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Updated POM

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working POM for build with Tethys. Note though that it's failing to get
rid of all signature files in the \META-INF\ folder, so the two files
META-INF\ECLIPSE_.SF and META-INF\ECLIPSE_.RSA must be removed before
the jar file can be used.
This commit is contained in:
Douglas Gillespie 2023-12-19 12:45:56 +00:00
commit ea6caecc67
7 changed files with 853 additions and 711 deletions
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5
.classpath
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@ -6,8 +6,9 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/jre">
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-11">
<attributes>
<attribute name="module" value="true"/>
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
@ -16,7 +17,5 @@
<attribute name="maven.pomderived" value="true"/>
</attributes>
</classpathentry>
<classpathentry combineaccessrules="false" kind="src" path="/nilusxmlgenerator"/>
<classpathentry combineaccessrules="false" kind="src" path="/TethysJavaClient"/>
<classpathentry kind="output" path="target/classes"/>
</classpath>

5
dependency-reduced-pom.xml
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@ -17,6 +17,7 @@
<resource>
<directory>src</directory>
<excludes>
<exclude>META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA</exclude>
<exclude>**/*.java</exclude>
<exclude>jars/*.*</exclude>
</excludes>
@ -196,6 +197,10 @@
<properties>
<maven.compiler.target>11</maven.compiler.target>
<maven.compiler.source>11</maven.compiler.source>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<javafx.version>16</javafx.version>
<jaxb.runtime.version>2.4.0-b180830.0438</jaxb.runtime.version>
<jaxb.xjc.version>2.4.0-b180830.0438</jaxb.xjc.version>
<jaxb.api.version>2.4.0-b180830.0359</jaxb.api.version>
</properties>
</project>

1477
pom.xml
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File diff suppressed because it is too large Load Diff

6
src/PamController/PamguardVersionInfo.java
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@ -24,19 +24,19 @@ public class PamguardVersionInfo {
* PAMGuard can work with.
*/
static public final String minJavaVersion = "11.0.0";
static public final String maxJavaVersion = "19.99.99";
static public final String maxJavaVersion = "21.99.99";
/**
* Version number, major version.minorversion.sub-release.
* Note: can't go higher than sub-release 'f'
*/
static public final String version = "2.02.09c";
static public final String version = "2.02.09f";
/**
* Release date
*/
static public final String date = "10 November 2023";
static public final String date = "18 December 2023";
// /**
// * Release type - Beta or Core

22
src/help/utilities/tethys/docs/tethys_overview.html
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@ -37,15 +37,29 @@ img {
experimental efforts based on a common attribute. This resulting
database can then be queried based on time, space, or any desired
attribute and the results can be integrated with external datasets
such as NASA’s Ocean Color, lunar illumination, etc. in a consistent
such as NASA's Ocean Color, lunar illumination, etc. in a consistent
manner. While Tethys is designed primarily for acoustic metadata from
marine mammals, the design is general enough to permit use in other
areas as well.
</p>
<br>
<br>
<p class="nextLink">
<p>PAMGuard is compatible with Tethys 3.0, released early in 2024. </p>
<p>The Tethys database is not a replacement for the existing
<a href="../../generalDatabaseHelp/docs/database_database.html">PAMGuard Database.</a>
Where the PAMGuard database only contains data from a single instrument or cruise, the Tethys
database contains data from many cruises and projects and can be used to hold a summary of all data
from a lab or organisation.
</p>
<p>Before using the module in PAMGuard, you should install the Tethys Server, which runs under
Windows. <a href="https://tethys.sdsu.edu/install/">
Instructions for installing the Tethys Server can be found here.</a></p>
<br><br>
<a href="tethys_configure.html">Next: Configuring the Tethys
Module</a>
</p>

41
src/pamguard/Pamguard.java
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@ -717,6 +717,47 @@ public class Pamguard {
}
}
}
/*
* Some bits that need added to Maven POM.
*
<!-- From NilusXMLGenerator POM at https://bitbucket.org/tethysacousticmetadata/nilusxmlgenerator/src/master/-->
<dependency>
<groupId>org.eclipse.persistence</groupId>
<artifactId>org.eclipse.persistence.moxy</artifactId>
<version>2.5.0</version>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.4.0-b180830.0359</version>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>2.4.0-b180830.0438</version>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-xjc</artifactId>
<version>2.4.0-b180830.0438</version>
</dependency>
<!-- Also not in Maven, so you may need to copy the javaclient and nilus folders from
e.g. C:\Users\dg50\source\repos\**your projectfolder**\repo\tethys\org
to C:\Users\dg50\.m2\repository\tethys\org
<dependency>
<groupId>tethys.org</groupId>
<artifactId>nilus</artifactId>
<version>3.0</version>
</dependency>
<dependency>
<groupId>tethys.org</groupId>
<artifactId>javaclient</artifactId>
<version>3.0</version>
</dependency>-->
*/
}

8
src/whistlesAndMoans/StubRemover.java
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@ -82,7 +82,13 @@ public class StubRemover {
private int searchStubSize(List<SliceData> sliceData, int currentSlice, int peakInd, int searchDir, int diagGap, int currentSize) {
int nSlice = sliceData.size();
int nextSliceInd = currentSlice + searchDir;
if (nextSliceInd < 0 || nextSliceInd >= nSlice-1) {
/**
* This function is only every used to throw away very small stubs, so there is no need to get the full size
* of every one. It's OK to return as soon as the size is bigger than the minimum required to make
* something worth keeping. This reduces the time spent tracing down every little alley which was
* severely impacting performance for larger whistles.
*/
if (nextSliceInd < 0 || nextSliceInd >= nSlice-1 || currentSize > whistleControl.getWhistleToneParameters().minPixels) {
return currentSize;
}
SliceData nextSlice = sliceData.get(nextSliceInd);