diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py
index 296d87d2d49..8bd7b4df400 100644
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -646,13 +646,15 @@ class RepositoryMetadataGrid( grids.Grid ):
class RepositoryNameColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository_metadata ):
- return escape_html( repository_metadata.repository.name )
+ repository = repository_metadata.repository
+ return escape_html( repository.name )
class RepositoryOwnerColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository_metadata ):
- return escape_html( repository_metadata.user.username )
+ repository = repository_metadata.repository
+ return escape_html( repository.user.username )
class ChangesetRevisionColumn( grids.TextColumn ):
@@ -763,18 +765,53 @@ class RepositoryMetadataGrid( grids.Grid ):
class RepositoryDependenciesGrid( RepositoryMetadataGrid ):
-
- title = "Repository dependencies available in this Tool Shed"
+
+
+ class RequiredRepositoryColumn( grids.TextColumn ):
+
+ def get_value( self, trans, grid, repository_metadata ):
+ rd_str = ''
+ if repository_metadata:
+ metadata = repository_metadata.metadata
+ if metadata:
+ rd_dict = metadata.get( 'repository_dependencies', {} )
+ if rd_dict:
+ rd_tups = rd_dict[ 'repository_dependencies' ]
+ # "repository_dependencies": [["http://localhost:9009", "bwa059", "test", "a07baa797d53"]]
+ # Sort rd_tups by by required repository name.
+ sorted_rd_tups = sorted( rd_tups, key=lambda rd_tup: rd_tup[ 1 ] )
+ num_tups = len( sorted_rd_tups )
+ for index, rd_tup in enumerate( sorted_rd_tups ):
+ name = rd_tup[ 1 ]
+ owner = rd_tup[ 2 ]
+ required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
+ if required_repository:
+ required_repository_id = trans.security.encode_id( required_repository.id )
+ rd_str += '' % required_repository_id
+ rd_str += 'name: %s | owner: %s | revision: %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 2 ] ), escape_html( rd_tup[ 3 ] ) )
+ if required_repository:
+ rd_str += ''
+ if index < num_tups - 1:
+ rd_str += '
'
+ return rd_str
+
+ title = "Repository dependency definitions in this tool shed"
columns = [
RepositoryMetadataGrid.RepositoryNameColumn( "Repository name",
- link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
- attach_popup=False ),
+ model_class=model.Repository,
+ link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ),
+ attach_popup=False,
+ key="Repository.name" ),
RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner",
model_class=model.User,
attach_popup=False,
- key="User.username" )
+ key="User.username" ),
+ RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision",
+ attach_popup=False ),
+ RequiredRepositoryColumn( "Repository dependency",
+ attach_popup=False )
]
- columns.append( grids.MulticolFilterColumn( "Search repository name, description",
+ columns.append( grids.MulticolFilterColumn( "Search repository name, owner",
cols_to_filter=[ columns[0], columns[1] ],
key="free-text-search",
visible=False,
@@ -790,9 +827,190 @@ class RepositoryDependenciesGrid( RepositoryMetadataGrid ):
.order_by( model.Repository.name )
+class ToolDependenciesGrid( RepositoryMetadataGrid ):
+
+
+ class ToolDependencyColumn( grids.TextColumn ):
+
+ def get_value( self, trans, grid, repository_metadata ):
+ td_str = ''
+ if repository_metadata:
+ metadata = repository_metadata.metadata
+ if metadata:
+ tds_dict = metadata.get( 'tool_dependencies', {} )
+ if tds_dict:
+ # Example: {"bwa/0.5.9": {"name": "bwa", "type": "package", "version": "0.5.9"}}
+ sorted_keys = sorted( [ k for k in tds_dict.keys() ] )
+ num_keys = len( sorted_keys )
+ # Handle environment settings first.
