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commit/galaxy-central: greg: Slight fix for viewing invalid tools - allow an admin user to view only his invalid tools if requesting from the repositories view.
by Bitbucket 04 Apr '12

04 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b11be06de890/ changeset: b11be06de890 user: greg date: 2012-04-04 19:56:22 summary: Slight fix for viewing invalid tools - allow an admin user to view only his invalid tools if requesting from the repositories view. affected #: 3 files diff -r e514944f0a38e6d88307251958b4407e5d20e51b -r b11be06de890f3ecb457e435726cd8e6ad9b6c63 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -405,9 +405,10 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) webapp = params.get( 'webapp', 'community' ) + cntrller = params.get( 'cntrller', 'repository' ) is_admin = trans.user_is_admin() invalid_tools_dict = odict() - if is_admin: + if is_admin and cntrller == 'admin': for repository in trans.sa_session.query( trans.model.Repository ) \ .filter( trans.model.Repository.table.c.deleted == False ) \ .order_by( trans.model.Repository.table.c.name ): diff -r e514944f0a38e6d88307251958b4407e5d20e51b -r b11be06de890f3ecb457e435726cd8e6ad9b6c63 templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -61,7 +61,7 @@ <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata', webapp='community' )}">Browse metadata</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', webapp='community' )}">Browse invalid tools</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='admin', webapp='community' )}">Browse invalid tools</a></div></div></div> diff -r e514944f0a38e6d88307251958b4407e5d20e51b -r b11be06de890f3ecb457e435726cd8e6ad9b6c63 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -72,7 +72,7 @@ <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', webapp='community' )}">Browse my invalid tools</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository', webapp='community' )}">Browse my invalid tools</a></div> %endif </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.

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commit/galaxy-central: greg: Apply fix for brand overflowing to the tool shed's base_panels.mako.
by Bitbucket 04 Apr '12

04 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e514944f0a38/ changeset: e514944f0a38 user: greg date: 2012-04-04 19:42:23 summary: Apply fix for brand overflowing to the tool shed's base_panels.mako. affected #: 1 file diff -r a3ffda11a38b4a863dae03c0a53e2428ffbda1a4 -r e514944f0a38e6d88307251958b4407e5d20e51b templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -117,12 +117,12 @@ </div> ## Logo, layered over tabs to be clickable - <div class="title" style="position: absolute; top: 0; left: 0; white-space: nowrap;"> + <div class="title"><a href="${app.config.get( 'logo_url', '/' )}"> - <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="display: inline; width: 26px; vertical-align: top;"> + <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}"> Galaxy Tool Shed %if app.config.brand: - <span class='brand'>/ ${app.config.brand}</span> + <span>/ ${app.config.brand}</span> %endif </a></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.

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commit/galaxy-central: greg: Add the ability to browse invalid tools in the tool shed - current user is restricted to seeing only their invalid tools if not an admin. Also a bit of cleanup in tool shed statistics.
by Bitbucket 04 Apr '12

04 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a3ffda11a38b/ changeset: a3ffda11a38b user: greg date: 2012-04-04 19:36:37 summary: Add the ability to browse invalid tools in the tool shed - current user is restricted to seeing only their invalid tools if not an admin. Also a bit of cleanup in tool shed statistics. affected #: 8 files diff -r 7aebce7e4aa1081643c69e23136765585b5097be -r a3ffda11a38b4a863dae03c0a53e2428ffbda1a4 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -50,9 +50,14 @@ for repository in self.sa_session.query( self.model.Repository ): self.repositories += 1 self.total_clones += repository.times_downloaded - if repository.deleted: + is_deleted = repository.deleted + is_new = repository.is_new + if is_deleted and is_new: self.deleted_repositories += 1 - elif repository.is_new: + self.new_repositories += 1 + elif is_deleted: + self.deleted_repositories += 1 + elif is_new: self.new_repositories += 1 else: processed_guids = [] diff -r 7aebce7e4aa1081643c69e23136765585b5097be -r a3ffda11a38b4a863dae03c0a53e2428ffbda1a4 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -461,21 +461,25 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - count = 0 - for repository in trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ): - try: - reset_all_repository_metadata( trans, trans.security.encode_id( repository.id ) ) - log.debug( "Reset metadata on repository %s" % repository.name ) - count += 1 - except Exception, e: - log.debug( "Error attempting to reset metadata on repository %s: %s" % ( repository.name, str( e ) ) ) - message = "Reset metadata on %d repositories" % count - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_repository_metadata', - webapp='community', - message=util.sanitize_text( message ), - status=status ) ) + if 'reset_all_repository_metadata_button' in kwd: + count = 0 + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.deleted == False ): + try: + reset_all_repository_metadata( trans, trans.security.encode_id( repository.id ) ) + log.debug( "Reset metadata on repository %s" % repository.name ) + count += 1 + except Exception, e: + log.debug( "Error attempting to reset metadata on repository %s: %s" % ( repository.name, str( e ) ) ) + message = "Reset metadata on %d repositories" % count + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_repository_metadata', + webapp='community', + message=util.sanitize_text( message ), + status=status ) ) + return trans.fill_template( '/webapps/community/admin/reset_all_repository_metadata.mako', + message=message, + status=status ) @web.expose @web.require_admin def browse_repositories( self, trans, **kwd ): @@ -549,12 +553,15 @@ @web.expose @web.require_admin def regenerate_statistics( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if 'regenerate_statistics_button' in kwd: trans.app.shed_counter.generate_statistics() - message = "Successfully regenerated statistics" + message = "Successfully regenerated statistics" return trans.fill_template( '/webapps/community/admin/statistics.mako', message=message, - status='done' ) + status=status ) @web.expose @web.require_admin def delete_repository( self, trans, **kwd ): diff -r 7aebce7e4aa1081643c69e23136765585b5097be -r a3ffda11a38b4a863dae03c0a53e2428ffbda1a4 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -400,6 +400,38 @@ # Render the list view return self.valid_repository_list_grid( trans, **kwd ) @web.expose + def browse_invalid_tools( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) + is_admin = trans.user_is_admin() + invalid_tools_dict = odict() + if is_admin: + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.deleted == False ) \ + .order_by( trans.model.Repository.table.c.name ): + for downloadable_revision in repository.downloadable_revisions: + metadata = downloadable_revision.metadata + invalid_tools = metadata.get( 'invalid_tools', [] ) + for invalid_tool_config in invalid_tools: + invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision ) + else: + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.user_id == trans.user.id ) ) \ + .order_by( trans.model.Repository.table.c.name ): + for downloadable_revision in repository.downloadable_revisions: + metadata = downloadable_revision.metadata + invalid_tools = metadata.get( 'invalid_tools', [] ) + for invalid_tool_config in invalid_tools: + invalid_tools_dict[ invalid_tool_config ] = ( repository.id, repository.name, downloadable_revision.changeset_revision ) + return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako', + invalid_tools_dict=invalid_tools_dict, + webapp=webapp, + message=message, + status=status ) + @web.expose def find_workflows( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) diff -r 7aebce7e4aa1081643c69e23136765585b5097be -r a3ffda11a38b4a863dae03c0a53e2428ffbda1a4 templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -60,6 +60,9 @@ <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata', webapp='community' )}">Browse metadata</a></div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', webapp='community' )}">Browse invalid tools</a> + </div></div></div><div class="toolSectionTitle"> diff -r 7aebce7e4aa1081643c69e23136765585b5097be -r a3ffda11a38b4a863dae03c0a53e2428ffbda1a4 templates/webapps/community/admin/reset_all_repository_metadata.mako --- /dev/null +++ b/templates/webapps/community/admin/reset_all_repository_metadata.mako @@ -0,0 +1,19 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Reset metadata on each change set of the repositories in this tool shed</div> + <form name="reset_all_repository_metadata" id="reset_all_repository_metadata" action="${h.url_for( controller='admin', action='reset_all_repository_metadata' )}" method="post" > + <div class="form-row"> + Click the button below to reset metadata on each change set of the repositories in this tool shed. + </div> + <div class="form-row"> + <input type="submit" name="reset_all_repository_metadata_button" value="Reset all repository metadata"/> + </div> + </form> + </div> +</div> diff -r 7aebce7e4aa1081643c69e23136765585b5097be -r a3ffda11a38b4a863dae03c0a53e2428ffbda1a4 templates/webapps/community/admin/statistics.mako --- a/templates/webapps/community/admin/statistics.mako +++ b/templates/webapps/community/admin/statistics.mako @@ -19,7 +19,7 @@ <td>${trans.app.shed_counter.repositories}</td></tr><tr> - <td>New repositories</td> + <td>Empty repositories</td><td>${trans.app.shed_counter.new_repositories}</td></tr><tr> diff -r 7aebce7e4aa1081643c69e23136765585b5097be -r a3ffda11a38b4a863dae03c0a53e2428ffbda1a4 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -71,6 +71,9 @@ <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_repositories', webapp='community' )}">Browse my repositories</a></div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', webapp='community' )}">Browse my invalid tools</a> + </div> %endif </div></div> diff -r 7aebce7e4aa1081643c69e23136765585b5097be -r a3ffda11a38b4a863dae03c0a53e2428ffbda1a4 templates/webapps/community/repository/browse_invalid_tools.mako --- /dev/null +++ b/templates/webapps/community/repository/browse_invalid_tools.mako @@ -0,0 +1,38 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + %if invalid_tools_dict: + <div class="toolFormTitle">Invalid tools<i> - click the tool config file name to see why the tool is invalid</i></div> + <div class="form-row"> + <table class="grid"> + <tr> + <th>Tool config</th> + <th>Repository name</th> + <th>Changeset revision</th> + </tr> + %for invalid_tool_config, repository_tup in invalid_tools_dict.items(): + <% repository_id, repository_name, changeset_revision = repository_tup %> + <tr> + <td> + <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}"> + ${invalid_tool_config} + </a> + </td> + <td>${repository_name}</td> + <td>${changeset_revision}</td> + </tr> + %endfor + </table> + </div> + </div> + %else: + <div class="form-row"> + You do not own any repositories that contain invalid tools. + </div> + %endif +</div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Rework the display of DrillDown form elements.
by Bitbucket 04 Apr '12

