Java lipid 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/lipid_validation/mslibrary-lipid-validator/app/src/main/resources/PNNL-LIPIDS-NEGATIVE-small.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.ElementTable;
+import org.lifstools.jgoslin.domain.LipidAdduct;
+import org.lifstools.jgoslin.domain.LipidParsingException;
+import org.lifstools.jgoslin.parser.LipidParser;
+import org.lifstools.jgoslin.parser.SumFormulaParser;
+
+/**
+ *
+ * @author nilshoffmann
+ */
+public class MsLibraryReader {
+
+    private final LipidParser lipidParser = new LipidParser();
+    private final SumFormulaParser sfp = new SumFormulaParser();
+
+    public void read(File mgfFile) throws IOException, UnsupportedFormatException {
+        AutoLibraryParser alp = new AutoLibraryParser(10, (spectralLibraryEntryList, alreadyProcessed) -> {
+            spectralLibraryEntryList.forEach((t) -> {
+                String name = t.getField(DBEntryField.NAME).map((dbentryname) -> dbentryname.toString()).orElse("NA");
+                System.out.println("Processing entry: " + name);
+                try {
+                    System.out.println("Checking if lipid name is parseable!");
+                    LipidAdduct lipidAdduct = lipidParser.parse(name);
+                    System.out.println(lipidAdduct.toString());
+                    String providedSumFormula = t.getField(DBEntryField.FORMULA).map((formula) -> formula.toString()).orElse("");
+                    ElementTable et = sfp.parse(providedSumFormula, sfp.newEventHandler());
+                    String calculatedSumFormula = lipidAdduct.getSumFormula();
+                    System.out.println("Sum Formulas: DB entry: " + et.getSumFormula() + " calculated: " + calculatedSumFormula);
+                    System.out.println("Sum Formulas are equal: " + calculatedSumFormula.equals(et.getSumFormula()));
+                    Object pepmass = t.getField(DBEntryField.MOLWEIGHT).orElse(Double.valueOf(0));
+                    System.out.println("Molweight: " + pepmass.toString());
+                    Object mw = t.getField(DBEntryField.PRECURSOR_MZ).orElse(Double.valueOf(0));
+                    System.out.println("Precursor MZ: " + mw.toString());
+                    double mwd = ((Double)mw).doubleValue();
+                    double calculatedMass = et.getMass().doubleValue();
+                    System.out.println("Calculated Precursor MZ: "+calculatedMass);
+                    System.out.println("Mass difference: "+(mwd-calculatedMass));
+                    double diffMass = Math.abs(mwd-calculatedMass);
+                    boolean massOk = diffMass<1.0E-3;
+                    System.out.println("Mass difference < 1.0E-3? "+massOk);
+                } catch (LipidParsingException e) {
+                    System.out.println("Goslin says no!");
+                }
+            });
+        });
+        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/main/resources/PNNL-LIPIDS-NEGATIVE-small.mgf

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+BEGIN IONS
+PEPMASS=450.262
+CHARGE=1
+MSLEVEL=2
+SOURCE_INSTRUMENT=LC-ESI-CID; Lumos
+FILENAME=/home/mingxun/Data/data/Metabolomics/Libraries/PNNL/Lipids/LibrariesCreation/PNNL_LipidSpectra_Neg.mgf
+SEQ=*..*
+IONMODE=Negative
+ORGANISM=PNNL-LIPIDS-NEGATIVE
+NAME=PE(16:1/0:0) [M-H]1-
+PI=Thomas Metz
+FORMULA=C21H41N1O7P1
+DATACOLLECTOR=Thomas Metz
+SMILES=N/A
+INCHI=N/A
+INCHIAUX=N/A
+PUBMED=N/A
+SUBMITUSER=mwang87
+LIBRARYQUALITY=1
+SPECTRUMID=CCMSLIB00010059112
+SCANS=1
+88.32769	245.804764
+93.972839	232.013443
+95.618507	268.045868
+100.635094	307.082031
+105.552155	291.909698
+123.586555	369.775604
+140.011139	1016.653503
+147.90979	356.798553
+151.629898	416.599426
+158.973969	371.781433
+196.037247	2644.280029
+205.488373	501.591583
+214.048126	15959.319336
+253.216827	668097.875
+261.997437	462.053406
+307.020447	728.224487
+409.645721	690.217773
+END IONS
+
+
+BEGIN IONS
+PEPMASS=450.262
+CHARGE=1
+MSLEVEL=2
+SOURCE_INSTRUMENT=LC-ESI-HCD; Lumos
+FILENAME=/home/mingxun/Data/data/Metabolomics/Libraries/PNNL/Lipids/LibrariesCreation/PNNL_LipidSpectra_Neg.mgf
+SEQ=*..*
+IONMODE=Negative
+ORGANISM=PNNL-LIPIDS-NEGATIVE
+NAME=PE(16:1/0:0) [M-H]1-
+PI=Thomas Metz
+FORMULA=C21H41N1O7P1
+DATACOLLECTOR=Thomas Metz
+SMILES=N/A
+INCHI=N/A
+INCHIAUX=N/A
+PUBMED=N/A
+SUBMITUSER=mwang87
+LIBRARYQUALITY=1
+SPECTRUMID=CCMSLIB00010059114
+SCANS=2
+100.93396	282.544464
+113.877197	307.384216
+140.011642	8027.749023
+152.9953	2096.166748
+178.184937	1374.054077
+196.03775	9324.954102
+214.048828	15460.44043
+235.208908	752.753296
+253.217422	967534.6875
+254.221176	771.921692
+262.387482	654.0802
+271.458923	780.599854
+294.089935	762.228088
+322.021149	839.201355
+END IONS
+
+
+BEGIN IONS
+PEPMASS=476.278
+CHARGE=1
+MSLEVEL=2
+SOURCE_INSTRUMENT=LC-ESI-CID; Lumos
+FILENAME=/home/mingxun/Data/data/Metabolomics/Libraries/PNNL/Lipids/LibrariesCreation/PNNL_LipidSpectra_Neg.mgf
+SEQ=*..*
+IONMODE=Negative
+ORGANISM=PNNL-LIPIDS-NEGATIVE
+NAME=PE(18:2/0:0) [M-H]1-
+PI=Thomas Metz
+FORMULA=C23H43N1O7P1
+DATACOLLECTOR=Thomas Metz
+SMILES=N/A
+INCHI=N/A
+INCHIAUX=N/A
+PUBMED=N/A
+SUBMITUSER=mwang87
+LIBRARYQUALITY=1
+SPECTRUMID=CCMSLIB00010059115
+SCANS=3
+99.012329	302.66864
+137.016525	441.67511
+140.011261	1204.163208
+150.551758	430.2565
+152.995499	834.349426
+178.209702	1269.476562
+196.037888	3227.924316
+214.048141	29480.539062
+214.071869	1270.914429
+247.366653	793.174438
+278.830505	852.584534
+279.232513	1467222.375
+280.235352	951.054077
+280.567749	942.396912
+285.79657	797.994751
+306.568115	913.472595
+394.96698	1693.546265
+432.089874	782.323792
+432.187653	1374.477661
+448.449188	640.251648
+455.015808	711.718628
+458.298615	1311.985596
+486.666687	717.959473
+END IONS
+
+

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