January 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Remove tipsy classes from base css.
by Bitbucket 15 Jan '13

15 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8d2fe975c13c/ changeset: 8d2fe975c13c user: jgoecks date: 2013-01-15 03:07:11 summary: Remove tipsy classes from base css. affected #: 2 files diff -r 311b636a72988f339f6b81837d5341a6505917a0 -r 8d2fe975c13c33439167903653c6c06217cab764 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1480,37 +1480,6 @@ padding: 0; } -.tipsy { - padding: 5px; - font-size: 10px; - filter: alpha(opacity=80); - background-repeat: no-repeat; - background-image: url(../images/tipsy.gif); -} -.tipsy-inner { - padding: 5px 8px 4px 8px; - background-color: black; - color: white; - max-width: 200px; - text-align: center; -} - -.tipsy-north { - background-position: top center; -} - -.tipsy-south { - background-position: bottom center; -} - -.tipsy-east { - background-position: right center; -} - -.tipsy-west { - background-position: left center; -} - .editable-text { cursor:pointer; } diff -r 311b636a72988f339f6b81837d5341a6505917a0 -r 8d2fe975c13c33439167903653c6c06217cab764 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -1047,12 +1047,6 @@ .text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;} .text-content th,.text-content td{padding:.8em;} .icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;background-repeat:no-repeat;background-position:0px 0px;padding:0;} -.tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} -.tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} -.tipsy-north{background-position:top center;} -.tipsy-south{background-position:bottom center;} -.tipsy-east{background-position:right center;} -.tipsy-west{background-position:left center;} .editable-text{cursor:pointer;} .editable-text:hover{cursor:text;border:dotted #999999 1px;} .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} 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: clements: Update Sphinx RST structural doc to reflect recent code changes.
by Bitbucket 15 Jan '13

15 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/311b636a7298/ changeset: 311b636a7298 user: clements date: 2013-01-15 02:01:17 summary: Update Sphinx RST structural doc to reflect recent code changes. affected #: 4 files diff -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 -r 311b636a72988f339f6b81837d5341a6505917a0 doc/source/lib/galaxy.jobs.runners.rst --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -72,4 +72,5 @@ galaxy.jobs.runners.cli_job galaxy.jobs.runners.cli_shell + galaxy.jobs.runners.lwr_client diff -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 -r 311b636a72988f339f6b81837d5341a6505917a0 doc/source/lib/galaxy.util.rst --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -159,4 +159,5 @@ .. toctree:: galaxy.util.backports + galaxy.util.log diff -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 -r 311b636a72988f339f6b81837d5341a6505917a0 doc/source/lib/galaxy.webapps.community.controllers.rst --- a/doc/source/lib/galaxy.webapps.community.controllers.rst +++ b/doc/source/lib/galaxy.webapps.community.controllers.rst @@ -65,11 +65,3 @@ :undoc-members: :show-inheritance: -:mod:`workflow` Module ----------------------- - -.. automodule:: galaxy.webapps.community.controllers.workflow - :members: - :undoc-members: - :show-inheritance: - diff -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 -r 311b636a72988f339f6b81837d5341a6505917a0 doc/source/lib/galaxy.webapps.community.util.rst --- a/doc/source/lib/galaxy.webapps.community.util.rst +++ b/doc/source/lib/galaxy.webapps.community.util.rst @@ -25,3 +25,11 @@ :undoc-members: :show-inheritance: +:mod:`workflow_util` Module +--------------------------- + +.. automodule:: galaxy.webapps.community.util.workflow_util + :members: + :undoc-members: + :show-inheritance: + 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: clements: Replaced "query" with "dataset" in a number of tool definition XML files.
