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Unverified Commit 91a091bb authored by kpepper's avatar kpepper Committed by GitHub
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Merge pull request #269 from kpepper/build-process-upgrade-merge 

Prep for Release 18.0.0
parents 7e690d98 70e68776
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ChangeLog
View file @ 91a091bb
Version 18
1) Switched build process to use Maven. Changed directory structure. Removed ant and Make files.
2) Retired a number of jars and upgraded others. Removed the ssh-plugin jar.
3) Upgraded to Picard 2.18.14 jar, which has a number of important bug fixes.
4) Removed old documentation functionality. HTML/PDF manuals are now stored in gh-pages branch and exported directly from word docs.
5) Changed application script jar paths.
6) Rewrote writedb_entry script.
7) Fixed broken Amigo, GO term, Uniprot and UniprotKB URLs, used in the Artemis gene builder/feature edit windows.
8) Updated README.md
9) Fix for RT ticket #400288: "GO term warnings in Artemis" - we now no longer put out a warning for ISM, as it's optional in certain cases
1) Switched build process to use Apache Maven. Changed directory structure. Removed ant and Make files. Most jar files are now pulled directly from the Maven repository.
2) Upgraded Java version as Java 8 will be going out of support. Artemis will now only build/run with Java versions 9 to 11 (RT ticket #589103).
3) Upgraded to Picard 2.18.14 jar, which has a number of important bug fixes, including:
i) RT tickets #625730 - Loading bams into Artemis
ii) RT ticket #624271 - Problems with some bams loaded into Artemis causing data not to be viewable
4) Removed broken documentation functionality.
HTML/PDF manuals are now stored in Github gh-pages branch and exported from word docs (RT ticket #618907).
5) Added run menu option to execute an InterPro sequence search for a selected feature - RT ticket #643820.
6) Updated application scripts.
7) Fixed broken Amigo, GO term, Uniprot (RT ticket #639930) and UniprotKB URLs, used in the Artemis gene builder/feature edit windows.
8) Updated README.md
9) Fix for RT ticket #400288: "GO term warnings in Artemis" - we now no longer put out a warning for ISM, as it's optional in certain cases
[http://wiki.geneontology.org/index.php/Inferred_from_Sequence_Model_(ISM)].
10) Upgrade of Java version as Java 8 will be going out of support. Artemis will now only build with Java versions 9 to 11.
11) Removed the INSTALL document as the content is covered elsewhere.
12) Changed error message displayed when multiple features are selected for pfam/rfam search.
13) Added temporary Java 9+ --add-opens flags to art/act scripts. These will be removed when Ibatis is replaced.
14) Added basic unit tests for Chado access to enable Postgres 10 testing.
15) Added Mockito for unit test mocking.
16) Updated/fixed run_blast<..> scripts in the etc folder. These now use blast+. Removed options to run Smart, Jalview, fasta & fastx.
Results are displayed using View->Search Results.
17) Removed the old icons/Readme doc for local blast setup and added an updated version to the main README.md.
18) Updated setup_blast_dbs.sh script and added to etc folder, for setup of local blast environment (See README.md).
19) Removed ability to run remote blast, fasta34 etc using SSH. This functionality is old, does not work and is not used.
20) Removed old ".sanger" and ".sanger.linux" scripts from etc folder - these were very out of date, with incorrect file paths etc.
21) Fixed RT ticket #642350: "GO term evidence codes in chado Artemis" - Added HTP, HDA, HMP, HGI, HEP GO evidence codes to Artemis.
22) Added fix for Java 9 JDK-8181568 issue across all apps, related to display of application icons on Macs.
23) Fixed incorrect Pfam URL, used in Feature Edit and Evidence Viewer screens.
24) Fixed error handling on Run->Pfam/Rfam search (RT Ticket #420623).
25) Enabled ability to drag and drop data files on to Artemis and BamView apps [Mac OS X] for immediate display.
26) Fixed RT ticket #642944: "ACT crunch-m8 file generation". ACT can now handle tblastx or blastn
hit table files produced from fasta comparisons on the NCBI Blast web site. This is an alternative to Web ACT / Double ACT.
