galaxy-commits August 2011

galaxy-commits@lists.galaxyproject.org

1 participants
106 discussions

commit/galaxy-central: dan: pdate EuPathDB datasource configuration file. Contributed by Mark Heiges.
by Bitbucket 23 Aug '11

23 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9de21817a7a5/ changeset: 9de21817a7a5 user: dan date: 2011-08-22 20:03:57 summary: pdate EuPathDB datasource configuration file. Contributed by Mark Heiges. affected #: 1 file (4 bytes) --- a/tools/data_source/eupathdb.xml Mon Aug 22 10:45:22 2011 -0400 +++ b/tools/data_source/eupathdb.xml Mon Aug 22 14:03:57 2011 -0400 @@ -7,7 +7,7 @@ </inputs><uihints minwidth="800"/><outputs> - <data name="output" format="txt" /> + <data name="output" format="tabular" /></outputs><options sanitize="False" refresh="True"/></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Add helper.py (posted to the -dev list as "galaxythinger.py" in the past), a command line tool for performing a couple common operations like encoding/decoding IDs and getting the disk path of HDAs.
by Bitbucket 22 Aug '11

22 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0f878ea61e98/ changeset: 0f878ea61e98 user: natefoo date: 2011-08-22 16:45:22 summary: Add helper.py (posted to the -dev list as "galaxythinger.py" in the past), a command line tool for performing a couple common operations like encoding/decoding IDs and getting the disk path of HDAs. affected #: 1 file (0 bytes) 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: kanwei: Spacing fix
by Bitbucket 20 Aug '11

20 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/fa7159dcb42e/ changeset: fa7159dcb42e user: kanwei date: 2011-08-20 08:56:33 summary: Spacing fix affected #: 2 files (0 bytes) --- a/lib/galaxy/web/form_builder.py Sat Aug 20 14:27:30 2011 +1000 +++ b/lib/galaxy/web/form_builder.py Sat Aug 20 02:56:33 2011 -0400 @@ -191,9 +191,9 @@ def get_html( self, prefix="" ): rval = FTPFileField.thead if self.dir is None: - rval += '<tr><td colspan="3"><em>Please <a href="%s">create</a> or <a href="%s">log in to</a> a Galaxy account to view files uploaded via FTP.</em></td></tr>' % ( url_for( controller='user', action='create', cntrller='user', referer=url_for( controller='root' ) ), url_for( controller='user', action='login', cntrller='user', referer=url_for( controller='root' ) ) ) + rval += '<tr><td colspan="4"><em>Please <a href="%s">create</a> or <a href="%s">log in to</a> a Galaxy account to view files uploaded via FTP.</em></td></tr>' % ( url_for( controller='user', action='create', cntrller='user', referer=url_for( controller='root' ) ), url_for( controller='user', action='login', cntrller='user', referer=url_for( controller='root' ) ) ) elif not os.path.exists( self.dir ): - rval += '<tr><td colspan="3"><em>Your FTP upload directory contains no files.</em></td></tr>' + rval += '<tr><td colspan="4"><em>Your FTP upload directory contains no files.</em></td></tr>' else: uploads = [] for ( dirpath, dirnames, filenames ) in os.walk( self.dir ): @@ -204,7 +204,7 @@ size=nice_size( statinfo.st_size ), ctime=time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) if not uploads: - rval += '<tr><td colspan="3"><em>Your FTP upload directory contains no files.</em></td></tr>' + rval += '<tr><td colspan="4"><em>Your FTP upload directory contains no files.</em></td></tr>' for upload in uploads: rval += FTPFileField.trow % ( prefix, self.name, upload['path'], upload['path'], upload['size'], upload['ctime'] ) rval += FTPFileField.tfoot --- a/tools/data_source/upload.xml Sat Aug 20 14:27:30 2011 +1000 +++ b/tools/data_source/upload.xml Sat Aug 20 02:56:33 2011 -0400 @@ -177,7 +177,7 @@ **MAF** -TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated "variable=value pairs". There should be no white space surrounding the "=". +TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated "variable=value" pairs. There should be no white space surrounding the "=". ----- 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: fubar: WebLogo3 wrapper repair to a string format edge case. Reports are good for finding these - user hadn't reported...
by Bitbucket 20 Aug '11