04 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7aebce7e4aa1/ changeset: 7aebce7e4aa1 user: dan date: 2012-04-04 18:24:43 summary: Rework the display of DrillDown form elements. affected #: 3 files diff -r 45735a13168bfa54ebcf232cbd9ebc2ffe10ee92 -r 7aebce7e4aa1081643c69e23136765585b5097be lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1056,26 +1056,35 @@ ... </param> ... ''' ) ) >>> print p.get_html() - <div><ul class="toolParameterExpandableCollapsable"> - <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="checkbox" name="some_name" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> - <li><input type="checkbox" name="some_name" value="option1"">Option 1 - </li> - <li><input type="checkbox" name="some_name" value="option2"">Option 2 - </li> - <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="checkbox" name="some_name" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> - <li><input type="checkbox" name="some_name" value="option3"">Option 3 - </li> - <li><input type="checkbox" name="some_name" value="option4"">Option 4 - </li> - </ul> - </li> - </ul> - </li> - <li><input type="checkbox" name="some_name" value="option5"">Option 5 - </li> - </ul></div> + <div class="form-row drilldown-container" id="drilldown--736f6d655f6e616d65"> + <div class="form-row-input"> + <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span> + <input type="checkbox" name="some_name" value="heading1" >Heading 1 + <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;"> + <div class="form-row-input"> + <input type="checkbox" name="some_name" value="option1" >Option 1 + </div> + <div class="form-row-input"> + <input type="checkbox" name="some_name" value="option2" >Option 2 + </div> + <div class="form-row-input"> + <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span> + <input type="checkbox" name="some_name" value="heading1" >Heading 1 + <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + <div class="form-row-input"> + <input type="checkbox" name="some_name" value="option3" >Option 3 + </div> + <div class="form-row-input"> + <input type="checkbox" name="some_name" value="option4" >Option 4 + </div> + </div> + </div> + </div> + </div> + <div class="form-row-input"> + <input type="checkbox" name="some_name" value="option5" >Option 5 + </div> + </div> >>> p = DrillDownSelectToolParameter( None, XML( ... ''' ... <param name="some_name" type="drill_down" display="radio" hierarchy="recurse" multiple="false"> @@ -1093,26 +1102,35 @@ ... </param> ... ''' ) ) >>> print p.get_html() - <div><ul class="toolParameterExpandableCollapsable"> - <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="radio" name="some_name" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> - <li><input type="radio" name="some_name" value="option1"">Option 1 - </li> - <li><input type="radio" name="some_name" value="option2"">Option 2 - </li> - <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="radio" name="some_name" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> - <li><input type="radio" name="some_name" value="option3"">Option 3 - </li> - <li><input type="radio" name="some_name" value="option4"">Option 4 - </li> - </ul> - </li> - </ul> - </li> - <li><input type="radio" name="some_name" value="option5"">Option 5 - </li> - </ul></div> + <div class="form-row drilldown-container" id="drilldown--736f6d655f6e616d65"> + <div class="form-row-input"> + <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-click"></span> + <input type="radio" name="some_name" value="heading1" >Heading 1 + <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-container" style="float: left; margin-left: 1em;"> + <div class="form-row-input"> + <input type="radio" name="some_name" value="option1" >Option 1 + </div> + <div class="form-row-input"> + <input type="radio" name="some_name" value="option2" >Option 2 + </div> + <div class="form-row-input"> + <span class="form-toggle icon-button toggle-expand" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-click"></span> + <input type="radio" name="some_name" value="heading1" >Heading 1 + <div class="form-row" id="drilldown--736f6d655f6e616d65-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + <div class="form-row-input"> + <input type="radio" name="some_name" value="option3" >Option 3 + </div> + <div class="form-row-input"> + <input type="radio" name="some_name" value="option4" >Option 4 + </div> + </div> + </div> + </div> + </div> + <div class="form-row-input"> + <input type="radio" name="some_name" value="option5" >Option 5 + </div> + </div> >>> print p.options [{'selected': False, 'name': 'Heading 1', 'value': 'heading1', 'options': [{'selected': False, 'name': 'Option 1', 'value': 'option1', 'options': []}, {'selected': False, 'name': 'Option 2', 'value': 'option2', 'options': []}, {'selected': False, 'name': 'Heading 1', 'value': 'heading1', 'options': [{'selected': False, 'name': 'Option 3', 'value': 'option3', 'options': []}, {'selected': False, 'name': 'Option 4', 'value': 'option4', 'options': []}]}]}, {'selected': False, 'name': 'Option 5', 'value': 'option5', 'options': []}] """ diff -r 45735a13168bfa54ebcf232cbd9ebc2ffe10ee92 -r 7aebce7e4aa1081643c69e23136765585b5097be lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -6,6 +6,7 @@ from cgi import escape from galaxy.util import restore_text, relpath, nice_size from galaxy.web import url_for +from binascii import hexlify log = logging.getLogger(__name__) @@ -391,48 +392,66 @@ >>> t = DrillDownField( "foo", multiple=True, display="checkbox", options=[{'name': 'Heading 1', 'value': 'heading1', 'options': [{'name': 'Option 1', 'value': 'option1', 'options': []}, {'name': 'Option 2', 'value': 'option2', 'options': []}, {'name': 'Heading 1', 'value': 'heading1', 'options': [{'name': 'Option 3', 'value': 'option3', 'options': []}, {'name': 'Option 4', 'value': 'option4', 'options': []}]}]}, {'name': 'Option 5', 'value': 'option5', 'options': []}] ) >>> print t.get_html() - <div><ul class="toolParameterExpandableCollapsable"> - <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="checkbox" name="foo" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> - <li><input type="checkbox" name="foo" value="option1"">Option 1 - </li> - <li><input type="checkbox" name="foo" value="option2"">Option 2 - </li> - <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="checkbox" name="foo" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> - <li><input type="checkbox" name="foo" value="option3"">Option 3 - </li> - <li><input type="checkbox" name="foo" value="option4"">Option 4 - </li> - </ul> - </li> - </ul> - </li> - <li><input type="checkbox" name="foo" value="option5"">Option 5 - </li> - </ul></div> + <div class="form-row drilldown-container" id="drilldown--666f6f"> + <div class="form-row-input"> + <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-click"></span> + <input type="checkbox" name="foo" value="heading1" >Heading 1 + <div class="form-row" id="drilldown--666f6f-68656164696e6731-container" style="float: left; margin-left: 1em;"> + <div class="form-row-input"> + <input type="checkbox" name="foo" value="option1" >Option 1 + </div> + <div class="form-row-input"> + <input type="checkbox" name="foo" value="option2" >Option 2 + </div> + <div class="form-row-input"> + <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-68656164696e6731-click"></span> + <input type="checkbox" name="foo" value="heading1" >Heading 1 + <div class="form-row" id="drilldown--666f6f-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + <div class="form-row-input"> + <input type="checkbox" name="foo" value="option3" >Option 3 + </div> + <div class="form-row-input"> + <input type="checkbox" name="foo" value="option4" >Option 4 + </div> + </div> + </div> + </div> + </div> + <div class="form-row-input"> + <input type="checkbox" name="foo" value="option5" >Option 5 + </div> + </div> >>> t = DrillDownField( "foo", multiple=False, display="radio", options=[{'name': 'Heading 1', 'value': 'heading1', 'options': [{'name': 'Option 1', 'value': 'option1', 'options': []}, {'name': 'Option 2', 'value': 'option2', 'options': []}, {'name': 'Heading 1', 'value': 'heading1', 'options': [{'name': 'Option 3', 'value': 'option3', 'options': []}, {'name': 'Option 4', 'value': 'option4', 'options': []}]}]}, {'name': 'Option 5', 'value': 'option5', 'options': []}] ) >>> print t.get_html() - <div><ul class="toolParameterExpandableCollapsable"> - <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="radio" name="foo" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> - <li><input type="radio" name="foo" value="option1"">Option 1 - </li> - <li><input type="radio" name="foo" value="option2"">Option 2 - </li> - <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="radio" name="foo" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> - <li><input type="radio" name="foo" value="option3"">Option 3 - </li> - <li><input type="radio" name="foo" value="option4"">Option 4 - </li> - </ul> - </li> - </ul> - </li> - <li><input type="radio" name="foo" value="option5"">Option 5 - </li> - </ul></div> + <div class="form-row drilldown-container" id="drilldown--666f6f"> + <div class="form-row-input"> + <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-click"></span> + <input type="radio" name="foo" value="heading1" >Heading 1 + <div class="form-row" id="drilldown--666f6f-68656164696e6731-container" style="float: left; margin-left: 1em;"> + <div class="form-row-input"> + <input type="radio" name="foo" value="option1" >Option 1 + </div> + <div class="form-row-input"> + <input type="radio" name="foo" value="option2" >Option 2 + </div> + <div class="form-row-input"> + <span class="form-toggle icon-button toggle-expand" id="drilldown--666f6f-68656164696e6731-68656164696e6731-click"></span> + <input type="radio" name="foo" value="heading1" >Heading 1 + <div class="form-row" id="drilldown--666f6f-68656164696e6731-68656164696e6731-container" style="float: left; margin-left: 1em;"> + <div class="form-row-input"> + <input type="radio" name="foo" value="option3" >Option 3 + </div> + <div class="form-row-input"> + <input type="radio" name="foo" value="option4" >Option 4 + </div> + </div> + </div> + </div> + </div> + <div class="form-row-input"> + <input type="radio" name="foo" value="option5" >Option 5 + </div> + </div> """ def __init__( self, name, multiple=None, display=None, refresh_on_change=False, options = [], value = [], refresh_on_change_values = [] ): self.name = name @@ -466,30 +485,34 @@ if option['options']: new_parents = list( parent_options ) + [ option['value'] ] find_expanded_options( expanded_options, option['options'], new_parents ) - def recurse_options( html, options, expanded_options = [] ): + def recurse_options( html, options, base_id, expanded_options = [] ): for option in options: + escaped_option_value = escape( str( option['value'] ), quote=True ) selected = ( option['value'] in self.value ) - if selected: selected = ' checked' - else: selected = '' + if selected: + selected = ' checked' + else: + selected = '' + span_class = 'form-toggle icon-button toggle' + if option['value'] not in expanded_options: + span_class = "%s-expand" % ( span_class ) + html.append( '<div class="form-row-input">') + drilldown_group_id = "%s-%s" % ( base_id, hexlify( option['value'] ) ) if option['options']: - default_state = 'collapsed' - default_icon = '[+]' - if option['value'] in expanded_options: - default_state = 'expanded' - default_icon = '[-]' - html.append( '<li><span class="toolParameterExpandableCollapsable">%s</span><input type="%s" name="%s%s" value="%s"%s">%s' % ( default_icon, self.display, prefix, self.name, escape(str(option['value']), quote=True), selected, option['name']) ) - html.append( '<ul class="toolParameterExpandableCollapsable" default_state="%s">' % default_state ) - recurse_options( html, option['options'], expanded_options ) - html.append( '</ul>') - else: - html.append( '<li><input type="%s" name="%s%s" value="%s"%s">%s' % ( self.display, prefix, self.name, escape(str(option['value']), quote=True), selected, option['name']) ) - html.append( '</li>' ) + html.append( '<span class="%s" id="%s-click"></span>' % ( span_class, drilldown_group_id ) ) + html.append( '<input type="%s" name="%s%s" value="%s" %s>%s' % ( self.display, prefix, self.name, escaped_option_value, selected, option['name']) ) + if option['options']: + html.append( '<div class="form-row" id="%s-container" style="float: left; margin-left: 1em;">' % ( drilldown_group_id ) ) + recurse_options( html, option['options'], drilldown_group_id, expanded_options ) + html.append( '</div>') + html.append( '</div>') + drilldown_id = "drilldown-%s-%s" % ( hexlify( prefix ), hexlify( self.name ) ) rval = [] - rval.append( '<div><ul class="toolParameterExpandableCollapsable">' ) + rval.append( '<div class="form-row drilldown-container" id="%s">' % ( drilldown_id ) ) expanded_options = [] find_expanded_options( expanded_options, self.options ) - recurse_options( rval, self.options, expanded_options ) - rval.append( '</ul></div>' ) + recurse_options( rval, self.options, drilldown_id, expanded_options ) + rval.append( '</div>' ) return '\n'.join( rval ) class AddressField(BaseField): diff -r 45735a13168bfa54ebcf232cbd9ebc2ffe10ee92 -r 7aebce7e4aa1081643c69e23136765585b5097be templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -32,23 +32,29 @@ }); // For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements - $( 'li ul.toolParameterExpandableCollapsable' ).each( function() { - var el = $(this), - parent_li = el.parent('li'), - sub_ul = el.remove(); - - parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() { - sub_ul.toggle(); - $(this).html( sub_ul.is(":hidden") ? '[+]' : '[-]' ); + $( 'div.drilldown-container' ).each( function() { + $(this).find('span.form-toggle' ).each( function() { + var show_hide_click_elt = $(this); + var group_id = show_hide_click_elt.attr('id').substring( 0, show_hide_click_elt.attr('id').lastIndexOf( '-click' ) ); + $('#' + group_id + '-container').each( function() { + var show_hide_elt = $(this); + if ( show_hide_click_elt.hasClass( 'toggle-expand' ) ) { + show_hide_elt.hide(); + } + show_hide_click_elt.click( function() { + if ( show_hide_click_elt.hasClass("toggle") ){ + show_hide_click_elt.removeClass("toggle"); + show_hide_click_elt.addClass("toggle-expand"); + show_hide_elt.hide() + } + else { + show_hide_click_elt.addClass("toggle"); + show_hide_click_elt.removeClass("toggle-expand"); + show_hide_elt.show(); + } + }); + }); }); - parent_li.append( sub_ul ); - }); - - $( 'ul ul.toolParameterExpandableCollapsable' ).each( function(i) { - var el = $(this); - if (el.attr("default_state") === "collapsed") { - el.hide(); - } }); function checkUncheckAll( name, check ) { 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: fubar: Reverted picard_FastqToSam.xml which I accidentally embellished with a bogus --tmpdir flag because it does not use picard_wrapper.py
by Bitbucket 04 Apr '12

04 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/45735a13168b/ changeset: 45735a13168b user: fubar date: 2012-04-04 18:16:12 summary: Reverted picard_FastqToSam.xml which I accidentally embellished with a bogus --tmpdir flag because it does not use picard_wrapper.py affected #: 1 file diff -r 440e50875343ff7d48464826ce819ef5a232882a -r 45735a13168bfa54ebcf232cbd9ebc2ffe10ee92 tools/picard/picard_FastqToSam.xml --- a/tools/picard/picard_FastqToSam.xml +++ b/tools/picard/picard_FastqToSam.xml @@ -4,7 +4,6 @@ <command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar" - --tmpdir "${__new_file_path__}" FASTQ="${input_fastq1}" #if str( $input_fastq2) != "None": FASTQ2="${input_fastq2}" 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: Fix bug that scrolled Trackster on double click when completely zoomed in.
by Bitbucket 04 Apr '12

04 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/440e50875343/ changeset: 440e50875343 user: jgoecks date: 2012-04-04 17:33:26 summary: Fix bug that scrolled Trackster on double click when completely zoomed in. affected #: 1 file diff -r 9ceb68fe691eb50509bf95b0e7641680b993c55d -r 440e50875343ff7d48464826ce819ef5a232882a static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1811,7 +1811,7 @@ } }, zoom_in: function (point, container) { - if (this.max_high === 0 || this.high - this.low < this.min_separation) { + if (this.max_high === 0 || this.high - this.low <= this.min_separation) { return; } var span = this.high - this.low, 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: dannon: Fix multi-input workflow selector to account for recent structural changes.
by Bitbucket 04 Apr '12