by Bitbucket 15 Jan '13

15 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e6f086d98d2/ changeset: 1e6f086d98d2 user: clements date: 2013-01-15 01:13:54 summary: Replaced "query" with "dataset" in a number of tool definition XML files. I got tired of coming across "query" when doing workshops. affected #: 7 files diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/extract/liftOver_wrapper.xml --- a/tools/extract/liftOver_wrapper.xml +++ b/tools/extract/liftOver_wrapper.xml @@ -39,8 +39,8 @@ <param name="minChainT" type="hidden" value="0" /></when><when value="1"> - <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in query" help="Recommended value: set to >= 300 bases for complete transcripts"/> - <param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in query"/> + <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in dataset" help="Recommended value: set to >= 300 bases for complete transcripts"/> + <param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in dataset"/><param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/></when></conditional> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/bed2gff.xml --- a/tools/filters/bed2gff.xml +++ b/tools/filters/bed2gff.xml @@ -2,7 +2,7 @@ <description>converter</description><command interpreter="python">bed_to_gff_converter.py $input $out_file1</command><inputs> - <param format="bed" name="input" type="data" label="Convert this query"/> + <param format="bed" name="input" type="data" label="Convert this dataset"/></inputs><outputs><data format="gff" name="out_file1" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/condense_characters.xml --- a/tools/filters/condense_characters.xml +++ b/tools/filters/condense_characters.xml @@ -12,7 +12,7 @@ <option value="U">Underscores</option><option value="P">Pipes</option></param> - <param format="txt" name="input" type="data" label="in this Query"/> + <param format="txt" name="input" type="data" label="in this Dataset"/></inputs><outputs><data format="input" name="out_file1" metadata_source="input" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/convert_characters.xml --- a/tools/filters/convert_characters.xml +++ b/tools/filters/convert_characters.xml @@ -13,7 +13,7 @@ <option value="P">Pipes</option><option value="Co">Colons</option></param> - <param format="txt" name="input" type="data" label="in Query"/> + <param format="txt" name="input" type="data" label="in Dataset"/></inputs><outputs><data format="tabular" name="out_file1" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/gff2bed.xml --- a/tools/filters/gff2bed.xml +++ b/tools/filters/gff2bed.xml @@ -2,7 +2,7 @@ <description>converter</description><command interpreter="python">gff_to_bed_converter.py $input $out_file1</command><inputs> - <param format="gff" name="input" type="data" label="Convert this query"/> + <param format="gff" name="input" type="data" label="Convert this dataset"/></inputs><outputs><data format="bed" name="out_file1" /> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/filters/sorter.xml --- a/tools/filters/sorter.xml +++ b/tools/filters/sorter.xml @@ -14,7 +14,7 @@ #end for </command><inputs> - <param format="tabular" name="input" type="data" label="Sort Query" /> + <param format="tabular" name="input" type="data" label="Sort Dataset" /><param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/><param name="style" type="select" label="with flavor"><option value="num">Numerical sort</option> diff -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a -r 1e6f086d98d20e2f5b25e9536d1fbe36bc8e4197 tools/new_operations/get_flanks.xml --- a/tools/new_operations/get_flanks.xml +++ b/tools/new_operations/get_flanks.xml @@ -50,11 +50,11 @@ **Example 1** -- For the following query:: +- For the following dataset:: chr22 1000 7000 NM_174568 0 + -- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Query positive strand; Blue: Flanks output)**:: +- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Dataset positive strand; Blue: Flanks output)**:: chr22 500 800 NM_174568 0 + @@ -62,11 +62,11 @@ **Example 2** -- For the following query:: +- For the following dataset:: chr22 1000 7000 NM_028946 0 - -- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Query negative strand; Magenta: Flanks output)**:: +- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**:: chr22 500 800 NM_028946 0 - @@ -75,4 +75,4 @@ </help> -</tool> \ No newline at end of file +</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fixes for discovering repository dependencies when resinstalling a tool shed repository when the repository dependencies were added to updated revisions of a repository after it was uninstalled.
