diff --git a/lipid_validation/mslibrary-lipid-validator/.gitattributes b/lipid_validation/mslibrary-lipid-validator/.gitattributes new file mode 100644 index 0000000..097f9f9 --- /dev/null +++ b/lipid_validation/mslibrary-lipid-validator/.gitattributes @@ -0,0 +1,9 @@ +# +# 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 + diff --git a/lipid_validation/mslibrary-lipid-validator/.gitignore b/lipid_validation/mslibrary-lipid-validator/.gitignore new file mode 100644 index 0000000..1b6985c --- /dev/null +++ b/lipid_validation/mslibrary-lipid-validator/.gitignore @@ -0,0 +1,5 @@ +# Ignore Gradle project-specific cache directory +.gradle + +# Ignore Gradle build output directory +build diff --git a/lipid_validation/mslibrary-lipid-validator/app/build.gradle b/lipid_validation/mslibrary-lipid-validator/app/build.gradle new file mode 100644 index 0000000..f403cd1 --- /dev/null +++ b/lipid_validation/mslibrary-lipid-validator/app/build.gradle @@ -0,0 +1,83 @@ +/* + * 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' +} diff --git a/lipid_validation/mslibrary-lipid-validator/app/src/main/java/org/mzmine/mslibrary/lipid/validator/App.java b/lipid_validation/mslibrary-lipid-validator/app/src/main/java/org/mzmine/mslibrary/lipid/validator/App.java new file mode 100644 index 0000000..eb08043 --- /dev/null +++ b/lipid_validation/mslibrary-lipid-validator/app/src/main/java/org/mzmine/mslibrary/lipid/validator/App.java @@ -0,0 +1,27 @@ +/* + * 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); + } + } +} diff --git a/lipid_validation/mslibrary-lipid-validator/app/src/main/java/org/mzmine/mslibrary/lipid/validator/MsLibraryReader.java b/lipid_validation/mslibrary-lipid-validator/app/src/main/java/org/mzmine/mslibrary/lipid/validator/MsLibraryReader.java new file mode 100644 index 0000000..3c7b454 --- /dev/null +++ b/lipid_validation/mslibrary-lipid-validator/app/src/main/java/org/mzmine/mslibrary/lipid/validator/MsLibraryReader.java @@ -0,0 +1,64 @@ +/* + * 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"))); + } + +} diff --git a/lipid_validation/mslibrary-lipid-validator/app/src/main/resources/PNNL-LIPIDS-NEGATIVE-small.mgf b/lipid_validation/mslibrary-lipid-validator/app/src/main/resources/PNNL-LIPIDS-NEGATIVE-small.mgf new file mode 100644 index 0000000..aa274a0 --- /dev/null +++ b/lipid_validation/mslibrary-lipid-validator/app/src/main/resources/PNNL-LIPIDS-NEGATIVE-small.mgf @@ -0,0 +1,126 @@ +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 + + diff --git a/lipid_validation/mslibrary-lipid-validator/app/src/test/java/org/mzmine/mslibrary/lipid/validator/AppTest.java b/lipid_validation/mslibrary-lipid-validator/app/src/test/java/org/mzmine/mslibrary/lipid/validator/AppTest.java new file mode 100644 index 0000000..6e44398 --- /dev/null +++ b/lipid_validation/mslibrary-lipid-validator/app/src/test/java/org/mzmine/mslibrary/lipid/validator/AppTest.java @@ -0,0 +1,14 @@ +/* + * 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"); + } +} diff --git a/lipid_validation/mslibrary-lipid-validator/gradle/wrapper/gradle-wrapper.jar b/lipid_validation/mslibrary-lipid-validator/gradle/wrapper/gradle-wrapper.jar new file mode 100644 index 0000000..7f93135 Binary files /dev/null and b/lipid_validation/mslibrary-lipid-validator/gradle/wrapper/gradle-wrapper.jar differ diff --git a/lipid_validation/mslibrary-lipid-validator/gradle/wrapper/gradle-wrapper.properties b/lipid_validation/mslibrary-lipid-validator/gradle/wrapper/gradle-wrapper.properties new file mode 100644 index 0000000..3fa8f86 --- /dev/null +++ b/lipid_validation/mslibrary-lipid-validator/gradle/wrapper/gradle-wrapper.properties @@ -0,0 +1,7 @@ +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 diff --git a/lipid_validation/mslibrary-lipid-validator/gradlew b/lipid_validation/mslibrary-lipid-validator/gradlew new file mode 100755 index 0000000..1aa94a4 --- /dev/null +++ b/lipid_validation/mslibrary-lipid-validator/gradlew @@ -0,0 +1,249 @@ +#!/bin/sh + +# +# Copyright © 2015-2021 the original authors. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# + +############################################################################## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# +############################################################################## + +# Attempt to set APP_HOME + +# Resolve links: $0 may be a link +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac +done + +# This is normally unused +# shellcheck disable=SC2034 +APP_BASE_NAME=${0##*/} +# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036) +APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit + +# Use the maximum available, or set MAX_FD != -1 to use that value. +MAX_FD=maximum + +warn () { + echo "$*" +} >&2 + +die () { + echo + echo "$*" + echo + exit 1 +} >&2 + +# OS specific support (must be 'true' or 'false'). +cygwin=false +msys=false +darwin=false +nonstop=false +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; +esac + +CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar + + +# Determine the Java command to use to start the JVM. +if [ -n "$JAVA_HOME" ] ; then + if [ -x "$JAVA_HOME/jre/sh/java" ] ; then + # IBM's JDK on AIX uses strange locations for the executables + JAVACMD=$JAVA_HOME/jre/sh/java + else + JAVACMD=$JAVA_HOME/bin/java + fi + if [ ! -x "$JAVACMD" ] ; then + die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." + fi +else + JAVACMD=java + if ! command -v java >/dev/null 2>&1 + then + die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. + +Please set the JAVA_HOME variable in your environment to match the +location of your Java installation." + fi +fi + +# Increase the maximum file descriptors if we can. +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked. + # shellcheck disable=SC2039,SC3045 + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked. + # shellcheck disable=SC2039,SC3045 + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac +fi + +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. + +# For Cygwin or MSYS, switch paths to Windows format before running java +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) + + # Now convert the arguments - kludge to limit ourselves to /bin/sh + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) + fi + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg + done +fi + + +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' + +# Collect all arguments for the java command: +# * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments, +# and any embedded shellness will be escaped. +# * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be +# treated as '${Hostname}' itself on the command line. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# Stop when "xargs" is not available. +if ! command -v xargs >/dev/null 2>&1 +then + die "xargs is not available" +fi + +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# + +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' + +exec "$JAVACMD" "$@" diff --git a/lipid_validation/mslibrary-lipid-validator/gradlew.bat b/lipid_validation/mslibrary-lipid-validator/gradlew.bat new file mode 100644 index 0000000..93e3f59 --- /dev/null +++ b/lipid_validation/mslibrary-lipid-validator/gradlew.bat @@ -0,0 +1,92 @@ +@rem +@rem Copyright 2015 the original author or authors. +@rem +@rem Licensed under the Apache License, Version 2.0 (the "License"); +@rem you may not use this file except in compliance with the License. +@rem You may obtain a copy of the License at +@rem +@rem https://www.apache.org/licenses/LICENSE-2.0 +@rem +@rem Unless required by applicable law or agreed to in writing, software +@rem distributed under the License is distributed on an "AS IS" BASIS, +@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +@rem See the License for the specific language governing permissions and +@rem limitations under the License. +@rem + +@if "%DEBUG%"=="" @echo off +@rem ########################################################################## +@rem +@rem Gradle startup script for Windows +@rem +@rem ########################################################################## + +@rem Set local scope for the variables with windows NT shell +if "%OS%"=="Windows_NT" setlocal + +set DIRNAME=%~dp0 +if "%DIRNAME%"=="" set DIRNAME=. +@rem This is normally unused +set APP_BASE_NAME=%~n0 +set APP_HOME=%DIRNAME% + +@rem Resolve any "." and ".." in APP_HOME to make it shorter. +for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi + +@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m" + +@rem Find java.exe +if defined JAVA_HOME goto findJavaFromJavaHome + +set JAVA_EXE=java.exe +%JAVA_EXE% -version >NUL 2>&1 +if %ERRORLEVEL% equ 0 goto execute + +echo. +echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:findJavaFromJavaHome +set JAVA_HOME=%JAVA_HOME:"=% +set JAVA_EXE=%JAVA_HOME%/bin/java.exe + +if exist "%JAVA_EXE%" goto execute + +echo. +echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% +echo. +echo Please set the JAVA_HOME variable in your environment to match the +echo location of your Java installation. + +goto fail + +:execute +@rem Setup the command line + +set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar + + +@rem Execute Gradle +"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %* + +:end +@rem End local scope for the variables with windows NT shell +if %ERRORLEVEL% equ 0 goto mainEnd + +:fail +rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of +rem the _cmd.exe /c_ return code! +set EXIT_CODE=%ERRORLEVEL% +if %EXIT_CODE% equ 0 set EXIT_CODE=1 +if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE% +exit /b %EXIT_CODE% + +:mainEnd +if "%OS%"=="Windows_NT" endlocal + +:omega diff --git a/lipid_validation/mslibrary-lipid-validator/settings.gradle b/lipid_validation/mslibrary-lipid-validator/settings.gradle new file mode 100644 index 0000000..ba7a857 --- /dev/null +++ b/lipid_validation/mslibrary-lipid-validator/settings.gradle @@ -0,0 +1,14 @@ +/* + * This file was generated by the Gradle 'init' task. + * + * The settings file is used to specify which projects to include in your build. + * For more detailed information on multi-project builds, please refer to https://docs.gradle.org/8.4/userguide/building_swift_projects.html in the Gradle documentation. + */ + +plugins { + // Apply the foojay-resolver plugin to allow automatic download of JDKs + id 'org.gradle.toolchains.foojay-resolver-convention' version '0.7.0' +} + +rootProject.name = 'mslibrary-lipid-validator' +include('app')