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merge

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This commit is contained in:
Jeremy Goecks
2012-10-19 21:08:16 -04:00
parent fefa6ac501 53426bcd1e
commit 6e5653bdff
16 changed files with 528 additions and 208 deletions
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lib/galaxy/datatypes/data.py
+3 -1
View File
@@ -536,7 +536,9 @@ class Data( object ):
TODO: Do we need to merge gzip files using gzjoin? cat seems to work,
but might be brittle. Need to revisit this.
"""
if len(split_files) == 1:
if not split_files:
raise ValueError('Asked to merge zero files as %s' % output_file)
elif len(split_files) == 1:
cmd = 'mv -f %s %s' % ( split_files[0], output_file )
else:
cmd = 'cat %s > %s' % ( ' '.join(split_files), output_file )
lib/galaxy/jobs/splitters/multi.py
+13 -4
View File
@@ -115,6 +115,7 @@ def do_merge( job_wrapper, task_wrappers):
try:
working_directory = job_wrapper.working_directory
task_dirs = [os.path.join(working_directory, x) for x in os.listdir(working_directory) if x.startswith('task_')]
assert task_dirs, "Should be at least one sub-task!"
# TODO: Output datasets can be very complex. This doesn't handle metadata files
outputs = job_wrapper.get_output_hdas_and_fnames()
pickone_done = []
@@ -129,10 +130,18 @@ def do_merge( job_wrapper, task_wrappers):
# Just include those files f in the output list for which the
# file f exists; some files may not exist if a task fails.
output_files = [ f for f in output_files if os.path.exists(f) ]
log.debug('files %s ' % output_files)
output_type.merge(output_files, output_file_name)
log.debug('merge finished: %s' % output_file_name)
pass # TODO: merge all the files
if output_files:
log.debug('files %s ' % output_files)
if len(output_files) < len(task_dirs):
log.debug('merging only %i out of expected %i files for %s'
% (len(output_files), len(task_dirs), output_file_name))
output_type.merge(output_files, output_file_name)
log.debug('merge finished: %s' % output_file_name)
else:
msg = 'nothing to merge for %s (expected %i files)' \
% (output_file_name, len(task_dirs))
log.debug(msg)
stderr += msg + "\n"
elif output in pickone_outputs:
# just pick one of them
if output not in pickone_done:
lib/galaxy/webapps/community/controllers/admin.py
+51 -48
View File
@@ -7,7 +7,7 @@ from galaxy.web.form_builder import SelectField
from galaxy.util import inflector
from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui
from common import *
from repository import RepositoryListGrid, CategoryListGrid
from repository import RepositoryGrid, CategoryGrid
from galaxy import eggs
eggs.require( 'mercurial' )
@@ -17,7 +17,7 @@ import logging
log = logging.getLogger( __name__ )
class UserListGrid( grids.Grid ):
class UserGrid( grids.Grid ):
# TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp.
class UserLoginColumn( grids.TextColumn ):
def get_value( self, trans, grid, user ):
@@ -66,10 +66,10 @@ class UserListGrid( grids.Grid ):
default_sort_key = "email"
columns = [
UserLoginColumn( "Email",
key="email",
link=( lambda item: dict( operation="information", id=item.id ) ),
attach_popup=True,
filterable="advanced" ),
key="email",
link=( lambda item: dict( operation="information", id=item.id ) ),
attach_popup=True,
filterable="advanced" ),
UserNameColumn( "User Name",
key="username",
attach_popup=False,
@@ -116,7 +116,7 @@ class UserListGrid( grids.Grid ):
def get_current_item( self, trans, **kwargs ):
return trans.user
class RoleListGrid( grids.Grid ):
class RoleGrid( grids.Grid ):
# TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp.
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, role ):
@@ -207,7 +207,7 @@ class RoleListGrid( grids.Grid ):
def apply_query_filter( self, trans, query, **kwd ):
return query.filter( model.Role.type != model.Role.types.PRIVATE )
class GroupListGrid( grids.Grid ):
class GroupGrid( grids.Grid ):
# TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp.
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, group ):
@@ -278,34 +278,35 @@ class GroupListGrid( grids.Grid ):
preserve_state = False
use_paging = True
class ManageCategoryListGrid( CategoryListGrid ):
columns = [ col for col in CategoryListGrid.columns ]
class ManageCategoryGrid( CategoryGrid ):
columns = [ col for col in CategoryGrid.columns ]
# Override the NameColumn to include an Edit link
columns[ 0 ] = CategoryListGrid.NameColumn( "Name",
key="Category.name",
link=( lambda item: dict( operation="Edit", id=item.id ) ),
model_class=model.Category,
attach_popup=False )
columns[ 0 ] = CategoryGrid.NameColumn( "Name",
key="Category.name",
link=( lambda item: dict( operation="Edit", id=item.id ) ),
model_class=model.Category,
attach_popup=False )
global_actions = [
grids.GridAction( "Add new category",
dict( controller='admin', action='manage_categories', operation='create' ) )
]
class AdminRepositoryListGrid( RepositoryListGrid ):
columns = [ RepositoryListGrid.NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoryListGrid.DescriptionColumn( "Synopsis",
key="description",
attach_popup=False ),
RepositoryListGrid.MetadataRevisionColumn( "Metadata Revisions" ),
RepositoryListGrid.UserColumn( "Owner",
model_class=model.User,
link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ),
attach_popup=False,
key="User.username" ),
RepositoryListGrid.EmailAlertsColumn( "Alert", attach_popup=False ),
class AdminRepositoryGrid( RepositoryGrid ):
columns = [ RepositoryGrid.NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoryGrid.DescriptionColumn( "Synopsis",
key="description",
attach_popup=False ),
RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ),
RepositoryGrid.UserColumn( "Owner",
model_class=model.User,
link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ),
attach_popup=False,
key="User.username" ),
RepositoryGrid.EmailAlertsColumn( "Alert", attach_popup=False ),
RepositoryGrid.DeprecatedColumn( "Deprecated", attach_popup=False ),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn( "Deleted",
