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Merge pull request #2269 from davebx/refactor_suc

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Move specific methods from shed_util_common.py to specific_util.py
This commit is contained in:
Martin Cech
2016-06-07 17:55:55 -04:00
parent e2f2193355 172a4778c3
commit c0b5a2840b
48 changed files with 1494 additions and 1471 deletions
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lib/galaxy/tools/__init__.py
+7 -6
View File
@@ -55,6 +55,7 @@ from galaxy.web.form_builder import SelectField
from galaxy.util.dictifiable import Dictifiable
from galaxy.work.context import WorkRequestContext
from tool_shed.util import common_util
import tool_shed.util.repository_util as repository_util
from tool_shed.util import shed_util_common as suc
from .loader import template_macro_params, raw_tool_xml_tree, imported_macro_paths
@@ -164,7 +165,7 @@ class ToolBox( BaseGalaxyToolBox ):
# Abstract toolbox doesn't have a dependency on the the database, so
# override _get_tool_shed_repository here to provide this information.
return suc.get_installed_repository(
return repository_util.get_installed_repository(
self.app,
tool_shed=tool_shed,
name=name,
@@ -323,11 +324,11 @@ class Tool( object, Dictifiable ):
def tool_shed_repository( self ):
# If this tool is included in an installed tool shed repository, return it.
if self.tool_shed:
return suc.get_installed_repository( self.app,
tool_shed=self.tool_shed,
name=self.repository_name,
owner=self.repository_owner,
installed_changeset_revision=self.installed_changeset_revision )
return repository_util.get_installed_repository( self.app,
tool_shed=self.tool_shed,
name=self.repository_name,
owner=self.repository_owner,
installed_changeset_revision=self.installed_changeset_revision )
return None
@property
lib/galaxy/tools/data_manager/manager.py
+6 -6
View File
@@ -8,7 +8,7 @@ from galaxy.util.odict import odict
from galaxy.util.template import fill_template
from galaxy.tools.data import TabularToolDataTable
from tool_shed.util import common_util
import tool_shed.util.shed_util_common as suc
from tool_shed.util import repository_util
import galaxy.queue_worker
# set up logger
@@ -150,11 +150,11 @@ class DataManager( object ):
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision )
tool_shed_repository = \
suc.get_installed_repository( self.data_managers.app,
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision )
repository_util.get_installed_repository( self.data_managers.app,
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision )
if tool_shed_repository is None:
log.warning( 'Could not determine tool shed repository from database. This should only ever happen when running tests.' )
# we'll set tool_path manually here from shed_conf_file
lib/galaxy/web/base/controllers/admin.py
+3 -3
View File
@@ -10,7 +10,7 @@ import galaxy.queue_worker
from galaxy import util, web
from galaxy.util import inflector
from galaxy.web.form_builder import CheckboxField
from tool_shed.util import shed_util_common as suc
from tool_shed.util import repository_util
from tool_shed.util.web_util import escape
log = logging.getLogger( __name__ )
@@ -35,7 +35,7 @@ class Admin( object ):
status = kwd.get( 'status', 'done' )
if trans.webapp.name == 'galaxy':
is_repo_installed = trans.install_model.context.query( trans.install_model.ToolShedRepository ).first() is not None
installing_repository_ids = suc.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=True )
installing_repository_ids = repository_util.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=True )
return trans.fill_template( '/webapps/galaxy/admin/index.mako',
is_repo_installed=is_repo_installed,
installing_repository_ids=installing_repository_ids,
@@ -53,7 +53,7 @@ class Admin( object ):
status = kwd.get( 'status', 'done' )
if trans.webapp.name == 'galaxy':
is_repo_installed = trans.install_model.context.query( trans.install_model.ToolShedRepository ).first() is not None
installing_repository_ids = suc.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=True )
installing_repository_ids = repository_util.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=True )
