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

package/dist/ts/ts/Core/Comment.d.ts

@@ -0,0 +1,35 @@
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { IComparable, IEquatable } from '@fable-org/fable-library-js/Util.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { Record } from '@fable-org/fable-library-js/Types.js';
+import { TypeInfo } from '@fable-org/fable-library-js/Reflection.js';
+export declare class Comment$ {
+    _name: Option<string>;
+    _value: Option<string>;
+    constructor(name?: string, value?: string);
+    get Name(): string | undefined;
+    set Name(name: Option<string>);
+    get Value(): string | undefined;
+    set Value(value: Option<string>);
+    static make(name: Option<string>, value: Option<string>): Comment$;
+    static create(name?: string, value?: string): Comment$;
+    static toString(comment: Comment$): [string, string];
+    Copy(): Comment$;
+    Equals(obj: any): boolean;
+    GetHashCode(): int32;
+    toString(): string;
+    static fromString(s: string): Comment$;
+}
+export declare function Comment$_$reflection(): TypeInfo;
+export declare function Comment_$ctor_40457300(name?: string, value?: string): Comment$;
+export declare class Remark extends Record implements IEquatable<Remark>, IComparable<Remark> {
+    readonly Line: int32;
+    readonly Value: string;
+    constructor(Line: int32, Value: string);
+    static make(line: int32, value: string): Remark;
+    static create(line: int32, value: string): Remark;
+    static toTuple(remark: Remark): [int32, string];
+    Copy(): Remark;
+}
+export declare function Remark_$reflection(): TypeInfo;
+//# sourceMappingURL=Comment.d.ts.map

package/dist/ts/ts/Core/Comment.d.ts.map

@@ -0,0 +1 @@
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package/dist/ts/ts/Core/Comment.js

@@ -0,0 +1,91 @@
+import { unwrap, defaultArg, map as map$1 } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+import { equals } from '../../node_modules/@fable-org/fable-library-js/Util.js';
+import { boxHashArray, boxHashOption } from './Helper/HashCodes.js';
+import { StringBuilder_$ctor, StringBuilder__Append_Z721C83C5 } from '../../node_modules/@fable-org/fable-library-js/System.Text.js';
+import { join, toText, printf, replace } from '../../node_modules/@fable-org/fable-library-js/String.js';
+import { map, choose, ofArray } from '../../node_modules/@fable-org/fable-library-js/List.js';
+import { toString, Record } from '../../node_modules/@fable-org/fable-library-js/Types.js';
+import { match, create } from '../../node_modules/@fable-org/fable-library-js/RegExp.js';
+import { Pattern_handleGroupPatterns } from './Helper/Regex.js';
+
+class Comment$ {
+  constructor(name, value) {
+    this._name = name;
+    this._value = value;
+  }
+  get Name() {
+    const this$ = this;
+    return unwrap(this$._name);
+  }
+  set Name(name) {
+    const this$ = this;
+    this$._name = name;
+  }
+  get Value() {
+    const this$ = this;
+    return unwrap(this$._value);
+  }
+  set Value(value) {
+    const this$ = this;
+    this$._value = value;
+  }
+  static make(name, value) {
+    return new Comment$(unwrap(name), unwrap(value));
+  }
+  static create(name, value) {
+    return Comment$.make(name, value);
+  }
+  static toString(comment) {
+    return [defaultArg(comment.Name, ""), defaultArg(comment.Value, "")];
+  }
+  Copy() {
+    const this$ = this;
+    const name = this$.Name;
+    const value = this$.Value;
+    return Comment$.make(name, value);
+  }
+  Equals(obj) {
+    let c;
+    const this$ = this;
+    return obj instanceof Comment$ && (c = obj, equals(c.Name, this$.Name) && equals(c.Value, this$.Value));
+  }
+  GetHashCode() {
+    const this$ = this;
+    return boxHashArray([boxHashOption(this$.Name), boxHashOption(this$.Value)]) | 0;
+  }
+  toString() {
+    const this$ = this;
+    const sb = StringBuilder_$ctor();
+    StringBuilder__Append_Z721C83C5(sb, "Comment {");
+    StringBuilder__Append_Z721C83C5(sb, join(", ", map((tupledArg_1) => toText(printf('%s = "%s"'))(tupledArg_1[0])(tupledArg_1[1]), choose((tupledArg) => map$1((o) => [tupledArg[0], o], tupledArg[1]), ofArray([["Name", this$.Name], ["Value", this$.Value]])))));
+    StringBuilder__Append_Z721C83C5(sb, "}");
+    return toString(sb);
+  }
+  static fromString(s) {
+    const nameResult = match(create(Pattern_handleGroupPatterns('Name = "[^"]*"')), s);
+    const valueResult = match(create(Pattern_handleGroupPatterns('Value = "[^"]*"')), s);
+    return new Comment$(unwrap(nameResult != null ? replace(replace(nameResult[0], "Name = ", ""), '"', "") : void 0), unwrap(valueResult != null ? replace(replace(valueResult[0], "Value = ", ""), '"', "") : void 0));
+  }
+}
+class Remark extends Record {
+  constructor(Line, Value) {
+    super();
+    this.Line = Line | 0;
+    this.Value = Value;
+  }
+  static make(line, value) {
+    return new Remark(line, value);
+  }
+  static create(line, value) {
+    return Remark.make(line, value);
+  }
+  static toTuple(remark) {
+    return [remark.Line, remark.Value];
+  }
+  Copy() {
+    const this$ = this;
+    return Remark.make(this$.Line, this$.Value);
+  }
+}
+
+export { Comment$, Remark };