key="deleted",
@@ -316,7 +317,7 @@ class AdminRepositoryListGrid( RepositoryListGrid ):
key="free-text-search",
visible=False,
filterable="standard" ) )
operations = [ operation for operation in RepositoryListGrid.operations ]
operations = [ operation for operation in RepositoryGrid.operations ]
operations.append( grids.GridOperation( "Delete",
allow_multiple=False,
condition=( lambda item: not item.deleted ),
@@ -327,7 +328,7 @@ class AdminRepositoryListGrid( RepositoryListGrid ):
async_compatible=False ) )
standard_filters = []
class RepositoryMetadataListGrid( grids.Grid ):
class RepositoryMetadataGrid( grids.Grid ):
class IdColumn( grids.IntegerColumn ):
def get_value( self, trans, grid, repository_metadata ):
return repository_metadata.id
@@ -414,17 +415,18 @@ class RepositoryMetadataListGrid( grids.Grid ):
preserve_state = False
use_paging = True
def build_initial_query( self, trans, **kwd ):
return trans.sa_session.query( self.model_class ) \
.join( model.Repository.table )
return trans.sa_session.query( model.RepositoryMetadata ) \
.join( model.Repository.table ) \
.filter( model.Repository.table.c.deprecated == False )
class AdminController( BaseUIController, Admin ):
user_list_grid = UserListGrid()
role_list_grid = RoleListGrid()
group_list_grid = GroupListGrid()
manage_category_list_grid = ManageCategoryListGrid()
repository_list_grid = AdminRepositoryListGrid()
repository_metadata_list_grid = RepositoryMetadataListGrid()
user_list_grid = UserGrid()
role_list_grid = RoleGrid()
group_list_grid = GroupGrid()
manage_category_grid = ManageCategoryGrid()
repository_grid = AdminRepositoryGrid()
repository_metadata_grid = RepositoryMetadataGrid()
@web.expose
@web.require_admin
@@ -477,7 +479,7 @@ class AdminController( BaseUIController, Admin ):
return self.delete_repository( trans, **kwd )
elif operation == "undelete":
return self.undelete_repository( trans, **kwd )
# The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change
# The changeset_revision_select_field in the RepositoryGrid 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
@@ -495,7 +497,7 @@ class AdminController( BaseUIController, Admin ):
id=trans.security.encode_id( repository.id ),
changeset_revision=v ) )
# Render the list view
return self.repository_list_grid( trans, **kwd )
return self.repository_grid( trans, **kwd )
@web.expose
@web.require_admin
def browse_repository_metadata( self, trans, **kwd ):
@@ -515,7 +517,7 @@ class AdminController( BaseUIController, Admin ):
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_repositories',
**kwd ) )
return self.repository_metadata_list_grid( trans, **kwd )
return self.repository_metadata_grid( trans, **kwd )
@web.expose
@web.require_admin
def create_category( self, trans, **kwd ):
@@ -645,9 +647,9 @@ class AdminController( BaseUIController, Admin ):
@web.require_admin
def manage_categories( self, trans, **kwd ):
if 'f-free-text-search' in kwd:
# Trick to enable searching repository name, description from the CategoryListGrid.
# What we've done is rendered the search box for the RepositoryListGrid on the grid.mako
# template for the CategoryListGrid. See ~/templates/webapps/community/category/grid.mako.
# Trick to enable searching repository name, description from the CategoryGrid.
# What we've done is rendered the search box for the RepositoryGrid on the grid.mako
# template for the CategoryGrid. See ~/templates/webapps/community/category/grid.mako.
# Since we are searching repositories and not categories, redirect to browse_repositories().
return trans.response.send_redirect( web.url_for( controller='admin',
action='browse_repositories',
@@ -674,7 +676,7 @@ class AdminController( BaseUIController, Admin ):
return trans.response.send_redirect( web.url_for( controller='admin',
action='edit_category',
**kwd ) )
return self.manage_category_list_grid( trans, **kwd )
return self.manage_category_grid( trans, **kwd )
@web.expose
@web.require_admin
def regenerate_statistics( self, trans, **kwd ):
@@ -732,7 +734,8 @@ class AdminController( BaseUIController, Admin ):
multiple=True,
display='checkboxes' )
for repository in trans.sa_session.query( trans.model.Repository ) \
.filter( trans.model.Repository.table.c.deleted == False ) \
.filter( and_( trans.model.Repository.table.c.deleted == False,
trans.model.Repository.table.c.deprecated == False ) ) \
.order_by( trans.model.Repository.table.c.name,
trans.model.Repository.table.c.user_id ):
owner = repository.user.username
lib/galaxy/webapps/community/controllers/repository.py
+245 -94
View File
@@ -25,7 +25,7 @@ log = logging.getLogger( __name__ )
VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" )
class CategoryListGrid( grids.Grid ):
class CategoryGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, category ):
return category.name
@@ -65,14 +65,14 @@ class CategoryListGrid( grids.Grid ):
preserve_state = False
use_paging = True
class ValidCategoryListGrid( CategoryListGrid ):
class ValidCategoryGrid( CategoryGrid ):
class RepositoriesColumn( grids.TextColumn ):
def get_value( self, trans, grid, category ):
if category.repositories:
viewable_repositories = 0
for rca in category.repositories:
repository = rca.repository
if repository.downloadable_revisions:
if not repository.deprecated and repository.downloadable_revisions:
viewable_repositories += 1
return viewable_repositories
return 0
@@ -81,13 +81,13 @@ class ValidCategoryListGrid( CategoryListGrid ):
template='/webapps/community/category/valid_grid.mako'
default_sort_key = "name"
columns = [
CategoryListGrid.NameColumn( "Name",
key="Category.name",
link=( lambda item: dict( operation="valid_repositories_by_category", id=item.id ) ),
attach_popup=False ),
CategoryListGrid.DescriptionColumn( "Description",
key="Category.description",
attach_popup=False ),
CategoryGrid.NameColumn( "Name",
key="Category.name",
link=( lambda item: dict( operation="valid_repositories_by_category", id=item.id ) ),
