- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b7e148067d62/ Changeset: b7e148067d62 User: dannon Date: 2013-09-26 15:13:32 Summary: Correctly shutdown HierarchicalObjectStore and DistributedObjectStore Affected #: 1 file diff -r ff806b8e5f18791641fa49a20d9bea9e65215310 -r b7e148067d62e0153a15d4c46f70eece3c938a7e lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -381,9 +381,8 @@ self.backends = {} def shutdown(self): - [b.shutdown() for b in self.backends.values()] - if self.sleeper is not None: - self.sleeper.wake() + for store in self.backends.values(): + store.shutdown() super(NestedObjectStore, self).shutdown() def exists(self, obj, **kwargs): @@ -452,11 +451,8 @@ self.original_weighted_backend_ids = [] self.max_percent_full = {} self.global_max_percent_full = 0.0 - random.seed() - self.__parse_distributed_config(config, config_xml) - self.sleeper = None if fsmon and ( self.global_max_percent_full or filter( lambda x: x != 0.0, self.max_percent_full.values() ) ): self.sleeper = Sleeper() @@ -501,6 +497,12 @@ self.weighted_backend_ids.append(id) self.original_weighted_backend_ids = self.weighted_backend_ids + + def shutdown(self): + super(NestedObjectStore, self).shutdown() + if self.sleeper is not None: + self.sleeper.wake() + def __filesystem_monitor(self): while self.running: new_weighted_backend_ids = self.original_weighted_backend_ids @@ -570,10 +572,6 @@ for b in config_xml.find('backends'): self.backends[int(b.get('order'))] = build_object_store_from_config(config, fsmon=fsmon, config_xml=b) - def shutdown(self): - for store in self.backends.values(): - store.shutdown() - super(HierarchicalObjectStore, self).shutdown() def exists(self, obj, **kwargs): """ https://bitbucket.org/galaxy/galaxy-central/commits/e890cd2464ac/ Changeset: e890cd2464ac User: dannon Date: 2013-09-26 15:13:50 Summary: merge Affected #: 11 files diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -172,6 +172,7 @@ self.job_stop_queue = self.job_manager.job_stop_queue # Initialize the external service types self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self ) + self.model.engine.dispose() def shutdown( self ): self.job_manager.shutdown() diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml @@ -9,7 +9,12 @@ grep -v '^#' $input | sort -k1,1 | ## Generate coverage bedgraph. - bedtools genomecov -bg -split -i stdin -g $chromInfo + bedtools genomecov -bg -i stdin -g $chromInfo + + ## Only use split option for bed and gff/gff3/gtf. + #if $input.ext in [ 'bed', 'gff', 'gff3', 'gtf' ]: + -split + #end if ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this ## should only be used on systems with large RAM. diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -226,7 +226,13 @@ if state == drmaa.JobState.RUNNING and not ajs.running: ajs.running = True ajs.job_wrapper.change_state( model.Job.states.RUNNING ) - if state in ( drmaa.JobState.DONE, drmaa.JobState.FAILED ): + if state == drmaa.JobState.FAILED: + if ajs.job_wrapper.get_state() != model.Job.states.DELETED: + ajs.stop_job = False + ajs.fail_message = "The cluster DRM system terminated this job" + self.work_queue.put( ( self.fail_job, ajs ) ) + continue + if state == drmaa.JobState.DONE: if ajs.job_wrapper.get_state() != model.Job.states.DELETED: self.work_queue.put( ( self.finish_job, ajs ) ) continue diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc 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 @@ -121,12 +121,12 @@ for exported_workflow_dict in exported_workflows: workflow_name = exported_workflow_dict[ 'workflow_name' ] workflow, status, message = workflow_util.import_workflow( trans, repository, workflow_name ) - if status == 'error': - log.error( message, exc_info=True ) - trans.response.status = 500 - return message - else: - imported_workflow_dicts.append( workflow.to_dict( view='element' ) ) + if status == 'error': + log.error( message, exc_info=True ) + trans.response.status = 500 + return message + else: + imported_workflow_dicts.append( workflow.to_dict( view='element' ) ) return imported_workflow_dicts @web.expose_api diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -705,9 +705,10 @@ if 'display_url' not in kwd or 'redirect_url' not in kwd: return trans.show_error_message( 'Invalid parameters specified for "display at" link, please contact a Galaxy administrator' ) try: - redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] ) + redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] ) except: - redirect_url = kwd['redirect_url'] # not all will need custom text + redirect_url = kwd['redirect_url'] # not all will need custom text + redirect_url = redirect_url.encode( 'utf-8' ) current_user_roles = trans.get_current_user_roles() if trans.app.security_agent.dataset_is_public( data.dataset ): return trans.response.send_redirect( redirect_url ) # anon access already permitted by rbac diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -1,16 +1,17 @@ import logging from galaxy.web.framework.helpers import time_ago +from galaxy import eggs from galaxy import web from galaxy import util from galaxy.web.base.controller import BaseAPIController import tool_shed.util.shed_util_common as suc from tool_shed.galaxy_install import repository_util -from galaxy import eggs -import pkg_resources +eggs.require( 'mercurial' ) -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 b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/tool_shed/grids/admin_grids.py --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -1,15 +1,19 @@ -import os, logging -from galaxy.web.framework.helpers import time_ago, grids +import logging +import os +from galaxy.web.framework.helpers import grids +from galaxy.web.framework.helpers import time_ago from galaxy.webapps.tool_shed import model from galaxy.model.orm import and_ import tool_shed.util.shed_util_common as suc -from tool_shed.grids.repository_grids import RepositoryGrid, CategoryGrid +from tool_shed.grids.repository_grids import CategoryGrid +from tool_shed.grids.repository_grids import RepositoryGrid from galaxy import eggs -import pkg_resources +eggs.require( 'mercurial' ) -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 b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -573,27 +573,23 @@ def build_readme_files_folder( trans, folder_id, readme_files_dict, label='Readme files' ): """Return a folder hierarchy containing readme text files.""" if readme_files_dict: - multiple_readme_files = len( readme_files_dict ) > 1 readme_id = 0 folder_id += 1 readme_files_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) - if multiple_readme_files: - folder_id += 1 - readme_files_folder = Folder( id=folder_id, key='readme_files', label=label, parent=readme_files_root_folder ) - readme_files_root_folder.folders.append( readme_files_folder ) + folder_id += 1 + readme_files_folder = Folder( id=folder_id, key='readme_files', label=label, parent=readme_files_root_folder ) + multiple_readme_files = len( readme_files_dict ) > 1 + readme_files_root_folder.folders.append( readme_files_folder ) for readme_file_name, readme_file_text in readme_files_dict.items(): readme_id += 1 readme = ReadMe( id=readme_id, name=readme_file_name, text=readme_file_text ) if multiple_readme_files: folder_id += 1 - folder = Folder( id=folder_id, key=readme.name, label=readme.name, parent=readme_files_folder ) + folder = Folder( id=folder_id, key=readme_file_name, label=readme_file_name, parent=readme_files_folder ) folder.readme_files.append( readme ) readme_files_folder.folders.append( folder ) else: - folder_id += 1 - readme_files_folder = Folder( id=folder_id, key='readme_files', label=readme.name, parent=readme_files_root_folder ) readme_files_folder.readme_files.append( readme ) - readme_files_root_folder.folders.append( readme_files_folder ) else: readme_files_root_folder = None return folder_id, readme_files_root_folder diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -589,7 +589,7 @@ original_repository_metadata = repository.metadata else: original_repository_metadata = None - readme_file_names = get_readme_file_names( repository.name ) + readme_file_names = readme_util.get_readme_file_names( str( repository.name ) ) if app.name == 'galaxy': # Shed related tool panel configs are only relevant to Galaxy. metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) } @@ -1046,16 +1046,6 @@ # The tool did not change through all of the changeset revisions. return old_id -def get_readme_file_names( repository_name ): - """Creates a list of valid filenames.""" - readme_files = [ 'readme', 'read_me', 'install' ] - valid_filenames = map( lambda f: '%s.txt' % f, readme_files ) - valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) ) - valid_filenames.extend( readme_files ) - valid_filenames.append( '%s.txt' % repository_name ) - valid_filenames.append( '%s.rst' % repository_name ) - return valid_filenames - def get_relative_path_to_repository_file( root, name, relative_install_dir, work_dir, shed_config_dict, resetting_all_metadata_on_repository ): if resetting_all_metadata_on_repository: full_path_to_file = os.path.join( root, name ) diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc lib/tool_shed/util/readme_util.py --- a/lib/tool_shed/util/readme_util.py +++ b/lib/tool_shed/util/readme_util.py @@ -70,3 +70,13 @@ raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) readme_files_dict = json.from_json_string( raw_text ) return readme_files_dict + +def get_readme_file_names( repository_name ): + """Return a list of file names that will be categorized as README files for the received repository_name.""" + readme_files = [ 'readme', 'read_me', 'install' ] + valid_filenames = map( lambda f: '%s.txt' % f, readme_files ) + valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) ) + valid_filenames.extend( readme_files ) + valid_filenames.append( '%s.txt' % repository_name ) + valid_filenames.append( '%s.rst' % repository_name ) + return valid_filenames diff -r b7e148067d62e0153a15d4c46f70eece3c938a7e -r e890cd2464ac2d14a7a4ccd9e4a4ef728e6f0cfc templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -425,7 +425,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rd-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;">${datatype.extension | h}</${cell_type}><${cell_type}>${datatype.type | h}</${cell_type}><${cell_type}>${datatype.mimetype | h}</${cell_type}> @@ -440,15 +440,15 @@ <%def name="render_failed_test( failed_test, pad, parent, row_counter, row_is_header=False )"><% from tool_shed.util.shed_util_common import to_html_string - encoded_id = trans.security.encode_id( failed_test.id ) + encoded_id = trans.security.encode_id( failed_test.id ) %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rft-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="failed_test_table" class="tool_test_results"> + <table id="test_environment"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${failed_test.test_id | h}</td></tr> @@ -475,7 +475,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-ridm-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;">${data_manager.index | h}</${cell_type}><${cell_type}>${data_manager.error | h}</${cell_type}></tr> @@ -493,7 +493,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rird-${encoded_id}"><td style="padding-left: ${pad+20}px;"> ${ invalid_repository_dependency.error | h } </td> @@ -510,7 +510,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rit-${encoded_id}"><td style="padding-left: ${pad+20}px;"> %if trans.webapp.name == 'tool_shed' and invalid_tool.repository_id and invalid_tool.tool_config and invalid_tool.changeset_revision: <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( invalid_tool.repository_id ), tool_config=invalid_tool.tool_config, changeset_revision=invalid_tool.changeset_revision, render_repository_actions_for=render_repository_actions_for )}"> @@ -545,7 +545,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-ritd-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="invalid_td_table"><tr><td>${ invalid_tool_dependency.error | h }</td></tr> @@ -559,14 +559,16 @@ </%def><%def name="render_missing_test_component( missing_test_component, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( missing_test_component.id ) %> + <% + encoded_id = trans.security.encode_id( missing_test_component.id ) + %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rmtc-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="missing_table" class="tool_test_results"> + <table id="test_environment"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${missing_test_component.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${missing_test_component.tool_version | h}</td></tr><tr><td><b>Tool guid:</b> ${missing_test_component.tool_guid | h}</td></tr> @@ -587,27 +589,17 @@ encoded_id = trans.security.encode_id( readme.id ) render_rst = readme.name.endswith( '.rst' ) %> - <style type="text/css"> - #readme_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><tr class="datasetRow" %if parent is not None: - parent="${parent}" + parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rr-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="readme_table"> + <table id="readme_files"> %if render_rst: <tr><td>${ rst_to_html( readme.text ) }</td></tr> %else: - <tr><td>${readme.name}<br/>${ to_html_string( readme.text ) }</td></tr> + <tr><td>${ to_html_string( readme.text ) }</td></tr> %endif </table></td> @@ -652,7 +644,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rrd-${encoded_id}"> %if trans.webapp.name == 'galaxy': <${cell_type} style="padding-left: ${pad+20}px;"> %if row_is_header: @@ -684,28 +676,31 @@ %></%def> -<%def name="render_tool_test_results_css()"> +<%def name="render_table_wrap_style( table_id )"><style type="text/css"> - table.tool_test_results{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } + table.${table_id}{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } </style></%def><%def name="render_tool_dependency_installation_error( installation_error, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( installation_error.id ) %> + <% + encoded_id = trans.security.encode_id( installation_error.id ) + %> + ${render_table_wrap_style( "td_install_error_table" )} <tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rtdie-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="td_install_error_table" class="tool_test_results"> + <table id="td_install_error_table"><tr bgcolor="#FFFFCC"><th>Type</th><th>Name</th><th>Version</th></tr> @@ -726,14 +721,17 @@ </%def><%def name="render_repository_installation_error( installation_error, pad, parent, row_counter, row_is_header=False, is_current_repository=False )"> - <% encoded_id = trans.security.encode_id( installation_error.id ) %> + <% + encoded_id = trans.security.encode_id( installation_error.id ) + %> + ${render_table_wrap_style( "rd_install_error_table" )} <tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rrie-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="rd_install_error_table" class="tool_test_results"> + <table id="rd_install_error_table"> %if not is_current_repository: <tr bgcolor="#FFFFCC"><th>Tool shed</th><th>Name</th><th>Owner</th><th>Changeset revision</th> @@ -757,14 +755,16 @@ </%def><%def name="render_not_tested( not_tested, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( not_tested.id ) %> + <% + encoded_id = trans.security.encode_id( not_tested.id ) + %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rnt-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="not_tested_table" class="tool_test_results"> + <table id="test_environment"><tr><td>${not_tested.reason | h}</td></tr></table></td> @@ -776,14 +776,16 @@ </%def><%def name="render_passed_test( passed_test, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( passed_test.id ) %> + <% + encoded_id = trans.security.encode_id( passed_test.id ) + %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rpt-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="passed_tests_table" class="tool_test_results"> + <table id="test_environment"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${passed_test.test_id | h}</td></tr> @@ -808,7 +810,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rt-${encoded_id}"> %if row_is_header: <th style="padding-left: ${pad+20}px;">${tool.name | h}</th> %else: @@ -857,7 +859,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rtd-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;"> %if row_is_header: ${tool_dependency.name | h} @@ -917,9 +919,9 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rte-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table class="grid" id="readme_table"> + <table class="grid" id="test_environment"><tr><td><b>Time tested:</b> ${test_environment.time_last_tested | h}</td></tr><tr><td><b>System:</b> ${test_environment.system | h}</td></tr><tr><td><b>Architecture:</b> ${test_environment.architecture | h}</td></tr> @@ -950,7 +952,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rvdm-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;">${data_manager.name | h}</${cell_type}><${cell_type}>${data_manager.version | h}</${cell_type}><${cell_type}>${data_manager.data_tables | h}</${cell_type}> @@ -981,7 +983,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rw-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;"> %if row_is_header: ${workflow.workflow_name | h} @@ -1045,6 +1047,8 @@ return str( self.count ) %> %if readme_files_root_folder: + ${render_table_wrap_style( "readme_files" )} + <p/><div class="toolForm"><div class="toolFormTitle">Repository README files - may contain important installation or license information</div><div class="toolFormBody"> @@ -1127,14 +1131,14 @@ %if valid_data_managers_root_folder: <p/><% row_counter = RowCounter() %> - <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="valid_tools"> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="valid_data_managers"> ${render_folder( valid_data_managers_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} </table> %endif %if invalid_data_managers_root_folder: <p/><% row_counter = RowCounter() %> - <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="invalid_tools"> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="invalid_data_managers"> ${render_folder( invalid_data_managers_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} </table> %endif @@ -1156,16 +1160,20 @@ </div> %endif %if tool_test_results_root_folder: - ${render_tool_test_results_css()} + ##${render_table_wrap_style( "failed_test_table" )} + ##${render_table_wrap_style( "missing_table" )} + ##${render_table_wrap_style( "not_tested_table" )} + ##${render_table_wrap_style( "passed_tests_table" )} + ${render_table_wrap_style( "test_environment" )} <p/><div class="toolForm"><div class="toolFormTitle">Automated tool test results</div><div class="toolFormBody"> - <p/> - <% row_counter = RowCounter() %> - <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="test_environment"> - ${render_folder( tool_test_results_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} - </table> + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="test_environment"> + ${render_folder( tool_test_results_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table></div></div> %endif 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.

