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Changed EBI DbFetch code so that the function works again. Added late…
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…st picard jar. More work on CRAM file loading. Updated/added scripts for application start. Small tweaks to makefile/ant. Removed gff2embl and gene_builder. Recreated evosuite tests.
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@kpepper
kpepper committed Jan 25, 2018
1 parent d058e6d commit c743a79
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3 changes: 1 addition & 2 deletions .classpath
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Expand Up @@ -23,10 +23,9 @@
<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="lib" path="lib/picard/htsjdk-2.12.0.jar" sourcepath="/Users/kp11/workspace/jarbuilds/htsjdk/src/main/java"/>
<classpathentry kind="lib" path="/Users/kp11/workspace/applications/Artemis/eclipse-classes"/>
<classpathentry kind="lib" path="test/evosuite-lib/evosuite-1.0.5.jar"/>
<classpathentry kind="lib" path="lib/commons-net-3.6.jar"/>
<classpathentry kind="lib" path="lib/picard/picard-2.13.2.jar"/>
<classpathentry kind="lib" path="lib/picard/picard.jar"/>
<classpathentry kind="output" path="eclipse-classes"/>
</classpath>
2 changes: 1 addition & 1 deletion .travis.yml
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Expand Up @@ -22,4 +22,4 @@ install:
- "$BUILD_CMD"
- "cd test"
- "ln -s $(pwd)/../etc/log4j.properties ."
script: ./RunManualUnitTestsOnly.sh | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ]
script: ./RunDefaultUnitTests.sh | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ]
2 changes: 1 addition & 1 deletion AUTHORS
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@@ -1,4 +1,4 @@
Kevin Pepper (path-help@sanger.ac.uk)
Tim Carver (path-help@sanger.ac.uk)
Sascha Steinbiss (path-help@sanger.ac.uk)
Kim Rutherford (path-help@sanger.ac.uk)
Kevin Pepper (path-help@sanger.ac.uk)
14 changes: 8 additions & 6 deletions ChangeLog
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Expand Up @@ -4,30 +4,32 @@ Version 17
BamView fixes/changes -
Improved mouse selection of reads.
Fixed exceptions thrown when zooming into an area with secondary reads or SNPs enabled - RT ticket #596489: Problem zooming in using isoseq data
Upgraded Samtools (htsjdk) and Picard libraries.
Removed Samtools (htsjdk) jar and updated Picard jar (which includes htsjdk).
Upgraded Apache Commons Net jar - used for ftp'ing.
Added Cram file loading and fixed defects around that code area (also related RT ticket #560982: Artemis fails to build from source).
Added display of bam secondary alignment flag to read details pop-up window.
Improved error handling/reporting for standalone BamView application.
Added buffer sizing to FTPSeekableStream.
Increased BAM file index creation speed.
Performance tweak for BAM file indexing.

Added EvoSuite unit tests and additional targeted tests (RT ticket #419534: Develop a test suite for Artemis).

Added Jacoco unit test coverage reporting - manual tests only currently. This may be switched to Clover in the future if this proves compatible with EvoSuite.

Removed redundant Corba libraries.

Upgraded Apache Commons Net jar to latest release.

Upgraded JUnit jar.

Changed Travis yml build file. RT ticket #597497: Set up artemis tests to run on travis.

Changed all build scripts.
Changed all build scripts and startup scripts. Removed building of artemis_mac.jar which is not used.
Removed etc/gene_builder script and the gff2embl script (and documentation references) - no longer supported. RT ticket #598617.

Fixed RT ticket #606061 - Using EBI-Dbfetch on ARTEMIS. Change to DbfetchEntrySource.java due to incorrect regular expression and EBI URL.


Resized splash screen.

Added error handling for dnaplotter template file loading in standalone mode.

Version 16
Add 'Features Within Selection' option to the 'Select' menu to select
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6 changes: 4 additions & 2 deletions INSTALL
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Expand Up @@ -68,6 +68,8 @@ Running the test suite
======================

cd test
RunAllUnitTests.sh

This will run manually written and EvoSuite generated unit tests. It will take a while to run.
RunDefaultUnitTests.sh - this runs all hand-written unit tests.
RunEvoSuiteUnitTests.sh - this runs all EvoSuite generated unit tests. It will take well over 30 mins to run.
RunAllUnitTests.sh - this runs all hand-written and EvoSuite generated unit tests. It will take well over 30 mins to run.