10) Removed the INSTALL document as the content is now covered elsewhere.
11) Changed error message displayed when multiple features are selected for pfam/rfam search.
12) Added temporary Java 9+ --add-opens flags to art/act scripts. These will be removed when Ibatis is replaced.
13) Added unit tests for Chado access to enable Postgres 10 testing (RT ticket #632896).
14) Added Mockito for unit test mocking.
15) Updated/fixed run_blast<..> scripts in the etc folder. Running blast from the run menu now uses blast+. Removed options to run Smart, Jalview, fasta & fastx.
Results are displayed using View->Search Results.
Related RT ticket #596281 also closed.
16) Removed the old icons/Readme doc for local blast setup and added an updated version to the main README.md.
17) Updated setup_blast_dbs.sh script and added to etc folder, for setup of a local blast environment (detailed in the README.md and manuals).
18) Removed ability to run remote blast, fasta34 etc using SSH. This functionality is being retired.
19) Removed old ".sanger" and ".sanger.linux" scripts from etc folder - these were very out of date, with incorrect file paths etc.
20) Fixed RT ticket #642350: "GO term evidence codes in chado Artemis" - Added HTP, HDA, HMP, HGI, HEP GO evidence codes to Artemis.
21) Added fix for Java 9 JDK-8181568 issue across all apps, related to display of application icons on Macs.
22) Fixed incorrect Pfam URL, used in Feature Edit and Evidence Viewer screens.
23) Fixed error handling on Run->Pfam/Rfam search (RT ticket #420623).
24) Enabled ability to drag and drop data files on to Artemis and BamView apps [Mac OS X] for immediate display.
25) Fixed RT ticket #642944: "ACT crunch-m8 file generation". ACT can now handle tblastx hit table files produced from comparisons
on the NCBI Blast web site. This is an alternative to Web ACT / Double ACT.
[e.g. https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=blasttab&LAST_PAGE=tblastx&BLAST_INIT=blast2seq]
27) Removed the /lustre/scratch101/blastdb/Pathogen/Kineto_aa run->blast menu option. This database path no longer exists.
28) Added new InterPro sequence search on the run menu - RT Ticket #643820.
29) RT Ticket #472601: Artemis RPKM and read count broken since version 16.0.6. Fixed bug related to intron region reads. New unit tests added.
26) Removed the /lustre/scratch101/blastdb/Pathogen/Kineto_aa run->blast menu option. This database path no longer exists.
27) RT ticket #472601: Artemis RPKM and read count broken since version 16.0.6. Fixed bug related to intron region reads. New unit tests added.
Version 17.0.2-test - patch release for Sanger. Changes incorporated into GitHub master.
......
LICENSE
View file @ 91a091bb
This software is Copyright (c) 2018 by Wellcome Trust Sanger Institute.
This software is Copyright (c) 2019 by Wellcome Trust Sanger Institute.
This is free software, licensed under:
......
act
View file @ 91a091bb
......@@ -5,7 +5,6 @@
#
QUIET=no
PRG=$0
usage () {
echo "SYNOPSIS"
......@@ -58,17 +57,16 @@ add_proxy_properties() {
}
#
# Resolve links - $0 may be a link
# Resolve script path (inc symlinks)
#
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '.*/.*' > /dev/null; then
PRG="$link"
else
PRG="`dirname $PRG`/$link"
fi
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
# Special Sanger override on chado PGUSER
if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
......@@ -95,7 +93,7 @@ do
shift
done
APPLICATION_HOME=`dirname "$PRG"`
JAR_NAME=act.jar
JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
......
