[med-svn] [Git][med-team/megan-ce][master] 6 commits: Skipping biom2 classes to avoid importing classes of sis-jhdf5

Pierre Gruet (@pgt) gitlab at salsa.debian.org
Sun Sep 8 14:47:14 BST 2024



Pierre Gruet pushed to branch master at Debian Med / megan-ce


Commits:
196aa1e5 by Pierre Gruet at 2024-09-08T13:10:11+02:00
Skipping biom2 classes to avoid importing classes of sis-jhdf5

- - - - -
5f880596 by Pierre Gruet at 2024-09-08T13:10:33+02:00
Raising Standards version to 4.7.0 (no change)

- - - - -
042acfa8 by Pierre Gruet at 2024-09-08T13:13:10+02:00
Adding url and developer_name fields to the MetaInfo file

- - - - -
387ca35f by Pierre Gruet at 2024-09-08T13:13:46+02:00
Skipping biom2 when copying sources

- - - - -
327eb116 by Pierre Gruet at 2024-09-08T15:11:30+02:00
Removing sis-jhdf5 jar from manifest

- - - - -
c2c5d356 by Pierre Gruet at 2024-09-08T15:12:34+02:00
Upload to unstable

- - - - -


8 changed files:

- debian/changelog
- debian/control
- debian/megan-ce.manifest
- debian/metainfo/io.github.danielhuson.megan_community_edition.metainfo.xml
- − debian/patches/altering_calls_to_sis-jhdf5.patch
- debian/patches/fix_class_path.patch
- + debian/patches/no_hdf5.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+megan-ce (6.21.1+dfsg-4) unstable; urgency=medium
+
+  * Stopping (build-)depending on libsis-jhdf5-java:
+    - Skipping biom2 classes to avoid importing classes of sis-jhdf5
+    - Removing sis-jhdf5 jar from the manifest
+  * Raising Standards version to 4.7.0 (no change)
+  * Adding url and developer_name fields to the MetaInfo file
+
+ -- Pierre Gruet <pgt at debian.org>  Sun, 08 Sep 2024 15:11:35 +0200
+
 megan-ce (6.21.1+dfsg-3) unstable; urgency=medium
 
   * Fixing the clean target (Closes: #1046802)


=====================================
debian/control
=====================================
@@ -16,9 +16,8 @@ Build-Depends: debhelper-compat (= 13),
                libgoogle-gson-java,
                libjbcrypt-java,
                libopenjfx-java,
-               libsis-jhdf5-java,
                libxerial-sqlite-jdbc-java
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/megan-ce
 Vcs-Git: https://salsa.debian.org/med-team/megan-ce.git
 Homepage: https://github.com/danielhuson/megan-ce
@@ -31,7 +30,6 @@ Depends: default-jre,
          libjloda-java,
          libjbcrypt-java,
          libopenjfx-java,
-         libsis-jhdf5-java,
          libxerial-sqlite-jdbc-java,
          ${misc:Depends}
 Description: interactive tool to explore and analyse microbiome sequencing data


=====================================
debian/megan-ce.manifest
=====================================
@@ -1,3 +1,3 @@
 /usr/share/java/megan.jar:
  Main-Class: megan.main.Megan6
- Class-Path: /usr/share/java/colt.jar /usr/share/java/commons-math3.jar /usr/share/java/gson.jar /usr/share/java/jama.jar /usr/share/java/javafx-base.jar /usr/share/java/javafx-controls.jar /usr/share/java/javafx-fxml.jar /usr/share/java/javafx-graphics.jar /usr/share/java/javafx-swing.jar /usr/share/java/jbcrypt.jar /usr/share/java/jloda.jar /usr/share/java/sis-jhdf5.jar /usr/share/java/xerial-sqlite-jdbc.jar
+ Class-Path: /usr/share/java/colt.jar /usr/share/java/commons-math3.jar /usr/share/java/gson.jar /usr/share/java/jama.jar /usr/share/java/javafx-base.jar /usr/share/java/javafx-controls.jar /usr/share/java/javafx-fxml.jar /usr/share/java/javafx-graphics.jar /usr/share/java/javafx-swing.jar /usr/share/java/jbcrypt.jar /usr/share/java/jloda.jar /usr/share/java/xerial-sqlite-jdbc.jar


=====================================
debian/metainfo/io.github.danielhuson.megan_community_edition.metainfo.xml
=====================================
@@ -7,6 +7,9 @@
   
