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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 06 Jun '13

06 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ba00a72c8008/ Changeset: ba00a72c8008 User: greg Date: 2013-06-06 21:05:10 Summary: A slight variation on Nick Soranzo's pull request # 176 for fixing large file downloades using download_by_url. Affected #: 3 files diff -r 5de636ce68faededc52d7b0c16167fbef98be786 -r ba00a72c8008bdec310b69ccf980d374341f0113 lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -222,9 +222,13 @@ dst = None try: src = urllib2.urlopen( download_url ) - data = src.read() - dst = open( file_path,'wb' ) - dst.write( data ) + dst = open( file_path, 'wb' ) + while True: + chunk = src.read( suc.CHUNK_SIZE ) + if chunk: + dst.write( chunk ) + else: + break except: raise finally: diff -r 5de636ce68faededc52d7b0c16167fbef98be786 -r ba00a72c8008bdec310b69ccf980d374341f0113 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -21,7 +21,6 @@ UNDESIRABLE_DIRS = [ '.hg', '.svn', '.git', '.cvs' ] UNDESIRABLE_FILES = [ '.hg_archival.txt', 'hgrc', '.DS_Store' ] -CHUNK_SIZE = 2**20 # 1Mb def check_archive( archive ): for member in archive.getmembers(): @@ -86,7 +85,7 @@ bzipped_file = bz2.BZ2File( uploaded_file_name, 'rb' ) while 1: try: - chunk = bzipped_file.read( CHUNK_SIZE ) + chunk = bzipped_file.read( suc.CHUNK_SIZE ) except IOError: os.close( fd ) os.remove( uncompressed ) @@ -170,7 +169,7 @@ gzipped_file = gzip.GzipFile( uploaded_file_name, 'rb' ) while 1: try: - chunk = gzipped_file.read( CHUNK_SIZE ) + chunk = gzipped_file.read( suc.CHUNK_SIZE ) except IOError, e: os.close( fd ) os.remove( uncompressed ) diff -r 5de636ce68faededc52d7b0c16167fbef98be786 -r ba00a72c8008bdec310b69ccf980d374341f0113 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -29,6 +29,7 @@ log = logging.getLogger( __name__ ) +CHUNK_SIZE = 2**20 # 1Mb INITIAL_CHANGELOG_HASH = '000000000000' MAX_CONTENT_SIZE = 1048576 MAX_DISPLAY_SIZE = 32768 https://bitbucket.org/galaxy/galaxy-central/commits/68db2c690037/ Changeset: 68db2c690037 Branch: stable User: greg Date: 2013-06-06 21:05:10 Summary: A slight variation on Nick Soranzo's pull request # 176 for fixing large file downloades using download_by_url. Affected #: 3 files diff -r 2a1459ef5bc402c585f24c904e0d5ad82a7326db -r 68db2c6900376fb8b56dae6b501c68cb598fd153 lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -222,9 +222,13 @@ dst = None try: src = urllib2.urlopen( download_url ) - data = src.read() - dst = open( file_path,'wb' ) - dst.write( data ) + dst = open( file_path, 'wb' ) + while True: + chunk = src.read( suc.CHUNK_SIZE ) + if chunk: + dst.write( chunk ) + else: + break except: raise finally: diff -r 2a1459ef5bc402c585f24c904e0d5ad82a7326db -r 68db2c6900376fb8b56dae6b501c68cb598fd153 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -21,7 +21,6 @@ UNDESIRABLE_DIRS = [ '.hg', '.svn', '.git', '.cvs' ] UNDESIRABLE_FILES = [ '.hg_archival.txt', 'hgrc', '.DS_Store' ] -CHUNK_SIZE = 2**20 # 1Mb def check_archive( archive ): for member in archive.getmembers(): @@ -86,7 +85,7 @@ bzipped_file = bz2.BZ2File( uploaded_file_name, 'rb' ) while 1: try: - chunk = bzipped_file.read( CHUNK_SIZE ) + chunk = bzipped_file.read( suc.CHUNK_SIZE ) except IOError: os.close( fd ) os.remove( uncompressed ) @@ -170,7 +169,7 @@ gzipped_file = gzip.GzipFile( uploaded_file_name, 'rb' ) while 1: try: - chunk = gzipped_file.read( CHUNK_SIZE ) + chunk = gzipped_file.read( suc.CHUNK_SIZE ) except IOError, e: os.close( fd ) os.remove( uncompressed ) diff -r 2a1459ef5bc402c585f24c904e0d5ad82a7326db -r 68db2c6900376fb8b56dae6b501c68cb598fd153 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -29,6 +29,7 @@ log = logging.getLogger( __name__ ) +CHUNK_SIZE = 2**20 # 1Mb INITIAL_CHANGELOG_HASH = '000000000000' MAX_CONTENT_SIZE = 1048576 MAX_DISPLAY_SIZE = 32768 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 06 Jun '13