by Bitbucket 14 Jan '13

14 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/76a8795d3a7e/ changeset: 76a8795d3a7e user: greg date: 2013-01-14 23:15:46 summary: Fixes for discovering repository dependencies when resinstalling a tool shed repository when the repository dependencies were added to updated revisions of a repository after it was uninstalled. affected #: 3 files diff -r b94fbc70b5be12b56852f811843092eeca6b2f98 -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -952,12 +952,16 @@ update_dict = encoding_util.tool_shed_decode( encoded_update_dict ) changeset_revision = update_dict[ 'changeset_revision' ] ctx_rev = update_dict[ 'ctx_rev' ] + includes_tools = update_dict.get( 'includes_tools', False ) + has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False ) response.close() except Exception, e: log.debug( "Error getting change set revision for update from the tool shed for repository '%s': %s" % ( repository.name, str( e ) ) ) + includes_tools = False + has_repository_dependencies = False changeset_revision = None ctx_rev = None - return changeset_revision, ctx_rev + return changeset_revision, ctx_rev, includes_tools, has_repository_dependencies def handle_missing_data_table_entry( app, relative_install_dir, tool_path, repository_tools_tups ): """ Inspect each tool to see if any have input parameters that are dynamically generated select lists that require entries in the diff -r b94fbc70b5be12b56852f811843092eeca6b2f98 -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1256,6 +1256,21 @@ @web.expose def get_changeset_revision_and_ctx_rev( self, trans, **kwd ): """Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated.""" + def has_tools_and_repository_dependencies( repository_metadata ): + includes_tools = False + has_repository_dependencies = False + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'tools' in metadata: + includes_tools = True + else: + includes_tools = False + if 'repository_dependencies' in metadata: + has_repository_dependencies = True + else: + has_repository_dependencies = False + return includes_tools, has_repository_dependencies params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1264,20 +1279,24 @@ owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans, name, owner ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + includes_tools, has_repository_dependencies = has_tools_and_repository_dependencies( repository_metadata ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) # Default to the received changeset revision and ctx_rev. update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) ctx_rev = str( update_to_ctx.rev() ) latest_changeset_revision = changeset_revision - update_dict = dict( changeset_revision=changeset_revision, ctx_rev=ctx_rev ) + update_dict = dict( changeset_revision=changeset_revision, + ctx_rev=ctx_rev, + includes_tools=includes_tools, + has_repository_dependencies=has_repository_dependencies ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. return encoding_util.tool_shed_encode( update_dict ) else: - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, - trans.security.encode_id( repository.id ), - changeset_revision ) if repository_metadata: # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates. return encoding_util.tool_shed_encode( update_dict ) @@ -1286,10 +1305,16 @@ # repository was installed. We need to find the changeset_revision to which we need to update. update_to_changeset_hash = None for changeset in repo.changelog: + includes_tools = False + has_repository_dependencies = False changeset_hash = str( repo.changectx( changeset ) ) ctx = suc.get_changectx_for_changeset( repo, changeset_hash ) if update_to_changeset_hash: - if suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ): + update_to_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_hash ) + if update_to_repository_metadata: + includes_tools, has_repository_dependencies = has_tools_and_repository_dependencies( update_to_repository_metadata ) # We found a RepositoryMetadata record. if changeset_hash == repository.tip( trans.app ): # The current ctx is the repository tip, so use it. @@ -1302,6 +1327,8 @@ elif not update_to_changeset_hash and changeset_hash == changeset_revision: # We've found the changeset in the changelog for which we need to get the next update. update_to_changeset_hash = changeset_hash + update_dict[ 'includes_tools' ] = includes_tools + update_dict[ 'has_repository_dependencies' ] = has_repository_dependencies update_dict[ 'changeset_revision' ] = str( latest_changeset_revision ) update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() ) return encoding_util.tool_shed_encode( update_dict ) diff -r b94fbc70b5be12b56852f811843092eeca6b2f98 -r 76a8795d3a7e2c662be4eab0d7f94d1d49de853a 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 @@ -372,27 +372,15 @@ if operation == "activate or reinstall": repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: - # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated so that we + # Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated so that we # can reset the metadata if necessary. This will ensure that information about repository dependencies and tool dependencies # will be current. - current_changeset_revision, current_ctx_rev = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) - if current_ctx_rev != repository.ctx_rev: - repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( repository.repo_path( trans.app ) ) ) - repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository ) - shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) - suc.update_repository( repo, ctx_rev=current_ctx_rev ) - shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) - shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) - metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, - repository=repository, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - persist=True ) - if repository.includes_tools or repository.has_repository_dependencies: + current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \ + shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) + if current_ctx_rev == repository.ctx_rev: + includes_tools = repository.includes_tools + has_repository_dependencies = repository.has_repository_dependencies + if includes_tools or has_repository_dependencies: # Only allow selecting a different section in the tool panel if the repository was uninstalled. return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='reselect_tool_panel_section', @@ -859,12 +847,12 @@ if cloned_ok: if reinstalling: # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated. - current_changeset_revision, current_ctx_rev = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) + current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \ + shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) if current_ctx_rev != ctx_rev: repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) ) shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) suc.update_repository( repo, ctx_rev=current_ctx_rev ) - self.handle_repository_contents( trans, tool_shed_repository=tool_shed_repository, tool_path=tool_path, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Get updates to the latest changset revision and reset metadata when reinstalling an uninstalled tool shed repository in Galaxy.