   <metadata_license>CC-BY-4.0</metadata_license>
   <project_license>GPL-3.0-or-later</project_license>
+
+  <url type="homepage">https://github.com/husonlab/megan-ce</url>
+  <developer_name>Daniel H. Huson</developer_name>
   
   <description>
     <p>


=====================================
debian/patches/altering_calls_to_sis-jhdf5.patch deleted
=====================================
@@ -1,63 +0,0 @@
-Description: rewriting some calls to classes of sis-jhdf5
- Many times methods are called, which are not in the class of the object they
- are applied to. We implement the right calls.
-Author: Pierre Gruet <pgt at debian.org>
-Forwarded: https://github.com/husonlab/megan-ce/issues/16
-Last-Update: 2022-01-15
-
---- a/src/megan/biom/biom2/Biom2ParserTest.java
-+++ b/src/megan/biom/biom2/Biom2ParserTest.java
-@@ -73,7 +73,7 @@
-                     classifications.add(taxonomyNameMetadata);
-                     // System.err.println("Elements:  " + reader.getDataSetInformation("/observation/metadata/"+taxonomyNameMetadata).getNumberOfElements());
- 
--                    final MDArray<String> array = reader.readStringMDArray("/observation/metadata/" + taxonomyNameMetadata);
-+                    final MDArray<String> array = reader.string().readMDArray("/observation/metadata/" + taxonomyNameMetadata);
-                     /*
-                     int[] dimensions = array.dimensions();
-                     if (dimensions.length == 2) {
---- a/src/megan/biom/biom2/ImportBiom2Taxonomy.java
-+++ b/src/megan/biom/biom2/ImportBiom2Taxonomy.java
-@@ -48,7 +48,7 @@
- 
-         for (final String metaKey : reader.getGroupMembers("/observation/metadata")) {
-             if (Basic.getIndexIgnoreCase(metaKey, keys) != -1) {
--                pathArray = reader.readStringMDArray("/observation/metadata/" + metaKey);
-+                pathArray = reader.string().readMDArray("/observation/metadata/" + metaKey);
-                 dimensions = pathArray.dimensions();
-                 if (dimensions != null && dimensions.length > 0)
-                     break;
-@@ -111,7 +111,7 @@
-     public static boolean hasTaxonomyMetadata(IHDF5Reader reader) {
-         for (final String metaKey : reader.getGroupMembers("/observation/metadata")) {
-             if (Basic.getIndexIgnoreCase(metaKey, keys) != -1) {
--                final MDArray<String> pathArray = reader.readStringMDArray("/observation/metadata/" + metaKey);
-+                final MDArray<String> pathArray = reader.string().readMDArray("/observation/metadata/" + metaKey);
-                 final int[] dimensions = pathArray.dimensions();
-                 if (dimensions != null && dimensions.length > 0)
-                     return true;
---- a/src/megan/biom/biom2/TopLevelAttributes.java
-+++ b/src/megan/biom/biom2/TopLevelAttributes.java
-@@ -93,14 +93,14 @@
-      */
-     private void read(IHDF5Reader reader) throws IOException {
-         try {
--            id = reader.getStringAttribute("/", "id");
--            type = reader.getStringAttribute("/", "type");
--            formatURL = reader.getStringAttribute("/", "format-url");
--            formatVersion = reader.getIntArrayAttribute("/", "format-version");
--            generatedBy = reader.getStringAttribute("/", "generated-by");
--            creationDate = reader.getStringAttribute("/", "creation-date");
--            shape = reader.getIntArrayAttribute("/", "shape");
--            nnz = reader.getIntAttribute("/", "nnz");
-+            id = reader.string().getAttr("/", "id");
-+            type = reader.string().getAttr("/", "type");
-+            formatURL = reader.string().getAttr("/", "format-url");
-+            formatVersion = reader.int32().getArrayAttr("/", "format-version");
-+            generatedBy = reader.string().getAttr("/", "generated-by");
-+            creationDate = reader.string().getAttr("/", "creation-date");
-+            shape = reader.int32().getArrayAttr("/", "shape");
-+            nnz = reader.int32().getAttr("/", "nnz");
-         } catch (Exception ex) {
-             System.err.println("BIOM2 parser: Some required top-level attribute(s) missing.");
-             throw new IOException(ex);


=====================================
debian/patches/fix_class_path.patch
=====================================
@@ -5,7 +5,7 @@ Forwarded: not-needed
 