06 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f9e3822c6407/ Changeset: f9e3822c6407 User: lance_parsons Date: 2012-12-10 22:23:11 Summary: Fix for Postgres versions < 9 (see https://trello.com/c/Z0EynAV2) Affected #: 1 file diff -r c3acc86490780d1949c4a3abf1263ace7c5ece6c -r f9e3822c64072c8466a39b5cbeaa4387e0c28ac8 scripts/set_user_disk_usage.py --- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -52,7 +52,7 @@ sql = """ UPDATE galaxy_user SET disk_usage = (SELECT COALESCE(SUM(total_size), 0) - FROM ( SELECT d.total_size + FROM ( SELECT DISTINCT ON (d.id) d.total_size, d.id FROM history_dataset_association hda JOIN history h ON h.id = hda.history_id JOIN dataset d ON hda.dataset_id = d.id @@ -62,7 +62,7 @@ AND d.purged = false AND d.id NOT IN (SELECT dataset_id FROM library_dataset_dataset_association) - GROUP BY d.id) sizes) + ) sizes) WHERE id = :id RETURNING disk_usage; """ https://bitbucket.org/galaxy/galaxy-central/commits/5de636ce68fa/ Changeset: 5de636ce68fa User: dannon Date: 2013-06-06 16:21:57 Summary: Merged in lance_parsons/galaxy-central_postgres-user-disk-usage-fix (pull request #97) Fix for Postgres versions < 9 Affected #: 1 file diff -r af91c734dbb76b8c0e3166c7471370f9ba8260b5 -r 5de636ce68faededc52d7b0c16167fbef98be786 scripts/set_user_disk_usage.py --- a/scripts/set_user_disk_usage.py +++ b/scripts/set_user_disk_usage.py @@ -52,7 +52,7 @@ sql = """ UPDATE galaxy_user SET disk_usage = (SELECT COALESCE(SUM(total_size), 0) - FROM ( SELECT d.total_size + FROM ( SELECT DISTINCT ON (d.id) d.total_size, d.id FROM history_dataset_association hda JOIN history h ON h.id = hda.history_id JOIN dataset d ON hda.dataset_id = d.id @@ -62,7 +62,7 @@ AND d.purged = false AND d.id NOT IN (SELECT dataset_id FROM library_dataset_dataset_association) - GROUP BY d.id) sizes) + ) sizes) WHERE id = :id RETURNING disk_usage; """ 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 05 Jun '13

05 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2a1459ef5bc4/ Changeset: 2a1459ef5bc4 Branch: stable User: natefoo Date: 2013-06-05 21:25:19 Summary: Fix a couple bugs in job recovery in the Condor runner found by Branden Timm. Affected #: 1 file diff -r 47b86d6a9077facb54804576be49ca545d18bd4e -r 2a1459ef5bc402c585f24c904e0d5ad82a7326db lib/galaxy/jobs/runners/condor.py --- a/lib/galaxy/jobs/runners/condor.py +++ b/lib/galaxy/jobs/runners/condor.py @@ -232,6 +232,7 @@ """Recovers jobs stuck in the queued/running state when Galaxy started""" # TODO Check if we need any changes here job_id = job.get_job_runner_external_id() + galaxy_id_tag = job_wrapper.get_id_tag() if job_id is None: self.put( job_wrapper ) return @@ -252,7 +253,7 @@ cjs.running = False self.monitor_queue.put( cjs ) - def __old_state_paths( self, cjs, job ): + def __old_state_paths( self, cjs ): """For recovery of jobs started prior to standardizing the naming of files in the AsychronousJobState object """ https://bitbucket.org/galaxy/galaxy-central/commits/af91c734dbb7/ Changeset: af91c734dbb7 User: natefoo Date: 2013-06-05 21:25:30 Summary: Merge stable Affected #: 1 file diff -r 89d391f23c1bfb9a745b03095dbcf0459b830e19 -r af91c734dbb76b8c0e3166c7471370f9ba8260b5 lib/galaxy/jobs/runners/condor.py --- a/lib/galaxy/jobs/runners/condor.py +++ b/lib/galaxy/jobs/runners/condor.py @@ -232,6 +232,7 @@ """Recovers jobs stuck in the queued/running state when Galaxy started""" # TODO Check if we need any changes here job_id = job.get_job_runner_external_id() + galaxy_id_tag = job_wrapper.get_id_tag() if job_id is None: self.put( job_wrapper ) return @@ -252,7 +253,7 @@ cjs.running = False self.monitor_queue.put( cjs ) - def __old_state_paths( self, cjs, job ): + def __old_state_paths( self, cjs ): """For recovery of jobs started prior to standardizing the naming of files in the AsychronousJobState object """ 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: 3 new changesets
by commits-noreply＠bitbucket.org 05 Jun '13

