galaxy-commits March 2013

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commit/galaxy-central: natefoo: merge next-stable.
by commits-noreply＠bitbucket.org 26 Mar '13

26 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3b918b912fe6/ Changeset: 3b918b912fe6 User: natefoo Date: 2013-03-26 20:40:59 Summary: merge next-stable. Affected #: 7 files diff -r 42b616e64d0575012d40acf69a355b98bf954db7 -r 3b918b912fe68718eb0b20c5c76e0e639f1cf42c lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -95,35 +95,43 @@ """ raise NotImplementedError() - # Runners must override the job handling methods - def queue_job(self, job_wrapper): + def prepare_job(self, job_wrapper, include_metadata=False, include_work_dir_outputs=True): """Some sanity checks that all runners' queue_job() methods are likely to want to do """ job_id = job_wrapper.get_id_tag() job_state = job_wrapper.get_state() job_wrapper.is_ready = False + job_wrapper.runner_command_line = None # Make sure the job hasn't been deleted if job_state == model.Job.states.DELETED: log.debug( "(%s) Job deleted by user before it entered the %s queue" % ( job_id, self.runner_name ) ) if self.app.config.cleanup_job in ( "always", "onsuccess" ): job_wrapper.cleanup() - return + return False elif job_state != model.Job.states.QUEUED: log.info( "(%d) Job is in state %s, skipping execution" % ( job_id, job_state ) ) # cleanup may not be safe in all states - return + return False # Prepare the job try: job_wrapper.prepare() - job_wrapper.runner_command_line = self.build_command_line( job_wrapper ) + job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) except: log.exception("(%s) Failure preparing job" % job_id) job_wrapper.fail( "failure preparing job", exception=True ) - return + return False - job_wrapper.is_ready = True + if not job_wrapper.runner_command_line: + job_wrapper.finish( '', '' ) + return False + + return True + + # Runners must override the job handling methods + def queue_job(self, job_wrapper): + raise NotImplementedError() def stop_job(self, job): raise NotImplementedError() diff -r 42b616e64d0575012d40acf69a355b98bf954db7 -r 3b918b912fe68718eb0b20c5c76e0e639f1cf42c lib/galaxy/jobs/runners/cli.py --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -75,12 +75,11 @@ def queue_job( self, job_wrapper ): """Create job script and submit it to the DRM""" - # Superclass method has some basic sanity checks - super( ShellJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=True ): return - # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line # Get shell and job execution interface diff -r 42b616e64d0575012d40acf69a355b98bf954db7 -r 3b918b912fe68718eb0b20c5c76e0e639f1cf42c lib/galaxy/jobs/runners/condor.py --- a/lib/galaxy/jobs/runners/condor.py +++ b/lib/galaxy/jobs/runners/condor.py @@ -58,12 +58,11 @@ def queue_job( self, job_wrapper ): """Create job script and submit it to the DRM""" - # Superclass method has some basic sanity checks - super( CondorJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=True ): return - # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line # get configured job destination diff -r 42b616e64d0575012d40acf69a355b98bf954db7 -r 3b918b912fe68718eb0b20c5c76e0e639f1cf42c lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -105,14 +105,13 @@ def queue_job( self, job_wrapper ): """Create job script and submit it to the DRM""" - # Superclass method has some basic sanity checks - super( DRMAAJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=True ): return - # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line - + # get configured job destination job_destination = job_wrapper.job_destination diff -r 42b616e64d0575012d40acf69a355b98bf954db7 -r 3b918b912fe68718eb0b20c5c76e0e639f1cf42c lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -35,15 +35,14 @@ self._init_worker_threads() def queue_job( self, job_wrapper ): - # Superclass method has some basic sanity checks - super( LocalJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper ): return stderr = stdout = '' exit_code = 0 - # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line job_id = job_wrapper.get_id_tag() diff -r 42b616e64d0575012d40acf69a355b98bf954db7 -r 3b918b912fe68718eb0b20c5c76e0e639f1cf42c lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -222,12 +222,11 @@ def queue_job( self, job_wrapper ): """Create PBS script for a job and submit it to the PBS queue""" - # Superclass method has some basic sanity checks - super( PBSJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=not( self.app.config.pbs_stage_path ) ): return - # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line job_destination = job_wrapper.job_destination diff -r 42b616e64d0575012d40acf69a355b98bf954db7 -r 3b918b912fe68718eb0b20c5c76e0e639f1cf42c lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -26,12 +26,14 @@ self._init_worker_threads() def queue_job( self, job_wrapper ): - super( TaskedJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper ): return + # command line has been added to the wrapper by prepare_job() + command_line = job_wrapper.runner_command_line + stderr = stdout = '' - command_line = job_wrapper.runner_command_line # Persist the destination job_wrapper.set_job_destination(job_wrapper.job_destination) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Fix setting of external metadata broken by refactoring job preparation.
