commit/galaxy-central: 4 new changesets
by commits-noreply@bitbucket.org
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/
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7 years, 3 months
commit/galaxy-central: jmchilton: Merged in jmchilton/galaxy-central-backport-2/stable (pull request #638)
by commits-noreply@bitbucket.org
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/
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7 years, 3 months
commit/galaxy-central: 25 new changesets
by commits-noreply@bitbucket.org
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/
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7 years, 3 months
commit/galaxy-central: jmchilton: Allow web-less job/workflow handlers.
by commits-noreply@bitbucket.org
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/
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7 years, 3 months