Merge pull request #233 from kpepper/artemis_unit_testing

Artemis unit testing v17.0.0 branch merge

.classpath

@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="corba"/>
-	<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|cobertura-lib|coverage-report|data|docs|evosuite-dependencies|evosuite-libs|evosuite-tests|jacoco-lib|lib|evosuite-tests/" including="uk/**" kind="src" output="eclipse-classes" path="test"/>
+	<classpathentry including="uk/**" kind="src" output="eclipse-classes" path="test/evosuite-tests"/>
+	<classpathentry excluding="main/" kind="src" path="ant-build/src"/>
+	<classpathentry excluding="ant-build/classes/|ant-build/src/|docs|test|test/evosuite-tests/|uk/ac/sanger/artemis/ExternalProgramUtils.java" including="org/|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"/>
@@ -14,9 +14,6 @@
 	<classpathentry kind="lib" path="lib/ibatis/ibatis-2.3.4.726.jar"/>
 	<classpathentry kind="lib" path="lib/ibatis/log4j-1.2.14.jar"/>
 	<classpathentry kind="lib" path="lib/postgresql-8.4-701.jdbc3.jar"/>
-	<classpathentry kind="lib" path="lib/picard/picard.jar"/>
-	<classpathentry kind="lib" path="lib/picard/sam.jar"/>
-	<classpathentry kind="lib" path="lib/commons-net-2.2.jar"/>
 	<classpathentry kind="lib" path="lib/batik/batik-awt-util.jar"/>
 	<classpathentry kind="lib" path="lib/batik/batik-codec.jar"/>
 	<classpathentry kind="lib" path="lib/batik/batik-dom.jar"/>
@@ -25,5 +22,10 @@
 	<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="output" path="ant-build/classes/main"/>
+	<classpathentry kind="lib" path="test/lib/junit-4.11.jar"/>
+	<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.jar"/>
+	<classpathentry kind="output" path="eclipse-classes"/>
 </classpath>

.gitignore

@@ -1 +1,12 @@
 *.class
+.settings
+ant-build
+test/ant-build
+**/.DS_Store
+**/*.log
+test/coverage-report
+jar_build
+tar_build
+artemis_compiled.tar
+/eclipse-classes/
+/test-kjp/

.travis.yml

@@ -1,16 +1,18 @@
 language: java
 jdk:
-  - openjdk7
-  - openjdk6
-  - oraclejdk7
+  - openjdk8
+  - oraclejdk8
 sudo: false
 env:
   global:
     - BUILD_CMD='make'
+    - RUN_TESTS=false
 matrix:
   include:
-    - jdk: openjdk7
-      env: BUILD_CMD='ant -f build.xml'
+    - jdk: oraclejdk8
+      env: 
+        - BUILD_CMD='ant -f build.xml'
+        - RUN_TESTS=true
 cache:
   directories:
   - "${HOME}/dependencies"
@@ -21,6 +23,9 @@ before_install:
   - "source install_dependencies.sh"
 install:
   - "$BUILD_CMD"
-  - "cd test"
-  - "ln -s $(pwd)/../etc/log4j.properties ."
-script: ant -f build-test.xml test -DEMBOSS_ROOT=$EMBOSS_ROOT | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ]
+script:
+  - if [ "$RUN_TESTS" == "true" ]; then
+      cd test;
+      ln -s $(pwd)/../etc/log4j.properties .;
+      ./RunDefaultUnitTests.sh | tee test.log && [ -z "$(grep 'Failures:\s[^0]\|Errors:\s[^0]' test.log)" ];
+    fi

AUTHORS

@@ -1,3 +1,4 @@
 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)