by commits-noreply＠bitbucket.org 26 Mar '13

26 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c5d7d2bd7928/ Changeset: c5d7d2bd7928 Branch: next-stable User: natefoo Date: 2013-03-26 20:40:36 Summary: Fix setting of external metadata broken by refactoring job preparation. Affected #: 7 files diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -95,35 +95,43 @@ """ raise NotImplementedError() - # Runners must override the job handling methods - def queue_job(self, job_wrapper): + def prepare_job(self, job_wrapper, include_metadata=False, include_work_dir_outputs=True): """Some sanity checks that all runners' queue_job() methods are likely to want to do """ job_id = job_wrapper.get_id_tag() job_state = job_wrapper.get_state() job_wrapper.is_ready = False + job_wrapper.runner_command_line = None # Make sure the job hasn't been deleted if job_state == model.Job.states.DELETED: log.debug( "(%s) Job deleted by user before it entered the %s queue" % ( job_id, self.runner_name ) ) if self.app.config.cleanup_job in ( "always", "onsuccess" ): job_wrapper.cleanup() - return + return False elif job_state != model.Job.states.QUEUED: log.info( "(%d) Job is in state %s, skipping execution" % ( job_id, job_state ) ) # cleanup may not be safe in all states - return + return False # Prepare the job try: job_wrapper.prepare() - job_wrapper.runner_command_line = self.build_command_line( job_wrapper ) + job_wrapper.runner_command_line = self.build_command_line( job_wrapper, include_metadata=include_metadata, include_work_dir_outputs=include_work_dir_outputs ) except: log.exception("(%s) Failure preparing job" % job_id) job_wrapper.fail( "failure preparing job", exception=True ) - return + return False - job_wrapper.is_ready = True + if not job_wrapper.runner_command_line: + job_wrapper.finish( '', '' ) + return False + + return True + + # Runners must override the job handling methods + def queue_job(self, job_wrapper): + raise NotImplementedError() def stop_job(self, job): raise NotImplementedError() diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/cli.py --- a/lib/galaxy/jobs/runners/cli.py +++ b/lib/galaxy/jobs/runners/cli.py @@ -75,12 +75,11 @@ def queue_job( self, job_wrapper ): """Create job script and submit it to the DRM""" - # Superclass method has some basic sanity checks - super( ShellJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=True ): return - # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line # Get shell and job execution interface diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/condor.py --- a/lib/galaxy/jobs/runners/condor.py +++ b/lib/galaxy/jobs/runners/condor.py @@ -58,12 +58,11 @@ def queue_job( self, job_wrapper ): """Create job script and submit it to the DRM""" - # Superclass method has some basic sanity checks - super( CondorJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=True ): return - # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line # get configured job destination diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -105,14 +105,13 @@ def queue_job( self, job_wrapper ): """Create job script and submit it to the DRM""" - # Superclass method has some basic sanity checks - super( DRMAAJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=True ): return - # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line - + # get configured job destination job_destination = job_wrapper.job_destination diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -35,15 +35,14 @@ self._init_worker_threads() def queue_job( self, job_wrapper ): - # Superclass method has some basic sanity checks - super( LocalJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper ): return stderr = stdout = '' exit_code = 0 - # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line job_id = job_wrapper.get_id_tag() diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -222,12 +222,11 @@ def queue_job( self, job_wrapper ): """Create PBS script for a job and submit it to the PBS queue""" - # Superclass method has some basic sanity checks - super( PBSJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper, include_metadata=not( self.app.config.pbs_stage_path ) ): return - # command line has been added to the wrapper by the superclass queue_job() + # command line has been added to the wrapper by prepare_job() command_line = job_wrapper.runner_command_line job_destination = job_wrapper.job_destination diff -r 55b651e70aef895545bf88039f6a5558976a1842 -r c5d7d2bd7928c160a5163fe9fc9a5e20aa5470ae lib/galaxy/jobs/runners/tasks.py --- a/lib/galaxy/jobs/runners/tasks.py +++ b/lib/galaxy/jobs/runners/tasks.py @@ -26,12 +26,14 @@ self._init_worker_threads() def queue_job( self, job_wrapper ): - super( TaskedJobRunner, self ).queue_job( job_wrapper ) - if not job_wrapper.is_ready: + # prepare the job + if not self.prepare_job( job_wrapper ): return + # command line has been added to the wrapper by prepare_job() + command_line = job_wrapper.runner_command_line + stderr = stdout = '' - command_line = job_wrapper.runner_command_line # Persist the destination job_wrapper.set_job_destination(job_wrapper.job_destination) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Mar '13

26 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/55b651e70aef/ Changeset: 55b651e70aef Branch: next-stable User: carlfeberhard Date: 2013-03-26 20:10:42 Summary: fix for exception handling in root.history Affected #: 1 file diff -r ea2a5e240c41c9d58a3982d21af362781db980da -r 55b651e70aef895545bf88039f6a5558976a1842 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -155,9 +155,9 @@ 'history_id': history_dictionary[ 'id' ], 'state' : trans.model.Dataset.states.ERROR, 'visible' : True, - 'misc_info' : str( exception ), + 'misc_info' : str( exc ), 'misc_blurb': 'Failed to retrieve dataset information.', - 'error' : str( exception ) + 'error' : str( exc ) } hda_dictionaries.append( return_val ) https://bitbucket.org/galaxy/galaxy-central/commits/42b616e64d05/ Changeset: 42b616e64d05 User: carlfeberhard Date: 2013-03-26 20:11:34 Summary: merge next-stable Affected #: 1 file diff -r eb7f1d35ad35e2410393362b636039714c873b5e -r 42b616e64d0575012d40acf69a355b98bf954db7 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -155,9 +155,9 @@ 'history_id': history_dictionary[ 'id' ], 'state' : trans.model.Dataset.states.ERROR, 'visible' : True, - 'misc_info' : str( exception ), + 'misc_info' : str( exc ), 'misc_blurb': 'Failed to retrieve dataset information.', - 'error' : str( exception ) + 'error' : str( exc ) } hda_dictionaries.append( return_val ) 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: james_taylor: biostar: pass slugified version of tool name as tag when sending to question form
by commits-noreply＠bitbucket.org 26 Mar '13

26 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb7f1d35ad35/ Changeset: eb7f1d35ad35 User: james_taylor Date: 2013-03-26 18:04:36 Summary: biostar: pass slugified version of tool name as tag when sending to question form Affected #: 1 file diff -r ac80dbfe7703102ff152760419361a55d3eb0f6f -r eb7f1d35ad35e2410393362b636039714c873b5e lib/galaxy/webapps/galaxy/controllers/biostar.py --- a/lib/galaxy/webapps/galaxy/controllers/biostar.py +++ b/lib/galaxy/webapps/galaxy/controllers/biostar.py @@ -8,16 +8,35 @@ from galaxy.util import json import hmac +# Slugifying from Armin Ronacher (http://flask.pocoo.org/snippets/5/) + +import re +from unicodedata import normalize + +_punct_re = re.compile(r'[\t !"#$%&\'()*\-/<=>?(a)\[\\\]^_`{|},.]+') + + +def slugify(text, delim=u'-'): + """Generates an slightly worse ASCII-only slug.""" + result = [] + for word in _punct_re.split(text.lower()): + word = normalize('NFKD', word).encode('ascii', 'ignore') + if word: + result.append(word) + return unicode(delim.join(result)) + + # Biostar requires all keys to be present, so we start with a template DEFAULT_PAYLOAD = { - 'email': "", - 'title': "Question about Galaxy", + 'email': "", + 'title': "Question about Galaxy", 'tags': 'galaxy', - 'tool_name': '', - 'tool_version': '', + 'tool_name': '', + 'tool_version': '', 'tool_id': '' } + def encode_data( key, data ): """ Encode data to send a question to Biostar @@ -28,6 +47,13 @@ return text, digest +def tag_for_tool( tool ): + """ + Generate a reasonavle biostar tag for a tool. + """ + return slugify( unicode( tool.name ) ) + + class BiostarController( BaseUIController ): """ Provides integration with Biostar through external authentication, see: http://liondb.com/help/x/ @@ -81,6 +107,10 @@ if not tool: return error( "No tool found matching '%s'" % tool_id ) # Tool specific information for payload - payload = { 'title': "Question about Galaxy tool '%s'" % tool.name, 'tool_name': tool.name, 'tool_version': tool.version, 'tool_id': tool.id } + payload = { 'title': "Question about Galaxy tool '%s'" % tool.name, + 'tool_name': tool.name, + 'tool_version': tool.version, + 'tool_id': tool.id, + 'tags': 'galaxy ' + tag_for_tool( tool ) } # Pass on to regular question method return self.biostar_question_redirect( trans, payload ) \ No newline at end of file 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: Fix tool shed utility file imports and withe space to follow new Galaxy dev team coding standards.