2 changes: 1 addition & 1 deletion LICENSE
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@@ -1,4 +1,4 @@
This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
This software is Copyright (c) 2018 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

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84 changes: 41 additions & 43 deletions Makefile
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Expand Up @@ -6,7 +6,7 @@ SHELL=/bin/sh

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-2.13.2.jar:lib/picard/htsjdk-2.12.0.jar:lib/commons-net-3.6.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:.
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/commons-net-3.6.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:.

ARTEMIS_DIRS = uk/ac/sanger/artemis \
uk/ac/sanger/artemis/chado \
Expand All @@ -21,6 +21,7 @@ uk/ac/sanger/artemis/components/genebuilder/cv \
uk/ac/sanger/artemis/components/genebuilder/gff \
uk/ac/sanger/artemis/components/genebuilder/ortholog \
uk/ac/sanger/artemis/components/variant \
uk/ac/sanger/artemis/components/ref \
uk/ac/sanger/artemis/editor \
uk/ac/sanger/artemis/io \
uk/ac/sanger/artemis/j2ssh \
Expand Down Expand Up @@ -63,59 +64,56 @@ dist :
rm -rf artemis_compiled.tar.gz tar_build
mkdir tar_build
mkdir tar_build/artemis
rm -f artemis_compiled_latest.tar.gz
tar cf - $(OTHER_FILES) act art Makefile etc | (cd tar_build/artemis; tar xf -)
tar cf - $(OTHER_FILES) act art dnaplotter bamview setenv 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

artemis.jar : $(CLASSES)
mkdir jar_build
rm -f artemis.jar
cd jar_build; \
if [ ! -d org ]; then \
for fileJar in ../lib/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../lib/j2ssh/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../lib/ibatis/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../lib/batik/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../lib/picard/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
fi; \
cp -R ../lib/LICENSE.Apache ../uk ../org ../etc ../images ../lib/j2ssh/j2ssh.properties \
../images/PSUlogo.gif ../images/icon.gif ../README.md ../artemis_sqlmap .
find jar_build -name '*.java' -print | xargs rm -f
find jar_build -name '.svn' -print | xargs rm -rf
cd jar_build; \
mkdir -p jar_build/build
rm -f *.jar
cd jar_build/build; \
for fileJar in ../../lib/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../../lib/j2ssh/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../../lib/ibatis/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../../lib/batik/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../../lib/picard/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
cp -R ../../lib/LICENSE.* ../../uk ../../org ../../etc ../../images ../../lib/j2ssh/j2ssh.properties \
../../images/PSUlogo.gif ../../images/icon.gif ../../README.md ../../artemis_sqlmap .
find jar_build/build -name '*.java' -print | xargs rm -f
find jar_build/build -name '.svn' -print | xargs rm -rf
find jar_build/build -name '*.DS_Store' -print | xargs rm -rf
cd jar_build/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 htsjdk picard LICENSE.Apache j2ssh.properties; \
jar cmf manifest-art ../artemis.jar META-INF/services images/PSUlogo.gif images/icon.gif README.md etc \
artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE 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/ htsjdk picard LICENSE.Apache j2ssh.properties; \
jar cmf manifest-circular ../DNAPlotter.jar images/PSUlogo.gif README.md etc \
org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE 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 htsjdk picard com/ibatis; \
jar cmf manifest-bamview ../bamview.jar META-INF/services etc org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE; \
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 htsjdk picard 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 htsjdk picard LICENSE.Apache artemis_sqlmap
jar cmf manifest-act ../act.jar META-INF/services images/PSUlogo.gif images/icon.gif README.md etc \
artemis_sqlmap org uk com net htsjdk picard gov joptsimple ngs freemarker LICENSE.Apache LICENSE.Picard LICENSE.JDBC LICENSE j2ssh.properties; \

rm -rf jar_build/build;

clean :
-rm -rf *.html artemis.jar resources uk/ac/sanger/jcon/ jar_build tar_build artemis_compiled.tar
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -39,7 +39,7 @@ For information on how to get Artemis see this web page:

# COPYRIGHT

Copyright (C) 1998-2016 Genome Research Limited
Copyright (C) 1998-2018 Genome Research Limited

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
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