attach_popup=False ),
CategoryGrid.DescriptionColumn( "Description",
key="Category.description",
attach_popup=False ),
# Columns that are valid for filtering but are not visible.
RepositoriesColumn( "Valid repositories",
model_class=model.Repository,
@@ -102,7 +102,7 @@ class ValidCategoryListGrid( CategoryListGrid ):
preserve_state = False
use_paging = True
class RepositoryListGrid( grids.Grid ):
class RepositoryGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository ):
return repository.name
@@ -188,6 +188,11 @@ class RepositoryListGrid( grids.Grid ):
if trans.user and repository.email_alerts and trans.user.email in from_json_string( repository.email_alerts ):
return 'yes'
return ''
class DeprecatedColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository ):
if repository.deprecated:
return 'yes'
return ''
# Grid definition
title = "Repositories"
model_class = model.Repository
@@ -248,21 +253,83 @@ class RepositoryListGrid( grids.Grid ):
.outerjoin( model.RepositoryCategoryAssociation.table ) \
.outerjoin( model.Category.table )
class EmailAlertsRepositoryListGrid( RepositoryListGrid ):
class RepositoriesIOwnGrid( RepositoryGrid ):
title = "Repositories I own"
columns = [
RepositoryListGrid.NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
RepositoryGrid.NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ),
RepositoryGrid.TipRevisionColumn( "Tip Revision" ),
RepositoryGrid.CategoryColumn( "Category",
model_class=model.Category,
key="Category.name",
attach_popup=False ),
RepositoryListGrid.DescriptionColumn( "Synopsis",
key="description",
attach_popup=False ),
RepositoryListGrid.UserColumn( "Owner",
model_class=model.User,
link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ),
attach_popup=False,
key="User.username" ),
RepositoryListGrid.EmailAlertsColumn( "Alert", attach_popup=False ),
RepositoryGrid.DeprecatedColumn( "Deprecated" )
]
columns.append( grids.MulticolFilterColumn( "Search repository name",
cols_to_filter=[ columns[0] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
operations = [ grids.GridOperation( "Mark as deprecated",
allow_multiple=False,
condition=( lambda item: not item.deleted and not item.deprecated ),
async_compatible=False ),
grids.GridOperation( "Mark as not deprecated",
allow_multiple=False,
condition=( lambda item: not item.deleted and item.deprecated ),
async_compatible=False ) ]
def build_initial_query( self, trans, **kwd ):
return trans.sa_session.query( model.Repository ) \
.filter( model.Repository.table.c.user_id == trans.user.id ) \
.join( model.User.table ) \
.outerjoin( model.RepositoryCategoryAssociation.table ) \
.outerjoin( model.Category.table )
class DeprecatedRepositoriesIOwnGrid( RepositoriesIOwnGrid ):
title = "Deprecated repositories I own"
columns = [
RepositoriesIOwnGrid.NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoriesIOwnGrid.MetadataRevisionColumn( "Metadata Revisions" ),
RepositoriesIOwnGrid.TipRevisionColumn( "Tip Revision" ),
RepositoriesIOwnGrid.CategoryColumn( "Category",
model_class=model.Category,
key="Category.name",
attach_popup=False ),
]
columns.append( grids.MulticolFilterColumn( "Search repository name",
cols_to_filter=[ columns[0] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
def build_initial_query( self, trans, **kwd ):
return trans.sa_session.query( model.Repository ) \
.filter( and_( model.Repository.table.c.user_id == trans.user.id,
model.Repository.table.c.deprecated == True ) ) \
.join( model.User.table ) \
.outerjoin( model.RepositoryCategoryAssociation.table ) \
.outerjoin( model.Category.table )
class EmailAlertsRepositoryGrid( RepositoryGrid ):
columns = [
RepositoryGrid.NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=False ),
RepositoryGrid.DescriptionColumn( "Synopsis",
key="description",
attach_popup=False ),
RepositoryGrid.UserColumn( "Owner",
model_class=model.User,
link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ),
attach_popup=False,
key="User.username" ),
RepositoryGrid.EmailAlertsColumn( "Alert", attach_popup=False ),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn( "Deleted",
key="deleted",
@@ -277,29 +344,67 @@ class EmailAlertsRepositoryListGrid( RepositoryListGrid ):
grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository' ) )
]
class WritableRepositoryListGrid( RepositoryListGrid ):
class MyWritableRepositoriesGrid( RepositoryGrid ):
# This grid filters out repositories that have been marked as deprecated.
columns = [
RepositoryGrid.NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ),
RepositoryGrid.TipRevisionColumn( "Tip Revision" ),
RepositoryGrid.UserColumn( "Owner",
model_class=model.User,
link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ),
attach_popup=False,
key="User.username" ),
RepositoryGrid.EmailAlertsColumn( "Alert", attach_popup=False ),
# Columns that are valid for filtering but are not visible.
RepositoryGrid.EmailColumn( "Email",
model_class=model.User,
key="email",
visible=False ),
RepositoryGrid.RepositoryCategoryColumn( "Category",
model_class=model.Category,
key="Category.name",
visible=False ),
grids.DeletedColumn( "Deleted",
key="deleted",
visible=False,
filterable="advanced" )
]
columns.append( grids.MulticolFilterColumn( "Search repository name",
cols_to_filter=[ columns[0] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
operations = [ grids.GridOperation( "Receive email alerts",
allow_multiple=False,
condition=( lambda item: not item.deleted ),
async_compatible=False ) ]
def build_initial_query( self, trans, **kwd ):
# TODO: improve performance by adding a db table associating users with repositories for which they have write access.
username = kwd[ 'username' ]
username = trans.user.username
clause_list = []
for repository in trans.sa_session.query( self.model_class ) \
.filter( self.model_class.table.c.deleted == False ):
for repository in trans.sa_session.query( model.Repository ) \
.filter( and_( model.Repository.table.c.deprecated == False,
model.Repository.table.c.deleted == False ) ):
allow_push = repository.allow_push
if allow_push:
allow_push_usernames = allow_push.split( ',' )
if username in allow_push_usernames:
clause_list.append( self.model_class.table.c.id == repository.id )
clause_list.append( model.Repository.table.c.id == repository.id )
if clause_list:
return trans.sa_session.query( self.model_class ) \
return trans.sa_session.query( model.Repository ) \
.filter( or_( *clause_list ) ) \
.join( model.User.table ) \
.outerjoin( model.RepositoryCategoryAssociation.table ) \
.outerjoin( model.Category.table )
# Return an empty query.
return trans.sa_session.query( self.model_class ) \
.filter( self.model_class.table.c.id < 0 )
return []
class ValidRepositoryListGrid( RepositoryListGrid ):
class ValidRepositoryGrid( RepositoryGrid ):
# This grid filters out repositories that have been marked as deprecated.
class CategoryColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository ):
rval = '<ul>'
@@ -330,16 +435,16 @@ class ValidRepositoryListGrid( RepositoryListGrid ):
return ''
title = "Valid repositories"
columns = [
RepositoryListGrid.NameColumn( "Name",
key="name",
attach_popup=True ),
RepositoryListGrid.DescriptionColumn( "Synopsis",
key="description",
attach_popup=False ),
RepositoryGrid.NameColumn( "Name",
key="name",
attach_popup=True ),
RepositoryGrid.DescriptionColumn( "Synopsis",
key="description",
attach_popup=False ),
RevisionColumn( "Installable Revisions" ),
RepositoryListGrid.UserColumn( "Owner",
model_class=model.User,
attach_popup=False ),
RepositoryGrid.UserColumn( "Owner",
model_class=model.User,
attach_popup=False ),
# Columns that are valid for filtering but are not visible.
RepositoryCategoryColumn( "Category",
model_class=model.Category,
@@ -355,22 +460,25 @@ class ValidRepositoryListGrid( RepositoryListGrid ):
def build_initial_query( self, trans, **kwd ):
if 'id' in kwd:
# The user is browsing categories of valid repositories, so filter the request by the received id, which is a category id.