20 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a9b3f9b82e84/ changeset: a9b3f9b82e84 user: fubar date: 2011-08-20 06:27:30 summary: WebLogo3 wrapper repair to a string format edge case. Reports are good for finding these - user hadn't reported... affected #: 1 file (7 bytes) --- a/tools/rgenetics/rgWebLogo3.py Fri Aug 19 14:37:51 2011 -0400 +++ b/tools/rgenetics/rgWebLogo3.py Sat Aug 20 14:27:30 2011 +1000 @@ -43,11 +43,6 @@ tlf = open(templog,'w') process = subprocess.Popen(cl, shell=True, stderr=tlf, stdout=tlf) rval = process.wait() - if rval <> 0: - print >> sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % cl - print >> sys.stderr, '## This may be a data problem or a tool dependency (%s) installation problem' % WEBLOGO - print >> sys.stderr, '## Please ensure %s is correctly installed and working on the command line -see http://code.google.com/p/weblogo' % WEBLOGO - sys.exit(1) tlf.close() tlogs = ''.join(open(templog,'r').readlines()) if len(tlogs) > 1: @@ -55,6 +50,11 @@ else: s = '## executing %s returned status %d. Nothing appeared on stderr/stdout\n' % (cl,rval) os.unlink(templog) # always + if rval <> 0: + print >> sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % (cl,rval) + print >> sys.stderr, '## This may be a data problem or a tool dependency (%s) installation problem' % WEBLOGO + print >> sys.stderr, '## Please ensure %s is correctly installed and working on the command line -see http://code.google.com/p/weblogo' % WEBLOGO + sys.exit(1) return s Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by Bitbucket 20 Aug '11

20 Aug '11

3 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c5fa48633c0b/ changeset: c5fa48633c0b branch: job_scripts user: peterjc date: 2011-07-29 15:18:15 summary: Catch problems creating job script affected #: 1 file (248 bytes) --- a/lib/galaxy/jobs/runners/drmaa.py Thu Jul 28 11:50:56 2011 -0400 +++ b/lib/galaxy/jobs/runners/drmaa.py Fri Jul 29 14:18:15 2011 +0100 @@ -156,10 +156,15 @@ jt.nativeSpecification = native_spec script = drm_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) - fh = file( jt.remoteCommand, "w" ) - fh.write( script ) - fh.close() - os.chmod( jt.remoteCommand, 0750 ) + try: + fh = file( jt.remoteCommand, "w" ) + fh.write( script ) + fh.close() + os.chmod( jt.remoteCommand, 0750 ) + except: + job_wrapper.fail( "failure preparing job script", exception=True ) + log.exception("failure running job %s" % job_wrapper.get_id_tag()) + return # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: http://bitbucket.org/galaxy/galaxy-central/changeset/769e04ccce29/ changeset: 769e04ccce29 branch: job_scripts user: natefoo date: 2011-08-19 19:30:21 summary: Closed branch job_scripts affected #: 0 files (0 bytes) http://bitbucket.org/galaxy/galaxy-central/changeset/8d8d9e8ef1a0/ changeset: 8d8d9e8ef1a0 user: natefoo date: 2011-08-19 19:30:36 summary: merge affected #: 1 file (248 bytes) --- a/lib/galaxy/jobs/runners/drmaa.py Thu Aug 18 14:20:48 2011 -0400 +++ b/lib/galaxy/jobs/runners/drmaa.py Fri Aug 19 13:30:36 2011 -0400 @@ -156,10 +156,15 @@ jt.nativeSpecification = native_spec script = drm_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) - fh = file( jt.remoteCommand, "w" ) - fh.write( script ) - fh.close() - os.chmod( jt.remoteCommand, 0750 ) + try: + fh = file( jt.remoteCommand, "w" ) + fh.write( script ) + fh.close() + os.chmod( jt.remoteCommand, 0750 ) + except: + job_wrapper.fail( "failure preparing job script", exception=True ) + log.exception("failure running job %s" % job_wrapper.get_id_tag()) + return # job was deleted while we were preparing it if job_wrapper.get_state() == model.Job.states.DELETED: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Add wrapper for Trinity, the de novo RNA-seq transcript assembler (http://http://trinityrnaseq.sourceforge.net/).
by Bitbucket 19 Aug '11