+ if 'set_environment' in sorted_keys:
+ # Example: "set_environment": [{"name": "JAVA_JAR_FILE", "type": "set_environment"}]
+ env_dicts = tds_dict[ 'set_environment' ]
+ num_env_dicts = len( env_dicts )
+ td_str += 'environment: '
+ for index, env_dict in enumerate( env_dicts ):
+ td_str += '%s' % escape_html( env_dict[ 'name' ] )
+ if index < num_env_dicts - 1:
+ td_str += ', '
+ td_str += '
'
+ for index, key in enumerate( sorted_keys ):
+ if key == 'set_environment':
+ continue
+ td_dict = tds_dict[ key ]
+ # Example: {"name": "bwa", "type": "package", "version": "0.5.9"}
+ name = td_dict[ 'name' ]
+ type = td_dict[ 'type' ]
+ version = td_dict[ 'version' ]
+ td_str += '%s version %s' % ( escape_html( name ), escape_html( version ) )
+ if index < num_keys - 1:
+ td_str += '
'
+ return td_str
+
+ title = "Tool dependency definitions in this tool shed"
+ columns = [
+ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name",
+ model_class=model.Repository,
+ link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ),
+ attach_popup=False,
+ key="Repository.name" ),
+ RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner",
+ model_class=model.User,
+ attach_popup=False,
+ key="User.username" ),
+ RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision",
+ attach_popup=False ),
+ ToolDependencyColumn( "Tool dependency",
+ attach_popup=False )
+ ]
+ columns.append( grids.MulticolFilterColumn( "Search repository name, owner",
+ cols_to_filter=[ columns[0], columns[1] ],
+ key="free-text-search",
+ visible=False,
+ filterable="standard" ) )
+
+ def build_initial_query( self, trans, **kwd ):
+ return trans.sa_session.query( model.RepositoryMetadata ) \
+ .join( model.Repository ) \
+ .filter( and_( model.RepositoryMetadata.table.c.includes_tool_dependencies == True,
+ model.Repository.table.c.deleted == False,
+ model.Repository.table.c.deprecated == False ) ) \
+ .join( model.User.table ) \
+ .order_by( model.Repository.name )
+
+
+class ToolsGrid( RepositoryMetadataGrid ):
+
+
+ class ToolsColumn( grids.TextColumn ):
+
+ def get_value( self, trans, grid, repository_metadata ):
+ tool_str = ''
+ if repository_metadata:
+ metadata = repository_metadata.metadata
+ if metadata:
+ tool_dicts = metadata.get( 'tools', [] )
+ if tool_dicts:
+ num_tool_dicts = len( tool_dicts )
+ for index, tool_dict in enumerate( tool_dicts ):
+ tool_id = tool_dict[ 'id' ]
+ name = tool_dict[ 'name' ]
+ version = tool_dict[ 'version' ]
+ tool_str += '%s | %s | %s' % ( escape_html( tool_id ), escape_html( name ), escape_html( version ) )
+ if index < num_tool_dicts - 1:
+ tool_str += '
'
+ return tool_str
+
+ title = "Valid tools in this tool shed"
+ columns = [
+ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name",
+ model_class=model.Repository,
+ link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ),
+ attach_popup=False,
+ key="Repository.name" ),
+ RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner",
+ model_class=model.User,
+ attach_popup=False,
+ key="User.username" ),
+ RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision",
+ attach_popup=False ),
+ ToolsColumn( "Tool id | name | version",
+ attach_popup=False )
+ ]
+ columns.append( grids.MulticolFilterColumn( "Search repository name, owner",
+ cols_to_filter=[ columns[0], columns[1] ],
+ key="free-text-search",
+ visible=False,
+ filterable="standard" ) )
+
+ def build_initial_query( self, trans, **kwd ):
+ return trans.sa_session.query( model.RepositoryMetadata ) \
+ .join( model.Repository ) \
+ .filter( and_( model.RepositoryMetadata.table.c.includes_tools == True,
+ model.Repository.table.c.deleted == False,
+ model.Repository.table.c.deprecated == False ) ) \
+ .join( model.User.table ) \
+ .order_by( model.Repository.name )
+
+
+class DatatypesGrid( RepositoryMetadataGrid ):
+
+
+ class DatatypesColumn( grids.TextColumn ):
+
+ def get_value( self, trans, grid, repository_metadata ):
+ datatype_str = ''
+ if repository_metadata:
+ metadata = repository_metadata.metadata
+ if metadata:
+ datatype_dicts = metadata.get( 'datatypes', [] )
+ if datatype_dicts:
+ num_datatype_dicts = len( datatype_dicts )
+ for index, datatype_dict in enumerate( datatype_dicts ):
+ # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"}
+ extension = datatype_dict[ 'extension' ]
+ dtype = datatype_dict[ 'dtype' ]
+ mimetype = datatype_dict[ 'mimetype' ]
+ display_in_upload = datatype_dict.get( 'display_in_upload', False )
+ datatype_str += '%s | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) )
+ if index < num_datatype_dicts - 1:
+ datatype_str += '
'
+ return datatype_str
+
+ title = "Custom datatypes in this tool shed"
+ columns = [
+ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name",
+ model_class=model.Repository,
+ link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ),
+ attach_popup=False,
+ key="Repository.name" ),
+ RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner",
+ model_class=model.User,
+ attach_popup=False,
+ key="User.username" ),
+ RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision",
+ attach_popup=False ),
+ DatatypesColumn( "Datatype extension | Type | Mimetype",
+ attach_popup=False )
+ ]
+ columns.append( grids.MulticolFilterColumn( "Search repository name, owner",
+ cols_to_filter=[ columns[0], columns[1] ],
+ key="free-text-search",
+ visible=False,
+ filterable="standard" ) )
+
+ def build_initial_query( self, trans, **kwd ):
+ return trans.sa_session.query( model.RepositoryMetadata ) \
+ .join( model.Repository ) \
+ .filter( and_( model.RepositoryMetadata.table.c.includes_datatypes == True,
+ model.Repository.table.c.deleted == False,
+ model.Repository.table.c.deprecated == False ) ) \
+ .join( model.User.table ) \
+ .order_by( model.Repository.name )
+
class RepositoryController( BaseUIController, common_util.ItemRatings ):
category_grid = CategoryGrid()
+ datatypes_grid = DatatypesGrid()
deprecated_repositories_i_own_grid = DeprecatedRepositoriesIOwnGrid()
email_alerts_repository_grid = EmailAlertsRepositoryGrid()
install_matched_repository_grid = InstallMatchedRepositoryGrid()
@@ -800,9 +1018,12 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
my_writable_repositories_grid = MyWritableRepositoriesGrid()
repositories_by_user_grid = RepositoriesByUserGrid()
repositories_i_own_grid = RepositoriesIOwnGrid()
+ repository_dependencies_grid = RepositoryDependenciesGrid()
repository_grid = RepositoryGrid()