04 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9ceb68fe691e/ changeset: 9ceb68fe691e user: dannon date: 2012-04-04 17:27:48 summary: Fix multi-input workflow selector to account for recent structural changes. affected #: 1 file diff -r 26403ed86d4ccf39ea88c2658012a9a99d453266 -r 9ceb68fe691eb50509bf95b0e7641680b993c55d templates/workflow/run.mako --- a/templates/workflow/run.mako +++ b/templates/workflow/run.mako @@ -37,7 +37,7 @@ placeholder = 'type to filter'; } else { $('.multiinput').addClass('disabled'); - $('.multiinput', select.parent().prev()).removeClass('disabled'); + $('.multiinput', select.closest('.form-row')).removeClass('disabled'); select.attr('multiple', 'multiple').attr('size', 8); placeholder = 'type to filter, [enter] to select all'; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Allow multiple output file collection from the job_working_directory.
by Bitbucket 03 Apr '12

03 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/26403ed86d4c/ changeset: 26403ed86d4c user: natefoo date: 2012-04-04 04:07:19 summary: Allow multiple output file collection from the job_working_directory. affected #: 4 files diff -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac -r 26403ed86d4ccf39ea88c2658012a9a99d453266 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -86,6 +86,7 @@ self.allow_user_dataset_purge = string_as_bool( kwargs.get( "allow_user_dataset_purge", "False" ) ) self.allow_user_impersonation = string_as_bool( kwargs.get( "allow_user_impersonation", "False" ) ) self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) ) + self.collect_outputs_from = [ x.strip() for x in kwargs.get( 'collect_outputs_from', 'new_file_path,job_working_directory' ).lower().split(',') ] self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root ) self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) ) diff -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac -r 26403ed86d4ccf39ea88c2658012a9a99d453266 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -443,7 +443,7 @@ # Check for and move associated_files self.tool.collect_associated_files(out_data, self.working_directory) # Create generated output children and primary datasets and add to param_dict - collected_datasets = {'children':self.tool.collect_child_datasets(out_data),'primary':self.tool.collect_primary_datasets(out_data)} + collected_datasets = {'children':self.tool.collect_child_datasets(out_data, self.working_directory),'primary':self.tool.collect_primary_datasets(out_data, self.working_directory)} param_dict.update({'__collected_datasets__':collected_datasets}) # Certain tools require tasks to be completed after job execution # ( this used to be performed in the "exec_after_process" hook, but hooks are deprecated ). diff -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac -r 26403ed86d4ccf39ea88c2658012a9a99d453266 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2153,7 +2153,7 @@ shutil.rmtree(temp_file_path) except: continue - def collect_child_datasets( self, output): + def collect_child_datasets( self, output, job_working_directory ): """ Look for child dataset files, create HDA and attach to parent. """ @@ -2161,7 +2161,12 @@ # Loop through output file names, looking for generated children in # form of 'child_parentId_designation_visibility_extension' for name, outdata in output.items(): - for filename in glob.glob(os.path.join(self.app.config.new_file_path,"child_%i_*" % outdata.id) ): + filenames = [] + if 'new_file_path' in self.app.config.collect_outputs_from: + filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path,"child_%i_*" % outdata.id) ) ) + if 'job_working_directory' in self.app.config.collect_outputs_from: + filenames.extend( glob.glob(os.path.join(job_working_directory,"child_%i_*" % outdata.id) ) ) + for filename in filenames: if not name in children: children[name] = {} fields = os.path.basename(filename).split("_") @@ -2213,7 +2218,7 @@ self.sa_session.add( child_dataset ) self.sa_session.flush() return children - def collect_primary_datasets( self, output): + def collect_primary_datasets( self, output, job_working_directory ): """ Find any additional datasets generated by a tool and attach (for cases where number of outputs is not known in advance). @@ -2223,7 +2228,12 @@ # datasets in form of: # 'primary_associatedWithDatasetID_designation_visibility_extension(_DBKEY)' for name, outdata in output.items(): - for filename in glob.glob(os.path.join(self.app.config.new_file_path,"primary_%i_*" % outdata.id) ): + filenames = [] + if 'new_file_path' in self.app.config.collect_outputs_from: + filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path,"primary_%i_*" % outdata.id) ) ) + if 'job_working_directory' in self.app.config.collect_outputs_from: + filenames.extend( glob.glob(os.path.join(job_working_directory,"primary_%i_*" % outdata.id) ) ) + for filename in filenames: if not name in primary_datasets: primary_datasets[name] = {} fields = os.path.basename(filename).split("_") diff -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac -r 26403ed86d4ccf39ea88c2658012a9a99d453266 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -151,7 +151,6 @@ # Directory where chrom len files are kept, currently mainly used by trackster #len_file_path = tool-data/shared/ucsc/chrom - # Datatypes config file, defines what data (file) types are available in # Galaxy. #datatypes_config_file = datatypes_conf.xml @@ -172,6 +171,14 @@ # Path to the directory containing the external_service_types defined in the config. #external_service_type_path = external_service_types +# Tools with a number of outputs not known until runtime can write these +# outputs to a directory for collection by Galaxy when the job is done. +# Previously, this directory was new_file_path, but using one global directory +# can cause performance problems, so using job_working_directory ('.' or cwd +# when a job is run) is encouraged. By default, both are checked to avoid +# breaking existing tools. +#collect_outputs_from = new_file_path,job_working_directory + # -- Mail and notification # Galaxy sends mail for various things: Subscribing users to the mailing list 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: fubar: Added --tmpdir "${__new_file_path__}" to some other Picard tool command lines so java uses that for temp space.
by Bitbucket 03 Apr '12

03 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/99419b4be32d/ changeset: 99419b4be32d user: fubar date: 2012-04-03 23:56:46 summary: Added --tmpdir "${__new_file_path__}" to some other Picard tool command lines so java uses that for temp space. affected #: 5 files diff -r d2758274580003a0cb94eecc65de8d2d358f9a37 -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac tools/picard/picard_BamIndexStats.xml --- a/tools/picard/picard_BamIndexStats.xml +++ b/tools/picard/picard_BamIndexStats.xml @@ -7,6 +7,7 @@ -t "$htmlfile" -d "$htmlfile.files_path" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/BamIndexStats.jar" + --tmpdir "${__new_file_path__}" </command><inputs><param format="bam" name="input_file" type="data" label="BAM dataset to generate statistics for" diff -r d2758274580003a0cb94eecc65de8d2d358f9a37 -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac tools/picard/picard_FastqToSam.xml --- a/tools/picard/picard_FastqToSam.xml +++ b/tools/picard/picard_FastqToSam.xml @@ -4,6 +4,7 @@ <command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar" + --tmpdir "${__new_file_path__}" FASTQ="${input_fastq1}" #if str( $input_fastq2) != "None": FASTQ2="${input_fastq2}" diff -r d2758274580003a0cb94eecc65de8d2d358f9a37 -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac tools/picard/picard_MarkDuplicates.xml --- a/tools/picard/picard_MarkDuplicates.xml +++ b/tools/picard/picard_MarkDuplicates.xml @@ -7,6 +7,7 @@ --opt-dup-dist="$optDupeDist" --output-format=$outputFormat --output-txt=$outMetrics + --tmpdir "${__new_file_path__}" #if str( $outputFormat ) == "sam" #if str( $remDups ) == "true" --output-sam=$outFileSamRemoved diff -r d2758274580003a0cb94eecc65de8d2d358f9a37 -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac tools/picard/picard_ReorderSam.xml --- a/tools/picard/picard_ReorderSam.xml +++ b/tools/picard/picard_ReorderSam.xml @@ -15,6 +15,7 @@ --allow-contig-len-discord=$allowContigLenDiscord --output-format=$outputFormat --output=$outFile + --tmpdir "${__new_file_path__}" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/ReorderSam.jar" </command><inputs> diff -r d2758274580003a0cb94eecc65de8d2d358f9a37 -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac tools/picard/rgPicardASMetrics.xml --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -2,7 +2,7 @@ <command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext" - -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectAlignmentSummaryMetrics.jar + -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectAlignmentSummaryMetrics.jar --tmpdir "${__new_file_path__}" #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" #else 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 03 Apr '12

03 Apr '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8407e8f932af/ changeset: 8407e8f932af user: jgoecks date: 2012-04-03 23:10:55 summary: Handle tool labels outside sections. affected #: 2 files diff -r 4d28b899b291c984b7ec5e38ed92124148e69f44 -r 8407e8f932af6cbbcf151be8fd3df9086bbb6468 static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ b/static/scripts/backbone/tools.js @@ -178,7 +178,13 @@ clear_search_results: function() { this.each(function(panel_elt) { - panel_elt.clear_search_results(); + if (panel_elt instanceof ToolPanelSection) { + panel_elt.clear_search_results(); + } + else { + // Label or tool, so just show. + panel_elt.show(); + } }); }, @@ -189,8 +195,24 @@ return; } + var cur_label = null; this.each(function(panel_elt) { - panel_elt.apply_search_results(results); + if (panel_elt instanceof ToolPanelLabel) { + cur_label = panel_elt; + cur_label.hide(); + } + else if (panel_elt instanceof Tool) { + if (panel_elt.apply_search_results(results)) { + if (cur_label) { + cur_label.show(); + } + } + } + else { + // Starting new section, so clear current label. + cur_label = null; + panel_elt.apply_search_results(results); + } }); } }); @@ -358,6 +380,11 @@ tool_view.render(); this_el.append(tool_view.$el); } + else if (panel_elt instanceof ToolPanelLabel) { + var label_view = new ToolPanelLabelView({model: panel_elt}); + label_view.render(); + this_el.append(label_view.$el); + } }); return this; }, diff -r 4d28b899b291c984b7ec5e38ed92124148e69f44 -r 8407e8f932af6cbbcf151be8fd3df9086bbb6468 static/scripts/packed/backbone/tools.js --- a/static/scripts/packed/backbone/tools.js +++ b/static/scripts/packed/backbone/tools.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this)},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file +var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){if(a instanceof ToolPanelSection){a.clear_search_results()}else{a.show()}})},apply_search_results:function(){var b=this.tool_search.attributes.results;if(b===null){this.clear_search_results();return}var a=null;this.each(function(c){if(c instanceof ToolPanelLabel){a=c;a.hide()}else{if(c instanceof Tool){if(c.apply_search_results(b)){if(a){a.show()}}}else{a=null;c.apply_search_results(b)}}})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this)},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();b.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();b.append(f.$el)}}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/d27582745800/ changeset: d27582745800 user: jgoecks date: 2012-04-03 23:41:13 summary: Update styles for standalone labels, tools in tool panel. affected #: 2 files diff -r 8407e8f932af6cbbcf151be8fd3df9086bbb6468 -r d2758274580003a0cb94eecc65de8d2d358f9a37 static/june_2007_style/blue/tool_menu.css --- a/static/june_2007_style/blue/tool_menu.css +++ b/static/june_2007_style/blue/tool_menu.css @@ -1,2 +1,4 @@ #tool-search{padding-top:5px;padding-bottom:10px;position:relative;} div.toolSectionWrapper{margin-bottom:5px;} +div.toolPanelLabel{padding-top:10px;padding-bottom:5px;font-weight:bold;color:gray;text-transform:uppercase;} +div.toolTitleNoSection{padding-bottom:5px;font-weight:bold;} diff -r 8407e8f932af6cbbcf151be8fd3df9086bbb6468 -r d2758274580003a0cb94eecc65de8d2d358f9a37 static/june_2007_style/tool_menu.css.tmpl --- a/static/june_2007_style/tool_menu.css.tmpl +++ b/static/june_2007_style/tool_menu.css.tmpl @@ -3,6 +3,21 @@ padding-bottom: 10px; position: relative; } + div.toolSectionWrapper { margin-bottom: 5px; +} + +div.toolPanelLabel { + padding-top: 10px; + padding-bottom: 5px; + font-weight: bold; + color: gray; + text-transform: uppercase; +} + +div.toolTitleNoSection +{ + padding-bottom: 5px; + font-weight: bold; } \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 03 Apr '12