1 0

commit/galaxy-central: natefoo: Handle unicode args passed to display_at.
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b914c26a33fe/ Changeset: b914c26a33fe User: natefoo Date: 2013-09-26 14:40:02 Summary: Handle unicode args passed to display_at. Affected #: 1 file diff -r 51760f44ba6d8994c5f46b26f77c9c3a7708b802 -r b914c26a33fe17e3e43115b2fa37bd3888d91399 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -705,9 +705,10 @@ if 'display_url' not in kwd or 'redirect_url' not in kwd: return trans.show_error_message( 'Invalid parameters specified for "display at" link, please contact a Galaxy administrator' ) try: - redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] ) + redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] ) except: - redirect_url = kwd['redirect_url'] # not all will need custom text + redirect_url = kwd['redirect_url'] # not all will need custom text + redirect_url = redirect_url.encode( 'utf-8' ) current_user_roles = trans.get_current_user_roles() if trans.app.security_agent.dataset_is_public( data.dataset ): return trans.response.send_redirect( redirect_url ) # anon access already permitted by rbac 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.

1 0

commit/galaxy-central: natefoo: Handle DRM failures in the DRMAA runner.
by commits-noreply＠bitbucket.org 26 Sep '13

26 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/51760f44ba6d/ Changeset: 51760f44ba6d User: natefoo Date: 2013-09-26 14:36:34 Summary: Handle DRM failures in the DRMAA runner. Affected #: 1 file diff -r ce0b8a3a966d24edd0ba8c7dc51213929c4de75d -r 51760f44ba6d8994c5f46b26f77c9c3a7708b802 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -226,7 +226,13 @@ if state == drmaa.JobState.RUNNING and not ajs.running: ajs.running = True ajs.job_wrapper.change_state( model.Job.states.RUNNING ) - if state in ( drmaa.JobState.DONE, drmaa.JobState.FAILED ): + if state == drmaa.JobState.FAILED: + if ajs.job_wrapper.get_state() != model.Job.states.DELETED: + ajs.stop_job = False + ajs.fail_message = "The cluster DRM system terminated this job" + self.work_queue.put( ( self.fail_job, ajs ) ) + continue + if state == drmaa.JobState.DONE: if ajs.job_wrapper.get_state() != model.Job.states.DELETED: self.work_queue.put( ( self.finish_job, ajs ) ) continue 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.

1 0

commit/galaxy-central: dannon: Fix app startup for uwsgi and multiprocess.
by commits-noreply＠bitbucket.org 25 Sep '13

25 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce0b8a3a966d/ Changeset: ce0b8a3a966d User: dannon Date: 2013-09-25 22:43:41 Summary: Fix app startup for uwsgi and multiprocess. Affected #: 1 file diff -r 9852a9c70535775c6423a42d6924eead6c4bdad1 -r ce0b8a3a966d24edd0ba8c7dc51213929c4de75d lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -172,6 +172,7 @@ self.job_stop_queue = self.job_manager.job_stop_queue # Initialize the external service types self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self ) + self.model.engine.dispose() def shutdown( self ): self.job_manager.shutdown() 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.

