@nfdi4plants/arctrl 1.0.0-alpha6

package/ISA/ISA/Regex.js

@@ -0,0 +1,588 @@
+import { create, match } from "../../fable_modules/fable-library.4.1.4/RegExp.js";
+import { value as value_1, map, some } from "../../fable_modules/fable-library.4.1.4/Option.js";
+import { parse } from "../../fable_modules/fable-library.4.1.4/Int32.js";
+
+export const Pattern_ExcelNumberFormat = `"(?<${"numberFormat"}>(.*?))"`;
+
+export const Pattern_TermAnnotationShortPattern = `(?<${"idspace"}>\\w+?):(?<${"localid"}>\\w+)`;
+
+export const Pattern_TermAnnotationURIPattern = `http://purl.obolibrary.org/obo/(?<${"idspace"}>\\w+?)_(?<${"localid"}>\\w+)`;
+
+export const Pattern_TermAnnotationURIPattern_lessRestrictive = `.*\\/(?<${"idspace"}>\\w+?)[:_](?<${"localid"}>\\w+)`;
+
+export const Pattern_IOTypePattern = `(Input|Output)\\s\\[(?<${"iotype"}>.+)\\]`;
+
+export const Pattern_InputPattern = `Input\\s\\[(?<${"iotype"}>.+)\\]`;
+
+export const Pattern_OutputPattern = `Output\\s\\[(?<${"iotype"}>.+)\\]`;
+
+/**
+ * Matches, if the input string matches the given regex pattern.
+ */
+export function ActivePatterns_$007CRegex$007C_$007C(pattern, input) {
+    const m = match(create(pattern), input.trim());
+    if (m != null) {
+        return m;
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches any column header starting with some text, followed by one whitespace and a term name inside squared brackets.
+ */
+export function ActivePatterns_$007CReferenceColumnHeader$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("(Term Source REF|Term Accession Number)\\s\\((?<id>.*)\\)", input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return {
+            Annotation: (r.groups && r.groups.id) || "",
+        };
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches any column header starting with some text, followed by one whitespace and a term name inside squared brackets.
+ */
+export function ActivePatterns_$007CTermColumn$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("(?<termcolumntype>.+)\\s\\[(?<termname>.+)\\]", input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return {
+            TermColumnType: (r.groups && r.groups.termcolumntype) || "",
+            TermName: (r.groups && r.groups.termname) || "",
+        };
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Unit" column header.
+ */
+export function ActivePatterns_$007CUnitColumnHeader$007C_$007C(input) {
+    if (ActivePatterns_$007CRegex$007C_$007C("Unit", input) != null) {
+        return some(void 0);
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Parameter [Term]" or "Parameter Value [Term]" column header and returns the Term string.
+ */
+export function ActivePatterns_$007CParameterColumnHeader$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CTermColumn$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        const matchValue = r.TermColumnType;
+        switch (matchValue) {
+            case "Parameter":
+            case "Parameter Value":
+                return r.TermName;
+            default:
+                return void 0;
+        }
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Factor [Term]" or "Factor Value [Term]" column header and returns the Term string.
+ */
+export function ActivePatterns_$007CFactorColumnHeader$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CTermColumn$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        const matchValue = r.TermColumnType;
+        switch (matchValue) {
+            case "Factor":
+            case "Factor Value":
+                return r.TermName;
+            default:
+                return void 0;
+        }
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Characteristic [Term]" or "Characteristics [Term]" or "Characteristics Value [Term]" column header and returns the Term string.
+ */
+export function ActivePatterns_$007CCharacteristicColumnHeader$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CTermColumn$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        const matchValue = r.TermColumnType;
+        switch (matchValue) {
+            case "Characteristic":
+            case "Characteristics":
+            case "Characteristics Value":
+                return r.TermName;
+            default:
+                return void 0;
+        }
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Component [Term]" or "Component Value [Term]" column header and returns the Term string.