package/dist/ts/ts/Core/CommentList.d.ts

@@ -0,0 +1,28 @@
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { Comment$ } from './Comment.js';
+import { FSharpMap } from '@fable-org/fable-library-js/Map.js';
+/**
+ * If a comment with the given key exists in the [], return its value, else return None
+ */
+export declare function tryItem(key: string, comments: Comment$[]): Option<string>;
+/**
+ * Returns true, if the key exists in the []
+ */
+export declare function containsKey(key: string, comments: Comment$[]): boolean;
+/**
+ * If a comment with the given key exists in the [], return its value
+ */
+export declare function item(key: string, comments: Comment$[]): string;
+/**
+ * Create a map of comment keys to comment values
+ */
+export declare function toMap(comments: Comment$[]): FSharpMap<string, Option<string>>;
+/**
+ * Add the given comment to the comment [] if it doesnt exist, else replace it
+ */
+export declare function set$(comment: Comment$, comments: Comment$[]): Comment$[];
+/**
+ * Returns a new comment [] where comments with the given key are filtered out
+ */
+export declare function dropByKey(key: string, comments: Comment$[]): Comment$[];
+//# sourceMappingURL=CommentList.d.ts.map

package/dist/ts/ts/Core/CommentList.d.ts.map

@@ -0,0 +1 @@
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package/dist/ts/ts/Core/CommentList.js

@@ -0,0 +1,27 @@
+import { tryPick } from '../../node_modules/@fable-org/fable-library-js/Seq.js';
+import { value } from '../../node_modules/@fable-org/fable-library-js/Option.js';
+
+function tryItem(key, comments) {
+  return tryPick((c) => {
+    const matchValue = c.Name;
+    let matchResult, n_1;
+    if (matchValue != null) {
+      if (value(matchValue) === key) {
+        matchResult = 0;
+        n_1 = value(matchValue);
+      } else {
+        matchResult = 1;
+      }
+    } else {
+      matchResult = 1;
+    }
+    switch (matchResult) {
+      case 0:
+        return c.Value;
+      default:
+        return void 0;
+    }
+  }, comments);
+}
+
+export { tryItem };