return trans.fill_template( '/webapps/galaxy/admin/center.mako',
is_repo_installed=is_repo_installed,
installing_repository_ids=installing_repository_ids,
lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+10 -10
View File
@@ -75,7 +75,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
# Since exported workflows are dictionaries with very few attributes that differentiate them from each
# other, we'll build the list based on the following dictionary of those few attributes.
exported_workflows = []
repository = suc.get_tool_shed_repository_by_id( self.app, id )
repository = repository_util.get_tool_shed_repository_by_id( self.app, id )
metadata = repository.metadata
if metadata:
exported_workflow_tups = metadata.get( 'workflows', [] )
@@ -172,7 +172,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
index = payload.get( 'index', None )
if index is None:
raise HTTPBadRequest( detail="Missing required parameter 'index'." )
repository = suc.get_tool_shed_repository_by_id( self.app, tool_shed_repository_id )
repository = repository_util.get_tool_shed_repository_by_id( self.app, tool_shed_repository_id )
exported_workflows = json.loads( self.exported_workflows( trans, tool_shed_repository_id ) )
# Since we don't have an in-memory object with an id, we'll identify the exported workflow via its location (i.e., index) in the list.
exported_workflow = exported_workflows[ int( index ) ]
@@ -199,7 +199,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
tool_shed_repository_id = kwd.get( 'id', '' )
if not tool_shed_repository_id:
raise HTTPBadRequest( detail="Missing required parameter 'id'." )
repository = suc.get_tool_shed_repository_by_id( self.app, tool_shed_repository_id )
repository = repository_util.get_tool_shed_repository_by_id( self.app, tool_shed_repository_id )
exported_workflows = json.loads( self.exported_workflows( trans, tool_shed_repository_id ) )
imported_workflow_dicts = []
for exported_workflow_dict in exported_workflows:
@@ -434,11 +434,11 @@ class ToolShedRepositoriesController( BaseAPIController ):
# Get the information about the repository to be installed from the payload.
tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload( payload, include_changeset=True )
tool_shed_repositories = []
tool_shed_repository = suc.get_installed_repository( self.app,
tool_shed=tool_shed_url,
name=name,
owner=owner,
changeset_revision=changeset_revision )
tool_shed_repository = repository_util.get_installed_repository( self.app,
tool_shed=tool_shed_url,
name=name,
owner=owner,
changeset_revision=changeset_revision )
rrm = RepairRepositoryManager( self.app )
repair_dict = rrm.get_repair_dict( tool_shed_repository )
ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] )
@@ -535,7 +535,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
:param id: the encoded id of the ToolShedRepository object
"""
# Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e
tool_shed_repository = suc.get_tool_shed_repository_by_id( self.app, id )
tool_shed_repository = repository_util.get_tool_shed_repository_by_id( self.app, id )
if tool_shed_repository is None:
log.debug( "Unable to locate tool_shed_repository record for id %s." % ( str( id ) ) )
return {}
@@ -555,7 +555,7 @@ class ToolShedRepositoriesController( BaseAPIController ):
:param id: the repository's encoded id
"""
tool_shed_repository = suc.get_tool_shed_repository_by_id( self.app, id )
tool_shed_repository = repository_util.get_tool_shed_repository_by_id( self.app, id )
if tool_shed_repository is None:
log.debug( "Unable to locate tool_shed_repository record for id %s." % ( str( id ) ) )
return {}
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+38 -38
View File
@@ -394,11 +394,11 @@ class AdminToolshed( AdminGalaxy ):
repository_id = kwd.get( 'repository_id', None )
relative_path_to_image_file = kwd.get( 'image_file', None )
if repository_id and relative_path_to_image_file:
repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
repository = repository_util.get_tool_shed_repository_by_id( trans.app, repository_id )
if repository:
repo_files_dir = repository.repo_files_directory( trans.app )
