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First commit of unit test changes. Added more manual unit tests, an E…
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…voSuite regression set and coverage reporting. Moved Java version for Artemis to Java 8. Ripped out redundant Corba code.
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@kpepper
kpepper committed Oct 2, 2017
1 parent 50c7da3 commit 695d03a
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5 changes: 4 additions & 1 deletion .classpath
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Original file line number Diff line number Diff line change
@@ -1,9 +1,11 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="corba"/>
<classpathentry including="uk" kind="src" path="test"/>
<classpathentry excluding="main/" kind="src" path="ant-build/src"/>
<classpathentry kind="src" path="lib"/>
<classpathentry including="nsdb/|seqdb/|type/" kind="src" path="ant-build/src/main"/>
<classpathentry excluding="ant-build/src/main/|uk/ac/sanger/artemis/ExternalProgramUtils.java" including="nsdb/|org/|seqdb/|type/|uk/" kind="src" path=""/>
<classpathentry excluding="ant-build/src/|ant-build/src/main/|uk/ac/sanger/artemis/ExternalProgramUtils.java|test/" including="nsdb/|org/|seqdb/|type/|uk/" kind="src" path=""/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="lib" path="lib/jemAlign.jar"/>
<classpathentry kind="lib" path="lib/jakarta-regexp-1.2.jar"/>
Expand All @@ -25,5 +27,6 @@
<classpathentry kind="lib" path="lib/batik/batik-util.jar"/>
<classpathentry kind="lib" path="lib/batik/batik-xml.jar"/>
<classpathentry kind="lib" path="lib/commons-lang-2.6.jar"/>
<classpathentry kind="lib" path="test/lib/junit-4.11.jar"/>
<classpathentry kind="output" path="ant-build/classes/main"/>
</classpath>
5 changes: 5 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1 +1,6 @@
*.class
.settings
ant-build
test/ant-build
**/.DS_Store
**/*.log
37 changes: 11 additions & 26 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ SHELL=/bin/sh

#OPT_FLAGS = -g -deprecation

JAVAC := javac -source 1.5 -target 1.5 $(OPT_FLAGS) $(EXTRA_FLAGS)
JAVAC := javac -source 1.8 -target 1.8 $(OPT_FLAGS) $(EXTRA_FLAGS)

REAL_CLASSPATH := CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/picard/sam.jar:lib/commons-net-2.2.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:.

Expand All @@ -31,35 +31,20 @@ uk/ac/sanger/artemis/util
SOURCES := $(foreach DIR,$(ARTEMIS_DIRS),$(wildcard $(DIR)/*.java))
CLASSES := $(SOURCES:%.java=%.class)

all: idl code
all: code

# Utils needs to be built before controller
uk/ac/sanger/artemis/circular/digest/CircularGenomeController.class:uk/ac/sanger/artemis/circular/digest/Utils.class
$(REAL_CLASSPATH) $(JAVAC) $(@:%.class=%.java)

code: $(CLASSES)

topdown: idl
topdown:
$(REAL_CLASSPATH) $(JAVAC) uk/ac/sanger/artemis/components/ArtemisMain.java

%.class : %.java
$(REAL_CLASSPATH) $(JAVAC) $<

idl : type/*.java nsdb/*.java seqdb/*.java

IDL = idlj
IDLCMD = $(IDL) -Icorba

type/*.java : corba/types.idl
$(IDLCMD) corba/types.idl

nsdb/*.java : corba/nsdb.idl corba/nsdb_write.idl
$(IDLCMD) corba/nsdb.idl
$(IDLCMD) corba/nsdb_write.idl

seqdb/*.java : corba/seqdb.idl
$(IDLCMD) corba/seqdb.idl

doc :
$(REAL_CLASSPATH) javadoc -J-mx200m -version \
AppGlobal.java \
Expand All @@ -70,7 +55,7 @@ doc :
manual :
(cd docs; make)

CLASS_FILES := `find org uk nsdb type seqdb -name '*.class' -print`
CLASS_FILES := `find org uk -name '*.class' -print`

OTHER_FILES := `find images/PSUlogo.gif images/icon.gif COPYING README.md`

Expand All @@ -79,8 +64,8 @@ dist :
mkdir tar_build
mkdir tar_build/artemis
rm -f artemis_compiled_latest.tar.gz
tar cf - $(OTHER_FILES) act art Makefile corba etc | (cd tar_build/artemis; tar xf -)
tar cf - artemis_sqlmap dnaplotter uk org nsdb type seqdb lib | (cd tar_build/artemis; tar xf -)
tar cf - $(OTHER_FILES) act art Makefile etc | (cd tar_build/artemis; tar xf -)
tar cf - artemis_sqlmap dnaplotter uk org lib | (cd tar_build/artemis; tar xf -)
(cd tar_build; find . -name 'CVS' -print | xargs rm -rf; find . -name '.svn' -print | xargs rm -rf; tar cvf ../artemis_compiled.tar artemis)