1 0

commit/galaxy-central: greg: Thanks to John Chilton - Fix for importing exported workflows contained in an installed tool shed repository.
by commits-noreply＠bitbucket.org 25 Sep '13

25 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9852a9c70535/ Changeset: 9852a9c70535 User: greg Date: 2013-09-25 22:37:52 Summary: Thanks to John Chilton - Fix for importing exported workflows contained in an installed tool shed repository. Affected #: 1 file diff -r 5ee26d53a18f9c66e21d0663f877b5f12fb4aabc -r 9852a9c70535775c6423a42d6924eead6c4bdad1 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 @@ -121,12 +121,12 @@ for exported_workflow_dict in exported_workflows: workflow_name = exported_workflow_dict[ 'workflow_name' ] workflow, status, message = workflow_util.import_workflow( trans, repository, workflow_name ) - if status == 'error': - log.error( message, exc_info=True ) - trans.response.status = 500 - return message - else: - imported_workflow_dicts.append( workflow.to_dict( view='element' ) ) + if status == 'error': + log.error( message, exc_info=True ) + trans.response.status = 500 + return message + else: + imported_workflow_dicts.append( workflow.to_dict( view='element' ) ) return imported_workflow_dicts @web.expose_api 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.

1 0

commit/galaxy-central: greg: Tool shed container style fixes.
by commits-noreply＠bitbucket.org 25 Sep '13

25 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5ee26d53a18f/ Changeset: 5ee26d53a18f User: greg Date: 2013-09-25 22:28:35 Summary: Tool shed container style fixes. Affected #: 1 file diff -r 872e942b497b22e30d73aada6df101bbef1a460f -r 5ee26d53a18f9c66e21d0663f877b5f12fb4aabc templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -440,7 +440,7 @@ <%def name="render_failed_test( failed_test, pad, parent, row_counter, row_is_header=False )"><% from tool_shed.util.shed_util_common import to_html_string - encoded_id = trans.security.encode_id( failed_test.id ) + encoded_id = trans.security.encode_id( failed_test.id ) %><tr class="datasetRow" %if parent is not None: @@ -448,7 +448,7 @@ %endif id="libraryItem-rft-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="failed_test_table" class="tool_test_results"> + <table id="test_environment"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${failed_test.test_id | h}</td></tr> @@ -559,14 +559,16 @@ </%def><%def name="render_missing_test_component( missing_test_component, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( missing_test_component.id ) %> + <% + encoded_id = trans.security.encode_id( missing_test_component.id ) + %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif id="libraryItem-rmtc-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="missing_table" class="tool_test_results"> + <table id="test_environment"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${missing_test_component.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${missing_test_component.tool_version | h}</td></tr><tr><td><b>Tool guid:</b> ${missing_test_component.tool_guid | h}</td></tr> @@ -674,41 +676,31 @@ %></%def> -<%def name="render_readme_files_css()"> +<%def name="render_table_wrap_style( table_id )"><style type="text/css"> - table.readme_files{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style> -</%def> - -<%def name="render_tool_test_results_css()"> - <style type="text/css"> - table.tool_test_results{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } + table.${table_id}{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } </style></%def><%def name="render_tool_dependency_installation_error( installation_error, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( installation_error.id ) %> + <% + encoded_id = trans.security.encode_id( installation_error.id ) + %> + ${render_table_wrap_style( "td_install_error_table" )} <tr class="datasetRow" %if parent is not None: parent="${parent}" %endif id="libraryItem-rtdie-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="td_install_error_table" class="tool_test_results"> + <table id="td_install_error_table"><tr bgcolor="#FFFFCC"><th>Type</th><th>Name</th><th>Version</th></tr> @@ -729,14 +721,17 @@ </%def><%def name="render_repository_installation_error( installation_error, pad, parent, row_counter, row_is_header=False, is_current_repository=False )"> - <% encoded_id = trans.security.encode_id( installation_error.id ) %> + <% + encoded_id = trans.security.encode_id( installation_error.id ) + %> + ${render_table_wrap_style( "rd_install_error_table" )} <tr class="datasetRow" %if parent is not None: parent="${parent}" %endif id="libraryItem-rrie-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="rd_install_error_table" class="tool_test_results"> + <table id="rd_install_error_table"> %if not is_current_repository: <tr bgcolor="#FFFFCC"><th>Tool shed</th><th>Name</th><th>Owner</th><th>Changeset revision</th> @@ -760,14 +755,16 @@ </%def><%def name="render_not_tested( not_tested, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( not_tested.id ) %> + <% + encoded_id = trans.security.encode_id( not_tested.id ) + %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif id="libraryItem-rnt-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="not_tested_table" class="tool_test_results"> + <table id="test_environment"><tr><td>${not_tested.reason | h}</td></tr></table></td> @@ -779,14 +776,16 @@ </%def><%def name="render_passed_test( passed_test, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( passed_test.id ) %> + <% + encoded_id = trans.security.encode_id( passed_test.id ) + %><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif id="libraryItem-rpt-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="passed_tests_table" class="tool_test_results"> + <table id="test_environment"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${passed_test.test_id | h}</td></tr> @@ -916,23 +915,13 @@ <%def name="render_test_environment( test_environment, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( test_environment.id ) %> - <style type="text/css"> - #test_environment_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif id="libraryItem-rte-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table class="grid" id="test_environment_table"> + <table class="grid" id="test_environment"><tr><td><b>Time tested:</b> ${test_environment.time_last_tested | h}</td></tr><tr><td><b>System:</b> ${test_environment.system | h}</td></tr><tr><td><b>Architecture:</b> ${test_environment.architecture | h}</td></tr> @@ -1058,7 +1047,7 @@ return str( self.count ) %> %if readme_files_root_folder: - ${render_readme_files_css()} + ${render_table_wrap_style( "readme_files" )} <p/><div class="toolForm"><div class="toolFormTitle">Repository README files - may contain important installation or license information</div> @@ -1142,14 +1131,14 @@ %if valid_data_managers_root_folder: <p/><% row_counter = RowCounter() %> - <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="valid_tools"> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="valid_data_managers"> ${render_folder( valid_data_managers_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} </table> %endif %if invalid_data_managers_root_folder: <p/><% row_counter = RowCounter() %> - <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="invalid_tools"> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="invalid_data_managers"> ${render_folder( invalid_data_managers_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} </table> %endif @@ -1171,7 +1160,11 @@ </div> %endif %if tool_test_results_root_folder: - ${render_tool_test_results_css()} + ##${render_table_wrap_style( "failed_test_table" )} + ##${render_table_wrap_style( "missing_table" )} + ##${render_table_wrap_style( "not_tested_table" )} + ##${render_table_wrap_style( "passed_tests_table" )} + ${render_table_wrap_style( "test_environment" )} <p/><div class="toolForm"><div class="toolFormTitle">Automated tool test results</div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix for rendering multiple readme files contained within a tool shed repository.
by commits-noreply＠bitbucket.org 25 Sep '13