return trans.sa_session.query( self.model_class ) \
return trans.sa_session.query( model.Repository ) \
.filter( model.Repository.table.c.deprecated == False ) \
.join( model.RepositoryMetadata.table ) \
.join( model.User.table ) \
.join( model.RepositoryCategoryAssociation.table ) \
.join( model.Category.table ) \
.filter( and_( model.Category.table.c.id == trans.security.decode_id( kwd[ 'id' ] ),
model.RepositoryMetadata.table.c.downloadable == True ) )
# The user performed a free text search on the ValidCategoryListGrid.
return trans.sa_session.query( self.model_class ) \
# The user performed a free text search on the ValidCategoryGrid.
return trans.sa_session.query( model.Repository ) \
.filter( model.Repository.table.c.deprecated == False ) \
.join( model.RepositoryMetadata.table ) \
.join( model.User.table ) \
.outerjoin( model.RepositoryCategoryAssociation.table ) \
.outerjoin( model.Category.table ) \
.filter( model.RepositoryMetadata.table.c.downloadable == True )
class MatchedRepositoryListGrid( grids.Grid ):
class MatchedRepositoryGrid( grids.Grid ):
# This grid filters out repositories that have been marked as deprecated.
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository_metadata ):
return repository_metadata.repository.name
@@ -413,38 +521,38 @@ class MatchedRepositoryListGrid( grids.Grid ):
if match_tuples:
for match_tuple in match_tuples:
repository_id, changeset_revision = match_tuple
clause_list.append( "%s=%d and %s='%s'" % ( self.model_class.table.c.repository_id,
clause_list.append( "%s=%d and %s='%s'" % ( model.RepositoryMetadata.table.c.repository_id,
int( repository_id ),
self.model_class.table.c.changeset_revision,
model.RepositoryMetadata.table.c.changeset_revision,
changeset_revision ) )
return trans.sa_session.query( self.model_class ) \
return trans.sa_session.query( model.RepositoryMetadata ) \
.join( model.Repository ) \
.filter( model.Repository.table.c.deprecated == False ) \
.join( model.User.table ) \
.filter( or_( *clause_list ) ) \
.order_by( model.Repository.name )
# Return an empty query
return trans.sa_session.query( self.model_class ) \
.join( model.Repository ) \
.join( model.User.table ) \
.filter( self.model_class.table.c.repository_id == 0 )
return []
class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ):
columns = [ col for col in MatchedRepositoryListGrid.columns ]
class InstallMatchedRepositoryGrid( MatchedRepositoryGrid ):
columns = [ col for col in MatchedRepositoryGrid.columns ]
# Override the NameColumn
columns[ 0 ] = MatchedRepositoryListGrid.NameColumn( "Name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=False )
columns[ 0 ] = MatchedRepositoryGrid.NameColumn( "Name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=False )
class RepositoryController( BaseUIController, ItemRatings ):
install_matched_repository_list_grid = InstallMatchedRepositoryListGrid()
matched_repository_list_grid = MatchedRepositoryListGrid()
valid_repository_list_grid = ValidRepositoryListGrid()
repository_list_grid = RepositoryListGrid()
email_alerts_repository_list_grid = EmailAlertsRepositoryListGrid()
category_list_grid = CategoryListGrid()
valid_category_list_grid = ValidCategoryListGrid()
writable_repository_list_grid = WritableRepositoryListGrid()
install_matched_repository_grid = InstallMatchedRepositoryGrid()
matched_repository_grid = MatchedRepositoryGrid()
valid_repository_grid = ValidRepositoryGrid()
repository_grid = RepositoryGrid()
email_alerts_repository_grid = EmailAlertsRepositoryGrid()
category_grid = CategoryGrid()
valid_category_grid = ValidCategoryGrid()
my_writable_repositories_grid = MyWritableRepositoriesGrid()
repositories_i_own_grid = RepositoriesIOwnGrid()
deprecated_repositories_i_own_grid = DeprecatedRepositoriesIOwnGrid()
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:
@@ -470,8 +578,8 @@ class RepositoryController( BaseUIController, ItemRatings ):
def browse_categories( self, trans, **kwd ):
# The request came from the tool shed.
if 'f-free-text-search' in kwd:
# Trick to enable searching repository name, description from the CategoryListGrid. What we've done is rendered the search box for the
# RepositoryListGrid on the grid.mako template for the CategoryListGrid. See ~/templates/webapps/community/category/grid.mako. Since we
# Trick to enable searching repository name, description from the CategoryGrid. What we've done is rendered the search box for the
# RepositoryGrid on the grid.mako template for the CategoryGrid. See ~/templates/webapps/community/category/grid.mako. Since we
# are searching repositories and not categories, redirect to browse_repositories().
if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]:
# The value of 'id' has been set to the search string, which is a repository name. We'll try to get the desired encoded repository id to pass on.
@@ -491,7 +599,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_repositories',
**kwd ) )
return self.category_list_grid( trans, **kwd )
return self.category_grid( trans, **kwd )
@web.expose
def browse_invalid_tools( self, trans, **kwd ):
params = util.Params( kwd )
@@ -564,13 +672,27 @@ class RepositoryController( BaseUIController, ItemRatings ):
for k, v in kwd.items():
if k.startswith( 'f-' ):
del kwd[ k ]
kwd[ 'f-email' ] = trans.user.email
return self.repositories_i_own_grid( trans, **kwd )
elif operation == "deprecated_repositories_i_own":
# Eliminate the current filters if any exist.
for k, v in kwd.items():
if k.startswith( 'f-' ):
del kwd[ k ]
return self.deprecated_repositories_i_own_grid( trans, **kwd )
elif operation in [ 'mark as deprecated', 'mark as not deprecated' ]:
# Eliminate the current filters if any exist.
for k, v in kwd.items():
if k.startswith( 'f-' ):
del kwd[ k ]
kwd[ 'mark_deprecated' ] = operation == 'mark as deprecated'
return trans.response.send_redirect( web.url_for( controller='repository',
action='deprecate',
**kwd ) )
elif operation == "reviewed_repositories_i_own":
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='reviewed_repositories_i_own' ) )
elif operation == "writable_repositories":
kwd[ 'username' ] = trans.user.username
return self.writable_repository_list_grid( trans, **kwd )
elif operation == "my_writable_repositories":
return self.my_writable_repositories_grid( trans, **kwd )
elif operation == "repositories_by_category":
# Eliminate the current filters if any exist.
for k, v in kwd.items():
@@ -590,7 +712,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
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
# The changeset_revision_select_field in the RepositoryGrid 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
@@ -607,7 +729,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
operation='view_or_manage_repository',
id=trans.security.encode_id( repository.id ),
changeset_revision=v ) )
return self.repository_list_grid( trans, **kwd )
return self.repository_grid( trans, **kwd )
@web.expose
def browse_repository( self, trans, id, **kwd ):
params = util.Params( kwd )
@@ -637,7 +759,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
if kwd[ 'f-free-text-search' ] == 'All':
# The user performed a search, then clicked the "x" to eliminate the search criteria.
new_kwd = {}
return self.valid_category_list_grid( trans, **new_kwd )
return self.valid_category_grid( trans, **new_kwd )
# Since we are searching valid repositories and not categories, redirect to browse_valid_repositories().
if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]:
# The value of 'id' has been set to the search string, which is a repository name.
@@ -658,7 +780,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_valid_repositories',
**kwd ) )
return self.valid_category_list_grid( trans, **kwd )
return self.valid_category_grid( trans, **kwd )
@web.expose
def browse_valid_repositories( self, trans, **kwd ):
galaxy_url = kwd.get( 'galaxy_url', None )
@@ -667,7 +789,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
# The user browsed to a category and then entered a search string, so get the category associated with it's value.
category_name = kwd[ 'f-Category.name' ]
category = get_category_by_name( trans, category_name )