19 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c4a82d645370/ changeset: c4a82d645370 user: jgoecks date: 2011-08-18 20:20:48 summary: Add wrapper for Trinity, the de novo RNA-seq transcript assembler (http://http://trinityrnaseq.sourceforge.net/). affected #: 2 files (105 bytes) --- a/tool_conf.xml.sample Thu Aug 18 14:01:28 2011 -0400 +++ b/tool_conf.xml.sample Thu Aug 18 14:20:48 2011 -0400 @@ -335,6 +335,8 @@ <tool file="ngs_rna/cufflinks_wrapper.xml" /><tool file="ngs_rna/cuffcompare_wrapper.xml" /><tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <label text="De novo Assembly" id="de_novo_assembly "/> + <tool file="ngs_rna/trinity_all.xml" /><label text="Filtering" id="filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Quota display nice_size bugfixes.
by Bitbucket 19 Aug '11

19 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/59beb8e9290d/ changeset: 59beb8e9290d user: natefoo date: 2011-08-18 20:01:28 summary: Quota display nice_size bugfixes. affected #: 1 file (72 bytes) --- a/lib/galaxy/quota/__init__.py Thu Aug 18 13:51:02 2011 -0400 +++ b/lib/galaxy/quota/__init__.py Thu Aug 18 14:01:28 2011 -0400 @@ -60,11 +60,13 @@ use_default = True max = 0 adjustment = 0 + rval = 0 for quota in quotas: if quota.deleted: continue if quota.operation == '=' and quota.bytes == -1: - return None + rval = None + break elif quota.operation == '=': use_default = False if quota.bytes > max: @@ -76,16 +78,17 @@ if use_default: max = self.default_registered_quota if max is None: - return None - quota = max + adjustment - if quota <= 0: - quota = 0 + rval = None + if rval is not None: + rval = max + adjustment + if rval <= 0: + rval = 0 if nice_size: - if quota is not None: - quota = util.nice_size( quota ) + if rval is not None: + rval = util.nice_size( rval ) else: - quota = 'unlimited' - return quota + rval = 'unlimited' + return rval @property def default_unregistered_quota( self ): return self._default_quota( self.model.DefaultQuotaAssociation.types.UNREGISTERED ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Enhancements and fixes for working with versions of repository tools in the tool shed.
by Bitbucket 19 Aug '11

