June 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Refinements for setting metadata on the entire change log of tool shed repositories.
by Bitbucket 06 Jun '12

06 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3db661b25774/ changeset: 3db661b25774 user: greg date: 2012-06-06 21:15:15 summary: Refinements for setting metadata on the entire change log of tool shed repositories. affected #: 1 file diff -r 8a06e3e264ec912b67fb8388cf3874b32399ac07 -r 3db661b25774e2cb3eba6c156220f181eb28cb95 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -962,6 +962,9 @@ # The list of changeset_revisions refers to repository_metadata records that have been created or updated. When the following loop # completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list. changeset_revisions = [] + # When a new repository_metadata record is created, it always uses the values of metadata_changeset_revision and metadata_dict. + metadata_changeset_revision = None + metadata_dict = None ancestor_changeset_revision = None ancestor_metadata_dict = None for changeset in repo.changelog: @@ -978,13 +981,16 @@ if deleted_sample_file not in missing_sample_files: missing_sample_files.append( deleted_sample_file ) if current_metadata_dict: + if not metadata_changeset_revision and not metadata_dict: + # We're at the first change set in the change log. + metadata_changeset_revision = current_changeset_revision + metadata_dict = current_metadata_dict if ancestor_changeset_revision: # Compare metadata from ancestor and current. The value of comparsion will be one of: # 'no metadata' - no metadata for either ancestor or current, so continue from current # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current # 'subset' - ancestor metadata is a subset of current metadata, so continue from current - # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current - # metadata, so persist ancestor metadata. + # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current metadata, so persist ancestor metadata. comparison = compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, @@ -993,30 +999,38 @@ ancestor_changeset_revision = current_changeset_revision ancestor_metadata_dict = current_metadata_dict elif comparison == 'not equal and not subset': - create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict ) + metadata_changeset_revision = ancestor_changeset_revision + metadata_dict = ancestor_metadata_dict + create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) # Keep track of the changeset_revisions that we've persisted. - changeset_revisions.append( ancestor_changeset_revision ) + changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = current_changeset_revision ancestor_metadata_dict = current_metadata_dict else: - # We're either at the first change set in the change log or we have just created or updated - # a repository_metadata record. At this point we set the ancestor changeset to the current - # changeset for comparison in the next iteration. + # We're either at the first change set in the change log or we have just created or updated a repository_metadata record. At + # this point we set the ancestor changeset to the current changeset for comparison in the next iteration. ancestor_changeset_revision = current_changeset_revision ancestor_metadata_dict = current_metadata_dict if not ctx.children(): + metadata_changeset_revision = current_changeset_revision + metadata_dict = current_metadata_dict # We're at the end of the change log. - create_or_update_repository_metadata( trans, id, repository, current_changeset_revision, current_metadata_dict ) - changeset_revisions.append( current_changeset_revision ) + create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None elif ancestor_metadata_dict: + # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. + ancestor_changeset_revision = current_changeset_revision + metadata_changeset_revision = current_changeset_revision + metadata_dict = ancestor_metadata_dict if not ctx.children(): # We're at the end of the change log. - create_or_update_repository_metadata( trans, id, repository, current_changeset_revision, ancestor_metadata_dict ) - changeset_revisions.append( current_changeset_revision ) + create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None + # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. clean_repository_metadata( trans, id, changeset_revisions ) add_repository_metadata_tool_versions( trans, id, changeset_revisions ) if missing_sample_files: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Update default and help for Tophat2 coverage search parameter.
by Bitbucket 06 Jun '12

06 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8a06e3e264ec/ changeset: 8a06e3e264ec user: jgoecks date: 2012-06-06 20:42:21 summary: Update default and help for Tophat2 coverage search parameter. affected #: 1 file diff -r 41f72445078999fd2a3f6471ee319a0be977097c -r 8a06e3e264ec912b67fb8388cf3874b32399ac07 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -231,9 +231,9 @@ <conditional name="coverage_search"> - <param name="use_search" type="select" label="Use Coverage Search"> - <option selected="true" value="Yes">Yes</option> - <option value="No">No</option> + <param name="use_search" type="select" label="Use Coverage Search" help="Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity."> + <option selected="true" value="No">No</option> + <option value="Yes">Yes</option></param><when value="Yes"><param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" /> 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: Fixes for getting updates to installed tool shed repositories.
by Bitbucket 06 Jun '12

06 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/41f724450789/ changeset: 41f724450789 user: greg date: 2012-06-06 19:26:15 summary: Fixes for getting updates to installed tool shed repositories. affected #: 2 files diff -r 5343150e167ea8682f25849e7b01e1f40c4b440d -r 41f72445078999fd2a3f6471ee319a0be977097c lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -174,6 +174,40 @@ return trans.response.send_redirect( url ) @web.expose @web.require_admin + def check_installed_tool_dependencies( self, trans, repository_id, relative_install_dir ): + """See if any tool dependencies need to be installed.""" + tool_dependencies_missing = False + repository = get_repository( trans, repository_id ) + if repository.includes_tool_dependencies: + # Get the tool_dependencies.xml file from the repository. + work_dir = make_tmp_directory() + tool_dependencies_config = get_config_from_repository( trans.app, + 'tool_dependencies.xml', + repository, + repository.changeset_revision, + work_dir, + install_dir=relative_install_dir ) + # Parse the tool_dependencies.xml config. + tree = ElementTree.parse( tool_dependencies_config ) + root = tree.getroot() + ElementInclude.include( root ) + fabric_version_checked = False + for elem in root: + if elem.tag == 'package': + package_name = elem.get( 'name', None ) + package_version = elem.get( 'version', None ) + if package_name and package_version: + install_dir = get_install_dir( trans.app, repository, repository.installed_changeset_revision, package_name, package_version ) + if not_installed( install_dir ): + tool_dependencies_missing = True + break + try: + shutil.rmtree( work_dir ) + except: + pass + return tool_dependencies_missing + @web.expose + @web.require_admin def deactivate_or_uninstall_repository( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -540,7 +574,8 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = get_repository( trans, kwd[ 'id' ] ) + repository_id = kwd[ 'id' ] + repository = get_repository( trans, repository_id ) description = util.restore_text( params.get( 'description', repository.description ) ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) @@ -558,34 +593,7 @@ trans.sa_session.add( repository ) trans.sa_session.flush() message = "Repository metadata has been reset." - tool_dependencies_missing = False - if repository.includes_tool_dependencies: - # See if any tool dependencies need to be installed, get the tool_dependencies.xml file from the repository. - work_dir = make_tmp_directory() - tool_dependencies_config = get_config_from_repository( trans.app, - 'tool_dependencies.xml', - repository, - repository.changeset_revision, - work_dir, - install_dir=relative_install_dir ) - # Parse the tool_dependencies.xml config. - tree = ElementTree.parse( tool_dependencies_config ) - root = tree.getroot() - ElementInclude.include( root ) - fabric_version_checked = False - for elem in root: - if elem.tag == 'package': - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - install_dir = get_install_dir( trans.app, repository, repository.installed_changeset_revision, package_name, package_version ) - if not_installed( install_dir ): - tool_dependencies_missing = True - break - try: - shutil.rmtree( work_dir ) - except: - pass + tool_dependencies_missing = self.check_installed_tool_dependencies( trans, repository_id, relative_install_dir ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=description, @@ -782,7 +790,7 @@ repository = get_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision ) if changeset_revision and latest_changeset_revision and latest_ctx_rev: if changeset_revision == latest_changeset_revision: - message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name + message = "The installed repository named '%s' is current, there are no updates available. " % name else: shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if relative_install_dir: @@ -801,13 +809,17 @@ repository.update_available = False trans.sa_session.add( repository ) trans.sa_session.flush() - message = "The cloned repository named '%s' has been updated to change set revision '%s'." % \ - ( name, latest_changeset_revision ) + message = "The installed repository named '%s' has been updated to change set revision '%s'. " % ( name, latest_changeset_revision ) + # See if any tool dependencies can be installed. + shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) + tool_dependencies_missing = self.check_installed_tool_dependencies( trans, trans.security.encode_id( repository.id ), relative_install_dir ) + if tool_dependencies_missing: + message += "Select <b>Install tool dependencies</b> from the repository's pop-up menu to install tool dependencies." else: - message = "The directory containing the cloned repository named '%s' cannot be found." % name + message = "The directory containing the installed repository named '%s' cannot be found. " % name status = 'error' else: - message = "The latest changeset revision could not be retrieved for the repository named '%s'." % name + message = "The latest changeset revision could not be retrieved for the installed repository named '%s'. " % name status = 'error' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repository', diff -r 5343150e167ea8682f25849e7b01e1f40c4b440d -r 41f72445078999fd2a3f6471ee319a0be977097c lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -599,6 +599,9 @@ repository = get_repository_by_name_and_owner( trans, name, owner ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) + # Default to the current changeset revision. + update_to_ctx = get_changectx_for_changeset( repo, changeset_revision ) + latest_changeset_revision = changeset_revision from_update_manager = webapp == 'update_manager' if from_update_manager: update = 'true' @@ -608,80 +611,45 @@ url = '%sadmin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '/', qualified=True ) ) url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % ( repository.name, repository.user.username, changeset_revision ) if changeset_revision == repository.tip: - # If changeset_revision is the repository tip, we know there are no additional updates for the tools. + # If changeset_revision is the repository tip, there are no additional updates. if from_update_manager: return no_update # Return the same value for changeset_revision and latest_changeset_revision. - url += repository.tip + url += latest_changeset_revision else: repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) if repository_metadata: - # If changeset_revision is in the repository_metadata table for this repository, then we know there are no additional updates - # for the tools. + # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates. if from_update_manager: return no_update else: # Return the same value for changeset_revision and latest_changeset_revision. - url += changeset_revision + url += latest_changeset_revision else: - # TODO: Re-engineer this to define the change set for update to be the one just before the next change set in the repository_metadata - # table for this repository. # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the - # repository was cloned. 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( repo, changeset_revision ) - if ctx is not None: - work_dir = make_tmp_directory() - tool_guids = [] - for filename in ctx: - # Find all tool configs in this repository changeset_revision. - if filename not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): - is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, - repo, - repo_dir, - ctx, - filename, - work_dir ) - if valid and tool is not None: - tool_guids.append( generate_tool_guid( trans, repository, tool ) ) - tool_guids.sort() - if tool_guids: - # Compare our list of tool guids against those in each repository_metadata record for the repository to find the - # repository_metadata record with the changeset_revision value we want to pass back to the caller. - found = False - for repository_metadata in get_repository_metadata_by_repository_id( trans, trans.security.encode_id( repository.id ) ): - metadata = repository_metadata.metadata - metadata_tool_guids = [] - for tool_dict in metadata[ 'tools' ]: - metadata_tool_guids.append( tool_dict[ 'guid' ] ) - metadata_tool_guids.sort() - if tool_guids == metadata_tool_guids: - # We've found the repository_metadata record whose changeset_revision value has been updated. - if from_update_manager: - return update - url += repository_metadata.changeset_revision - # Get the ctx_rev for the discovered changeset_revision. - latest_ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) - found = True - break - if not found: - # There must be a problem in the data, so we'll just send back the received changeset_revision. - log.debug( "Possible data corruption - updated repository_metadata cannot be found for repository id %d." % repository.id ) - if from_update_manager: - return no_update - url += changeset_revision - else: - # There are no tools in the changeset_revision, so no tool updates are possible. - if from_update_manager: - return no_update - url += changeset_revision - try: - shutil.rmtree( work_dir ) - except: - pass - url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) + # repository was installed. We need to find the changeset_revision to which we need to update. + update_to_changeset_hash = None + for changeset in repo.changelog: + changeset_hash = str( repo.changectx( changeset ) ) + ctx = get_changectx_for_changeset( repo, changeset_hash ) + if update_to_changeset_hash: + if get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ): + # We found a RepositoryMetadata record. + if changeset_hash == repository.tip: + # The current ctx is the repository tip, so use it. + update_to_ctx = get_changectx_for_changeset( repo, changeset_hash ) + latest_changeset_revision = changeset_hash + else: + update_to_ctx = get_changectx_for_changeset( repo, update_to_changeset_hash ) + latest_changeset_revision = update_to_changeset_hash + break + elif not update_to_changeset_hash and changeset_hash == changeset_revision: + # We've found the changeset in the changelog for which we need to get the next update. + update_to_changeset_hash = changeset_hash + url += str( latest_changeset_revision ) + url += '&latest_ctx_rev=%s' % str( update_to_ctx.rev() ) return trans.response.send_redirect( url ) @web.expose def contact_owner( self, trans, id, **kwd ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for rendering the url for cloning a tool shed repository.
by Bitbucket 06 Jun '12

06 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5343150e167e/ changeset: 5343150e167e user: greg date: 2012-06-06 15:48:15 summary: Fix for rendering the url for cloning a tool shed repository. affected #: 1 file diff -r da5b91a86b2f739eb9deb8dc51fe16446e5cda35 -r 5343150e167ea8682f25849e7b01e1f40c4b440d lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -407,12 +407,13 @@ def generate_clone_url( trans, repository_id ): """Generate the URL for cloning a repository.""" repository = get_repository( trans, repository_id ) - protocol, base = trans.request.base.split( '://' ) + base_url = url_for( '/', qualified=True ).rstrip( '/' ) if trans.user: + protocol, base = base_url.split( '://' ) username = '%s@' % trans.user.username + return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) else: - username = '' - return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) + return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name ) def generate_metadata_for_changeset_revision( trans, repo, id, ctx, changeset_revision, repo_dir, updating_tip=False ): if updating_tip: # If a push from the command line is occurring, update the repository files on disk before setting 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: fubar: Added __admin_users__ as a parameter so tools can check __user_email__ and refuse to run unless
by Bitbucket 05 Jun '12

05 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/da5b91a86b2f/ changeset: da5b91a86b2f user: fubar date: 2012-06-06 06:02:41 summary: Added __admin_users__ as a parameter so tools can check __user_email__ and refuse to run unless being invoked by a local admin - useful for any potentially dangerous tools. affected #: 1 file diff -r a4196ffaf11e22b9b0a76fe6aa1cbbcccd2fb219 -r da5b91a86b2f739eb9deb8dc51fe16446e5cda35 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2056,6 +2056,7 @@ # datatypes conf path, so we can load the datatypes registry param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root ) param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.integrated_datatypes_configs + param_dict['__admin_users__'] = self.app.config.admin_users # Return the dictionary of parameters return param_dict def build_param_file( self, param_dict, directory=None ): 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: Adding a new datatype to datatypes_conf.xml.sample - toolshed compatible gzips created by a new automated
by Bitbucket 05 Jun '12

05 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a4196ffaf11e/ changeset: a4196ffaf11e user: fubar date: 2012-06-06 04:08:55 summary: Adding a new datatype to datatypes_conf.xml.sample - toolshed compatible gzips created by a new automated script wrapper. affected #: 1 file diff -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 -r a4196ffaf11e22b9b0a76fe6aa1cbbcccd2fb219 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -89,6 +89,7 @@ <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/></datatype> + <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /><datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/><datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Foundation for parameter sweeping visualization.