25 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/872e942b497b/ Changeset: 872e942b497b User: greg Date: 2013-09-25 21:15:41 Summary: Fix for rendering multiple readme files contained within a tool shed repository. Affected #: 6 files diff -r b8d8f81bed872e58b4691643de8a08fa41662e71 -r 872e942b497b22e30d73aada6df101bbef1a460f lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -1,16 +1,17 @@ import logging from galaxy.web.framework.helpers import time_ago +from galaxy import eggs from galaxy import web from galaxy import util from galaxy.web.base.controller import BaseAPIController import tool_shed.util.shed_util_common as suc from tool_shed.galaxy_install import repository_util -from galaxy import eggs -import pkg_resources +eggs.require( 'mercurial' ) -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 b8d8f81bed872e58b4691643de8a08fa41662e71 -r 872e942b497b22e30d73aada6df101bbef1a460f lib/tool_shed/grids/admin_grids.py --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -1,15 +1,19 @@ -import os, logging -from galaxy.web.framework.helpers import time_ago, grids +import logging +import os +from galaxy.web.framework.helpers import grids +from galaxy.web.framework.helpers import time_ago from galaxy.webapps.tool_shed import model from galaxy.model.orm import and_ import tool_shed.util.shed_util_common as suc -from tool_shed.grids.repository_grids import RepositoryGrid, CategoryGrid +from tool_shed.grids.repository_grids import CategoryGrid +from tool_shed.grids.repository_grids import RepositoryGrid from galaxy import eggs -import pkg_resources +eggs.require( 'mercurial' ) -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 b8d8f81bed872e58b4691643de8a08fa41662e71 -r 872e942b497b22e30d73aada6df101bbef1a460f lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -573,27 +573,23 @@ def build_readme_files_folder( trans, folder_id, readme_files_dict, label='Readme files' ): """Return a folder hierarchy containing readme text files.""" if readme_files_dict: - multiple_readme_files = len( readme_files_dict ) > 1 readme_id = 0 folder_id += 1 readme_files_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) - if multiple_readme_files: - folder_id += 1 - readme_files_folder = Folder( id=folder_id, key='readme_files', label=label, parent=readme_files_root_folder ) - readme_files_root_folder.folders.append( readme_files_folder ) + folder_id += 1 + readme_files_folder = Folder( id=folder_id, key='readme_files', label=label, parent=readme_files_root_folder ) + multiple_readme_files = len( readme_files_dict ) > 1 + readme_files_root_folder.folders.append( readme_files_folder ) for readme_file_name, readme_file_text in readme_files_dict.items(): readme_id += 1 readme = ReadMe( id=readme_id, name=readme_file_name, text=readme_file_text ) if multiple_readme_files: folder_id += 1 - folder = Folder( id=folder_id, key=readme.name, label=readme.name, parent=readme_files_folder ) + folder = Folder( id=folder_id, key=readme_file_name, label=readme_file_name, parent=readme_files_folder ) folder.readme_files.append( readme ) readme_files_folder.folders.append( folder ) else: - folder_id += 1 - readme_files_folder = Folder( id=folder_id, key='readme_files', label=readme.name, parent=readme_files_root_folder ) readme_files_folder.readme_files.append( readme ) - readme_files_root_folder.folders.append( readme_files_folder ) else: readme_files_root_folder = None return folder_id, readme_files_root_folder diff -r b8d8f81bed872e58b4691643de8a08fa41662e71 -r 872e942b497b22e30d73aada6df101bbef1a460f lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -589,7 +589,7 @@ original_repository_metadata = repository.metadata else: original_repository_metadata = None - readme_file_names = get_readme_file_names( repository.name ) + readme_file_names = readme_util.get_readme_file_names( str( repository.name ) ) if app.name == 'galaxy': # Shed related tool panel configs are only relevant to Galaxy. metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) } @@ -1046,16 +1046,6 @@ # The tool did not change through all of the changeset revisions. return old_id -def get_readme_file_names( repository_name ): - """Creates a list of valid filenames.""" - readme_files = [ 'readme', 'read_me', 'install' ] - valid_filenames = map( lambda f: '%s.txt' % f, readme_files ) - valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) ) - valid_filenames.extend( readme_files ) - valid_filenames.append( '%s.txt' % repository_name ) - valid_filenames.append( '%s.rst' % repository_name ) - return valid_filenames - def get_relative_path_to_repository_file( root, name, relative_install_dir, work_dir, shed_config_dict, resetting_all_metadata_on_repository ): if resetting_all_metadata_on_repository: full_path_to_file = os.path.join( root, name ) diff -r b8d8f81bed872e58b4691643de8a08fa41662e71 -r 872e942b497b22e30d73aada6df101bbef1a460f lib/tool_shed/util/readme_util.py --- a/lib/tool_shed/util/readme_util.py +++ b/lib/tool_shed/util/readme_util.py @@ -70,3 +70,13 @@ raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) readme_files_dict = json.from_json_string( raw_text ) return readme_files_dict + +def get_readme_file_names( repository_name ): + """Return a list of file names that will be categorized as README files for the received repository_name.""" + readme_files = [ 'readme', 'read_me', 'install' ] + valid_filenames = map( lambda f: '%s.txt' % f, readme_files ) + valid_filenames.extend( map( lambda f: '%s.rst' % f, readme_files ) ) + valid_filenames.extend( readme_files ) + valid_filenames.append( '%s.txt' % repository_name ) + valid_filenames.append( '%s.rst' % repository_name ) + return valid_filenames diff -r b8d8f81bed872e58b4691643de8a08fa41662e71 -r 872e942b497b22e30d73aada6df101bbef1a460f templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -425,7 +425,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rd-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;">${datatype.extension | h}</${cell_type}><${cell_type}>${datatype.type | h}</${cell_type}><${cell_type}>${datatype.mimetype | h}</${cell_type}> @@ -446,7 +446,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rft-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="failed_test_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr> @@ -475,7 +475,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-ridm-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;">${data_manager.index | h}</${cell_type}><${cell_type}>${data_manager.error | h}</${cell_type}></tr> @@ -493,7 +493,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rird-${encoded_id}"><td style="padding-left: ${pad+20}px;"> ${ invalid_repository_dependency.error | h } </td> @@ -510,7 +510,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rit-${encoded_id}"><td style="padding-left: ${pad+20}px;"> %if trans.webapp.name == 'tool_shed' and invalid_tool.repository_id and invalid_tool.tool_config and invalid_tool.changeset_revision: <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( invalid_tool.repository_id ), tool_config=invalid_tool.tool_config, changeset_revision=invalid_tool.changeset_revision, render_repository_actions_for=render_repository_actions_for )}"> @@ -545,7 +545,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-ritd-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="invalid_td_table"><tr><td>${ invalid_tool_dependency.error | h }</td></tr> @@ -564,7 +564,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rmtc-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="missing_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${missing_test_component.tool_id | h}</td></tr> @@ -587,27 +587,17 @@ encoded_id = trans.security.encode_id( readme.id ) render_rst = readme.name.endswith( '.rst' ) %> - <style type="text/css"> - #readme_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><tr class="datasetRow" %if parent is not None: - parent="${parent}" + parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rr-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table id="readme_table"> + <table id="readme_files"> %if render_rst: <tr><td>${ rst_to_html( readme.text ) }</td></tr> %else: - <tr><td>${readme.name}<br/>${ to_html_string( readme.text ) }</td></tr> + <tr><td>${ to_html_string( readme.text ) }</td></tr> %endif </table></td> @@ -652,7 +642,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rrd-${encoded_id}"> %if trans.webapp.name == 'galaxy': <${cell_type} style="padding-left: ${pad+20}px;"> %if row_is_header: @@ -684,6 +674,19 @@ %></%def> +<%def name="render_readme_files_css()"> + <style type="text/css"> + table.readme_files{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } + </style> +</%def> + <%def name="render_tool_test_results_css()"><style type="text/css"> table.tool_test_results{ table-layout:fixed; @@ -703,7 +706,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rtdie-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="td_install_error_table" class="tool_test_results"><tr bgcolor="#FFFFCC"> @@ -731,7 +734,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rrie-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="rd_install_error_table" class="tool_test_results"> %if not is_current_repository: @@ -762,7 +765,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rnt-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="not_tested_table" class="tool_test_results"><tr><td>${not_tested.reason | h}</td></tr> @@ -781,7 +784,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rpt-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table id="passed_tests_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr> @@ -808,7 +811,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rt-${encoded_id}"> %if row_is_header: <th style="padding-left: ${pad+20}px;">${tool.name | h}</th> %else: @@ -857,7 +860,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rtd-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;"> %if row_is_header: ${tool_dependency.name | h} @@ -913,13 +916,23 @@ <%def name="render_test_environment( test_environment, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( test_environment.id ) %> + <style type="text/css"> + #test_environment_table{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } + </style><tr class="datasetRow" %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rte-${encoded_id}"><td style="padding-left: ${pad+20}px;"> - <table class="grid" id="readme_table"> + <table class="grid" id="test_environment_table"><tr><td><b>Time tested:</b> ${test_environment.time_last_tested | h}</td></tr><tr><td><b>System:</b> ${test_environment.system | h}</td></tr><tr><td><b>Architecture:</b> ${test_environment.architecture | h}</td></tr> @@ -950,7 +963,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rvdm-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;">${data_manager.name | h}</${cell_type}><${cell_type}>${data_manager.version | h}</${cell_type}><${cell_type}>${data_manager.data_tables | h}</${cell_type}> @@ -981,7 +994,7 @@ %if parent is not None: parent="${parent}" %endif - id="libraryItem-${encoded_id}"> + id="libraryItem-rw-${encoded_id}"><${cell_type} style="padding-left: ${pad+20}px;"> %if row_is_header: ${workflow.workflow_name | h} @@ -1045,6 +1058,8 @@ return str( self.count ) %> %if readme_files_root_folder: + ${render_readme_files_css()} + <p/><div class="toolForm"><div class="toolFormTitle">Repository README files - may contain important installation or license information</div><div class="toolFormBody"> @@ -1161,11 +1176,11 @@ <div class="toolForm"><div class="toolFormTitle">Automated tool test results</div><div class="toolFormBody"> - <p/> - <% row_counter = RowCounter() %> - <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="test_environment"> - ${render_folder( tool_test_results_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} - </table> + <p/> + <% row_counter = RowCounter() %> + <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table" id="test_environment"> + ${render_folder( tool_test_results_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )} + </table></div></div> %endif 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.