19 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4e3494acdb97/ changeset: 4e3494acdb97 user: greg date: 2011-08-18 19:51:02 summary: Enhancements and fixes for working with versions of repository tools in the tool shed. affected #: 13 files (6.6 KB) --- a/lib/galaxy/webapps/community/controllers/admin.py Thu Aug 18 13:13:35 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Thu Aug 18 13:51:02 2011 -0400 @@ -347,7 +347,7 @@ title = "Repository Metadata" model_class = model.RepositoryMetadata template='/webapps/community/repository/grid.mako' - default_sort_key = "repository_id" + default_sort_key = "name" columns = [ IdColumn( "Id", visible=False, @@ -355,8 +355,8 @@ NameColumn( "Name", key="name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", - id=item.repository.id, + link=( lambda item: dict( operation="view_or_manage_repository_revision", + id=item.id, webapp="community" ) ), attach_popup=True ), RevisionColumn( "Revision", @@ -396,7 +396,15 @@ operation = kwd[ 'operation' ].lower() if operation == "delete": return self.delete_repository_metadata( trans, **kwd ) - if operation == "view_or_manage_repository": + if operation == "view_or_manage_repository_revision": + # The received id is a RepositoryMetadata object id, so we need to get the + # associated Repository and redirect to view_or_manage_repository with the + # changeset_revision. + repository_metadata = get_repository_metadata_by_id( trans, kwd[ 'id' ] ) + repository = repository_metadata.repository + kwd[ 'id' ] = trans.security.encode_id( repository.id ) + kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision + kwd[ 'operation' ] = 'view_or_manage_repository' return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', **kwd ) ) --- a/lib/galaxy/webapps/community/controllers/common.py Thu Aug 18 13:13:35 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Thu Aug 18 13:51:02 2011 -0400 @@ -81,13 +81,24 @@ def get_repository_metadata_by_id( trans, id ): """Get repository metadata from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) +def get_revision_label( trans, repository, changeset_revision ): + """ + Return a string consisting of the human read-able + 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 ) + if ctx: + return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + return "-1:%s" % changeset_revision def get_latest_repository_metadata( trans, id ): """Get last metadata defined for a specified repository from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ) \ .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ .order_by( trans.model.RepositoryMetadata.table.c.update_time.desc() ) \ .first() -def generate_workflow_metadata( trans, id, change_set_revision, exported_workflow_dict, metadata_dict ): +def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): """ Update the received metadata_dict with changes that have been applied to the received exported_workflow_dict. Store everything except the @@ -120,7 +131,7 @@ # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table # record is not needed. return False -def generate_tool_metadata( trans, id, change_set_revision, root, name, tool, metadata_dict ): +def generate_tool_metadata( trans, id, changeset_revision, root, name, tool, metadata_dict ): """ Update the received metadata_dict with changes that have been applied to the received tool. @@ -163,15 +174,25 @@ if repository_metadata: metadata = repository_metadata.metadata if metadata and 'tools' in metadata: + saved_tool_ids = [] # The metadata for one or more tools was successfully generated in the past - # for this repository, so we compare the version string for each tool id + # for this repository, so we first compare the version string for each tool id # in metadata_dict with what was previously saved to see if we need to create # a new table record or if we can simply update the existing record. for new_tool_metadata_dict in metadata_dict[ 'tools' ]: for saved_tool_metadata_dict in metadata[ 'tools' ]: + if saved_tool_metadata_dict[ 'id' ] not in saved_tool_ids: + saved_tool_ids.append( saved_tool_metadata_dict[ 'id' ] ) if new_tool_metadata_dict[ 'id' ] == saved_tool_metadata_dict[ 'id' ]: if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]: return True + # So far, a new metadata record is not required, but we still have to check to see if + # any new tool ids exist in metadata_dict that are not in the saved metadata. We do + # this because if a new tarball was uploaded to a repository that included tools, it + # may have removed existing tool files if they were not included in the uploaded tarball. + for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids: + return True else: # We have repository metadata that does not include metadata for any tools in the # repository, so we can update the existing repository metadata. @@ -183,7 +204,7 @@ # The received metadata_dict includes no metadata for tools, so a new repository_metadata table # record is not needed. return False -def set_repository_metadata( trans, id, change_set_revision, **kwd ): +def set_repository_metadata( trans, id, changeset_revision, **kwd ): """Set repository metadata""" message = '' status = 'done' @@ -191,7 +212,7 @@ repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) invalid_files = [] - ctx = get_changectx_for_changeset( trans, repo, change_set_revision ) + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) if ctx is not None: metadata_dict = {} for root, dirs, files in os.walk( repo_dir ): @@ -211,7 +232,7 @@ tool = load_tool( trans, full_path ) if tool is not None: # Update the list metadata dictionaries for tools in metadata_dict. - metadata_dict = generate_tool_metadata( trans, id, change_set_revision, root, name, tool, metadata_dict ) + metadata_dict = generate_tool_metadata( trans, id, changeset_revision, root, name, tool, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) # Find all exported workflows @@ -224,27 +245,28 @@ fp.close() exported_workflow_dict = from_json_string( workflow_text ) # Update the list of metadata dictionaries for workflows in metadata_dict. - metadata_dict = generate_workflow_metadata( trans, id, change_set_revision, exported_workflow_dict, metadata_dict ) + metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) except