package/dist/ts/ts/Core/Conversion.d.ts

@@ -0,0 +1,215 @@
+import { Person } from './Person.js';
+import { Comment$ } from './Comment.js';
+import { Option } from '@fable-org/fable-library-js/Option.js';
+import { OntologyAnnotation } from './OntologyAnnotation.js';
+import { Value_$union } from './Value.js';
+import { CompositeCell_$union } from './Table/CompositeCell.js';
+import { Component } from './Process/Component.js';
+import { CompositeHeader_$union } from './Table/CompositeHeader.js';
+import { ProtocolParameter } from './Process/ProtocolParameter.js';
+import { ProcessParameterValue } from './Process/ProcessParameterValue.js';
+import { FactorValue } from './Process/FactorValue.js';
+import { Factor } from './Process/Factor.js';
+import { MaterialAttributeValue } from './Process/MaterialAttributeValue.js';
+import { MaterialAttribute } from './Process/MaterialAttribute.js';
+import { ProcessInput_$union } from './Process/ProcessInput.js';
+import { ProcessOutput_$union } from './Process/ProcessOutput.js';
+import { int32 } from '@fable-org/fable-library-js/Int32.js';
+import { ArcTable } from './Table/ArcTable.js';
+import { FSharpList } from '@fable-org/fable-library-js/List.js';
+import { Process } from './Process/Process.js';
+import { Protocol } from './Process/Protocol.js';
+import { ArcTables } from './Table/ArcTables.js';
+export declare const Person_orcidKey = "ORCID";
+export declare const Person_AssayIdentifierPrefix = "performer (ARC:00000168)";
+export declare const Person_createAssayIdentifierKey: ((arg0: string) => string);
+export declare function Person_setSourceAssayComment(person: Person, assayIdentifier: string): Person;
+/**
+ * This functions helps encoding/decoding ISA-JSON. It returns a sequence of ArcAssay-Identifiers.
+ */
+export declare function Person_getSourceAssayIdentifiersFromComments(person: Person): Iterable<string>;
+export declare function Person_removeSourceAssayComments(person: Person): Comment$[];
+export declare function Person_setOrcidFromComments(person: Person): Person;
+export declare function Person_setCommentFromORCID(person: Person): Person;
+/**
+ * Convert a CompositeCell to a ISA Value and Unit tuple.
+ */
+export declare function JsonTypes_valueOfCell(value: CompositeCell_$union): [Option<Value_$union>, Option<OntologyAnnotation>];
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA Component
+ */
+export declare function JsonTypes_composeComponent(header: CompositeHeader_$union, value: CompositeCell_$union): Component;
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA ProcessParameterValue
+ */
+export declare function JsonTypes_composeParameterValue(header: CompositeHeader_$union, value: CompositeCell_$union): ProcessParameterValue;
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA FactorValue
+ */
+export declare function JsonTypes_composeFactorValue(header: CompositeHeader_$union, value: CompositeCell_$union): FactorValue;
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA MaterialAttributeValue
+ */
+export declare function JsonTypes_composeCharacteristicValue(header: CompositeHeader_$union, value: CompositeCell_$union): MaterialAttributeValue;
+export declare function JsonTypes_composeFreetextMaterialName(headerFT: string, name: string): string;
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA ProcessInput
+ */
+export declare function JsonTypes_composeProcessInput(header: CompositeHeader_$union, value: CompositeCell_$union): ProcessInput_$union;
+/**
+ * Convert a CompositeHeader and Cell tuple to a ISA ProcessOutput
+ */
+export declare function JsonTypes_composeProcessOutput(header: CompositeHeader_$union, value: CompositeCell_$union): ProcessOutput_$union;
+/**
+ * Convert an ISA Value and Unit tuple to a CompositeCell
+ */
+export declare function JsonTypes_cellOfValue(value: Option<Value_$union>, unit: Option<OntologyAnnotation>): CompositeCell_$union;
+/**
+ * Convert an ISA Component to a CompositeHeader and Cell tuple
+ */
+export declare function JsonTypes_decomposeComponent(c: Component): [CompositeHeader_$union, CompositeCell_$union];
