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Clean up recently introduced tool shed repository Galaxy utilities grids.

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This commit is contained in:
Greg Von Kuster
2013-03-04 13:01:33 -05:00
parent d08546152a
commit 3a7fe470f2
2 changed files with 54 additions and 33 deletions
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lib/galaxy/webapps/tool_shed/controllers/repository.py
+2 -2
View File
@@ -280,9 +280,9 @@ class RepositoryController( BaseUIController, common_util.ItemRatings ):
def browse_tool_dependencies( self, trans, **kwd ):
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
if operation == "browse_repository":
if operation == "view_or_manage_repository":
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_repository',
action='view_or_manage_repository',
**kwd ) )
return self.tool_dependencies_grid( trans, **kwd )
lib/tool_shed/grids/repository_grids.py
+52 -31
View File
@@ -643,7 +643,10 @@ class RepositoryMetadataGrid( grids.Grid ):
class ChangesetRevisionColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository_metadata ):
return escape_html( repository_metadata.changeset_revision )
repository = repository_metadata.repository
changeset_revision = repository_metadata.changeset_revision
changeset_revision_label = suc.get_revision_label( trans, repository, changeset_revision )
return escape_html( changeset_revision_label )
class MaliciousColumn( grids.BooleanColumn ):
@@ -719,6 +722,7 @@ class RepositoryMetadataGrid( grids.Grid ):
default_sort_key = "Repository.name"
columns = [
RepositoryNameColumn( "Repository name",
key="Repository.name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=False ),
RepositoryOwnerColumn( "Owner",
@@ -743,8 +747,7 @@ class RepositoryMetadataGrid( grids.Grid ):
.join( model.Repository ) \
.filter( and_( model.Repository.table.c.deleted == False,
model.Repository.table.c.deprecated == False ) ) \
.join( model.User.table ) \
.order_by( model.Repository.name )
.join( model.User.table )
class RepositoryDependenciesGrid( RepositoryMetadataGrid ):
@@ -767,22 +770,24 @@ class RepositoryDependenciesGrid( RepositoryMetadataGrid ):
for index, rd_tup in enumerate( sorted_rd_tups ):
name = rd_tup[ 1 ]
owner = rd_tup[ 2 ]
changeset_revision = rd_tup[ 3 ]
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 += '<a href="browse_repository_dependencies?operation=browse_repository&id=%s">' % required_repository_id
rd_str += '<b>name:</b> %s | <b>owner:</b> %s | <b>revision:</b> %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 2 ] ), escape_html( rd_tup[ 3 ] ) )
rd_str += '<a href="browse_repository_dependencies?operation=view_or_manage_repository&id=%s&changeset_revision=%s">' % ( required_repository_id, changeset_revision )
rd_str += 'Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 3 ] ), escape_html( rd_tup[ 2 ] ) )
if required_repository:
rd_str += '</a>'
if index < num_tups - 1:
rd_str += '<br/>'
return rd_str
title = "Repository dependency definitions in this tool shed"
title = "Valid repository dependency definitions in this tool shed"
default_sort_key = "Repository.name"
columns = [
RepositoryMetadataGrid.RepositoryNameColumn( "Repository name",
model_class=model.Repository,
link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ),
link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ),
attach_popup=False,
key="Repository.name" ),
RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner",
@@ -806,8 +811,7 @@ class RepositoryDependenciesGrid( RepositoryMetadataGrid ):
.filter( and_( model.RepositoryMetadata.table.c.has_repository_dependencies == True,
model.Repository.table.c.deleted == False,
model.Repository.table.c.deprecated == False ) ) \
.join( model.User.table ) \
.order_by( model.Repository.name )
.join( model.User.table )
class ToolDependenciesGrid( RepositoryMetadataGrid ):
@@ -850,10 +854,11 @@ class ToolDependenciesGrid( RepositoryMetadataGrid ):
return td_str
title = "Tool dependency definitions in this tool shed"
default_sort_key = "Repository.name"
columns = [
RepositoryMetadataGrid.RepositoryNameColumn( "Repository name",
model_class=model.Repository,
link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ),
link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ),
attach_popup=False,
key="Repository.name" ),
RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner",
@@ -877,8 +882,7 @@ class ToolDependenciesGrid( RepositoryMetadataGrid ):
.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 )
.join( model.User.table )
class ToolsGrid( RepositoryMetadataGrid ):
@@ -893,21 +897,30 @@ class ToolsGrid( RepositoryMetadataGrid ):
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 += '<b>%s</b> | %s | %s' % ( escape_html( tool_id ), escape_html( name ), escape_html( version ) )
if index < num_tool_dicts - 1:
# Create tuples of the attributes we want so we can sort them by extension.
tool_tups = []
for tool_dict in tool_dicts:
tool_id = tool_dict.get( 'id', '' )
version = tool_dict.get( 'version', '' )
# For now we'll just display tool id and version.
if tool_id and version:
tool_tups.append( ( tool_id, version ) )
sorted_tool_tups = sorted( tool_tups, key=lambda tool_tup: tool_tup[ 0 ] )
num_tool_tups = len( sorted_tool_tups )
for index, tool_tup in enumerate( sorted_tool_tups ):
tool_id = tool_tup[ 0 ]
version = tool_tup[ 1 ]
tool_str += '<b>%s:</b> %s' % ( escape_html( tool_id ), escape_html( version ) )
if index < num_tool_tups - 1:
tool_str += '<br/>'
return tool_str
title = "Valid tools in this tool shed"
default_sort_key = "Repository.name"
columns = [
RepositoryMetadataGrid.RepositoryNameColumn( "Repository name",
model_class=model.Repository,
link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ),
link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ),
attach_popup=False,
key="Repository.name" ),
RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner",
@@ -916,7 +929,7 @@ class ToolsGrid( RepositoryMetadataGrid ):
key="User.username" ),
RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision",
attach_popup=False ),
ToolsColumn( "Tool id | name | version",
ToolsColumn( "Tool id and version",
attach_popup=False )
]
columns.append( grids.MulticolFilterColumn( "Search repository name, owner",
@@ -931,8 +944,7 @@ class ToolsGrid( RepositoryMetadataGrid ):
.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 )
.join( model.User.table )
class DatatypesGrid( RepositoryMetadataGrid ):
@@ -947,23 +959,33 @@ class DatatypesGrid( RepositoryMetadataGrid ):
if metadata:
datatype_dicts = metadata.get( 'datatypes', [] )
if datatype_dicts:
num_datatype_dicts = len( datatype_dicts )
for index, datatype_dict in enumerate( datatype_dicts ):
# Create tuples of the attributes we want so we can sort them by extension.
datatype_tups = []
for datatype_dict in datatype_dicts:
# Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"}
extension = datatype_dict.get( 'extension', '' )
dtype = datatype_dict.get( 'dtype', '' )
mimetype = datatype_dict.get( 'mimetype', '' )
display_in_upload = datatype_dict.get( 'display_in_upload', False )
datatype_str += '<b>%s</b> | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) )
if index < num_datatype_dicts - 1:
# For now we'll just display extension and dtype.
if extension and dtype:
datatype_tups.append( ( extension, dtype ) )
sorted_datatype_tups = sorted( datatype_tups, key=lambda datatype_tup: datatype_tup[ 0 ] )
num_datatype_tups = len( sorted_datatype_tups )
for index, datatype_tup in enumerate( sorted_datatype_tups ):
extension = datatype_tup[ 0 ]
dtype = datatype_tup[ 1 ]
datatype_str += '<b>%s:</b> %s' % ( escape_html( extension ), escape_html( dtype ) )
if index < num_datatype_tups - 1:
datatype_str += '<br/>'
return datatype_str
title = "Custom datatypes in this tool shed"
default_sort_key = "Repository.name"
columns = [
RepositoryMetadataGrid.RepositoryNameColumn( "Repository name",
model_class=model.Repository,
link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ),
link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ),
attach_popup=False,
key="Repository.name" ),
RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner",
@@ -972,7 +994,7 @@ class DatatypesGrid( RepositoryMetadataGrid ):
key="User.username" ),
RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision",
attach_popup=False ),
DatatypesColumn( "Datatype extension | Type | Mimetype",
DatatypesColumn( "Datatype extension and class",
attach_popup=False )
]
columns.append( grids.MulticolFilterColumn( "Search repository name, owner",
@@ -987,5 +1009,4 @@ class DatatypesGrid( RepositoryMetadataGrid ):
.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 )
.join( model.User.table )