Exception, e: invalid_files.append( ( name, str( e ) ) ) if metadata_dict: if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ): # Create a new repository_metadata table row. - repository_metadata = trans.model.RepositoryMetadata( repository.id, change_set_revision, metadata_dict ) + repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) trans.sa_session.add( repository_metadata ) trans.sa_session.flush() else: - # Update the last saved repository_metadata table row. - repository_metadata = get_latest_repository_metadata( trans, id ) - repository_metadata.metadata = metadata_dict - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() + # Update the last saved repository_metadata table row. + repository_metadata = get_latest_repository_metadata( trans, id ) + repository_metadata.changeset_revision = changeset_revision + repository_metadata.metadata = metadata_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() else: # change_set is None - message = "Repository does not include changeset revision '%s'." % str( change_set_revision ) + message = "Repository does not include changeset revision '%s'." % str( changeset_revision ) status = 'error' if invalid_files: - message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( change_set_revision ) + message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.<br/>" % str( changeset_revision ) for itc_tup in invalid_files: tool_file = itc_tup[0] exception_msg = itc_tup[1] @@ -284,16 +306,16 @@ def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( app.model.Repository ).filter_by( name=name ).one() -def get_changectx_for_changeset( trans, repo, change_set_revision, **kwd ): +def get_changectx_for_changeset( trans, repo, changeset_revision, **kwd ): """Retrieve a specified changectx from a repository""" for changeset in repo.changelog: ctx = repo.changectx( changeset ) - if str( ctx ) == change_set_revision: + if str( ctx ) == changeset_revision: return ctx return None -def change_set_is_malicious( trans, id, change_set_revision, **kwd ): +def change_set_is_malicious( trans, id, changeset_revision, **kwd ): """Check the malicious flag in repository metadata for a specified change set""" - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, change_set_revision ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: return repository_metadata.malicious return False @@ -440,8 +462,7 @@ 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 ) - revision_label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + revision_label = get_revision_label( trans, repository, changeset_revision ) options.append( ( revision_label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) if add_id_to_name: --- a/lib/galaxy/webapps/community/controllers/repository.py Thu Aug 18 13:13:35 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Thu Aug 18 13:51:02 2011 -0400 @@ -83,7 +83,9 @@ strings of all downloadable_revisions of this repository. """ select_field = build_changeset_revision_select_field( trans, repository ) - return select_field.get_html() + if len( select_field.options ) > 1: + return select_field.get_html() + return repository.revision class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): return repository.description @@ -220,7 +222,7 @@ if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "view_or_manage_repository": - repository_id = kwd.get( 'id', None ) + repository_id = kwd[ 'id' ] repository = get_repository( trans, repository_id ) is_admin = trans.user_is_admin() if is_admin or repository.user == trans.user: @@ -582,8 +584,7 @@ repository, selected_value=changeset_revision, add_id_to_name=False ) - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) - revision_label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata @@ -721,8 +722,7 @@ repository, selected_value=changeset_revision, add_id_to_name=False ) - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) - revision_label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata @@ -989,8 +989,6 @@ # Reload the tool_data_table_conf entries trans.app.tool_data_tables = galaxy.tools.data.ToolDataTableManager( trans.app.config.tool_data_table_config_path ) message = "The new entry has been added to the tool_data_table_conf.xml file, so click the <b>Reset metadata</b> button below." - # TODO: what if ~/tool-data/<loc_filename> doesn't exist? We need to figure out how to - # force the user to upload it's sample to the repository in order to generate metadata. return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', id=repository_id, @@ -1025,29 +1023,56 @@ break return column_fields @web.expose - def display_tool( self, trans, repository_id, tool_config, **kwd ): + def display_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', 'done' ) repository = get_repository( trans, repository_id ) + old_version_msg = "Your selected version of this tool does not exist in the repository tip, so it " + \ + "cannot be previewed, but you can inspect the tool version's metadata using it's pop-up menu and " + \ + "you can download your selected version of this tool from the <b>Repository Actions</b> menu." try: tool = load_tool( trans, os.path.abspath( tool_config ) ) - tool_state = self.__new_state( trans ) - is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) - return trans.fill_template( "/webapps/community/repository/tool_form.mako", - repository=repository, - tool=tool, - tool_state=tool_state, - is_malicious=is_malicious, - message=message, - status=status ) + can_preview = True + if changeset_revision != repository.tip: + # See if we are attempting to preview an old version of a tool. + # TODO: Previewing an old version of a tool is not currently supported because + # the received tool_config is a file on the file system. We need to implement + # an enhancement here to look at the repository manifest files if previewing an + # old version of a tool. + repo_changeset_repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + repo_changeset_metadata = repo_changeset_repository_metadata.metadata + if 'tools' in repo_changeset_metadata: + for tool_metadata_dict in repo_changeset_metadata[ 'tools' ]: + if tool_metadata_dict[ 'id' ] == tool.id: + if tool_metadata_dict[ 'version' ] != tool.version: + can_preview = False + message = old_version_msg + if can_preview: + tool_state = self.