December 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dannon: Delete *ancient* cron/cleanup_datsets.py content, but leave a nice deprecation warning and pointer for those who might actually be using it in cron jobs.
by commits-noreply＠bitbucket.org 17 Dec '14

17 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7e7a0c518d50/ Changeset: 7e7a0c518d50 User: dannon Date: 2014-12-17 16:00:29+00:00 Summary: Delete *ancient* cron/cleanup_datsets.py content, but leave a nice deprecation warning and pointer for those who might actually be using it in cron jobs. Affected #: 1 file diff -r 78597d2278e28ac962b80179d15eacd5849a4c79 -r 7e7a0c518d503cfc489dcb1fd8b1b9a113ed0e88 cron/cleanup_datasets.py --- a/cron/cleanup_datasets.py +++ b/cron/cleanup_datasets.py @@ -1,63 +1,8 @@ #!/usr/bin/env python -#This script removes deleted dataset files. -#Takes 3 arguments: -# 1: database directory to clean -# 2: postgres database name -# 3 (optional): number of days to allow as a buffer, defaults to 2 -#python cleanup_datasets.py /home/universe/server-home/wsgi-postgres/database/files/ galaxy_test 2 +import sys -import sys, os, tempfile, time -try: - database_dir = sys.argv[1] - database_name = sys.argv[2] - num_days = 2 - try: - num_days = int(sys.argv[3]) - except: - print "Using Default of 2 days buffer on delete" -except: - print "Usage: python %s path_to_files:/home/universe/server-home/wsgi-postgres/database/files/ database_name:galaxy_test [num_days_buffer:2]" % sys.argv[0] - sys.exit(0) -id_file = tempfile.NamedTemporaryFile('w') -id_filename = id_file.name -id_file.close() -ids = [] +print ("This script has been deprecated, replaced by the set of scripts in <galaxy_distribution>/scripts/cleanup_datsets/." + "See https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%2… for more information.") -command = "psql -d %s -c \"select id from dataset;\" -o %s" % (database_name, id_filename) -print "Getting IDs:", command -id_file = os.popen(command) -id_file.close() -for line in open(id_filename,'r'): - try: - ids.append(int(line.strip())) - except: - print line.strip(),"is not a valid id, skipping." -os.unlink(id_filename) -if len(ids) < 1: - print "Less than 1 IDs have been found! Deleting proccess has been canceled." - sys.exit(0) -print "-----%i IDs Retrieved -----" % len(ids) -print "----- Checking database directory for deleted ids: %s -----" % database_dir -file_size = 0 -num_delete = 0 -for result in os.walk(database_dir): - this_base_dir,sub_dirs,files = result - for file in files: - if file.startswith("dataset_") and file.endswith(".dat"): - id = int(file.replace("dataset_","").replace(".dat","")) - file_name = os.path.join(this_base_dir,file) - if id not in ids: - file_time = os.path.getctime(file_name) - if time.time() > file_time + (num_days*60*60*24): #num_days (default=2) days buffer room - num_delete += 1 - size = os.path.getsize(file_name) - file_size += size - os.unlink(file_name) -print file_size, "bytes" -print float(file_size) / 1024, "kilobytes" -print float(file_size) / 1024 / 1024, "Megabytes" -print float(file_size) / 1024 / 1024 / 1024, "Gigabytes" -print "%i files deleted" % num_delete - -sys.exit(0) \ No newline at end of file +sys.exit(1) 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: jmchilton: Fix a74d320.
by commits-noreply＠bitbucket.org 17 Dec '14

17 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/05604a5d31c1/ Changeset: 05604a5d31c1 Branch: next-stable User: jmchilton Date: 2014-12-17 15:57:44+00:00 Summary: Fix a74d320. Affected #: 1 file diff -r a74d32014b0512613042c2a44d0b946703a1fbcd -r 05604a5d31c1b150d4a04347e68c0f30f2d0a598 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -195,8 +195,7 @@ if isinstance( value, basic.DataToolParameter ): if not isinstance(param_value, list): param_value = [ param_value ] - map( lambda v: self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ), -param_value ) + map( lambda v: self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ), param_value ) processed_value = param_value elif isinstance( value, basic.DataCollectionToolParameter ): assert 'collection' in param_extra 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: jmchilton: Merge next-stable.
by commits-noreply＠bitbucket.org 17 Dec '14