by commits-noreply＠bitbucket.org 26 Mar '13

26 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ac80dbfe7703/ Changeset: ac80dbfe7703 User: greg Date: 2013-03-26 16:41:49 Summary: Fix tool shed utility file imports and withe space to follow new Galaxy dev team coding standards. Affected #: 12 files diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f 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 @@ -1,17 +1,25 @@ -import os, logging, urllib2 -import tool_shed.util.shed_util_common as suc -from tool_shed.util import encoding_util, data_manager_util, datatype_util, tool_util -from tool_shed.galaxy_install.tool_dependencies.install_util import install_package, set_environment +import logging +import os +import urllib2 +from galaxy import eggs from galaxy import util from galaxy.util import json from galaxy.webapps.tool_shed.util import container_util +import tool_shed.util.shed_util_common as suc +from tool_shed.util import encoding_util +from tool_shed.util import data_manager_util +from tool_shed.util import datatype_util +from tool_shed.util import tool_util +from tool_shed.galaxy_install.tool_dependencies.install_util import install_package +from tool_shed.galaxy_install.tool_dependencies.install_util import set_environment -from galaxy import eggs import pkg_resources pkg_resources.require( 'elementtree' ) -from elementtree import ElementTree, ElementInclude -from elementtree.ElementTree import Element, SubElement +from elementtree import ElementTree +from elementtree import ElementInclude +from elementtree.ElementTree import Element +from elementtree.ElementTree import SubElement log = logging.getLogger( __name__ ) diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f lib/tool_shed/util/common_util.py --- a/lib/tool_shed/util/common_util.py +++ b/lib/tool_shed/util/common_util.py @@ -1,4 +1,5 @@ -import os, urllib2 +import os +import urllib2 from galaxy import util from galaxy.util.odict import odict from tool_shed.util import encoding_util @@ -63,6 +64,7 @@ exception_msg += 'The entry for this tool shed must always be available in this file, so re-add it before attempting to start your Galaxy server.\n' raise Exception( exception_msg ) return tool_shed_accessible, missing_tool_configs_dict + def check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ): file_path = elem.get( 'file', None ) if file_path: @@ -71,6 +73,7 @@ tool_dependencies = migrated_tool_configs_dict[ name ] missing_tool_configs_dict[ name ] = tool_dependencies return missing_tool_configs_dict + def get_non_shed_tool_panel_configs( app ): # Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml. config_filenames = [] @@ -83,6 +86,7 @@ if tool_path is None: config_filenames.append( config_filename ) return config_filenames + def get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ): search_str = '://%s' % tool_shed for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items(): diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f lib/tool_shed/util/data_manager_util.py --- a/lib/tool_shed/util/data_manager_util.py +++ b/lib/tool_shed/util/data_manager_util.py @@ -1,4 +1,5 @@ -import os, logging +import logging +import os from galaxy import util import tool_shed.util.shed_util_common as suc diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f lib/tool_shed/util/datatype_util.py --- a/lib/tool_shed/util/datatype_util.py +++ b/lib/tool_shed/util/datatype_util.py @@ -1,13 +1,17 @@ -import os, logging, tempfile +import logging +import os +import tempfile +from galaxy import eggs +from galaxy import util import tool_shed.util.shed_util_common as suc -from galaxy import util -from galaxy import eggs import pkg_resources pkg_resources.require( 'elementtree' ) -from elementtree import ElementTree, ElementInclude -from elementtree.ElementTree import Element, SubElement +from elementtree import ElementTree +from elementtree import ElementInclude +from elementtree.ElementTree import Element +from elementtree.ElementTree import SubElement log = logging.getLogger( __name__ ) diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f lib/tool_shed/util/encoding_util.py --- a/lib/tool_shed/util/encoding_util.py +++ b/lib/tool_shed/util/encoding_util.py @@ -1,8 +1,9 @@ -import binascii, logging +import binascii +import logging +from galaxy import eggs from galaxy.util.hash_util import hmac_new from galaxy.util.json import json_fix -from galaxy import eggs import pkg_resources pkg_resources.require( "simplejson" ) @@ -34,6 +35,7 @@ if values is None: values = value return values + def tool_shed_encode( val ): if isinstance( val, dict ): value = simplejson.dumps( val ) diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1,21 +1,32 @@ -import os, tempfile, logging, urllib2 -from galaxy import web, util -from galaxy.util import inflector, json +import logging +import os +import tempfile +import urllib2 +from galaxy import eggs +from galaxy import util +from galaxy import web +from galaxy.datatypes import checkers +from galaxy.model.orm import and_ +from galaxy.tools.data_manager.manager import DataManager +from galaxy.util import inflector +from galaxy.util import json from galaxy.webapps.tool_shed.util import container_util -from galaxy.datatypes import checkers -from galaxy.tools.data_manager.manager import DataManager import tool_shed.util.shed_util_common as suc -from tool_shed.util import common_install_util, readme_util, tool_dependency_util, tool_util -from galaxy.model.orm import and_ +from tool_shed.util import common_install_util +from tool_shed.util import readme_util +from tool_shed.util import tool_dependency_util +from tool_shed.util import tool_util -from galaxy import eggs import pkg_resources pkg_resources.require( 'mercurial' ) -from mercurial import hg, ui, commands +from mercurial import commands +from mercurial import hg +from mercurial import ui pkg_resources.require( 'elementtree' ) -from elementtree import ElementTree, ElementInclude +from elementtree import ElementTree +from elementtree import ElementInclude log = logging.getLogger( __name__ ) diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f lib/tool_shed/util/readme_util.py --- a/lib/tool_shed/util/readme_util.py +++ b/lib/tool_shed/util/readme_util.py @@ -1,6 +1,8 @@ -import os, logging, urllib2 +import logging +import os +import urllib2 +from galaxy.util import json import tool_shed.util.shed_util_common as suc -from galaxy.util import json log = logging.getLogger( __name__ ) diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -1,14 +1,20 @@ -import os, logging +import logging +import os +from galaxy import eggs from galaxy.util import json +from galaxy.webapps.tool_shed.util import container_util import tool_shed.util.shed_util_common as suc -from tool_shed.util import common_install_util, encoding_util, metadata_util, tool_util -from galaxy.webapps.tool_shed.util import container_util +from tool_shed.util import common_install_util +from tool_shed.util import encoding_util +from tool_shed.util import metadata_util +from tool_shed.util import tool_util -from galaxy import eggs import pkg_resources pkg_resources.require( 'mercurial' ) -from mercurial import hg, ui, commands +from mercurial import commands +from mercurial import hg +from mercurial import ui log = logging.getLogger( __name__ ) diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f lib/tool_shed/util/review_util.py --- a/lib/tool_shed/util/review_util.py +++ b/lib/tool_shed/util/review_util.py @@ -1,13 +1,16 @@ -import os, logging +import logging +import os +from galaxy import eggs +from galaxy.model.orm import and_ from galaxy.util.odict import odict import tool_shed.util.shed_util_common as suc -from galaxy.model.orm import and_ -from galaxy import eggs import pkg_resources pkg_resources.require( 'mercurial' ) -from mercurial import hg, ui, commands +from mercurial import commands +from mercurial import hg +from mercurial import ui log = logging.getLogger( __name__ ) diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -1,15 +1,14 @@ import logging import os import shutil - from galaxy import eggs -eggs.require( 'elementtree' ) -from elementtree import ElementTree, ElementInclude - +from galaxy import util from galaxy.model.orm import and_ import tool_shed.util.shed_util_common as suc -from galaxy import util +eggs.require( 'elementtree' ) +from elementtree import ElementTree +from elementtree import ElementInclude log = logging.getLogger( __name__ ) diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -4,6 +4,7 @@ import shutil import tempfile import galaxy.tools +from galaxy import eggs from galaxy import util from galaxy.datatypes import checkers from galaxy.model.orm import and_ @@ -13,15 +14,18 @@ from galaxy.web.form_builder import SelectField import tool_shed.util.shed_util_common as suc -from galaxy import eggs import pkg_resources pkg_resources.require( 'mercurial' ) -from mercurial import hg, ui, commands +from mercurial import commands +from mercurial import hg +from mercurial import ui pkg_resources.require( 'elementtree' ) -from elementtree import ElementTree, ElementInclude -from elementtree.ElementTree import Element, SubElement +from elementtree import ElementTree +from elementtree import ElementInclude +from elementtree.ElementTree import Element +from elementtree.ElementTree import SubElement log = logging.getLogger( __name__ ) diff -r 504264153fe1804c409c775be2c6db3f160b8fe2 -r ac80dbfe7703102ff152760419361a55d3eb0f6f lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -1,19 +1,25 @@ +import logging +import galaxy.tools +import galaxy.tools.parameters +import galaxy.webapps.galaxy.controllers.workflow from galaxy import eggs +from galaxy.util import json +from galaxy.workflow.modules import InputDataModule +from galaxy.workflow.modules import ToolModule +from galaxy.workflow.modules import WorkflowModuleFactory +import tool_shed.util.shed_util_common as suc +from tool_shed.util import encoding_util +from tool_shed.util import metadata_util +from tool_shed.util import tool_util + import pkg_resources pkg_resources.require( "SVGFig" ) - -import logging, svgfig -from galaxy.util import json -import tool_shed.util.shed_util_common as suc -from tool_shed.util import encoding_util, metadata_util, tool_util -from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory -import galaxy.webapps.galaxy.controllers.workflow -import galaxy.tools -import galaxy.tools.parameters +import svgfig log = logging.getLogger( __name__ ) + class RepoInputDataModule( InputDataModule ): type = "data_input" @@ -24,12 +30,14 @@ module = Class( trans ) module.state = dict( name="Input Dataset" ) return module + @classmethod def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata=None, secure=True ): module = Class( trans ) state = json.from_json_string( step_dict[ "tool_state" ] ) module.state = dict( name=state.get( "name", "Input Dataset" ) ) return module + @classmethod def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): module = Class( trans ) @@ -38,6 +46,7 @@ module.state[ 'name' ] = step.tool_inputs[ 'name' ] return module + class RepoToolModule( ToolModule ): type = "tool" @@ -64,11 +73,13 @@ self.post_job_actions = {} self.workflow_outputs = [] self.state = None + @classmethod def new( Class, trans, repository_id, changeset_revision, tools_metadata, tool_id=None ): module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) module.state = module.tool.new_state( trans, all_pages=True ) return module + @classmethod def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata, secure=True ): tool_id = step_dict[ 'tool_id' ] @@ -78,6 +89,7 @@ module.state.decode( step_dict[ "tool_state" ], module.tool, module.trans.app, secure=secure ) module.errors = step_dict.get( "tool_errors", None ) return module + @classmethod def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): module = Class( trans, repository_id, changeset_revision, tools_metadata, step.tool_id ) @@ -88,6 +100,7 @@ module.state.inputs = {} module.errors = step.tool_errors return module + def get_data_inputs( self ): data_inputs = [] def callback( input, value, prefixed_name, prefixed_label ): @@ -98,6 +111,7 @@ if self.tool: galaxy.tools.parameters.visit_input_values( self.tool.inputs, self.state.inputs, callback ) return data_inputs + def get_data_outputs( self ): data_outputs = [] if self.tool: @@ -124,18 +138,23 @@ data_outputs.append( dict( name=name, extensions=formats ) ) return data_outputs + class RepoWorkflowModuleFactory( WorkflowModuleFactory ): + def __init__( self, module_types ): self.module_types = module_types + def new( self, trans, type, tools_metadata=None, tool_id=None ): """Return module for type and (optional) tool_id initialized with new / default state.""" assert type in self.module_types return self.module_types[type].new( trans, tool_id ) + def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ): """Return module initialized from the data in dictionary `step_dict`.""" type = step_dict[ 'type' ] assert type in self.module_types return self.module_types[ type ].from_dict( trans, repository_id, changeset_revision, step_dict, **kwd ) + def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ): """Return module initialized from the WorkflowStep object `step`.""" type = step.type @@ -292,6 +311,7 @@ canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height ) trans.response.set_content_type( "image/svg+xml" ) return canvas.standalone_xml() + def get_workflow_data_inputs( step, module ): if module.type == 'tool': if module.tool: @@ -306,6 +326,7 @@ data_inputs.append( data_inputs_dict ) return data_inputs return module.get_data_inputs() + def get_workflow_data_outputs( step, module, steps ): if module.type == 'tool': if module.tool: @@ -329,6 +350,7 @@ data_outputs.append( data_outputs_dict ) return data_outputs return module.get_data_outputs() + def get_workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision ): """ Return an in-memory Workflow object from the dictionary object created when it was exported. This method is called from @@ -383,6 +405,7 @@ galaxy.webapps.galaxy.controllers.workflow.attach_ordered_steps( workflow, steps ) # Return the in-memory Workflow object for display or later persistence to the Galaxy database. return workflow, missing_tool_tups + def get_workflow_module_name( module, missing_tool_tups ): module_name = module.get_name() if module.type == 'tool' and module_name == 'unavailable': @@ -392,6 +415,7 @@ module_name = '%s' % missing_tool_name break return module_name + def save_workflow( trans, workflow ): """Use the received in-memory Workflow object for saving to the Galaxy database.""" stored = trans.model.StoredWorkflow() 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: inithello: Set do_not_test = True if the repository fails functional tests. Set do_not_test = False if the repository passes functional tests, so that the repository will always be re-tested against the most recent code.
