galaxy-commits February 2015

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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 02 Feb '15

02 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d387a165eed/ Changeset: 1d387a165eed User: nsoranzo Date: 2015-01-24 00:24:17+00:00 Summary: Use spaces instead of tabs. Affected #: 1 file diff -r 49d651198b3a7756936c4b578ccdd824b2c55e4e -r 1d387a165eedb70f81baac629128e3c8be40ac7e rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -2,18 +2,18 @@ cd `dirname $0` check_if_not_started(){ - # Search for all pids in the logs and tail for the last one - latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` - # Grab the current pid from the file we were given - current_pid_in_file=$(cat $2); - # If they're equivalent, then the current pid file agrees with our logs - # and we've succesfully started - if [ $latest_pid -eq $current_pid_in_file ]; - then - echo 0; - else - echo 1; - fi + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + # Grab the current pid from the file we were given + current_pid_in_file=$(cat $2); + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + if [ $latest_pid -eq $current_pid_in_file ]; + then + echo 0; + else + echo 1; + fi } # If there is a .venv/ directory, assume it contains a virtualenv that we @@ -37,30 +37,30 @@ servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` for server in $servers; do - # If there's a pid - if [ -e $server.pid ] - then - # Then kill it - echo "Killing $server" - pid=`cat $server.pid` - kill $pid - else - # Otherwise just continue - echo "$server not running" - fi - # Start the server (and background) (should this be nohup'd?) - python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ - # Wait for the server to start - sleep 1 - # Grab the new pid - pid=`cat $server.pid` - result=1 - # Wait for the latest pid in the file to be the pid we've grabbed - while [ $result -eq 1 ] - do - result=$(check_if_not_started $server.log $server.pid) - printf "." - sleep 1 - done - echo + # If there's a pid + if [ -e $server.pid ] + then + # Then kill it + echo "Killing $server" + pid=`cat $server.pid` + kill $pid + else + # Otherwise just continue + echo "$server not running" + fi + # Start the server (and background) (should this be nohup'd?) + python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ + # Wait for the server to start + sleep 1 + # Grab the new pid + pid=`cat $server.pid` + result=1 + # Wait for the latest pid in the file to be the pid we've grabbed + while [ $result -eq 1 ] + do + result=$(check_if_not_started $server.log $server.pid) + printf "." + sleep 1 + done + echo done https://bitbucket.org/galaxy/galaxy-central/commits/228796a3cafc/ Changeset: 228796a3cafc User: nsoranzo Date: 2015-01-24 00:40:41+00:00 Summary: Reduce differences with run.sh . Affected #: 1 file diff -r 1d387a165eedb70f81baac629128e3c8be40ac7e -r 228796a3cafcca474319c7b71f1633349d024dbe rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -1,4 +1,5 @@ #!/bin/sh + cd `dirname $0` check_if_not_started(){ @@ -23,6 +24,15 @@ . .venv/bin/activate fi +python ./scripts/check_python.py +[ $? -ne 0 ] && exit 1 + +./scripts/common_startup.sh + +if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then + python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" +fi + if [ -z "$GALAXY_CONFIG_FILE" ]; then if [ -f universe_wsgi.ini ]; then GALAXY_CONFIG_FILE=universe_wsgi.ini https://bitbucket.org/galaxy/galaxy-central/commits/40958c314026/ Changeset: 40958c314026 User: nsoranzo Date: 2015-01-24 01:04:13+00:00 Summary: Simplify code. Check if a server process died. Affected #: 1 file diff -r 228796a3cafcca474319c7b71f1633349d024dbe -r 40958c314026031614321b421e84d41c0513df5c rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -2,21 +2,6 @@ cd `dirname $0` -check_if_not_started(){ - # Search for all pids in the logs and tail for the last one - latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` - # Grab the current pid from