# Set the id value in kwd since it is required by the ValidRepositoryListGrid.build_initial_query method.
# Set the id value in kwd since it is required by the ValidRepositoryGrid.build_initial_query method.
kwd[ 'id' ] = trans.security.encode_id( category.id )
if galaxy_url:
trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
@@ -690,7 +812,7 @@ class RepositoryController( BaseUIController, ItemRatings ):
category_id = kwd.get( 'id', None )
category = get_category( trans, category_id )
kwd[ 'f-Category.name' ] = category.name
# The changeset_revision_select_field in the ValidRepositoryListGrid performs a refresh_on_change which sends in request parameters like
# The changeset_revision_select_field in the ValidRepositoryGrid 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.
@@ -708,11 +830,11 @@ class RepositoryController( BaseUIController, ItemRatings ):
url_args = dict( action='browse_valid_repositories',
operation='preview_tools_in_changeset',
repository_id=repository_id )
self.valid_repository_list_grid.operations = [ grids.GridOperation( "Preview and install",
self.valid_repository_grid.operations = [ grids.GridOperation( "Preview and install",
url_args=url_args,
allow_multiple=False,
async_compatible=False ) ]
return self.valid_repository_list_grid( trans, **kwd )
return self.valid_repository_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 ):
@@ -931,6 +1053,27 @@ class RepositoryController( BaseUIController, ItemRatings ):
message=message,
status=status )
@web.expose
@web.require_login( "deprecate repository" )
def deprecate( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
repository_id = params.get( 'id', None )
repository = get_repository( trans, repository_id )
mark_deprecated = util.string_as_bool( params.get( 'mark_deprecated', False ) )
repository.deprecated = mark_deprecated
trans.sa_session.add( repository )
trans.sa_session.flush()
if mark_deprecated:
message = 'The repository <b>%s</b> has been marked as deprecated.' % repository.name
else:
message = 'The repository <b>%s</b> has been marked as not deprecated.' % repository.name
trans.response.send_redirect( web.url_for( controller='repository',
action='browse_repositories',
operation='repositories_i_own',
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', '' ) )
@@ -1049,16 +1192,16 @@ class RepositoryController( BaseUIController, ItemRatings ):
dict( controller='repository', action='find_tools' ) ),
grids.GridAction( "Search for workflows",
dict( controller='repository', action='find_workflows' ) ) ]
self.install_matched_repository_list_grid.global_actions = global_actions
self.install_matched_repository_grid.global_actions = global_actions
install_url_args = dict( controller='repository', action='find_tools' )
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 )
self.install_matched_repository_grid.operations = operations
return self.install_matched_repository_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 )
self.matched_repository_grid.title = "Repositories with matching tools"
return self.matched_repository_grid( trans, **kwd )
else:
message = "No search performed - each field must contain the same number of comma-separated items."
status = "error"
@@ -1135,16 +1278,16 @@ class RepositoryController( BaseUIController, ItemRatings ):
dict( controller='repository', action='find_tools' ) ),
grids.GridAction( "Search for workflows",
dict( controller='repository', action='find_workflows' ) ) ]
self.install_matched_repository_list_grid.global_actions = global_actions
self.install_matched_repository_grid.global_actions = global_actions
install_url_args = dict( controller='repository', action='find_workflows' )
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 )
self.install_matched_repository_grid.operations = operations
return self.install_matched_repository_grid( trans, **kwd )
else:
kwd[ 'message' ] = "workflow name: <b>%s</b><br/>exact matches only: <b>%s</b>" % \
( self.__stringify( workflow_names ), str( exact_matches_checked ) )
self.matched_repository_list_grid.title = "Repositories with matching workflows"
return self.matched_repository_list_grid( trans, **kwd )
self.matched_repository_grid.title = "Repositories with matching workflows"
return self.matched_repository_grid( trans, **kwd )
else:
message = "No search performed - each field must contain the same number of comma-separated items."
status = "error"
@@ -1407,17 +1550,24 @@ class RepositoryController( BaseUIController, ItemRatings ):
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()
# See if the current user owns any repositories that have been reviewed.
has_reviewed_repositories = False
current_user = trans.user
has_reviewed_repositories = False
has_deprecated_repositories = False
if current_user:
# See if the current user owns any repositories that have been reviewed.
for repository in current_user.active_repositories:
if repository.reviewed_revisions:
has_reviewed_repositories = True
break
# See if the current user has any repositories that have been marked as deprecated.
for repository in current_user.active_repositories:
if repository.deprecated:
has_deprecated_repositories = True
break
return trans.fill_template( '/webapps/community/index.mako',
repository_metadata=repository_metadata,
has_reviewed_repositories=has_reviewed_repositories,
has_deprecated_repositories=has_deprecated_repositories,
message=message,
status=status )
@web.expose
@@ -1738,7 +1888,8 @@ class RepositoryController( BaseUIController, ItemRatings ):
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 )
self.email_alerts_repository_grid.title = "Set email alerts for repository changes"
return self.email_alerts_repository_grid( trans, **kwd )
def __new_state( self, trans, all_pages=False ):
"""
Create a new `DefaultToolState` for this tool. It will not be initialized
lib/galaxy/webapps/community/controllers/repository_review.py
+91 -37
View File
@@ -7,7 +7,7 @@ from galaxy.web.framework.helpers import time_ago, iff, grids
from galaxy.model.orm import *
from sqlalchemy.sql.expression import func
from common import *
from repository import RepositoryListGrid
from repository import RepositoryGrid
from galaxy.util.shed_util import get_configured_ui
from galaxy.util.odict import odict
@@ -48,36 +48,33 @@ class ComponentGrid( grids.Grid ):
preserve_state = False
use_paging = True
class RepositoriesWithReviewsGrid( RepositoryListGrid ):
class RepositoriesWithReviewsGrid( RepositoryGrid ):