by Bitbucket 14 Jan '13

14 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b94fbc70b5be/ changeset: b94fbc70b5be user: greg date: 2013-01-14 21:16:06 summary: Get updates to the latest changset revision and reset metadata when reinstalling an uninstalled tool shed repository in Galaxy. affected #: 2 files diff -r dc575517a5f2d3081e1795c5d5e91c77e4488bc5 -r b94fbc70b5be12b56852f811843092eeca6b2f98 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -46,9 +46,9 @@ """ for dependency_key, requirements_dict in tool_dependencies.items(): if dependency_key not in [ 'set_environment' ]: - repository_name = requirements_dict[ 'repository_name' ] - repository_owner = requirements_dict[ 'repository_owner' ] - changeset_revision = requirements_dict[ 'changeset_revision' ] + repository_name = requirements_dict.get( 'repository_name', 'unknown' ) + repository_owner = requirements_dict.get( 'repository_owner', 'unknown' ) + changeset_revision = requirements_dict.get( 'changeset_revision', 'unknown' ) dependency_name = requirements_dict[ 'name' ] version = requirements_dict[ 'version' ] type = requirements_dict[ 'type' ] diff -r dc575517a5f2d3081e1795c5d5e91c77e4488bc5 -r b94fbc70b5be12b56852f811843092eeca6b2f98 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 @@ -372,6 +372,26 @@ if operation == "activate or reinstall": repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: + # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated so that we + # can reset the metadata if necessary. This will ensure that information about repository dependencies and tool dependencies + # will be current. + current_changeset_revision, current_ctx_rev = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) + if current_ctx_rev != repository.ctx_rev: + repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( repository.repo_path( trans.app ) ) ) + repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository ) + shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) + suc.update_repository( repo, ctx_rev=current_ctx_rev ) + shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) + shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) + metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, + repository=repository, + repository_clone_url=repository_clone_url, + shed_config_dict=shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=True, + persist=True ) if repository.includes_tools or repository.has_repository_dependencies: # Only allow selecting a different section in the tool panel if the repository was uninstalled. return trans.response.send_redirect( web.url_for( controller='admin_toolshed', @@ -811,6 +831,7 @@ @web.require_admin def install_tool_shed_repositories( self, trans, tool_shed_repositories, reinstalling=False, **kwd ): """Install specified tool shed repositories.""" + shed_tool_conf = kwd.get( 'shed_tool_conf', '' ) tool_path = kwd[ 'tool_path' ] includes_tool_dependencies = util.string_as_bool( kwd[ 'includes_tool_dependencies' ] ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) @@ -843,6 +864,7 @@ repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) ) shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) suc.update_repository( repo, ctx_rev=current_ctx_rev ) + self.handle_repository_contents( trans, tool_shed_repository=tool_shed_repository, tool_path=tool_path, @@ -850,7 +872,7 @@ relative_install_dir=relative_install_dir, tool_shed=tool_shed_repository.tool_shed, tool_section=tool_section, - shed_tool_conf=kwd.get( 'shed_tool_conf', '' ), + shed_tool_conf=shed_tool_conf, reinstalling=reinstalling ) trans.sa_session.refresh( tool_shed_repository ) metadata = tool_shed_repository.metadata @@ -1389,12 +1411,12 @@ repository_id=repository_id, repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, - changeset_revision=tool_shed_repository.installed_changeset_revision ) + changeset_revision=tool_shed_repository.changeset_revision ) else: repository_dependencies = None repo_info_dict = suc.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, + changeset_revision=tool_shed_repository.changeset_revision, ctx_rev=ctx_rev, repository_owner=tool_shed_repository.owner, repository_name=tool_shed_repository.name, @@ -1475,7 +1497,7 @@ repository_id=repository_id, repository_name=tool_shed_repository.name, repository_owner=tool_shed_repository.owner, - changeset_revision=tool_shed_repository.installed_changeset_revision ) + changeset_revision=tool_shed_repository.changeset_revision ) if repository_dependencies: includes_repository_dependencies = True else: @@ -1483,7 +1505,7 @@ includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies repo_info_dict = suc.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, + changeset_revision=tool_shed_repository.changeset_revision, ctx_rev=ctx_rev, repository_owner=tool_shed_repository.owner, repository_name=tool_shed_repository.name, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Add tool id for when clause warnings that are output when tool XML is parsed.