03 Apr '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3704881a59f0/ changeset: 3704881a59f0 user: fubar date: 2012-04-03 22:11:54 summary: Patch for picard_AddOrReplaceReadGroups.xml to add --tmpdir "${__new_file_path__}" to the command line generated. That will over-ride the default value "/tmp" for opts.tmpdir in picard_wrapper.py and solve the problem with /tmp filling reported by Matt Shirley. affected #: 1 file diff -r 84d0e16fad2cb311503a8e688de4808fd65d78f0 -r 3704881a59f067437247d65b3e5b195f6358cc6c tools/picard/picard_AddOrReplaceReadGroups.xml --- a/tools/picard/picard_AddOrReplaceReadGroups.xml +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml @@ -16,6 +16,7 @@ --output-format=$outputFormat --output=$outFile -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/AddOrReplaceReadGroups.jar" + --tmpdir "${__new_file_path__}" </command><inputs><param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in" https://bitbucket.org/galaxy/galaxy-central/changeset/4d28b899b291/ changeset: 4d28b899b291 user: fubar date: 2012-04-03 22:12:48 summary: branch merge affected #: 2 files diff -r 3704881a59f067437247d65b3e5b195f6358cc6c -r 4d28b899b291c984b7ec5e38ed92124148e69f44 static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ b/static/scripts/backbone/tools.js @@ -285,7 +285,6 @@ * Toggle visibility of tool section. */ toggle: function() { - this.$el.children(".toolSectionBody").toggle("fast"); this.model.set("open", !this.model.attributes.open); }, @@ -294,8 +293,8 @@ */ update_open: function() { (this.model.attributes.open ? - this.$el.children(".toolSectionBody").show("fast") : - this.$el.children(".toolSectionBody").hide("fast") + this.$el.children(".toolSectionBody").slideDown("fast") : + this.$el.children(".toolSectionBody").slideUp("fast") ); } }); diff -r 3704881a59f067437247d65b3e5b195f6358cc6c -r 4d28b899b291c984b7ec5e38ed92124148e69f44 static/scripts/packed/backbone/tools.js --- a/static/scripts/packed/backbone/tools.js +++ b/static/scripts/packed/backbone/tools.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this)},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.$el.children(".toolSectionBody").toggle("fast");this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").show("fast"):this.$el.children(".toolSectionBody").hide("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file +var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this)},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 03 Apr '12

03 Apr '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d77454603237/ changeset: d77454603237 user: jgoecks date: 2012-04-03 22:00:17 summary: Prettify tool section show/hide using sliding. affected #: 2 files diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r d774546032374648823f29aad4fb178086e169e4 static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ b/static/scripts/backbone/tools.js @@ -285,7 +285,6 @@ * Toggle visibility of tool section. */ toggle: function() { - this.$el.children(".toolSectionBody").toggle("fast"); this.model.set("open", !this.model.attributes.open); }, @@ -294,8 +293,8 @@ */ update_open: function() { (this.model.attributes.open ? - this.$el.children(".toolSectionBody").show("fast") : - this.$el.children(".toolSectionBody").hide("fast") + this.$el.children(".toolSectionBody").slideDown("fast") : + this.$el.children(".toolSectionBody").slideUp("fast") ); } }); diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r d774546032374648823f29aad4fb178086e169e4 static/scripts/packed/backbone/tools.js --- a/static/scripts/packed/backbone/tools.js +++ b/static/scripts/packed/backbone/tools.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this)},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.$el.children(".toolSectionBody").toggle("fast");this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").show("fast"):this.$el.children(".toolSectionBody").hide("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file +var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this)},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/4ae471a236a3/ changeset: 4ae471a236a3 user: jgoecks date: 2012-04-03 22:00:48 summary: Merge affected #: 9 files diff -r d774546032374648823f29aad4fb178086e169e4 -r 4ae471a236a381022d87779b033e49d2f8b321bd lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -24,35 +24,73 @@ class ShedCounter( object ): def __init__( self, model ): self.model = model - self.count_time = strftime( "%b %d, %Y", gmtime() ) - self.valid_tools = self.count_valid_tools() + self.generation_time = strftime( "%b %d, %Y", gmtime() ) + self.repositories = 0 + self.new_repositories = 0 + self.deleted_repositories = 0 + self.invalid_tools = 0 + self.valid_tools = 0 + self.workflows = 0 + self.proprietary_datatypes = 0 + self.total_clones = 0 + self.generate_statistics() @property def sa_session( self ): """Returns a SQLAlchemy session""" return self.model.context - def count_valid_tools( self ): - valid_tools = 0 - processed_repository_ids = [] - for repository_metadata in self.sa_session.query( self.model.RepositoryMetadata ) \ - .filter( and_( self.model.RepositoryMetadata.table.c.malicious == False, - self.model.RepositoryMetadata.table.c.metadata is not None, - self.model.RepositoryMetadata.table.c.tool_versions is not None ) ): - processed_guids = [] - repository = repository_metadata.repository - if repository.id not in processed_repository_ids: - for revision_metadata in repository.downloadable_revisions: - metadata = revision_metadata.metadata + def generate_statistics( self ): + self.repositories = 0 + self.new_repositories = 0 + self.deleted_repositories = 0 + self.invalid_tools = 0 + self.valid_tools = 0 + self.workflows = 0 + self.proprietary_datatypes = 0 + self.total_clones = 0 + for repository in self.sa_session.query( self.model.Repository ): + self.repositories += 1 + self.total_clones += repository.times_downloaded + if repository.deleted: + self.deleted_repositories += 1 + elif repository.is_new: + self.new_repositories += 1 + else: + processed_guids = [] + processed_invalid_tool_configs = [] + processed_relative_workflow_paths = [] + processed_datatypes = [] + for downloadable_revision in repository.downloadable_revisions: + metadata = downloadable_revision.metadata if 'tools' in metadata: tool_dicts = metadata[ 'tools' ] for tool_dict in tool_dicts: if 'guid' in tool_dict: guid = tool_dict[ 'guid' ] if guid not in processed_guids: - valid_tools += 1 + self.valid_tools += 1 processed_guids.append( guid ) - processed_repository_ids.append( repository.id ) - return valid_tools - + if 'invalid_tools' in metadata: + invalid_tool_configs = metadata[ 'invalid_tools' ] + for invalid_tool_config in invalid_tool_configs: + if invalid_tool_config not in processed_invalid_tool_configs: + self.invalid_tools += 1 + processed_invalid_tool_configs.append( invalid_tool_config ) + if 'datatypes' in metadata: + datatypes = metadata[ 'datatypes' ] + for datatypes_dict in datatypes: + if 'extension' in datatypes_dict: + extension = datatypes_dict[ 'extension' ] + if extension not in processed_datatypes: + self.proprietary_datatypes += 1 + processed_datatypes.append( extension ) + if 'workflows' in metadata: + workflows = metadata[ 'workflows' ] + for workflow_tup in workflows: + relative_path, exported_workflow_dict = workflow_tup + if relative_path not in processed_relative_workflow_paths: + self.workflows += 1 + processed_relative_workflow_paths.append( relative_path ) + self.generation_time = strftime( "%b %d, %Y", gmtime() ) def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ): # A tool shed repository is being installed so change the shed_tool_conf file. Parse the config file to generate the entire list # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have diff -r d774546032374648823f29aad4fb178086e169e4 -r 4ae471a236a381022d87779b033e49d2f8b321bd lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -457,6 +457,27 @@ status=status ) ) @web.expose @web.require_admin + def reset_all_repository_metadata( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + count = 0 + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.deleted == False ): + try: + reset_all_repository_metadata( trans, trans.security.encode_id( repository.id ) ) + log.debug( "Reset metadata on repository %s" % repository.name ) + count += 1 + except Exception, e: + log.debug( "Error attempting to reset metadata on repository %s: %s" % ( repository.name, str( e ) ) ) + message = "Reset metadata on %d repositories" % count + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_repository_metadata', + webapp='community', + message=util.sanitize_text( message ), + status=status ) ) + @web.expose + @web.require_admin def browse_repositories( self, trans, **kwd ): # We add params to the keyword dict in this method in order to rename the param # with an "f-" prefix, simulating filtering by clicking a search link. We have @@ -527,6 +548,15 @@ return self.repository_list_grid( trans, **kwd ) @web.expose @web.require_admin + def regenerate_statistics( self, trans, **kwd ): + if 'regenerate_statistics_button' in kwd: + trans.app.shed_counter.generate_statistics() + message = "Successfully regenerated statistics" + return trans.fill_template( '/webapps/community/admin/statistics.mako', + message=message, + status='done' ) + @web.expose + @web.require_admin def delete_repository( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) diff -r d774546032374648823f29aad4fb178086e169e4 -r 4ae471a236a381022d87779b033e49d2f8b321bd lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -201,7 +201,7 @@ can_set_metadata = False correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. " correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " - correction_msg += "that includes the required entry to resolve this issue.<br/>" + correction_msg += "that includes the required entry to correct this error.<br/>" invalid_files.append( ( name, correction_msg ) ) if options.index_file or options.missing_index_file: # Make sure the repository contains the required xxx.loc.sample file. @@ -290,6 +290,7 @@ # repository tip, we handle things like .loc.sample files here. metadata_dict = {} invalid_files = [] + invalid_tool_configs = [] sample_files = [] datatypes_config = None # Find datatypes_conf.xml if it exists. @@ -324,6 +325,7 @@ except Exception, e: valid = False invalid_files.append( ( name, str( e ) ) ) + invalid_tool_configs.append( name ) if valid and tool is not None: can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) if can_set_metadata: @@ -331,6 +333,8 @@ tool_config = os.path.join( root, name ) repository_clone_url = generate_clone_url( trans, id ) metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) + else: + invalid_tool_configs.append( name ) # Find all exported workflows elif name.endswith( '.ga' ): try: @@ -344,11 +348,14 @@ metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) + if invalid_tool_configs: + metadata_dict[ 'invalid_tools' ] = invalid_tool_configs return metadata_dict, invalid_files def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision, repo_dir ): # Browse repository files within a change set to generate metadata. metadata_dict = {} invalid_files = [] + invalid_tool_configs = [] sample_files = [] tmp_datatypes_config = None # Find datatypes_conf.xml if it exists. @@ -392,6 +399,7 @@ valid = True except Exception, e: invalid_files.append( ( filename, str( e ) ) ) + invalid_tool_configs.append( filename ) valid = False if valid and tool is not None: # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename @@ -403,6 +411,8 @@ # tip, we do not have to handle any .loc.sample files since they would have been handled previously. repository_clone_url = generate_clone_url( trans, id ) metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict ) + else: + invalid_tool_configs.append( filename ) try: os.unlink( tmp_filename ) except: @@ -417,6 +427,8 @@ metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) + if invalid_tool_configs: + metadata_dict[ 'invalid_tools' ] = invalid_tool_configs return metadata_dict, invalid_files def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ): """Set repository metadata""" diff -r d774546032374648823f29aad4fb178086e169e4 -r 4ae471a236a381022d87779b033e49d2f8b321bd lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -770,15 +770,14 @@ """ If the received changeset_revision includes a file named readme (case ignored), return it's contents. """ - name = kwd[ 'name' ] - owner = kwd[ 'owner' ] + repository_name = kwd[ 'name' ] + repository_owner = kwd[ 'owner' ] changeset_revision = kwd[ 'changeset_revision' ] - repository = get_repository_by_name_and_owner( trans, name, owner ) + repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) for root, dirs, files in os.walk( repo_dir ): for name in files: - if name.lower() in [ 'readme', 'readme.txt', 'read_me', 'read_me.txt' ]: + if name.lower() in [ 'readme', 'readme.txt', 'read_me', 'read_me.txt', '%s.txt' % repository_name ]: f = open( os.path.join( root, name ), 'r' ) text = f.read() f.close() @@ -1814,6 +1813,81 @@ changeset_revision=changeset_revision, message=message, status='error' ) ) + @web.expose + def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'error' ) + webapp = params.get( 'webapp', 'community' ) + repository = get_repository( trans, repository_id ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) + invalid_message = '' + if changeset_revision == repository.tip: + for root, dirs, files in os.walk( repo_dir ): + found = False + for name in files: + if name == tool_config: + tool_config_path = os.path.join( root, name ) + found = True + break + if found: + break + else: + for filename in ctx: + if filename == tool_config: + fctx = ctx[ filename ] + # Write the contents of datatypes_config.xml to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tool_config_path = fh.name + fh.close() + fh = open( tool_config_path, 'w' ) + fh.write( fctx.data() ) + fh.close() + break + metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, repository_id, ctx, changeset_revision, repo_dir ) + for invalid_file_tup in invalid_files: + invalid_tool_config, invalid_msg = invalid_file_tup + if tool_config == invalid_tool_config: + invalid_message = invalid_msg + break + tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_path ) + tool_state = self.__new_state( trans ) + is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) + if changeset_revision != repository.tip: + try: + os.unlink( tool_config_path ) + except: + pass + try: + if invalid_message: + message = invalid_message + return trans.fill_template( "/webapps/community/repository/tool_form.mako", + repository=repository, + changeset_revision=changeset_revision, + tool=tool, + tool_state=tool_state, + is_malicious=is_malicious, + webapp=webapp, + message=message, + status='error' ) + except Exception, e: + message = "This tool is invalid because: %s." % str( e ) + if webapp == 'galaxy': + return trans.response.send_redirect( web.url_for( controller='repository', + action='preview_tools_in_changeset', + repository_id=repository_id, + changeset_revision=changeset_revision, + message=message, + status='error' ) ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation='view_or_manage_repository', + id=repository_id, + changeset_revision=changeset_revision, + message=message, + status='error' ) ) def __new_state( self, trans, all_pages=False ): """ Create a new `DefaultToolState` for this tool. It will not be initialized diff -r d774546032374648823f29aad4fb178086e169e4 -r 4ae471a236a381022d87779b033e49d2f8b321bd templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -84,6 +84,7 @@ $("iframe#galaxy_main").contents().find("body").find("div[class='errormessage']").text( msg ); } } + var uploads_in_progress = 0; jQuery( function() { $("iframe#galaxy_main").load( function() { $(this).contents().find("form").each( function() { @@ -134,7 +135,16 @@ $(this).append("<input type='hidden' name='ajax_upload' value='true'>"); } // iframe submit is required for nginx (otherwise the encoding is wrong) - $(this).ajaxSubmit( { iframe: true } ); + $(this).ajaxSubmit( { iframe: true, + complete: function (xhr, stat) { + uploads_in_progress--; + if (uploads_in_progress == 0) { + window.onbeforeunload = null; + } + } + } ); + uploads_in_progress++; + window.onbeforeunload = function() { return "Navigating away from the Galaxy analysis interface will interrupt the file upload(s) currently in progress. Do you really want to do this?"; } if ( $(this).find("input[name='folder_id']").val() != undefined ) { var library_id = $(this).find("input[name='library_id']").val(); var show_deleted = $(this).find("input[name='show_deleted']").val(); diff -r d774546032374648823f29aad4fb178086e169e4 -r 4ae471a236a381022d87779b033e49d2f8b321bd templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -55,6 +55,9 @@ <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories', webapp='community' )}">Browse all repositories</a></div><div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_all_repository_metadata', webapp='community' )}">Reset all metadata</a> + </div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata', webapp='community' )}">Browse metadata</a></div></div> @@ -86,6 +89,12 @@ </div></div></div> + <div class="toolSectionTitle"> + Statistics + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='regenerate_statistics', webapp='community' )}">View shed statistics</a> + </div></div></div></div> diff -r d774546032374648823f29aad4fb178086e169e4 -r 4ae471a236a381022d87779b033e49d2f8b321bd templates/webapps/community/admin/statistics.mako --- /dev/null +++ b/templates/webapps/community/admin/statistics.mako @@ -0,0 +1,56 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Tool shed statistics generated on ${trans.app.shed_counter.generation_time}</div> + <form name="regenerate_statistics" id="regenerate_statistics" action="${h.url_for( controller='admin', action='regenerate_statistics', webapp='community' )}" method="post" > + <div class="form-row"> + <table class="grid"> + <tr> + <th>Item</th> + <th>Count</th> + </tr> + <tr> + <td>Total repositories</td> + <td>${trans.app.shed_counter.repositories}</td> + </tr> + <tr> + <td>New repositories</td> + <td>${trans.app.shed_counter.new_repositories}</td> + </tr> + <tr> + <td>Deleted repositories</td> + <td>${trans.app.shed_counter.deleted_repositories}</td> + </tr> + <tr> + <td>Valid tools</td> + <td>${trans.app.shed_counter.valid_tools}</td> + </tr> + <tr> + <td>Invalid tools</td> + <td>${trans.app.shed_counter.invalid_tools}</td> + </tr> + <tr> + <td>Workflows</td> + <td>${trans.app.shed_counter.workflows}</td> + </tr> + <tr> + <td>Proprietary datatypes</td> + <td>${trans.app.shed_counter.proprietary_datatypes}</td> + </tr> + <tr> + <td>Total clones</td> + <td>${trans.app.shed_counter.total_clones}</td> + </tr> + </table> + </div> + <div class="form-row"> + <input type="submit" name="regenerate_statistics_button" value="Regenerate statistics"/> + </div> + </form> + </div> +</div> diff -r d774546032374648823f29aad4fb178086e169e4 -r 4ae471a236a381022d87779b033e49d2f8b321bd templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -39,7 +39,7 @@ <%def name="left_panel()"><div class="unified-panel-header" unselectable="on"> - <div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools} valid tools on ${trans.app.shed_counter.count_time}</div> + <div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools} valid tools on ${trans.app.shed_counter.generation_time}</div></div><div class="page-container" style="padding: 10px;"><div class="toolMenu"> diff -r d774546032374648823f29aad4fb178086e169e4 -r 4ae471a236a381022d87779b033e49d2f8b321bd templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -95,7 +95,7 @@ <div class="form-row"><table width="100%"><tr bgcolor="#D8D8D8" width="100%"> - <td><b>Tools</b><i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i></td> + <td><b>Valid tools</b><i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i></td></tr></table></div> @@ -147,6 +147,31 @@ </div><div style="clear: both"></div> %endif + %if 'invalid_tools' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Invalid tools</b><i> - click the tool config file name to see why the tool is invalid</i></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% invalid_tool_configs = metadata[ 'invalid_tools' ] %> + <table class="grid"> + %for invalid_tool_config in invalid_tool_configs: + <tr> + <td> + <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}"> + ${invalid_tool_config} + </a> + </td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif %if 'workflows' in metadata: ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for shed statistics.
by Bitbucket 03 Apr '12