+/**
+ * Convert an ISA ProcessParameterValue to a CompositeHeader and Cell tuple
+ */
+export declare function JsonTypes_decomposeParameterValue(ppv: ProcessParameterValue): [CompositeHeader_$union, CompositeCell_$union];
+/**
+ * Convert an ISA FactorValue to a CompositeHeader and Cell tuple
+ */
+export declare function JsonTypes_decomposeFactorValue(fv: FactorValue): [CompositeHeader_$union, CompositeCell_$union];
+/**
+ * Convert an ISA MaterialAttributeValue to a CompositeHeader and Cell tuple
+ */
+export declare function JsonTypes_decomposeCharacteristicValue(cv: MaterialAttributeValue): [CompositeHeader_$union, CompositeCell_$union];
+/**
+ * Convert an ISA ProcessOutput to a CompositeHeader and Cell tuple
+ */
+export declare function JsonTypes_decomposeProcessInput(pi: ProcessInput_$union): [CompositeHeader_$union, CompositeCell_$union];
+/**
+ * Convert an ISA ProcessOutput to a CompositeHeader and Cell tuple
+ */
+export declare function JsonTypes_decomposeProcessOutput(po: ProcessOutput_$union): [CompositeHeader_$union, CompositeCell_$union];
+/**
+ * This function creates a string containing the name and the ontology short-string of the given ontology annotation term
+ *
+ * TechnologyPlatforms are plain strings in ISA-JSON.
+ *
+ * This function allows us, to parse them as an ontology term.
+ */
+export declare function JsonTypes_composeTechnologyPlatform(tp: OntologyAnnotation): string;
+/**
+ * This function parses the given string containing the name and the ontology short-string of the given ontology annotation term
+ *
+ * TechnologyPlatforms are plain strings in ISA-JSON.
+ *
+ * This function allows us, to parse them as an ontology term.
+ */
+export declare function JsonTypes_decomposeTechnologyPlatform(name: string): OntologyAnnotation;
+/**
+ * If the given headers depict a component, returns a function for parsing the values of the matrix to the values of this component
+ */
+export declare function ProcessParsing_tryComponentGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => Component))>;
+/**
+ * If the given headers depict a parameter, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessParsing_tryParameterGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => ProcessParameterValue))>;
+/**
+ * If the given headers depict a factor, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessParsing_tryFactorGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => FactorValue))>;
+/**
+ * If the given headers depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessParsing_tryCharacteristicGetter(generalI: int32, valueI: int32, valueHeader: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => MaterialAttributeValue))>;
+/**
+ * If the given headers depict a protocolType, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessParsing_tryGetProtocolTypeGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => OntologyAnnotation))>;
+/**
+ * If the given headers depict a protocolREF, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessParsing_tryGetProtocolREFGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
+/**
+ * If the given headers depict a protocolDescription, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessParsing_tryGetProtocolDescriptionGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
+/**
+ * If the given headers depict a protocolURI, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessParsing_tryGetProtocolURIGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
+/**
+ * If the given headers depict a protocolVersion, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessParsing_tryGetProtocolVersionGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => string))>;
+/**
+ * If the given headers depict an input, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessParsing_tryGetInputGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => ProcessInput_$union))>;
+/**
+ * If the given headers depict an output, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessParsing_tryGetOutputGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => ProcessOutput_$union))>;
