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Merge pull request #1321 from virtualcell/BioFormatsFix
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Bio formats fix
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@jcschaff
jcschaff authored Jul 16, 2024
2 parents fb949ea + f593b3e commit 126bde7
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Showing 10 changed files with 799 additions and 288 deletions.
12 changes: 6 additions & 6 deletions docker/build/installers/VCell.install4j
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<launcher name="VCell-${compiler:Site}-MacOSX" id="102" icnsFile="${compiler:vcellIcnsFile}">
<executable name="VCell-${compiler:Site}" iconSet="true" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
<splashScreen show="true" bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" textOverlay="true" />
<java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<classPath>
<variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
</classPath>
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<launcher name="VCell-${compiler:Site}-Windows64" id="345" icnsFile="${compiler:vcellIcnsFile}">
<executable name="VCell-${compiler:Site}" iconSet="true" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
<splashScreen show="true" bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" textOverlay="true" />
<java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<classPath>
<variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
</classPath>
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<launcher name="VCell-${compiler:Site}-Windows32" id="447" icnsFile="${compiler:vcellIcnsFile}">
<executable name="VCell-${compiler:Site}" iconSet="true" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
<splashScreen show="true" bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" textOverlay="true" />
<java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<classPath>
<variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
</classPath>
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<launcher name="VCell-${compiler:Site}-Linux32" id="534" icnsFile="${compiler:vcellIcnsFile}">
<executable name="VCell-${compiler:Site}" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
<splashScreen bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" />
<java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<classPath>
<variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
</classPath>
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<launcher name="VCell-${compiler:Site}-Linux64" id="627" icnsFile="${compiler:vcellIcnsFile}">
<executable name="VCell-${compiler:Site}" failOnStderrOutput="false" executableMode="gui" checkConsoleParameter="true" dpiAware="false" />
<splashScreen bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" />
<java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<java mainClass="cbit.vcell.client.VCellClientMain" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<classPath>
<variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
</classPath>
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<launcher name="VCell-${compiler:Site}-Linux64-sbmltovcml" id="1880" excludeFromMenu="true">
<executable name="VCell-${compiler:Site}-sbmltovcml" iconSet="true" redirectStderr="false" failOnStderrOutput="false" executableMode="console" checkConsoleParameter="true" dpiAware="false" />
<splashScreen bitmapFile="${compiler:vcell5SplashScreenPngFilePath}" />
<java mainClass="org.vcell.sbml.SbmlVcmlConverter" vmParameters="&quot;-Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<java mainClass="org.vcell.sbml.SbmlVcmlConverter" vmParameters="&quot;--add-exports java.desktop/sun.awt.image=ALL-UNNAMED -Dvcell.installDir=${launcher:sys.launcherDirectory}&quot;">
<classPath>
<variable name="vcellClasspathColonSep" separator=":" useRelativePrefix="true" relativePrefix="lib" />
</classPath>
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8 changes: 4 additions & 4 deletions pom.xml
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Expand Up @@ -99,8 +99,7 @@
<axis-wsdl4j.version>1.2</axis-wsdl4j.version>
<bcprov-jdk15on.version>1.70</bcprov-jdk15on.version>
<bcpkix-jdk15on.version>1.70</bcpkix-jdk15on.version>
<bio-formats.version>6.7.0</bio-formats.version>
<bio-formats_plugins.version>${bio-formats.version}</bio-formats_plugins.version>
<bio-formats.version>6.1.1</bio-formats.version>
<biojava.version>6.0.4</biojava.version>
<biomodels-wslib.version>1.21</biomodels-wslib.version>
<colt.version>1.2.0</colt.version>
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<jhdf5.version>0.7.0-alpha</jhdf5.version>
<jhdf5-2-10.version>2.9</jhdf5-2-10.version>
<jmatio.version>1.0</jmatio.version>
<joda-time.version>2.3</joda-time.version>
<joda-time.version>2.12.2</joda-time.version>
<jai-core.version>1.1.3</jai-core.version>
<javax-mail.version>1.4</javax-mail.version>
<jsbml.version>1.6.1</jsbml.version>
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<sesame-rio-n3.version>2.9.0</sesame-rio-n3.version>
<slf4j-api.version>2.0.9</slf4j-api.version>
<sshj.version>0.35.0</sshj.version>
<xercesImpl.version>2.8.0</xercesImpl.version>
<xercesImpl.version>2.8.1</xercesImpl.version>
<xstream.version>1.4.20</xstream.version>
<xalan.version>2.7.3</xalan.version>
<xom.version>1.2.5</xom.version>

<!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
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4 changes: 4 additions & 0 deletions vcell-api/pom.xml
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Expand Up @@ -151,6 +151,10 @@
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
</exclusion>
<exclusion>
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- <dependency>-->
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6 changes: 6 additions & 0 deletions vcell-client/pom.xml
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Expand Up @@ -150,6 +150,12 @@
<artifactId>picocli</artifactId>
<version>${picocli.version}</version>
</dependency>

<dependency>
<groupId>xalan</groupId>
<artifactId>xalan</artifactId>
<version>${xalan.version}</version>
</dependency>

<dependency>
<groupId>org.eclipse.jetty</groupId>
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95 changes: 94 additions & 1 deletion vcell-core/pom.xml
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Expand Up @@ -277,7 +277,82 @@
<artifactId>commons-lang3</artifactId>
<version>3.13.0</version>
</dependency>

<!-- https://mvnrepository.com/artifact/org.openmicroscopy/ome-common -->
<dependency>
<groupId>org.openmicroscopy</groupId>
<artifactId>ome-common</artifactId>
<version>6.0.22</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</exclusion>
<exclusion>
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- https://mvnrepository.com/artifact/com.github.ome.bioformats/formats-bsd -->
<dependency>
<groupId>com.github.ome.bioformats</groupId>
<artifactId>formats-bsd</artifactId>
<version>${bio-formats.version}</version>
<exclusions>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
</exclusion>
<exclusion>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</exclusion>
<exclusion>
<groupId>joda-time</groupId>
<artifactId>joda-time</artifactId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
</exclusion>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</exclusion>
<exclusion>
<groupId>org.openmicroscopy</groupId>
<artifactId>ome-common</artifactId>
</exclusion>
<exclusion>
<groupId>xalan</groupId>
<artifactId>xalan</artifactId>
</exclusion>
<exclusion>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>kryo</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-configuration2</artifactId>
Expand Down Expand Up @@ -337,6 +412,12 @@
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
<version>${jaxen.version}</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.sbml.jsbml</groupId>
Expand Down Expand Up @@ -518,10 +599,22 @@
<artifactId>xom</artifactId>
<version>${xom.version}</version>
<exclusions>
<exclusion>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
</exclusion>
<exclusion>
<groupId>org.bouncycastle</groupId>
<artifactId>bctsp-jdk14</artifactId>
</exclusion>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
<exclusion>
<groupId>xalan</groupId>
<artifactId>xalan</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
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