First PoC for lipid ms lib parsing and validation.

lipid_validation/mslibrary-lipid-validator/.gitattributes

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+#
+# https://help.github.com/articles/dealing-with-line-endings/
+#
+# Linux start script should use lf
+/gradlew        text eol=lf
+
+# These are Windows script files and should use crlf
+*.bat           text eol=crlf
+

lipid_validation/mslibrary-lipid-validator/.gitignore

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+# Ignore Gradle project-specific cache directory
+.gradle
+
+# Ignore Gradle build output directory
+build

lipid_validation/mslibrary-lipid-validator/app/build.gradle

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+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * This generated file contains a sample Java application project to get you started.
+ * For more details on building Java & JVM projects, please refer to https://docs.gradle.org/8.4/userguide/building_java_projects.html in the Gradle documentation.
+ */
+
+plugins {
+    // Apply the application plugin to add support for building a CLI application in Java.
+    id 'application'
+}
+
+repositories {
+    // Use Maven Central for resolving dependencies.
+    mavenCentral()
+    maven {
+        url "https://m.lifs-tools.org/artifactory/libs-release"
+    }
+    maven { url = "file://" + projectDir + "/src/main/lib" }
+    // For jmzml, etc.
+    maven { url = "https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/" }
+    // For SIRIUS ID modules
+    maven { url = "https://bio.informatik.uni-jena.de/repository/libs-oss/" }
+    maven { url = "https://jitpack.io" }
+    maven { url = "https://www.xypron.de/repository/" }
+    // For cpdetector
+    maven { url = "https://nexus.nuiton.org/nexus/content/groups/releases/" }
+    // For jimzml
+    // maven { url = "https://mvnrepository.com/artifact/com.alanmrace/jimzmlparser" }
+}
+
+ext {
+    jgoslinVersion = '2.1.0'
+}
+
+dependencies {
+    // Use JUnit Jupiter for testing.
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.9.3'
+
+    testRuntimeOnly 'org.junit.platform:junit-platform-launchchemspider-apier'
+
+    // This dependency is used by the application.
+    implementation 'com.google.guava:guava:32.1.1-jre'
+
+    implementation('io.github.mzmine:mzmine3:3.9.3') {
+        exclude group: 'org.rsc.chemspider', module: 'chemspider-api'
+        exclude group: 'mzmine', module: 'jmprojection'
+        exclude group: 'mzmine', module: 'gslibml'
+        exclude group: 'org.du-lab.adap', module: 'adap'
+        exclude group: 'gnf', module: 'clustering'
+    }
+    implementation "org.lifs-tools:jgoslin-parsers:$jgoslinVersion"
+}
+
+// Apply a specific Java toolchain to ease working on different environments.
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(20)
+    }
+}
+
+application {
+    // Define the main class for the application.
+    mainClass = 'org.mzmine.mslibrary.lipid.validator.App'
+}
+
+tasks.named('test') {
+    // Use JUnit Platform for unit tests.
+    useJUnitPlatform()
+}
+
+tasks.withType(JavaCompile) {
+    options.encoding = "UTF-8"
+    options.compilerArgs += ['--enable-preview']
+}
+
+tasks.withType(Test) {
+    jvmArgs += "--enable-preview"
+}
+
+tasks.withType(JavaExec) {
+    jvmArgs += '--enable-preview'
+}

lipid_validation/mslibrary-lipid-validator/app/src/main/java/org/mzmine/mslibrary/lipid/validator/App.java

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+/*
+ * This Java source file was generated by the Gradle 'init' task.
+ */
+package org.mzmine.mslibrary.lipid.validator;
+
+import io.github.mzmine.util.spectraldb.parser.UnsupportedFormatException;
+import java.io.File;
+import java.io.IOException;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+public class App {
+
+    public String getGreeting() {
+        return "Hello World!";
+    }
+
+    public static void main(String[] args) {
+        try {
+            new MsLibraryReader().read(new File("/home/nilshoffmann/Projects/github.com/nilshoffmann/biohack23_p15/library_spectra_validation/tests/examples/test_case_correct.mgf"));
+        } catch (IOException ex) {
+            Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
+        } catch (UnsupportedFormatException ex) {
+            Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
+        }
+    }
+}

lipid_validation/mslibrary-lipid-validator/app/src/main/java/org/mzmine/mslibrary/lipid/validator/MsLibraryReader.java

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+/*
+ * Click nbfs://nbhost/SystemFileSystem/Templates/Licenses/license-default.txt to change this license
+ * Click nbfs://nbhost/SystemFileSystem/Templates/Classes/Class.java to edit this template
+ */
+package org.mzmine.mslibrary.lipid.validator;
+
+import io.github.mzmine.util.MemoryMapStorage;
+import io.github.mzmine.util.spectraldb.entry.DBEntryField;
+import io.github.mzmine.util.spectraldb.entry.SpectralLibrary;
+import io.github.mzmine.util.spectraldb.parser.AutoLibraryParser;
+import io.github.mzmine.util.spectraldb.parser.UnsupportedFormatException;
+import java.io.File;
+import java.io.IOException;
+import java.util.UUID;
+import org.lifstools.jgoslin.domain.LipidParsingException;
+import org.lifstools.jgoslin.parser.LipidParser;
+
+/**
+ *
+ * @author nilshoffmann
+ */
+public class MsLibraryReader {
+
+    private final LipidParser lipidParser = new LipidParser();
+
+    public void read(File mgfFile) throws IOException, UnsupportedFormatException {
+        AutoLibraryParser alp = new AutoLibraryParser(10, (spectralLibraryEntryList, alreadyProcessed) -> {
+            spectralLibraryEntryList.forEach((t) -> {
+                String name = t.getField(DBEntryField.NAME).orElse("NA");
+                System.out.println("Processing entry: " + name);
+                try {
+                    lipidParser.parse(name);
+                } catch (LipidParsingException e) {
+                    System.out.println("");
+                }
+            });
+        });
+        String prefix = "lipid-spec-lib-" + UUID.randomUUID();
+        boolean parseSuccess = alp.parse(null, mgfFile, new SpectralLibrary(MemoryMapStorage.create(), prefix, File.createTempFile(prefix, ".slib")));
+    }
+
+}

lipid_validation/mslibrary-lipid-validator/app/src/test/java/org/mzmine/mslibrary/lipid/validator/AppTest.java

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+/*
+ * This Java source file was generated by the Gradle 'init' task.
+ */
+package org.mzmine.mslibrary.lipid.validator;
+
+import org.junit.jupiter.api.Test;
+import static org.junit.jupiter.api.Assertions.*;
+
+class AppTest {
+    @Test void appHasAGreeting() {
+        App classUnderTest = new App();
+        assertNotNull(classUnderTest.getGreeting(), "app should have a greeting");
+    }
+}

lipid_validation/mslibrary-lipid-validator/gradle/wrapper/gradle-wrapper.properties

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+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists