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commit/galaxy-central: greg: Handle exceptions attempting to open a README file contained in a tool shed repository.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/124ac431a5dc/ changeset: 124ac431a5dc user: greg date: 2012-10-24 19:42:01 summary: Handle exceptions attempting to open a README file contained in a tool shed repository. affected #: 2 files diff -r 87e6251af95f57e4fa24d6e0c9eaefec6016025d -r 124ac431a5dc96087fc95fd4e1985033e20ba13f lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1333,10 +1333,14 @@ repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) metadata = repository_metadata.metadata if metadata and 'readme' in metadata: - f = open( metadata[ 'readme' ], 'r' ) - text = f.read() - f.close() - return str( text ) + try: + f = open( metadata[ 'readme' ], 'r' ) + text = f.read() + f.close() + return str( text ) + except Exception, e: + log.debug( "Error attempting to read README file '%s' defined in metadata for repository '%s', revision '%s': %s" % \ + ( str( metadata[ 'readme' ] ), str( repository_name ), str( changeset_revision ), str( e ) ) ) return '' @web.expose def get_tool_dependencies( self, trans, **kwd ): diff -r 87e6251af95f57e4fa24d6e0c9eaefec6016025d -r 124ac431a5dc96087fc95fd4e1985033e20ba13f lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1764,10 +1764,15 @@ readme_filename = metadata[ 'readme' ] if tool_path: readme_filename = os.path.join( tool_path, readme_filename ) - f = open( readme_filename, 'r' ) - raw_text = f.read() - f.close() - readme_text = translate_string( raw_text, to_html=True ) + try: + f = open( readme_filename, 'r' ) + raw_text = f.read() + f.close() + readme_text = translate_string( raw_text, to_html=True ) + except Exception, e: + log.debug( "Error attempting to read README file '%s' defined in metadata for repository '%s', revision '%s': %s" % \ + ( str( readme_filename ), str( repository.name ), str( repository.changeset_revision ), str( e ) ) ) + readme_text = '' else: readme_text = '' is_malicious = False 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 Bitbucket 24 Oct '12

24 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ce8cabd05c3b/ changeset: ce8cabd05c3b user: dan date: 2012-10-24 18:33:34 summary: Enhance GenomeSpace import tool to display a better history item name for additional primary datasets. affected #: 1 file diff -r 3fe486853787d10c2ba6f0b79f82aa59aaed8790 -r ce8cabd05c3b5cb4d441eac42beaebaeb048aa9a tools/genomespace/genomespace_importer.py --- a/tools/genomespace/genomespace_importer.py +++ b/tools/genomespace/genomespace_importer.py @@ -100,7 +100,7 @@ datasource_params = json_params.get( 'param_dict' ) assert None not in [ username, token ], "Missing GenomeSpace username or token." output_filename = datasource_params.get( "output_file1", None ) - dataset_id = json_params['output_data'][0]['dataset_id'] + dataset_id = base_dataset_id = json_params['output_data'][0]['dataset_id'] hda_id = json_params['output_data'][0]['hda_id'] url_opener = get_cookie_opener( username, token ) #load and set genomespace format ids to galaxy exts @@ -182,12 +182,18 @@ name = "GenomeSpace importer on %s" % ( filename ) ) ) ) #if using tmp file, move the file to the new file path dir to get scooped up later if using_temp_file: + original_filename = filename filename = ''.join( c in VALID_CHARS and c or '-' for c in filename ) while filename in used_filenames: filename = "-%s" % filename used_filenames.append( filename ) - shutil.move( output_filename, os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, file_type ) ) ) - + target_output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, file_type ) ) + shutil.move( output_filename, target_output_filename ) + metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'new_primary_dataset', + base_dataset_id = base_dataset_id, + ext = file_type, + filename = target_output_filename, + name = "GenomeSpace importer on %s" % ( original_filename ) ) ) ) dataset_id = None #only one primary dataset available output_filename = None #only have one filename available metadata_parameter_file.close() https://bitbucket.org/galaxy/galaxy-central/changeset/87e6251af95f/ changeset: 87e6251af95f user: dan date: 2012-10-24 18:33:34 summary: Enhance GenomeSpace filebrowser importer to display a better history item name for additional primary datasets. affected #: 1 file diff -r ce8cabd05c3b5cb4d441eac42beaebaeb048aa9a -r 87e6251af95f57e4fa24d6e0c9eaefec6016025d tools/genomespace/genomespace_file_browser.py --- a/tools/genomespace/genomespace_file_browser.py +++ b/tools/genomespace/genomespace_file_browser.py @@ -140,11 +140,17 @@ if not filename: filename = download_url if output_filename is None: + original_filename = filename filename = ''.join( c in VALID_CHARS and c or '-' for c in filename ) while filename in used_filenames: filename = "-%s" % filename used_filenames.append( filename ) output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, galaxy_ext ) ) + metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'new_primary_dataset', + base_dataset_id = dataset_id, + ext = galaxy_ext, + filename = output_filename, + name = "GenomeSpace import on %s" % ( original_filename ) ) ) ) else: if dataset_id is not None: metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'dataset', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Allow setting dataset attributes of additional primary datasets through galaxy.json.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3fe486853787/ changeset: 3fe486853787 user: dan date: 2012-10-24 18:28:46 summary: Allow setting dataset attributes of additional primary datasets through galaxy.json. affected #: 1 file diff -r 0c56502c7fd78431001012cb56b3df1224472769 -r 3fe486853787d10c2ba6f0b79f82aa59aaed8790 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2623,10 +2623,19 @@ Find any additional datasets generated by a tool and attach (for cases where number of outputs is not known in advance). """ - primary_datasets = {} + new_primary_datasets = {} + try: + json_file = open( os.path.join( job_working_directory, jobs.TOOL_PROVIDED_JOB_METADATA_FILE ), 'r' ) + for line in json_file: + line = simplejson.loads( line ) + if line.get( 'type' ) == 'new_primary_dataset': + new_primary_datasets[ os.path.split( line.get( 'filename' ) )[-1] ] = line + except Exception, e: + log.debug( "Error opening galaxy.json file: %s" % e ) # Loop through output file names, looking for generated primary # datasets in form of: # 'primary_associatedWithDatasetID_designation_visibility_extension(_DBKEY)' + primary_datasets = {} for name, outdata in output.items(): filenames = [] if 'new_file_path' in self.app.config.collect_outputs_from: @@ -2664,8 +2673,6 @@ primary_data.info = outdata.info primary_data.init_meta( copy_from=outdata ) primary_data.dbkey = dbkey - primary_data.set_meta() - primary_data.set_peek() # Associate new dataset with job job = None for assoc in outdata.creating_job_associations: @@ -2677,6 +2684,15 @@ self.sa_session.add( assoc ) self.sa_session.flush() primary_data.state = outdata.state + #add tool/metadata provided information + new_primary_datasets_attributes = new_primary_datasets.get( os.path.split( filename )[-1] ) + if new_primary_datasets_attributes: + dataset_att_by_name = dict( ext='extension' ) + for att_set in [ 'name', 'info', 'ext', 'dbkey' ]: + dataset_att_name = dataset_att_by_name.get( att_set, att_set ) + setattr( primary_data, dataset_att_name, new_primary_datasets_attributes.get( att_set, getattr( primary_data, dataset_att_name ) ) ) + primary_data.set_meta() + primary_data.set_peek() self.sa_session.add( primary_data ) self.sa_session.flush() outdata.history.add_dataset( primary_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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commit/galaxy-central: greg: Apply patch from Peter Cock which issues a warning if loading a loc file with inconsistent numbers of tabs.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0c56502c7fd7/ changeset: 0c56502c7fd7 user: greg date: 2012-10-24 17:44:32 summary: Apply patch from Peter Cock which issues a warning if loading a loc file with inconsistent numbers of tabs. affected #: 1 file diff -r 7c671a79de1ed98fb2b7253e91fae551c0222a29 -r 0c56502c7fd78431001012cb56b3df1224472769 lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -471,6 +471,7 @@ def parse_file_fields( self, reader ): rval = [] + field_count = None for line in reader: if line.startswith( '#' ) or ( self.line_startswith and not line.startswith( self.line_startswith ) ): continue @@ -478,6 +479,16 @@ if line: fields = line.split( self.separator ) if self.largest_index < len( fields ): + if not field_count: + field_count = len( fields ) + elif field_count != len( fields ): + try: + name = reader.name + except AttributeError: + name = "a configuration file" + # Perhaps this should be an error, but even a warning is useful. + log.warn( "Inconsistent number of fields (%i vs %i) in %s using separator %r, check line: %r" % \ + ( field_count, len( fields ), name, self.separator, line ) ) rval.append( fields ) return rval Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add the free text search feature (enabling searching on repository name) to the tool shed's RepositoryMetadata grid in the admin controller.