# The following line sometimes returns None. TODO: Figure out why.
path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file )
path_to_file = repository_util.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file )
if path_to_file and os.path.exists( path_to_file ):
file_name = os.path.basename( relative_path_to_image_file )
try:
@@ -500,7 +500,7 @@ class AdminToolshed( AdminGalaxy ):
status = kwd.get( 'status', 'done' )
if workflow_name:
workflow_name = encoding_util.tool_shed_decode( workflow_name )
repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
repository = repository_util.get_tool_shed_repository_by_id( trans.app, repository_id )
if repository:
workflow, status, message = workflow_util.import_workflow( trans, repository, workflow_name )
if workflow:
@@ -593,7 +593,7 @@ class AdminToolshed( AdminGalaxy ):
tmp_clone_url = util.build_url( tool_shed_url, pathspec=[ 'repos', owner, name ] )
tmp_repo_info_tuple = ( None, tmp_clone_url, latest_downloadable_revision, None, owner, None, None )
installed_repository, installed_changeset_revision = \
suc.repository_was_previously_installed( trans.app, tool_shed_url, name, tmp_repo_info_tuple, from_tip=False )
repository_util.repository_was_previously_installed( trans.app, tool_shed_url, name, tmp_repo_info_tuple, from_tip=False )
if installed_repository:
current_changeset_revision = str( installed_repository.changeset_revision )
message = 'Revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b> has already been installed.' % \
@@ -829,7 +829,7 @@ class AdminToolshed( AdminGalaxy ):
# The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a
# tool dependency, but they didn't check any of the available tool dependencies on which to perform the action.
repository_id = kwd.get( 'repository_id', None )
tool_shed_repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
tool_shed_repository = repository_util.get_tool_shed_repository_by_id( trans.app, repository_id )
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
if not tool_dependency_ids:
@@ -911,7 +911,7 @@ class AdminToolshed( AdminGalaxy ):
else:
# The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a
# tool dependency, but they didn't check any of the available tool dependencies on which to perform the action.
tool_shed_repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
tool_shed_repository = repository_util.get_tool_shed_repository_by_id( trans.app, repository_id )
self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies" % escape( tool_shed_repository.name )
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
@@ -963,7 +963,7 @@ class AdminToolshed( AdminGalaxy ):
def monitor_repository_installation( self, trans, **kwd ):
tsridslist = common_util.get_tool_shed_repository_ids( **kwd )
if not tsridslist:
tsridslist = suc.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=False )
tsridslist = repository_util.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=False )
kwd[ 'tool_shed_repository_ids' ] = tsridslist
return self.repository_installation_grid( trans, **kwd )
@@ -1029,7 +1029,7 @@ class AdminToolshed( AdminGalaxy ):
# but the received repository id is from the Galaxy side (the caller is this controller's
# update_to_changeset_revision() method. We need to get the id of the same repository from the
# Tool Shed side.
repository = suc.get_tool_shed_repository_by_id( trans.app, updating_repository_id )
repository = repository_util.get_tool_shed_repository_by_id( trans.app, updating_repository_id )
# For backward compatibility to the 12/20/12 Galaxy release.
try:
params = dict( name=str( repository.name ), owner=str( repository.owner ) )
@@ -1074,7 +1074,7 @@ class AdminToolshed( AdminGalaxy ):
if ( ( not includes_tools_for_display_in_tool_panel and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or
( includes_tools_for_display_in_tool_panel and kwd.get( 'select_tool_panel_section_button', False ) ) ):
if updating:
repository = suc.get_tool_shed_repository_by_id( trans.app, updating_repository_id )
repository = repository_util.get_tool_shed_repository_by_id( trans.app, updating_repository_id )
decoded_updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata )
# Now that the user has decided whether they will handle dependencies, we can update
# the repository to the latest revision.
@@ -1379,17 +1379,17 @@ class AdminToolshed( AdminGalaxy ):
suc.clean_dependency_relationships(trans, new_meta, tool_shed_repository, tool_shed_url)