05 Jun '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/81a20de198df/ Changeset: 81a20de198df User: dannon Date: 2013-06-05 17:24:55 Summary: Require decorator in manage_db.py -- resolves decorator not found for particular deployments Affected #: 1 file diff -r 4612c80302918943c3b4375613554a4f4960e8c8 -r 81a20de198df2480ef9ba4dfb87201ba14e048cc scripts/manage_db.py --- a/scripts/manage_db.py +++ b/scripts/manage_db.py @@ -6,6 +6,7 @@ from galaxy import eggs +eggs.require( "decorator" ) eggs.require( "Tempita" ) eggs.require( "SQLAlchemy" ) eggs.require( "sqlalchemy_migrate" ) https://bitbucket.org/galaxy/galaxy-central/commits/47b86d6a9077/ Changeset: 47b86d6a9077 Branch: stable User: dannon Date: 2013-06-05 17:24:55 Summary: Require decorator in manage_db.py -- resolves decorator not found for particular deployments Affected #: 1 file diff -r c4096b030f10eb346b24da98ce16b72d23672f03 -r 47b86d6a9077facb54804576be49ca545d18bd4e scripts/manage_db.py --- a/scripts/manage_db.py +++ b/scripts/manage_db.py @@ -6,6 +6,7 @@ from galaxy import eggs +eggs.require( "decorator" ) eggs.require( "Tempita" ) eggs.require( "SQLAlchemy" ) eggs.require( "sqlalchemy_migrate" ) https://bitbucket.org/galaxy/galaxy-central/commits/89d391f23c1b/ Changeset: 89d391f23c1b User: dannon Date: 2013-06-05 17:25:24 Summary: Merge with stable Affected #: 0 files 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: 3 new changesets
by commits-noreply＠bitbucket.org 05 Jun '13

05 Jun '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4c31bdad50d2/ Changeset: 4c31bdad50d2 User: dannon Date: 2013-06-05 16:13:40 Summary: Strip select2 behavior from quota, role, and group creation in the admin panel Affected #: 3 files diff -r a6e2e099e89ad9d59d4bd40531b8ea6d0673879e -r 4c31bdad50d226f6eb8ae11b74100d3f7d248b6c templates/admin/dataset_security/group/group_create.mako --- a/templates/admin/dataset_security/group/group_create.mako +++ b/templates/admin/dataset_security/group/group_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> diff -r a6e2e099e89ad9d59d4bd40531b8ea6d0673879e -r 4c31bdad50d226f6eb8ae11b74100d3f7d248b6c templates/admin/dataset_security/role/role_create.mako --- a/templates/admin/dataset_security/role/role_create.mako +++ b/templates/admin/dataset_security/role/role_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> diff -r a6e2e099e89ad9d59d4bd40531b8ea6d0673879e -r 4c31bdad50d226f6eb8ae11b74100d3f7d248b6c templates/admin/quota/quota_create.mako --- a/templates/admin/quota/quota_create.mako +++ b/templates/admin/quota/quota_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> https://bitbucket.org/galaxy/galaxy-central/commits/c4096b030f10/ Changeset: c4096b030f10 Branch: stable User: dannon Date: 2013-06-05 16:13:40 Summary: Strip select2 behavior from quota, role, and group creation in the admin panel Affected #: 3 files diff -r 7f26e0efb93bfb139798593ba1049c639db2ccd2 -r c4096b030f10eb346b24da98ce16b72d23672f03 templates/admin/dataset_security/group/group_create.mako --- a/templates/admin/dataset_security/group/group_create.mako +++ b/templates/admin/dataset_security/group/group_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> diff -r 7f26e0efb93bfb139798593ba1049c639db2ccd2 -r c4096b030f10eb346b24da98ce16b72d23672f03 templates/admin/dataset_security/role/role_create.mako --- a/templates/admin/dataset_security/role/role_create.mako +++ b/templates/admin/dataset_security/role/role_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> diff -r 7f26e0efb93bfb139798593ba1049c639db2ccd2 -r c4096b030f10eb346b24da98ce16b72d23672f03 templates/admin/quota/quota_create.mako --- a/templates/admin/quota/quota_create.mako +++ b/templates/admin/quota/quota_create.mako @@ -40,6 +40,8 @@ $(this).attr("selected", "selected"); }); }); + //Temporary removal of select2 for inputs -- refactor this later. + $('select').select2("destroy"); }); </script> https://bitbucket.org/galaxy/galaxy-central/commits/4612c8030291/ Changeset: 4612c8030291 User: dannon Date: 2013-06-05 16:14:37 Summary: Merge w/ stable Affected #: 4 files diff -r 4c31bdad50d226f6eb8ae11b74100d3f7d248b6c -r 4612c80302918943c3b4375613554a4f4960e8c8 .hgtags --- a/.hgtags +++ b/.hgtags @@ -2,3 +2,4 @@ 1c717491139269651bb59687563da9410b84c65d release_2013.02.08 75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 +524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 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 05 Jun '13