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7c671a79de1e/ changeset: 7c671a79de1e user: greg date: 2012-10-24 17:35:59 summary: Add the free text search feature (enabling searching on repository name) to the tool shed's RepositoryMetadata grid in the admin controller. affected #: 1 file diff -r bb365c782b64c37b90333d964f55cba0acd401da -r 7c671a79de1ed98fb2b7253e91fae551c0222a29 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -424,6 +424,11 @@ DeprecatedColumn( "Deprecated", attach_popup=False ), MaliciousColumn( "Malicious", attach_popup=False ) ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) operations = [ grids.GridOperation( "Delete", allow_multiple=False, allow_popup=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: natefoo: Implement job_walltime for the local runner.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bb365c782b64/ changeset: bb365c782b64 user: natefoo date: 2012-10-24 17:34:16 summary: Implement job_walltime for the local runner. affected #: 3 files diff -r a5db4601ddbe117b5eb393f5d92982e50a866c7d -r bb365c782b64c37b90333d964f55cba0acd401da lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -5,6 +5,7 @@ import sys, os, tempfile import logging, logging.config import ConfigParser +from datetime import timedelta from galaxy.util import string_as_bool, listify, parse_xml from galaxy import eggs @@ -99,6 +100,10 @@ self.output_size_limit = int( kwargs.get( 'output_size_limit', 0 ) ) self.retry_job_output_collection = int( kwargs.get( 'retry_job_output_collection', 0 ) ) self.job_walltime = kwargs.get( 'job_walltime', None ) + self.job_walltime_delta = None + if self.job_walltime is not None: + h, m, s = [ int( v ) for v in self.job_walltime.split( ':' ) ] + self.job_walltime_delta = timedelta( 0, s, 0, 0, m, h ) self.admin_users = kwargs.get( "admin_users", "" ) self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) diff -r a5db4601ddbe117b5eb393f5d92982e50a866c7d -r bb365c782b64c37b90333d964f55cba0acd401da lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -1,6 +1,7 @@ import logging import subprocess import tempfile +import datetime from Queue import Queue import threading @@ -89,28 +90,36 @@ preexec_fn = os.setpgrp ) job_wrapper.set_runner( 'local:///', proc.pid ) job_wrapper.change_state( model.Job.states.RUNNING ) - if self.app.config.output_size_limit > 0: - sleep_time = 1 - while proc.poll() is None: + sleep_time = 1 + job_start = datetime.datetime.now() + while proc.poll() is None: + if self.app.config.output_size_limit > 0: for outfile, size in job_wrapper.check_output_sizes(): if size > self.app.config.output_size_limit: # Error the job immediately - job_wrapper.fail( 'Job output grew too large (greater than %s), please try different job parameters or' \ + job_wrapper.fail( 'Job output grew too large (greater than %s), please try different job parameters' \ % nice_size( self.app.config.output_size_limit ) ) log.warning( 'Terminating job %s due to output %s growing larger than %s limit' \ % ( job_wrapper.job_id, os.path.basename( outfile ), nice_size( self.app.config.output_size_limit ) ) ) # Then kill it - os.killpg( proc.pid, 15 ) - sleep( 1 ) - if proc.poll() is None: - os.killpg( proc.pid, 9 ) - proc.wait() # reap + self._terminate( proc ) log.debug( 'Job %s (pid %s) terminated' % ( job_wrapper.job_id, proc.pid ) ) return sleep( sleep_time ) - if sleep_time < 8: - # So we don't stat every second - sleep_time *= 2 + if self.app.config.job_walltime_delta is not None: + time_executing = datetime.datetime.now() - job_start + if time_executing > self.app.config.job_walltime_delta: + # Error the job immediately + job_wrapper.fail( 'Job ran longer than maximum allowed execution time (%s), please try different job parameters' \ + % self.app.config.job_walltime ) + log.warning( 'Terminating job %s since walltime has been reached' % job_wrapper.job_id ) + # Then kill it + self._terminate( proc ) + log.debug( 'Job %s (pid %s) terminated' % ( job_wrapper.job_id, proc.pid ) ) + return + if sleep_time < 8: + # So we don't stat every second + sleep_time *= 2 # Reap the process and get the exit code. exit_code = proc.wait() stdout_file.seek( 0 ) @@ -202,3 +211,9 @@ # local jobs can't be recovered job_wrapper.change_state( model.Job.states.ERROR, info = "This job was killed when Galaxy was restarted. Please retry the job." ) + def _terminate( self, proc ): + os.killpg( proc.pid, 15 ) + sleep( 1 ) + if proc.poll() is None: + os.killpg( proc.pid, 9 ) + return proc.wait() # reap diff -r a5db4601ddbe117b5eb393f5d92982e50a866c7d -r bb365c782b64c37b90333d964f55cba0acd401da lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py +++ b/lib/galaxy/jobs/runners/pbs.py @@ -128,10 +128,6 @@ # set the default server during startup self.default_pbs_server = None self.determine_pbs_server( 'pbs:///' ) - self.job_walltime = None - if self.app.config.job_walltime is not None: - h, m, s = [ int( v ) for v in self.app.config.job_walltime.split( ':' ) ] - self.job_walltime = timedelta( 0, s, 0, 0, m, h ) self.monitor_thread = threading.Thread( target=self.monitor ) self.monitor_thread.start() self.work_queue = Queue() @@ -422,7 +418,7 @@ fail = False for outfile, size in pbs_job_state.job_wrapper.check_output_sizes(): if size > self.app.config.output_size_limit: - pbs_job_state.fail_message = 'Job output grew too large (greater than %s), please try different job parameters or' \ + pbs_job_state.fail_message = 'Job output grew too large (greater than %s), please try different job parameters' \ % nice_size( self.app.config.output_size_limit ) log.warning( '(%s/%s) Dequeueing job due to output %s growing larger than %s limit' \ % ( galaxy_job_id, job_id, os.path.basename( outfile ), nice_size( self.app.config.output_size_limit ) ) ) @@ -432,14 +428,14 @@ break if fail: continue - if self.job_walltime is not None: + if self.app.config.job_walltime_delta is not None: # Check the job's execution time if status.get( 'resources_used', False ): # resources_used may not be in the status for new jobs h, m, s = [ int( i ) for i in status.resources_used.walltime.split( ':' ) ] time_executing = timedelta( 0, s, 0, 0, m, h ) - if time_executing > self.job_walltime: - pbs_job_state.fail_message = 'Job ran longer than maximum allowed execution time (%s), please try different job parameters or' \ + if time_executing > self.app.config.job_walltime_delta: + pbs_job_state.fail_message = 'Job ran longer than maximum allowed execution time (%s), please try different job parameters' \ % self.app.config.job_walltime log.warning( '(%s/%s) Dequeueing job since walltime has been reached' \ % ( galaxy_job_id, job_id ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Make sure repository component reviews that have been marked private are restricted to those that are authorized to access them.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a5db4601ddbe/ changeset: a5db4601ddbe user: greg date: 2012-10-24 17:28:27 summary: Make sure repository component reviews that have been marked private are restricted to those that are authorized to access them. affected #: 1 file diff -r ae5b674b4342a87863a17cea8ad3a46adef2b51f -r a5db4601ddbe117b5eb393f5d92982e50a866c7d templates/webapps/community/repository_review/browse_review.mako --- a/templates/webapps/community/repository_review/browse_review.mako +++ b/templates/webapps/community/repository_review/browse_review.mako @@ -61,15 +61,15 @@ <table class="grid"> %for component_review in review.component_reviews: <% + can_browse = trans.app.security_agent.user_can_browse_component_review( component_review, trans.user ) component = component_review.component - - # Initialize Private check box. - private_check_box_name = '%s%sprivate' % ( component.name, STRSEP ) - private_check_box = CheckboxField( name=private_check_box_name, checked=component_review.private ) - - # Initialize star rating. - rating_name = '%s%srating' % ( component.name, STRSEP ) - + if can_browse: + # Initialize Private check box. + private_check_box_name = '%s%sprivate' % ( component.name, STRSEP ) + private_check_box = CheckboxField( name=private_check_box_name, checked=component_review.private ) + + # Initialize star rating. + rating_name = '%s%srating' % ( component.name, STRSEP ) %><tr><td bgcolor="#D8D8D8"><b>${component.name | h}</b></td> @@ -77,41 +77,45 @@ </tr><tr><td colspan="2"> - <table class="grid"> - <tr> - <td> - <label>Private:</label> - ${private_check_box.get_html( disabled=True )} - <div