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Updated dependencies to Java 17 #15

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Updated dependencies to Java 17 #15

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a61a49c
Updated dependencies to Java 17
nilshoffmann Dec 15, 2023
fdc228b
Add DIA workflow to CV table
bittremieux Oct 6, 2023
a78bfff
Add table for deconvoluted data
bittremieux Oct 6, 2023
2921e22
Update mzML1.1.1.xsd to use declared namespace
mobiusklein Dec 13, 2023
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10 changes: 5 additions & 5 deletions schema/schema_1.1/mzML1.1.1.xsd
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Expand Up @@ -542,11 +542,11 @@
<xs:annotation>
<xs:documentation>A unique string identifier for this run.</xs:documentation>
</xs:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:minLength value="1"/>
</xsd:restriction>
</xsd:simpleType>
<xs:simpleType>
<xs:restriction base="xs:string">
<xs:minLength value="1"/>
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name="defaultInstrumentConfigurationRef" type="xs:IDREF" use="required">
<xs:annotation>
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19 changes: 19 additions & 0 deletions specification_document/dia_workflow_cv.md
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@@ -0,0 +1,19 @@
Adjustments for **raw** DIA data such as SONAR, HDMSE, or diaPASEF data:

| Workflow | Description | CV term set |
| --- | --- | --- |
| MSE<br>AIF<br>p2cid | data independent acquisition from dissociation of full mass range | - data independent acquisition<br>- dissociation of full mass range |
| SONAR | data independent acquisition from dissociation of scanning quadrupole across mass range | - data independent acquisition<br>- dissociation of scanning quadrupole across a specified mass range |
| SWATH-MS<br>FT-ARM<br>HRM<br>PAcIFIC | data independent acquisition from dissociation of sequential mass ranges | - data independent acquisition<br>- dissociation of sequential mass ranges |
| diaPASEF | data independent acquisition from dissociation of sequential mass ranges separated by ion mobility | - data independent acquisition<br>- dissociation of sequential mass ranges<br>- ion mobility separation |
| HDMSE<br>IMS-AIF | data independent acquisition from dissociation of full mass range separated by ion mobility | - data independent acquisition<br>- dissociation of full mass range<br>- ion mobility separation |

Adjustments for **deconvoluted** DIA data such as SONAR or HDMSE data

| Workflow | Description | CV term set |
| --- | --- | --- |
| MSE<br>AIF<br>p2cid | data independent acquisition from dissociation of full mass range | - data independent acquisition<br>- dissociation of full mass range<br>- deconvoluted data |
| SONAR | data independent acquisition from dissociation of scanning quadrupole across mass range | - data independent acquisition<br>- dissociation of scanning quadrupole across a specified mass range<br>- deconvoluted data |
| SWATH-MS<br>FT-ARM<br>HRM<br>PAcIFIC | data independent acquisition from dissociation of sequential mass ranges | - data independent acquisition<br>- dissociation of sequential mass ranges<br>- deconvoluted data |
| diaPASEF | data independent acquisition from dissociation of sequential mass ranges separated by ion mobility | - data independent acquisition<br>- dissociation of sequential mass ranges<br>- ion mobility separation<br>- deconvoluted data |
| HDMSE<br>IMS-AIF | data independent acquisition from dissociation of full mass range separated by ion mobility | - data independent acquisition<br>- dissociation of full mass range<br>- ion mobility separation<br>- deconvoluted data |
223 changes: 119 additions & 104 deletions validator/pom.xml
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Expand Up @@ -21,57 +21,67 @@
<!-- Additions Florian -->

<build>
<!-- fix the versions of the plugins used in the build -->
<pluginManagement>
<!-- fix the versions of the plugins used in the build -->
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.3.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.11.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>3.5.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.1.2</version>
<configuration>
<argLine>--add-modules java.xml.bind</argLine>
<argLine>--add-modules java.activation</argLine>
<argLine>--add-opens=java.base/java.lang=ALL-UNNAMED --illegal-access=deny</argLine>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.5.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.4</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<!-- To compile with JDK5.0 -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.5</source>
<target>1.5</target>
<source>17</source>
<target>17</target>
</configuration>
</plugin>

<!-- Additions Florian -->
<!-- To copy the dependencies from the maven repository to the lib directory -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/${lib.dir}</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/${lib.dir}</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
</plugin>
<!-- Additions Florian -->

Expand Down Expand Up @@ -102,11 +112,11 @@
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
<id>make-assembly</id>
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
Expand All @@ -121,19 +131,19 @@
<build>
<plugins>
<!-- to create a executable jar to start the MzMLValidatorGUI -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>psidev.psi.ms.MzMLValidatorGUI</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>${lib.dir}</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>psidev.psi.ms.MzMLValidatorGUI</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>${lib.dir}</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
</profile>
Expand All @@ -143,17 +153,17 @@
<plugins>
<!-- to create a executable jar to start the MzMLSchemaValidator -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>psidev.psi.ms.MzMLSchemaValidator</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>${lib.dir}</classpathPrefix>
</manifest>
</archive>
</configuration>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>psidev.psi.ms.MzMLSchemaValidator</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>${lib.dir}</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
Expand All @@ -164,17 +174,17 @@
<plugins>
<!-- to create a executable jar to start the command line MzMLValidator -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>psidev.psi.ms.MzMLValidator</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>${lib.dir}</classpathPrefix>
</manifest>
</archive>
</configuration>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>psidev.psi.ms.MzMLValidator</mainClass>
<addClasspath>true</addClasspath>
<classpathPrefix>${lib.dir}</classpathPrefix>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
Expand All @@ -183,26 +193,18 @@
<!-- Additions Florian -->