by Bitbucket 05 Jun '12

05 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0b2d939a7870/ changeset: 0b2d939a7870 user: jgoecks date: 2012-06-05 23:10:23 summary: Foundation for parameter sweeping visualization. affected #: 6 files diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2407,10 +2407,19 @@ if isinstance( input, DataToolParameter ): param_dict.update( { 'type' : 'data', 'html' : urllib.quote( input.get_html( trans ) ) } ) elif isinstance( input, SelectToolParameter ): - param_dict.update( { 'type' : 'select', 'html' : urllib.quote( input.get_html( trans ) ) } ) + param_dict.update( { 'type' : 'select', + 'html' : urllib.quote( input.get_html( trans ) ), + 'options': input.static_options + } ) elif isinstance( input, Conditional ): # TODO. pass + elif isinstance( input, ( IntegerToolParameter, FloatToolParameter ) ): + param_dict.update( { 'type' : 'number', 'init_value' : input.value, + 'html' : urllib.quote( input.get_html( trans ) ), + 'min': input.min, + 'max': input.max + } ) else: param_dict.update( { 'type' : '??', 'init_value' : input.value, \ 'html' : urllib.quote( input.get_html( trans ) ) } ) diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -762,6 +762,15 @@ output_dataset = joda.dataset return self.add_track_async( trans, output_dataset.id ) + + @web.expose + @web.require_login( "use Galaxy visualizations", use_panels=True ) + def paramamonster( self, trans, hda_ldda, dataset_id ): + # Get dataset. + dataset = self._get_dataset( trans, hda_ldda, dataset_id ) + + return trans.fill_template_mako( "visualization/paramamonster.mako", dataset=dataset, + tool=self.app.toolbox.tools_by_id[ 'cufflinks' ].to_dict( trans, for_display=True ) ) @web.expose @web.require_login( "use Galaxy visualizations", use_panels=True ) diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 static/scripts/packed/viz/paramamonster.js --- /dev/null +++ b/static/scripts/packed/viz/paramamonster.js @@ -0,0 +1,1 @@ +var ToolParameterTree=Backbone.Model.extend({defaults:{tool:null,samples:4},initialize:function(d){var c=this.get("tool"),b=this.get("samples"),a=c.get("inputs").filter(function(h){return(["number","select"].indexOf(h.get("type"))!==-1)}),f=_.map(a,function(h){return h.get("name")});sampling=_.map(a,function(h){var i=h.get("type");if(i==="number"){return d3.scale.linear().domain([h.get("min"),h.get("max")]).ticks(b)}else{if(i==="select"){return _.map(h.get("options"),function(j){return j[0]})}}});var g=function(j,h,i){if(h.length-1===i){return _.map(h[i],function(k){return{name:k}})}return _.map(h[i],function(k){return{name:j[i]+":"+k,children:g(j,h,i+1)}})};var e={name:"Parameter Tree for "+c.get("name"),children:g(f,sampling,0)};this.set("valid_inputs",a);this.set("tree_data",e)}});var TileView=Backbone.View.extend({});var ToolParameterTreeView=Backbone.View.extend({className:"paramamonster",initialize:function(a){this.model=a.model},render:function(){var e=960,b=2000;var a=d3.layout.cluster().size([b,e-160]);var d=d3.svg.diagonal().projection(function(i){return[i.y,i.x]});var h=d3.select(this.$el[0]).append("svg").attr("width",e).attr("height",b).append("g").attr("transform","translate(80, 0)");var c=a.nodes(this.model.get("tree_data"));var g=h.selectAll("path.link").data(a.links(c)).enter().append("path").attr("class","link").attr("d",d);var f=h.selectAll("g.node").data(c).enter().append("g").attr("class","node").attr("transform",function(i){return"translate("+i.y+","+i.x+")"});f.append("circle").attr("r",4.5);f.append("text").attr("dx",function(i){return i.children?-8:8}).attr("dy",3).attr("text-anchor",function(i){return i.children?"end":"start"}).text(function(i){return i.name})}}); \ No newline at end of file diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 static/scripts/viz/paramamonster.js --- /dev/null +++ b/static/scripts/viz/paramamonster.js @@ -0,0 +1,123 @@ +/** + * Visualization and components for ParamaMonster, a visualization for exploring a tool's parameter space via + * genomic visualization. + */ + +var ToolParameterTree = Backbone.Model.extend({ + defaults: { + tool: null, + samples: 4 + }, + + + initialize: function(options) { + // + // -- Create tree data from tool. -- + // + + // Valid inputs for tree are number, select parameters. + var tool = this.get('tool'), + samples = this.get('samples'), + inputs = tool.get('inputs').filter(function(input) { + return ( ['number', 'select'].indexOf(input.get('type')) !== -1 ); + }), + inputs_names = _.map(inputs, function(i) { return i.get('name')}); + // Sample from all valid inputs. + sampling = _.map(inputs, function(input) { + var type = input.get('type'); + if (type === 'number') { + return d3.scale.linear().domain([input.get('min'), input.get('max')]).ticks(samples); + } + else if (type === 'select') { + return _.map(input.get('options'), function(option) { + return option[0]; + }); + } + }); + + /** + * Returns tree data. + */ + var create_tree_data = function(param_names, param_settings, index) { + // Terminate when last parameter setting is reached. + if (param_settings.length - 1 === index) { + return _.map(param_settings[index], function(setting) { + return { + name: setting + } + }); + } + + // Recurse to handle other parameters. + return _.map(param_settings[index], function(setting) { + return { + name: param_names[index] + ':' + setting, + children: create_tree_data(param_names, param_settings, index + 1) + } + }); + }; + + var tree_data = { + name: 'Parameter Tree for ' + tool.get('name'), + children: create_tree_data(inputs_names, sampling, 0) + }; + + // Set valid inputs, tree data for later use. + this.set('valid_inputs', inputs); + this.set('tree_data', tree_data); + } + +}); + +var TileView = Backbone.View.extend({ + +}); + +var ToolParameterTreeView = Backbone.View.extend({ + className: 'paramamonster', + + initialize: function(options) { + this.model = options.model; + }, + + render: function() { + var width = 960, + height = 2000; + + var cluster = d3.layout.cluster() + .size([height, width - 160]); + + var diagonal = d3.svg.diagonal() + .projection(function(d) { return [d.y, d.x]; }); + + var vis = d3.select(this.$el[0]) + .append("svg") + .attr("width", width) + .attr("height", height) + .append("g") + .attr("transform", "translate(80, 0)"); + + var nodes = cluster.nodes(this.model.get('tree_data')); + + var link = vis.selectAll("path.link") + .data(cluster.links(nodes)) + .enter().append("path") + .attr("class", "link") + .attr("d", diagonal); + + var node = vis.selectAll("g.node") + .data(nodes) + .enter().append("g") + .attr("class", "node") + .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; }) + + node.append("circle") + .attr("r", 4.5); + + node.append("text") + .attr("dx", function(d) { return d.children ? -8 : 8; }) + .attr("dy", 3) + .attr("text-anchor", function(d) { return d.children ? "end" : "start"; }) + .text(function(d) { return d.name; }); + } +}); \ No newline at end of file diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -16,7 +16,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "libs/d3", "mvc/visualization" )} + ${h.js( "libs/d3", "viz/visualization" )} <script type="text/javascript"> $(function() { @@ -81,7 +81,7 @@ // -- Render viz. -- circster.render(); - $('#vis').append(circster.$el); + $('#vis').append(circster.$el); }); </script></%def> diff -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 -r 0b2d939a7870074977a30d7e9b57cd0c434fe637 templates/visualization/paramamonster.mako --- /dev/null +++ b/templates/visualization/paramamonster.mako @@ -0,0 +1,62 @@ +<%inherit file="/webapps/galaxy/base_panels.mako"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.active_view="visualization" + self.message_box_visible=False +%> +</%def> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + <style> + .unified-panel-body { + overflow: auto; + } + .link { + fill: none; + stroke: #ccc; + stroke-width: 1.5px; + } + .node { + font: 10px sans-serif; + } + .node circle { + fill: #fff; + stroke: steelblue; + stroke-width: 1.5px; + } + </style> +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + + ${h.templates( "tool_link", "panel_section", "tool_search" )} + ${h.js( "libs/d3", "viz/visualization", "viz/paramamonster", "mvc/tools" )} + + <script type="text/javascript"> + $(function() { + // -- Viz set up. -- + + var tool = new Tool(JSON.parse('${ h.to_json_string( tool ) }')), + tool_param_tree = new ToolParameterTree({ tool: tool }), + tool_param_tree_view = new ToolParameterTreeView({ model: tool_param_tree }); + + tool_param_tree_view.render(); + $('#vis').append(tool_param_tree_view.$el); + }); + </script> +</%def> + +<%def name="center_panel()"> + <div class="unified-panel-header" unselectable="on"> + <div class="unified-panel-header-inner"> + <div style="float:left;" id="title"></div> + </div> + <div style="clear: both"></div> + </div> + <div id="vis" class="unified-panel-body"></div> +</%def> 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: Fixes for setting metadata on tool shed repoistories.
by Bitbucket 05 Jun '12

05 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/91217d6ead5a/ changeset: 91217d6ead5a user: greg date: 2012-06-05 20:59:42 summary: Fixes for setting metadata on tool shed repoistories. affected #: 2 files diff -r d7580315fa206bcc64bc7607ee52bccfbf95e42f -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1010,12 +1010,12 @@ ancestor_changeset_revision = None ancestor_metadata_dict = None elif ancestor_metadata_dict: - # Our current change set has no metadata, but our ancestor change set has metadata, so save it. - create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict ) - # Keep track of the changeset_revisions that we've persisted. - changeset_revisions.append( ancestor_changeset_revision ) - ancestor_changeset_revision = None - ancestor_metadata_dict = None + if not ctx.children(): + # We're at the end of the change log. + create_or_update_repository_metadata( trans, id, repository, current_changeset_revision, ancestor_metadata_dict ) + changeset_revisions.append( current_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None clean_repository_metadata( trans, id, changeset_revisions ) add_repository_metadata_tool_versions( trans, id, changeset_revisions ) if missing_sample_files: @@ -1083,7 +1083,7 @@ repository_metadata.metadata = metadata_dict trans.sa_session.add( repository_metadata ) trans.sa_session.flush() - elif not invalid_files: + elif updating_tip and len( repo ) == 1 and not invalid_files: message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( changeset_revision ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" @@ -1120,7 +1120,6 @@ status = 'error' return message, status def set_repository_metadata_due_to_new_tip( trans, id, repository, content_alert_str=None, **kwd ): - message = util.restore_text( kwd.get( 'message', '' ) ) # Set metadata on the repository tip. error_message, status = set_repository_metadata( trans, id, repository.tip, content_alert_str=content_alert_str, **kwd ) if not error_message: diff -r d7580315fa206bcc64bc7607ee52bccfbf95e42f -r 91217d6ead5a58609e0cc0ac839d2c2a6bc94691 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -158,6 +158,8 @@ message += " %d files were removed from the repository root. " % len( files_to_remove ) kwd[ 'message' ] = message set_repository_metadata_due_to_new_tip( trans, repository_id, repository, content_alert_str=content_alert_str, **kwd ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) trans.response.send_redirect( web.url_for( controller='repository', action='browse_repository', id=repository_id, 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: Fixes for handling tool shed repository files that have been renamed or deleted.
by Bitbucket 05 Jun '12

05 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d7580315fa20/ changeset: d7580315fa20 user: greg date: 2012-06-05 18:51:54 summary: Fixes for handling tool shed repository files that have been renamed or deleted. affected #: 3 files diff -r f551610b687003fc09cd6ff7bbc506d237c67a75 -r d7580315fa206bcc64bc7607ee52bccfbf95e42f lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -856,14 +856,26 @@ response.close() return ctx_rev def get_named_tmpfile_from_ctx( ctx, filename, dir ): - fctx = ctx[ filename ] - fh = tempfile.NamedTemporaryFile( 'wb', dir=dir ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'wb' ) - fh.write( fctx.data() ) - fh.close() - return tmp_filename + filename = strip_path( filename ) + for ctx_file in ctx.files(): + ctx_file_name = strip_path( ctx_file ) + if filename == ctx_file_name: + try: + # If the file was moved, its destination file contents will be returned here. + fctx = ctx[ ctx_file ] + except LookupError, e: + # Continue looking in case the file was moved. + fctx = None + continue + if fctx: + fh = tempfile.NamedTemporaryFile( 'wb', dir=dir ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return tmp_filename + return None def get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): sa_session = app.model.context.current if tool_shed.find( '//' ) > 0: diff -r f551610b687003fc09cd6ff7bbc506d237c67a75 -r d7580315fa206bcc64bc7607ee52bccfbf95e42f lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -529,17 +529,22 @@ def get_file_context_from_ctx( ctx, filename ): # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to - # the latter: - # ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample'] + # the latter: ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample']. Another scenario + # is that the file has been deleted. + deleted = False filename = strip_path( filename ) for ctx_file in ctx.files(): ctx_file_name = strip_path( ctx_file ) if filename == ctx_file_name: try: + # If the file was moved, its destination will be returned here. fctx = ctx[ ctx_file ] return fctx except LookupError, e: - return 'DELETED' + # Set deleted for now, and continue looking in case the file was moved instead of deleted. + deleted = True + if deleted: + return 'DELETED' return None def get_latest_repository_metadata( trans, id ): """Get last metadata defined for a specified repository from the database""" @@ -772,37 +777,37 @@ def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ): """ Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename. The value of changeset_revision - is a valid (downloadable) changset revision. If changeset_revision is the repository tip, then the tool will be loaded from it's file on disk. - Otherwise, the tool config will be located in the repository manifest between the received valid changeset revision and the previous valid - changeset revision (if one exists) or the first changeset revision in the repository (if one doesn't). + is a valid (downloadable) changset revision. The tool config will be located in the repository manifest between the received valid changeset + revision and the first changeset revision in the repository, searching backwards. """ def load_from_tmp_config( ctx, ctx_file, work_dir ): tool = None message = '' tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) - element_tree = util.parse_xml( tmp_tool_config ) - element_tree_root = element_tree.getroot() - # Look for code files required by the tool config. - tmp_code_files = [] - for code_elem in element_tree_root.findall( 'code' ): - code_file_name = code_elem.get( 'file' ) - tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) - if tmp_code_file_name: - tmp_code_files.append( tmp_code_file_name ) - try: - tool = load_tool( trans, tmp_tool_config ) - except Exception, e: - tool = None - message = "Error loading tool: %s. " % str( e ) - for tmp_code_file in tmp_code_files: + if tmp_tool_config: + element_tree = util.parse_xml( tmp_tool_config ) + element_tree_root = element_tree.getroot() + # Look for code files required by the tool config. + tmp_code_files = [] + for code_elem in element_tree_root.findall( 'code' ): + code_file_name = code_elem.get( 'file' ) + tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) + if tmp_code_file_name: + tmp_code_files.append( tmp_code_file_name ) try: - os.unlink( tmp_code_file ) + tool = load_tool( trans, tmp_tool_config ) + except Exception, e: + tool = None + message = "Error loading tool: %s. " % str( e ) + for tmp_code_file in tmp_code_files: + try: + os.unlink( tmp_code_file ) + except: + pass + try: + os.unlink( tmp_tool_config ) except: pass - try: - os.unlink( tmp_tool_config ) - except: - pass return tool, message tool_config_filename = strip_path( tool_config_filename ) repository = get_repository( trans, repository_id ) @@ -842,41 +847,42 @@ valid = False error_message = '' tmp_config = get_named_tmpfile_from_ctx( ctx, filename, dir ) - if not ( check_binary( tmp_config ) or check_image( tmp_config ) or check_gzip( tmp_config )[ 0 ] - or check_bz2( tmp_config )[ 0 ] or check_zip( tmp_config ) ): - try: - # Make sure we're looking at a tool config and not a display application config or something else. - element_tree = util.parse_xml( tmp_config ) - element_tree_root = element_tree.getroot() - is_tool_config = element_tree_root.tag == 'tool' - except Exception, e: - log.debug( "Error parsing %s, exception: %s" % ( tmp_config, str( e ) ) ) - is_tool_config = False - if is_tool_config: - # Load entries into the tool_data_tables if the tool requires them. - tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', dir ) - if tool_data_table_config: - error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) - # Look for code files required by the tool config. The directory to which dir refers should be removed by the caller. - for code_elem in element_tree_root.findall( 'code' ): - code_file_name = code_elem.get( 'file' ) - if not os.path.exists( os.path.join( dir, code_file_name ) ): - tmp_code_file_name = copy_file_from_disk( code_file_name, repo_dir, dir ) - if tmp_code_file_name is None: - tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, dir ) + if tmp_config: + if not ( check_binary( tmp_config ) or check_image( tmp_config ) or check_gzip( tmp_config )[ 0 ] + or check_bz2( tmp_config )[ 0 ] or check_zip( tmp_config ) ): try: - tool = load_tool( trans, tmp_config ) - valid = True - except KeyError, e: - valid = False - error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str( e ) - error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct ' - error_message += 'this error. ' + # Make sure we're looking at a tool config and not a display application config or something else. + element_tree = util.parse_xml( tmp_config ) + element_tree_root = element_tree.getroot() + is_tool_config = element_tree_root.tag == 'tool' except Exception, e: - valid = False - error_message = str( e ) - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - reset_tool_data_tables( trans.app ) + log.debug( "Error parsing %s, exception: %s" % ( tmp_config, str( e ) ) ) + is_tool_config = False + if is_tool_config: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', dir ) + if tool_data_table_config: + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) + # Look for code files required by the tool config. The directory to which dir refers should be removed by the caller. + for code_elem in element_tree_root.findall( 'code' ): + code_file_name = code_elem.get( 'file' ) + if not os.path.exists( os.path.join( dir, code_file_name ) ): + tmp_code_file_name = copy_file_from_disk( code_file_name, repo_dir, dir ) + if tmp_code_file_name is None: + tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, dir ) + try: + tool = load_tool( trans, tmp_config ) + valid = True + except KeyError, e: + valid = False + error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str( e ) + error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct ' + error_message += 'this error. ' + except Exception, e: + valid = False + error_message = str( e ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) return is_tool_config, valid, tool, error_message def new_tool_metadata_required( trans, id, metadata_dict ): """ diff -r f551610b687003fc09cd6ff7bbc506d237c67a75 -r d7580315fa206bcc64bc7607ee52bccfbf95e42f lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -10,7 +10,7 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * -from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, get_named_tmpfile_from_ctx, make_tmp_directory, NOT_TOOL_CONFIGS, strip_path +from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, make_tmp_directory, NOT_TOOL_CONFIGS, strip_path from galaxy.tool_shed.encoding_util import * from common import * @@ -1257,12 +1257,6 @@ repo = hg.repository( get_configured_ui(), repo_dir ) ctx = get_changectx_for_changeset( repo, changeset_revision ) invalid_message = '' - work_dir = make_tmp_directory() - for filename in ctx: - ctx_file_name = strip_path( filename ) - if ctx_file_name == tool_config: - tool_config_path = get_named_tmpfile_from_ctx( ctx, filename, work_dir ) - break metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans, repo, repository_id, @@ -1275,17 +1269,11 @@ invalid_tool_config_name = strip_path( invalid_tool_config ) if tool_config == invalid_tool_config_name: invalid_message = invalid_msg - break + break tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) - #if error_message: - # message += error_message tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) try: - shutil.rmtree( work_dir ) - except: - pass - try: if invalid_message: message = invalid_message return trans.fill_template( "/webapps/community/repository/tool_form.mako", Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Refinements for locating desired files within a tool shed repository manifest and setting metadata on tool shed repositories.