17 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/78597d2278e2/ Changeset: 78597d2278e2 User: jmchilton Date: 2014-12-17 14:41:26+00:00 Summary: Merge next-stable. Affected #: 3 files diff -r e614c7c1e0e9648076759c06dc33ed48b1847b13 -r 78597d2278e28ac962b80179d15eacd5849a4c79 test/functional/tools/gzipped_inputs.xml --- /dev/null +++ b/test/functional/tools/gzipped_inputs.xml @@ -0,0 +1,19 @@ +<tool id="gzipped_inputs" name="Echo Dataset"> + <command> + cat $input1 > $out_file1 + </command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset"/> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + </outputs> + <tests> + <test> + <param name="input1" value="4.bed.gz" /> + <output name="out_file1" file="4.bed" /> + </test> + </tests> + <help> + </help> +</tool> diff -r e614c7c1e0e9648076759c06dc33ed48b1847b13 -r 78597d2278e28ac962b80179d15eacd5849a4c79 test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -13,6 +13,7 @@ <tool file="multi_output_assign_primary.xml" /><tool file="composite_output.xml" /><tool file="metadata.xml" /> + <tool file="gzipped_inputs.xml" /><tool file="output_order.xml" /><tool file="output_format.xml" /><tool file="output_filter.xml" /> 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: jmchilton: Fix gz/zip upload of files to test framework.
by commits-noreply＠bitbucket.org 17 Dec '14

17 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a74d32014b05/ Changeset: a74d32014b05 Branch: next-stable User: jmchilton Date: 2014-12-17 14:38:49+00:00 Summary: Fix gz/zip upload of files to test framework. With test case to ensure they don't break again. Problem was due to a small switch of an if to an elif in 7114d15a6d22 which had been sort of masking over an older bug. Thanks to Peter Cock for reporting the issue. Affected #: 3 files diff -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a -r a74d32014b0512613042c2a44d0b946703a1fbcd lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -195,7 +195,9 @@ if isinstance( value, basic.DataToolParameter ): if not isinstance(param_value, list): param_value = [ param_value ] - processed_value = [ self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ) for v in param_value ] + map( lambda v: self.__add_uploaded_dataset( context.for_state(), v, param_extra, value ), +param_value ) + processed_value = param_value elif isinstance( value, basic.DataCollectionToolParameter ): assert 'collection' in param_extra collection_def = param_extra[ 'collection' ] diff -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a -r a74d32014b0512613042c2a44d0b946703a1fbcd test/functional/tools/gzipped_inputs.xml --- /dev/null +++ b/test/functional/tools/gzipped_inputs.xml @@ -0,0 +1,19 @@ +<tool id="gzipped_inputs" name="Echo Dataset"> + <command> + cat $input1 > $out_file1 + </command> + <inputs> + <param name="input1" type="data" label="Concatenate Dataset"/> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + </outputs> + <tests> + <test> + <param name="input1" value="4.bed.gz" /> + <output name="out_file1" file="4.bed" /> + </test> + </tests> + <help> + </help> +</tool> diff -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a -r a74d32014b0512613042c2a44d0b946703a1fbcd test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -11,6 +11,7 @@ <tool file="multi_output_configured.xml" /><tool file="composite_output.xml" /><tool file="metadata.xml" /> + <tool file="gzipped_inputs.xml" /><tool file="output_order.xml" /><tool file="output_format.xml" /><tool file="output_filter.xml" /> 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: natefoo: Update tag latest_2014.10.06 for changeset 5834b1066462
by commits-noreply＠bitbucket.org 17 Dec '14