by commits-noreply＠bitbucket.org 26 Mar '13

26 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/504264153fe1/ Changeset: 504264153fe1 User: inithello Date: 2013-03-26 15:02:17 Summary: Set do_not_test = True if the repository fails functional tests. Set do_not_test = False if the repository passes functional tests, so that the repository will always be re-tested against the most recent code. Affected #: 1 file diff -r b756a49b424565f5ec4037f25a89e987a47d184b -r 504264153fe1804c409c775be2c6db3f160b8fe2 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 @@ -241,8 +241,7 @@ listing = file( location, 'r' ).read() elif source == 'url': assert tool_shed_api_key is not None, 'Cannot proceed without tool shed API key.' - params = urllib.urlencode( dict( tools_functionally_correct='false', - do_not_test='false', + params = urllib.urlencode( dict( do_not_test='false', downloadable='true', malicious='false', includes_tools='true' ) ) @@ -281,10 +280,15 @@ return from_json_string( url_contents ) def register_test_result( url, metadata_id, test_results_dict, tests_passed=False ): + ''' + Set do_not_test = True if the repository fails functional tests. Set do_not_test = False + if the repository passes functional tests, so that the repository will always be re-tested + against the most recent code. + ''' params = {} if tests_passed: params[ 'tools_functionally_correct' ] = 'true' - params[ 'do_not_test' ] = 'true' + params[ 'do_not_test' ] = 'false' else: params[ 'tools_functionally_correct' ] = 'false' params[ 'do_not_test' ] = 'true' 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: Enhance and correct documentation in the new tool_shed_repositories Galaxy API controller as well as the documentation in the example API install scripts. Fix discovery of the tool_path setting in the selected shed-related tool panel config file in the tool_shed_repositories controller's install_repository_revision method.
by commits-noreply＠bitbucket.org 26 Mar '13

26 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b756a49b4245/ Changeset: b756a49b4245 User: greg Date: 2013-03-26 14:29:02 Summary: Enhance and correct documentation in the new tool_shed_repositories Galaxy API controller as well as the documentation in the example API install scripts. Fix discovery of the tool_path setting in the selected shed-related tool panel config file in the tool_shed_repositories controller's install_repository_revision method. Affected #: 3 files diff -r 50e8e5efacadef15969a663ac3849883e0a49727 -r b756a49b424565f5ec4037f25a89e987a47d184b lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -58,7 +58,7 @@ GET /api/tool_shed_repositories/{encoded_tool_shed_repsository_id} Display a dictionary containing information about a specified tool_shed_repository. - :param tool_shed_repository_id: the encoded id of the `ToolShedRepository` object + :param id: the encoded id of the ToolShedRepository object """ # Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e try: @@ -80,18 +80,32 @@ POST /api/tool_shed_repositories/install_repository_revision Install a specified repository revision from a specified tool shed into Galaxy. - :param tool_shed_url: the base URL of the Tool Shed from which to install the Repository - :param name: the name of the Repository - :param owner: the owner of the Repository - :param changset_revision: the changset_revision of the RepositoryMetadata object associated with the Repository :param key: the current Galaxy admin user's API key - :param new_tool_panel_section_label: optional label of a new section to be added to the Galaxy tool panel in which to load - tools contained in the Repository. Either this parameter must be an empty string or - the tool_panel_section_id parameter must be an empty string, as both cannot be used. - :param tool_panel_section_id: optional id of the Galaxy tool panel section in which to load tools contained in the Repository. - If not set, tools will be loaded outside of any sections in the tool panel. Either this - parameter must be an empty string or the tool_panel_section_id parameter must be an empty string, - as both cannot be used. + + The following parameters are included in the payload. + :param tool_shed_url (required): the base URL of the Tool Shed from which to install the Repository + :param name (required): the name of the Repository + :param owner (required): the owner of the Repository + :param changset_revision (required): the changset_revision of the RepositoryMetadata object associated with the Repository + :param new_tool_panel_section_label (optional): label of a new section to be added to the Galaxy tool panel in which to load + tools contained in the Repository. Either this parameter must be an empty string or + the tool_panel_section_id parameter must be an empty string or both must be an empty + string (both cannot be used simultaneously). + :param tool_panel_section_id (optional): id of the Galaxy tool panel section in which to load tools contained in the Repository. + If this parameter is an empty string and the above new_tool_panel_section_label parameter is an + empty string, tools will be loaded outside of any sections in the tool panel. Either this + parameter must be an empty string or the tool_panel_section_id parameter must be an empty string + of both must be an empty string (both cannot be used simultaneously). + :param install_repository_dependencies (optional): Set to True if you want to install repository dependencies defined for the specified + repository being installed. The default setting is False. + :param install_tool_dependencies (optional): Set to True if you want to install tool dependencies defined for the specified repository being + installed. The default setting is False. + :param shed_tool_conf (optional): The shed-related tool panel configuration file configured in the "tool_config_file" setting in the Galaxy config file + (e.g., universe_wsgi.ini). At least one shed-related tool panel config file is required to be configured. Setting + this parameter to a specific file enables you to choose where the specified repository will be installed because + the tool_path attribute of the <toolbox> from the specified file is used as the installation location + (e.g., <toolbox tool_path="../shed_tools">). If this parameter is not set, a shed-related tool panel configuration + file will be selected automatically. """ # Get the information about the repository to be installed from the payload. tool_shed_url = payload.get( 'tool_shed_url', '' ) @@ -160,29 +174,30 @@ includes_tools_for_display_in_tool_panel = repository_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] except: raise HTTPBadRequest( detail="Missing required parameter 'includes_tools_for_display_in_tool_panel'." ) - # Get the information about the Galaxy components (e.g., tool pane section, tool config file, etc) that will contain the repository - # information. + # Get the information about the Galaxy components (e.g., tool pane section, tool config file, etc) that will contain the repository information. install_repository_dependencies = payload.get( 'install_repository_dependencies', False ) install_tool_dependencies = payload.get( 