@nfdi4plants/arctrl 1.0.0-alpha6

package/ISA/ISA/Identifier.js

@@ -0,0 +1,76 @@
+import { match, isMatch } from "../../fable_modules/fable-library.4.1.4/RegExp.js";
+import { newGuid } from "../../fable_modules/fable-library.4.1.4/Guid.js";
+import { combineMany } from "../../FileSystem/Path.js";
+
+export function checkValidCharacters(identifier) {
+    if (!isMatch(/^[a-zA-Z0-9_\- ]+$/gu, identifier)) {
+        throw new Error("New identifier contains forbidden characters! Allowed characters are: letters, digits, underscore (_), dash (-) and whitespace ( ).");
+    }
+}
+
+export function createMissingIdentifier() {
+    let copyOfStruct;
+    return "MISSING_IDENTIFIER_" + ((copyOfStruct = newGuid(), copyOfStruct));
+}
+
+export function isMissingIdentifier(str) {
+    return str.indexOf("MISSING_IDENTIFIER_") === 0;
+}
+
+export function removeMissingIdentifier(str) {
+    if (str.indexOf("MISSING_IDENTIFIER_") === 0) {
+        return "";
+    }
+    else {
+        return str;
+    }
+}
+
+/**
+ * On read-in the FileName can be any combination of "assays" (assay folder name), assayIdentifier and "isa.assay.xlsx" (the actual file name).
+ * 
+ * This functions extracts assayIdentifier from any of these combinations and returns it.
+ */
+export function Assay_identifierFromFileName(fileName) {
+    const m = match(/^(assays(\/|\\))?(?<identifier>[a-zA-Z0-9_\- ]+)((\/|\\)isa.assay.xlsx)?$/gu, fileName);
+    const matchValue = m != null;
+    if (matchValue) {
+        return (m.groups && m.groups.identifier) || "";
+    }
+    else {
+        throw new Error(`Cannot parse identifier from FileName \`${fileName}\``);
+    }
+}
+
+/**
+ * On writing a xlsx file we unify our output to a relative path to ARC root. So: `assays/assayIdentifier/isa.assay.xlsx`.
+ */
+export function Assay_fileNameFromIdentifier(identifier) {
+    checkValidCharacters(identifier);
+    return combineMany(["assays", identifier, "isa.assay.xlsx"]);
+}
+
+/**
+ * On read-in the FileName can be any combination of "studies" (study folder name), studyIdentifier and "isa.study.xlsx" (the actual file name).
+ * 
+ * This functions extracts studyIdentifier from any of these combinations and returns it.
+ */
+export function Study_identifierFromFileName(fileName) {
+    const m = match(/^(studies(\/|\\))?(?<identifier>[a-zA-Z0-9_\- ]+)((\/|\\)isa.study.xlsx)?$/gu, fileName);
+    const matchValue = m != null;
+    if (matchValue) {
+        return (m.groups && m.groups.identifier) || "";
+    }
+    else {
+        throw new Error(`Cannot parse identifier from FileName \`${fileName}\``);
+    }
+}
+
+/**
+ * On writing a xlsx file we unify our output to a relative path to ARC root. So: `studies/studyIdentifier/isa.study.xlsx`.
+ */
+export function Study_fileNameFromIdentifier(identifier) {
+    checkValidCharacters(identifier);
+    return combineMany(["studies", identifier, "isa.study.xlsx"]);
+}
+

package/ISA/ISA/JsonTypes/AnnotationValue.js

@@ -0,0 +1,56 @@
+import { Union } from "../../../fable_modules/fable-library.4.1.4/Types.js";
+import { union_type, int32_type, float64_type, string_type } from "../../../fable_modules/fable-library.4.1.4/Reflection.js";
+import { parse } from "../../../fable_modules/fable-library.4.1.4/Double.js";
+import { parse as parse_1 } from "../../../fable_modules/fable-library.4.1.4/Int32.js";
+import { int32ToString } from "../../../fable_modules/fable-library.4.1.4/Util.js";
+
+export class AnnotationValue extends Union {
+    constructor(tag, fields) {
+        super();
+        this.tag = tag;
+        this.fields = fields;
+    }
+    cases() {
+        return ["Text", "Float", "Int"];
+    }
+}
+
+export function AnnotationValue_$reflection() {
+    return union_type("ARCtrl.ISA.AnnotationValue", [], AnnotationValue, () => [[["Item", string_type]], [["Item", float64_type]], [["Item", int32_type]]]);
+}
+
+export function AnnotationValue_get_empty() {
+    return new AnnotationValue(0, [""]);
+}
+
+/**
+ * Create a ISAJson Annotation value from a ISATab string entry
+ */
+export function AnnotationValue_fromString_Z721C83C5(s) {
+    try {
+        return new AnnotationValue(2, [parse_1(s, 511, false, 32)]);
+    }
+    catch (matchValue) {
+        try {
+            return new AnnotationValue(1, [parse(s)]);
+        }
+        catch (matchValue_1) {
+            return new AnnotationValue(0, [s]);
+        }
+    }
+}
+
+/**
+ * Get a ISATab string Annotation Name from a ISAJson object
+ */
+export function AnnotationValue_toString_Z6FAD7738(v) {
+    switch (v.tag) {
+        case 2:
+            return int32ToString(v.fields[0]);
+        case 1:
+            return v.fields[0].toString();
+        default:
+            return v.fields[0];
+    }
+}
+