17 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7197e949d3ab/ Changeset: 7197e949d3ab Branch: stable User: natefoo Date: 2014-12-17 14:00:15+00:00 Summary: Update tag latest_2014.10.06 for changeset 5834b1066462 Affected #: 1 file diff -r 5834b1066462dd219f67c1c3cbd77c78e7cf3a6c -r 7197e949d3ab990ceb76c193ebc940d90aa04cad .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06 +5834b1066462dd219f67c1c3cbd77c78e7cf3a6c latest_2014.10.06 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: 2 new changesets
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d13f2b265dbf/ Changeset: d13f2b265dbf User: Nitesh Turaga Date: 2014-12-16 16:04:58+00:00 Summary: "shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also. Affected #: 1 file diff -r bd380f15c1b3b8a8b81d2759eaacd30e94c58d68 -r d13f2b265dbf58c60ce4f13bcc902c4848c65c7c config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -136,7 +136,7 @@ # Tools can be locally developed or installed from Galaxy tool sheds. # (config/tool_conf.xml.sample will be used if left unset and # config/tool_conf.xml does not exist). -#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml +#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml # Enable / disable checking if any tools defined in the above non-shed tool_config_files # (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool https://bitbucket.org/galaxy/galaxy-central/commits/e614c7c1e0e9/ Changeset: e614c7c1e0e9 User: dannon Date: 2014-12-16 20:48:44+00:00 Summary: Merged in nitesh1989/galaxy-central3 (pull request #615) "shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also. Affected #: 1 file diff -r 1cf0af0a6324e24a0008f5ceff598573262f14ca -r e614c7c1e0e9648076759c06dc33ed48b1847b13 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -136,7 +136,7 @@ # Tools can be locally developed or installed from Galaxy tool sheds. # (config/tool_conf.xml.sample will be used if left unset and # config/tool_conf.xml does not exist). -#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml +#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml # Enable / disable checking if any tools defined in the above non-shed tool_config_files # (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool 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: dannon: Merged in nitesh1989/galaxy-central3 (pull request #615)
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e614c7c1e0e9/ Changeset: e614c7c1e0e9 User: dannon Date: 2014-12-16 20:48:44+00:00 Summary: Merged in nitesh1989/galaxy-central3 (pull request #615) "shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also. Affected #: 1 file diff -r 1cf0af0a6324e24a0008f5ceff598573262f14ca -r e614c7c1e0e9648076759c06dc33ed48b1847b13 config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -136,7 +136,7 @@ # Tools can be locally developed or installed from Galaxy tool sheds. # (config/tool_conf.xml.sample will be used if left unset and # config/tool_conf.xml does not exist). -#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml +#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml # Enable / disable checking if any tools defined in the above non-shed tool_config_files # (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool 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: 2 new changesets
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31f0b0cbb4ef/ Changeset: 31f0b0cbb4ef Branch: next-stable User: davebgx Date: 2014-12-16 20:15:57+00:00 Summary: Merge stable into next-stable. Affected #: 2 files diff -r d1f9d077c2288b25a35ae97e306cdf2924548d62 -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -e416697be38e66f18be89a4cfca70457c9784294 latest_2014.10.06 +7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06 diff -r d1f9d077c2288b25a35ae97e306cdf2924548d62 -r 31f0b0cbb4ef7d2af357bbe43a77127d7b546c5a lib/tool_shed/util/repository_util.py --- a/lib/tool_shed/util/repository_util.py +++ b/lib/tool_shed/util/repository_util.py @@ -322,8 +322,8 @@ return 'You have a deleted repository named %s, so choose a different name.' % name else: return "You already have a repository named %s, so choose a different name." % name - if len( name ) < 4: - return "Repository names must be at least 4 characters in length." + if len( name ) < 2: + return "Repository names must be at least 2 characters in length." if len( name ) > 80: return "Repository names cannot be more than 80 characters in length." if not( VALID_REPOSITORYNAME_RE.match( name ) ): https://bitbucket.org/galaxy/galaxy-central/commits/1cf0af0a6324/ Changeset: 1cf0af0a6324 User: davebgx Date: 2014-12-16 20:16:18+00:00 Summary: Merge next-stable into default. Affected #: 2 files diff -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 -r 1cf0af0a6324e24a0008f5ceff598573262f14ca .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -e416697be38e66f18be89a4cfca70457c9784294 latest_2014.10.06 +7086b87d83a9092cbece0fec6f3e3ed03266be0c latest_2014.10.06 diff -r 1210ec53702661e4c04d4b741d90d0d49d44bba7 -r 1cf0af0a6324e24a0008f5ceff598573262f14ca lib/tool_shed/util/repository_util.py --- a/lib/tool_shed/util/repository_util.py +++ b/lib/tool_shed/util/repository_util.py @@ -325,8 +325,8 @@ return 'You have a deleted repository named %s, so choose a different name.' % name else: return "You already have a repository named %s, so choose a different name." % name - if len( name ) < 4: - return "Repository names must be at least 4 characters in length." + if len( name ) < 2: + return "Repository names must be at least 2 characters in length." if len( name ) > 80: return "Repository names cannot be more than 80 characters in length." if not( VALID_REPOSITORYNAME_RE.match( name ) ): 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: davebgx: Reduce minimum length of repository names from 4 characters to 2.
by commits-noreply＠bitbucket.org 16 Dec '14

16 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5834b1066462/ Changeset: 5834b1066462 Branch: stable User: davebgx Date: 2014-12-16 20:00:50+00:00 Summary: Reduce minimum length of repository names from 4 characters to 2. Affected #: 1 file diff -r c265480083ecb81f1e968521932342137807601c -r 5834b1066462dd219f67c1c3cbd77c78e7cf3a6c lib/tool_shed/util/repository_util.py --- a/lib/tool_shed/util/repository_util.py +++ b/lib/tool_shed/util/repository_util.py @@ -322,8 +322,8 @@ return 'You have a deleted repository named %s, so choose a different name.' % name else: return "You already have a repository named %s, so choose a different name." % name - if len( name ) < 4: - return "Repository names must be at least 4 characters in length." + if len( name ) < 2: + return "Repository names must be at least 2 characters in length." if len( name ) > 80: return "Repository names cannot be more than 80 characters in length." if not( VALID_REPOSITORYNAME_RE.match( name ) ): 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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[galaxyproject/usegalaxy-playbook] d5c9a8: Updated shed tools on Test
by GitHub 16 Dec '14

16 Dec '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d5c9a8fcc4942c1e0b8d6a7edb118c243e6cc7cb https://github.com/galaxyproject/usegalaxy-playbook/commit/d5c9a8fcc4942c1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-12-16 (Tue, 16 Dec 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- Updated shed tools on Test Commit: 8977b7af2dd8512a34aaa3dcbd7711a54d6c1228 https://github.com/galaxyproject/usegalaxy-playbook/commit/8977b7af2dd8512a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-12-16 (Tue, 16 Dec 2014) Changed paths: M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Remove downtime banner. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/e8119d8b39f7...…

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