jar : all artemis.jar
Expand Down Expand Up @@ -111,28 +96,28 @@ artemis.jar : $(CLASSES)
rm -rf META-INF/MANIFEST.MF; \
done; \
fi; \
cp -R ../lib/LICENSE.Apache ../uk ../org ../nsdb ../type ../seqdb ../etc ../images ../lib/j2ssh/j2ssh.properties \
cp -R ../lib/LICENSE.Apache ../uk ../org ../etc ../images ../lib/j2ssh/j2ssh.properties \
../images/PSUlogo.gif ../images/icon.gif ../README.md ../artemis_sqlmap .
find jar_build -name '*.java' -print | xargs rm -f
find jar_build -name '.svn' -print | xargs rm -rf
cd jar_build; \
rm -rf META-INF/MANIFEST.MF; \
echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions" > manifest-art; \
jar cmf manifest-art artemis.jar META-INF/services images/PSUlogo.gif images/icon.gif README.md etc \
artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
artemis_sqlmap org uk com net LICENSE.Apache j2ssh.properties; \
echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \
jar cmf manifest-circular DNAPlotter.jar images/PSUlogo.gif README.md etc \
uk org/gmod org/w3c org/apache org/biojava/bio/ com/ibatis/common/jdbc/ net/sf/samtools/ LICENSE.Apache j2ssh.properties; \
echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \
jar cmf manifest-bamview BamView.jar META-INF/services etc uk org/apache org/biojava org/biojavax org/gmod org/w3c net/sf com/ibatis; \
echo "Main-Class: uk.ac.sanger.artemis.components.ActMain\nPermissions: all-permissions" > manifest-act; \
jar cmf manifest-act act.jar META-INF/services images/PSUlogo.gif images/icon.gif README.md etc \
artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
artemis_sqlmap org uk com net LICENSE.Apache j2ssh.properties; \
rm -f etc/log4j.properties; \
jar cmf manifest-art artemis_mac.jar images/PSUlogo.gif images/icon.gif README.md \
uk org/gmod nsdb type seqdb LICENSE.Apache artemis_sqlmap
uk org/gmod LICENSE.Apache artemis_sqlmap

clean :
-rm -rf *.html artemis.jar seqdb nsdb type resources uk/ac/sanger/jcon/ jar_build tar_build artemis_compiled.tar
-rm -rf *.html artemis.jar resources uk/ac/sanger/jcon/ jar_build tar_build artemis_compiled.tar
-rm -rf TAGS* *.o
-find . -name '*.class' -print | xargs rm -f
26 changes: 8 additions & 18 deletions build.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -95,32 +95,17 @@
</target>

<target name="prepare-src" depends="init,prepare-core" />

<!-- Compile IDL stub classes into the build directory (jar preparation) -->
<target name="compile-idl" depends="init,prepare-core">
<exec executable="idlj" dir="${build.src.main}">
<arg line="-Icorba corba/types.idl" />
</exec>
<exec executable="idlj" dir="${build.src.main}">
<arg line="-Icorba corba/nsdb.idl" />
</exec>
<exec executable="idlj" dir="${build.src.main}">
<arg line="-Icorba corba/nsdb_write.idl" />
</exec>
<exec executable="idlj" dir="${build.src.main}">
<arg line="-Icorba corba/seqdb.idl" />
</exec>
</target>

<!-- Compiles the source directory -->
<target name="compile" depends="init,compile-idl,prepare-src">
<target name="compile" depends="init,print-version,prepare-src">
<javac
target="1.8"
fork="true"
memoryinitialsize="256m"
memorymaximumsize="256m"
srcdir="${build.src.main}"
destdir="${build.dest.main}"
excludes="nsdb/**,seqdb/**,type/**,lib/**,src/**,uk/ac/sanger/artemis/components/MacHandler.java,uk/ac/sanger/artemis/components/filetree/FileTree.java,uk/ac/sanger/artemis/components/filetree/SshFileTree.java,uk/ac/sanger/artemis/ExternalProgramUtils.java"
excludes="lib/**,src/**,uk/ac/sanger/artemis/components/MacHandler.java,uk/ac/sanger/artemis/components/filetree/FileTree.java,uk/ac/sanger/artemis/components/filetree/SshFileTree.java,uk/ac/sanger/artemis/ExternalProgramUtils.java"
deprecation="false"
depend="no"
debug="true">
Expand Down Expand Up @@ -163,4 +148,9 @@
<delete file="${name}-${version}.tar" />
<delete file="${name}-${version}.zip" />
</target>

<target name="print-version">
<echo>Java/JVM version: ${ant.java.version}</echo>
<echo>Java/JVM detail version: ${java.version}</echo>
</target>
</project>
206 changes: 0 additions & 206 deletions corba/apollo.idl
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