__new_state( trans ) + is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) + return trans.fill_template( "/webapps/community/repository/tool_form.mako", + repository=repository, + tool=tool, + tool_state=tool_state, + is_malicious=is_malicious, + message=message, + status=status ) except Exception, e: - message = 'Error loading tool: %s. Click <b>Reset metadata</b> to correct this error.' % str( e ) - return trans.response.send_redirect( web.url_for( controller='repository', - action='manage_repository', - id=repository_id, - message=message, - status='error' ) ) + # TODO: enhance this to check the repository manifest for the files and + # display the tool using them. + exception_str = str( e ) + if exception_str.find( 'No such file or directory' ) >= 0: + message = old_version_msg + else: + message = "Error loading tool: %s. Click <b>Reset metadata</b> to correct this error." % exception_str + 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 @@ -1067,18 +1092,25 @@ repository = get_repository( trans, repository_id ) metadata = {} tool = None + revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ).metadata if 'tools' in repository_metadata: for tool_metadata_dict in repository_metadata[ 'tools' ]: if tool_metadata_dict[ 'id' ] == tool_id: metadata = tool_metadata_dict - tool = load_tool( trans, os.path.abspath( metadata[ 'tool_config' ] ) ) + try: + # We may be attempting to load a tool that no longer exists in the repository tip. + tool = load_tool( trans, os.path.abspath( metadata[ 'tool_config' ] ) ) + except: + tool = None break is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", repository=repository, tool=tool, metadata=metadata, + changeset_revision=changeset_revision, + revision_label=revision_label, is_malicious=is_malicious, message=message, status=status ) @@ -1147,6 +1179,7 @@ action='browse_repositories', operation="view_or_manage_repository", id=trans.security.encode_id( repository.id ), + changeset_revision=repository.tip, status=status, message=message ) ) return output.split() --- a/templates/webapps/community/repository/add_tool_data_table_entry.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/add_tool_data_table_entry.mako Thu Aug 18 13:51:02 2011 -0400 @@ -46,9 +46,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif --- a/templates/webapps/community/repository/browse_repository.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/browse_repository.mako Thu Aug 18 13:51:02 2011 -0400 @@ -68,9 +68,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> @@ -82,9 +82,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif --- a/templates/webapps/community/repository/manage_repository.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Thu Aug 18 13:51:02 2011 -0400 @@ -97,26 +97,28 @@ ${render_msg( message, status )} %endif -<div class="toolForm"> - <div class="toolFormTitle">Revision</div> - <div class="toolFormBody"> - <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > - <div class="form-row"> - <% - if changeset_revision == repository.tip: - tip_str = 'repository tip' - else: - tip_str = '' - %> - ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> - <div class="toolParamHelp" style="clear: both;"> - Select a revision to preview download-able versions of tools from this repository. +%if len( changeset_revision_select_field.options ) > 1: + <div class="toolForm"> + <div class="toolFormTitle">Repository revision</div> + <div class="toolFormBody"> + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <% + if changeset_revision == repository.tip: + tip_str = 'repository tip' + else: + tip_str = '' + %> + ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> + <div class="toolParamHelp" style="clear: both;"> + Select a revision to inspect and download versions of tools from this repository. + </div></div> - </div> - </form> + </form> + </div></div> -</div> -<p/> + <p/> +%endif <div class="toolForm"><div class="toolFormTitle">${repository.name}</div><div class="toolFormBody"> @@ -181,7 +183,7 @@ %if can_set_metadata: <p/><div class="toolForm"> - <div class="toolFormTitle">Preview tools and inspect metadata</div> + <div class="toolFormTitle">Preview tools in repository tip and inspect metadata by tool version</div><div class="toolFormBody"> %if metadata: %if 'tools' in metadata: @@ -205,12 +207,12 @@ <tr><td><div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision )}"> ${tool_dict[ 'name' ]} </a></div><div popupmenu="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View tool metadata</a></div></td><td>${tool_dict[ 'description' ]}</td> @@ -269,16 +271,20 @@ <div style="clear: both"></div> %endif %endif - <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="set_metadata_button" value="Reset metadata"/> + %if repository.tip == changeset_revision: + ## TODO: when we support previewing older versions of tools, we + ## should allow resetting metadata on the older versions as well. + <form name="set_metadata" action="${h.url_for( controller='repository', action='set_metadata', id=trans.security.encode_id( repository.id ), ctx_str=changeset_revision )}" method="post"> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="set_metadata_button" value="Reset metadata"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + Inspect the repository and reset the above attributes for the repository tip. + </div></div> - <div class="toolParamHelp" style="clear: both;"> - Inspect the repository and reset the above attributes for the repository tip. - </div> - </div> - </form> + </form> + %endif </div></div> %endif --- a/templates/webapps/community/repository/rate_repository.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/rate_repository.mako Thu Aug 18 13:51:02 2011 -0400 @@ -75,9 +75,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> @@ -89,9 +89,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif --- a/templates/webapps/community/repository/tool_form.