the file we were given - current_pid_in_file=$(cat $2); - # If they're equivalent, then the current pid file agrees with our logs - # and we've succesfully started - if [ $latest_pid -eq $current_pid_in_file ]; - then - echo 0; - else - echo 1; - fi -} - # If there is a .venv/ directory, assume it contains a virtualenv that we # should run this instance in. if [ -d .venv ]; @@ -45,11 +30,9 @@ fi servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` -for server in $servers; -do +for server in $servers; do # If there's a pid - if [ -e $server.pid ] - then + if [ -e $server.pid ]; then # Then kill it echo "Killing $server" pid=`cat $server.pid` @@ -60,17 +43,19 @@ fi # Start the server (and background) (should this be nohup'd?) python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ - # Wait for the server to start - sleep 1 - # Grab the new pid - pid=`cat $server.pid` - result=1 - # Wait for the latest pid in the file to be the pid we've grabbed - while [ $result -eq 1 ] - do - result=$(check_if_not_started $server.log $server.pid) + while true; do + sleep 1 printf "." - sleep 1 + # Grab the current pid from the pid file + if ! current_pid_in_file=$(cat $server.pid); then + echo "A Galaxy process died, interrupting" >&2 + exit 1 + fi + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + [ -n "$latest_pid" ] && [ $latest_pid -eq $current_pid_in_file ] && break done echo done https://bitbucket.org/galaxy/galaxy-central/commits/a56fdaab0e25/ Changeset: a56fdaab0e25 User: jmchilton Date: 2015-02-02 14:14:09+00:00 Summary: Merged in nsoranzo/galaxy-central (pull request #647) More enhancements to rolling_restart.sh Affected #: 1 file diff -r 16efc5713d85f631c8ef9ad11895730f4747ea7e -r a56fdaab0e25011febcd98fe376adf39c7ebfb10 rolling_restart.sh --- a/rolling_restart.sh +++ b/rolling_restart.sh @@ -1,21 +1,7 @@ #!/bin/sh + cd `dirname $0` -check_if_not_started(){ - # Search for all pids in the logs and tail for the last one - latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $1 -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` - # Grab the current pid from the file we were given - current_pid_in_file=$(cat $2); - # If they're equivalent, then the current pid file agrees with our logs - # and we've succesfully started - if [ $latest_pid -eq $current_pid_in_file ]; - then - echo 0; - else - echo 1; - fi -} - # If there is a .venv/ directory, assume it contains a virtualenv that we # should run this instance in. if [ -d .venv ]; @@ -23,6 +9,15 @@ . .venv/bin/activate fi +python ./scripts/check_python.py +[ $? -ne 0 ] && exit 1 + +./scripts/common_startup.sh + +if [ -n "$GALAXY_UNIVERSE_CONFIG_DIR" ]; then + python ./scripts/build_universe_config.py "$GALAXY_UNIVERSE_CONFIG_DIR" +fi + if [ -z "$GALAXY_CONFIG_FILE" ]; then if [ -f universe_wsgi.ini ]; then GALAXY_CONFIG_FILE=universe_wsgi.ini @@ -35,32 +30,32 @@ fi servers=`sed -n 's/^\[server:$.*$\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo` -for server in $servers; -do - # If there's a pid - if [ -e $server.pid ] - then - # Then kill it - echo "Killing $server" - pid=`cat $server.pid` - kill $pid - else - # Otherwise just continue - echo "$server not running" - fi - # Start the server (and background) (should this be nohup'd?) - python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ - # Wait for the server to start - sleep 1 - # Grab the new pid - pid=`cat $server.pid` - result=1 - # Wait for the latest pid in the file to be the pid we've grabbed - while [ $result -eq 1 ] - do - result=$(check_if_not_started $server.log $server.pid) - printf "." - sleep 1 - done - echo +for server in $servers; do + # If there's a pid + if [ -e $server.pid ]; then + # Then kill it + echo "Killing $server" + pid=`cat $server.pid` + kill $pid + else + # Otherwise just continue + echo "$server not running" + fi + # Start the server (and background) (should this be nohup'd?) + python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log --daemon $@ + while true; do + sleep 1 + printf "." + # Grab the current pid from the pid file + if ! current_pid_in_file=$(cat $server.pid); then + echo "A Galaxy process died, interrupting" >&2 + exit 1 + fi + # Search for all pids in the logs and tail for the last one + latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1` + # If they're equivalent, then the current pid file agrees with our logs + # and we've succesfully started + [ -n "$latest_pid" ] && [ $latest_pid -eq $current_pid_in_file ] && break + done + echo done Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Merged in jmchilton/galaxy-central-backport-2/stable (pull request #638)
by commits-noreply＠bitbucket.org 02 Feb '15

02 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fd75aaee91cf/ Changeset: fd75aaee91cf Branch: stable User: jmchilton Date: 2015-02-02 14:10:43+00:00 Summary: Merged in jmchilton/galaxy-central-backport-2/stable (pull request #638) [STABLE] Backport pull request #636 to all relevant latest_* releases Affected #: 3 files diff -r a7ae7afffa8fa7551ea760ca01e9c1808809391b -r fd75aaee91cf3e8a0916689dfea72e0c752c447c .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,18 +8,18 @@ 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -9bce3f426863f8ba88062f67c7efc1836e82ee7c latest_2014.06.02 -8f9dcac033694e4cabcf5daae5cca1cfefbe967f latest_2014.04.14 +c52dc4c72b77e4b0849a596b6d05e4341236642a latest_2014.06.02 +b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 -19e56e66b0b344c6e2afa4541f6988e4fdb9af29 latest_2013.06.03 -cee903b8b3eee9145627ee89742555dac581791e latest_2013.08.12 -7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 -0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 +aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 +db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 +52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 +746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 +6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 +782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 c5e7535b4d229dbbe52d48ea35a27ab601205b7b latest_2015.01.13 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.

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commit/galaxy-central: 25 new changesets
by commits-noreply＠bitbucket.org 02 Feb '15

02 Feb '15

25 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aae74ee09e46/ Changeset: aae74ee09e46 Branch: stable User: jmchilton Date: 2015-01-15 21:01:03+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 19e56e66b0b344c6e2afa4541f6988e4fdb9af29 -r aae74ee09e4667e270750711327c8167e1dfae05 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2575,7 +2575,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.template_macro_params.keys() if not self.options or self.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/f15cc980e3ca/ Changeset: f15cc980e3ca Branch: stable User: jmchilton Date: 2015-01-15 21:01:05+00:00 Summary: Update tag latest_2013.06.03 for changeset aae74ee09e46 Affected #: 1 file diff -r f7235d0ad14fd90b8977e88f68715a7dedc5bab9 -r f15cc980e3ca5bf1f15fe9a11d420e3022c787de .hgtags --- a/.hgtags +++ b/.hgtags @@ -13,7 +13,7 @@ 9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 -19e56e66b0b344c6e2afa4541f6988e4fdb9af29 latest_2013.06.03 +aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 cee903b8b3eee9145627ee89742555dac581791e latest_2013.08.12 7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 https://bitbucket.org/galaxy/galaxy-central/commits/8b183b869448/ Changeset: 8b183b869448 Branch: stable User: jmchilton Date: 2015-01-15 21:01:11+00:00 Summary: Merge head created for backport bug fix on latest_2013.06.03 Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/db967a25c5db/ Changeset: db967a25c5db Branch: stable User: jmchilton Date: 2015-01-15 21:01:13+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r cee903b8b3eee9145627ee89742555dac581791e -r db967a25c5db969ee4b3e138fe2be4d979665bdf lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2585,7 +2585,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.template_macro_params.keys() if not self.options or self.