'install_tool_dependencies', False ) new_tool_panel_section = payload.get( 'new_tool_panel_section_label', '' ) shed_tool_conf = payload.get( 'shed_tool_conf', None ) - tool_path = payload.get( 'tool_path', None ) - tool_panel_section_id = payload.get( 'tool_panel_section_id', '' ) - if tool_panel_section_id not in [ None, '' ]: - tool_panel_section = trans.app.toolbox.tool_panel[ tool_panel_section_id ] + if shed_tool_conf: + # Get the tool_path setting. + index, shed_conf_dict = suc.get_shed_tool_conf_dict( trans.app, shed_tool_conf ) + tool_path = shed_config_dict[ 'tool_path' ] else: - tool_panel_section = '' - if not shed_tool_conf or not tool_path: - # Pick a semi-random shed-related tool panel configuration file. + # Pick a semi-random shed-related tool panel configuration file and get the tool_path setting. for shed_config_dict in trans.app.toolbox.shed_tool_confs: + # Don't use migrated_tools_conf.xml. if shed_config_dict[ 'config_filename' ] != trans.app.config.migrated_tools_config: break shed_tool_conf = shed_config_dict[ 'config_filename' ] tool_path = shed_config_dict[ 'tool_path' ] if not shed_tool_conf: raise HTTPBadRequest( detail="Missing required parameter 'shed_tool_conf'." ) - if not tool_path: - raise HTTPBadRequest( detail="Missing required parameter 'tool_path'." ) + tool_panel_section_id = payload.get( 'tool_panel_section_id', '' ) + if tool_panel_section_id not in [ None, '' ]: + tool_panel_section = trans.app.toolbox.tool_panel[ tool_panel_section_id ] + else: + tool_panel_section = '' # Build the dictionary of information necessary for creating tool_shed_repository database records for each repository being installed. installation_dict = dict( install_repository_dependencies=install_repository_dependencies, new_tool_panel_section=new_tool_panel_section, diff -r 50e8e5efacadef15969a663ac3849883e0a49727 -r b756a49b424565f5ec4037f25a89e987a47d184b scripts/api/install_repository_tools_into_existing_tool_panel_section.py --- a/scripts/api/install_repository_tools_into_existing_tool_panel_section.py +++ b/scripts/api/install_repository_tools_into_existing_tool_panel_section.py @@ -9,7 +9,7 @@ <section id="from_test_tool_shed" name="From Test Tool Shed" version=""></section> -usage: ./install_repository_tools_into_existing_tool_panel_section <api_key <galaxy base url> tool_shed_url name owner changeset_revision tool_panel_section_id +usage: ./install_repository_tools_into_existing_tool_panel_section.py <api_key <galaxy base url> tool_shed_url name owner changeset_revision tool_panel_section_id Here is a working example of how to use this script to install a repository from the test tool shed. ./install_repository_tools_into_existing_tool_panel_section.py <api key><galaxy base url>/api/tool_shed_repositories/new/install_repository_revision http://testtoolshed.g2.bx.psu.edu gregs_filter greg f28d5018f9cb from_test_tool_shed diff -r 50e8e5efacadef15969a663ac3849883e0a49727 -r b756a49b424565f5ec4037f25a89e987a47d184b scripts/api/install_repository_tools_into_new_tool_panel_section.py --- a/scripts/api/install_repository_tools_into_new_tool_panel_section.py +++ b/scripts/api/install_repository_tools_into_new_tool_panel_section.py @@ -4,10 +4,10 @@ valid tools, loading them into a new section of the Galaxy tool panel. The repository has no tool dependencies or repository dependencies, so only a single repository will be installed. -usage: ./install_repository_tools_into_new_tool_panel_section <api_key <galaxy base url> tool_shed_url name owner changeset_revision new_tool_panel_section_label +usage: ./install_repository_tools_into_new_tool_panel_section.py <api_key <galaxy base url> tool_shed_url name owner changeset_revision new_tool_panel_section_label Here is a working example of how to use this script to install a repository from the test tool shed. -./install_repository_tools_into_new_tool_panel_section.py <api key><galaxy base url>/api/tool_shed_repositories/new/install_repository_revision http://testtoolshed.g2.bx.psu.edu gregs_filter greg f28d5018f9cb From%20Test%20Tool%20Shed +./install_repository_tools_into_new_tool_panel_section.py <api key><galaxy base url>/api/tool_shed_repositories/new/install_repository_revision http://testtoolshed.g2.bx.psu.edu gregs_filter greg f28d5018f9cb 'From Test Tool Shed' """ import os Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: More explicit specification of return codes, documentation of same.
by commits-noreply＠bitbucket.org 26 Mar '13

26 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/50e8e5efacad/ Changeset: 50e8e5efacad User: inithello Date: 2013-03-26 14:27:39 Summary: More explicit specification of return codes, documentation of same. Affected #: 1 file diff -r 5b7bc81c3fc7712894a1ff1bd75476259bf6c591 -r 50e8e5efacadef15969a663ac3849883e0a49727 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 @@ -787,14 +787,19 @@ print '# ----------------------------------------------------------------------------------' print "# %d repositories not installed correctly:" % len( repositories_failed_install ) show_summary_output( repositories_failed_install ) + else: + success = True + else: + success = True print "####################################################################################" - if repositories_tested > 0: - if success: - return 0 - else: - return 1 + # Normally, the value of 'success' would determine whether this test suite is marked as passed or failed + # in the automated buildbot framework. However, due to the procedure used here, we only want to report + # failure if a repository fails to install correctly. Therefore, we have overriden the value of 'success' + # here based on what actions the script has executed. + if success: + return 0 else: - return 0 + return 1 if __name__ == "__main__": now = strftime( "%Y-%m-%d %H:%M:%S" ) 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 26 Mar '13

26 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ea2a5e240c41/ Changeset: ea2a5e240c41 Branch: next-stable User: carlfeberhard Date: 2013-03-26 00:04:37 Summary: history panel: better bootstrapped history and hda data; UsesHistoryDatasetAssociationMixin: don't try to provide full data for deleted, purged, or non-accessible hda Affected #: 3 files diff -r 388648deecffe1d5d3c46525aabd5b4d55549248 -r ea2a5e240c41c9d58a3982d21af362781db980da lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -334,31 +334,40 @@ def get_hda_dict( self, trans, hda ): hda_dict = hda.get_api_value( view='element' ) history = hda.history + hda_dict[ 'api_type' ] = "file" # Add additional attributes that depend on trans can hence must be added here rather than at the model level. + can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) + can_access_hda = ( trans.user_is_admin() or can_access_hda ) + hda_dict[ 'accessible' ] = can_access_hda + + # return here if deleted and purged or can't access + purged = ( hda.purged or hda.dataset.purged ) + if ( hda.deleted and purged ) or not can_access_hda: + return trans.security.encode_dict_ids( hda_dict ) + if trans.user_is_admin() or trans.app.config.expose_dataset_path: hda_dict[ 'file_name' ] = hda.file_name - if not hda_dict[ 'deleted' ]: - hda_dict[ 