[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5dd5952050c8/ Changeset: 5dd5952050c8 User: davebgx Date: 2014-06-13 22:39:59 Summary: Abstract common startup tasks into scripts/common_startup.sh, which used to be copy_sample_files.sh. Affected #: 5 files diff -r 6e39473e4c51151ef71ef0f5a5e05134e5d5aaa4 -r 5dd5952050c822282ecb12ed3a5fc2f262a8f921 run.sh --- a/run.sh +++ b/run.sh @@ -5,31 +5,12 @@ python ./scripts/check_python.py [ $? -ne 0 ] && exit 1 -./scripts/copy_sample_files.sh +./scripts/common_startup.sh if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" fi -# explicitly attempt to fetch eggs before running -FETCH_EGGS=1 -for arg in "$@"; do - [ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0; break -done -if [ $FETCH_EGGS -eq 1 ]; then - python ./scripts/check_eggs.py -q - if [ $? -ne 0 ]; then - echo "Some eggs are out of date, attempting to fetch..." - python ./scripts/fetch_eggs.py - if [ $? -eq 0 ]; then - echo "Fetch successful." - else - echo "Fetch failed." - exit 1 - fi - fi -fi - if [ -n "$GALAXY_RUN_ALL" ]; then servers=`sed -n 's/^\[server:\(.*\)\]/\1/ p' universe_wsgi.ini | xargs echo` daemon=`echo "$@" | grep -q daemon` diff -r 6e39473e4c51151ef71ef0f5a5e05134e5d5aaa4 -r 5dd5952050c822282ecb12ed3a5fc2f262a8f921 run_reports.sh --- a/run_reports.sh +++ b/run_reports.sh @@ -11,6 +11,8 @@ cd `dirname $0` +./scripts/common_startup.sh --skip-samples + GALAXY_REPORTS_CONFIG=${GALAXY_REPORTS_CONFIG:-reports_wsgi.ini} GALAXY_REPORTS_PID=${GALAXY_REPORTS_PID:-reports_webapp.pid} GALAXY_REPORTS_LOG=${GALAXY_REPORTS_LOG:-reports_webapp.log} diff -r 6e39473e4c51151ef71ef0f5a5e05134e5d5aaa4 -r 5dd5952050c822282ecb12ed3a5fc2f262a8f921 run_tool_shed.sh --- a/run_tool_shed.sh +++ b/run_tool_shed.sh @@ -2,7 +2,7 @@ cd `dirname $0` -./scripts/copy_sample_files.sh +./scripts/common_startup.sh tool_shed=`./lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh $@` args=$@ diff -r 6e39473e4c51151ef71ef0f5a5e05134e5d5aaa4 -r 5dd5952050c822282ecb12ed3a5fc2f262a8f921 scripts/common_startup.sh --- /dev/null +++ b/scripts/common_startup.sh @@ -0,0 +1,63 @@ +#!/bin/bash + +# explicitly attempt to fetch eggs before running +FETCH_EGGS=1 +COPY_SAMPLE_FILES=1 +for arg in "$@"; do + [ "$arg" = "--skip-eggs" ] && FETCH_EGGS=0 + [ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0 + [ "$arg" = "--skip-samples" ] && COPY_SAMPLE_FILES=0 +done +if [ $FETCH_EGGS -eq 1 ]; then + python ./scripts/check_eggs.py -q + if [ $? -ne 0 ]; then + echo "Some eggs are out of date, attempting to fetch..." + python ./scripts/fetch_eggs.py + if [ $? -eq 0 ]; then + echo "Fetch successful." + else + echo "Fetch failed." + exit 1 + fi + fi +fi + +SAMPLES=" + tool_shed_wsgi.ini.sample + datatypes_conf.xml.sample + external_service_types_conf.xml.sample + migrated_tools_conf.xml.sample + reports_wsgi.ini.sample + shed_tool_conf.xml.sample + tool_conf.xml.sample + shed_tool_data_table_conf.xml.sample + tool_data_table_conf.xml.sample + tool_sheds_conf.xml.sample + data_manager_conf.xml.sample + shed_data_manager_conf.xml.sample + openid_conf.xml.sample + job_metrics_conf.xml.sample + universe_wsgi.ini.sample + lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample + tool-data/shared/ncbi/builds.txt.sample + tool-data/shared/ensembl/builds.txt.sample + tool-data/shared/ucsc/builds.txt.sample + tool-data/shared/ucsc/publicbuilds.txt.sample + tool-data/shared/ucsc/ucsc_build_sites.txt.sample + tool-data/shared/igv/igv_build_sites.txt.sample + tool-data/shared/rviewer/rviewer_build_sites.txt.sample + tool-data/*.sample + static/welcome.html.sample +" + +if [ $COPY_SAMPLE_FILES -eq 1 ]; then + # Create any missing config/location files + for sample in $SAMPLES; do + file=${sample%.sample} + if [ ! -f "$file" -a -f "$sample" ]; then + echo "Initializing $file from `basename $sample`" + cp $sample $file + fi + done +fi + diff -r 6e39473e4c51151ef71ef0f5a5e05134e5d5aaa4 -r 5dd5952050c822282ecb12ed3a5fc2f262a8f921 scripts/copy_sample_files.sh --- a/scripts/copy_sample_files.sh +++ /dev/null @@ -1,39 +0,0 @@ -#!/bin/bash - -SAMPLES=" - tool_shed_wsgi.ini.sample - datatypes_conf.xml.sample - external_service_types_conf.xml.sample - migrated_tools_conf.xml.sample - reports_wsgi.ini.sample - shed_tool_conf.xml.sample - tool_conf.xml.sample - shed_tool_data_table_conf.xml.sample - tool_data_table_conf.xml.sample - tool_sheds_conf.xml.sample - data_manager_conf.xml.sample - shed_data_manager_conf.xml.sample - openid_conf.xml.sample - job_metrics_conf.xml.sample - universe_wsgi.ini.sample - lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample - tool-data/shared/ncbi/builds.txt.sample - tool-data/shared/ensembl/builds.txt.sample - tool-data/shared/ucsc/builds.txt.sample - tool-data/shared/ucsc/publicbuilds.txt.sample - tool-data/shared/ucsc/ucsc_build_sites.txt.sample - tool-data/shared/igv/igv_build_sites.txt.sample - tool-data/shared/rviewer/rviewer_build_sites.txt.sample - tool-data/*.sample - static/welcome.html.sample -" - -# Create any missing config/location files -for sample in $SAMPLES; do - file=${sample%.sample} - if [ ! -f "$file" -a -f "$sample" ]; then - echo "Initializing $file from `basename $sample`" - cp $sample $file - fi -done - https://bitbucket.org/galaxy/galaxy-central/commits/867208553d9d/ Changeset: 867208553d9d User: davebgx Date: 2014-06-13 22:41:00 Summary: Merge with incoming. Affected #: 1 file diff -r 5dd5952050c822282ecb12ed3a5fc2f262a8f921 -r 867208553d9dba216acd6669543714e3aa1ebed2 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -34,6 +34,9 @@ def __getitem__( self, key ): return self.data_tables.__getitem__( key ) + def __setitem__( self, key, value ): + return self.data_tables.__setitem__( key, value ) + def __contains__( self, key ): return self.data_tables.__contains__( key ) @@ -43,6 +46,9 @@ except KeyError: return default + def set( self, name, value ): + self[ name ] = value + def get_tables( self ): return self.data_tables Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.