1 0

commit/galaxy-central: jgoecks: For bed/gff/vcf converter, only use -split option when appropriate.
by commits-noreply＠bitbucket.org 25 Sep '13

25 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b8d8f81bed87/ Changeset: b8d8f81bed87 User: jgoecks Date: 2013-09-25 20:45:25 Summary: For bed/gff/vcf converter, only use -split option when appropriate. Affected #: 1 file diff -r ff806b8e5f18791641fa49a20d9bea9e65215310 -r b8d8f81bed872e58b4691643de8a08fa41662e71 lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml @@ -9,7 +9,12 @@ grep -v '^#' $input | sort -k1,1 | ## Generate coverage bedgraph. - bedtools genomecov -bg -split -i stdin -g $chromInfo + bedtools genomecov -bg -i stdin -g $chromInfo + + ## Only use split option for bed and gff/gff3/gtf. + #if $input.ext in [ 'bed', 'gff', 'gff3', 'gtf' ]: + -split + #end if ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this ## should only be used on systems with large RAM. 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.

1 0

commit/galaxy-central: dannon: Oops. Prints.
by commits-noreply＠bitbucket.org 25 Sep '13

25 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff806b8e5f18/ Changeset: ff806b8e5f18 User: dannon Date: 2013-09-25 20:42:29 Summary: Oops. Prints. Affected #: 1 file diff -r 751e7989d0766d101df5c3175e6164afc86ba7c8 -r ff806b8e5f18791641fa49a20d9bea9e65215310 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -209,9 +209,6 @@ self.extra_dirs[e.tag] = e.get('path') if extra_dirs is not None: self.extra_dirs.update( extra_dirs ) - print "DISK OBJECT STORE:" - print self.file_path - print self.extra_dirs def _get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """Class method that returns the absolute path for the file corresponding @@ -613,7 +610,6 @@ store = config.object_store if store == 'disk': - print "BUILDING DISK OBJECT STORE" return DiskObjectStore(config=config, config_xml=config_xml) elif store == 's3' or store == 'swift': from galaxy.objectstore.s3 import S3ObjectStore 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.