'download_url' ] = url_for( 'history_contents_display', history_id = trans.security.encode_id( history.id ), - history_content_id = trans.security.encode_id( hda.id ) ) + hda_dict[ 'download_url' ] = url_for( 'history_contents_display', + history_id = trans.security.encode_id( history.id ), + history_content_id = trans.security.encode_id( hda.id ) ) - can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) - hda_dict[ 'accessible' ] = ( trans.user_is_admin() or can_access_hda ) - hda_dict[ 'api_type' ] = "file" - - if not( hda.purged or hda.deleted or hda.dataset.purged ): - meta_files = [] - for meta_type in hda.metadata.spec.keys(): - if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ): - meta_files.append( dict( file_type=meta_type ) ) - if meta_files: - hda_dict[ 'meta_files' ] = meta_files + meta_files = [] + for meta_type in hda.metadata.spec.keys(): + if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ): + meta_files.append( dict( file_type=meta_type ) ) + if meta_files: + hda_dict[ 'meta_files' ] = meta_files hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) hda_dict[ 'visualizations' ] = hda.get_visualizations() + # return here if deleted + if hda.deleted and not purged: + return trans.security.encode_dict_ids( hda_dict ) + if hda.creating_job and hda.creating_job.tool_id: tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) if tool_used and tool_used.force_history_refresh: @@ -813,7 +822,6 @@ history = self.get_object( trans, id, 'History', check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) return self.security_check( trans, history, check_ownership, check_accessible ) - def get_history_datasets( self, trans, history, show_deleted=False, show_hidden=False, show_purged=False ): """ Returns history's datasets. """ query = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \ diff -r 388648deecffe1d5d3c46525aabd5b4d55549248 -r ea2a5e240c41c9d58a3982d21af362781db980da lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -11,7 +11,7 @@ log = logging.getLogger( __name__ ) -class RootController( BaseUIController, UsesHistoryMixin, UsesAnnotations ): +class RootController( BaseUIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesAnnotations ): @web.expose def default(self, trans, target1=None, target2=None, **kwd): @@ -130,8 +130,39 @@ else: # get all datasets server-side, client-side will get flags and render appropriately - datasets = self.get_history_datasets( trans, history, - show_deleted=True, show_hidden=True, show_purged=True ) + hdas = self.get_history_datasets( trans, history, + show_deleted=True, show_hidden=True, show_purged=True ) + + #TODO: would be good to re-use the hdas above to get the history data... + history_dictionary = self.get_history_dict( trans, history ) + + #TODO: blech - all here for now - duplication of hist. contents, index + hda_dictionaries = [] + for hda in hdas: + try: + hda_dictionaries.append( self.get_hda_dict( trans, hda ) ) + + except Exception, exc: + # don't fail entire list if hda err's, record and move on + # (making sure http recvr knows it's err'd) + encoded_hda_id = trans.security.encode_id( hda.id ) + log.error( "Error in history API at listing contents with history %s, hda %s: (%s) %s", + history_dictionary[ 'id' ], encoded_hda_id, type( exc ), str( exc ) ) + return_val = { + 'id' : encoded_hda_id, + 'name' : hda.name, + 'hid' : hda.hid, + 'history_id': history_dictionary[ 'id' ], + 'state' : trans.model.Dataset.states.ERROR, + 'visible' : True, + 'misc_info' : str( exception ), + 'misc_blurb': 'Failed to retrieve dataset information.', + 'error' : str( exception ) + } + hda_dictionaries.append( return_val ) + + history = history_dictionary + datasets = hda_dictionaries return trans.stream_template_mako( history_panel_template, history = history, diff -r 388648deecffe1d5d3c46525aabd5b4d55549248 -r ea2a5e240c41c9d58a3982d21af362781db980da templates/webapps/galaxy/root/alternate_history.mako --- a/templates/webapps/galaxy/root/alternate_history.mako +++ b/templates/webapps/galaxy/root/alternate_history.mako @@ -90,7 +90,7 @@ <% from urllib import unquote_plus - history_class_name = history.__class__.__name__ + history_class_name = 'History' encoded_id_template = '<%= id %>' url_dict = { @@ -189,12 +189,9 @@ ## I'd rather do without these (esp. the get_hdas which hits the db twice) ## but we'd need a common map producer (something like get_api_value but more complete) ##TODO: api/web controllers should use common code, and this section should call that code -<%def name="get_history( id )"> +<%def name="get_history( history )"><% - history_json = trans.webapp.api_controllers[ 'histories' ].show( trans, trans.security.encode_id( id ) ) - #assert isinstance( history, dict ), ( - # 'Bootstrapped history was expecting a dictionary: %s' %( str( history ) ) ) - return history_json + return h.to_json_string( history ) %></%def> @@ -207,16 +204,9 @@ %></%def> -<%def name="get_hdas( history_id, hdas )"> +<%def name="get_hdas( hdas )"><% - #BUG: one inaccessible dataset will error entire list - if not hdas: - return '[]' - # rather just use the history.id (wo the datasets), but... - hda_json = trans.webapp.api_controllers[ 'history_contents' ].index( - trans, trans.security.encode_id( history_id ), - ids=( ','.join([ trans.security.encode_id( hda.id ) for hda in hdas ]) ) ) - return hda_json + return h.to_json_string( hdas ) %></%def> @@ -324,8 +314,8 @@ page_show_hidden = ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) }, user = ${ get_current_user() }, - history = ${ get_history( history.id ) }, - hdas = ${ get_hdas( history.id, datasets ) }; + history = ${ get_history( history ) }, + hdas = ${ get_hdas( datasets ) }; // add user data to history // i don't like this history+user relationship, but user authentication changes views/behaviour https://bitbucket.org/galaxy/galaxy-central/commits/5b7bc81c3fc7/ Changeset: 5b7bc81c3fc7 User: carlfeberhard Date: 2013-03-26 00:05:30 Summary: merge next-stable Affected #: 3 files diff -r b437eece023175a6ac8ea87f7a4dae6582ad7892 -r 5b7bc81c3fc7712894a1ff1bd75476259bf6c591 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -334,31 +334,40 @@ def get_hda_dict( self, trans, hda ): hda_dict = hda.get_api_value( view='element' ) history = hda.history + hda_dict[ 'api_type' ] = "file" # Add additional attributes that depend on trans can hence must be added here rather than at the model level. + can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) + can_access_hda = ( trans.user_is_admin() or can_access_hda ) + hda_dict[ 'accessible' ] = can_access_hda + + # return here if deleted and purged or can't access + purged = ( hda.purged or hda.dataset.purged ) + if ( hda.deleted and purged ) or not can_access_hda: + return trans.security.encode_dict_ids( hda_dict ) + if trans.user_is_admin() or trans.app.config.expose_dataset_path: hda_dict[ 'file_name' ] = hda.file_name - if not hda_dict[ 'deleted' ]: - hda_dict[ 'download_url' ] = url_for( 'history_contents_display', history_id = trans.security.encode_id( history.id ), - history_content_id = trans.security.encode_id( hda.id ) ) + hda_dict[ 'download_url' ] = url_for( 'history_contents_display', + history_id = trans.security.encode_id( history.id ), + history_content_id = trans.security.encode_id( hda.id ) ) - can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) - hda_dict[ 'accessible' ] = ( trans.user_is_admin() or can_access_hda ) - hda_dict[ 'api_type' ] = "file" - - if not( hda.purged or hda.deleted or hda.dataset.purged ): - meta_files = [] - for meta_type in hda.metadata.spec.keys(): - if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ): - meta_files.append( dict( file_type=meta_type ) ) - if meta_files: - hda_dict[ 'meta_files' ] = meta_files + meta_files = [] + for meta_type in hda.metadata.spec.keys(): + if isinstance( hda.metadata.spec[ meta_type ].param, FileParameter ): + meta_files.append( dict( file_type=meta_type ) ) + if meta_files: + hda_dict[ 'meta_files' ] = meta_files hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) hda_dict[ 'visualizations' ] = hda.get_visualizations() + # return here if deleted + if hda.deleted and not purged: + return trans.security.encode_dict_ids( hda_dict ) + if hda.creating_job and hda.creating_job.tool_id: tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) if tool_used and tool_used.force_history_refresh: @@ -813,7 +822,6 @@ history = self.get_object( trans, id, 'History', check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted ) return self.security_check( trans, history, check_ownership, check_accessible ) - def get_history_datasets( self, trans, history, show_deleted=False, show_hidden=False, show_purged=False ): """ Returns history's datasets. """ query = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \ diff -r b437eece023175a6ac8ea87f7a4dae6582ad7892 -r 5b7bc81c3fc7712894a1ff1bd75476259bf6c591 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -11,7 +11,7 @@ log = logging.getLogger( __name__ ) -class RootController( BaseUIController, UsesHistoryMixin, UsesAnnotations ): +class RootController( BaseUIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesAnnotations ): @web.expose def default(self, trans, target1=None, target2=None, **kwd): @@ -130,8 +130,39 @@ else: # get all datasets server-side, client-side will get flags and render appropriately - datasets = self.get_history_datasets( trans, history, - show_deleted=True, show_hidden=True, show_purged=True ) + hdas = self.get_history_datasets( trans, history, + show_deleted=True, show_hidden=True, show_purged=True ) + + #TODO: would be good to re-use the hdas above to get the history data... + history_dictionary = self.get_history_dict( trans, history ) + + #TODO: blech - all here for now - duplication of hist. contents, index + hda_dictionaries = [] + for hda in hdas: + try: + hda_dictionaries.append( self.get_hda_dict( trans, hda ) ) + + except Exception, exc: + # don't fail entire list if hda err's, record and move on + # (making sure http recvr knows it's err'd) + encoded_hda_id = trans.security.encode_id( hda.id ) + log.error( "Error in history API at listing contents with history %s, hda %s: (%s) %s", + history_dictionary[ 'id' ], encoded_hda_id, type( exc ), str( exc ) ) + return_val = { + 'id' : encoded_hda_id, + 'name' : hda.name, + 'hid' : hda.hid, + 'history_id': history_dictionary[ 'id' ], + 'state' : trans.model.Dataset.states.ERROR, + 'visible' : True, + 'misc_info' : str( exception ), + 'misc_blurb': 'Failed to retrieve dataset information.', + 'error' : str( exception ) + } + hda_dictionaries.append( return_val ) + + history = history_dictionary + datasets = hda_dictionaries return trans.stream_template_mako( history_panel_template, history = history, diff -r b437eece023175a6ac8ea87f7a4dae6582ad7892 -r 5b7bc81c3fc7712894a1ff1bd75476259bf6c591 templates/webapps/galaxy/root/alternate_history.mako --- a/templates/webapps/galaxy/root/alternate_history.mako +++ b/templates/webapps/galaxy/root/alternate_history.mako @@ -90,7 +90,7 @@ <% from urllib import unquote_plus - history_class_name = history.__class__.__name__ + history_class_name = 'History' encoded_id_template = '<%= id %>' url_dict = { @@ -189,12 +189,9 @@ ## I'd rather do without these (esp. the get_hdas which hits the db twice) ## but we'd need a common map producer (something like get_api_value but more complete) ##TODO: api/web controllers should use common code, and this section should call that code -<%def name="get_history( id )"> +<%def name="get_history( history )"><% - history_json = trans.webapp.api_controllers[ 'histories' ].show( trans, trans.security.encode_id( id ) ) - #assert isinstance( history, dict ), ( - # 'Bootstrapped history was expecting a dictionary: %s' %( str( history ) ) ) - return history_json + return h.to_json_string( history ) %></%def> @@ -207,16 +204,9 @@ %></%def> -<%def name="get_hdas( history_id, hdas )"> +<%def name="get_hdas( hdas )"><% - #BUG: one inaccessible dataset will error entire list - if not hdas: - return '[]' - # rather just use the history.id (wo the datasets), but... - hda_json = trans.webapp.api_controllers[ 'history_contents' ].index( - trans, trans.security.encode_id( history_id ), - ids=( ','.join([ trans.security.encode_id( hda.id ) for hda in hdas ]) ) ) - return hda_json + return h.to_json_string( hdas ) %></%def> @@ -324,8 +314,8 @@ page_show_hidden = ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) }, user = ${ get_current_user() }, - history = ${ get_history( history.id ) }, - hdas = ${ get_hdas( history.id, datasets ) }; + history = ${ get_history( history ) }, + hdas = ${ get_hdas( datasets ) }; // add user data to history // i don't like this history+user relationship, but user authentication changes views/behaviour Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 25 Mar '13

25 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/388648deecff/ Changeset: 388648deecff Branch: next-stable User: natefoo Date: 2013-03-25 23:22:11 Summary: Don't misuse PBS parameters in the sample job config. Affected #: 1 file diff -r 75ba4f814129bb24ef85feb5fde99c115a707d4d -r 388648deecffe1d5d3c46525aabd5b4d55549248 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -29,7 +29,7 @@ <destination id="pbs" runner="pbs" tags="mycluster"/><destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs"> - <param id="Execution_Time">72:00:00</param> + <param id="Resource_List">walltime=72:00:00</param></destination><destination id="remote_cluster" runner="drmaa" tags="longjobs"/><destination id="real_user_cluster" runner="drmaa"> https://bitbucket.org/galaxy/galaxy-central/commits/b437eece0231/ Changeset: b437eece0231 User: natefoo Date: 2013-03-25 23:22:25 Summary: merge next-stable Affected #: 1 file diff -r 7df0d7eb3a0670a299d571683daba26cbc692f0b -r b437eece023175a6ac8ea87f7a4dae6582ad7892 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -29,7 +29,7 @@ <destination id="pbs" runner="pbs" tags="mycluster"/><destination id="pbs_longjobs" runner="pbs" tags="mycluster,longjobs"> - <param id="Execution_Time">72:00:00</param> + <param id="Resource_List">walltime=72:00:00</param></destination><destination id="remote_cluster" runner="drmaa" tags="longjobs"/><destination id="real_user_cluster" runner="drmaa"> 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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galaxy-commits March 2013