# This grid filters out repositories that have been marked as deprecated.
class ReviewersColumn( grids.TextColumn ):
def get_value( self, trans, grid, repository ):
rval = ''
if repository.reviewers:
rval = ''
for user in repository.reviewers:
rval += '%s<br/>' % user.username
return rval
return ''
title = "All reviewed Repositories"
rval += '<a class="view-info" href="repository_reviews_by_user?id=%s">' % trans.security.encode_id( user.id )
rval += '%s</a> | ' % user.username
rval = rval.rstrip( ' | ' )
return rval
title = "All reviewed repositories"
model_class = model.Repository
template='/webapps/community/repository_review/grid.mako'
default_sort_key = "Repository.name"
columns = [
RepositoryListGrid.NameColumn( "Repository name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoryListGrid.DescriptionColumn( "Synopsis",
key="description",
attach_popup=False ),
RepositoryListGrid.WithReviewsRevisionColumn( "Reviewed revisions" ),
RepositoryListGrid.WithoutReviewsRevisionColumn( "Revisions for review" ),
RepositoryListGrid.UserColumn( "Owner",
attach_popup=False ),
ReviewersColumn( "Reviewers",
attach_popup=False )
RepositoryGrid.NameColumn( "Repository name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoryGrid.WithReviewsRevisionColumn( "Reviewed revisions" ),
RepositoryGrid.WithoutReviewsRevisionColumn( "Revisions for review" ),
RepositoryGrid.UserColumn( "Owner", attach_popup=False ),
ReviewersColumn( "Reviewers", attach_popup=False )
]
columns.append( grids.MulticolFilterColumn( "Search repository name, description",
cols_to_filter=[ columns[0], columns[1] ],
columns.append( grids.MulticolFilterColumn( "Search repository name",
cols_to_filter=[ columns[0] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
@@ -89,12 +86,14 @@ class RepositoriesWithReviewsGrid( RepositoryListGrid ):
]
def build_initial_query( self, trans, **kwd ):
return trans.sa_session.query( model.Repository ) \
.filter( model.Repository.table.c.deprecated == False ) \
.join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \
.join( ( model.User.table, model.User.table.c.id == model.Repository.table.c.user_id ) ) \
.outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \
.outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) )
class RepositoriesWithoutReviewsGrid( RepositoriesWithReviewsGrid ):
# This grid filters out repositories that have been marked as deprecated.
title = "Repositories with no reviews"
columns = [
RepositoriesWithReviewsGrid.NameColumn( "Repository name",
@@ -119,12 +118,15 @@ class RepositoriesWithoutReviewsGrid( RepositoriesWithReviewsGrid ):
async_compatible=False ) ]
def build_initial_query( self, trans, **kwd ):
return trans.sa_session.query( model.Repository ) \
.filter( model.Repository.reviews == None ) \
.filter( and_( model.Repository.table.c.deprecated == False,
model.Repository.reviews == None ) ) \
.join( model.User.table )
class RepositoriesReviewedByMeGrid( RepositoriesWithReviewsGrid ):
# This grid filters out repositories that have been marked as deprecated.
def build_initial_query( self, trans, **kwd ):
return trans.sa_session.query( model.Repository ) \
.filter( model.Repository.table.c.deprecated == False ) \
.join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \
.filter( model.RepositoryReview.table.c.user_id == trans.user.id ) \
.join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \
@@ -132,6 +134,7 @@ class RepositoriesReviewedByMeGrid( RepositoriesWithReviewsGrid ):
.outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) )
class RepositoryReviewsByUserGrid( grids.Grid ):
# This grid filters out repositories that have been marked as deprecated.
class RepositoryNameColumn( grids.TextColumn ):
def get_value( self, trans, grid, review ):
return review.repository.name
@@ -166,33 +169,61 @@ class RepositoryReviewsByUserGrid( grids.Grid ):
default_sort_key = 'repository_id'
columns = [
RepositoryNameColumn( "Repository Name",
model_class=model.Repository,
key="Repository.name",
attach_popup=False ),
model_class=model.Repository,
key="Repository.name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoryDescriptionColumn( "Description",
model_class=model.Repository,
key="Repository.description",
attach_popup=False ),
RevisionColumn( "Revision",
attach_popup=False ),
RatingColumn( "Rating",
attach_popup=False )
model_class=model.Repository,
key="Repository.description",
attach_popup=False ),
RevisionColumn( "Revision", attach_popup=False ),
RatingColumn( "Rating", attach_popup=False ),
]
# Override these
default_filter = {}
global_actions = []
operations = []
operations = [
grids.GridOperation( "Inspect repository revisions",
allow_multiple=False,
condition=( lambda item: not item.deleted ),
async_compatible=False )
]
standard_filters = []
num_rows_per_page = 50
preserve_state = False
use_paging = True
def build_initial_query( self, trans, **kwd ):
user_id = trans.security.decode_id( kwd[ 'id' ] )
return trans.sa_session.query( self.model_class ) \
return trans.sa_session.query( model.RepositoryReview ) \
.filter( and_( model.RepositoryReview.table.c.deleted == False, \
model.RepositoryReview.table.c.user_id == user_id ) )
model.RepositoryReview.table.c.user_id == user_id ) ) \
.join( ( model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \
.filter( model.Repository.table.c.deprecated == False )
class ReviewedRepositoriesIOwnGrid( RepositoriesWithReviewsGrid ):
title = "Reviewed repositories I own"
columns = [
RepositoriesWithReviewsGrid.NameColumn( "Repository name",
key="name",
link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ),
attach_popup=True ),
RepositoriesWithReviewsGrid.WithReviewsRevisionColumn( "Reviewed revisions" ),
RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ),
RepositoriesWithReviewsGrid.ReviewersColumn( "Reviewers", attach_popup=False ),
RepositoryGrid.DeprecatedColumn( "Deprecated" )
]
columns.append( grids.MulticolFilterColumn( "Search repository name",
cols_to_filter=[ columns[0] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
operations = [
grids.GridOperation( "Inspect repository revisions",
allow_multiple=False,
condition=( lambda item: not item.deleted ),
async_compatible=False )
]
def build_initial_query( self, trans, **kwd ):
return trans.sa_session.query( model.Repository ) \
.join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \
@@ -655,10 +686,26 @@ class RepositoryReviewController( BaseUIController, ItemRatings ):
@web.expose
@web.require_login( "repository reviews by user" )
def repository_reviews_by_user( self, trans, **kwd ):
# The user may not be the current user. The value of the received id is the encoded user id.
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
if 'operation' in kwd:
operation = kwd['operation'].lower()
# The value of the received id is the encoded review id.
review = get_review( trans, kwd[ 'id' ] )
repository = review.repository
kwd[ 'id' ] = trans.security.encode_id( repository.id )
if operation == "inspect repository revisions":
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='manage_repository_reviews',
**kwd ) )
if operation == "view_or_manage_repository":
kwd[ 'changeset_revision' ] = review.changeset_revision
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='view_or_manage_repository',
**kwd ) )
# The user may not be the current user. The value of the received id is the encoded user id.
user = get_user( trans, kwd[ 'id' ] )
self.repository_reviews_by_user_grid.title = "All repository revision reviews for user '%s'" % user.username
return self.repository_reviews_by_user_grid( trans, **kwd )
@@ -668,6 +715,13 @@ class RepositoryReviewController( BaseUIController, ItemRatings ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