03 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/84d0e16fad2c/ changeset: 84d0e16fad2c user: greg date: 2012-04-03 21:26:05 summary: Fix for shed statistics. affected #: 1 file diff -r 69aab50e8e18b3cda8ffd9acf4537e01a0c6c31f -r 84d0e16fad2cb311503a8e688de4808fd65d78f0 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -48,18 +48,18 @@ self.proprietary_datatypes = 0 self.total_clones = 0 for repository in self.sa_session.query( self.model.Repository ): + self.repositories += 1 self.total_clones += repository.times_downloaded if repository.deleted: self.deleted_repositories += 1 elif repository.is_new: self.new_repositories += 1 else: - self.repositories += 1 + processed_guids = [] + processed_invalid_tool_configs = [] + processed_relative_workflow_paths = [] + processed_datatypes = [] for downloadable_revision in repository.downloadable_revisions: - processed_guids = [] - processed_invalid_tool_configs = [] - processed_relative_workflow_paths = [] - processed_datatypes = [] metadata = downloadable_revision.metadata if 'tools' in metadata: tool_dicts = metadata[ 'tools' ] 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: Enable an admin to be able to view and regenerate tool shed statistics.
by Bitbucket 03 Apr '12

03 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/69aab50e8e18/ changeset: 69aab50e8e18 user: greg date: 2012-04-03 21:18:29 summary: Enable an admin to be able to view and regenerate tool shed statistics. affected #: 5 files diff -r 12a3c47995d6269f49b4695fb9acc5c7fbf630a9 -r 69aab50e8e18b3cda8ffd9acf4537e01a0c6c31f lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -24,35 +24,73 @@ class ShedCounter( object ): def __init__( self, model ): self.model = model - self.count_time = strftime( "%b %d, %Y", gmtime() ) - self.valid_tools = self.count_valid_tools() + self.generation_time = strftime( "%b %d, %Y", gmtime() ) + self.repositories = 0 + self.new_repositories = 0 + self.deleted_repositories = 0 + self.invalid_tools = 0 + self.valid_tools = 0 + self.workflows = 0 + self.proprietary_datatypes = 0 + self.total_clones = 0 + self.generate_statistics() @property def sa_session( self ): """Returns a SQLAlchemy session""" return self.model.context - def count_valid_tools( self ): - valid_tools = 0 - processed_repository_ids = [] - for repository_metadata in self.sa_session.query( self.model.RepositoryMetadata ) \ - .filter( and_( self.model.RepositoryMetadata.table.c.malicious == False, - self.model.RepositoryMetadata.table.c.metadata is not None, - self.model.RepositoryMetadata.table.c.tool_versions is not None ) ): - processed_guids = [] - repository = repository_metadata.repository - if repository.id not in processed_repository_ids: - for revision_metadata in repository.downloadable_revisions: - metadata = revision_metadata.metadata + def generate_statistics( self ): + self.repositories = 0 + self.new_repositories = 0 + self.deleted_repositories = 0 + self.invalid_tools = 0 + self.valid_tools = 0 + self.workflows = 0 + self.proprietary_datatypes = 0 + self.total_clones = 0 + for repository in self.sa_session.query( self.model.Repository ): + self.total_clones += repository.times_downloaded + if repository.deleted: + self.deleted_repositories += 1 + elif repository.is_new: + self.new_repositories += 1 + else: + self.repositories += 1 + for downloadable_revision in repository.downloadable_revisions: + processed_guids = [] + processed_invalid_tool_configs = [] + processed_relative_workflow_paths = [] + processed_datatypes = [] + metadata = downloadable_revision.metadata if 'tools' in metadata: tool_dicts = metadata[ 'tools' ] for tool_dict in tool_dicts: if 'guid' in tool_dict: guid = tool_dict[ 'guid' ] if guid not in processed_guids: - valid_tools += 1 + self.valid_tools += 1 processed_guids.append( guid ) - processed_repository_ids.append( repository.id ) - return valid_tools - + if 'invalid_tools' in metadata: + invalid_tool_configs = metadata[ 'invalid_tools' ] + for invalid_tool_config in invalid_tool_configs: + if invalid_tool_config not in processed_invalid_tool_configs: + self.invalid_tools += 1 + processed_invalid_tool_configs.append( invalid_tool_config ) + if 'datatypes' in metadata: + datatypes = metadata[ 'datatypes' ] + for datatypes_dict in datatypes: + if 'extension' in datatypes_dict: + extension = datatypes_dict[ 'extension' ] + if extension not in processed_datatypes: + self.proprietary_datatypes += 1 + processed_datatypes.append( extension ) + if 'workflows' in metadata: + workflows = metadata[ 'workflows' ] + for workflow_tup in workflows: + relative_path, exported_workflow_dict = workflow_tup + if relative_path not in processed_relative_workflow_paths: + self.workflows += 1 + processed_relative_workflow_paths.append( relative_path ) + self.generation_time = strftime( "%b %d, %Y", gmtime() ) def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ): # A tool shed repository is being installed so change the shed_tool_conf file. Parse the config file to generate the entire list # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have diff -r 12a3c47995d6269f49b4695fb9acc5c7fbf630a9 -r 69aab50e8e18b3cda8ffd9acf4537e01a0c6c31f lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -548,6 +548,15 @@ return self.repository_list_grid( trans, **kwd ) @web.expose @web.require_admin + def regenerate_statistics( self, trans, **kwd ): + if 'regenerate_statistics_button' in kwd: + trans.app.shed_counter.generate_statistics() + message = "Successfully regenerated statistics" + return trans.fill_template( '/webapps/community/admin/statistics.mako', + message=message, + status='done' ) + @web.expose + @web.require_admin def delete_repository( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) diff -r 12a3c47995d6269f49b4695fb9acc5c7fbf630a9 -r 69aab50e8e18b3cda8ffd9acf4537e01a0c6c31f templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -89,6 +89,12 @@ </div></div></div> + <div class="toolSectionTitle"> + Statistics + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='regenerate_statistics', webapp='community' )}">View shed statistics</a> + </div></div></div></div> diff -r 12a3c47995d6269f49b4695fb9acc5c7fbf630a9 -r 69aab50e8e18b3cda8ffd9acf4537e01a0c6c31f templates/webapps/community/admin/statistics.mako --- /dev/null +++ b/templates/webapps/community/admin/statistics.mako @@ -0,0 +1,56 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Tool shed statistics generated on ${trans.app.shed_counter.generation_time}</div> + <form name="regenerate_statistics" id="regenerate_statistics" action="${h.url_for( controller='admin', action='regenerate_statistics', webapp='community' )}" method="post" > + <div class="form-row"> + <table class="grid"> + <tr> + <th>Item</th> + <th>Count</th> + </tr> + <tr> + <td>Total repositories</td> + <td>${trans.app.shed_counter.repositories}</td> + </tr> + <tr> + <td>New repositories</td> + <td>${trans.app.shed_counter.new_repositories}</td> + </tr> + <tr> + <td>Deleted repositories</td> + <td>${trans.app.shed_counter.deleted_repositories}</td> + </tr> + <tr> + <td>Valid tools</td> + <td>${trans.app.shed_counter.valid_tools}</td> + </tr> + <tr> + <td>Invalid tools</td> + <td>${trans.app.shed_counter.invalid_tools}</td> + </tr> + <tr> + <td>Workflows</td> + <td>${trans.app.shed_counter.workflows}</td> + </tr> + <tr> + <td>Proprietary datatypes</td> + <td>${trans.app.shed_counter.proprietary_datatypes}</td> + </tr> + <tr> + <td>Total clones</td> + <td>${trans.app.shed_counter.total_clones}</td> + </tr> + </table> + </div> + <div class="form-row"> + <input type="submit" name="regenerate_statistics_button" value="Regenerate statistics"/> + </div> + </form> + </div> +</div> diff -r 12a3c47995d6269f49b4695fb9acc5c7fbf630a9 -r 69aab50e8e18b3cda8ffd9acf4537e01a0c6c31f templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -39,7 +39,7 @@ <%def name="left_panel()"><div class="unified-panel-header" unselectable="on"> - <div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools} valid tools on ${trans.app.shed_counter.count_time}</div> + <div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools} valid tools on ${trans.app.shed_counter.generation_time}</div></div><div class="page-container" style="padding: 10px;"><div class="toolMenu"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Warn users against navigating away from Galaxy while uploads are in progress, to prevent interrupting uploads.
by Bitbucket 03 Apr '12

