCtrl_Process_ProtocolParameter__ProtocolParameter_TryGetColumnIndex(pp));
         }
     }
     finally {
@@ -970,7 +1009,7 @@ export function ARCtrl_ArcTable__ArcTable_fromProtocol_Static_3BF20962(p) {
         while (enumerator_1["System.Collections.IEnumerator.MoveNext"]()) {
             const c = enumerator_1["System.Collections.Generic.IEnumerator`1.get_Current"]();
             const v_1 = map((arg) => singleton_2(ARCtrl_CompositeCell__CompositeCell_fromValue_Static_6B24B5AD(arg, unwrap(c.ComponentUnit))), c.ComponentValue);
-            t.AddColumn(new CompositeHeader(3, [value_9(c.ComponentType)]), v_1, ARCtrl_Process_Component__Component_TryGetColumnIndex(c));
+            t.AddColumn(new CompositeHeader(3, [value_10(c.ComponentType)]), v_1, ARCtrl_Process_Component__Component_TryGetColumnIndex(c));
         }
     }
     finally {

package/Core/Helper/Regex.js

@@ -20,6 +20,8 @@ export const Pattern_InputPattern = `Input\\s\\[(?<${"iotype"}>.+)\\]`;
 
 export const Pattern_OutputPattern = `Output\\s\\[(?<${"iotype"}>.+)\\]`;
 
+export const Pattern_CommentPattern = `Comment\\s\\[(?<${"commentKey"}>.+)\\]`;
+
 /**
  * Matches, if the input string matches the given regex pattern.
  */
@@ -324,6 +326,17 @@ export function ActivePatterns_$007CAutoGeneratedTableName$007C_$007C(input) {
     }
 }
 
+export function ActivePatterns_$007CComment$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Pattern_CommentPattern, input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return (r.groups && r.groups.commentKey) || "";
+    }
+    else {
+        return void 0;
+    }
+}
+
 export function tryParseReferenceColumnHeader(str) {
     const matchValue = str.trim();
     const activePatternResult = ActivePatterns_$007CReferenceColumnHeader$007C_$007C(matchValue);

package/Core/OntologyAnnotation.js

@@ -4,8 +4,9 @@ import { StringBuilder__Append_Z721C83C5, StringBuilder_$ctor } from "../fable_m
 import { printf, toText, join } from "../fable_modules/fable-library-js.4.16.0/String.js";
 import { toArray, empty, singleton, append, delay, toList } from "../fable_modules/fable-library-js.4.16.0/Seq.js";
 import { toString } from "../fable_modules/fable-library-js.4.16.0/Types.js";
-import { hash, boxHashOption, boxHashArray } from "./Helper/HashCodes.js";
+import { hash as hash_1, boxHashOption, boxHashArray } from "./Helper/HashCodes.js";
 import { ResizeArray_map } from "./Helper/Collections.js";
+import { safeHash } from "../fable_modules/fable-library-js.4.16.0/Util.js";
 import { class_type } from "../fable_modules/fable-library-js.4.16.0/Reflection.js";
 
 export class OntologyAnnotation {
@@ -166,7 +167,7 @@ export class OntologyAnnotation {
     }
     Equals(obj) {
         const this$ = this;
-        return hash(this$) === hash(obj);
+        return hash_1(this$) === hash_1(obj);
     }
     Copy() {
         const this$ = this;
@@ -184,6 +185,18 @@ export class OntologyAnnotation {
         const this$ = this;
         return "OA " + this$.NameText;
     }
+    CompareTo(obj) {
+        const this$ = this;
+        if (obj instanceof OntologyAnnotation) {
+            const oa = obj;
+            const hash = safeHash(this$) | 0;
+            const otherHash = safeHash(oa) | 0;
+            return ((hash === otherHash) ? 0 : ((hash < otherHash) ? -1 : 1)) | 0;
+        }
+        else {
+            return 1;
+        }
+    }
 }
 
 export function OntologyAnnotation_$reflection() {