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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. You are receiving this because you have the service enabled, addressing the recipient of this email.

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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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commit/galaxy-central: greg: Fix a few typos in my last commit.
by commits-noreply＠bitbucket.org 25 Mar '13

25 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7df0d7eb3a06/ Changeset: 7df0d7eb3a06 User: greg Date: 2013-03-25 22:18:17 Summary: Fix a few typos in my last commit. Affected #: 3 files diff -r efe376544e2263ec8f9788d71d25dd2b4b49a39d -r 7df0d7eb3a0670a299d571683daba26cbc692f0b 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 @@ -168,7 +168,7 @@ 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 is not None: + if tool_panel_section_id not in [ None, '' ]: tool_panel_section = trans.app.toolbox.tool_panel[ tool_panel_section_id ] else: tool_panel_section = '' diff -r efe376544e2263ec8f9788d71d25dd2b4b49a39d -r 7df0d7eb3a0670a299d571683daba26cbc692f0b 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_existing_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 <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_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%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%20Test%20Tool%20Shed """ import os diff -r efe376544e2263ec8f9788d71d25dd2b4b49a39d -r 7df0d7eb3a0670a299d571683daba26cbc692f0b scripts/api/install_repository_with_repository_dependencies.py --- a/scripts/api/install_repository_with_repository_dependencies.py +++ b/scripts/api/install_repository_with_repository_dependencies.py @@ -4,10 +4,10 @@ repository dependencies, so multiple repositories will ultimately be installed. Since no Galaxy tool panel section information is used, all tools contained in the installed repositories will be loaded into the Galaxy tool panel outside of any sections. -usage: ./install_repository_tools_into_existing_tool_panel_section <api_key <galaxy base url> tool_shed_url name owner changeset_revision True +usage: ./install_repository_with_repository_dependencies.py <api_key <galaxy base url> tool_shed_url name owner changeset_revision True 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 emboss_5 devteam 8ddad0c9a75a True +./install_repository_with_repository_dependencies.py <api key><galaxy base url>/api/tool_shed_repositories/new/install_repository_revision http://testtoolshed.g2.bx.psu.edu emboss_5 devteam 8ddad0c9a75a True """ import os @@ -32,4 +32,4 @@ print 'usage: %s key url tool_shed_url name owner changeset_revision install_repository_dependencies' % os.path.basename( sys.argv[ 0 ] ) sys.exit( 1 ) -submit( sys.argv[ 1 ], sys.argv[ 2 ], data ) \ No newline at end of file +submit( sys.argv[ 1 ], sys.argv[ 2 ], data ) 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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