# The repository's status must be updated from 'Uninstalled' to 'New' when initiating reinstall
# so the repository_installation_updater will function.
tool_shed_repository = suc.create_or_update_tool_shed_repository( trans.app,
tool_shed_repository.name,
tool_shed_repository.description,
tool_shed_repository.installed_changeset_revision,
tool_shed_repository.ctx_rev,
repository_clone_url,
metadata,
trans.install_model.ToolShedRepository.installation_status.NEW,
tool_shed_repository.changeset_revision,
tool_shed_repository.owner,
tool_shed_repository.dist_to_shed )
tool_shed_repository = repository_util.create_or_update_tool_shed_repository( trans.app,
tool_shed_repository.name,
tool_shed_repository.description,
tool_shed_repository.installed_changeset_revision,
tool_shed_repository.ctx_rev,
repository_clone_url,
metadata,
trans.install_model.ToolShedRepository.installation_status.NEW,
tool_shed_repository.changeset_revision,
tool_shed_repository.owner,
tool_shed_repository.dist_to_shed )
ctx_rev = suc.get_ctx_rev( trans.app,
tool_shed_url,
tool_shed_repository.name,
@@ -1775,13 +1775,13 @@ class AdminToolshed( AdminGalaxy ):
"""An error occurred while cloning the repository, so reset everything necessary to enable another attempt."""
repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] )
if kwd.get( 'reset_repository', False ):
suc.set_repository_attributes( trans.app,
repository,
status=trans.install_model.ToolShedRepository.installation_status.NEW,
error_message=None,
deleted=False,
uninstalled=False,
remove_from_disk=True )
repository_util.set_repository_attributes( trans.app,
repository,
status=trans.install_model.ToolShedRepository.installation_status.NEW,
error_message=None,
deleted=False,
uninstalled=False,
remove_from_disk=True )
new_kwd = {}
new_kwd[ 'message' ] = "You can now attempt to install the repository named <b>%s</b> again." % escape( str( repository.name ) )
new_kwd[ 'status' ] = "done"
@@ -1910,11 +1910,11 @@ class AdminToolshed( AdminGalaxy ):
changeset_revision = kwd.get( 'changeset_revision', None )
latest_changeset_revision = kwd.get( 'latest_changeset_revision', None )
latest_ctx_rev = kwd.get( 'latest_ctx_rev', None )
repository = suc.get_installed_repository( trans.app,
tool_shed=tool_shed_url,
name=name,
owner=owner,
changeset_revision=changeset_revision )
repository = repository_util.get_installed_repository( trans.app,
tool_shed=tool_shed_url,
name=name,
owner=owner,
changeset_revision=changeset_revision )
original_metadata_dict = repository.metadata
original_repository_dependencies_dict = original_metadata_dict.get( 'repository_dependencies', {} )
original_repository_dependencies = original_repository_dependencies_dict.get( 'repository_dependencies', [] )
@@ -2001,11 +2001,11 @@ class AdminToolshed( AdminGalaxy ):
# we set from_tip to True to make sure we get the entire set of changeset revisions
# from the Tool Shed.
new_repository_db_record, installed_changeset_revision = \
suc.repository_was_previously_installed( trans.app,
tool_shed_url,
new_name,
repo_info_tuple,
from_tip=True )
repository_util.repository_was_previously_installed( trans.app,
tool_shed_url,
new_name,
repo_info_tuple,
from_tip=True )
if new_repository_db_record:
if new_repository_db_record.status in [ trans.install_model.ToolShedRepository.installation_status.ERROR,
trans.install_model.ToolShedRepository.installation_status.NEW,
@@ -2120,7 +2120,7 @@ class AdminToolshed( AdminGalaxy ):
status = kwd.get( 'status', 'done' )
if workflow_name:
workflow_name = encoding_util.tool_shed_decode( workflow_name )
repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
repository = repository_util.get_tool_shed_repository_by_id( trans.app, repository_id )
changeset_revision = repository.changeset_revision
metadata = repository.metadata
return trans.fill_template( "/admin/tool_shed_repository/view_workflow.mako",
lib/galaxy/webapps/tool_shed/api/categories.py
+2 -1
View File
@@ -7,6 +7,7 @@ from galaxy.web import require_admin as require_admin
from galaxy.web import _future_expose_api as expose_api
from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless
from galaxy.web.base.controller import BaseAPIController
from tool_shed.util import repository_util
import tool_shed.util.shed_util_common as suc
log = logging.getLogger( __name__ )
@@ -81,7 +82,7 @@ class CategoriesController( BaseAPIController ):
category_dict[ 'url' ] = web.url_for( controller='categories',
action='show',
id=trans.security.encode_id( category.id ) )
repositories = suc.get_repositories_by_category( self.app, category.id )
repositories = repository_util.get_repositories_by_category( self.app, category.id )
category_dict[ 'repositories' ] = repositories
return category_dict
lib/galaxy/webapps/tool_shed/api/repositories.py
+21 -22
View File
@@ -36,7 +36,6 @@ from tool_shed.util import hg_util
from tool_shed.util import metadata_util
from tool_shed.util import repository_content_util
from tool_shed.util import repository_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import tool_util
log = logging.getLogger( __name__ )
@@ -73,7 +72,7 @@ class RepositoriesController( BaseAPIController ):
owner = payload.get( 'owner', '' )
if not owner:
raise HTTPBadRequest( detail="Missing required parameter 'owner'." )
repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( self.app, name, owner )
if repository is None:
error_message = 'Cannot locate repository with name %s and owner %s,' % ( str( name ), str( owner ) )
log.debug( error_message )
@@ -106,12 +105,12 @@ class RepositoriesController( BaseAPIController ):
tsr_id = kwd.get( 'tsr_id', None )
if None not in [ name, owner ]:
# Get the repository information.
repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( self.app, name, owner )
if repository is None:
trans.response.status = 404
return { 'status': 'error', 'message': 'No repository named %s found with owner %s' % ( name, owner ) }
elif tsr_id is not None:
repository = suc.get_repository_in_tool_shed( self.app, tsr_id )
repository = repository_util.get_repository_in_tool_shed( self.app, tsr_id )
else:
error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
error_message += "invalid parameters received."
@@ -190,7 +189,7 @@ class RepositoriesController( BaseAPIController ):
# http://<xyz>/api/repositories/get_repository_revision_install_info?name=<n>&owner=<o>&changeset_revision=<cr>
if name and owner and changeset_revision:
# Get the repository information.
repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( self.app, name, owner )
if repository is None:
log.debug( 'Cannot locate repository %s owned by %s' % ( str( name ), str( owner ) ) )
return {}, {}, {}
@@ -201,17 +200,17 @@ class RepositoriesController( BaseAPIController ):
action='show',
id=encoded_repository_id )
# Get the repository_metadata information.
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
changeset_revision )
if repository_metadata is None:
# The changeset_revision column in the repository_metadata table has been updated with a new
# value value, so find the changeset_revision to which we need to update.
repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False )
new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
new_changeset_revision )
new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
new_changeset_revision )
changeset_revision = new_changeset_revision
if repository_metadata is not None:
encoded_repository_metadata_id = trans.security.encode_id( repository_metadata.id )
@@ -257,7 +256,7 @@ class RepositoriesController( BaseAPIController ):
# Example URL: http://localhost:9009/api/repositories/get_installable_revisions?tsr_id=9d37e53072ff9fa4
tsr_id = kwd.get( 'tsr_id', None )
if tsr_id is not None:
repository = suc.get_repository_in_tool_shed( self.app, tsr_id )
repository = repository_util.get_repository_in_tool_shed( self.app, tsr_id )
else:
error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
error_message += "missing or invalid parameter received."