# The repository_metadata_grid is not currently displayed, but is sub-classed by several grids.
repository_metadata_grid = RepositoryMetadataGrid()
+ tool_dependencies_grid = ToolDependenciesGrid()
+ tools_grid = ToolsGrid()
valid_category_grid = ValidCategoryGrid()
valid_repository_grid = ValidRepositoryGrid()
@@ -824,7 +1045,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
pass
return self.browse_repositories( trans, **kwd )
if 'operation' in kwd:
- operation = kwd['operation'].lower()
+ operation = kwd[ 'operation' ].lower()
if operation in [ "repositories_by_category", "repositories_by_user" ]:
# Eliminate the current filters if any exist.
for k, v in kwd.items():
@@ -835,6 +1056,16 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
**kwd ) )
return self.category_grid( trans, **kwd )
+ @web.expose
+ def browse_datatypes( self, trans, **kwd ):
+ if 'operation' in kwd:
+ operation = kwd[ 'operation' ].lower()
+ if operation == "view_or_manage_repository":
+ return trans.response.send_redirect( web.url_for( controller='repository',
+ action='view_or_manage_repository',
+ **kwd ) )
+ return self.datatypes_grid( trans, **kwd )
+
@web.expose
def browse_invalid_tools( self, trans, **kwd ):
params = util.Params( kwd )
@@ -881,7 +1112,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
# 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 'operation' in kwd:
- operation = kwd['operation'].lower()
+ operation = kwd[ 'operation' ].lower()
if operation == "view_or_manage_repository":
return trans.response.send_redirect( web.url_for( controller='repository',
action='view_or_manage_repository',
@@ -999,6 +1230,40 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
message=message,
status=status )
+ @web.expose
+ def browse_repository_dependencies( self, trans, **kwd ):
+ if 'operation' in kwd:
+ operation = kwd[ 'operation' ].lower()
+ if operation == "browse_repository":
+ return trans.response.send_redirect( web.url_for( controller='repository',
+ action='browse_repository',
+ **kwd ) )
+ if operation == "view_or_manage_repository":
+ return trans.response.send_redirect( web.url_for( controller='repository',
+ action='view_or_manage_repository',
+ **kwd ) )
+ return self.repository_dependencies_grid( trans, **kwd )
+
+ @web.expose
+ def browse_tools( self, trans, **kwd ):
+ if 'operation' in kwd:
+ operation = kwd[ 'operation' ].lower()
+ if operation == "view_or_manage_repository":
+ return trans.response.send_redirect( web.url_for( controller='repository',
+ action='view_or_manage_repository',
+ **kwd ) )
+ return self.tools_grid( trans, **kwd )
+
+ @web.expose
+ def browse_tool_dependencies( self, trans, **kwd ):
+ if 'operation' in kwd:
+ operation = kwd[ 'operation' ].lower()
+ if operation == "browse_repository":
+ return trans.response.send_redirect( web.url_for( controller='repository',
+ action='browse_repository',
+ **kwd ) )
+ return self.tool_dependencies_grid( trans, **kwd )
+
@web.expose
def browse_valid_categories( self, trans, **kwd ):
# The request came from Galaxy, so restrict category links to display only valid repository changeset revisions.
@@ -1022,7 +1287,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
pass
return self.browse_valid_repositories( trans, **kwd )
if 'operation' in kwd:
- operation = kwd['operation'].lower()
+ operation = kwd[ 'operation' ].lower()
if operation in [ "valid_repositories_by_category", "valid_repositories_by_user" ]:
# Eliminate the current filters if any exist.
for k, v in kwd.items():
@@ -2420,7 +2685,7 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
if 'operation' in kwd:
- operation = kwd['operation'].lower()
+ operation = kwd[ 'operation' ].lower()
if operation == "receive email alerts":
if trans.user:
if kwd[ 'id' ]:
diff --git a/templates/webapps/tool_shed/index.mako b/templates/webapps/tool_shed/index.mako
index f2dc225dfce..965c1a78fd6 100644
--- a/templates/webapps/tool_shed/index.mako
+++ b/templates/webapps/tool_shed/index.mako
@@ -67,6 +67,22 @@
Search for workflows
+
+
+ Valid Galaxy Utilities
+
+
+
+
+
%endif