<repositories>
<!-- removed java.net repositories, these are now mirrored in maven central -->
<!-- removed java.net repositories, these are now mirrored in maven central -->
<!-- EBI repositories -->
<repository>
<id>ebi-repo</id>
<name>The EBI internal repository</name>
<url>http://www.ebi.ac.uk/~maven/m2repo</url>
<releases>
<enabled>true</enabled>
</releases>
<id>nexus-ebi-release-repo</id>
<url>https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/</url>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>ebi-repo-snapshots</id>
<name>The EBI internal repository</name>
<url>http://www.ebi.ac.uk/~maven/m2repo_snapshots</url>
<releases>
<enabled>false</enabled>
</releases>
<id>nexus-ebi-snapshot-repo</id>
<url>https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-snapshots/</url>
<snapshots>
<enabled>true</enabled>
</snapshots>
Expand All @@ -213,27 +215,40 @@
<dependency>
<groupId>psidev.psi.tools</groupId>
<artifactId>validator</artifactId>
<version>2.0.3-SNAPSHOT</version>
<version>2.1.0</version>
</dependency>

<dependency>
<groupId>uk.ac.ebi.jmzml</groupId>
<artifactId>jmzml</artifactId>
<version>1.6.8-SNAPSHOT</version>
<version>1.7.11</version>
</dependency>

<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.1</version>
<scope>test</scope>
</dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.2</version>
<scope>test</scope>
</dependency>

<dependency>
<groupId>net.java.dev.swing-layout</groupId>
<artifactId>swing-layout</artifactId>
<version>1.0.2</version>
</dependency>
<dependency>
<groupId>net.java.dev.swing-layout</groupId>
<artifactId>swing-layout</artifactId>
<version>1.0.2</version>
</dependency>

<dependency>
<groupId>jakarta.annotation</groupId>
<artifactId>jakarta.annotation-api</artifactId>
<version>1.3.5</version>
</dependency>

<dependency>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>4.0.0</version>
</dependency>

</dependencies>

<distributionManagement>
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2 changes: 1 addition & 1 deletion validator/src/main/java/psidev/psi/ms/MzMLValidator.java
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Expand Up @@ -62,7 +62,7 @@
* This class represents the PSI mzML semantic validator.
*
* @author Lennart Martens, modified by Juan Antonio Vizcaino and Salvador
* Mart�nez
* Martinez
* @version $Id$
*/
public class MzMLValidator extends Validator {
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16 changes: 5 additions & 11 deletions validator/src/main/java/psidev/psi/ms/MzMLValidatorGUI.java
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Expand Up @@ -20,8 +20,6 @@
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JOptionPane;
import javax.swing.UIManager;
import javax.swing.UnsupportedLookAndFeelException;
import javax.swing.filechooser.FileFilter;
import javax.xml.bind.JAXBException;

Expand All @@ -33,10 +31,6 @@
import psidev.psi.tools.validator.ValidatorMessage;
import psidev.psi.tools.validator.util.ValidatorReport;

import com.sun.java.swing.plaf.windows.WindowsLookAndFeel;
import java.util.logging.Level;
import java.util.logging.Logger;

/**
*
* @author __USER__
Expand Down Expand Up @@ -885,11 +879,11 @@ public void setProgress(int value, String message) {
}

public static void main(String[] args) {
try {
UIManager.setLookAndFeel(new WindowsLookAndFeel());
} catch (UnsupportedLookAndFeelException e) {
System.out.println("No Windows lookAndFeel found");
}
// try {
// UIManager.setLookAndFeel(new WindowsLookAndFeel());
// } catch (UnsupportedLookAndFeelException e) {
// System.out.println("No Windows lookAndFeel found");
// }
MzMLValidatorGUI jpanValidator = new MzMLValidatorGUI();

if (args != null && args.length == 1) {
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3 changes: 1 addition & 2 deletions validator/src/main/java/psidev/psi/ms/mzml/mapping/jaxb/BinaryDataArrayType.java
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Expand Up @@ -8,7 +8,6 @@

package psidev.psi.ms.mzml.mapping.jaxb;

import com.sun.org.apache.xerces.internal.impl.dv.util.Base64;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
Expand Down Expand Up @@ -125,7 +124,7 @@ protected void create(Node node) {
// we only expect one such element!
if (nl.getLength() == 1) {
Node data = nl.item(0);
binary = Base64.decode(data.getTextContent());
binary = java.util.Base64.getDecoder().decode(data.getTextContent());
} else {
throw new IllegalStateException("Expected only one 'binary' element, but found: " + nl.getLength());
}
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