by Bitbucket 14 Jan '13

14 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc575517a5f2/ changeset: dc575517a5f2 user: jgoecks date: 2013-01-14 20:14:41 summary: Add tool id for when clause warnings that are output when tool XML is parsed. affected #: 1 file diff -r 7b30a0fd0a042eb6db92e43e005ccd6634184e66 -r dc575517a5f2d3081e1795c5d5e91c77e4488bc5 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1600,9 +1600,11 @@ try: possible_cases.remove( case.value ) except: - log.warning( "A when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % ( group.name, group.test_param.name, case.value ) ) + log.warning( "Tool %s: a when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % + ( self.id, group.name, group.test_param.name, case.value ) ) for unspecified_case in possible_cases: - log.warning( "A when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % ( group.name, group.test_param.name, unspecified_case ) ) + log.warning( "Tool %s: a when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % + ( self.id, group.name, group.test_param.name, unspecified_case ) ) case = ConditionalWhen() case.value = unspecified_case case.inputs = odict() 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: jgoecks: Remove unused test parameter.
by Bitbucket 14 Jan '13

14 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b30a0fd0a04/ changeset: 7b30a0fd0a04 user: jgoecks date: 2013-01-14 20:00:21 summary: Remove unused test parameter. affected #: 1 file diff -r 58e3f00d02b8c09da2f1172fcadb7c8e65493ee3 -r 7b30a0fd0a042eb6db92e43e005ccd6634184e66 tools/rgenetics/rgGRR.xml --- a/tools/rgenetics/rgGRR.xml +++ b/tools/rgenetics/rgGRR.xml @@ -28,7 +28,6 @@ <param name='title' value='rgGRRtest1' /><param name='n' value='100' /><param name='Z' value='6' /> - <param name='force' value='true' /><output name='out_file1' file='rgtestouts/rgGRR/rgGRRtest1.html' ftype='html' compare="diff" lines_diff='350'><extra_files type="file" name='Log_rgGRRtest1.txt' value="rgtestouts/rgGRR/Log_rgGRRtest1.txt" compare="diff" lines_diff="170"/><extra_files type="file" name='rgGRRtest1.svg' value="rgtestouts/rgGRR/rgGRRtest1.svg" compare="diff" lines_diff="1000" /> 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 14 Jan '13

14 Jan '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/46fc972bb869/ changeset: 46fc972bb869 user: jgoecks date: 2013-01-14 19:56:50 summary: Improve error message for test parameters that could not be added. affected #: 1 file diff -r f57b2bfb2365bef93b7974d990d663a0660a67d9 -r 46fc972bb869a4d3807bc11dcad7f279efc3a878 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -35,11 +35,13 @@ value = new_value break if not found_parameter: - raise ValueError( "Unable to determine parameter type of test input '%s'. Ensure that the parameter exists and that any container groups are defined first." % name ) + raise ValueError( "Unable to determine parameter type of test input '%s'. " + "Ensure that the parameter exists and that any container groups are defined first." + % name ) elif isinstance( self.tool.inputs[name], basic.DataToolParameter ): value = self.__add_uploaded_dataset( name, value, extra, self.tool.inputs[name] ) except Exception, e: - log.debug( "Error in add_param for %s: %s" % ( name, e ) ) + log.debug( "Error for tool %s: could not add test parameter %s. %s" % ( self.tool.id, name, e ) ) self.inputs.append( ( name, value, extra ) ) def add_output( self, name, file, extra ): self.outputs.append( ( name, file, extra ) ) https://bitbucket.org/galaxy/galaxy-central/commits/58e3f00d02b8/ changeset: 58e3f00d02b8 user: jgoecks date: 2013-01-14 19:57:19 summary: Fix issues in Tophat color wrapper tests. affected #: 1 file diff -r 46fc972bb869a4d3807bc11dcad7f279efc3a878 -r 58e3f00d02b8c09da2f1172fcadb7c8e65493ee3 tools/ngs_rna/tophat_color_wrapper.xml --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -503,7 +503,7 @@ <test> @@ -564,7 +564,7 @@  @@ -591,7 +591,10 @@ <param name="max_insertion_length" value="3"/><param name="max_deletion_length" value="3"/><param name="use_junctions" value="No" /> - <param name="use_search" value="No" /> + <param name="use_search" value="Yes" /> + <param name="min_closure_exon" value="50" /> + <param name="min_closure_intron" value="50" /> + <param name="max_closure_intron" value="5000" /><param name="use_search" value="Yes" /><param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /> 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: Ensure each repository dependency container contains only unique entries.