 --- a/antbuild/build.xml
 +++ b/antbuild/build.xml
-@@ -22,22 +22,30 @@
+@@ -22,22 +22,29 @@
  		<property name="ant.build.javac.target" value="13"/>-->
  
  		<property name="jfxDir" value="../../javafx/lib"/>
@@ -26,7 +26,6 @@ Forwarded: not-needed
 +                        <fileset dir="/usr/share/java/"  includes="javafx-swing.jar"/>
 +			<fileset dir="/usr/share/java/"  includes="jbcrypt.jar"/>
 +			<fileset dir="/usr/share/java/"  includes="jloda.jar"/>
-+                        <fileset dir="/usr/share/java/"  includes="sis-jhdf5.jar"/>
 +                        <fileset dir="/usr/share/java/"  includes="xerial-sqlite-jdbc.jar"/>
  		</path>
  
@@ -41,7 +40,7 @@ Forwarded: not-needed
  			<fileset dir="../antbuild"  includes="megan.jar"/>
  		</path>
  
-@@ -48,10 +56,6 @@
+@@ -48,10 +55,6 @@
  			<mkdir dir="${buildModulesDir}/megan"/>
  		</target>
  
@@ -52,7 +51,7 @@ Forwarded: not-needed
  		<target name="copy_sources" depends="init">
  			<copy todir="${buildSrcDir}/megan">
  				<fileset dir="../src"/>
-@@ -98,7 +102,6 @@
+@@ -98,7 +101,6 @@
  			<delete dir="${buildModulesDir}" includeEmptyDirs="true"/>
  			<delete dir="${buildSrcDir}" includeEmptyDirs="true"/>
  			<delete file="megan.jar"/>


=====================================
debian/patches/no_hdf5.patch
=====================================
@@ -0,0 +1,40 @@
+Description: omitting biom2 classes so that we don't need the classes from
+ sis-jhdf5
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: not-needed
+Last-Update: 2024-09-07
+
+--- a/antbuild/build.xml
++++ b/antbuild/build.xml
+@@ -57,7 +57,8 @@
+ 
+ 		<target name="copy_sources" depends="init">
+ 			<copy todir="${buildSrcDir}/megan">
+-				<fileset dir="../src"/>
++                <!-- Exluding biom2 to avoid importing sis-jhdf5 classes -->
++				<fileset dir="../src" excludes="**/biom2/*.java"/>
+ 			</copy>
+ 		</target>
+ 
+--- a/src/megan/commands/ImportBIOMCommand.java
++++ b/src/megan/commands/ImportBIOMCommand.java
+@@ -26,7 +26,6 @@
+ import jloda.util.ProgramProperties;
+ import jloda.util.parse.NexusStreamParser;
+ import megan.biom.biom1.BIOM1Importer;
+-import megan.biom.biom2.Biom2Importer;
+ import megan.core.Director;
+ import megan.core.Document;
+ import megan.inspector.InspectorWindow;
+@@ -82,8 +81,9 @@
+ 
+             if (BiomFileFilter.isBiom1File(fileName))
+                 BIOM1Importer.apply(fileName, doc, type, taxonomyIgnorePath);
+-            else if (BiomFileFilter.isBiom2File(fileName))
+-                Biom2Importer.apply(fileName, doc, type, taxonomyIgnorePath);
++            // Not supporting Biom2, which requires sis-jhdf5.
++            /*else if (BiomFileFilter.isBiom2File(fileName))
++                Biom2Importer.apply(fileName, doc, type, taxonomyIgnorePath);*/
+ 
+             if (dir.getViewerByClass(InspectorWindow.class) != null)
+                 ((InspectorWindow) dir.getViewerByClass(InspectorWindow.class)).clear();


=====================================
debian/patches/series
=====================================
@@ -4,4 +4,4 @@ do_not_check_for_update.patch
 no_module_info.patch
 omit_ComputeContrastsCommand.patch
 BCrypt_replacement.patch
-altering_calls_to_sis-jhdf5.patch
+no_hdf5.patch



View it on GitLab: https://salsa.debian.org/med-team/megan-ce/-/compare/dc6533d4830ee907045ccd05c04cc475f3b81eb7...c2c5d356501ca02f223951bdc3779f944ec13451

-- 
View it on GitLab: https://salsa.debian.org/med-team/megan-ce/-/compare/dc6533d4830ee907045ccd05c04cc475f3b81eb7...c2c5d356501ca02f223951bdc3779f944ec13451
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