+/**
+ * If the given headers depict a comment, returns a function for parsing the values of the matrix to the values of this type
+ */
+export declare function ProcessParsing_tryGetCommentGetter(generalI: int32, header: CompositeHeader_$union): Option<((arg0: ArcTable) => ((arg0: int32) => Comment$))>;
+/**
+ * Given the header sequence of an ArcTable, returns a function for parsing each row of the table to a process
+ */
+export declare function ProcessParsing_getProcessGetter(processNameRoot: string, headers: Iterable<CompositeHeader_$union>): ((arg0: ArcTable) => ((arg0: int32) => Process));
+/**
+ * Groups processes by their name, or by the name of the protocol they execute
+ *
+ * Process names are taken from the Worksheet name and numbered: SheetName_1, SheetName_2, etc.
+ *
+ * This function decomposes this name into a root name and a number, and groups processes by root name.
+ */
+export declare function ProcessParsing_groupProcesses(ps: FSharpList<Process>): FSharpList<[string, FSharpList<Process>]>;
+/**
+ * Merges processes with the same name, protocol and param values
+ */
+export declare function ProcessParsing_mergeIdenticalProcesses(processes: FSharpList<Process>): FSharpList<Process>;
+export declare function ProcessParsing_processToRows(p: Process): FSharpList<FSharpList<[CompositeHeader_$union, CompositeCell_$union]>>;
+export declare function ARCtrl_CompositeHeader__CompositeHeader_TryParameter(this$: CompositeHeader_$union): Option<ProtocolParameter>;
+export declare function ARCtrl_CompositeHeader__CompositeHeader_TryFactor(this$: CompositeHeader_$union): Option<Factor>;
+export declare function ARCtrl_CompositeHeader__CompositeHeader_TryCharacteristic(this$: CompositeHeader_$union): Option<MaterialAttribute>;
+export declare function ARCtrl_CompositeHeader__CompositeHeader_TryComponent(this$: CompositeHeader_$union): Option<Component>;
+/**
+ * This function is used to improve interoperability with ISA-JSON types. It is not recommended for default ARCtrl usage.
+ */
+export declare function ARCtrl_CompositeCell__CompositeCell_fromValue_Static_Z6986DF18(value: Value_$union, unit?: OntologyAnnotation): CompositeCell_$union;
+export declare function CompositeRow_toProtocol(tableName: string, row: Iterable<[CompositeHeader_$union, CompositeCell_$union]>): Protocol;
+/**
+ * Create a new table from an ISA protocol.
+ *
+ * The table will have at most one row, with the protocol information and the component values
+ */
+export declare function ARCtrl_ArcTable__ArcTable_fromProtocol_Static_3BF20962(p: Protocol): ArcTable;
+/**
+ * Returns the list of protocols executed in this ArcTable
+ */
+export declare function ARCtrl_ArcTable__ArcTable_GetProtocols(this$: ArcTable): FSharpList<Protocol>;
+/**
+ * Returns the list of processes specidified in this ArcTable
+ */
+export declare function ARCtrl_ArcTable__ArcTable_GetProcesses(this$: ArcTable): FSharpList<Process>;
+/**
+ * Create a new table from a list of processes
+ *
+ * The name will be used as the sheet name
+ *
+ * The processes SHOULD have the same headers, or even execute the same protocol
+ */
+export declare function ARCtrl_ArcTable__ArcTable_fromProcesses_Static(name: string, ps: FSharpList<Process>): ArcTable;
+/**
+ * Return a list of all the processes in all the tables.
+ */
+export declare function ARCtrl_ArcTables__ArcTables_GetProcesses(this$: ArcTables): FSharpList<Process>;
+/**
+ * Create a collection of tables from a list of processes.
+ *
+ * For this, the processes are grouped by nameroot ("nameroot_1", "nameroot_2" ...) or exectued protocol if no name exists
+ *
+ * Then each group is converted to a table with this nameroot as sheetname
+ */
+export declare function ARCtrl_ArcTables__ArcTables_fromProcesses_Static_62A3309D(ps: FSharpList<Process>): ArcTables;
+//# sourceMappingURL=Conversion.d.ts.map

package/dist/ts/ts/Core/Conversion.d.ts.map

@@ -0,0 +1 @@
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