by Bitbucket 14 Jan '13

14 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f57b2bfb2365/ changeset: f57b2bfb2365 user: greg date: 2013-01-14 17:22:07 summary: Ensure each repository dependency container contains only unique entries. affected #: 1 file diff -r 937966b77a10fb229ee265f2a85eac6634fb7d08 -r f57b2bfb2365bef93b7974d990d663a0660a67d9 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -235,11 +235,8 @@ for name, repo_info_tuple in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tuple ) - clone_dir = os.path.join( tool_path, generate_tool_path( repository_clone_url, changeset_revision ) ) - relative_install_dir = os.path.join( clone_dir, name ) # Make sure the repository was not already installed. - installed_tool_shed_repository, installed_changeset_revision = \ - repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple, clone_dir ) + installed_tool_shed_repository, installed_changeset_revision = repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple ) if installed_tool_shed_repository: tool_section, new_tool_panel_section, tool_panel_section_key = handle_tool_panel_selection( trans=trans, metadata=installed_tool_shed_repository.metadata, @@ -602,8 +599,7 @@ installed_rd, missing_rd = \ get_installed_and_missing_repository_dependencies( trans, repository ) else: - installed_rd, missing_rd = \ - get_installed_and_missing_repository_dependencies_for_new_install( trans, repository_dependencies ) + installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ) # Discover all repository dependencies and retrieve information for installing them. required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) # Display tool dependencies defined for each of the repository dependencies. @@ -697,7 +693,7 @@ missing_repository_dependencies[ root_key ] = missing_rd_tups missing_repository_dependencies[ 'description' ] = description return installed_repository_dependencies, missing_repository_dependencies -def get_installed_and_missing_repository_dependencies_for_new_install( trans, repository_dependencies ): +def get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ): """ Parse the received repository_dependencies dictionary that is associated with a repository being installed into Galaxy for the first time and attempt to determine repository dependencies that are already installed and those that are not. @@ -706,28 +702,32 @@ installed_repository_dependencies = {} missing_rd_tups = [] installed_rd_tups = [] - description = repository_dependencies[ 'description' ] - root_key = repository_dependencies[ 'root_key' ] - # The repository dependencies container will include only the immediate repository dependencies of this repository, so the container will be - # only a single level in depth. - for key, rd_tups in repository_dependencies.items(): - if key in [ 'description', 'root_key' ]: - continue - for rd_tup in rd_tups: - tool_shed, name, owner, changeset_revision = rd_tup - # This is tricky because updates to installed repository revisions may have occurred making it difficult to discover installed repository - # revisions. If installed repositories are not discovered in this method, they will be returned in the list of missing_repository_dependencies, - # but should be discovered later during the installation process since that process inspects all appropriate changeset revisions. - repository = suc.get_repository_for_dependency_relationship( trans.app, tool_shed, name, owner, changeset_revision ) - if repository: - new_rd_tup = [ tool_shed, name, owner, changeset_revision, repository.id, repository.status ] - if repository.status == trans.model.ToolShedRepository.installation_status.INSTALLED: - installed_rd_tups.append( new_rd_tup ) + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + if repository_dependencies: + description = repository_dependencies[ 'description' ] + root_key = repository_dependencies[ 'root_key' ] + # The repository dependencies container will include only the immediate repository dependencies of this repository, so the container will be + # only a single level in depth. + for key, rd_tups in repository_dependencies.items(): + if key in [ 'description', 'root_key' ]: + continue + for rd_tup in rd_tups: + tool_shed, name, owner, changeset_revision = rd_tup + # Updates to installed repository revisions may have occurred, so make sure to locate the appropriate repository revision if one exists. + repository, current_changeset_revision = repository_was_previously_installed( trans, tool_shed, name, repo_info_tuple ) + if repository: + new_rd_tup = [ tool_shed, name, owner, changeset_revision, repository.id, repository.status ] + if repository.status == trans.model.ToolShedRepository.installation_status.INSTALLED: + if new_rd_tup not in installed_rd_tups: + installed_rd_tups.append( new_rd_tup ) + else: + if new_rd_tup not in missing_rd_tups: + missing_rd_tups.append( new_rd_tup ) else: - missing_rd_tups.append( new_rd_tup ) - else: - new_rd_tup = [ tool_shed, name, owner, changeset_revision, None, 'Never installed' ] - missing_rd_tups.append( new_rd_tup ) + new_rd_tup = [ tool_shed, name, owner, changeset_revision, None, 'Never installed' ] + if new_rd_tup not in missing_rd_tups: + missing_rd_tups.append( new_rd_tup ) if installed_rd_tups: installed_repository_dependencies[ 'root_key' ] = root_key installed_repository_dependencies[ root_key ] = installed_rd_tups @@ -1415,16 +1415,11 @@ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ suc.get_repo_info_tuple_contents( repo_info_tuple ) if tool_dependencies: - clone_dir = os.path.join( tool_path, generate_tool_path( repository_clone_url, changeset_revision ) ) # Add the install_dir attribute to the tool_dependencies. tool_dependencies = suc.add_installation_directories_to_tool_dependencies( trans=trans, tool_dependencies=tool_dependencies ) # The required_repository may have been installed with a different changeset revision. - required_repository, installed_changeset_revision = repository_was_previously_installed( trans, - tool_shed_url, - name, - repo_info_tuple, - clone_dir ) + required_repository, installed_changeset_revision = repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple ) if required_repository: required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \ get_installed_and_missing_tool_dependencies( trans, required_repository, tool_dependencies ) @@ -1610,7 +1605,7 @@ trans.sa_session.add( tool_dependency ) trans.sa_session.flush() return removed, error_message -def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple, clone_dir ): +def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple ): """ Handle the case where the repository was previously installed using an older changeset_revsion, but later the repository was updated in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: clements: Reindented license text to make it render better at bitbucket.
by Bitbucket 12 Jan '13

12 Jan '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/937966b77a10/ changeset: 937966b77a10 user: clements date: 2013-01-12 01:00:01 summary: Reindented license text to make it render better at bitbucket. Also dropped non-informative link from outside the license. affected #: 1 file diff -r 2e96c23c760b7d9259168e007bec52ffcdfa00a9 -r 937966b77a10fb229ee265f= 2a85eac6634fb7d08 LICENSE.txt --- a/LICENSE.txt +++ b/LICENSE.txt @@ -2,49 +2,178 @@ =20 Licensed under the Academic Free License version 3.0 =20 -1) Grant of Copyright License. Licensor grants You a worldwide, royalty-fr= ee, non-exclusive, sublicensable license, for the duration of the copyright= , to do the following: + 1) Grant of Copyright License. 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If, at any time, You expressly assented to=20 + this License, that assent indicates your clear and irrevocable accepta= nce=20 + of this License and all of its terms and conditions. If You distribute= or=20 + communicate copies of the Original Work or a Derivative Work, You must=20 + make a reasonable effort under the circumstances to obtain the express=20 + assent of recipients to the terms of this License. This License=20 + conditions your rights to undertake the activities listed in Section 1= ,=20 + including your right to create Derivative Works based upon the Origina= l=20 + Work, and doing so without honoring these terms and conditions is=20 + prohibited by copyright law and international treaty. Nothing in this=20 + License is intended to affect copyright exceptions and limitations=20 + (including "fair use" or "fair dealing"). 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This License shall terminate=20 + automatically and You may no longer exercise any of the rights granted=20 + to You by this License as of the date You commence an action, includin= g=20 + a cross-claim or counterclaim, against Licensor or any licensee allegi= ng=20 + that the Original Work infringes a patent. This termination provision=20 + shall not apply for an action alleging patent infringement by=20 + combinations of the Original Work with other software or hardware. =20 -11) Jurisdiction, Venue and Governing Law. Any action or suit relating to = this License may be brought only in the courts of a jurisdiction wherein th= e Licensor resides or in which Licensor conducts its primary business, and = under the laws of that jurisdiction excluding its conflict-of-law provision= s. The application of the United Nations Convention on Contracts for the In= ternational Sale of Goods is expressly excluded. Any use of the Original Wo= rk outside the scope of this License or after its termination shall be subj= ect to the requirements and penalties of copyright or patent law in the app= ropriate jurisdiction. This section shall survive the termination of this L= icense. +11) Jurisdiction, Venue and Governing Law. Any action or suit relating to=20 + this License may be brought only in the courts of a jurisdiction where= in=20 + the Licensor resides or in which Licensor conducts its primary busines= s,=20 + and under the laws of that jurisdiction excluding its conflict-of-law=20 + provisions. The application of the United Nations Convention on=20 + Contracts for the International Sale of Goods is expressly excluded. A= ny=20 + use of the Original Work outside the scope of this License or after it= s=20 + termination shall be subject to the requirements and penalties of=20 + copyright or patent law in the appropriate jurisdiction. 