+ */
+export function ActivePatterns_$007CComponentColumnHeader$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CTermColumn$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        const matchValue = r.TermColumnType;
+        switch (matchValue) {
+            case "Component":
+            case "Component Value":
+                return r.TermName;
+            default:
+                return void 0;
+        }
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a short term string and returns the term source ref and the annotation number strings.
+ * 
+ * Example: "MS:1003022" --> term source ref: "MS"; annotation number: "1003022"
+ */
+export function ActivePatterns_$007CTermAnnotationShort$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Pattern_TermAnnotationShortPattern, input);
+    if (activePatternResult != null) {
+        const value = activePatternResult;
+        return {
+            IDSpace: (value.groups && value.groups.idspace) || "",
+            LocalID: (value.groups && value.groups.localid) || "",
+        };
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a term string (either short or URI) and returns the term source ref and the annotation number strings.
+ * 
+ * Example 1: "MS:1003022" --> term source ref: "MS"; annotation number: "1003022"
+ * 
+ * Example 2: "http://purl.obolibrary.org/obo/MS_1003022" --> term source ref: "MS"; annotation number: "1003022"
+ */
+export function ActivePatterns_$007CTermAnnotation$007C_$007C(input) {
+    let matchResult, value;
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Pattern_TermAnnotationShortPattern, input);
+    if (activePatternResult != null) {
+        matchResult = 0;
+        value = activePatternResult;
+    }
+    else {
+        const activePatternResult_1 = ActivePatterns_$007CRegex$007C_$007C(Pattern_TermAnnotationURIPattern, input);
+        if (activePatternResult_1 != null) {
+            matchResult = 0;
+            value = activePatternResult_1;
+        }
+        else {
+            const activePatternResult_2 = ActivePatterns_$007CRegex$007C_$007C(Pattern_TermAnnotationURIPattern_lessRestrictive, input);
+            if (activePatternResult_2 != null) {
+                matchResult = 0;
+                value = activePatternResult_2;
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+    }
+    switch (matchResult) {
+        case 0:
+            return {
+                IDSpace: (value.groups && value.groups.idspace) || "",
+                LocalID: (value.groups && value.groups.localid) || "",
+            };
+        default:
+            return void 0;
+    }
+}
+
+/**
+ * Matches a "Term Source REF (ShortTerm)" column header and returns the ShortTerm as Term Source Ref and Annotation Number.
+ * 
+ * Example: "Term Source REF (MS:1003022)" --> term source ref: "MS"; annotation number: "1003022"
+ */
+export function ActivePatterns_$007CTSRColumnHeader$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("Term Source REF\\s\\((?<id>.*)\\)", input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        const matchValue = (r.groups && r.groups.id) || "";
+        const activePatternResult_1 = ActivePatterns_$007CTermAnnotation$007C_$007C(matchValue);
+        if (activePatternResult_1 != null) {
+            const r_1 = activePatternResult_1;
+            return r_1;
+        }
+        else {
+            return {
+                IDSpace: "",
+                LocalID: "",
+            };
+        }
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Term Accession Number (ShortTerm)" column header and returns the ShortTerm as Term Source Ref and Annotation Number.
+ * 
+ * Example: "Term Accession Number (MS:1003022)" --> term source ref: "MS"; annotation number: "1003022"
+ */
+export function ActivePatterns_$007CTANColumnHeader$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("Term Accession Number\\s\\((?<id>.*)\\)", input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        const matchValue = (r.groups && r.groups.id) || "";
+        const activePatternResult_1 = ActivePatterns_$007CTermAnnotation$007C_$007C(matchValue);
+        if (activePatternResult_1 != null) {
+            const r_1 = activePatternResult_1;
+            return r_1;
+        }
+        else {
+            return {
+                IDSpace: "",
+                LocalID: "",
+            };
+        }
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Input [InputType]" column header and returns the InputType as string.