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/f405d17de085/ Changeset: f405d17de085 Branch: stable User: jmchilton Date: 2015-01-15 21:01:15+00:00 Summary: Update tag latest_2013.08.12 for changeset db967a25c5db Affected #: 1 file diff -r 8b183b869448efd44c5e4dd452421392bcfdd295 -r f405d17de085663dc0392dadfa51d20956c39bfa .hgtags --- a/.hgtags +++ b/.hgtags @@ -14,7 +14,7 @@ b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 -cee903b8b3eee9145627ee89742555dac581791e latest_2013.08.12 +db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 https://bitbucket.org/galaxy/galaxy-central/commits/cb12cb063a9b/ Changeset: cb12cb063a9b Branch: stable User: jmchilton Date: 2015-01-15 21:01:17+00:00 Summary: Merge head created for backport bug fix on latest_2013.08.12 Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/52a18b44474f/ Changeset: 52a18b44474f Branch: stable User: jmchilton Date: 2015-01-15 21:01:18+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 7d5aa19a166cba9039e15f338a1e3fc924c43d3a -r 52a18b44474f017fce92850fb3892a4f76a7374a lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2592,7 +2592,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.template_macro_params.keys() if not self.options or self.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/9ae14630ca77/ Changeset: 9ae14630ca77 Branch: stable User: jmchilton Date: 2015-01-15 21:01:20+00:00 Summary: Update tag latest_2013.11.04 for changeset 52a18b44474f Affected #: 1 file diff -r cb12cb063a9b326fc435189264c4fb6fa66cffb6 -r 9ae14630ca7716e6a7eef34865c65356a9abb4d5 .hgtags --- a/.hgtags +++ b/.hgtags @@ -15,7 +15,7 @@ dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 -7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 +52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 https://bitbucket.org/galaxy/galaxy-central/commits/4dc0e41df66e/ Changeset: 4dc0e41df66e Branch: stable User: jmchilton Date: 2015-01-15 21:01:22+00:00 Summary: Merge head created for backport bug fix on latest_2013.11.04 Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/746db2bf4da0/ Changeset: 746db2bf4da0 Branch: stable User: jmchilton Date: 2015-01-15 21:01:23+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 -r 746db2bf4da081a7491b5a4602aeadd2611b3b1d lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -323,7 +323,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys() if not self.tool or not self.tool.options or self.tool.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/30fe131b672e/ Changeset: 30fe131b672e Branch: stable User: jmchilton Date: 2015-01-15 21:01:25+00:00 Summary: Update tag latest_2014.02.10 for changeset 746db2bf4da0 Affected #: 1 file diff -r 4dc0e41df66ecbb2b5c7e9e8fe39295d5eb7ad09 -r 30fe131b672e6ea459459f8cabab81118e551e3b .hgtags --- a/.hgtags +++ b/.hgtags @@ -16,7 +16,7 @@ aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 -0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 +746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 https://bitbucket.org/galaxy/galaxy-central/commits/d9cdccfc0225/ Changeset: d9cdccfc0225 Branch: stable User: jmchilton Date: 2015-01-15 21:01:25+00:00 Summary: Merge head created for backport bug fix on latest_2014.02.10 Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/b2c0570f52e1/ Changeset: b2c0570f52e1 Branch: stable User: jmchilton Date: 2015-01-15 21:01:27+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 8f9dcac033694e4cabcf5daae5cca1cfefbe967f -r b2c0570f52e18d8661ca1d80c42867e4b036f22b lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -323,7 +323,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys() if not self.tool or not self.tool.options or self.tool.