art
View file @ 91a091bb
......@@ -5,7 +5,6 @@
#
QUIET=no
PRG=$0
usage () {
echo "SYNOPSIS"
......@@ -64,17 +63,16 @@ add_proxy_properties() {
}
#
# Resolve links - $0 may be a link
# Resolve script path (inc symlinks)
#
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '.*/.*' > /dev/null; then
PRG="$link"
else
PRG="`dirname $PRG`/$link"
fi
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
# Special Sanger override on chado PGUSER
if [[ "$ARTEMIS_SANGER_DBUSER" != "" ]]
......@@ -89,8 +87,8 @@ APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environme
while test $# != 0
do
case $1 in
-options) APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dextra_options=$2"; shift ;;
-chado) APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dchado=$PGHOST:$PGPORT/$PGDATABASE?$PGUSER -Dibatis" ;;
-options) APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dextra_options=$2"; shift ;;
-chado) APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Dchado=$PGHOST:$PGPORT/$PGDATABASE?$PGUSER -Dibatis" ;;
-D*) APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES $1" ;;
-quiet) QUIET=yes ; APPLICATION_PROPERTIES="$APPLICATION_PROPERTIES -Drun_quietly=true" ;;
-help) usage ;;
......@@ -101,7 +99,7 @@ do
shift
done
APPLICATION_HOME=`dirname "$PRG"`
JAR_NAME=artemis.jar
JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
......
bamview
View file @ 91a091bb
......@@ -5,7 +5,6 @@
#
QUIET=no
PRG=$0
add_proxy_properties() {
......@@ -26,20 +25,18 @@ add_proxy_properties() {
}
#
# Resolve links - $0 may be a link
# Resolve script path (inc symlinks)
#
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '.*/.*' > /dev/null; then
PRG="$link"
else
PRG="`dirname $PRG`/$link"
fi
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
APPLICATION_PROPERTIES="-Djdbc.drivers=org.postgresql.Driver -Dartemis.environment=UNIX $SANGER_ARTEMIS_OPTIONS"
APPLICATION_HOME=`dirname "$PRG"`
JAR_NAME=bamview.jar
JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
......
dnaplotter
View file @ 91a091bb
......@@ -5,7 +5,6 @@
#
QUIET=no
PRG=$0
usage () {
echo "SYNOPSIS"
......@@ -44,18 +43,18 @@ add_proxy_properties() {
fi
}
#
# Resolve links - $0 may be a link
# Resolve script path (inc symlinks)
#
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '.*/.*' > /dev/null; then
PRG="$link"
else
PRG="`dirname $PRG`/$link"
fi
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
APPLICATION_HOME="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
#
# Parse arguments.
......@@ -76,7 +75,7 @@ do
shift
done
APPLICATION_HOME=`dirname "$PRG"`
JAR_NAME=dnaplotter.jar
JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
......
etc/versions
View file @ 91a091bb
Artemis Release 18.0.0-RC1
ACT Release 18.0.0-RC1
DNAPlotter Release 18.0.0-RC1
BamView 18.0.0-RC1
\ No newline at end of file
Artemis Release 18.0.0
ACT Release 18.0.0
DNAPlotter Release 18.0.0
BamView 18.0.0
\ No newline at end of file
etc/writedb_entry
View file @ 91a091bb
......@@ -11,7 +11,6 @@
#
QUIET=no
PRG=$0
PROXY_SETTINGS=
add_proxy_properties() {
......@@ -32,18 +31,17 @@ add_proxy_properties() {
fi
}
#
# Resolve links - $0 may be a link
# Resolve script path (inc symlinks)
#
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '.*/.*' > /dev/null; then
PRG="$link"
else
PRG="`dirname $PRG`/$link"
fi
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
PRG="$( cd -P "$( dirname "$SOURCE" )" && pwd )"; # get final path of this script
#
# Allow URLs to work from behind firewalls.
......@@ -52,7 +50,7 @@ add_proxy_properties
FLAGS="-mx2048m -ms20m -Djdbc.drivers=org.postgresql.Driver -Dibatis"
DEFAULT_CONNECTION="-Dchado=db.genedb.org:5432/snapshot?genedb_ro -Dread_only"
APPLICATION_HOME=`dirname "$PRG"`/..
APPLICATION_HOME="$PRG/.."