+ */
+export function ActivePatterns_$007CInputColumnHeader$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Pattern_InputPattern, input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return (r.groups && r.groups.iotype) || "";
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Output [OutputType]" column header and returns the OutputType as string.
+ */
+export function ActivePatterns_$007COutputColumnHeader$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Pattern_OutputPattern, input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return (r.groups && r.groups.iotype) || "";
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches auto-generated readable table names. Mainly used in ArcAssay.addTable(). Default tables will get such a name.
+ * 
+ * Will match "New Table 10" and return the number `10`.
+ */
+export function ActivePatterns_$007CAutoGeneratedTableName$007C_$007C(input) {
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C("^New\\sTable\\s(?<number>\\d+)$", input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return parse((r.groups && r.groups.number) || "", 511, false, 32);
+    }
+    else {
+        return void 0;
+    }
+}
+
+export function tryParseReferenceColumnHeader(str) {
+    const matchValue = str.trim();
+    const activePatternResult = ActivePatterns_$007CReferenceColumnHeader$007C_$007C(matchValue);
+    if (activePatternResult != null) {
+        const v = activePatternResult;
+        return v;
+    }
+    else {
+        return void 0;
+    }
+}
+
+export function tryParseTermAnnotationShort(str) {
+    const matchValue = str.trim();
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Pattern_TermAnnotationShortPattern, matchValue);
+    if (activePatternResult != null) {
+        const value = activePatternResult;
+        return {
+            IDSpace: (value.groups && value.groups.idspace) || "",
+            LocalID: (value.groups && value.groups.localid) || "",
+        };
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * This function can be used to extract `IDSPACE:LOCALID` (or: `Term Accession`) from Swate header strings or obofoundry conform URI strings.
+ * 
+ * **Example 1:** "http://purl.obolibrary.org/obo/GO_000001" --> "GO:000001"
+ * 
+ * **Example 2:** "Term Source REF (NFDI4PSO:0000064)" --> "NFDI4PSO:0000064"
+ */
+export function tryParseTermAnnotation(str) {
+    const matchValue = str.trim();
+    let matchResult, value;
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Pattern_TermAnnotationShortPattern, matchValue);
+    if (activePatternResult != null) {
+        matchResult = 0;
+        value = activePatternResult;
+    }
+    else {
+        const activePatternResult_1 = ActivePatterns_$007CRegex$007C_$007C(Pattern_TermAnnotationURIPattern, matchValue);
+        if (activePatternResult_1 != null) {
+            matchResult = 0;
+            value = activePatternResult_1;
+        }
+        else {
+            const activePatternResult_2 = ActivePatterns_$007CRegex$007C_$007C(Pattern_TermAnnotationURIPattern_lessRestrictive, matchValue);
+            if (activePatternResult_2 != null) {
+                matchResult = 0;
+                value = activePatternResult_2;
+            }
+            else {
+                matchResult = 1;
+            }
+        }
+    }
+    switch (matchResult) {
+        case 0:
+            return {
+                IDSpace: (value.groups && value.groups.idspace) || "",
+                LocalID: (value.groups && value.groups.localid) || "",
+            };
+        default:
+            return void 0;
+    }
+}
+
+/**
+ * Tries to parse 'str' to term accession and returns it in the format `Some "termsourceref:localtan"`. Exmp.: `Some "MS:000001"`
+ */
+export function tryGetTermAnnotationShortString(str) {
+    return map((r) => ((r.IDSpace + ":") + r.LocalID), tryParseTermAnnotation(str));
+}
+
+/**
+ * Parses 'str' to term accession and returns it in the format "termsourceref:localtan". Exmp.: "MS:000001"
+ */
+export function getTermAnnotationShortString(str) {
+    const matchValue = tryGetTermAnnotationShortString(str);
+    if (matchValue == null) {
+        throw new Error(`Unable to parse '${str}' to term accession.`);
+    }
+    else {
+        return matchValue;
+    }
+}
+
+/**
+ * This function is used to parse Excel numberFormat string to term name.