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/05c5df09ecba/ Changeset: 05c5df09ecba Branch: stable User: jmchilton Date: 2015-01-15 21:01:28+00:00 Summary: Update tag latest_2014.04.14 for changeset b2c0570f52e1 Affected #: 1 file diff -r d9cdccfc0225023736550f66b2da46f2abc47767 -r 05c5df09ecbac4adb5b32c24a55f9f056a72fc7c .hgtags --- a/.hgtags +++ b/.hgtags @@ -9,7 +9,7 @@ 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 9bce3f426863f8ba88062f67c7efc1836e82ee7c latest_2014.06.02 -8f9dcac033694e4cabcf5daae5cca1cfefbe967f latest_2014.04.14 +b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 https://bitbucket.org/galaxy/galaxy-central/commits/ae4d7fb3f647/ Changeset: ae4d7fb3f647 Branch: stable User: jmchilton Date: 2015-01-15 21:01:29+00:00 Summary: Merge head created for backport bug fix on latest_2014.04.14 Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/c52dc4c72b77/ Changeset: c52dc4c72b77 Branch: stable User: jmchilton Date: 2015-01-15 21:01:30+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 9bce3f426863f8ba88062f67c7efc1836e82ee7c -r c52dc4c72b77e4b0849a596b6d05e4341236642a lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -348,7 +348,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys() if not self.tool or not self.tool.options or self.tool.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/a430a10e3db9/ Changeset: a430a10e3db9 Branch: stable User: jmchilton Date: 2015-01-15 21:01:31+00:00 Summary: Update tag latest_2014.06.02 for changeset c52dc4c72b77 Affected #: 1 file diff -r ae4d7fb3f6478e32b46eddbfc3b5f7f10c6ee246 -r a430a10e3db976c0981a782d54593923f00a20d7 .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,7 +8,7 @@ 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -9bce3f426863f8ba88062f67c7efc1836e82ee7c latest_2014.06.02 +c52dc4c72b77e4b0849a596b6d05e4341236642a latest_2014.06.02 b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 https://bitbucket.org/galaxy/galaxy-central/commits/4b8e3b14abc5/ Changeset: 4b8e3b14abc5 Branch: stable User: jmchilton Date: 2015-01-15 21:01:32+00:00 Summary: Merge head created for backport bug fix on latest_2014.06.02 Affected #: 1 file https://bitbucket.org/galaxy/galaxy-central/commits/6d6d7f8b3217/ Changeset: 6d6d7f8b3217 Branch: stable User: jmchilton Date: 2015-01-15 21:01:33+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r f3fc4602e22b39468d780b955a1a05caf867a7e9 -r 6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -348,7 +348,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys() if not self.tool or not self.tool.options or self.tool.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/93eeb569386c/ Changeset: 93eeb569386c Branch: stable User: jmchilton Date: 2015-01-15 21:01:34+00:00 Summary: Update tag latest_2014.08.11 for changeset 6d6d7f8b3217 Affected #: 1 file diff -r 4b8e3b14abc5e18d14985f8736ee652796e4f782 -r 93eeb569386c4af71a211e58621d180a5f3e963e .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,7 +18,7 @@ 52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 +6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 https://bitbucket.org/galaxy/galaxy-central/commits/464f7083f431/ Changeset: 464f7083f431 Branch: stable User: jmchilton Date: 2015-01-15 21:01:34+00:00 Summary: Merge head created for backport bug fix on latest_2014.08.11 Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/782fa60fc654/ Changeset: 782fa60fc654 Branch: stable User: jmchilton Date: 2015-01-15 21:01:35+00:00 Summary: Bugfix: Skip extra wrapping around template-style macros. Affected #: 1 file diff -r 9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 -r 782fa60fc65488aea0c618d723e9a63d42caf865 lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -348,7 +348,7 @@ Note: this method follows the style of the similar populate calls, in that param_dict is modified in-place. """ # chromInfo is a filename, do not sanitize it. - skip = [ 'chromInfo' ] + skip = [ 'chromInfo' ] + self.tool.template_macro_params.keys() if not self.tool or not self.tool.options or self.tool.options.sanitize: for key, value in param_dict.items(): if key not in skip: https://bitbucket.org/galaxy/galaxy-central/commits/cfdcc366831c/ Changeset: cfdcc366831c Branch: stable User: jmchilton Date: 2015-01-15 21:01:36+00:00 Summary: Update tag latest_2014.10.06 for changeset 782fa60fc654 Affected #: 1 file diff -r 464f7083f43112e1676af0271329eb4fe820bb25 -r cfdcc366831c310ef3eb413d9611dfac1b27b4d0 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,6 +20,6 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 +782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 3b559c4b9399236ae2a76ea1f061fcd660e76ed5 latest_2015.01.13 https://bitbucket.org/galaxy/galaxy-central/commits/cd6c14de33c5/ Changeset: cd6c14de33c5 Branch: stable User: jmchilton Date: 2015-01-15 21:01:37+00:00 Summary: Merge head created for backport bug fix on latest_2014.10.06 Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/fd75aaee91cf/ Changeset: fd75aaee91cf Branch: stable User: jmchilton Date: 2015-02-02 14:10:43+00:00 Summary: Merged in jmchilton/galaxy-central-backport-2/stable (pull request #638) [STABLE] Backport pull request #636 to all relevant latest_* releases Affected #: 3 files diff -r a7ae7afffa8fa7551ea760ca01e9c1808809391b -r fd75aaee91cf3e8a0916689dfea72e0c752c447c .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,18 +8,18 @@ 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -9bce3f426863f8ba88062f67c7efc1836e82ee7c latest_2014.06.02 -8f9dcac033694e4cabcf5daae5cca1cfefbe967f latest_2014.04.14 +c52dc4c72b77e4b0849a596b6d05e4341236642a latest_2014.06.02 +b2c0570f52e18d8661ca1d80c42867e4b036f22b latest_2014.04.14 9c323aad4ffdd65a3deb06a4a36f6b2c5115a60f latest_2013.01.13 b986c184be88947b5d1d90be7f36cfd2627dd938 latest_2013.02.08 dec9431d66b837a208e2f060d90afd913c721227 latest_2013.04.01 -19e56e66b0b344c6e2afa4541f6988e4fdb9af29 latest_2013.06.03 -cee903b8b3eee9145627ee89742555dac581791e latest_2013.08.12 -7d5aa19a166cba9039e15f338a1e3fc924c43d3a latest_2013.11.04 -0c000cc2f9c05bf4c1c2bc3a10215014fd64e696 latest_2014.02.10 +aae74ee09e4667e270750711327c8167e1dfae05 latest_2013.06.03 +db967a25c5db969ee4b3e138fe2be4d979665bdf latest_2013.08.12 +52a18b44474f017fce92850fb3892a4f76a7374a latest_2013.11.04 +746db2bf4da081a7491b5a4602aeadd2611b3b1d latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -f3fc4602e22b39468d780b955a1a05caf867a7e9 latest_2014.08.11 +6d6d7f8b321725a21a96ce21e7d18a3a66f7b72e latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 +782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 c5e7535b4d229dbbe52d48ea35a27ab601205b7b latest_2015.01.13 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Allow web-less job/workflow handlers.
by commits-noreply＠bitbucket.org 02 Feb '15

02 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/16efc5713d85/ Changeset: 16efc5713d85 User: jmchilton Date: 2015-02-02 05:54:51+00:00 Summary: Allow web-less job/workflow handlers. See notes in lib/galaxy/main.py for usage. lib/galaxy/main.py basically sets up an app (minus web controllers) very much in the way paste would but without binding it to a port. Pass --server-name to specify a server name (presumably a job handler found in job_conf.xml). An optional --daemonize mode is available - though it requires the daemonize library (install with `pip install daemonize`). Based on similar initial work in Pulsar (see https://github.com/galaxyproject/pulsar/blob/master/pulsar/daemon.py). Affected #: 2 files diff -r 57217275bebe445be7bdae43b9072bcca47ff3e7 -r 16efc5713d85f631c8ef9ad11895730f4747ea7e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -318,6 +318,9 @@ # Crummy, but PasteScript does not give you a way to determine this if arg.lower().startswith('--server-name='): self.server_name = arg.split('=', 1)[-1] + # Allow explicit override of server name in confg params + if "server_name" in kwargs: + self.server_name = kwargs.get("server_name") # Store all configured server names self.server_names = [] for section in global_conf_parser.sections(): diff -r 57217275bebe445be7bdae43b9072bcca47ff3e7 -r 16efc5713d85f631c8ef9ad11895730f4747ea7e