JAR_NAME=artemis.jar
JAR_FILE_DEFAULT=$APPLICATION_HOME/target/jars/$JAR_NAME
JAR_FILE_INSTALLED=$APPLICATION_HOME/dist/$JAR_NAME
......
pom.xml
View file @ 91a091bb
......@@ -5,7 +5,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>uk.ac.sanger</groupId>
<artifactId>artemis</artifactId>
<version>18.0.0-RC1</version>
<version>18.0.0</version>
<name>Artemis</name>
<description>Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
......@@ -66,7 +66,7 @@ Artemis is written in Java, and is available for UNIX, Macintosh and Windows sys
<version.file>${project.basedir}/etc/versions</version.file>
<copyright.text>2018 Wellcome Trust Sanger Institute</copyright.text>
<copyright.text>2019 Wellcome Trust Sanger Institute</copyright.text>
<!-- Properties passed into Maven on command line -->
<emboss.installation.root>${env.EMBOSS_ROOT}</emboss.installation.root>
......
src/main/java/uk/ac/sanger/artemis/Entry.java
View file @ 91a091bb
......@@ -1196,7 +1196,8 @@ public class Entry implements FeatureChangeListener, Selectable
final Location location = feature.getLocation();
final RangeVector ranges = location.getRanges();
for(int i = 0 ; i < ranges.size() ; ++i)
int numRanges = ranges.size();
for(int i = 0 ; i < numRanges ; ++i)
{
if(((Range)ranges.elementAt(i)).getEnd() > getBases().getLength())
{
......
src/main/java/uk/ac/sanger/artemis/components/Splash.java
View file @ 91a091bb
/* Splash.java
/* Splash.java
*
* This file is part of Artemis
*
......@@ -454,7 +454,7 @@ abstract public class Splash extends JFrame
g.drawString(geneticCode,
left_margin, yPos+(font_height * 3));
g.drawString("Copyright 1998 - 2018",
g.drawString("Copyright 1998 - 2019",
left_margin, yPos+(font_height * 9 / 2));
g.drawString("Genome Research Limited",
left_margin, yPos+(font_height * 11 / 2));
......
src/main/java/uk/ac/sanger/artemis/io/ChadoCanonicalGene.java
View file @ 91a091bb
......@@ -485,7 +485,8 @@ public class ChadoCanonicalGene
*/
public Feature containsTranscript(final StringVector names)
{
for(int i=0; i<transcripts.size(); i++)
final int numTranscripts = transcripts.size();
for(int i=0; i < numTranscripts; i++)
{
try
{
......@@ -510,7 +511,9 @@ public class ChadoCanonicalGene
{
List<Feature> splicedFeaturesOfTranscript = splicedFeatures.get(transcript_name);
List<Feature> results = new Vector<Feature>();
for(int i=0; i<splicedFeaturesOfTranscript.size(); i++)
int numSplicedFeatures = splicedFeaturesOfTranscript.size();
for(int i=0; i < numSplicedFeatures; i++)
{
Feature feature = (Feature)splicedFeaturesOfTranscript.get(i);
if(feature.getKey().getKeyString().equals(type))
......@@ -533,7 +536,9 @@ public class ChadoCanonicalGene
{
List<Feature> splicedFeaturesOfTranscript = splicedFeatures.get(transcript_name);
Set<String> splicedTypes = new HashSet<String>();
for(int i=0; i<splicedFeaturesOfTranscript.size(); i++)
int numSplicedfeatures = splicedFeaturesOfTranscript.size();
for(int i=0; i < numSplicedfeatures; i++)
{
Feature feature = (Feature)splicedFeaturesOfTranscript.get(i);
splicedTypes.add( feature.getKey().getKeyString() );
......
src/main/java/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
View file @ 91a091bb
......@@ -544,7 +544,8 @@ abstract public class SimpleDocumentEntry
final Key new_key = feature.getKey();
// check the qualifiers
for(int i = 0 ; i < new_qualifiers.size() ; ++i)
int numQual = new_qualifiers.size();
for(int i = 0 ; i < numQual ; ++i)
{
final Qualifier this_qualifier = (Qualifier)new_qualifiers.elementAt(i);
final String this_qualifier_name = this_qualifier.getName();
......
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