05 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a6e2e099e89a/ Changeset: a6e2e099e89a User: greg Date: 2013-06-05 15:58:11 Summary: Fix for handling multiple repository installations simultaneously when handle repository dependencies is checked and at least 1 selected repository for installation has no repository dependencies while at least one selected repository for installation does. This scenario occurs only when searching the tool shed for tools rather than browssing it for repositories. Affected #: 1 file diff -r 583f5edfc5977d92f884d86eb9f1af22294fe4c7 -r a6e2e099e89ad9d59d4bd40531b8ea6d0673879e lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -252,6 +252,8 @@ # We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool shed to discover repository ids. required_repository_tups = [] for repo_info_dict in repo_info_dicts: + if repo_info_dict not in all_repo_info_dicts: + all_repo_info_dicts.append( repo_info_dict ) for repository_name, repo_info_tup in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tup ) https://bitbucket.org/galaxy/galaxy-central/commits/7f26e0efb93b/ Changeset: 7f26e0efb93b Branch: stable User: greg Date: 2013-06-05 15:58:11 Summary: Fix for handling multiple repository installations simultaneously when handle repository dependencies is checked and at least 1 selected repository for installation has no repository dependencies while at least one selected repository for installation does. This scenario occurs only when searching the tool shed for tools rather than browssing it for repositories. Affected #: 1 file diff -r 2dd18c7198ad7ff1c354dbefa0715b2344360487 -r 7f26e0efb93bfb139798593ba1049c639db2ccd2 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -252,6 +252,8 @@ # We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool shed to discover repository ids. required_repository_tups = [] for repo_info_dict in repo_info_dicts: + if repo_info_dict not in all_repo_info_dicts: + all_repo_info_dicts.append( repo_info_dict ) for repository_name, repo_info_tup in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tup ) 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: Dave Bouvier: Add information on why a repository was not tested, if it has been configured not to be tested.
by commits-noreply＠bitbucket.org 04 Jun '13

04 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/583f5edfc597/ Changeset: 583f5edfc597 User: Dave Bouvier Date: 2013-06-04 21:54:28 Summary: Add information on why a repository was not tested, if it has been configured not to be tested. Affected #: 1 file diff -r 393b3d86fbf1b8c1471faef828de31110d3a90f5 -r 583f5edfc5977d92f884d86eb9f1af22294fe4c7 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -743,6 +743,10 @@ skip_because = reason break if skip_this_repository: + repository_status[ 'not_tested' ] = dict( reason=skip_because ) + params[ 'tools_functionally_correct' ] = False + params[ 'do_not_test' ] = False + register_test_result( galaxy_tool_shed_url, metadata_revision_id, repository_status, repository_info_dict, params ) log.info( "Not testing revision %s of repository %s owned by %s.", changeset_revision, name, owner ) continue else: @@ -854,6 +858,10 @@ # "missing_components": "Which components are missing, e.g. the test data filename, or the test-data directory." # }, # ] + # "not_tested": + # { + # "reason": "The Galaxy development team has determined that this repository should not be installed and tested by the automated framework." + # } # } failed_tool_dependencies = repository.includes_tool_dependencies and repository.tool_dependencies_with_installation_errors failed_repository_dependencies = repository.repository_dependencies_with_installation_errors 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: greg: Add a not tested container for the automated tool test results in the tool shed.