by Bitbucket 05 Jun '12

05 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f551610b6870/ changeset: f551610b6870 user: greg date: 2012-06-05 17:15:14 summary: Refinements for locating desired files within a tool shed repository manifest and setting metadata on tool shed repositories. affected #: 5 files diff -r 29b8e39db1094cb5a5586c4f7b404428641d518c -r f551610b687003fc09cd6ff7bbc506d237c67a75 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -21,6 +21,7 @@ log = logging.getLogger( __name__ ) +INITIAL_CHANGELOG_HASH = '000000000000' # Characters that must be html escaped MAPPED_CHARS = { '>' :'>', '<' :'<', @@ -771,28 +772,15 @@ if str( ctx ) == changeset_revision: return ctx return None -def get_config( config_file, repo, repo_dir, ctx, dir ): - """Return config_filename if it exists in some changeset of the repository.""" - # First look on disk. - for root, dirs, files in os.walk( repo_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name == config_file: - dest_file_name = os.path.join( dir, name ) - shutil.copy( os.path.abspath( os.path.join( root, name ) ), dest_file_name ) - return os.path.abspath( dest_file_name ) - # Next look in the current change set. - for filename in ctx: - ctx_file_name = strip_path( filename ) - if ctx_file_name == config_file: - return get_named_tmpfile_from_ctx( ctx, filename, dir ) - # Finally look in the repository manifest. - for changeset in repo.changelog: - prev_ctx = repo.changectx( changeset ) - for ctx_file in prev_ctx.files(): +def get_config( config_file, repo, ctx, dir ): + """Return the latest version of config_filename from the repository manifest.""" + config_file = strip_path( config_file ) + for changeset in reversed_upper_bounded_changelog( repo, ctx ): + changeset_ctx = repo.changectx( changeset ) + for ctx_file in changeset_ctx.files(): ctx_file_name = strip_path( ctx_file ) if ctx_file_name == config_file: - return get_named_tmpfile_from_ctx( prev_ctx, filename, dir ) + return get_named_tmpfile_from_ctx( changeset_ctx, ctx_file, dir ) return None def get_config_from_disk( config_file, relative_install_dir ): for root, dirs, files in os.walk( relative_install_dir ): @@ -808,7 +796,7 @@ repo_files_dir = os.path.join( install_dir, repository.name ) repo = hg.repository( get_configured_ui(), repo_files_dir ) ctx = get_changectx_for_changeset( repo, changeset_revision ) - config = get_config( config_file, repo, repo_files_dir, ctx, dir ) + config = get_config( config_file, repo, ctx, dir ) return config def get_configured_ui(): # Configure any desired ui settings. @@ -867,6 +855,15 @@ ctx_rev = response.read() response.close() return ctx_rev +def get_named_tmpfile_from_ctx( ctx, filename, dir ): + fctx = ctx[ filename ] + fh = tempfile.NamedTemporaryFile( 'wb', dir=dir ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return tmp_filename def get_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): sa_session = app.model.context.current if tool_shed.find( '//' ) > 0: @@ -1383,6 +1380,31 @@ def reset_tool_data_tables( app ): # Reset the tool_data_tables to an empty dictionary. app.tool_data_tables.data_tables = {} +def reversed_lower_upper_bounded_changelog( repo, excluded_lower_bounds_changeset_revision, included_upper_bounds_changeset_revision ): + """ + Return a reversed list of changesets in the repository changelog after the excluded_lower_bounds_changeset_revision, but up to and + including the included_upper_bounds_changeset_revision. The value of excluded_lower_bounds_changeset_revision will be the value of + INITIAL_CHANGELOG_HASH if no valid changesets exist before included_upper_bounds_changeset_revision. + """ + # To set excluded_lower_bounds_changeset_revision, calling methods should do the following, where the value of changeset_revision + # is a downloadable changeset_revision. + # excluded_lower_bounds_changeset_revision = get_previous_valid_changset_revision( repository, repo, changeset_revision ) + if excluded_lower_bounds_changeset_revision == INITIAL_CHANGELOG_HASH: + appending_started = True + else: + appending_started = False + reversed_changelog = [] + for changeset in repo.changelog: + changeset_hash = str( repo.changectx( changeset ) ) + if appending_started: + reversed_changelog.insert( 0, changeset ) + if changeset_hash == excluded_lower_bounds_changeset_revision and not appending_started: + appending_started = True + if changeset_hash == included_upper_bounds_changeset_revision: + break + return reversed_changelog +def reversed_upper_bounded_changelog( repo, included_upper_bounds_changeset_revision ): + return reversed_lower_upper_bounded_changelog( repo, INITIAL_CHANGELOG_HASH, included_upper_bounds_changeset_revision ) def strip_path( fpath ): file_path, file_name = os.path.split( fpath ) return file_name diff -r 29b8e39db1094cb5a5586c4f7b404428641d518c -r f551610b687003fc09cd6ff7bbc506d237c67a75 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -473,9 +473,12 @@ .filter( trans.model.Repository.table.c.deleted == False ): try: error_message, status = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) ) - if error_message: + if status not in [ 'ok' ] and error_message: log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, error_message ) ) unsuccessful_count += 1 + elif status in [ 'ok' ] and error_message: + log.debug( "Successfully reset metadata on repository %s, but encountered this problem: %s" % ( repository.name, error_message ) ) + successful_count += 1 else: log.debug( "Successfully reset metadata on repository %s" % repository.name ) successful_count += 1 diff -r 29b8e39db1094cb5a5586c4f7b404428641d518c -r f551610b687003fc09cd6ff7bbc506d237c67a75 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -6,8 +6,9 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * from galaxy.util.shed_util import copy_sample_file, generate_datatypes_metadata, generate_tool_dependency_metadata, generate_tool_metadata -from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_configured_ui, handle_sample_tool_data_table_conf_file -from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables, strip_path, to_html_escaped, to_html_str, update_repository +from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_configured_ui, get_named_tmpfile_from_ctx +from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH, make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables +from galaxy.util.shed_util import reversed_upper_bounded_changelog, strip_path, to_html_escaped, to_html_str, update_repository from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -201,7 +202,7 @@ if options: if options.tool_data_table or options.missing_tool_data_table_name: # Make sure the repository contains a tool_data_table_conf.xml.sample file. - sample_tool_data_table_conf = get_config( 'tool_data_table_conf.xml.sample', repo, repo_dir, ctx, dir ) + sample_tool_data_table_conf = get_config( 'tool_data_table_conf.xml.sample', repo, ctx, dir ) if sample_tool_data_table_conf: error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, sample_tool_data_table_conf ) if error: @@ -254,9 +255,9 @@ # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision is an ancestor of # current_changeset_revision which is associated with current_metadata_dict. # - # TODO: a new repository_metadata record will be created only when this method returns the string 'not equal and not subset'. However, - # we're currently also returning the strings 'no metadata', 'equal' and 'subset', depending upon how the 2 change sets compare. We'll - # leave things this way for the current time in case we discover a use for these additional result strings. + # A new repository_metadata record will be created only when this method returns the string 'not equal and not subset'. However, we're + # currently also returning the strings 'no metadata', 'equal' and 'subset', depending upon how the 2 change sets compare. We'll leave + # things this way for the current time in case we discover a use for these additional result strings. ancestor_datatypes = ancestor_metadata_dict.get( 'datatypes', [] ) ancestor_tools = ancestor_metadata_dict.get( 'tools', [] ) ancestor_guids = [ tool_dict[ 'guid' ] for tool_dict in ancestor_tools ] @@ -357,41 +358,18 @@ tmp_filename = None return tmp_filename def copy_file_from_manifest( repo, ctx, filename, dir ): - """Copy a file named filename from somewhere in the repository manifest to the directory to which dir refers.""" - filename = strip_path( filename ) - fctx = None - found = False - # First see if the file is in ctx. We have to be careful in determining if we found the correct file because multiple files - # with the same name may be in different directories within ctx if the repository owner moved the files as part of the change set. - # For example, in the following ctx.files() list, the former may have been moved to the latter: - # ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample'] - for ctx_file in ctx.files(): - ctx_file_name = strip_path( ctx_file ) - if filename == ctx_file_name: - try: - fctx = ctx[ ctx_file ] - found = True - break - except: - continue - if not found: - # Find the file in the repository manifest. - for changeset in repo.changelog: - prev_ctx = repo.changectx( changeset ) - for ctx_file in prev_ctx.files(): - ctx_file_name = strip_path( ctx_file ) - if filename == ctx_file_name: - try: - fctx = prev_ctx[ ctx_file ] - break - except: - continue - if fctx: - file_path = os.path.join( dir, filename ) - fh = open( file_path, 'wb' ) - fh.write( fctx.data() ) - fh.close() - return file_path + """ + Copy the latest version of the file named filename from the repository manifest to the directory to which dir refers. + """ + for changeset in reversed_upper_bounded_changelog( repo, ctx ): + changeset_ctx = repo.changectx( changeset ) + fctx = get_file_context_from_ctx( changeset_ctx, filename ) + if fctx and fctx not in [ 'DELETED' ]: + file_path = os.path.join( dir, filename ) + fh = open( file_path, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return file_path return None def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ): repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) @@ -444,10 +422,10 @@ invalid_tool_configs = [] original_tool_data_path = trans.app.config.tool_data_path work_dir = make_tmp_directory() - datatypes_config = get_config( 'datatypes_conf.xml', repo, repo_dir, ctx, work_dir ) + datatypes_config = get_config( 'datatypes_conf.xml', repo, ctx, work_dir ) if datatypes_config: metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) - sample_files = get_sample_files( repo, repo_dir, dir=work_dir ) + sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) # Handle the tool_data_table_conf.xml.sample file if it is included in the repository. if 'tool_data_table_conf.xml.sample' in sample_files: tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) @@ -515,7 +493,7 @@ invalid_files.append( ( ctx_file_name, str( e ) ) ) if 'tools' in metadata_dict: # Find tool_dependencies.xml if it exists. This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config( 'tool_dependencies.xml', repo, repo_dir, ctx, work_dir ) + tool_dependencies_config = get_config( 'tool_dependencies.xml', repo, ctx, work_dir ) if tool_dependencies_config: metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) if invalid_tool_configs: @@ -529,7 +507,7 @@ shutil.rmtree( work_dir ) except: pass - return metadata_dict, invalid_files + return metadata_dict, invalid_files, deleted_sample_files def generate_tool_guid( trans, repository, tool ): """ Generate a guid for the received tool. The form of the guid is @@ -548,21 +526,59 @@ return trans.sa_session.query( trans.model.Category ) \ .filter( trans.model.Category.table.c.deleted==False ) \ .order_by( trans.model.Category.table.c.name ).all() +def get_file_context_from_ctx( ctx, filename ): + # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories + # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to + # the latter: + # ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample'] + filename = strip_path( filename ) + for ctx_file in ctx.files(): + ctx_file_name = strip_path( ctx_file ) + if filename == ctx_file_name: + try: + fctx = ctx[ ctx_file ] + return fctx + except LookupError, e: + return 'DELETED' + return None 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.id.desc() ) \ .first() -def get_named_tmpfile_from_ctx( ctx, filename, dir ): - fctx = ctx[ filename ] - fh = tempfile.NamedTemporaryFile( 'wb', dir=dir ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'wb' ) - fh.write( fctx.data() ) - fh.close() - return tmp_filename +def get_list_of_copied_sample_files( repo, ctx, dir ): + """ + Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy + each discovered file to dir and return the list of filenames. If a .sample file was added in a changeset and then deleted in a later + changeset, it will be returned in the deleted_sample_files list. The caller will set the value of app.config.tool_data_path to dir in + order to load the tools and generate metadata for them. + """ + deleted_sample_files = [] + sample_files = [] + for changeset in reversed_upper_bounded_changelog( repo, ctx ): + changeset_ctx = repo.changectx( changeset ) + for ctx_file in changeset_ctx.files(): + ctx_file_name = strip_path( ctx_file ) + # If we decide in the future that files deleted later in the changelog should not be used, we can use the following if statement. + # if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files: + if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files: + fctx = get_file_context_from_ctx( changeset_ctx, ctx_file ) + if fctx in [ 'DELETED' ]: + # Since the possibly future used if statement above is commented out, the same file that was initially added will be + # discovered in an earlier changeset in the change log and fall through to the else block below. In other words, if + # a file named blast2go.loc.sample was added in change set 0 and then deleted in changeset 3, the deleted file in changeset + # 3 will be handled here, but the later discovered file in changeset 0 will be handled in the else block below. In this + # way, the file contents will always be found for future tools even though the file was deleted. + if ctx_file_name not in deleted_sample_files: + deleted_sample_files.append( ctx_file_name ) + else: + sample_files.append( ctx_file_name ) + tmp_ctx_file_name = os.path.join( dir, ctx_file_name.replace( '.sample', '' ) ) + fh = open( tmp_ctx_file_name, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return sample_files, deleted_sample_files def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ): parent_id = None # Compare from most recent to oldest. @@ -582,6 +598,10 @@ # The tool did not change through all of the changeset revisions. return old_id def get_previous_valid_changset_revision( repository, repo, before_changeset_revision ): + """ + Return the downloadable changeset_revision in the repository changelog just prior to the changeset to which before_changeset_revision + refers. If there isn't one, return the hash value of an empty repository changlog, INITIAL_CHANGELOG_HASH. + """ changeset_tups = [] for repository_metadata in repository.downloadable_revisions: changeset_revision = repository_metadata.changeset_revision @@ -600,7 +620,7 @@ return previous_changeset_revision else: # Return the hash value of an empty repository changlog - note that this will not be a valid changset revision. - return '000000000000' + return INITIAL_CHANGELOG_HASH else: previous_changeset_revision = current_changeset_revision def get_repository( trans, id ): @@ -640,29 +660,6 @@ return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) else: return "-1:%s" % changeset_revision -def get_sample_files( repo, repo_dir, dir ): - """Return a list of all files in the repository with the special .sample extension""" - sample_files = [] - # Copy all discovered sample files to dir, and the caller will set the value of app.config.tool_data_path to dir - # in order to load the tools and generate metadata for them. First look on disk. - for root, dirs, files in os.walk( repo_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name.endswith( '.sample' ) and name not in sample_files: - new_name = name.replace( '.sample', '' ) - file_path = os.path.join( dir, new_name ) - shutil.copy( os.path.abspath( os.path.join( root, name ) ), file_path ) - sample_files.append( name ) - # Next look in the repository manifest. - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - for ctx_file in ctx.files(): - ctx_file_name = strip_path( ctx_file ) - if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files: - new_ctx_file_name = ctx_file_name.replace( '.sample', '' ) - copy_file_from_manifest( repo, ctx, ctx_file, dir ) - sample_files.append( ctx_file_name ) - return sample_files def get_user( trans, id ): """Get a user from the database by id""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) @@ -796,7 +793,7 @@ tool = load_tool( trans, tmp_tool_config ) except Exception, e: tool = None - message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) + message = "Error loading tool: %s. " % str( e ) for tmp_code_file in tmp_code_files: try: os.unlink( tmp_code_file ) @@ -819,40 +816,19 @@ tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) if tool_data_table_config: error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) - if changeset_revision == repository.tip: - # Load the tool fron it's config file on disk. - try: - copied_tool_config = copy_file_from_disk( tool_config_filename, repo_files_dir, work_dir ) - tool = load_tool( trans, copied_tool_config ) - except Exception, e: - tool = None - message = "Error loading tool from config '%s': %s." % ( tool_config_filename, str( e ) ) - else: - found = False - tool = None - # Get the tool config from ctx if present. - for ctx_file in ctx.files(): + found = False + # Get the latest revision of the tool config from the repository manifest up to the value of changeset_revision. + for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): + manifest_changeset_revision = str( repo.changectx( changeset ) ) + manifest_ctx = repo.changectx( changeset ) + for ctx_file in manifest_ctx.files(): ctx_file_name = strip_path( ctx_file ) if ctx_file_name == tool_config_filename: found = True break if found: - if found: - tool, message = load_from_tmp_config( ctx, ctx_file, work_dir ) - else: - # Get the tool config from the repository manifest between valid changeset revisions. - previous_valid_changset_revision = get_previous_valid_changset_revision( repository, repo, changeset_revision ) - for changeset in reversed_filtered_changelog( repo, previous_valid_changset_revision, changeset_revision ): - manifest_changeset_revision = str( repo.changectx( changeset ) ) - manifest_ctx = repo.changectx( changeset ) - for ctx_file in manifest_ctx.files(): - ctx_file_name = strip_path( ctx_file ) - if ctx_file_name == tool_config_filename: - found = True - break - if found: - tool, message = load_from_tmp_config( manifest_ctx, ctx_file, work_dir ) - break + tool, message = load_from_tmp_config( manifest_ctx, ctx_file, work_dir ) + break # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) try: @@ -968,6 +944,7 @@ log.debug( "Resetting all metadata on repository: %s" % repository.name ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) + missing_sample_files = [] if len( repo ) == 1: error_message, status = set_repository_metadata( trans, id, repository.tip, **kwd ) if error_message: @@ -983,13 +960,16 @@ for changeset in repo.changelog: current_changeset_revision = str( repo.changectx( changeset ) ) ctx = get_changectx_for_changeset( repo, current_changeset_revision ) - current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, - repo, - id, - ctx, - current_changeset_revision, - repo_dir, - updating_tip=current_changeset_revision==repository.tip ) + current_metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans, + repo, + id, + ctx, + current_changeset_revision, + repo_dir, + updating_tip=current_changeset_revision==repository.tip ) + for deleted_sample_file in deleted_sample_files: + if deleted_sample_file not in missing_sample_files: + missing_sample_files.append( deleted_sample_file ) if current_metadata_dict: if ancestor_changeset_revision: # Compare metadata from ancestor and current. The value of comparsion will be one of: @@ -1032,27 +1012,12 @@ ancestor_metadata_dict = None clean_repository_metadata( trans, id, changeset_revisions ) add_repository_metadata_tool_versions( trans, id, changeset_revisions ) + if missing_sample_files: + message += "Metadata was successfully reset, but the following required sample files have been deleted from the repository so the version " + message += "of each file just prior to its deletion is being used. These files should be re-added to the repository as soon as possible: " + message += "<b>%s</b><br/>" % ', '.join( missing_sample_files ) + return message, 'ok' return '', 'ok' -def reversed_filtered_changelog( repo, excluded_lower_bounds_changeset_revision, included_upper_bounds_changeset_revision ): - """ - Return a reversed list of changesets in the repository changelog after the excluded_lower_bounds_changeset_revision, but up to and - including the included_upper_bounds_changeset_revision. The value of excluded_lower_bounds_changeset_revision will be '000000000000' - if no valid changesets exist before included_upper_bounds_changeset_revision. - """ - if excluded_lower_bounds_changeset_revision == '000000000000': - appending_started = True - else: - appending_started = False - reversed_changelog = [] - for changeset in repo.changelog: - changeset_hash = str( repo.changectx( changeset ) ) - if appending_started: - reversed_changelog.insert( 0, changeset ) - if changeset_hash == excluded_lower_bounds_changeset_revision and not appending_started: - appending_started = True - if changeset_hash == included_upper_bounds_changeset_revision: - break - return reversed_changelog def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ): """ Set repository metadata on the repository tip, returning specific error messages (if any) to alert the repository owner that the changeset @@ -1068,13 +1033,13 @@ invalid_files = [] updating_tip = changeset_revision == repository.tip if ctx is not None: - metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, - repo, - id, - ctx, - changeset_revision, - repo_dir, - updating_tip=updating_tip ) + metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans, + repo, + id, + ctx, + changeset_revision, + repo_dir, + updating_tip=updating_tip ) if metadata_dict: if updating_tip: if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ): @@ -1120,6 +1085,10 @@ # Here ctx is None. message = "This repository does not include revision '%s'." % str( changeset_revision ) status = 'error' + if deleted_sample_files: + message += "Metadata was successfully reset, but the following required sample files have been deleted from the repository so the version " + message += "of each file just prior to its deletion is being used. These files should be re-added to the repository as soon as possible: " + message += "<b>%s</b><br/>" % ', '.join( deleted_sample_files ) if invalid_files: if metadata_dict: message = "Metadata was defined for some items in revision '%s'. " % str( changeset_revision ) diff -r 29b8e39db1094cb5a5586c4f7b404428641d518c -r f551610b687003fc09cd6ff7bbc506d237c67a75 lib/galaxy/webapps/community/controllers/hg.py --- a/lib/galaxy/webapps/community/controllers/hg.py +++ b/lib/galaxy/webapps/community/controllers/hg.py @@ -27,8 +27,10 @@ repository = get_repository_by_name_and_owner( trans, name, owner ) if repository: error_message, status = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) ) - if error_message: - log.debug( "Error resetting all metadata on repository '%s': %s" % ( str( repository.name ), str( error_message ) ) ) + if status not in [ 'ok' ] and error_message: + log.debug( "Error resetting metadata on repository '%s': %s" % ( str( repository.name ), str( error_message ) ) ) + elif status in [ 'ok' ] and error_message: + log.debug( "Successfully reset metadata on repository %s, but encountered problem: %s" % ( str( repository.name ), str( error_message ) ) ) return wsgi_app def make_web_app(): diff -r 29b8e39db1094cb5a5586c4f7b404428641d518c -r f551610b687003fc09cd6ff7bbc506d237c67a75 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -10,7 +10,7 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * -from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, make_tmp_directory, NOT_TOOL_CONFIGS, strip_path +from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, get_named_tmpfile_from_ctx, make_tmp_directory, NOT_TOOL_CONFIGS, strip_path from galaxy.tool_shed.encoding_util import * from common import * @@ -323,17 +323,26 @@ email_alerts_repository_list_grid = EmailAlertsRepositoryListGrid() category_list_grid = CategoryListGrid() - @web.expose - def index( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - # See if there are any RepositoryMetadata records since menu items require them. - repository_metadata = trans.sa_session.query( model.RepositoryMetadata ).first() - return trans.fill_template( '/webapps/community/index.mako', - repository_metadata=repository_metadata, - message=message, - status=status ) + def __add_hgweb_config_entry( self, trans, repository, repository_path ): + # Add an entry in the hgweb.config file for a new repository. An entry looks something like: + # repos/test/mira_assembler = database/community_files/000/repo_123. + hgweb_config = "%s/hgweb.config" % trans.app.config.root + if repository_path.startswith( './' ): + repository_path = repository_path.replace( './', '', 1 ) + entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path ) + tmp_fd, tmp_fname = tempfile.mkstemp() + if os.path.exists( hgweb_config ): + # Make a backup of the hgweb.config file since we're going to be changing it. + self.__make_hgweb_config_copy( trans, hgweb_config ) + new_hgweb_config = open( tmp_fname, 'wb' ) + for i, line in enumerate( open( hgweb_config ) ): + new_hgweb_config.write( line ) + else: + new_hgweb_config = open( tmp_fname, 'wb' ) + new_hgweb_config.write( '[paths]\n' ) + new_hgweb_config.write( "%s\n" % entry ) + new_hgweb_config.flush() + shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) @web.expose def browse_categories( self, trans, **kwd ): if 'f-free-text-search' in kwd: @@ -360,9 +369,146 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', **kwd ) ) - # Render the list view return self.category_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' ) + cntrller = params.get( 'cntrller', 'repository' ) + is_admin = trans.user_is_admin() + invalid_tools_dict = odict() + 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 ): + 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', + cntrller=cntrller, + invalid_tools_dict=invalid_tools_dict, + webapp=webapp, + message=message, + status=status ) + @web.expose + 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 + # to take this approach because the "-" character is illegal in HTTP requests. + if 'webapp' not in kwd: + kwd[ 'webapp' ] = 'community' + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "view_or_manage_repository": + repository_id = kwd[ 'id' ] + repository = get_repository( trans, repository_id ) + is_admin = trans.user_is_admin() + if is_admin or repository.user == trans.user: + return trans.response.send_redirect( web.url_for( controller='repository', + action='manage_repository', + **kwd ) ) + else: + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_repository', + **kwd ) ) + elif operation == "edit_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='edit_repository', + **kwd ) ) + elif operation == "repositories_by_user": + # Eliminate the current filters if any exist. + for k, v in kwd.items(): + if k.startswith( 'f-' ): + del kwd[ k ] + if 'user_id' in kwd: + user = get_user( trans, kwd[ 'user_id' ] ) + kwd[ 'f-email' ] = user.email + del kwd[ 'user_id' ] + else: + # The received id is the repository id, so we need to get the id of the user + # that uploaded the repository. + repository_id = kwd.get( 'id', None ) + repository = get_repository( trans, repository_id ) + kwd[ 'f-email' ] = repository.user.email + elif operation == "my_repositories": + # Eliminate the current filters if any exist. + for k, v in kwd.items(): + if k.startswith( 'f-' ): + del kwd[ k ] + kwd[ 'f-email' ] = trans.user.email + elif operation == "repositories_by_category": + # Eliminate the current filters if any exist. + for k, v in kwd.items(): + if k.startswith( 'f-' ): + del kwd[ k ] + category_id = kwd.get( 'id', None ) + category = get_category( trans, category_id ) + kwd[ 'f-Category.name' ] = category.name + elif operation == "receive email alerts": + if trans.user: + if kwd[ 'id' ]: + kwd[ 'caller' ] = 'browse_repositories' + return trans.response.send_redirect( web.url_for( controller='repository', + action='set_email_alerts', + **kwd ) ) + else: + kwd[ 'message' ] = 'You must be logged in to set email alerts.' + kwd[ 'status' ] = 'error' + del kwd[ 'operation' ] + # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change + # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One + # of the many select fields on the grid performed the refresh_on_change, so we loop through + # all of the received values to see which value is not the repository tip. If we find it, we + # know the refresh_on_change occurred, and we have the necessary repository id and change set + # revision to pass on. + for k, v in kwd.items(): + changset_revision_str = 'changeset_revision_' + if k.startswith( changset_revision_str ): + repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) + repository = get_repository( trans, repository_id ) + if repository.tip != v: + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + operation='view_or_manage_repository', + id=trans.security.encode_id( repository.id ), + changeset_revision=v ) ) + return self.repository_list_grid( trans, **kwd ) + @web.expose + def browse_repository( self, trans, id, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) + commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) + repository = get_repository( trans, id ) + repo = hg.repository( get_configured_ui(), repository.repo_path ) + current_working_dir = os.getcwd() + # Update repository files for browsing. + update_repository( repo ) + is_malicious = changeset_is_malicious( trans, id, repository.tip ) + return trans.fill_template( '/webapps/community/repository/browse_repository.mako', + repo=repo, + repository=repository, + commit_message=commit_message, + is_malicious=is_malicious, + webapp=webapp, + message=message, + status=status ) + @web.expose def browse_valid_repositories( self, trans, **kwd ): webapp = kwd.get( 'webapp', 'community' ) galaxy_url = kwd.get( 'galaxy_url', None ) @@ -404,40 +550,400 @@ allow_multiple=False, async_compatible=False ) ] return self.valid_repository_list_grid( trans, **kwd ) + def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ): + options = [] + for user in trans.sa_session.query( trans.model.User ): + if user.username not in current_push_list: + options.append( user ) + return build_select_field( trans, + objs=options, + label_attr='username', + select_field_name='allow_push', + selected_value=selected_value, + refresh_on_change=False, + multiple=True ) + def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ): + # Change an entry in the hgweb.config file for a repository. This only happens when + # the owner changes the name of the repository. An entry looks something like: + # repos/test/mira_assembler = database/community_files/000/repo_123. + hgweb_config = "%s/hgweb.config" % trans.app.config.root + # Make a backup of the hgweb.config file since we're going to be changing it. + self.__make_hgweb_config_copy( trans, hgweb_config ) + repo_dir = repository.repo_path + old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) + new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir ) + tmp_fd, tmp_fname = tempfile.mkstemp() + new_hgweb_config = open( tmp_fname, 'wb' ) + for i, line in enumerate( open( hgweb_config ) ): + if line.startswith( old_lhs ): + new_hgweb_config.write( new_entry ) + else: + new_hgweb_config.write( line ) + new_hgweb_config.flush() + shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) @web.expose - def browse_invalid_tools( self, trans, **kwd ): + def check_for_updates( self, trans, **kwd ): + """ + Handle a request from a local Galaxy instance. If the request originated with the Galaxy instances' UpdateManager, the value of 'webapp' + will be 'update_manager'. + """ + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + # If the request originated with the UpdateManager, it will not include a galaxy_url. + galaxy_url = kwd.get( 'galaxy_url', '' ) + name = params.get( 'name', None ) + owner = params.get( 'owner', None ) + changeset_revision = params.get( 'changeset_revision', None ) + webapp = params.get( 'webapp', 'community' ) + repository = get_repository_by_name_and_owner( trans, name, owner ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + from_update_manager = webapp == 'update_manager' + if from_update_manager: + update = 'true' + no_update = 'false' + else: + # Start building up the url to redirect back to the calling Galaxy instance. + url = '%sadmin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '/', qualified=True ) ) + url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % ( repository.name, repository.user.username, changeset_revision ) + if changeset_revision == repository.tip: + # If changeset_revision is the repository tip, we know there are no additional updates for the tools. + if from_update_manager: + return no_update + # Return the same value for changeset_revision and latest_changeset_revision. + url += repository.tip + else: + repository_metadata = get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + # If changeset_revision is in the repository_metadata table for this repository, then we know there are no additional updates + # for the tools. + if from_update_manager: + return no_update + else: + # Return the same value for changeset_revision and latest_changeset_revision. + url += changeset_revision + else: + # TODO: Re-engineer this to define the change set for update to be the one just before the next change set in the repository_metadata + # table for this repository. + # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the + # repository was cloned. 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( repo, changeset_revision ) + if ctx is not None: + work_dir = make_tmp_directory() + tool_guids = [] + for filename in ctx: + # Find all tool configs in this repository changeset_revision. + if filename not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): + is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, + repo, + repo_dir, + ctx, + filename, + work_dir ) + if valid and tool is not None: + tool_guids.append( generate_tool_guid( trans, repository, tool ) ) + tool_guids.sort() + if tool_guids: + # Compare our list of tool guids against those in each repository_metadata record for the repository to find the + # repository_metadata record with the changeset_revision value we want to pass back to the caller. + found = False + for repository_metadata in get_repository_metadata_by_repository_id( trans, trans.security.encode_id( repository.id ) ): + metadata = repository_metadata.metadata + metadata_tool_guids = [] + for tool_dict in metadata[ 'tools' ]: + metadata_tool_guids.append( tool_dict[ 'guid' ] ) + metadata_tool_guids.sort() + if tool_guids == metadata_tool_guids: + # We've found the repository_metadata record whose changeset_revision value has been updated. + if from_update_manager: + return update + url += repository_metadata.changeset_revision + # Get the ctx_rev for the discovered changeset_revision. + latest_ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) + found = True + break + if not found: + # There must be a problem in the data, so we'll just send back the received changeset_revision. + log.debug( "Possible data corruption - updated repository_metadata cannot be found for repository id %d." % repository.id ) + if from_update_manager: + return no_update + url += changeset_revision + else: + # There are no tools in the changeset_revision, so no tool updates are possible. + if from_update_manager: + return no_update + url += changeset_revision + try: + shutil.rmtree( work_dir ) + except: + pass + url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) + return trans.response.send_redirect( url ) + @web.expose + def contact_owner( self, trans, id, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository = get_repository( trans, id ) + if trans.user and trans.user.email: + return trans.fill_template( "/webapps/community/repository/contact_owner.mako", + repository=repository, + message=message, + status=status ) + else: + # Do all we can to eliminate spam. + return trans.show_error_message( "You must be logged in to contact the owner of a repository." ) + def __create_hgrc_file( self, repository ): + # At this point, an entry for the repository is required to be in the hgweb.config file so we can call repository.repo_path. + # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api. + # The hg purge extension purges all files and directories not being tracked by mercurial in the current repository. It'll + # remove unknown files and empty directories. This is not currently used because it is not supported in the mercurial API. + repo = hg.repository( get_configured_ui(), path=repository.repo_path ) + fp = repo.opener( 'hgrc', 'wb' ) + fp.write( '[paths]\n' ) + fp.write( 'default = .\n' ) + fp.write( 'default-push = .\n' ) + fp.write( '[web]\n' ) + fp.write( 'allow_push = %s\n' % repository.user.username ) + fp.write( 'name = %s\n' % repository.name ) + fp.write( 'push_ssl = false\n' ) + fp.write( '[extensions]\n' ) + fp.write( 'hgext.purge=' ) + fp.close() + @web.expose + def create_repository( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + categories = get_categories( trans ) + if not categories: + message = 'No categories have been configured in this instance of the Galaxy Tool Shed. ' + \ + 'An administrator needs to create some via the Administrator control panel before creating repositories.', + status = 'error' + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + message=message, + status=status ) ) + name = util.restore_text( params.get( 'name', '' ) ) + description = util.restore_text( params.get( 'description', '' ) ) + long_description = util.restore_text( params.get( 'long_description', '' ) ) + category_ids = util.listify( params.get( 'category_id', '' ) ) + selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] + if params.get( 'create_repository_button', False ): + error = False + message = self.__validate_repository_name( name, trans.user ) + if message: + error = True + if not description: + message = 'Enter a description.' + error = True + if not error: + # Add the repository record to the db + repository = trans.app.model.Repository( name=name, + description=description, + long_description=long_description, + user_id=trans.user.id ) + # Flush to get the id + trans.sa_session.add( repository ) + trans.sa_session.flush() + # Determine the repository's repo_path on disk + dir = os.path.join( trans.app.config.file_path, *directory_hash_id( repository.id ) ) + # Create directory if it does not exist + if not os.path.exists( dir ): + os.makedirs( dir ) + # Define repo name inside hashed directory + repository_path = os.path.join( dir, "repo_%d" % repository.id ) + # Create local repository directory + if not os.path.exists( repository_path ): + os.makedirs( repository_path ) + # Create the local repository + repo = hg.repository( get_configured_ui(), repository_path, create=True ) + # Add an entry in the hgweb.config file for the local repository + # This enables calls to repository.repo_path + self.