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/tool_form.mako Thu Aug 18 13:51:02 2011 -0400 @@ -115,9 +115,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> @@ -132,9 +132,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif @@ -145,7 +145,7 @@ %endif <div class="toolForm" id="${tool.id}"> - <div class="toolFormTitle">${tool.name}</div> + <div class="toolFormTitle">${tool.name} ${tool.version}</div><div class="toolFormBody"><form id="tool_form" name="tool_form" action="" method="get"><input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> --- a/templates/webapps/community/repository/upload.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/upload.mako Thu Aug 18 13:51:02 2011 -0400 @@ -48,9 +48,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> --- a/templates/webapps/community/repository/view_changelog.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/view_changelog.mako Thu Aug 18 13:51:02 2011 -0400 @@ -46,9 +46,9 @@ <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> %endif %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> @@ -57,9 +57,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div></ul> --- a/templates/webapps/community/repository/view_changeset.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/view_changeset.mako Thu Aug 18 13:51:02 2011 -0400 @@ -47,9 +47,9 @@ <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> %endif %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_view_change_log: <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> @@ -61,9 +61,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='zip' )}">Download as a zip file</a> %endif </div></ul> --- a/templates/webapps/community/repository/view_repository.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Thu Aug 18 13:51:02 2011 -0400 @@ -94,26 +94,28 @@ ${render_msg( message, status )} %endif -<div class="toolForm"> - <div class="toolFormTitle">Revision</div> - <div class="toolFormBody"> - <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > - <div class="form-row"> - <% - if changeset_revision == repository.tip: - tip_str = 'repository tip' - else: - tip_str = '' - %> - ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> - <div class="toolParamHelp" style="clear: both;"> - Select a revision to preview download-able versions of tools from this repository. +%if len( changeset_revision_select_field.options ) > 1: + <div class="toolForm"> + <div class="toolFormTitle">Repository revision</div> + <div class="toolFormBody"> + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <% + if changeset_revision == repository.tip: + tip_str = 'repository tip' + else: + tip_str = '' + %> + ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> + <div class="toolParamHelp" style="clear: both;"> + Select a revision to inspect and download versions of tools from this repository. + </div></div> - </div> - </form> + </form> + </div></div> -</div> -<p/> + <p/> +%endif <div class="toolForm"><div class="toolFormTitle">${repository.name}</div><div class="toolFormBody"> @@ -173,7 +175,7 @@ %if metadata: <p/><div class="toolForm"> - <div class="toolFormTitle">Preview tools and inspect metadata</div> + <div class="toolFormTitle">Preview tools in repository tip and inspect metadata by tool version</div><div class="toolFormBody"> %if 'tools' in metadata: <div class="form-row"> @@ -196,12 +198,12 @@ <tr><td><div style="float: left; margin-left: 1px;" class="menubutton split popup" id="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ] )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision )}"> ${tool_dict[ 'name' ]} </a></div><div popupmenu="tool-${tool_dict[ 'id' ].replace( ' ', '_' )}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View all metadata for this tool</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View tool metadata</a></div></td><td>${tool_dict[ 'description' ]}</td> --- a/templates/webapps/community/repository/view_tool_metadata.mako Thu Aug 18 13:13:35 2011 -0400 +++ b/templates/webapps/community/repository/view_tool_metadata.mako Thu Aug 18 13:51:02 2011 -0400 @@ -38,9 +38,9 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a> %endif %if can_upload: <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> @@ -52,9 +52,9 @@ <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif @@ -64,6 +64,20 @@ ${render_msg( message, status )} %endif +<div class="toolForm"> + <div class="toolFormTitle">Repository revision</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Revision:</label> + %if can_view_change_log: + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> + %else: + ${revision_label} + %endif + </div> + </div> +</div> +<p/> %if can_download: <div class="toolForm"><div class="toolFormTitle">${repository.name}</div> @@ -85,7 +99,7 @@ <div class="toolFormBody"><div class="form-row"><label>Name:</label> - <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=metadata[ 'tool_config' ] )}">${metadata[ 'name' ]}</a> + <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=metadata[ 'tool_config' ], changeset_revision=changeset_revision )}">${metadata[ 'name' ]}</a><div style="clear: both"></div></div> %if 'description' in metadata: @@ -116,31 +130,33 @@ <div style="clear: both"></div></div> %endif - <div class="form-row"> - <label>Command:</label> - <pre>${tool.command}</pre> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Interpreter:</label> - ${tool.interpreter} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Is multi-byte:</label> - ${tool.is_multi_byte} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Forces a history refresh:</label> - ${tool.force_history_refresh} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Parallelism:</label> - ${tool.parallelism} - <div style="clear: both"></div> - </div> + %if tool: + <div class="form-row"> + <label>Command:</label> + <pre>${tool.command}</pre> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Interpreter:</label> + ${tool.interpreter} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Is multi-byte:</label> + ${tool.is_multi_byte} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Forces a history refresh:</label> + ${tool.force_history_refresh} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Parallelism:</label> + ${tool.parallelism} + <div style="clear: both"></div> + </div> + %endif <% if 'requirements' in metadata: requirements = metadata[ 'requirements' ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Don't count library datasets against the creating user upon dataset creation.
by Bitbucket 19 Aug '11