03 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/12a3c47995d6/ changeset: 12a3c47995d6 user: natefoo date: 2012-04-03 20:49:28 summary: Warn users against navigating away from Galaxy while uploads are in progress, to prevent interrupting uploads. affected #: 1 file diff -r e7420c93edfab1766ec32a0002adee1dec8d30b3 -r 12a3c47995d6269f49b4695fb9acc5c7fbf630a9 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -84,6 +84,7 @@ $("iframe#galaxy_main").contents().find("body").find("div[class='errormessage']").text( msg ); } } + var uploads_in_progress = 0; jQuery( function() { $("iframe#galaxy_main").load( function() { $(this).contents().find("form").each( function() { @@ -134,7 +135,16 @@ $(this).append("<input type='hidden' name='ajax_upload' value='true'>"); } // iframe submit is required for nginx (otherwise the encoding is wrong) - $(this).ajaxSubmit( { iframe: true } ); + $(this).ajaxSubmit( { iframe: true, + complete: function (xhr, stat) { + uploads_in_progress--; + if (uploads_in_progress == 0) { + window.onbeforeunload = null; + } + } + } ); + uploads_in_progress++; + window.onbeforeunload = function() { return "Navigating away from the Galaxy analysis interface will interrupt the file upload(s) currently in progress. Do you really want to do this?"; } if ( $(this).find("input[name='folder_id']").val() != undefined ) { var library_id = $(this).find("input[name='library_id']").val(); var show_deleted = $(this).find("input[name='show_deleted']").val(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Handle exceptions when resetting all repository metadata in the tool shed.
by Bitbucket 03 Apr '12

03 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e7420c93edfa/ changeset: e7420c93edfa user: greg date: 2012-04-03 20:15:53 summary: Handle exceptions when resetting all repository metadata in the tool shed. affected #: 1 file diff -r e380ade65ea1684025099e4b3543a77d07f3e3fe -r e7420c93edfab1766ec32a0002adee1dec8d30b3 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -464,9 +464,12 @@ count = 0 for repository in trans.sa_session.query( trans.model.Repository ) \ .filter( trans.model.Repository.table.c.deleted == False ): - reset_all_repository_metadata( trans, trans.security.encode_id( repository.id ) ) - log.debug( "Reset metadata on repository %s" % repository.name ) - count += 1 + try: + reset_all_repository_metadata( trans, trans.security.encode_id( repository.id ) ) + log.debug( "Reset metadata on repository %s" % repository.name ) + count += 1 + except Exception, e: + log.debug( "Error attempting to reset metadata on repository %s: %s" % ( repository.name, str( e ) ) ) message = "Reset metadata on %d repositories" % count trans.response.send_redirect( web.url_for( controller='admin', action='browse_repository_metadata', 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: Include invalid tools in repository metadata, and enable the admin to reset all repository metadata.
by Bitbucket 03 Apr '12

03 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e380ade65ea1/ changeset: e380ade65ea1 user: greg date: 2012-04-03 19:52:50 summary: Include invalid tools in repository metadata, and enable the admin to reset all repository metadata. affected #: 5 files diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r e380ade65ea1684025099e4b3543a77d07f3e3fe lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -457,6 +457,24 @@ status=status ) ) @web.expose @web.require_admin + def reset_all_repository_metadata( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + count = 0 + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.deleted == False ): + reset_all_repository_metadata( trans, trans.security.encode_id( repository.id ) ) + log.debug( "Reset metadata on repository %s" % repository.name ) + count += 1 + message = "Reset metadata on %d repositories" % count + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_repository_metadata', + webapp='community', + message=util.sanitize_text( message ), + status=status ) ) + @web.expose + @web.require_admin def browse_repositories( self, trans, **kwd ): # We add params to the keyword dict in this method in order to rename the param # with an "f-" prefix, simulating filtering by clicking a search link. We have diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r e380ade65ea1684025099e4b3543a77d07f3e3fe lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -201,7 +201,7 @@ can_set_metadata = False correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. " correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " - correction_msg += "that includes the required entry to resolve this issue.<br/>" + correction_msg += "that includes the required entry to correct this error.<br/>" invalid_files.append( ( name, correction_msg ) ) if options.index_file or options.missing_index_file: # Make sure the repository contains the required xxx.loc.sample file. @@ -290,6 +290,7 @@ # repository tip, we handle things like .loc.sample files here. metadata_dict = {} invalid_files = [] + invalid_tool_configs = [] sample_files = [] datatypes_config = None # Find datatypes_conf.xml if it exists. @@ -324,6 +325,7 @@ except Exception, e: valid = False invalid_files.append( ( name, str( e ) ) ) + invalid_tool_configs.append( name ) if valid and tool is not None: can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) if can_set_metadata: @@ -331,6 +333,8 @@ tool_config = os.path.join( root, name ) repository_clone_url = generate_clone_url( trans, id ) metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) + else: + invalid_tool_configs.append( name ) # Find all exported workflows elif name.endswith( '.ga' ): try: @@ -344,11 +348,14 @@ metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) + if invalid_tool_configs: + metadata_dict[ 'invalid_tools' ] = invalid_tool_configs return metadata_dict, invalid_files def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision, repo_dir ): # Browse repository files within a change set to generate metadata. metadata_dict = {} invalid_files = [] + invalid_tool_configs = [] sample_files = [] tmp_datatypes_config = None # Find datatypes_conf.xml if it exists. @@ -392,6 +399,7 @@ valid = True except Exception, e: invalid_files.append( ( filename, str( e ) ) ) + invalid_tool_configs.append( filename ) valid = False if valid and tool is not None: # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename @@ -403,6 +411,8 @@ # tip, we do not have to handle any .loc.sample files since they would have been handled previously. repository_clone_url = generate_clone_url( trans, id ) metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict ) + else: + invalid_tool_configs.append( filename ) try: os.unlink( tmp_filename ) except: @@ -417,6 +427,8 @@ metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) + if invalid_tool_configs: + metadata_dict[ 'invalid_tools' ] = invalid_tool_configs return metadata_dict, invalid_files def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ): """Set repository metadata""" diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r e380ade65ea1684025099e4b3543a77d07f3e3fe lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -770,15 +770,14 @@ """ If the received changeset_revision includes a file named readme (case ignored), return it's contents. """ - name = kwd[ 'name' ] - owner = kwd[ 'owner' ] + repository_name = kwd[ 'name' ] + repository_owner = kwd[ 'owner' ] changeset_revision = kwd[ 'changeset_revision' ] - repository = get_repository_by_name_and_owner( trans, name, owner ) + repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) for root, dirs, files in os.walk( repo_dir ): for name in files: - if name.lower() in [ 'readme', 'readme.txt', 'read_me', 'read_me.txt' ]: + if name.lower() in [ 'readme', 'readme.txt', 'read_me', 'read_me.txt', '%s.txt' % repository_name ]: f = open( os.path.join( root, name ), 'r' ) text = f.read() f.close() @@ -1814,6 +1813,81 @@ changeset_revision=changeset_revision, message=message, status='error' ) ) + @web.expose + def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'error' ) + webapp = params.get( 'webapp', 'community' ) + repository = get_repository( trans, repository_id ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) + invalid_message = '' + if changeset_revision == repository.tip: + for root, dirs, files in os.walk( repo_dir ): + found = False + for name in files: + if name == tool_config: + tool_config_path = os.path.join( root, name ) + found = True + break + if found: + break + else: + for filename in ctx: + if filename == tool_config: + fctx = ctx[ filename ] + # Write the contents of datatypes_config.xml to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tool_config_path = fh.name + fh.close() + fh = open( tool_config_path, 'w' ) + fh.write( fctx.data() ) + fh.close() + break + metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, repository_id, ctx, changeset_revision, repo_dir ) + for invalid_file_tup in invalid_files: + invalid_tool_config, invalid_msg = invalid_file_tup + if tool_config == invalid_tool_config: + invalid_message = invalid_msg + break + tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_path ) + tool_state = self.__new_state( trans ) + is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) + if changeset_revision != repository.tip: + try: + os.unlink( tool_config_path ) + except: + pass + try: + if invalid_message: + message = invalid_message + return trans.fill_template( "/webapps/community/repository/tool_form.mako", + repository=repository, + changeset_revision=changeset_revision, + tool=tool, + tool_state=tool_state, + is_malicious=is_malicious, + webapp=webapp, + message=message, + status='error' ) + except Exception, e: + message = "This tool is invalid because: %s." % str( e ) + if webapp == 'galaxy': + return trans.response.send_redirect( web.url_for( controller='repository', + action='preview_tools_in_changeset', + repository_id=repository_id, + changeset_revision=changeset_revision, + message=message, + status='error' ) ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation='view_or_manage_repository', + id=repository_id, + changeset_revision=changeset_revision, + message=message, + status='error' ) ) def __new_state( self, trans, all_pages=False ): """ Create a new `DefaultToolState` for this tool. It will not be initialized diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r e380ade65ea1684025099e4b3543a77d07f3e3fe templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -55,6 +55,9 @@ <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories', webapp='community' )}">Browse all repositories</a></div><div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_all_repository_metadata', webapp='community' )}">Reset all metadata</a> + </div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata', webapp='community' )}">Browse metadata</a></div></div> diff -r a0f64b544cc6412516a62459808e0026d2897dc0 -r e380ade65ea1684025099e4b3543a77d07f3e3fe templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -95,7 +95,7 @@ <div class="form-row"><table width="100%"><tr bgcolor="#D8D8D8" width="100%"> - <td><b>Tools</b><i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i></td> + <td><b>Valid tools</b><i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i></td></tr></table></div> @@ -147,6 +147,31 @@ </div><div style="clear: both"></div> %endif + %if 'invalid_tools' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Invalid tools</b><i> - click the tool config file name to see why the tool is invalid</i></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% invalid_tool_configs = metadata[ 'invalid_tools' ] %> + <table class="grid"> + %for invalid_tool_config in invalid_tool_configs: + <tr> + <td> + <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}"> + ${invalid_tool_config} + </a> + </td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif %if 'workflows' in metadata: ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: In the DistributedObjectStore, when update_from_file is called with create=True, call DistributedObjectStore.create().
by Bitbucket 03 Apr '12

03 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a0f64b544cc6/ changeset: a0f64b544cc6 user: natefoo date: 2012-04-03 17:55:56 summary: In the DistributedObjectStore, when update_from_file is called with create=True, call DistributedObjectStore.create(). affected #: 1 file diff -r 8a572a3e1685e58212533c6141714c323bc67159 -r a0f64b544cc6412516a62459808e0026d2897dc0 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -963,6 +963,9 @@ 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): 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 03 Apr '12