__add_hgweb_config_entry( trans, repository, repository_path ) + # Create a .hg/hgrc file for the local repository + self.__create_hgrc_file( repository ) + flush_needed = False + if category_ids: + # Create category associations + for category_id in category_ids: + category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) + rca = trans.app.model.RepositoryCategoryAssociation( repository, category ) + trans.sa_session.add( rca ) + flush_needed = True + if flush_needed: + trans.sa_session.flush() + message = "Repository '%s' has been created." % repository.name + trans.response.send_redirect( web.url_for( controller='repository', + action='view_repository', + webapp='community', + message=message, + id=trans.security.encode_id( repository.id ) ) ) + return trans.fill_template( '/webapps/community/repository/create_repository.mako', + name=name, + description=description, + long_description=long_description, + selected_categories=selected_categories, + categories=categories, + message=message, + status=status ) + @web.expose + 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' ) webapp = params.get( 'webapp', 'community' ) - cntrller = params.get( 'cntrller', 'repository' ) - is_admin = trans.user_is_admin() - invalid_tools_dict = odict() - 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 ): - 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', - cntrller=cntrller, - invalid_tools_dict=invalid_tools_dict, + repository = get_repository( trans, repository_id ) + tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) + tool_state = self.__new_state( trans ) + is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) + try: + 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=status ) + except Exception, e: + message = "Error displaying tool, probably due to a problem in the tool config. The exception is: %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' ) ) + @web.expose + def download( self, trans, repository_id, changeset_revision, file_type, **kwd ): + # Download an archive of the repository files compressed as zip, gz or bz2. + params = util.Params( kwd ) + repository = get_repository( trans, repository_id ) + # Allow hgweb to handle the download. This requires the tool shed + # server account's .hgrc file to include the following setting: + # [web] + # allow_archive = bz2, gz, zip + if file_type == 'zip': + file_type_str = '%s.zip' % changeset_revision + elif file_type == 'bz2': + file_type_str = '%s.tar.bz2' % changeset_revision + elif file_type == 'gz': + file_type_str = '%s.tar.gz' % changeset_revision + repository.times_downloaded += 1 + trans.sa_session.add( repository ) + trans.sa_session.flush() + download_url = '/repos/%s/%s/archive/%s' % ( repository.user.username, repository.name, file_type_str ) + return trans.response.send_redirect( download_url ) + def __encode_repo_info_dict( self, trans, webapp, repository_metadata_ids ): + repo_info_dict = {} + includes_tools = False + for repository_metadata_id in repository_metadata_ids: + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + if not includes_tools and 'tools' in repository_metadata.metadata: + includes_tools = True + repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + # Get the changelog rev for this changeset_revision. + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + changeset_revision = repository_metadata.changeset_revision + ctx = get_changectx_for_changeset( repo, changeset_revision ) + repository_id = trans.security.encode_id( repository.id ) + repository_clone_url = generate_clone_url( trans, repository_id ) + repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision, str( ctx.rev() ) ) + return encode( repo_info_dict ), includes_tools + @web.expose + def find_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' ) + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + if 'operation' in kwd: + item_id = kwd.get( 'id', '' ) + if item_id: + operation = kwd[ 'operation' ].lower() + is_admin = trans.user_is_admin() + if operation == "view_or_manage_repository": + # The received id is a RepositoryMetadata id, so we have to get the repository id. + repository_metadata = get_repository_metadata_by_id( trans, item_id ) + repository_id = trans.security.encode_id( repository_metadata.repository.id ) + repository = get_repository( trans, repository_id ) + kwd[ 'id' ] = repository_id + kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision + if webapp == 'community' and ( is_admin or repository.user == trans.user ): + a = 'manage_repository' + else: + a = 'view_repository' + return trans.response.send_redirect( web.url_for( controller='repository', + action=a, + **kwd ) ) + if operation == "install": + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) + url = '%sadmin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \ + ( galaxy_url, url_for( '/', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) ) + return trans.response.send_redirect( url ) + else: + # This can only occur when there is a multi-select grid with check boxes and an operation, + # and the user clicked the operation button without checking any of the check boxes. + return trans.show_error_message( "No items were selected." ) + tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ] + tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ] + tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ] + exact_matches = params.get( 'exact_matches', '' ) + exact_matches_checked = CheckboxField.is_checked( exact_matches ) + match_tuples = [] + ok = True + if tool_ids or tool_names or tool_versions: + ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, tool_versions=tool_versions ) + if ok: + kwd[ 'match_tuples' ] = match_tuples + # Render the list view + if webapp == 'galaxy': + # Our initial request originated from a Galaxy instance. + global_actions = [ grids.GridAction( "Browse valid repositories", + dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), + grids.GridAction( "Search for valid tools", + dict( controller='repository', action='find_tools', webapp=webapp ) ), + grids.GridAction( "Search for workflows", + dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] + self.install_matched_repository_list_grid.global_actions = global_actions + install_url_args = dict( controller='repository', action='find_tools', webapp=webapp ) + operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] + self.install_matched_repository_list_grid.operations = operations + return self.install_matched_repository_list_grid( trans, **kwd ) + else: + kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ + ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) ) + self.matched_repository_list_grid.title = "Repositories with matching tools" + return self.matched_repository_list_grid( trans, **kwd ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" + exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) + return trans.fill_template( '/webapps/community/repository/find_tools.mako', webapp=webapp, + tool_id=self.__stringify( tool_ids ), + tool_name=self.__stringify( tool_names ), + tool_version=self.__stringify( tool_versions ), + exact_matches_check_box=exact_matches_check_box, message=message, - status=status ) + status=status ) @web.expose def find_workflows( self, trans, **kwd ): params = util.Params( kwd ) @@ -521,160 +1027,127 @@ message=message, status=status ) @web.expose - def find_tools( self, trans, **kwd ): + def get_ctx_rev( self, trans, **kwd ): + """Given a repository and changeset_revision, return the correct ctx.rev() value.""" + repository_name = kwd[ 'name' ] + repository_owner = kwd[ 'owner' ] + changeset_revision = kwd[ 'changeset_revision' ] + 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 ) + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + return str( ctx.rev() ) + return '' + @web.json + def get_file_contents( self, trans, file_path ): + # Avoid caching + trans.response.headers['Pragma'] = 'no-cache' + trans.response.headers['Expires'] = '0' + if is_gzip( file_path ): + to_html = to_html_str( '\ngzip compressed file\n' ) + elif is_bz2( file_path ): + to_html = to_html_str( '\nbz2 compressed file\n' ) + elif check_zip( file_path ): + to_html = to_html_str( '\nzip compressed file\n' ) + elif check_binary( file_path ): + to_html = to_html_str( '\nBinary file\n' ) + else: + to_html = '' + for i, line in enumerate( open( file_path ) ): + to_html = '%s%s' % ( to_html, to_html_str( line ) ) + if len( to_html ) > MAX_CONTENT_SIZE: + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) + to_html = '%s%s' % ( to_html, to_html_str( large_str ) ) + break + return to_html + def __get_files( self, trans, folder_path ): + contents = [] + for item in os.listdir( folder_path ): + # Skip .hg directories + if str( item ).startswith( '.hg' ): + continue + if os.path.isdir( os.path.join( folder_path, item ) ): + # Append a '/' character so that our jquery dynatree will + # function properly. + item = '%s/' % item + contents.append( item ) + if contents: + contents.sort() + return contents + @web.expose + def get_readme( self, trans, **kwd ): + """If the received changeset_revision includes a file named readme (case ignored), return it's contents.""" + repository_name = kwd[ 'name' ] + repository_owner = kwd[ 'owner' ] + changeset_revision = kwd[ 'changeset_revision' ] + valid_filenames = [ r for r in README_FILES ] + for r in README_FILES: + valid_filenames.append( '%s.txt' % r ) + valid_filenames.append( '%s.txt' % repository_name ) + repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) + repo_dir = repository.repo_path + for root, dirs, files in os.walk( repo_dir ): + for name in files: + if name.lower() in valid_filenames: + f = open( os.path.join( root, name ), 'r' ) + text = f.read() + f.close() + return str( text ) + return '' + @web.expose + def get_tool_dependencies( self, trans, **kwd ): + # Handle a request from a local Galaxy instance. If the request originated with the Galaxy instances' InstallManager, the value of 'webapp' + # will be 'install_manager'. params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + # If the request originated with the UpdateManager, it will not include a galaxy_url. + galaxy_url = kwd.get( 'galaxy_url', '' ) + name = params.get( 'name', None ) + owner = params.get( 'owner', None ) + changeset_revision = params.get( 'changeset_revision', None ) webapp = params.get( 'webapp', 'community' ) - galaxy_url = kwd.get( 'galaxy_url', None ) - if galaxy_url: - trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) - if 'operation' in kwd: - item_id = kwd.get( 'id', '' ) - if item_id: - operation = kwd[ 'operation' ].lower() - is_admin = trans.user_is_admin() - if operation == "view_or_manage_repository": - # The received id is a RepositoryMetadata id, so we have to get the repository id. - repository_metadata = get_repository_metadata_by_id( trans, item_id ) - repository_id = trans.security.encode_id( repository_metadata.repository.id ) - repository = get_repository( trans, repository_id ) - kwd[ 'id' ] = repository_id - kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision - if webapp == 'community' and ( is_admin or repository.user == trans.user ): - a = 'manage_repository' - else: - a = 'view_repository' - return trans.response.send_redirect( web.url_for( controller='repository', - action=a, - **kwd ) ) - if operation == "install": - galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) ) - url = '%sadmin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \ - ( galaxy_url, url_for( '/', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) ) - return trans.response.send_redirect( url ) - else: - # This can only occur when there is a multi-select grid with check boxes and an operation, - # and the user clicked the operation button without checking any of the check boxes. - return trans.show_error_message( "No items were selected." ) - tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ] - tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ] - tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ] - exact_matches = params.get( 'exact_matches', '' ) - exact_matches_checked = CheckboxField.is_checked( exact_matches ) - match_tuples = [] - ok = True - if tool_ids or tool_names or tool_versions: - ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, tool_versions=tool_versions ) - if ok: - kwd[ 'match_tuples' ] = match_tuples - # Render the list view - if webapp == 'galaxy': - # Our initial request originated from a Galaxy instance. - global_actions = [ grids.GridAction( "Browse valid repositories", - dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), - grids.GridAction( "Search for valid tools", - dict( controller='repository', action='find_tools', webapp=webapp ) ), - grids.GridAction( "Search for workflows", - dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] - self.install_matched_repository_list_grid.global_actions = global_actions - install_url_args = dict( controller='repository', action='find_tools', webapp=webapp ) - operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] - self.install_matched_repository_list_grid.operations = operations - return self.install_matched_repository_list_grid( trans, **kwd ) - else: - kwd[ 'message' ] = "tool id: <b>%s</b><br/>tool name: <b>%s</b><br/>tool version: <b>%s</b><br/>exact matches only: <b>%s</b>" % \ - ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) ) - self.matched_repository_list_grid.title = "Repositories with matching tools" - return self.matched_repository_list_grid( trans, **kwd ) - else: - message = "No search performed - each field must contain the same number of comma-separated items." - status = "error" - exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) - return trans.fill_template( '/webapps/community/repository/find_tools.mako', - webapp=webapp, - tool_id=self.__stringify( tool_ids ), - tool_name=self.__stringify( tool_names ), - tool_version=self.__stringify( tool_versions ), - exact_matches_check_box=exact_matches_check_box, - message=message, - status=status ) - def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ): - match_tuples = [] - ok = True - for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): - metadata = repository_metadata.metadata - if tool_ids or tool_names or tool_versions: - if 'tools' in metadata: - tools = metadata[ 'tools' ] - else: - tools = [] - for tool_dict in tools: - if tool_ids and not tool_names and not tool_versions: - for tool_id in tool_ids: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_names and not tool_ids and not tool_versions: - for tool_name in tool_names: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_versions and not tool_ids and not tool_names: - for tool_version in tool_versions: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_ids and tool_names and not tool_versions: - if len( tool_ids ) == len( tool_names ): - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - elif len( tool_ids ) == 1 or len( tool_names ) == 1: - tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - else: - ok = False - elif tool_ids and tool_versions and not tool_names: - if len( tool_ids ) == len( tool_versions ): - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - elif len( tool_ids ) == 1 or len( tool_versions ) == 1: - tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and not tool_ids: - if len( tool_versions ) == len( tool_names ): - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - elif len( tool_versions ) == 1 or len( tool_names ) == 1: - tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and tool_ids: - if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): - for i, tool_version in enumerate( tool_versions ): - tool_name = tool_names[ i ] - tool_id = tool_ids[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - else: - ok = False - elif workflow_names: - 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> ] - workflow_tups = metadata[ 'workflows' ] - workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ] - else: - workflows = [] - for workflow_dict in workflows: - for workflow_name in workflow_names: - if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif all_workflows and 'workflows' in metadata: - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - return ok, match_tuples - def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ): - workflow_dict_workflow_name = workflow_dict[ 'name' ].lower() - return ( workflow_name == workflow_dict_workflow_name ) or \ - ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 ) + repository = get_repository_by_name_and_owner( trans, name, owner ) + for downloadable_revision in repository.downloadable_revisions: + if downloadable_revision.changeset_revision == changeset_revision: + break + metadata = downloadable_revision.metadata + tool_dependencies = metadata.get( 'tool_dependencies', '' ) + if webapp == 'install_manager': + if tool_dependencies: + return tool_shed_encode( tool_dependencies ) + return '' + # TODO: future handler where request comes from some Galaxy admin feature. + @web.expose + def get_tool_versions( self, trans, **kwd ): + """ + For each valid /downloadable change set (up to the received changeset_revision) in the repository's change log, append the change + set's tool_versions dictionary to the list that will be returned. + """ + name = kwd[ 'name' ] + owner = kwd[ 'owner' ] + changeset_revision = kwd[ 'changeset_revision' ] + repository = get_repository_by_name_and_owner( trans, name, owner ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + tool_version_dicts = [] + for changeset in repo.changelog: + current_changeset_revision = str( repo.changectx( changeset ) ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), current_changeset_revision ) + if repository_metadata and repository_metadata.tool_versions: + tool_version_dicts.append( repository_metadata.tool_versions ) + if current_changeset_revision == changeset_revision: + break + if tool_version_dicts: + return to_json_string( tool_version_dicts ) + return '' + @web.expose + def help( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + return trans.fill_template( '/webapps/community/repository/help.mako', message=message, status=status, **kwd ) def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): found = False if tool_id and not tool_name and not tool_version: @@ -716,83 +1189,19 @@ tool_dict_tool_name.find( tool_name ) >= 0 and \ tool_dict_tool_id.find( tool_id ) >= 0 ) return found - def __stringify( self, list ): - if list: - return ','.join( list ) - return '' - def __make_same_length( self, list1, list2 ): - # If either list is 1 item, we'll append to it until its - # length is the same as the other. - if len( list1 ) == 1: - for i in range( 1, len( list2 ) ): - list1.append( list1[ 0 ] ) - elif len( list2 ) == 1: - for i in range( 1, len( list1 ) ): - list2.append( list2[ 0 ] ) - return list1, list2 - def __search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ): - for i, tool_id in enumerate( tool_ids ): - tool_name = tool_names[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - return match_tuples - def __search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ): - for i, tool_id in enumerate( tool_ids ): - tool_version = tool_versions[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - return match_tuples - def __search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ): - for i, tool_name in enumerate( tool_names ): - tool_version = tool_versions[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - return match_tuples - def __encode_repo_info_dict( self, trans, webapp, repository_metadata_ids ): - repo_info_dict = {} - includes_tools = False - for repository_metadata_id in repository_metadata_ids: - repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) - if not includes_tools and 'tools' in repository_metadata.metadata: - includes_tools = True - repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) - # Get the changelog rev for this changeset_revision. - repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) - changeset_revision = repository_metadata.changeset_revision - ctx = get_changectx_for_changeset( repo, changeset_revision ) - repository_id = trans.security.encode_id( repository.id ) - repository_clone_url = generate_clone_url( trans, repository_id ) - repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision, str( ctx.rev() ) ) - return encode( repo_info_dict ), includes_tools + def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ): + workflow_dict_workflow_name = workflow_dict[ 'name' ].lower() + return ( workflow_name == workflow_dict_workflow_name ) or \ + ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 ) @web.expose - def preview_tools_in_changeset( self, trans, repository_id, **kwd ): + def index( self, trans, **kwd ): params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) + message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = params.get( 'webapp', 'community' ) - repository = get_repository( trans, repository_id ) - changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) - repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) - if repository_metadata: - repository_metadata_id = trans.security.encode_id( repository_metadata.id ), - metadata = repository_metadata.metadata - else: - repository_metadata_id = None - metadata = None - revision_label = get_revision_label( trans, repository, changeset_revision ) - changeset_revision_select_field = build_changeset_revision_select_field( trans, - repository, - selected_value=changeset_revision, - add_id_to_name=False ) - return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', - repository=repository, - repository_metadata_id=repository_metadata_id, - changeset_revision=changeset_revision, - revision_label=revision_label, - changeset_revision_select_field=changeset_revision_select_field, - metadata=metadata, - webapp=webapp, + # See if there are any RepositoryMetadata records since menu items require them. + repository_metadata = trans.sa_session.query( model.RepositoryMetadata ).first() + return trans.fill_template( '/webapps/community/index.mako', + repository_metadata=repository_metadata, message=message, status=status ) @web.expose @@ -838,633 +1247,117 @@ ( galaxy_url, url_for( '/', qualified=True ), encoded_repo_info_dict, str( includes_tools ) ) return trans.response.send_redirect( url ) @web.expose - def get_ctx_rev( self, trans, **kwd ): - """Given a repository and changeset_revision, return the correct ctx.rev() value.""" - repository_name = kwd[ 'name' ] - repository_owner = kwd[ 'owner' ] - changeset_revision = kwd[ 'changeset_revision' ] - repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) + 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 ) - if ctx: - return str( ctx.rev() ) - return '' - @web.expose - def get_readme( self, trans, **kwd ): - """If the received changeset_revision includes a file named readme (case ignored), return it's contents.""" - repository_name = kwd[ 'name' ] - repository_owner = kwd[ 'owner' ] - changeset_revision = kwd[ 'changeset_revision' ] - valid_filenames = [ r for r in README_FILES ] - for r in README_FILES: - valid_filenames.append( '%s.txt' % r ) - valid_filenames.append( '%s.txt' % repository_name ) - repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner ) - repo_dir = repository.repo_path - for root, dirs, files in os.walk( repo_dir ): - for name in files: - if name.lower() in valid_filenames: - f = open( os.path.join( root, name ), 'r' ) - text = f.read() - f.close() - return str( text ) - return '' - @web.expose - def get_tool_versions( self, trans, **kwd ): - """ - For each valid /downloadable change set (up to the received changeset_revision) in the repository's change log, append the change - set's tool_versions dictionary to the list that will be returned. - """ - name = kwd[ 'name' ] - owner = kwd[ 'owner' ] - changeset_revision = kwd[ 'changeset_revision' ] - repository = get_repository_by_name_and_owner( trans, name, owner ) - repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) - tool_version_dicts = [] - for changeset in repo.changelog: - current_changeset_revision = str( repo.changectx( changeset ) ) - repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), current_changeset_revision ) - if repository_metadata and repository_metadata.tool_versions: - tool_version_dicts.append( repository_metadata.tool_versions ) - if current_changeset_revision == changeset_revision: - break - if tool_version_dicts: - return to_json_string( tool_version_dicts ) - return '' - @web.expose - def check_for_updates( self, trans, **kwd ): - # Handle a request from a local Galaxy instance. If the request originated with the - # Galaxy instances' UpdateManager, the value of 'webapp' will be 'update_manager'. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - # If the request originated with the UpdateManager, it will not include a galaxy_url. - galaxy_url = kwd.get( 'galaxy_url', '' ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) - webapp = params.get( 'webapp', 'community' ) - repository = get_repository_by_name_and_owner( trans, name, owner ) - repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) - latest_ctx = get_changectx_for_changeset( repo, changeset_revision ) - from_update_manager = webapp == 'update_manager' - if from_update_manager: - update = 'true' - no_update = 'false' - else: - # Start building up the url to redirect back to the calling Galaxy instance. - url = '%sadmin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '/', qualified=True ) ) - url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ - ( repository.name, repository.user.username, changeset_revision ) - if changeset_revision == repository.tip: - # If changeset_revision is the repository tip, we know there are no additional updates for the tools. - if from_update_manager: - return no_update - # Return the same value for changeset_revision and latest_changeset_revision. - url += repository.tip - else: - repository_metadata = get_repository_metadata_by_changeset_revision( trans, - trans.security.encode_id( repository.id ), - changeset_revision ) - if repository_metadata: - # If changeset_revision is in the repository_metadata table for this repository, then we know there are no additional updates - # for the tools. - if from_update_manager: - return no_update - else: - # Return the same value for changeset_revision and latest_changeset_revision. - url += changeset_revision - else: - # TODO: Re-engineer this to define the change set for update to be the one just before the next change set in the repository_metadata - # table for this repository. - # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the - # repository was cloned. 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( repo, changeset_revision ) - if ctx is not None: - work_dir = make_tmp_directory() - tool_guids = [] - for filename in ctx: - # Find all tool configs in this repository changeset_revision. - if filename not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): - is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, + invalid_message = '' + work_dir = make_tmp_directory() + for filename in ctx: + ctx_file_name = strip_path( filename ) + if ctx_file_name == tool_config: + tool_config_path = get_named_tmpfile_from_ctx( ctx, filename, work_dir ) + break + metadata_dict, invalid_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans, repo, + repository_id, + ctx, + changeset_revision, repo_dir, - ctx, - filename, - work_dir ) - if valid and tool is not None: - tool_guids.append( generate_tool_guid( trans, repository, tool ) ) - tool_guids.sort() - if tool_guids: - # Compare our list of tool guids against those in each repository_metadata record for the repository to find the - # repository_metadata record with the changeset_revision value we want to pass back to the caller. - found = False - for repository_metadata in get_repository_metadata_by_repository_id( trans, trans.security.encode_id( repository.id ) ): - metadata = repository_metadata.metadata - metadata_tool_guids = [] - for tool_dict in metadata[ 'tools' ]: - metadata_tool_guids.append( tool_dict[ 'guid' ] ) - metadata_tool_guids.sort() - if tool_guids == metadata_tool_guids: - # We've found the repository_metadata record whose changeset_revision value has been updated. - if from_update_manager: - return update - url += repository_metadata.changeset_revision - # Get the ctx_rev for the discovered changeset_revision. - latest_ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) - found = True - break - if not found: - # There must be a problem in the data, so we'll just send back the received changeset_revision. - log.debug( "Possible data corruption - updated repository_metadata cannot be found for repository id %d." % repository.id ) - if from_update_manager: - return no_update - url += changeset_revision - else: - # There are no tools in the changeset_revision, so no tool updates are possible. - if from_update_manager: - return no_update - url += changeset_revision - try: - shutil.rmtree( work_dir ) - except: - pass - url += '&latest_ctx_rev=%s' % str( latest_ctx.rev() ) - return trans.response.send_redirect( url ) - @web.expose - def get_tool_dependencies( self, trans, **kwd ): - # Handle a request from a local Galaxy instance. If the request originated with the Galaxy instances' InstallManager, the value of 'webapp' - # will be 'install_manager'. - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - # If the request originated with the UpdateManager, it will not include a galaxy_url. - galaxy_url = kwd.get( 'galaxy_url', '' ) - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) - webapp = params.get( 'webapp', 'community' ) - repository = get_repository_by_name_and_owner( trans, name, owner ) - for downloadable_revision in repository.downloadable_revisions: - if downloadable_revision.changeset_revision == changeset_revision: - break - metadata = downloadable_revision.metadata - tool_dependencies = metadata.get( 'tool_dependencies', '' ) - if webapp == 'install_manager': - if tool_dependencies: - return tool_shed_encode( tool_dependencies ) - return '' - # TODO: future handler where request comes from some Galaxy admin feature. - @web.expose - 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 - # to take this approach because the "-" character is illegal in HTTP requests. - if 'webapp' not in kwd: - kwd[ 'webapp' ] = 'community' - if 'operation' in kwd: - operation = kwd['operation'].lower() - if operation == "view_or_manage_repository": - repository_id = kwd[ 'id' ] - repository = get_repository( trans, repository_id ) - is_admin = trans.user_is_admin() - if is_admin or repository.user == trans.user: - return trans.response.send_redirect( web.url_for( controller='repository', - action='manage_repository', - **kwd ) ) - else: - return trans.response.send_redirect( web.url_for( controller='repository', - action='view_repository', - **kwd ) ) - elif operation == "edit_repository": - return trans.response.send_redirect( web.url_for( controller='repository', - action='edit_repository', - **kwd ) ) - elif operation == "repositories_by_user": - # Eliminate the current filters if any exist. - for k, v in kwd.items(): - if k.startswith( 'f-' ): - del kwd[ k ] - if 'user_id' in kwd: - user = get_user( trans, kwd[ 'user_id' ] ) - kwd[ 'f-email' ] = user.email - del kwd[ 'user_id' ] - else: - # The received id is the repository id, so we need to get the id of the user - # that uploaded the repository. - repository_id = kwd.get( 'id', None ) - repository = get_repository( trans, repository_id ) - kwd[ 'f-email' ] = repository.user.email - elif operation == "my_repositories": - # Eliminate the current filters if any exist. - for k, v in kwd.items(): - if k.startswith( 'f-' ): - del kwd[ k ] - kwd[ 'f-email' ] = trans.user.email - elif operation == "repositories_by_category": - # Eliminate the current filters if any exist. - for k, v in kwd.items(): - if k.startswith( 'f-' ): - del kwd[ k ] - category_id = kwd.get( 'id', None ) - category = get_category( trans, category_id ) - kwd[ 'f-Category.name' ] = category.name - elif operation == "receive email alerts": - if trans.user: - if kwd[ 'id' ]: - kwd[ 'caller' ] = 'browse_repositories' - return trans.response.send_redirect( web.url_for( controller='repository', - action='set_email_alerts', - **kwd ) ) - else: - kwd[ 'message' ] = 'You must be logged in to set email alerts.' - kwd[ 'status' ] = 'error' - del kwd[ 'operation' ] - # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change - # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One - # of the many select fields on the grid performed the refresh_on_change, so we loop through - # all of the received values to see which value is not the repository tip. If we find it, we - # know the refresh_on_change occurred, and we have the necessary repository id and change set - # revision to pass on. - for k, v in kwd.items(): - changset_revision_str = 'changeset_revision_' - if k.startswith( changset_revision_str ): - repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) ) - repository = get_repository( trans, repository_id ) - if repository.tip != v: - return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repositories', - operation='view_or_manage_repository', - id=trans.security.encode_id( repository.id ), - changeset_revision=v ) ) - # Render the list view - return self.repository_list_grid( trans, **kwd ) - @web.expose - def create_repository( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - categories = get_categories( trans ) - if not categories: - message = 'No categories have been configured in this instance of the Galaxy Tool Shed. ' + \ - 'An administrator needs to create some via the Administrator control panel before creating repositories.', - status = 'error' + updating_tip=changeset_revision==repository.tip ) + for invalid_file_tup in invalid_files: + invalid_tool_config, invalid_msg = invalid_file_tup + invalid_tool_config_name = strip_path( invalid_tool_config ) + if tool_config == invalid_tool_config_name: + invalid_message = invalid_msg + break + tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) + #if error_message: + # message += error_message + tool_state = self.__new_state( trans ) + is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) + try: + shutil.rmtree( work_dir ) + 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='browse_repositories', + action='preview_tools_in_changeset', + repository_id=repository_id, + changeset_revision=changeset_revision, message=message, - status=status ) ) - name = util.restore_text( params.get( 'name', '' ) ) - description = util.restore_text( params.get( 'description', '' ) ) - long_description = util.restore_text( params.get( 'long_description', '' ) ) - category_ids = util.listify( params.get( 'category_id', '' ) ) - selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] - if params.get( 'create_repository_button', False ): - error = False - message = self.__validate_repository_name( name, trans.user ) - if message: - error = True - if not description: - message = 'Enter a description.' - error = True - if not error: - # Add the repository record to the db - repository = trans.app.model.Repository( name=name, - description=description, - long_description=long_description, - user_id=trans.user.id ) - # Flush to get the id - trans.sa_session.add( repository ) - trans.sa_session.flush() - # Determine the repository's repo_path on disk - dir = os.path.join( trans.app.config.file_path, *directory_hash_id( repository.id ) ) - # Create directory if it does not exist - if not os.path.exists( dir ): - os.makedirs( dir ) - # Define repo name inside hashed directory - repository_path = os.path.join( dir, "repo_%d" % repository.id ) - # Create local repository directory - if not os.path.exists( repository_path ): - os.makedirs( repository_path ) - # Create the local repository - repo = hg.repository( get_configured_ui(), repository_path, create=True ) - # Add an entry in the hgweb.config file for the local repository - # This enables calls to repository.repo_path - self.__add_hgweb_config_entry( trans, repository, repository_path ) - # Create a .hg/hgrc file for the local repository - self.__create_hgrc_file( repository ) - flush_needed = False - if category_ids: - # Create category associations - for category_id in category_ids: - category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) - rca = trans.app.model.RepositoryCategoryAssociation( repository, category ) - trans.sa_session.add( rca ) - flush_needed = True - if flush_needed: - trans.sa_session.flush() - message = "Repository '%s' has been created." % repository.name - trans.response.send_redirect( web.url_for( controller='repository', - action='view_repository', - webapp='community', - message=message, - id=trans.security.encode_id( repository.id ) ) ) - return trans.fill_template( '/webapps/community/repository/create_repository.mako', - name=name, - description=description, - long_description=long_description, - selected_categories=selected_categories, - categories=categories, - message=message, - status=status ) - def __validate_repository_name( self, name, user ): - # Repository names must be unique for each user, must be at least four characters - # in length and must contain only lower-case letters, numbers, and the '_' character. - if name in [ 'None', None, '' ]: - return 'Enter the required repository name.' - for repository in user.active_repositories: - if repository.name == name: - return "You already have a repository named '%s', so choose a different name." % name - if len( name ) < 4: - return "Repository names must be at least 4 characters in length." - if len( name ) > 80: - return "Repository names cannot be more than 80 characters in length." - if not( VALID_REPOSITORYNAME_RE.match( name ) ): - return "Repository names must contain only lower-case letters, numbers and underscore '_'." - return '' + 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 __make_hgweb_config_copy( self, trans, hgweb_config ): # Make a backup of the hgweb.config file today = date.today() backup_date = today.strftime( "%Y_%m_%d" ) hgweb_config_copy = '%s/hgweb.config_%s_backup' % ( trans.app.config.root, backup_date ) shutil.copy( os.path.abspath( hgweb_config ), os.path.abspath( hgweb_config_copy ) ) - def __add_hgweb_config_entry( self, trans, repository, repository_path ): - # Add an entry in the hgweb.config file for a new repository. An entry looks something like: - # repos/test/mira_assembler = database/community_files/000/repo_123. - hgweb_config = "%s/hgweb.config" % trans.app.config.root - if repository_path.startswith( './' ): - repository_path = repository_path.replace( './', '', 1 ) - entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path ) - tmp_fd, tmp_fname = tempfile.mkstemp() - if os.path.exists( hgweb_config ): - # Make a backup of the hgweb.config file since we're going to be changing it. - self.__make_hgweb_config_copy( trans, hgweb_config ) - new_hgweb_config = open( tmp_fname, 'wb' ) - for i, line in enumerate( open( hgweb_config ) ): - new_hgweb_config.write( line ) - else: - new_hgweb_config = open( tmp_fname, 'wb' ) - new_hgweb_config.write( '[paths]\n' ) - new_hgweb_config.write( "%s\n" % entry ) - new_hgweb_config.flush() - shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) - def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ): - # Change an entry in the hgweb.config file for a repository. This only happens when - # the owner changes the name of the repository. An entry looks something like: - # repos/test/mira_assembler = database/community_files/000/repo_123. - hgweb_config = "%s/hgweb.config" % trans.app.config.root - # Make a backup of the hgweb.config file since we're going to be changing it. - self.