# The value of the received id is the encoded repository id.
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "view_or_manage_repository":
return trans.response.send_redirect( web.url_for( controller='repository_review',
action='view_or_manage_repository',
**kwd ) )
return self.reviewed_repositories_i_own_grid( trans, **kwd )
@web.expose
@web.require_login( "select previous review" )
lib/galaxy/webapps/community/model/__init__.py
+3 -1
View File
@@ -109,7 +109,8 @@ class Repository( object ):
MARKED_FOR_REMOVAL = 'r',
MARKED_FOR_ADDITION = 'a',
NOT_TRACKED = '?' )
def __init__( self, name=None, description=None, long_description=None, user_id=None, private=False, email_alerts=None, times_downloaded=0 ):
def __init__( self, name=None, description=None, long_description=None, user_id=None, private=False, email_alerts=None, times_downloaded=0,
deprecated=False ):
self.name = name or "Unnamed repository"
self.description = description
self.long_description = long_description
@@ -117,6 +118,7 @@ class Repository( object ):
self.private = private
self.email_alerts = email_alerts
self.times_downloaded = times_downloaded
self.deprecated = deprecated
@property
def repo_path( self ):
# Repository locations on disk are defined in the hgweb.config file
lib/galaxy/webapps/community/model/mapping.py
+6 -2
View File
@@ -111,7 +111,8 @@ Repository.table = Table( "repository", metadata,
Column( "private", Boolean, default=False ),
Column( "deleted", Boolean, index=True, default=False ),
Column( "email_alerts", JSONType, nullable=True ),
Column( "times_downloaded", Integer ) )
Column( "times_downloaded", Integer ),
Column( "deprecated", Boolean, default=False ) )
RepositoryMetadata.table = Table( "repository_metadata", metadata,
Column( "id", Integer, primary_key=True ),
@@ -218,7 +219,10 @@ assign_mapper( context, Tag, Tag.table,
properties=dict( children=relation(Tag, backref=backref( 'parent', remote_side=[ Tag.table.c.id ] ) ) ) )
assign_mapper( context, Category, Category.table,
properties=dict( repositories=relation( RepositoryCategoryAssociation ) ) )
properties=dict( repositories=relation( RepositoryCategoryAssociation,
secondary=Repository.table,
primaryjoin=( Category.table.c.id == RepositoryCategoryAssociation.table.c.category_id ),
secondaryjoin=( ( RepositoryCategoryAssociation.table.c.repository_id == Repository.table.c.id ) & ( Repository.table.c.deprecated == False ) ) ) ) )
assign_mapper( context, Repository, Repository.table,
properties = dict(
lib/galaxy/webapps/community/model/migrate/versions/0014_add_deprecated_column.py
+53
View File
@@ -0,0 +1,53 @@
"""
Migration script to add the deprecated column to the repository table.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
# Need our custom types, but don't import anything else from model
from galaxy.model.custom_types import *
import sys, logging
log = logging.getLogger( __name__ )
log.setLevel(logging.DEBUG)
handler = logging.StreamHandler( sys.stdout )
format = "%(name)s %(levelname)s %(asctime)s %(message)s"
formatter = logging.Formatter( format )
handler.setFormatter( formatter )
log.addHandler( handler )
metadata = MetaData( migrate_engine )
db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
def upgrade():
print __doc__
metadata.reflect()
# Create and initialize imported column in job table.
Repository_table = Table( "repository", metadata, autoload=True )
c = Column( "deprecated", Boolean, default=False )
try:
# Create
c.create( Repository_table )
assert c is Repository_table.c.deprecated
# Initialize.
if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
default_false = "0"
elif migrate_engine.name == 'postgres':
default_false = "false"
db_session.execute( "UPDATE repository SET deprecated=%s" % default_false )
except Exception, e:
print "Adding deprecated column to the repository table failed: %s" % str( e )
log.debug( "Adding deprecated column to the repository table failed: %s" % str( e ) )
def downgrade():
metadata.reflect()
# Drop email_alerts column from repository table.
Repository_table = Table( "repository", metadata, autoload=True )
try:
Repository_table.c.deprecated.drop()
except Exception, e:
print "Dropping column deprecated from the repository table failed: %s" % str( e )
log.debug( "Dropping column deprecated from the repository table failed: %s" % str( e ) )
templates/webapps/community/category/grid.mako
+2 -2
View File
@@ -49,8 +49,8 @@
<%def name="grid_body( grid )">
<%
from galaxy.webapps.community.controllers.repository import RepositoryListGrid
repo_grid = RepositoryListGrid()
from galaxy.webapps.community.controllers.repository import RepositoryGrid
repo_grid = RepositoryGrid()
%>
${self.make_grid( grid, repo_grid )}
</%def>
templates/webapps/community/category/valid_grid.mako
+2 -2
View File
@@ -48,8 +48,8 @@
<%def name="grid_body( grid )">
<%
from galaxy.webapps.community.controllers.repository import ValidRepositoryListGrid
repo_grid = ValidRepositoryListGrid()
from galaxy.webapps.community.controllers.repository import ValidRepositoryGrid
repo_grid = ValidRepositoryGrid()
%>
${self.make_grid( grid, repo_grid )}
</%def>
templates/webapps/community/index.mako
+6 -1
View File
@@ -78,8 +78,13 @@
<a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='reviewed_repositories_i_own' )}">Reviewed repositories I own</a>
</div>
%endif
%if has_deprecated_repositories:
<div class="toolTitle">
<a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='deprecated_repositories_i_own' )}">Deprecated repositories I own</a>
</div>
%endif
<div class="toolTitle">
<a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='writable_repositories' )}">My writable repositories</a>
<a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_writable_repositories' )}">My writable repositories</a>
</div>
<div class="toolTitle">
<a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository' )}">My invalid tools</a>
templates/webapps/community/repository/manage_repository.mako
+22 -7
View File
@@ -7,22 +7,25 @@
from galaxy.web.framework.helpers import time_ago
is_admin = trans.user_is_admin()
is_new = repository.is_new
is_deprecated = repository.deprecated
can_contact_owner = trans.user and trans.user != repository.user
can_push = trans.app.security_agent.can_push( trans.user, repository )
can_push = not is_deprecated and trans.app.security_agent.can_push( trans.user, repository )
can_upload = can_push
can_download = not is_new and ( not is_malicious or can_push )
can_download = not is_deprecated and not is_new and ( not is_malicious or can_push )
can_browse_contents = not is_new
can_set_metadata = not is_new
can_rate = not is_new and trans.user and repository.user != trans.user
can_set_metadata = not is_new and not is_deprecated
can_rate = not is_new and not is_deprecated and trans.user and repository.user != trans.user
can_view_change_log = not is_new
if can_push:
browse_label = 'Browse or delete repository tip files'
else:
browse_label = 'Browse repository tip files'
can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip
can_reset_all_metadata = is_admin and len( repo ) > 0
can_deprecate = not is_new and trans.user and ( is_admin or repository.user == trans.user ) and not is_deprecated
can_undeprecate = trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated
can_reset_all_metadata = not is_deprecated and is_admin and len( repo ) > 0
has_readme = metadata and 'readme' in metadata
can_review_repository = trans.app.security_agent.user_can_review_repositories( trans.user )
can_review_repository = not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user )
reviewing_repository = cntrller and cntrller == 'repository_review'
if changeset_revision == repository.tip:
tip_str = 'repository tip'
@@ -87,6 +90,12 @@
%if can_reset_all_metadata:
<a class="action-button" href="${h.url_for( controller='repository', action='reset_all_metadata', id=trans.security.encode_id( repository.id ) )}">Reset all repository metadata</a>
%endif
%if can_deprecate:
<a class="action-button" href="${h.url_for( controller='repository', action='deprecate', id=trans.security.encode_id( repository.id ), mark_deprecated=True )}">Mark repository as deprecated</a>
%endif
%if can_undeprecate:
<a class="action-button" href="${h.url_for( controller='repository', action='deprecate', id=trans.security.encode_id( repository.id ), mark_deprecated=False )}">Mark repository as not deprecated</a>
%endif
%if can_download:
<a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>
<a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a>
@@ -101,6 +110,12 @@
${render_msg( message, status )}
%endif
%if repository.deprecated:
<div class="warningmessage">
This repository has been marked as deprecated, so some tool shed features may be restricted.