1 0

commit/galaxy-central: dannon: NestedObjectStore/HierarchicalObjectStore. Object store configuration now possible through object_store_conf.xml (which overrides all universe objectstore settings).
by commits-noreply＠bitbucket.org 25 Sep '13

25 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/751e7989d076/ Changeset: 751e7989d076 User: dannon Date: 2013-09-25 20:41:51 Summary: NestedObjectStore/HierarchicalObjectStore. Object store configuration now possible through object_store_conf.xml (which overrides all universe objectstore settings). Affected #: 6 files diff -r e5301506fcbe9dc5b1ae92d347b200254a3c63fa -r 751e7989d0766d101df5c3175e6164afc86ba7c8 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -242,6 +242,9 @@ self.os_is_secure = string_as_bool( kwargs.get( 'os_is_secure', True ) ) self.os_conn_path = kwargs.get( 'os_conn_path', '/' ) self.object_store_cache_size = float(kwargs.get( 'object_store_cache_size', -1 )) + self.object_store_config_file = kwargs.get( 'object_store_config_file', None ) + if self.object_store_config_file is not None: + self.object_store_config_file = resolve_path( self.object_store_config_file, self.root ) self.distributed_object_store_config_file = kwargs.get( 'distributed_object_store_config_file', None ) if self.distributed_object_store_config_file is not None: self.distributed_object_store_config_file = resolve_path( self.distributed_object_store_config_file, self.root ) diff -r e5301506fcbe9dc5b1ae92d347b200254a3c63fa -r 751e7989d0766d101df5c3175e6164afc86ba7c8 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -5,7 +5,6 @@ """ import os -import time import random import shutil import logging @@ -25,7 +24,7 @@ """ ObjectStore abstract interface """ - def __init__(self, config, **kwargs): + def __init__(self, config, config_xml=None, **kwargs): self.running = True self.extra_dirs = {} @@ -194,15 +193,25 @@ True >>> assert s.get_filename(obj) == file_path + '/000/dataset_1.dat' """ - def __init__(self, config, file_path=None, extra_dirs=None): - super(DiskObjectStore, self).__init__(config, file_path=file_path, extra_dirs=extra_dirs) + def __init__(self, config, config_xml=None, file_path=None, extra_dirs=None): + super(DiskObjectStore, self).__init__(config, config_xml=None, file_path=file_path, extra_dirs=extra_dirs) self.file_path = file_path or config.file_path self.config = config self.check_old_style = config.object_store_check_old_style self.extra_dirs['job_work'] = config.job_working_directory self.extra_dirs['temp'] = config.new_file_path + #The new config_xml overrides universe settings. + if config_xml: + for e in config_xml: + if e.tag == 'files_dir': + self.file_path = e.get('path') + else: + self.extra_dirs[e.tag] = e.get('path') if extra_dirs is not None: self.extra_dirs.update( extra_dirs ) + print "DISK OBJECT STORE:" + print self.file_path + print self.extra_dirs def _get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """Class method that returns the absolute path for the file corresponding @@ -364,6 +373,69 @@ super(CachingObjectStore, self).__init__(self, path, backend) +class NestedObjectStore(ObjectStore): + """ + Base for ObjectStores that use other ObjectStores + (DistributedObjectStore, HierarchicalObjectStore) + """ + + def __init__(self, config, config_xml=None): + super(NestedObjectStore, self).__init__(config, config_xml=config_xml) + self.backends = {} + + def shutdown(self): + [b.shutdown() for b in self.backends.values()] + if self.sleeper is not None: + self.sleeper.wake() + super(NestedObjectStore, self).shutdown() + + def exists(self, obj, **kwargs): + return self.__call_method('exists', obj, False, False, **kwargs) + + def file_ready(self, obj, **kwargs): + return self.__call_method('file_ready', obj, False, False, **kwargs) + + def create(self, obj, **kwargs): + random.choice(self.backends.values()).create(obj, **kwargs) + + def empty(self, obj, **kwargs): + return self.__call_method('empty', obj, True, False, **kwargs) + + def size(self, obj, **kwargs): + return self.__call_method('size', obj, 0, False, **kwargs) + + def delete(self, obj, **kwargs): + return self.__call_method('delete', obj, False, False, **kwargs) + + def get_data(self, obj, **kwargs): + return self.__call_method('get_data', obj, ObjectNotFound, True, **kwargs) + + def get_filename(self, obj, **kwargs): + return self.__call_method('get_filename', obj, ObjectNotFound, True, **kwargs) + + def update_from_file(self, obj, **kwargs): + if kwargs.get('create', False): + self.create(obj, **kwargs) + kwargs['create'] = False + return self.__call_method('update_from_file', obj, ObjectNotFound, True, **kwargs) + + def get_object_url(self, obj, **kwargs): + return self.__call_method('get_object_url', obj, None, False, **kwargs) + + def __call_method(self, method, obj, default, default_is_exception, **kwargs): + """ + Check all children object stores for the first one with the dataset + """ + for key, store in self.backends.items(): + if store.exists(obj, **kwargs): + return store.__getattribute__(method)(obj, **kwargs) + if default_is_exception: + raise default( 'objectstore, __call_method failed: %s on %s, kwargs: %s' + %( method, str( obj ), str( kwargs ) ) ) + else: + return default + + class DistributedObjectStore(ObjectStore): """ ObjectStore that defers to a list of backends, for getting objects the @@ -371,12 +443,13 @@ store selected randomly, but with weighting. """ - def __init__(self, config, fsmon=False): - super(DistributedObjectStore, self).__init__(config) - self.distributed_config = config.distributed_object_store_config_file - assert self.distributed_config is not None, "distributed object store ('object_store = distributed') " \ - "requires a config file, please set one in " \ - "'distributed_object_store_config_file')" + def __init__(self, config, config_xml=None, fsmon=False): + super(DistributedObjectStore, self).__init__(config, config_xml=config_xml) + if not config_xml: + self.distributed_config = config.distributed_object_store_config_file + assert self.distributed_config is not None, "distributed object store ('object_store = distributed') " \ + "requires a config file, please set one in " \ + "'distributed_object_store_config_file')" self.backends = {} self.weighted_backend_ids = [] self.original_weighted_backend_ids = [] @@ -385,7 +458,7 @@ random.seed() - self.__parse_distributed_config(config) + self.__parse_distributed_config(config, config_xml) self.sleeper = None if fsmon and ( self.global_max_percent_full or filter( lambda x: x != 0.0, self.max_percent_full.values() ) ): @@ -395,10 +468,14 @@ self.filesystem_monitor_thread.start() log.info("Filesystem space monitor started") - def __parse_distributed_config(self, config): - tree = util.parse_xml(self.distributed_config) - root = tree.getroot() - log.debug('Loading backends for distributed object store from %s' % self.distributed_config) + def __parse_distributed_config(self, config, config_xml = None): + if not config_xml: + tree = util.parse_xml(self.distributed_config) + root = tree.getroot() + log.debug('Loading backends for distributed object store from %s' % self.distributed_config) + else: + root = config_xml.find('backends') + log.debug('Loading backends for distributed object store from %s' % config_xml.get('id')) self.global_max_percent_full = float(root.get('maxpctfull', 0)) for elem in [ e for e in root if e.tag == 'backend' ]: id = elem.get('id') @@ -438,17 +515,6 @@ self.weighted_backend_ids = new_weighted_backend_ids self.sleeper.sleep(120) # Test free space every 2 minutes - def shutdown(self): - super(DistributedObjectStore, self).shutdown() - if self.sleeper is not None: - self.sleeper.wake() - - def exists(self, obj, **kwargs): - return self.