__make_hgweb_config_copy( trans, hgweb_config ) - repo_dir = repository.repo_path - old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) - new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir ) - tmp_fd, tmp_fname = tempfile.mkstemp() - new_hgweb_config = open( tmp_fname, 'wb' ) - for i, line in enumerate( open( hgweb_config ) ): - if line.startswith( old_lhs ): - new_hgweb_config.write( new_entry ) - else: - new_hgweb_config.write( line ) - new_hgweb_config.flush() - shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) - def __create_hgrc_file( self, repository ): - # At this point, an entry for the repository is required to be in the hgweb.config file so we can call repository.repo_path. - # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api. - # The hg purge extension purges all files and directories not being tracked by mercurial in the current repository. It'll - # remove unknown files and empty directories. This is not currently used because it is not supported in the mercurial API. - repo = hg.repository( get_configured_ui(), path=repository.repo_path ) - fp = repo.opener( 'hgrc', 'wb' ) - fp.write( '[paths]\n' ) - fp.write( 'default = .\n' ) - fp.write( 'default-push = .\n' ) - fp.write( '[web]\n' ) - fp.write( 'allow_push = %s\n' % repository.user.username ) - fp.write( 'name = %s\n' % repository.name ) - fp.write( 'push_ssl = false\n' ) - fp.write( '[extensions]\n' ) - fp.write( 'hgext.purge=' ) - fp.close() + def __make_same_length( self, list1, list2 ): + # If either list is 1 item, we'll append to it until its length is the same as the other. + if len( list1 ) == 1: + for i in range( 1, len( list2 ) ): + list1.append( list1[ 0 ] ) + elif len( list2 ) == 1: + for i in range( 1, len( list1 ) ): + list2.append( list2[ 0 ] ) + return list1, list2 @web.expose - def browse_repository( self, trans, id, **kwd ): + @web.require_login( "manage email alerts" ) + def manage_email_alerts( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = params.get( 'webapp', 'community' ) - commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) - repository = get_repository( trans, id ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) - current_working_dir = os.getcwd() - # Update repository files for browsing. - update_repository( repo ) - is_malicious = changeset_is_malicious( trans, id, repository.tip ) - return trans.fill_template( '/webapps/community/repository/browse_repository.mako', - repo=repo, - repository=repository, - commit_message=commit_message, - is_malicious=is_malicious, - webapp=webapp, - message=message, - status=status ) - @web.expose - def contact_owner( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - repository = get_repository( trans, id ) - if trans.user and trans.user.email: - return trans.fill_template( "/webapps/community/repository/contact_owner.mako", - repository=repository, - message=message, - status=status ) - else: - # Do all we can to eliminate spam. - return trans.show_error_message( "You must be logged in to contact the owner of a repository." ) - @web.expose - def send_to_owner( self, trans, id, message='' ): - repository = get_repository( trans, id ) - if not message: - message = 'Enter a message' - status = 'error' - elif trans.user and trans.user.email: - smtp_server = trans.app.config.smtp_server - from_address = trans.app.config.email_from - if smtp_server is None or from_address is None: - return trans.show_error_message( "Mail is not configured for this Galaxy tool shed instance" ) - to_address = repository.user.email - # Get the name of the server hosting the tool shed instance. - host = trans.request.host - # Build the email message - body = string.Template( contact_owner_template ) \ - .safe_substitute( username=trans.user.username, - repository_name=repository.name, - email=trans.user.email, - message=message, - host=host ) - subject = "Regarding your tool shed repository named %s" % repository.name - # Send it - try: - util.send_mail( from_address, to_address, subject, body, trans.app.config ) - message = "Your message has been sent" - status = "done" - except Exception, e: - message = "An error occurred sending your message by email: %s" % str( e ) - status = "error" - else: - # Do all we can to eliminate spam. - return trans.show_error_message( "You must be logged in to contact the owner of a repository." ) - return trans.response.send_redirect( web.url_for( controller='repository', - action='contact_owner', - id=id, - message=message, - status=status ) ) - @web.expose - def select_files_to_delete( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) - repository = get_repository( trans, id ) - repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) - selected_files_to_delete = util.restore_text( params.get( 'selected_files_to_delete', '' ) ) - if params.get( 'select_files_to_delete_button', False ): - if selected_files_to_delete: - selected_files_to_delete = selected_files_to_delete.split( ',' ) - current_working_dir = os.getcwd() - # Get the current repository tip. - tip = repository.tip - for selected_file in selected_files_to_delete: - try: - commands.remove( repo.ui, repo, selected_file, force=True ) - except Exception, e: - log.debug( "Error removing files using the mercurial API, so trying a different approach, the error was: %s" % str( e )) - relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) - repo.dirstate.remove( relative_selected_file ) - repo.dirstate.write() - absolute_selected_file = os.path.abspath( selected_file ) - if os.path.isdir( absolute_selected_file ): - try: - os.rmdir( absolute_selected_file ) - except OSError, e: - # The directory is not empty - pass - elif os.path.isfile( absolute_selected_file ): - os.remove( absolute_selected_file ) - dir = os.path.split( absolute_selected_file )[0] - try: - os.rmdir( dir ) - except OSError, e: - # The directory is not empty - pass - # Commit the change set. - if not commit_message: - commit_message = 'Deleted selected files' - commands.commit( repo.ui, repo, repo_dir, user=trans.user.username, message=commit_message ) - handle_email_alerts( trans, repository ) - # Update the repository files for browsing. - update_repository( repo ) - # Get the new repository tip. - repo = hg.repository( get_configured_ui(), repo_dir ) - if tip == repository.tip: - message += 'No changes to repository. ' - kwd[ 'message' ] = message - - else: - message += 'The selected files were deleted from the repository. ' - kwd[ 'message' ] = message - set_repository_metadata_due_to_new_tip( trans, id, repository, **kwd ) + new_repo_alert = params.get( 'new_repo_alert', '' ) + new_repo_alert_checked = CheckboxField.is_checked( new_repo_alert ) + user = trans.user + if params.get( 'new_repo_alert_button', False ): + user.new_repo_alert = new_repo_alert_checked + trans.sa_session.add( user ) + trans.sa_session.flush() + if new_repo_alert_checked: + message = 'You will receive email alerts for all new valid tool shed repositories.' else: - message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." - status = "error" - is_malicious = changeset_is_malicious( trans, id, repository.tip ) - return trans.fill_template( '/webapps/community/repository/browse_repository.mako', - repo=repo, - repository=repository, - commit_message=commit_message, - is_malicious=is_malicious, - message=message, - status=status ) - @web.expose - def view_repository( self, trans, id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - repository = get_repository( trans, id ) - webapp = params.get( 'webapp', 'community' ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) - avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) - changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) - display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) - alerts = params.get( 'alerts', '' ) - alerts_checked = CheckboxField.is_checked( alerts ) - if repository.email_alerts: - email_alerts = from_json_string( repository.email_alerts ) - else: - email_alerts = [] - user = trans.user - if user and params.get( 'receive_email_alerts_button', False ): - flush_needed = False - if alerts_checked: - if user.email not in email_alerts: - email_alerts.append( user.email ) - repository.email_alerts = to_json_string( email_alerts ) - flush_needed = True - else: - if user.email in email_alerts: - email_alerts.remove( user.email ) - repository.email_alerts = to_json_string( email_alerts ) - flush_needed = True - if flush_needed: - trans.sa_session.add( repository ) - trans.sa_session.flush() - checked = alerts_checked or ( user and user.email in email_alerts ) - alerts_check_box = CheckboxField( 'alerts', checked=checked ) - changeset_revision_select_field = build_changeset_revision_select_field( trans, - repository, - selected_value=changeset_revision, - add_id_to_name=False ) - revision_label = get_revision_label( trans, repository, changeset_revision ) - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) - if repository_metadata: - repository_metadata_id = trans.security.encode_id( repository_metadata.id ), - metadata = repository_metadata.metadata - else: - repository_metadata_id = None - metadata = None - is_malicious = changeset_is_malicious( trans, id, repository.tip ) - if is_malicious: - if trans.app.security_agent.can_push( trans.user, repository ): - message += malicious_error_can_push - else: - message += malicious_error - status = 'error' - return trans.fill_template( '/webapps/community/repository/view_repository.mako', - repo=repo, - repository=repository, - repository_metadata_id=repository_metadata_id, - metadata=metadata, - avg_rating=avg_rating, - display_reviews=display_reviews, - num_ratings=num_ratings, - alerts_check_box=alerts_check_box, - changeset_revision=changeset_revision, - changeset_revision_select_field=changeset_revision_select_field, - revision_label=revision_label, - is_malicious=is_malicious, - webapp=webapp, + message = 'You will not receive any email alerts for new valid tool shed repositories.' + checked = new_repo_alert_checked or ( user and user.new_repo_alert ) + new_repo_alert_check_box = CheckboxField( 'new_repo_alert', checked=checked ) + email_alert_repositories = [] + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.email_alerts != None ) ) \ + .order_by( trans.model.Repository.table.c.name ): + if user.email in repository.email_alerts: + email_alert_repositories.append( repository ) + return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako", + webapp='community', + new_repo_alert_check_box=new_repo_alert_check_box, + email_alert_repositories=email_alert_repositories, message=message, status=status ) @web.expose @@ -1621,6 +1514,429 @@ message=message, status=status ) @web.expose + @web.require_login( "multi select email alerts" ) + def multi_select_email_alerts( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if 'webapp' not in kwd: + kwd[ 'webapp' ] = 'community' + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "receive email alerts": + if trans.user: + if kwd[ 'id' ]: + kwd[ 'caller' ] = 'multi_select_email_alerts' + return trans.response.send_redirect( web.url_for( controller='repository', + action='set_email_alerts', + **kwd ) ) + else: + kwd[ 'message' ] = 'You must be logged in to set email alerts.' + kwd[ 'status' ] = 'error' + del kwd[ 'operation' ] + return self.email_alerts_repository_list_grid( trans, **kwd ) + def __new_state( self, trans, all_pages=False ): + """ + Create a new `DefaultToolState` for this tool. It will not be initialized + with default values for inputs. + + Only inputs on the first page will be initialized unless `all_pages` is + True, in which case all inputs regardless of page are initialized. + """ + state = DefaultToolState() + state.inputs = {} + return state + @web.json + def open_folder( self, trans, repository_id, key ): + # The tool shed includes a repository source file browser, which currently depends upon + # copies of the hg repository file store in the repo_path for browsing. + # Avoid caching + trans.response.headers['Pragma'] = 'no-cache' + trans.response.headers['Expires'] = '0' + repository = trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( repository_id ) ) + folder_path = key + try: + files_list = self.__get_files( trans, folder_path ) + except OSError, e: + if str( e ).find( 'No such file or directory' ) >= 0: + # We have a repository with no contents. + return [] + folder_contents = [] + for filename in files_list: + is_folder = False + if filename and filename[-1] == os.sep: + is_folder = True + if filename: + full_path = os.path.join( folder_path, filename ) + node = { "title": filename, + "isFolder": is_folder, + "isLazy": is_folder, + "tooltip": full_path, + "key": full_path } + folder_contents.append( node ) + return folder_contents + @web.expose + def preview_tools_in_changeset( self, trans, repository_id, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) + repository = get_repository( trans, repository_id ) + changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ), + metadata = repository_metadata.metadata + else: + repository_metadata_id = None + metadata = None + revision_label = get_revision_label( trans, repository, changeset_revision ) + changeset_revision_select_field = build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False ) + return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', + repository=repository, + repository_metadata_id=repository_metadata_id, + changeset_revision=changeset_revision, + revision_label=revision_label, + changeset_revision_select_field=changeset_revision_select_field, + metadata=metadata, + webapp=webapp, + message=message, + status=status ) + @web.expose + @web.require_login( "rate repositories" ) + def rate_repository( self, trans, **kwd ): + """ Rate a repository and return updated rating data. """ + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + message='Select a repository to rate', + status='error' ) ) + repository = get_repository( trans, id ) + repo = hg.repository( get_configured_ui(), repository.repo_path ) + if repository.user == trans.user: + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repositories', + message="You are not allowed to rate your own repository", + status='error' ) ) + if params.get( 'rate_button', False ): + rating = int( params.get( 'rating', '0' ) ) + comment = util.restore_text( params.get( 'comment', '' ) ) + rating = self.rate_item( trans, trans.user, repository, rating, comment ) + avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) + display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) + rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) + is_malicious = changeset_is_malicious( trans, id, repository.tip ) + return trans.fill_template( '/webapps/community/repository/rate_repository.mako', + repository=repository, + avg_rating=avg_rating, + display_reviews=display_reviews, + num_ratings=num_ratings, + rra=rra, + is_malicious=is_malicious, + message=message, + status=status ) + @web.expose + def reset_all_metadata( self, trans, id, **kwd ): + error_message, status = reset_all_metadata_on_repository( trans, id, **kwd ) + if error_message: + message = error_message + status = 'error' + else: + message = "All repository metadata has been reset." + status = 'done' + return trans.response.send_redirect( web.url_for( controller='repository', + action='manage_repository', + id=id, + message=message, + status=status ) ) + def __search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ): + for i, tool_id in enumerate( tool_ids ): + tool_name = tool_names[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples + def __search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ): + for i, tool_id in enumerate( tool_ids ): + tool_version = tool_versions[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples + def __search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ): + for i, tool_name in enumerate( tool_names ): + tool_version = tool_versions[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples + def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ): + match_tuples = [] + ok = True + for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): + metadata = repository_metadata.metadata + if tool_ids or tool_names or tool_versions: + if 'tools' in metadata: + tools = metadata[ 'tools' ] + else: + tools = [] + for tool_dict in tools: + if tool_ids and not tool_names and not tool_versions: + for tool_id in tool_ids: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_names and not tool_ids and not tool_versions: + for tool_name in tool_names: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_versions and not tool_ids and not tool_names: + for tool_version in tool_versions: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_ids and tool_names and not tool_versions: + if len( tool_ids ) == len( tool_names ): + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + elif len( tool_ids ) == 1 or len( tool_names ) == 1: + tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + else: + ok = False + elif tool_ids and tool_versions and not tool_names: + if len( tool_ids ) == len( tool_versions ): + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + elif len( tool_ids ) == 1 or len( tool_versions ) == 1: + tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and not tool_ids: + if len( tool_versions ) == len( tool_names ): + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + elif len( tool_versions ) == 1 or len( tool_names ) == 1: + tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and tool_ids: + if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): + for i, tool_version in enumerate( tool_versions ): + tool_name = tool_names[ i ] + tool_id = tool_ids[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + ok = False + elif workflow_names: + 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> ] + workflow_tups = metadata[ 'workflows' ] + workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ] + else: + workflows = [] + for workflow_dict in workflows: + for workflow_name in workflow_names: + if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif all_workflows and 'workflows' in metadata: + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return ok, match_tuples + @web.expose + def select_files_to_delete( self, trans, id, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) + repository = get_repository( trans, id ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + selected_files_to_delete = util.restore_text( params.get( 'selected_files_to_delete', '' ) ) + if params.get( 'select_files_to_delete_button', False ): + if selected_files_to_delete: + selected_files_to_delete = selected_files_to_delete.split( ',' ) + current_working_dir = os.getcwd() + # Get the current repository tip. + tip = repository.tip + for selected_file in selected_files_to_delete: + try: + commands.remove( repo.ui, repo, selected_file, force=True ) + except Exception, e: + log.debug( "Error removing files using the mercurial API, so trying a different approach, the error was: %s" % str( e )) + relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) + repo.dirstate.remove( relative_selected_file ) + repo.dirstate.write() + absolute_selected_file = os.path.abspath( selected_file ) + if os.path.isdir( absolute_selected_file ): + try: + os.rmdir( absolute_selected_file ) + except OSError, e: + # The directory is not empty + pass + elif os.path.isfile( absolute_selected_file ): + os.remove( absolute_selected_file ) + dir = os.path.split( absolute_selected_file )[0] + try: + os.rmdir( dir ) + except OSError, e: + # The directory is not empty + pass + # Commit the change set. + if not commit_message: + commit_message = 'Deleted selected files' + commands.commit( repo.ui, repo, repo_dir, user=trans.user.username, message=commit_message ) + handle_email_alerts( trans, repository ) + # Update the repository files for browsing. + update_repository( repo ) + # Get the new repository tip. + repo = hg.repository( get_configured_ui(), repo_dir ) + if tip == repository.tip: + message += 'No changes to repository. ' + kwd[ 'message' ] = message + + else: + message += 'The selected files were deleted from the repository. ' + kwd[ 'message' ] = message + set_repository_metadata_due_to_new_tip( trans, id, repository, **kwd ) + else: + message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." + status = "error" + is_malicious = changeset_is_malicious( trans, id, repository.tip ) + return trans.fill_template( '/webapps/community/repository/browse_repository.mako', + repo=repo, + repository=repository, + commit_message=commit_message, + is_malicious=is_malicious, + message=message, + status=status ) + @web.expose + def send_to_owner( self, trans, id, message='' ): + repository = get_repository( trans, id ) + if not message: + message = 'Enter a message' + status = 'error' + elif trans.user and trans.user.email: + smtp_server = trans.app.config.smtp_server + from_address = trans.app.config.email_from + if smtp_server is None or from_address is None: + return trans.show_error_message( "Mail is not configured for this Galaxy tool shed instance" ) + to_address = repository.user.email + # Get the name of the server hosting the tool shed instance. + host = trans.request.host + # Build the email message + body = string.Template( contact_owner_template ) \ + .safe_substitute( username=trans.user.username, + repository_name=repository.name, + email=trans.user.email, + message=message, + host=host ) + subject = "Regarding your tool shed repository named %s" % repository.name + # Send it + try: + util.send_mail( from_address, to_address, subject, body, trans.app.config ) + message = "Your message has been sent" + status = "done" + except Exception, e: + message = "An error occurred sending your message by email: %s" % str( e ) + status = "error" + else: + # Do all we can to eliminate spam. + return trans.show_error_message( "You must be logged in to contact the owner of a repository." ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='contact_owner', + id=id, + message=message, + status=status ) ) + @web.expose + @web.require_login( "set email alerts" ) + def set_email_alerts( self, trans, **kwd ): + # Set email alerts for selected repositories + # This method is called from multiple grids, so + # the caller must be passed. + caller = kwd[ 'caller' ] + user = trans.user + if user: + repository_ids = util.listify( kwd.get( 'id', '' ) ) + total_alerts_added = 0 + total_alerts_removed = 0 + flush_needed = False + for repository_id in repository_ids: + repository = get_repository( trans, repository_id ) + if repository.email_alerts: + email_alerts = from_json_string( repository.email_alerts ) + else: + email_alerts = [] + if user.email in email_alerts: + email_alerts.remove( user.email ) + repository.email_alerts = to_json_string( email_alerts ) + trans.sa_session.add( repository ) + flush_needed = True + total_alerts_removed += 1 + else: + email_alerts.append( user.email ) + repository.email_alerts = to_json_string( email_alerts ) + trans.sa_session.add( repository ) + flush_needed = True + total_alerts_added += 1 + if flush_needed: + trans.sa_session.flush() + message = 'Total alerts added: %d, total alerts removed: %d' % ( total_alerts_added, total_alerts_removed ) + kwd[ 'message' ] = message + kwd[ 'status' ] = 'done' + del kwd[ 'operation' ] + return trans.response.send_redirect( web.url_for( controller='repository', + action=caller, + **kwd ) ) + @web.expose + @web.require_login( "set repository metadata" ) + def set_metadata( self, trans, id, ctx_str, **kwd ): + malicious = kwd.get( 'malicious', '' ) + if kwd.get( 'malicious_button', False ): + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, ctx_str ) + malicious_checked = CheckboxField.is_checked( malicious ) + repository_metadata.malicious = malicious_checked + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + if malicious_checked: + message = "The repository tip has been defined as malicious." + else: + message = "The repository tip has been defined as <b>not</b> malicious." + status = 'done' + else: + # The set_metadata_button was clicked + message, status = set_repository_metadata( trans, id, ctx_str, **kwd ) + if not message: + message = "Metadata for change set revision '%s' has been reset." % str( ctx_str ) + return trans.response.send_redirect( web.url_for( controller='repository', + action='manage_repository', + id=id, + changeset_revision=ctx_str, + malicious=malicious, + message=message, + status=status ) ) + def __stringify( self, list ): + if list: + return ','.join( list ) + return '' + def __validate_repository_name( self, name, user ): + # Repository names must be unique for each user, must be at least four characters + # in length and must contain only lower-case letters, numbers, and the '_' character. + if name in [ 'None', None, '' ]: + return 'Enter the required repository name.' + for repository in user.active_repositories: + if repository.name == name: + return "You already have a repository named '%s', so choose a different name." % name + if len( name ) < 4: + return "Repository names must be at least 4 characters in length." + if len( name ) > 80: + return "Repository names cannot be more than 80 characters in length." + if not( VALID_REPOSITORYNAME_RE.match( name ) ): + return "Repository names must contain only lower-case letters, numbers and underscore '_'." + return '' + @web.expose def view_changelog( self, trans, id, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -1694,291 +2010,76 @@ message=message, status=status ) @web.expose - @web.require_login( "rate repositories" ) - def rate_repository( self, trans, **kwd ): - """ Rate a repository and return updated rating data. """ + def view_repository( self, trans, id, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - id = params.get( 'id', None ) - if not id: - return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repositories', - message='Select a repository to rate', - status='error' ) ) repository = get_repository( trans, id ) + webapp = params.get( 'webapp', 'community' ) repo = hg.repository( get_configured_ui(), repository.repo_path ) - if repository.user == trans.user: - return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repositories', - message="You are not allowed to rate your own repository", - status='error' ) ) - if params.get( 'rate_button', False ): - rating = int( params.get( 'rating', '0' ) ) - comment = util.restore_text( params.get( 'comment', '' ) ) - rating = self.rate_item( trans, trans.user, repository, rating, comment ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) + changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) ) - rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) + alerts = params.get( 'alerts', '' ) + alerts_checked = CheckboxField.is_checked( alerts ) + if repository.email_alerts: + email_alerts = from_json_string( repository.email_alerts ) + else: + email_alerts = [] + user = trans.user + if user and params.get( 'receive_email_alerts_button', False ): + flush_needed = False + if alerts_checked: + if user.email not in email_alerts: + email_alerts.append( user.email ) + repository.email_alerts = to_json_string( email_alerts ) + flush_needed = True + else: + if user.email in email_alerts: + email_alerts.remove( user.email ) + repository.email_alerts = to_json_string( email_alerts ) + flush_needed = True + if flush_needed: + trans.sa_session.add( repository ) + trans.sa_session.flush() + checked = alerts_checked or ( user and user.email in email_alerts ) + alerts_check_box = CheckboxField( 'alerts', checked=checked ) + changeset_revision_select_field = build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False ) + revision_label = get_revision_label( trans, repository, changeset_revision ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ), + metadata = repository_metadata.metadata + else: + repository_metadata_id = None + metadata = None is_malicious = changeset_is_malicious( trans, id, repository.tip ) - return trans.fill_template( '/webapps/community/repository/rate_repository.mako', + if is_malicious: + if trans.app.security_agent.can_push( trans.user, repository ): + message += malicious_error_can_push + else: + message += malicious_error + status = 'error' + return trans.fill_template( '/webapps/community/repository/view_repository.mako', + repo=repo, repository=repository, + repository_metadata_id=repository_metadata_id, + metadata=metadata, avg_rating=avg_rating, display_reviews=display_reviews, num_ratings=num_ratings, - rra=rra, + alerts_check_box=alerts_check_box, + changeset_revision=changeset_revision, + changeset_revision_select_field=changeset_revision_select_field, + revision_label=revision_label, is_malicious=is_malicious, + webapp=webapp, message=message, status=status ) @web.expose - @web.require_login( "set email alerts" ) - def set_email_alerts( self, trans, **kwd ): - # Set email alerts for selected repositories - # This method is called from multiple grids, so - # the caller must be passed. - caller = kwd[ 'caller' ] - user = trans.user - if user: - repository_ids = util.listify( kwd.get( 'id', '' ) ) - total_alerts_added = 0 - total_alerts_removed = 0 - flush_needed = False - for repository_id in repository_ids: - repository = get_repository( trans, repository_id ) - if repository.email_alerts: - email_alerts = from_json_string( repository.email_alerts ) - else: - email_alerts = [] - if user.email in email_alerts: - email_alerts.remove( user.email ) - repository.email_alerts = to_json_string( email_alerts ) - trans.sa_session.add( repository ) - flush_needed = True - total_alerts_removed += 1 - else: - email_alerts.append( user.email ) - repository.email_alerts = to_json_string( email_alerts ) - trans.sa_session.add( repository ) - flush_needed = True - total_alerts_added += 1 - if flush_needed: - trans.sa_session.flush() - message = 'Total alerts added: %d, total alerts removed: %d' % ( total_alerts_added, total_alerts_removed ) - kwd[ 'message' ] = message - kwd[ 'status' ] = 'done' - del kwd[ 'operation' ] - return trans.response.send_redirect( web.url_for( controller='repository', - action=caller, - **kwd ) ) - @web.expose - @web.require_login( "manage email alerts" ) - def manage_email_alerts( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - new_repo_alert = params.get( 'new_repo_alert', '' ) - new_repo_alert_checked = CheckboxField.is_checked( new_repo_alert ) - user = trans.user - if params.get( 'new_repo_alert_button', False ): - user.new_repo_alert = new_repo_alert_checked - trans.sa_session.add( user ) - trans.sa_session.flush() - if new_repo_alert_checked: - message = 'You will receive email alerts for all new valid tool shed repositories.' - else: - message = 'You will not receive any email alerts for new valid tool shed repositories.' - checked = new_repo_alert_checked or ( user and user.new_repo_alert ) - new_repo_alert_check_box = CheckboxField( 'new_repo_alert', checked=checked ) - email_alert_repositories = [] - for repository in trans.sa_session.query( trans.model.Repository ) \ - .filter( and_( trans.model.Repository.table.c.deleted == False, - trans.model.Repository.table.c.email_alerts != None ) ) \ - .order_by( trans.model.Repository.table.c.name ): - if user.email in repository.email_alerts: - email_alert_repositories.append( repository ) - return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako", - webapp='community', - new_repo_alert_check_box=new_repo_alert_check_box, - email_alert_repositories=email_alert_repositories, - message=message, - status=status ) - @web.expose - @web.require_login( "manage email alerts" ) - def multi_select_email_alerts( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - if 'webapp' not in kwd: - kwd[ 'webapp' ] = 'community' - if 'operation' in kwd: - operation = kwd['operation'].lower() - if operation == "receive email alerts": - if trans.user: - if kwd[ 'id' ]: - kwd[ 'caller' ] = 'multi_select_email_alerts' - return trans.response.send_redirect( web.url_for( controller='repository', - action='set_email_alerts', - **kwd ) ) - else: - kwd[ 'message' ] = 'You must be logged in to set email alerts.' - kwd[ 'status' ] = 'error' - del kwd[ 'operation' ] - return self.email_alerts_repository_list_grid( trans, **kwd ) - @web.expose - @web.require_login( "set repository metadata" ) - def set_metadata( self, trans, id, ctx_str, **kwd ): - malicious = kwd.get( 'malicious', '' ) - if kwd.get( 'malicious_button', False ): - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, ctx_str ) - malicious_checked = CheckboxField.is_checked( malicious ) - repository_metadata.malicious = malicious_checked - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - if malicious_checked: - message = "The repository tip has been defined as malicious." - else: - message = "The repository tip has been defined as <b>not</b> malicious." - status = 'done' - else: - # The set_metadata_button was clicked - message, status = set_repository_metadata( trans, id, ctx_str, **kwd ) - if not message: - message = "Metadata for change set revision '%s' has been reset." % str( ctx_str ) - return trans.response.send_redirect( web.url_for( controller='repository', - action='manage_repository', - id=id, - changeset_revision=ctx_str, - malicious=malicious, - message=message, - status=status ) ) - @web.expose - def reset_all_metadata( self, trans, id, **kwd ): - error_message, status = reset_all_metadata_on_repository( trans, id, **kwd ) - if error_message: - message = error_message - else: - message = "All repository metadata has been reset." - status = 'done' - return trans.response.send_redirect( web.url_for( controller='repository', - action='manage_repository', - id=id, - message=message, - status=status ) ) - @web.expose - 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' ) - webapp = params.get( 'webapp', 'community' ) - repository = get_repository( trans, repository_id ) - tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) - tool_state = self.__new_state( trans ) - is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) - try: - 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=status ) - except Exception, e: - message = "Error displaying tool, probably due to a problem in the tool config. The exception is: %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' ) ) - @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 = '' - work_dir = make_tmp_directory() - for filename in ctx: - ctx_file_name = strip_path( filename ) - if ctx_file_name == tool_config: - tool_config_path = get_named_tmpfile_from_ctx( ctx, filename, work_dir ) - break - metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, - repo, - repository_id, - ctx, - changeset_revision, - repo_dir, - updating_tip=changeset_revision==repository.tip ) - for invalid_file_tup in invalid_files: - invalid_tool_config, invalid_msg = invalid_file_tup - invalid_tool_config_name = strip_path( invalid_tool_config ) - if tool_config == invalid_tool_config_name: - invalid_message = invalid_msg - break - tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) - if error_message: - message += error_message - tool_state = self.__new_state( trans ) - is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) - try: - shutil.rmtree( work_dir ) - 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 - with default values for inputs. - - Only inputs on the first page will be initialized unless `all_pages` is - True, in which case all inputs regardless of page are initialized. - """ - state = DefaultToolState() - state.inputs = {} - return state - @web.expose def view_tool_metadata( self, trans, repository_id, changeset_revision, tool_id, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -2015,106 +2116,3 @@ webapp=webapp, message=message, status=status ) - @web.expose - def download( self, trans, repository_id, changeset_revision, file_type, **kwd ): - # Download an archive of the repository files compressed as zip, gz or bz2. - params = util.Params( kwd ) - repository = get_repository( trans, repository_id ) - # Allow hgweb to handle the download. This requires the tool shed - # server account's .hgrc file to include the following setting: - # [web] - # allow_archive = bz2, gz, zip - if file_type == 'zip': - file_type_str = '%s.zip' % changeset_revision - elif file_type == 'bz2': - file_type_str = '%s.tar.bz2' % changeset_revision - elif file_type == 'gz': - file_type_str = '%s.tar.gz' % changeset_revision - repository.times_downloaded += 1 - trans.sa_session.add( repository ) - trans.sa_session.flush() - download_url = '/repos/%s/%s/archive/%s' % ( repository.user.username, repository.name, file_type_str ) - return trans.response.send_redirect( download_url ) - @web.json - def open_folder( self, trans, repository_id, key ): - # The tool shed includes a repository source file browser, which currently depends upon - # copies of the hg repository file store in the repo_path for browsing. - # Avoid caching - trans.response.headers['Pragma'] = 'no-cache' - trans.response.headers['Expires'] = '0' - repository = trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( repository_id ) ) - folder_path = key - try: - files_list = self.__get_files( trans, folder_path ) - except OSError, e: - if str( e ).find( 'No such file or directory' ) >= 0: - # We have a repository with no contents. - return [] - folder_contents = [] - for filename in files_list: - is_folder = False - if filename and filename[-1] == os.sep: - is_folder = True - if filename: - full_path = os.path.join( folder_path, filename ) - node = { "title": filename, - "isFolder": is_folder, - "isLazy": is_folder, - "tooltip": full_path, - "key": full_path } - folder_contents.append( node ) - return folder_contents - def __get_files( self, trans, folder_path ): - contents = [] - for item in os.listdir( folder_path ): - # Skip .hg directories - if str( item ).startswith( '.hg' ): - continue - if os.path.isdir( os.path.join( folder_path, item ) ): - # Append a '/' character so that our jquery dynatree will - # function properly. - item = '%s/' % item - contents.append( item ) - if contents: - contents.sort() - return contents - @web.json - def get_file_contents( self, trans, file_path ): - # Avoid caching - trans.response.headers['Pragma'] = 'no-cache' - trans.response.headers['Expires'] = '0' - if is_gzip( file_path ): - to_html = to_html_str( '\ngzip compressed file\n' ) - elif is_bz2( file_path ): - to_html = to_html_str( '\nbz2 compressed file\n' ) - elif check_zip( file_path ): - to_html = to_html_str( '\nzip compressed file\n' ) - elif check_binary( file_path ): - to_html = to_html_str( '\nBinary file\n' ) - else: - to_html = '' - for i, line in enumerate( open( file_path ) ): - to_html = '%s%s' % ( to_html, to_html_str( line ) ) - if len( to_html ) > MAX_CONTENT_SIZE: - large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) - to_html = '%s%s' % ( to_html, to_html_str( large_str ) ) - break - return to_html - @web.expose - def help( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - return trans.fill_template( '/webapps/community/repository/help.mako', message=message, status=status, **kwd ) - def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ): - options = [] - for user in trans.sa_session.query( trans.model.User ): - if user.username not in current_push_list: - options.append( user ) - return build_select_field( trans, - objs=options, - label_attr='username', - select_field_name='allow_push', - selected_value=selected_value, - refresh_on_change=False, - multiple=True ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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