19 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5710c02b60ca/ changeset: 5710c02b60ca user: natefoo date: 2011-08-18 19:13:35 summary: Don't count library datasets against the creating user upon dataset creation. affected #: 1 file (30 bytes) --- a/lib/galaxy/jobs/__init__.py Thu Aug 18 13:08:39 2011 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Aug 18 13:13:35 2011 -0400 @@ -681,7 +681,7 @@ bytes = 0 # Once datasets are collected, set the total dataset size (includes extra files) - for dataset_assoc in job.output_datasets + job.output_library_datasets: + for dataset_assoc in job.output_datasets: dataset_assoc.dataset.dataset.set_total_size() bytes += dataset_assoc.dataset.dataset.get_total_size() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Decrease disk usage and actually remove datasets (if applicable) when purging a history.
by Bitbucket 19 Aug '11

19 Aug '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3c87cb241165/ changeset: 3c87cb241165 user: natefoo date: 2011-08-18 19:08:39 summary: Decrease disk usage and actually remove datasets (if applicable) when purging a history. affected #: 1 file (167 bytes) --- a/lib/galaxy/web/controllers/history.py Thu Aug 18 11:08:47 2011 -0400 +++ b/lib/galaxy/web/controllers/history.py Thu Aug 18 13:08:39 2011 -0400 @@ -271,9 +271,12 @@ n_deleted += 1 if purge and trans.app.config.allow_user_dataset_purge: for hda in history.datasets: + if trans.user: + trans.user.total_disk_usage -= hda.quota_amount( trans.user ) hda.purged = True trans.sa_session.add( hda ) trans.log_event( "HDA id %s has been purged" % hda.id ) + trans.sa_session.flush() if hda.dataset.user_can_purge: try: hda.dataset.full_delete() @@ -1207,4 +1210,4 @@ def get_item( self, trans, id ): return self.get_history( trans, id ) - \ 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

← Newer
1
2
3
4
5
6
7
8
...
11
Older →

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

galaxy-commits August 2011