03 Apr '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5fdeb38b1e65/ changeset: 5fdeb38b1e65 user: james_taylor date: 2012-04-03 08:25:52 summary: style: fixes for history state images affected #: 3 files diff -r 243ad28621be905cdd09625520f3fe0ec0424f6d -r 5fdeb38b1e6526296343078e146914e395b8bd47 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1401,8 +1401,6 @@ padding: 0; } -@import "base_sprites"; - .tipsy { padding: 5px; font-size: 10px; @@ -1521,19 +1519,19 @@ div.historyItem-error { // border-color: @history_error_border; background: @history_error_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_error.png; - } + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_error.png; + // } } div.historyItem-empty { // border-color: @history_error_border; background: @history_error_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_empty.png; - } + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_empty.png; + // } } div.historyItem-running { @@ -1561,11 +1559,11 @@ } div.historyItem-queued { - // background: @history_queued_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_queued.png; - } + background: @history_queued_bg; + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_queued.png; + // } } div.historyItem-noPermission { @@ -1681,3 +1679,4 @@ font-weight: bold; } +@import "base_sprites"; diff -r 243ad28621be905cdd09625520f3fe0ec0424f6d -r 5fdeb38b1e6526296343078e146914e395b8bd47 static/june_2007_style/base_sprites.less.tmpl --- a/static/june_2007_style/base_sprites.less.tmpl +++ b/static/june_2007_style/base_sprites.less.tmpl @@ -99,4 +99,20 @@ -sprite-group: fugue; -sprite-image: fugue/control-270.png; -sprite-horiz-position: right; +} + + +div.historyItem-error .state-icon { + -sprite-group: history-states; + -sprite-image: data_error.png; +} + +div.historyItem-empty .state-icon { + -sprite-group: history-states; + -sprite-image: data_empty.png; +} + +div.historyItem-queued .state-icon { + -sprite-group: history-states; + -sprite-image: data_queued.png; } \ No newline at end of file diff -r 243ad28621be905cdd09625520f3fe0ec0424f6d -r 5fdeb38b1e6526296343078e146914e395b8bd47 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -224,7 +224,7 @@ .navbar-form .radio,.navbar-form .checkbox{margin-top:5px;} .navbar-form input[type="image"],.navbar-form input[type="checkbox"],.navbar-form input[type="radio"]{margin-top:3px;} .navbar-search{position:relative;float:left;margin-top:6px;margin-bottom:0;}.navbar-search .search-query{padding:4px 9px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:13px;font-weight:normal;line-height:1;color:#ffffff;color:rgba(255, 255, 255, 0.75);background:#666;background:rgba(255, 255, 255, 0.3);border:1px solid #111;-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1),0 1px 0px rgba(255, 255, 255, 0.15);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1),0 1px 0px rgba(255, 255, 255, 0.15);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1),0 1px 0px rgba(255, 255, 255, 0.15);-webkit-transition:none;-moz-transition:none;-ms-transition:none;-o-transition:none;transition:none;}.navbar-search .search-query :-moz-placeholder{color:#eeeeee;} -.navbar-search .search-query::-webkit-input-placeholder{color:#eeeeee;} +.navbar-search .search-query ::-webkit-input-placeholder{color:#eeeeee;} .navbar-search .search-query:hover{color:#ffffff;background-color:#999999;background-color:rgba(255, 255, 255, 0.5);} .navbar-search .search-query:focus,.navbar-search .search-query.focused{padding:5px 10px;color:#333333;text-shadow:0 1px 0 #ffffff;background-color:#ffffff;border:0;-webkit-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);-moz-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);box-shadow:0 0 3px rgba(0, 0, 0, 0.15);outline:0;} .navbar-fixed-top{position:fixed;top:0;right:0;left:0;z-index:1030;} @@ -677,6 +677,45 @@ .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;} +.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} +.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} +body.historyPage{background:#dfe5f9;color:#303030;margin:5px;border:0;padding:0;} +div.historyLinks{margin:5px 5px;} +div.historyItem{margin:0px -5px;padding:8px 10px;border-top:solid #999999 1px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} +div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} +.historyItemContainer:last-child div.historyItem{border-bottom:solid #999999 1px;} +div.historyItem div.historyItem{margin-right:-11px;} +div.historyItem-ok,div.historyItem-failed_metadata{background:#ccffcc;}div.historyItem-ok .state-icon,div.historyItem-failed_metadata .state-icon{display:none;} +div.historyItem-error{background:#ffcccc;} +div.historyItem-empty{background:#ffcccc;} +div.historyItem-running{background:#ffffcc;}div.historyItem-running .state-icon{background-image:url(data_running.gif);} +div.historyItem-setting_metadata{background:#ffffcc;}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif);} +div.historyItem-upload{background:#ccccff;}div.historyItem-upload .state-icon{background-image:url(data_upload.gif);} +div.historyItem-queued{background:#eeeeee;} +div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} +div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} +div.historyItemButtons{float:right;} +div.historyItemBody div{padding-top:2px;} +pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} +pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} +body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} +hr{border:none;height:0px;margin-top:0px;} +div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} +div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} +div.toolSectionTitle{font-weight:bold;} +div.toolPanelLabel{font-weight:bold;color:gray;text-transform:uppercase;} +div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;} +div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} +div.toolTitleNoSection{padding-bottom:0px;font-weight:bold;} .icon-button.display{background:url(history-buttons.png) no-repeat 0px 0px;} .icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} .icon-button.display_disabled{background:url(history-buttons.png) no-repeat 0px -52px;} @@ -702,42 +741,6 @@ .icon-button.plus-button{background:url(fugue.png) no-repeat 0px -338px;} .icon-button.gear{background:url(fugue.png) no-repeat 0px -364px;} .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -390px;} -.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;} -.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} -.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} -body.historyPage{background:#dfe5f9;color:#303030;margin:5px;border:0;padding:0;} -div.historyLinks{margin:5px 5px;} -div.historyItem{margin:0px -5px;padding:8px 10px;border-top:solid #999999 1px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} -div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} -.historyItemContainer:last-child div.historyItem{border-bottom:solid #999999 1px;} -div.historyItem div.historyItem{margin-right:-11px;} -div.historyItem-ok,div.historyItem-failed_metadata{background:#ccffcc;}div.historyItem-ok .state-icon,div.historyItem-failed_metadata .state-icon{display:none;} -div.historyItem-error{background:#ffcccc;}div.historyItem-error .state-icon{-sprite-group:history-states;-sprite-image:data_error.png;} -div.historyItem-empty{background:#ffcccc;}div.historyItem-empty .state-icon{-sprite-group:history-states;-sprite-image:data_empty.png;} -div.historyItem-running{background:#ffffcc;}div.historyItem-running .state-icon{background-image:url(data_running.gif);} -div.historyItem-setting_metadata{background:#ffffcc;}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif);} -div.historyItem-upload{background:#ccccff;}div.historyItem-upload .state-icon{background-image:url(data_upload.gif);} -div.historyItem-queued .state-icon{-sprite-group:history-states;-sprite-image:data_queued.png;} -div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} -div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} -div.historyItemButtons{float:right;} -div.historyItemBody div{padding-top:2px;} -pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} -pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} -body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} -hr{border:none;height:0px;margin-top:0px;} -div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} -div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} -div.toolSectionTitle{font-weight:bold;} -div.toolPanelLabel{font-weight:bold;color:gray;text-transform:uppercase;} -div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;} -div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} -div.toolTitleNoSection{padding-bottom:0px;font-weight:bold;} +div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px 0px;} +div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} +div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} https://bitbucket.org/galaxy/galaxy-central/changeset/8a572a3e1685/ changeset: 8a572a3e1685 user: james_taylor date: 2012-04-03 08:29:00 summary: merge affected #: 3 files diff -r 1200112cd51a35c47b9a35bd055dc4c825983cd5 -r 8a572a3e1685e58212533c6141714c323bc67159 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1422,8 +1422,6 @@ padding: 0; } -@import "base_sprites"; - .tipsy { padding: 5px; font-size: 10px; @@ -1542,19 +1540,19 @@ div.historyItem-error { // border-color: @history_error_border; background: @history_error_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_error.png; - } + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_error.png; + // } } div.historyItem-empty { // border-color: @history_error_border; background: @history_error_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_empty.png; - } + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_empty.png; + // } } div.historyItem-running { @@ -1582,11 +1580,11 @@ } div.historyItem-queued { - // background: @history_queued_bg; - .state-icon { - -sprite-group: history-states; - -sprite-image: data_queued.png; - } + background: @history_queued_bg; + // .state-icon { + // -sprite-group: history-states; + // -sprite-image: data_queued.png; + // } } div.historyItem-noPermission { @@ -1695,3 +1693,4 @@ font-weight: bold; } +@import "base_sprites"; diff -r 1200112cd51a35c47b9a35bd055dc4c825983cd5 -r 8a572a3e1685e58212533c6141714c323bc67159 static/june_2007_style/base_sprites.less.tmpl --- a/static/june_2007_style/base_sprites.less.tmpl +++ b/static/june_2007_style/base_sprites.less.tmpl @@ -103,4 +103,20 @@ -sprite-group: fugue; -sprite-image: fugue/control-270.png; -sprite-horiz-position: right; +} + + +div.historyItem-error .state-icon { + -sprite-group: history-states; + -sprite-image: data_error.png; +} + +div.historyItem-empty .state-icon { + -sprite-group: history-states; + -sprite-image: data_empty.png; +} + +div.historyItem-queued .state-icon { + -sprite-group: history-states; + -sprite-image: data_queued.png; } \ No newline at end of file diff -r 1200112cd51a35c47b9a35bd055dc4c825983cd5 -r 8a572a3e1685e58212533c6141714c323bc67159 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -682,6 +682,44 @@ .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;} +.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} +.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} +body.historyPage{background:#dfe5f9;color:#303030;margin:5px;border:0;padding:0;} +div.historyLinks{margin:5px 5px;} +div.historyItem{margin:0px -5px;padding:8px 10px;border-top:solid #999999 1px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} +div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} +.historyItemContainer:last-child div.historyItem{border-bottom:solid #999999 1px;} +div.historyItem div.historyItem{margin-right:-11px;} +div.historyItem-ok,div.historyItem-failed_metadata{background:#ccffcc;}div.historyItem-ok .state-icon,div.historyItem-failed_metadata .state-icon{display:none;} +div.historyItem-error{background:#ffcccc;} +div.historyItem-empty{background:#ffcccc;} +div.historyItem-running{background:#ffffcc;}div.historyItem-running .state-icon{background-image:url(data_running.gif);} +div.historyItem-setting_metadata{background:#ffffcc;}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif);} +div.historyItem-upload{background:#ccccff;}div.historyItem-upload .state-icon{background-image:url(data_upload.gif);} +div.historyItem-queued{background:#eeeeee;} +div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} +div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} +div.historyItemButtons{float:right;} +div.historyItemBody div{padding-top:2px;} +pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} +pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} +body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} +div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} +div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} +div.toolSectionTitle{font-weight:bold;} +div.toolPanelLabel{font-weight:bold;color:gray;text-transform:uppercase;} +div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;} +div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} +div.toolTitleNoSection{padding-bottom:0px;font-weight:bold;} .icon-button.display{background:url(history-buttons.png) no-repeat 0px 0px;} .icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} .icon-button.display_disabled{background:url(history-buttons.png) no-repeat 0px -52px;} @@ -708,41 +746,6 @@ .icon-button.gear{background:url(fugue.png) no-repeat 0px -364px;} .icon-button.chart_curve{background:url(fugue.png) no-repeat 0px -390px;} .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -416px;} -.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;} -.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} -.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px;} -body.historyPage{background:#dfe5f9;color:#303030;margin:5px;border:0;padding:0;} -div.historyLinks{margin:5px 5px;} -div.historyItem{margin:0px -5px;padding:8px 10px;border-top:solid #999999 1px;border-right:none;word-wrap:break-word;background:#eeeeee;}div.historyItem .state-icon{display:inline-block;vertical-align:middle;width:16px;height:16px;background-position:0 1px;background-repeat:no-repeat;} -div.historyItem .historyItemTitle{font-weight:bold;line-height:16px;} -.historyItemContainer:last-child div.historyItem{border-bottom:solid #999999 1px;} -div.historyItem div.historyItem{margin-right:-11px;} -div.historyItem-ok,div.historyItem-failed_metadata{background:#ccffcc;}div.historyItem-ok .state-icon,div.historyItem-failed_metadata .state-icon{display:none;} -div.historyItem-error{background:#ffcccc;}div.historyItem-error .state-icon{-sprite-group:history-states;-sprite-image:data_error.png;} -div.historyItem-empty{background:#ffcccc;}div.historyItem-empty .state-icon{-sprite-group:history-states;-sprite-image:data_empty.png;} -div.historyItem-running{background:#ffffcc;}div.historyItem-running .state-icon{background-image:url(data_running.gif);} -div.historyItem-setting_metadata{background:#ffffcc;}div.historyItem-setting_metadata .state-icon{background-image:url(data_running.gif);} -div.historyItem-upload{background:#ccccff;}div.historyItem-upload .state-icon{background-image:url(data_upload.gif);} -div.historyItem-queued .state-icon{-sprite-group:history-states;-sprite-image:data_queued.png;} -div.historyItem-noPermission{filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60;} -div.historyItemTitleBar.spinner .state-icon{background:url(data_running.gif) 0 1px no-repeat !important;} -div.historyItemButtons{float:right;} -div.historyItemBody div{padding-top:2px;} -pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} -pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} -body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} -div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} -div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} -div.toolSectionTitle{font-weight:bold;} -div.toolPanelLabel{font-weight:bold;color:gray;text-transform:uppercase;} -div.toolTitle{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:square outside;} -div.toolSectionBody div.toolPanelLabel{padding-top:5px;padding-bottom:5px;margin-left:16px;margin-right:10px;display:list-item;list-style:none outside;} -div.toolTitleNoSection{padding-bottom:0px;font-weight:bold;} +div.historyItem-error .state-icon{background:url(history-states.png) no-repeat 0px 0px;} +div.historyItem-empty .state-icon{background:url(history-states.png) no-repeat 0px -25px;} +div.historyItem-queued .state-icon{background:url(history-states.png) no-repeat 0px -50px;} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Fix inflector for n == 0
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1200112cd51a/ changeset: 1200112cd51a user: dannon date: 2012-04-02 22:58:16 summary: Fix inflector for n == 0 affected #: 1 file diff -r 3f9b7d8a617d60cc319d6e00c485839fc1ec4e6c -r 1200112cd51a35c47b9a35bd055dc4c825983cd5 lib/galaxy/util/inflection.py --- a/lib/galaxy/util/inflection.py +++ b/lib/galaxy/util/inflection.py @@ -14,7 +14,7 @@ def cond_plural(self, number_of_records, word) : '''Returns the plural form of a word if first parameter is greater than 1''' - if number_of_records > 1 : + if number_of_records != 1: return self.pluralize(word) else : return word @@ -385,4 +385,4 @@ # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THIS SOFTWARE OR THE USE OR OTHER DEALINGS IN -# THIS SOFTWARE. \ No newline at end of file +# THIS SOFTWARE. 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: Fix variable name bug that occurred when rendering tool links outside a section.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3f9b7d8a617d/ changeset: 3f9b7d8a617d user: jgoecks date: 2012-04-02 22:25:17 summary: Fix variable name bug that occurred when rendering tool links outside a section. affected #: 2 files diff -r 2ec5e00abdc56eb3bd0c453cfc5e7707c7aab593 -r 3f9b7d8a617d60cc319d6e00c485839fc1ec4e6c static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ b/static/scripts/backbone/tools.js @@ -355,7 +355,7 @@ this_el.append(section_title_view.$el); } else if (panel_elt instanceof Tool) { - var tool_view = new ToolLinkView({model: elt, className: "toolTitleNoSection"}); + var tool_view = new ToolLinkView({model: panel_elt, className: "toolTitleNoSection"}); tool_view.render(); this_el.append(tool_view.$el); } diff -r 2ec5e00abdc56eb3bd0c453cfc5e7707c7aab593 -r 3f9b7d8a617d60cc319d6e00c485839fc1ec4e6c static/scripts/packed/backbone/tools.js --- a/static/scripts/packed/backbone/tools.js +++ b/static/scripts/packed/backbone/tools.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this)},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.$el.children(".toolSectionBody").toggle("fast");this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").show("fast"):this.$el.children(".toolSectionBody").hide("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:elt,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file +var BaseModel=Backbone.Model.extend({defaults:{id:null,name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,params:[]},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()}});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{spinner_url:"",search_url:"",visible:true,query:"",results:null},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<3){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide()},"json")},200)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this)},clear_search_results:function(){this.each(function(a){a.clear_search_results()})},apply_search_results:function(){var a=this.tool_search.attributes.results;if(a===null){this.clear_search_results();return}this.each(function(b){b.apply_search_results(a)})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this)},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",template:Handlebars.templates.panel_label,render:function(){this.$el.append(this.template(this.model.toJSON()));return this},});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.$el.children(".toolSectionBody").toggle("fast");this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").show("fast"):this.$el.children(".toolSectionBody").hide("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},query_changed:function(){this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(a){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var b=this.$el;var a=new ToolSearchView({model:this.collection.tool_search});a.render();b.append(a.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();b.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();b.append(e.$el)}}});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Make sure a valid tool has a guid.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2ec5e00abdc5/ changeset: 2ec5e00abdc5 user: greg date: 2012-04-02 22:16:37 summary: Make sure a valid tool has a guid. affected #: 1 file diff -r 080242921d9fb538b280a31260c687a0053a3eb7 -r 2ec5e00abdc56eb3bd0c453cfc5e7707c7aab593 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -45,10 +45,11 @@ if 'tools' in metadata: tool_dicts = metadata[ 'tools' ] for tool_dict in tool_dicts: - guid = tool_dict[ 'guid' ] - if guid not in processed_guids: - valid_tools += 1 - processed_guids.append( guid ) + if 'guid' in tool_dict: + guid = tool_dict[ 'guid' ] + if guid not in processed_guids: + valid_tools += 1 + processed_guids.append( guid ) processed_repository_ids.append( repository.id ) return valid_tools Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add a counter utility to the tool shed.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/080242921d9f/ changeset: 080242921d9f user: greg date: 2012-04-02 22:13:08 summary: Add a counter utility to the tool shed. affected #: 7 files diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,6 +1,6 @@ import os, tempfile, shutil, subprocess, logging, string from datetime import date, datetime, timedelta -from time import strftime +from time import strftime, gmtime from galaxy import util from galaxy.datatypes.checkers import * from galaxy.util.json import * @@ -21,6 +21,37 @@ '\'' : ''' } VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) +class ShedCounter( object ): + def __init__( self, model ): + self.model = model + self.count_time = strftime( "%b %d, %Y", gmtime() ) + self.valid_tools = self.count_valid_tools() + @property + def sa_session( self ): + """Returns a SQLAlchemy session""" + return self.model.context + def count_valid_tools( self ): + valid_tools = 0 + processed_repository_ids = [] + for repository_metadata in self.sa_session.query( self.model.RepositoryMetadata ) \ + .filter( and_( self.model.RepositoryMetadata.table.c.malicious == False, + self.model.RepositoryMetadata.table.c.metadata is not None, + self.model.RepositoryMetadata.table.c.tool_versions is not None ) ): + processed_guids = [] + repository = repository_metadata.repository + if repository.id not in processed_repository_ids: + for revision_metadata in repository.downloadable_revisions: + metadata = revision_metadata.metadata + if 'tools' in metadata: + tool_dicts = metadata[ 'tools' ] + for tool_dict in tool_dicts: + guid = tool_dict[ 'guid' ] + if guid not in processed_guids: + valid_tools += 1 + processed_guids.append( guid ) + processed_repository_ids.append( repository.id ) + return valid_tools + def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ): # A tool shed repository is being installed so change the shed_tool_conf file. Parse the config file to generate the entire list # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -43,6 +43,8 @@ # Load security policy self.security_agent = self.model.security_agent self.quota_agent = galaxy.quota.NoQuotaAgent( self.model ) - self.openid_providers = OpenIDProviders() #TODO: Add OpenID support + # TODO: Add OpenID support + self.openid_providers = OpenIDProviders() + self.shed_counter = self.model.shed_counter def shutdown( self ): pass diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -321,7 +321,7 @@ def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository repo = hg.repository( get_configured_ui(), repository.repo_path ) - ctx = get_changectx_for_changeset( trans, repo, repository_metadata.changeset_revision ) + ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) class ToolsColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -140,7 +140,7 @@ changeset rev and the changeset revision string. """ repo = hg.repository( get_configured_ui(), repository.repo_path ) - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) else: @@ -425,7 +425,7 @@ repository = get_repository( trans, id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) metadata_dict = {} invalid_files = [] if ctx is not None: @@ -514,7 +514,7 @@ ancestor_metadata_dict = None for changeset in repo.changelog: current_changeset_revision = str( repo.changectx( changeset ) ) - ctx = get_changectx_for_changeset( trans, repo, current_changeset_revision ) + ctx = get_changectx_for_changeset( repo, current_changeset_revision ) if current_changeset_revision == repository.tip: current_metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, id, ctx, current_changeset_revision, repo_dir ) else: @@ -740,7 +740,7 @@ def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() -def get_changectx_for_changeset( trans, repo, changeset_revision, **kwd ): +def get_changectx_for_changeset( repo, changeset_revision, **kwd ): """Retrieve a specified changectx from a repository""" for changeset in repo.changelog: ctx = repo.changectx( changeset ) @@ -963,7 +963,7 @@ # Get the tool config file name from the hgweb url, something like: # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml old_tool_config_file_name = tool_config.split( '/' )[ -1 ] - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) fctx = None for filename in ctx: filename_head, filename_tail = os.path.split( filename ) @@ -1001,7 +1001,7 @@ refresh_on_change_values = [] for repository_metadata in repository.downloadable_revisions: changeset_revision = repository_metadata.changeset_revision - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: rev = '%04d' % ctx.rev() label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -854,7 +854,7 @@ repo = hg.repository( get_configured_ui(), repo_dir ) # Load each tool in the repository's changeset_revision to generate a list of # tool guids, since guids differentiate tools by id and version. - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx is not None: tool_guids = [] for filename in ctx: @@ -1579,7 +1579,7 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) - ctx = get_changectx_for_changeset( trans, repo, ctx_str ) + ctx = get_changectx_for_changeset( repo, ctx_str ) if ctx is None: message = "Repository does not include changeset revision '%s'." % str( ctx_str ) status = 'error' diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -13,6 +13,7 @@ from galaxy.model.orm.ext.assignmapper import * from galaxy.model.custom_types import * from galaxy.util.bunch import Bunch +from galaxy.util.shed_util import ShedCounter from galaxy.webapps.community.security import CommunityRBACAgent metadata = MetaData() @@ -247,4 +248,5 @@ result.create_tables = create_tables #load local galaxy security policy result.security_agent = CommunityRBACAgent( result ) + result.shed_counter = ShedCounter( result ) return result diff -r babda116a4c0193c2ee4941d09ac78940098fece -r 080242921d9fb538b280a31260c687a0053a3eb7 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -39,7 +39,7 @@ <%def name="left_panel()"><div class="unified-panel-header" unselectable="on"> - <div class='unified-panel-header-inner'>Galaxy Tool Shed</div> + <div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools} valid tools on ${trans.app.shed_counter.count_time}</div></div><div class="page-container" style="padding: 10px;"><div class="toolMenu"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: I missed a call to a renamed method in the job manager.
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/babda116a4c0/ changeset: babda116a4c0 user: natefoo date: 2012-04-02 21:38:02 summary: I missed a call to a renamed method in the job manager. affected #: 1 file diff -r 07eb5affb4c0c74f1bf95d2fb850f926d4defaf2 -r babda116a4c0193c2ee4941d09ac78940098fece lib/galaxy/jobs/manager.py --- a/lib/galaxy/jobs/manager.py +++ b/lib/galaxy/jobs/manager.py @@ -89,7 +89,7 @@ log.warning( "(%s) Tool '%s' removed from tool config, unable to recover job" % ( job.id, job.tool_id ) ) JobWrapper( job, self ).fail( 'This tool was disabled before the job completed. Please contact your Galaxy administrator.' ) else: - job.handler = self.__select_handler( job ) # handler's recovery method will take it from here + job.handler = self.__get_handler( job ) # handler's recovery method will take it from here log.info( "(%d) Job in '%s' state had no handler at job manager startup, assigned '%s' handler" % ( job.id, job.state, job.handler ) ) if self.sa_session.dirty: self.sa_session.flush() 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: richard_burhans: changes to aaChanges interface
by Bitbucket 02 Apr '12