by commits-noreply＠bitbucket.org 04 Jun '13

04 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/393b3d86fbf1/ Changeset: 393b3d86fbf1 User: greg Date: 2013-06-04 21:50:25 Summary: Add a not tested container for the automated tool test results in the tool shed. Affected #: 2 files diff -r 4466b12313cc7e22e941c1255ba989e3adbbadf1 -r 393b3d86fbf1b8c1471faef828de31110d3a90f5 lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -36,6 +36,7 @@ self.tool_dependencies = [] self.failed_tests = [] self.missing_test_components = [] + self.not_tested = [] self.passed_tests = [] self.test_environments = [] self.repository_dependencies = [] @@ -161,6 +162,14 @@ self.tool_version = tool_version +class NotTested( object ): + """NotTested object""" + + def __init__( self, id=None, reason=None ): + self.id = id + self.reason = reason + + class PassedTest( object ): """Passed tool tests object""" @@ -1048,6 +1057,15 @@ tool_shed_mercurial_version=test_environment_dict.get( 'tool_shed_mercurial_version', '' ), tool_shed_revision=test_environment_dict.get( 'tool_shed_revision', '' ) ) folder.test_environments.append( test_environment ) + not_tested_dict = tool_test_results_dict.get( 'not_tested', {} ) + if not_tested_dict: + folder_id += 1 + folder = Folder( id=folder_id, key='not_tested', label='Not tested', parent=test_results_folder ) + test_results_folder.folders.append( folder ) + not_tested_id = 0 + not_tested = NotTested( id=not_tested_id, + reason=not_tested_dict.get( 'reason', '' ) ) + folder.not_tested.append( not_tested ) passed_tests_dicts = tool_test_results_dict.get( 'passed_tests', [] ) if passed_tests_dicts: folder_id += 1 diff -r 4466b12313cc7e22e941c1255ba989e3adbbadf1 -r 393b3d86fbf1b8c1471faef828de31110d3a90f5 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -337,6 +337,11 @@ ${render_failed_test( failed_test, pad, my_row, row_counter )} %endfor %endif + %if folder.not_tested: + %for not_tested in folder.not_tested: + ${render_not_tested( not_tested, pad, my_row, row_counter )} + %endfor + %endif %if folder.passed_tests: %for passed_test in folder.passed_tests: ${render_passed_test( passed_test, pad, my_row, row_counter )} @@ -731,6 +736,35 @@ %></%def> +<%def name="render_not_tested( not_tested, pad, parent, row_counter, row_is_header=False )"> + <% encoded_id = trans.security.encode_id( not_tested.id ) %> + <style type="text/css"> + #not_tested_table{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } + </style> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-${encoded_id}"> + <td style="padding-left: ${pad+20}px;"> + <table id="not_tested_table"> + <tr><td>${not_tested.reason | h}</td></tr> + </table> + </td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + <%def name="render_passed_test( passed_test, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( passed_test.id ) %><style type="text/css"> 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: afgane: Add tabindex to cloudlaunch and set the width for select boxes
by commits-noreply＠bitbucket.org 04 Jun '13

04 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4466b12313cc/ Changeset: 4466b12313cc User: afgane Date: 2013-06-04 20:24:10 Summary: Add tabindex to cloudlaunch and set the width for select boxes Affected #: 1 file diff -r a28faa6ac188594a60cd495327661a15efd37ea5 -r 4466b12313cc7e22e941c1255ba989e3adbbadf1 templates/webapps/galaxy/cloud/index.mako --- a/templates/webapps/galaxy/cloud/index.mako +++ b/templates/webapps/galaxy/cloud/index.mako @@ -186,16 +186,16 @@ <div class="form-row"><label for="id_key_id">Key ID</label> - <input type="text" size="30" maxlength="20" name="key_id" id="id_key_id" value=""/><br/> + <input type="text" size="30" maxlength="20" name="key_id" id="id_key_id" value="" tabindex="1"/><br/><div class="toolParamHelp"> - This is the text string that uniquely identifies your account, found in the + This is the text string that uniquely identifies your account, found in the <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security Credentials section of the AWS Console</a>. </div></div><div class="form-row"><label for="id_secret">Secret Key</label> - <input type="text" size="50" maxlength="40" name="secret" id="id_secret" value=""/><br/> + <input type="text" size="50" maxlength="40" name="secret" id="id_secret" value="" tabindex="2"/><br/><div class="toolParamHelp"> This is your AWS Secret Key, also found in the <a href="https://portal.aws.amazon.com/gp/aws/securityCredentials">Security Credentials section of the AWS Console</a>. </div> @@ -205,7 +205,7 @@ %if not share_string: <div id='existing_instance_wrapper' style="display:none;" class="form-row"><label for="id_existing_instance">Instances in your account</label> - <select name="existing_instance" id="id_existing_instance"> + <select name="existing_instance" id="id_existing_instance" style="min-width: 228px"></select><input id='id_zone' type='hidden' name='zone' value=''/></div> @@ -231,7 +231,7 @@ <div class="form-row"><label for="id_keypair">Key Pair</label> - <select name="keypair" id="id_keypair"> + <select name="keypair" id="id_keypair" style="min-width: 228px"><option name="Create" value="cloudman_keypair">cloudman_keypair</option></select></div> 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: dan: Data Managers: allow multiple value translations to be specifed per column and also allow multiple types of value translations.