lib/galaxy/main.py --- /dev/null +++ b/lib/galaxy/main.py @@ -0,0 +1,245 @@ +""" Entry point for starting Galaxy without starting as part of a web server. + +Example Usage: Start a job/workflow handler without a web server and with +a given name using. + +python lib/galaxy/main.py --server-name handler0 + +Start as a daemon with (requires daemonized - install with 'pip install daemonize'): + +python lib/galaxy/main.py -d --daemon-log-file=handler0-daemon.log --pid-file handler0.pid --server-name handler0 + +In daemon mode logging of Galaxy (as opposed to this script) is configured via +a loggers section in Galaxy's ini file - this can be overridden with sensible +defaults logging to a single file with the following: + +python lib/galaxy/main.py -d --server-name handler0 --daemon-log-file=handler0-daemon.log --pid-file handler0.pid --log-file handler0.log + +""" +import logging +from logging.config import fileConfig + +import functools +import os +import time +import sys + +try: + import ConfigParser as configparser +except ImportError: + import configparser + +try: + from daemonize import Daemonize +except ImportError: + Daemonize = None + +# Vaguely Python 2.6 compatibile ArgumentParser import +try: + from argparser import ArgumentParser +except ImportError: + from optparse import OptionParser + + class ArgumentParser(OptionParser): + + def __init__(self, **kwargs): + self.delegate = OptionParser(**kwargs) + + def add_argument(self, *args, **kwargs): + if "required" in kwargs: + del kwargs["required"] + return self.delegate.add_option(*args, **kwargs) + + def parse_args(self, args=None): + (options, args) = self.delegate.parse_args(args) + return options + +REQUIRES_DAEMONIZE_MESSAGE = "Attempted to use Galaxy in daemon mode, but daemonize is unavailable." + +log = logging.getLogger(__name__) + +GALAXY_ROOT_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")) +GALAXY_LIB_DIR = os.path.join(GALAXY_ROOT_DIR, "lib") +DEFAULT_INI_APP = "main" +DEFAULT_INIS = ["config/galaxy.ini", "universe_wsgi.ini", "config/galaxy.ini.sample"] + +DEFAULT_PID = "galaxy.pid" +DEFAULT_VERBOSE = True +DESCRIPTION = "Daemonized entry point for Galaxy." + + +def load_galaxy_app( + config_builder, + config_env=False, + log=None, + **kwds +): + # Allow specification of log so daemon can reuse properly configured one. + if log is None: + log = logging.getLogger(__name__) + + # If called in daemon mode, set the ROOT directory and ensure Galaxy is on + # sys.path. + if config_env: + try: + os.chdir(GALAXY_ROOT_DIR) + except Exception: + log.exception("Failed to chdir") + raise + try: + sys.path.append(GALAXY_LIB_DIR) + except Exception: + log.exception("Failed to add Galaxy to sys.path") + raise + + config_builder.setup_logging() + from galaxy.util.properties import load_app_properties + kwds = config_builder.app_kwds() + kwds = load_app_properties(**kwds) + from galaxy.app import UniverseApplication + app = UniverseApplication( + global_conf={"__file__": config_builder.ini_path}, + **kwds + ) + return app + + +def app_loop(args, log): + try: + config_builder = GalaxyConfigBuilder(args) + galaxy_app = load_galaxy_app( + config_builder, + config_env=True, + log=log, + ) + except BaseException: + log.exception("Failed to initialize Galaxy application") + raise + sleep = True + while sleep: + try: + time.sleep(5) + except KeyboardInterrupt: + sleep = False + except SystemExit: + sleep = False + except Exception: + pass + try: + galaxy_app.shutdown() + except Exception: + log.exception("Failed to shutdown Galaxy application") + raise + + +def absolute_config_path(path, galaxy_root): + if path and not os.path.isabs(path): + path = os.path.join(galaxy_root, path) + return path + + +def find_ini(supplied_ini, galaxy_root): + if supplied_ini: + return supplied_ini + + # If not explicitly supplied an ini, check server.ini and then + # just restort to sample if that has not been configured. + for guess in DEFAULT_INIS: + ini_path = os.path.join(galaxy_root, guess) + if