+ * 
+ * **Example 1:** "0.00 "degree Celsius"" --> "degree Celsius"
+ */
+export function tryParseExcelNumberFormat(headerStr) {
+    const matchValue = headerStr.trim();
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Pattern_ExcelNumberFormat, matchValue);
+    if (activePatternResult != null) {
+        const value = activePatternResult;
+        return (value.groups && value.groups.numberFormat) || "";
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * This function is used to match both Input and Output columns and capture the IOType as `iotype` group.
+ * 
+ * **Example 1:** "Input [Sample]" --> "Sample"
+ */
+export function tryParseIOTypeHeader(headerStr) {
+    const matchValue = headerStr.trim();
+    const activePatternResult = ActivePatterns_$007CRegex$007C_$007C(Pattern_IOTypePattern, matchValue);
+    if (activePatternResult != null) {
+        const value = activePatternResult;
+        return (value.groups && value.groups.iotype) || "";
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches any column header starting with some text, followed by one whitespace and a term name inside squared brackets.
+ */
+export function tryParseTermColumn(input) {
+    const activePatternResult = ActivePatterns_$007CTermColumn$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return r;
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Unit" column header.
+ */
+export function tryParseUnitColumnHeader(input) {
+    const activePatternResult = ActivePatterns_$007CUnitColumnHeader$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = value_1(activePatternResult);
+        return some(void 0);
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Parameter [Term]" or "Parameter Value [Term]" column header and returns the Term string.
+ */
+export function tryParseParameterColumnHeader(input) {
+    const activePatternResult = ActivePatterns_$007CParameterColumnHeader$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return r;
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Factor [Term]" or "Factor Value [Term]" column header and returns the Term string.
+ */
+export function tryParseFactorColumnHeader(input) {
+    const activePatternResult = ActivePatterns_$007CFactorColumnHeader$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return r;
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Characteristic [Term]" or "Characteristics [Term]" or "Characteristics Value [Term]" column header and returns the Term string.
+ */
+export function tryParseCharacteristicColumnHeader(input) {
+    const activePatternResult = ActivePatterns_$007CCharacteristicColumnHeader$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return r;
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Component [Term]" or "Characteristics [Term]" or "Component Value [Term]" column header and returns the Term string.
+ */
+export function tryParseComponentColumnHeader(input) {
+    const activePatternResult = ActivePatterns_$007CComponentColumnHeader$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return r;
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Term Source REF (ShortTerm)" column header and returns the ShortTerm as Term Source Ref and Annotation Number.
+ * 
+ * Example: "Term Source REF (MS:1003022)" --> term source ref: "MS"; annotation number: "1003022"
+ */
+export function tryParseTSRColumnHeader(input) {
+    const activePatternResult = ActivePatterns_$007CTSRColumnHeader$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return r;
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Term Accession Number (ShortTerm)" column header and returns the ShortTerm as Term Source Ref and Annotation Number.
+ * 
+ * Example: "Term Accession Number (MS:1003022)" --> term source ref: "MS"; annotation number: "1003022"
+ */
+export function tryParseTANColumnHeader(input) {
+    const activePatternResult = ActivePatterns_$007CTANColumnHeader$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return r;
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Input [InputType]" column header and returns the InputType as string.
+ */
+export function tryParseInputColumnHeader(input) {
+    const activePatternResult = ActivePatterns_$007CInputColumnHeader$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return r;
+    }
+    else {
+        return void 0;
+    }
+}
+
+/**
+ * Matches a "Output [OutputType]" column header and returns the OutputType as string.
+ */
+export function tryParseOutputColumnHeader(input) {
+    const activePatternResult = ActivePatterns_$007COutputColumnHeader$007C_$007C(input);
+    if (activePatternResult != null) {
+        const r = activePatternResult;
+        return r;
+    }
+    else {
+        return void 0;
+    }
+}
+