by commits-noreply＠bitbucket.org 04 Jun '13

04 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a28faa6ac188/ Changeset: a28faa6ac188 User: dan Date: 2013-06-04 20:05:20 Summary: Data Managers: allow multiple value translations to be specifed per column and also allow multiple types of value translations. Affected #: 1 file diff -r df488dbd5bdb22dc78549118834788992e5cabcb -r a28faa6ac188594a60cd495327661a15efd37ea5 lib/galaxy/tools/data_manager/manager.py --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -16,6 +16,8 @@ log = logging.getLogger( __name__ ) SUPPORTED_DATA_TABLE_TYPES = ( TabularToolDataTable ) +VALUE_TRANSLATION_FUNCTIONS = dict( abspath=os.path.abspath ) +DEFAULT_VALUE_TRANSLATION_TYPE = 'template' class DataManagers( object ): def __init__( self, app, xml_filename=None ): @@ -160,15 +162,24 @@ if data_table_name not in self.output_ref_by_data_table: self.output_ref_by_data_table[ data_table_name ] = {} self.output_ref_by_data_table[ data_table_name ][ data_table_coumn_name ] = output_ref - value_translation_elem = column_elem.find( 'value_translation' ) - if value_translation_elem is not None: - value_translation = value_translation_elem.text - else: - value_translation = None - if value_translation is not None: - if data_table_name not in self.value_translation_by_data_table_column: - self.value_translation_by_data_table_column[ data_table_name ] = {} - self.value_translation_by_data_table_column[ data_table_name ][ data_table_coumn_name ] = value_translation + value_translation_elems = column_elem.findall( 'value_translation' ) + if value_translation_elems is not None: + for value_translation_elem in value_translation_elems: + value_translation = value_translation_elem.text + if value_translation is not None: + value_translation_type = value_translation_elem.get( 'type', DEFAULT_VALUE_TRANSLATION_TYPE ) + if data_table_name not in self.value_translation_by_data_table_column: + self.value_translation_by_data_table_column[ data_table_name ] = {} + if data_table_coumn_name not in self.value_translation_by_data_table_column[ data_table_name ]: + self.value_translation_by_data_table_column[ data_table_name ][ data_table_coumn_name ] = [] + if value_translation_type == 'function': + if value_translation in VALUE_TRANSLATION_FUNCTIONS: + value_translation = VALUE_TRANSLATION_FUNCTIONS[ value_translation ] + else: + raise ValueError( "Unsupported value translation function: '%s'" % ( value_translation ) ) + else: + assert value_translation_type == DEFAULT_VALUE_TRANSLATION_TYPE, ValueError( "Unsupported value translation type: '%s'" % ( value_translation_type ) ) + self.value_translation_by_data_table_column[ data_table_name ][ data_table_coumn_name ].append( value_translation ) for move_elem in column_elem.findall( 'move' ): move_type = move_elem.get( 'type', 'directory' ) @@ -290,8 +301,11 @@ def process_value_translation( self, data_table_name, column_name, **kwd ): value = kwd.get( column_name ) if data_table_name in self.value_translation_by_data_table_column and column_name in self.value_translation_by_data_table_column[ data_table_name ]: - value_translation = self.value_translation_by_data_table_column[ data_table_name ][ column_name ] - value = fill_template( value_translation, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd ) + for value_translation in self.value_translation_by_data_table_column[ data_table_name ][ column_name ]: + if isinstance( value_translation, basestring ): + value = fill_template( value_translation, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd ) + else: + value = value_translation( value ) return value def get_tool_shed_repository_info_dict( self ): 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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