class="toolParamHelp" style="clear: both;"> - A private review can be accessed only by the owner of the repository and authorized repository reviewers. - </div> - <div style="clear: both"></div> - </td> - </tr> - %if component_review.comment: + %if can_browse: + <table class="grid"><tr><td> - <div overflow-wrap:normal;overflow:hidden;word-break:keep-all;word-wrap:break-word;line-break:strict;> - ${ escape_html_add_breaks( component_review.comment ) } + <label>Private:</label> + ${private_check_box.get_html( disabled=True )} + <div class="toolParamHelp" style="clear: both;"> + A private review can be accessed only by the owner of the repository and authorized repository reviewers. </div> + <div style="clear: both"></div></td></tr> - %endif - <tr> - <td> - <label>Approved:</label> - ${component_review.approved | h} - <div style="clear: both"></div> - </td> - </tr> - <tr> - <td> - <label>Rating:</label> - ${render_star_rating( rating_name, component_review.rating, disabled=True )} - <div style="clear: both"></div> - </td> - </tr> - </table> + %if component_review.comment: + <tr> + <td> + <div overflow-wrap:normal;overflow:hidden;word-break:keep-all;word-wrap:break-word;line-break:strict;> + ${ escape_html_add_breaks( component_review.comment ) } + </div> + </td> + </tr> + %endif + <tr> + <td> + <label>Approved:</label> + ${component_review.approved | h} + <div style="clear: both"></div> + </td> + </tr> + <tr> + <td> + <label>Rating:</label> + ${render_star_rating( rating_name, component_review.rating, disabled=True )} + <div style="clear: both"></div> + </td> + </tr> + </table> + %else: + You are not authorized to access the review of this component since it has been marked private. + %endif </td></tr> %endfor 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 for determing a Checkbox setting when reviewing repositories.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ae5b674b4342/ changeset: ae5b674b4342 user: greg date: 2012-10-24 17:27:16 summary: Fix for determing a Checkbox setting when reviewing repositories. affected #: 1 file diff -r a239f666d5ba8ce3f24198e7054fdd03ab60ada0 -r ae5b674b4342a87863a17cea8ad3a46adef2b51f lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -509,7 +509,7 @@ elif component_review_attr == 'comment': comment = str( v ) elif component_review_attr == 'private': - private = CheckboxField.is_checked( str( v ) ) + private = CheckboxField.is_checked( v ) elif component_review_attr == 'approved': approved = str( v ) elif component_review_attr == 'rating': 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 the tool shed security agent to enable restriction of component reviews that have been marked private.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a239f666d5ba/ changeset: a239f666d5ba user: greg date: 2012-10-24 17:26:00 summary: Enhance the tool shed security agent to enable restriction of component reviews that have been marked private. affected #: 1 file diff -r 409fec0598f944d30f69e9faaac193b71d6541b8 -r a239f666d5ba8ce3f24198e7054fdd03ab60ada0 lib/galaxy/webapps/community/security/__init__.py --- a/lib/galaxy/webapps/community/security/__init__.py +++ b/lib/galaxy/webapps/community/security/__init__.py @@ -170,6 +170,21 @@ repository_reviewer_role = self.get_repository_reviewer_role() return repository_reviewer_role and repository_reviewer_role in roles return False + def user_can_browse_component_review( self, component_review, user ): + if component_review and user: + if component_review.private: + if self.user_can_review_repositories( user ): + # Reviewers can access private component reviews. + return True + repository_review = component_review.repository_review + repository = repository_review.repository + if repository.user == user: + # The repository owner can access private component reviews. + return True + return False + # The component_review is not marked private. + return True + return False def get_permitted_actions( filter=None ): '''Utility method to return a subset of RBACAgent's permitted actions''' 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: Migrate Picard tools to the tool shed.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/409fec0598f9/ changeset: 409fec0598f9 user: inithello date: 2012-10-24 17:09:20 summary: Migrate Picard tools to the tool shed. affected #: 82 files Diff too large to display. 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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