ChangeLog

@@ -1,3 +1,52 @@
+Version 17
+
+	Artemis/ACT and associated applications have been upgraded to Java 8. Java 7/6/5 are now no longer supported - RT ticket #589103
+
+	BamView fixes/changes - 
+		1) Improved mouse selection of reads.
+		2) Fixed exceptions thrown when zooming into an area with secondary reads or SNPs enabled - RT ticket #596489: Problem zooming in using isoseq data
+		3) Removed Samtools (htsjdk) jar and updated Picard jar (which includes htsjdk).
+		4) Upgraded Apache Commons Net jar - used for ftp'ing. 
+		5) Added Cram file loading and fixed defects around that code area (also related RT ticket #560982: Artemis fails to build from source).
+		6) Added display of bam secondary & supplementary alignment flags to read details pop-up window.
+		7) Improved error handling/reporting for standalone BamView application.
+		8) Added buffer sizing to FTPSeekableStream.
+		9) Performance tweak for BAM file indexing.
+		10) Fixed issue in BamView whereby if you went to the end of a long contig and then switched to a shorter one (via the combo), you would end up off the end of the sequence
+			resulting in a negative array index exception. Code has been changed to reset display to the start of sequence when the combo is changed (i.e. same as Artemis).
+		11) Added bamview_perform_detailed_validation boolean property that can be set to perform more detailed sam validation during loading - this can be slow for large files.
+
+	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
+		- for the moment we are stuck with two coverage reports - evosuite and Jacoco.
+
+	Removed redundant Corba libraries.
+
+	Upgraded JUnit jar.
+
+	Changed Travis yml build file. RT ticket #597497: Set up artemis tests to run on travis build.
+
+	Changed all build scripts and startup scripts - RT ticket #598617. 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. 
+
+	Fixed RT ticket #606061 - Using EBI-Dbfetch on ARTEMIS. Change to DbfetchEntrySource.java due to incorrect regular expression and EBI URL.
+
+	Resized splash screen, as it was too small to the accommodate text info.
+
+	Added error handling for dnaplotter template file loading in standalone mode.
+
+	Added Bioconda recipe. RT ticket #341139 .
+
+	Fixed RT ticket #467433 - Genbank DBSOURCE field was not recognised by Artemis. DBLINK was already added.
+
+	Fixed RT ticket #503254 - Act doesn't detect if file does not exist.
+
+	KNOWN ISSUES: 
+		1) Java JDKs 1.8.0_131 and above have a Swing bug related to overlaying of modal dialogs for Mac OS X: https://bugs.openjdk.java.net/browse/JDK-8179335
+		2) There is a current bug in htsjdk whereby calls to the queryMate functionality can throw an exception on reads with secondaries and/or supplementals. 
+		   This affects looking up properties for a selected read on bamview - https://github.com/samtools/htsjdk/issues/1065
+
 Version 16
 	Add 'Features Within Selection' option to the 'Select' menu to select
 	features that are contained by a selected base range.

INSTALL

@@ -68,4 +68,8 @@ Running the test suite
 ======================
 
 cd test
-ant -f build-test.xml
+
+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.
+

LICENSE

@@ -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:
 

Makefile

@@ -4,9 +4,9 @@ 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:.
+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 \
@@ -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 \
@@ -31,35 +32,20 @@ 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 \
@@ -70,69 +56,66 @@ 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`
+OTHER_FILES := `find images/PSUlogo.gif images/icon.gif README.md`
 
 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 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 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 $$fileJar; \
-            rm -rf META-INF/MANIFEST.MF; \
-          done; \
-        fi; \
-	cp -R ../lib/LICENSE.Apache ../uk ../org ../nsdb ../type ../seqdb ../etc ../images ../lib/j2ssh/j2ssh.properties \
-	      ../images/PSUlogo.gif ../images/icon.gif ../README.md ../artemis_sqlmap .
-	find jar_build -name '*.java' -print | xargs rm -f
-	find jar_build -name '.svn' -print | xargs rm -rf
-	cd jar_build; \
+	mkdir -p jar_build/build
+	rm -f *.jar
+	cd jar_build/build; \
+    for fileJar in ../../lib/*.jar; do \
+      jar xvf $$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 nsdb type seqdb 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; \
+	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 \
+                         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 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 nsdb type seqdb 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
+	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 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

README.md

@@ -21,7 +21,14 @@ The Artemis user manual is at:
   http://www.sanger.ac.uk/science/tools/artemis
 
 The ACT user manual is at:
-  http://www.sanger.ac.uk/science/tools/act
+  http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
+
+The DNA plotter user manual is at:
+  http://www.sanger.ac.uk/science/tools/dnaplotter
+
+The BAM View user manual is at:
+  http://www.sanger.ac.uk/science/tools/bamview
+
 
 # INSTALLATION
 
@@ -39,7 +46,7 @@ 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