__call_method('exists', obj, False, False, **kwargs) - - def file_ready(self, obj, **kwargs): - return self.__call_method('file_ready', obj, False, False, **kwargs) - def create(self, obj, **kwargs): """ create() is the only method in which obj.object_store_id may be None @@ -467,30 +533,6 @@ log.debug("Using preferred backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id)) self.backends[obj.object_store_id].create(obj, **kwargs) - def empty(self, obj, **kwargs): - return self.__call_method('empty', obj, True, False, **kwargs) - - def size(self, obj, **kwargs): - return self.__call_method('size', obj, 0, False, **kwargs) - - def delete(self, obj, **kwargs): - return self.__call_method('delete', obj, False, False, **kwargs) - - def get_data(self, obj, **kwargs): - return self.__call_method('get_data', obj, ObjectNotFound, True, **kwargs) - - def get_filename(self, obj, **kwargs): - return self.__call_method('get_filename', obj, ObjectNotFound, True, **kwargs) - - def update_from_file(self, obj, **kwargs): - if kwargs.get('create', False): - self.create(obj, **kwargs) - kwargs['create'] = False - return self.__call_method('update_from_file', obj, ObjectNotFound, True, **kwargs) - - def get_object_url(self, obj, **kwargs): - return self.__call_method('get_object_url', obj, None, False, **kwargs) - def __call_method(self, method, obj, default, default_is_exception, **kwargs): object_store_id = self.__get_store_id_for(obj, **kwargs) if object_store_id is not None: @@ -519,33 +561,70 @@ return None -class HierarchicalObjectStore(ObjectStore): +class HierarchicalObjectStore(NestedObjectStore): """ ObjectStore that defers to a list of backends, for getting objects the first store where the object exists is used, objects are always created in the first store. """ - def __init__(self, backends=[]): - super(HierarchicalObjectStore, self).__init__() + def __init__(self, config, config_xml=None, fsmon=False): + super(HierarchicalObjectStore, self).__init__(config, config_xml=config_xml) + for b in config_xml.find('backends'): + self.backends[int(b.get('order'))] = build_object_store_from_config(config, fsmon=fsmon, config_xml=b) + def shutdown(self): + for store in self.backends.values(): + store.shutdown() + super(HierarchicalObjectStore, self).shutdown() -def build_object_store_from_config(config, fsmon=False): - """ Depending on the configuration setting, invoke the appropriate object store + def exists(self, obj, **kwargs): + """ + Exists must check all child object stores + """ + for store in self.backends.values(): + if store.exists(obj, **kwargs): + return True + return False + + def create(self, obj, **kwargs): + """ + Create will always be called by the primary object_store + """ + self.backends[0].create(obj, **kwargs) + + +def build_object_store_from_config(config, fsmon=False, config_xml=None): """ - store = config.object_store + Depending on the configuration setting, invoke the appropriate object store + """ + + if not config_xml and config.object_store_config_file: + # This is a top level invocation of build_object_store_from_config, and + # we have an object_store_conf.xml -- read the .xml and build + # accordingly + tree = util.parse_xml(config.object_store_config_file) + root = tree.getroot() + store = root.get('type') + config_xml = root + elif config_xml: + store = config_xml.get('type') + else: + store = config.object_store + if store == 'disk': - return DiskObjectStore(config=config) + print "BUILDING DISK OBJECT STORE" + return DiskObjectStore(config=config, config_xml=config_xml) elif store == 's3' or store == 'swift': from galaxy.objectstore.s3 import S3ObjectStore - return S3ObjectStore(config=config) + return S3ObjectStore(config=config, config_xml=config_xml) elif store == 'distributed': - return DistributedObjectStore(config=config, fsmon=fsmon) + return DistributedObjectStore(config=config, fsmon=fsmon, config_xml=config_xml) elif store == 'hierarchical': - return HierarchicalObjectStore() + return HierarchicalObjectStore(config=config, config_xml=config_xml) elif store == 'irods': from galaxy.objectstore.rods import IRODSObjectStore - return IRODSObjectStore(config=config) + return IRODSObjectStore(config=config, config_xml=config_xml) else: log.error("Unrecognized object store definition: {0}".format(store)) diff -r e5301506fcbe9dc5b1ae92d347b200254a3c63fa -r 751e7989d0766d101df5c3175e6164afc86ba7c8 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -33,7 +33,7 @@ cache exists that is used as an intermediate location for files between Galaxy and S3. """ - def __init__(self, config): + def __init__(self, config, config_xml=None): super(S3ObjectStore, self).__init__() self.config = config self.staging_path = self.config.file_path diff -r e5301506fcbe9dc5b1ae92d347b200254a3c63fa -r 751e7989d0766d101df5c3175e6164afc86ba7c8 object_store_conf.xml.sample --- /dev/null +++ b/object_store_conf.xml.sample @@ -0,0 +1,24 @@ +<?xml version="1.0"?> +<object_store type="hierarchical"> + <backends> + <object_store type="distributed" id="primary" order="0"> + <backends> + <backend id="files1" type="disk" weight="1"> + <files_dir path="database/files1"/> + <extra_dir type="temp" path="database/tmp1"/> + <extra_dir type="job_work" path="database/job_working_directory1"/> + </backend> + <backend id="files2" type="disk" weight="1"> + <files_dir path="database/files2"/> + <extra_dir type="temp" path="database/tmp2"/> + <extra_dir type="job_work" path="database/job_working_directory2"/> + </backend> + </backends> + </object_store> + <object_store type="disk" id="secondary" order="1"> + <files_dir path="database/files3"/> + <extra_dir type="temp" path="database/tmp3"/> + <extra_dir type="job_work" path="database/job_working_directory3"/> + </object_store> + </backends> +</object_store> diff -r e5301506fcbe9dc5b1ae92d347b200254a3c63fa -r 751e7989d0766d101df5c3175e6164afc86ba7c8 templates/webapps/galaxy/history/display.mako --- a/templates/webapps/galaxy/history/display.mako +++ b/templates/webapps/galaxy/history/display.mako @@ -81,4 +81,4 @@ %endif ${_("This history is empty.")} </div> -</%def> \ No newline at end of file +</%def> diff -r e5301506fcbe9dc5b1ae92d347b200254a3c63fa -r 751e7989d0766d101df5c3175e6164afc86ba7c8 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -204,6 +204,10 @@ #collect_outputs_from = new_file_path,job_working_directory # -- Data Storage (Object Store) +# +# Configuration file for the object store +# If this is set and exists, it overrides any other objectstore settings. +# object_store_config_file = object_store_conf.xml # Object store backend module (valid options are: disk, s3, swift, irods, # distributed, hierarchical) 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.

1 0