</div>
%endif
%if len( changeset_revision_select_field.options ) > 1:
<div class="toolForm">
<div class="toolFormTitle">Repository revision</div>
@@ -122,7 +137,7 @@
<p/>
%endif
<div class="toolForm">
<div class="toolFormTitle">${repository.name}</div>
<div class="toolFormTitle">Repository '${repository.name}'</div>
<div class="toolFormBody">
<form name="edit_repository" id="edit_repository" action="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
%if can_download:
templates/webapps/community/repository/view_repository.mako
+12 -5
View File
@@ -6,11 +6,12 @@
<%
from galaxy.web.framework.helpers import time_ago
is_new = repository.is_new
is_deprecated = repository.deprecated
can_contact_owner = trans.user and trans.user != repository.user
can_push = trans.app.security_agent.can_push( trans.user, repository )
can_rate = not is_new and trans.user and repository.user != trans.user
can_push = not is_deprecated and trans.app.security_agent.can_push( trans.user, repository )
can_rate = not is_deprecated and not is_new and trans.user and repository.user != trans.user
can_upload = can_push
can_download = not is_new and ( not is_malicious or can_push )
can_download = not is_deprecated and not is_new and ( not is_malicious or can_push )
can_browse_contents = trans.webapp.name == 'community' and not is_new
can_view_change_log = trans.webapp.name == 'community' and not is_new
if can_push:
@@ -19,7 +20,7 @@
browse_label = 'Browse repository tip files'
has_readme = metadata and 'readme' in metadata
reviewing_repository = cntrller and cntrller == 'repository_review'
can_review_repository = trans.app.security_agent.user_can_review_repositories( trans.user )
can_review_repository = not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user )
%>
<%!
@@ -100,6 +101,12 @@
${render_msg( message, status )}
%endif
%if repository.deprecated:
<div class="warningmessage">
This repository has been marked as deprecated, so some tool shed features may be restricted.
</div>
%endif
%if len( changeset_revision_select_field.options ) > 1:
<div class="toolForm">
<div class="toolFormTitle">Repository revision</div>
@@ -123,7 +130,7 @@
<p/>
%endif
<div class="toolForm">
<div class="toolFormTitle">${repository.name}</div>
<div class="toolFormTitle">Repository '${repository.name}'</div>
<div class="toolFormBody">
%if can_download:
<div class="form-row">
templates/webapps/community/repository/view_tool_metadata.mako
+1 -1
View File
@@ -110,7 +110,7 @@
<p/>
%if can_download:
<div class="toolForm">
<div class="toolFormTitle">${repository.name}</div>
<div class="toolFormTitle">Repository '${repository.name}'</div>
<div class="toolFormBody">
<div class="form-row">
<label>Clone this repository:</label>
tools/genomespace/genomespace_file_browser.py
+9 -1
View File
@@ -39,6 +39,7 @@ GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles',
'gmt': 'gmt',
'gct': 'gct'}
VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
def chunk_write( source_stream, target_stream, source_method = "read", target_method="write" ):
source_method = getattr( source_stream, source_method )
@@ -113,6 +114,7 @@ def download_from_genomespace_file_browser( json_parameter_file, genomespace_sit
name = name[len( file_url_prefix ):]
file_numbers.append( int( name ) )
file_numbers.sort()
used_filenames = []
for file_num in file_numbers:
url_key = "%s%i" % ( file_url_prefix, file_num )
download_url = datasource_params.get( url_key, None )
@@ -135,8 +137,14 @@ def download_from_genomespace_file_browser( json_parameter_file, genomespace_sit
parsed_url = urlparse.urlparse( download_url )
query_params = urlparse.parse_qs( parsed_url[4] )
filename = urllib.unquote_plus( parsed_url[2].split( '/' )[-1] )
if not filename:
filename = download_url
if output_filename is None:
output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_output%i_visible_%s' % ( hda_id, file_num, galaxy_ext ) )
filename = ''.join( c in VALID_CHARS and c or '-' for c in filename )
while filename in used_filenames:
filename = "-%s" % filename
used_filenames.append( filename )
output_filename = os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, galaxy_ext ) )
else:
if dataset_id is not None:
metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'dataset',
tools/genomespace/genomespace_importer.py
+9 -2
View File
@@ -43,7 +43,7 @@ GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles',
'gmt': 'gmt',
'gct': 'gct'}
VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
def chunk_write( source_stream, target_stream, source_method = "read", target_method="write" ):
source_method = getattr( source_stream, source_method )
@@ -112,6 +112,7 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
datatypes_registry = Registry()
datatypes_registry.load_datatypes( root_dir = json_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = json_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] )
url_param = datasource_params.get( file_url_name, None )
used_filenames = []
for download_url in url_param.split( ',' ):
using_temp_file = False
parsed_url = urlparse.urlparse( download_url )
@@ -129,6 +130,8 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
parsed_url = urlparse.urlparse( download_url )
query_params = urlparse.parse_qs( parsed_url[4] )
filename = urllib.unquote_plus( parsed_url[2].split( '/' )[-1] )
if not filename:
filename = download_url
if output_filename is None:
#need to use a temp file here, because we do not know the ext yet
using_temp_file = True
@@ -179,7 +182,11 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
name = "GenomeSpace importer on %s" % ( filename ) ) ) )
#if using tmp file, move the file to the new file path dir to get scooped up later
if using_temp_file:
shutil.move( output_filename, os.path.join( datasource_params['__new_file_path__'], 'primary_%i_output%s_visible_%s' % ( hda_id, ''.join( c in VALID_CHARS and c or '-' for c in filename ), file_type ) ) )
filename = ''.join( c in VALID_CHARS and c or '-' for c in filename )
while filename in used_filenames:
filename = "-%s" % filename
used_filenames.append( filename )
shutil.move( output_filename, os.path.join( datasource_params['__new_file_path__'], 'primary_%i_%s_visible_%s' % ( hda_id, filename, file_type ) ) )
dataset_id = None #only one primary dataset available
output_filename = None #only have one filename available