02 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/07eb5affb4c0/ changeset: 07eb5affb4c0 user: richard_burhans date: 2012-04-02 20:28:08 summary: changes to aaChanges interface affected #: 1 file diff -r 758f425498670dbe992701df81d277dbc7cd6de7 -r 07eb5affb4c0c74f1bf95d2fb850f926d4defaf2 tools/evolution/codingSnps.xml --- a/tools/evolution/codingSnps.xml +++ b/tools/evolution/codingSnps.xml @@ -2,7 +2,7 @@ <description>amino-acid changes caused by a set of SNPs</description><command interpreter="perl"> - codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep strand=${strand_source.strand_col} > $out_file1 + codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep strand=${strand_source.strand_col} unique=$uniqpos > $out_file1 </command><inputs> @@ -17,6 +17,10 @@ <option value="0" selected="true">No</option><option value="1">Yes</option></param> + <param name="uniqpos" type="select" label="Only report each SNP position once"> + <option value="1" selected="true">Yes</option> + <option value="0">No</option> + </param><conditional name="strand_source"><param name="strand_choice" type="select" label="Strand info"><option value="data_column">a column in the dataset</option> @@ -54,6 +58,7 @@ <param name="input2" ftype="interval" value="codingSnps_inputGenes1.bed" dbkey="hg18" /><param name="strand_choice" value="all_pos" /><param name="strand_col" value="+" /> + <param name="uniqpos" value="0" /><output name="output" file="codingSnps_output1.interval" /></test><test> @@ -62,6 +67,7 @@ <param name="col1" value="4" /><param name="strand_choice" value="all_pos" /><param name="strand_col" value="+" /> + <param name="uniqpos" value="0" /><output name="output" file="codingSnps_output2.interval" /></test><test> 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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