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If any provision of this License is held to be unenforc= eable, such provision shall be reformed only to the extent necessary to mak= e it enforceable. +13) Miscellaneous. If any provision of this License is held to be=20 + unenforceable, such provision shall be reformed only to the extent=20 + necessary to make it enforceable. =20 -14) Definition of "You" in This License. "You" throughout this License, wh= ether in upper or lower case, means an individual or a legal entity exercis= ing rights under, and complying with all of the terms of, this License. For= legal entities, "You" includes any entity that controls, is controlled by,= or is under common control with you. For purposes of this definition, "con= trol" means (i) the power, direct or indirect, to cause the direction or ma= nagement of such entity, whether by contract or otherwise, or (ii) ownershi= p of fifty percent (50%) or more of the outstanding shares, or (iii) benefi= cial ownership of such entity. +14) Definition of "You" in This License. "You" throughout this License,=20 + whether in upper or lower case, means an individual or a legal entity=20 + exercising rights under, and complying with all of the terms of, this=20 + License. For legal entities, "You" includes any entity that controls, = is=20 + controlled by, or is under common control with you. For purposes of th= is=20 + definition, "control" means (i) the power, direct or indirect, to caus= e=20 + the direction or management of such entity, whether by contract or=20 + otherwise, or (ii) ownership of fifty percent (50%) or more of the=20 + outstanding shares, or (iii) beneficial ownership of such entity. =20 -15) Right to Use. You may use the Original Work in all ways not otherwise = restricted or conditioned by this License or by law, and Licensor promises = not to interfere with or be responsible for such uses by You. +15) Right to Use. You may use the Original Work in all ways not otherwise=20 + restricted or conditioned by this License or by law, and Licensor=20 + promises not to interfere with or be responsible for such uses by You. =20 -16) Modification of This License. This License is Copyright =C2=A9 2005 La= wrence Rosen. Permission is granted to copy, distribute, or communicate thi= s License without modification. Nothing in this License permits You to modi= fy this License as applied to the Original Work or to Derivative Works. How= ever, You may modify the text of this License and copy, distribute or commu= nicate your modified version (the "Modified License") and apply it to other= original works of authorship subject to the following conditions: (i) You = may not indicate in any way that your Modified License is the "Academic Fre= e License" or "AFL" and you may not use those names in the name of your Mod= ified License; (ii) You must replace the notice specified in the first para= graph above with the notice "Licensed under <insert your license name here>= " or with a notice of your own that is not confusingly similar to the notic= e in this License; and (iii) You may not claim that your original works are= open source software unless your Modified License has been approved by Ope= n Source Initiative (OSI) and You comply with its license review and certif= ication process. +16) Modification of This License. This License is Copyright =C2=A9 2005 La= wrence=20 + Rosen. Permission is granted to copy, distribute, or communicate this=20 + License without modification. Nothing in this License permits You to=20 + modify this License as applied to the Original Work or to Derivative=20 + Works. However, You may modify the text of this License and copy,=20 + distribute or communicate your modified version (the "Modified=20 + License") and apply it to other original works of authorship subject t= o=20 + the following conditions: (i) You may not indicate in any way that you= r=20 + Modified License is the "Academic Free License" or "AFL" and you may n= ot=20 + use those names in the name of your Modified License; (ii) You must=20 + replace the notice specified in the first paragraph above with the=20 + notice "Licensed under <insert your license name here>" or with a noti= ce=20 + of your own that is not confusingly similar to the notice in this=20 + License; and (iii) You may not claim that your original works are open=20 + source software unless your Modified License has been approved by Open=20 + Source Initiative (OSI) and You comply with its license review and=20 + certification process. =20 -A brief explanation of this license is available: http://www.rosenlaw.com/= OSL3.0-explained.pdf =20 Some icons found in Galaxy are from the Silk Icons set, available under the Creative Commons Attribution 2.5 License, from: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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