os.path.exists(ini_path): + return ini_path + + return guess + + +class GalaxyConfigBuilder(object): + """ Generate paste-like configuration from supplied command-line arguments. + """ + + def __init__(self, args=None, **kwds): + ini_path = kwds.get("ini_path", None) or (args and args.ini_path) + # If given app_conf_path - use that - else we need to ensure we have an + # ini path. + if not ini_path: + galaxy_root = kwds.get("galaxy_root", GALAXY_ROOT_DIR) + ini_path = find_ini(ini_path, galaxy_root) + ini_path = absolute_config_path(ini_path, galaxy_root=galaxy_root) + self.ini_path = ini_path + self.app_name = kwds.get("app") or (args and args.app) or DEFAULT_INI_APP + self.log_file = (args and args.log_file) + + @classmethod + def populate_options(cls, arg_parser): + arg_parser.add_argument("-c", "--ini-path", default=None, help="Galaxy ini config file (defaults to config/galaxy.ini)") + arg_parser.add_argument("--app", default=DEFAULT_INI_APP, help="app section in ini file (defaults to main)") + arg_parser.add_argument("-d", "--daemonize", default=False, help="Daemonzie process", action="store_true") + arg_parser.add_argument("--daemon-log-file", default=None, help="log file for daemon script ") + arg_parser.add_argument("--log-file", default=None, help="Galaxy log file (overrides log configuration in ini_path if set)") + arg_parser.add_argument("--pid-file", default=DEFAULT_PID, help="pid file (default is %s)" % DEFAULT_PID) + arg_parser.add_argument("--server-name", default=None, help="set a galaxy server name") + + def app_kwds(self): + config = dict( + ini_file=self.ini_path, + ini_section="app:%s" % self.app_name, + ) + return config + + def setup_logging(self): + # Galaxy will attempt to setup logging if loggers is not present in + # ini config file - this handles that loggers block however if present + # (the way paste normally would) + if not self.ini_path: + return + raw_config = configparser.ConfigParser() + raw_config.read([self.ini_path]) + if raw_config.has_section('loggers'): + config_file = os.path.abspath(self.ini_path) + fileConfig( + config_file, + dict(__file__=config_file, here=os.path.dirname(config_file)) + ) + + +def main(): + if Daemonize is None: + raise ImportError(REQUIRES_DAEMONIZE_MESSAGE) + + arg_parser = ArgumentParser(description=DESCRIPTION) + GalaxyConfigBuilder.populate_options(arg_parser) + args = arg_parser.parse_args() + if args.log_file: + os.environ["GALAXY_CONFIG_LOG_DESTINATION"] = os.path.abspath(args.log_file) + if args.server_name: + os.environ["GALAXY_CONFIG_SERVER_NAME"] = args.server_name + pid_file = args.pid_file + + log.setLevel(logging.DEBUG) + log.propagate = False + if args.daemonize: + keep_fds = [] + if args.daemon_log_file: + fh = logging.FileHandler(args.daemon_log_file, "w") + fh.setLevel(logging.DEBUG) + log.addHandler(fh) + keep_fds.append(fh.stream.fileno()) + else: + fh = logging.StreamHandler(sys.stderr) + fh.setLevel(logging.DEBUG) + log.addHandler(fh) + + daemon = Daemonize( + app="galaxy", + pid=pid_file, + action=functools.partial(app_loop, args, log), + verbose=DEFAULT_VERBOSE, + logger=log, + keep_fds=keep_fds, + ) + daemon.start() + else: + app_loop(args, log) + + +if __name__ == "__main__": + main() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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[galaxyproject/usegalaxy-playbook] 284bbd: Dropped GCC TDay vote slide, added SupAgro trainin...
by GitHub 01 Feb '15

01 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 284bbd124a086ea48aeaff6be978fe638c10d374 https://github.com/galaxyproject/usegalaxy-playbook/commit/284bbd124a086ea4… Author: Dave Clements <clements(a)Clements-Galaxy.local> Date: 2015-01-31 (Sat, 31 Jan 2015) Changed paths: A files/galaxy/common/static/welcome_img/SupAgro201502.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped GCC TDay vote slide, added SupAgro training slide.

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galaxy-commits February 2015