@@ -494,7 +493,7 @@ class RepositoriesController( BaseAPIController ):
owner = payload.get( 'owner', '' )
if not owner:
raise HTTPBadRequest( detail="Missing required parameter 'owner'." )
repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( self.app, name, owner )
if repository is None:
error_message = 'Cannot locate repository with name %s and owner %s,' % ( str( name ), str( owner ) )
log.debug( error_message )
@@ -679,7 +678,7 @@ class RepositoriesController( BaseAPIController ):
repository_id = payload.get( 'repository_id', None )
if repository_id is not None:
repository = suc.get_repository_in_tool_shed( self.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( self.app, repository_id )
start_time = strftime( "%Y-%m-%d %H:%M:%S" )
log.debug( "%s...resetting metadata on repository %s" % ( start_time, str( repository.name ) ) )
results = handle_repository( trans, start_time, repository )
@@ -708,7 +707,7 @@ class RepositoriesController( BaseAPIController ):
except Exception:
raise MalformedId( 'The given id is invalid.' )
repository = suc.get_repository_in_tool_shed( self.app, id )
repository = repository_util.get_repository_in_tool_shed( self.app, id )
if repository is None:
raise ObjectNotFound( 'Unable to locate repository for the given id.' )
repository_dict = repository.to_dict( view='element',
@@ -720,9 +719,9 @@ class RepositoriesController( BaseAPIController ):
@expose_api_anonymous_and_sessionless
def show_tools( self, trans, id, changeset, **kwd ):
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
id,
changeset )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app,
id,
changeset )
if repository_metadata is not None:
encoded_repository_metadata_id = trans.security.encode_id( repository_metadata.id )
repository_metadata_dict = repository_metadata.to_dict( view='collection',
@@ -770,9 +769,9 @@ class RepositoriesController( BaseAPIController ):
raise MalformedId( 'The given id is invalid.' )
recursive = util.asbool( kwd.get( 'recursive', 'True' ) )
all_metadata = {}
repository = suc.get_repository_in_tool_shed( self.app, id )
repository = repository_util.get_repository_in_tool_shed( self.app, id )
for changeset, changehash in repository.installable_revisions( self.app ):
metadata = suc.get_current_repository_metadata_for_changeset_revision( self.app, repository, changehash )
metadata = metadata_util.get_current_repository_metadata_for_changeset_revision( self.app, repository, changehash )
if metadata is None:
continue
metadata_dict = metadata.to_dict( value_mapper={ 'id': self.app.security.encode_id, 'repository_id': self.app.security.encode_id } )
@@ -931,7 +930,7 @@ class RepositoriesController( BaseAPIController ):
rdah = attribute_handlers.RepositoryDependencyAttributeHandler( self.app, unpopulate=False )
tdah = attribute_handlers.ToolDependencyAttributeHandler( self.app, unpopulate=False )
repository = suc.get_repository_in_tool_shed( self.app, id )
repository = repository_util.get_repository_in_tool_shed( self.app, id )
if not ( trans.user_is_admin() or
self.app.security_agent.user_can_administer_repository( trans.user, repository ) or
lib/galaxy/webapps/tool_shed/api/repository_revisions.py
+10 -10
View File
@@ -2,13 +2,13 @@ import logging
from sqlalchemy import and_
import tool_shed.util.shed_util_common as suc
from galaxy import util
from galaxy import web
from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest
from tool_shed.capsule import capsule_manager
from tool_shed.util import hg_util
from tool_shed.util import metadata_util
from tool_shed.util import repository_util
log = logging.getLogger( __name__ )
@@ -47,7 +47,7 @@ class RepositoryRevisionsController( BaseAPIController ):
# We'll currently support only gzip-compressed tar archives.
export_repository_dependencies = util.asbool( export_repository_dependencies )
# Get the repository information.
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
if repository is None:
error_message = 'Cannot locate repository with name %s and owner %s,' % ( str( name ), str( owner ) )
log.debug( error_message )
@@ -131,13 +131,13 @@ class RepositoryRevisionsController( BaseAPIController ):
rd_tups = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ]
for rd_tup in rd_tups:
tool_shed, name, owner, changeset_revision = rd_tup[ 0:4 ]
repository_dependency = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository_dependency = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
if repository_dependency is None:
log.dbug( 'Cannot locate repository dependency %s owned by %s.' % ( name, owner ) )
continue
repository_dependency_id = trans.security.encode_id( repository_dependency.id )
repository_dependency_repository_metadata = \
suc.get_repository_metadata_by_changeset_revision( trans.app, repository_dependency_id, changeset_revision )
metadata_util.get_repository_metadata_by_changeset_revision( trans.app, repository_dependency_id, changeset_revision )
if repository_dependency_repository_metadata is None:
# The changeset_revision column in the repository_metadata table has been updated with a new
# value value, so find the changeset_revision to which we need to update.
@@ -145,14 +145,14 @@ class RepositoryRevisionsController( BaseAPIController ):
repository=repository_dependency,
repo_path=None,
create=False )
new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository_dependency,
repo,
changeset_revision )
new_changeset_revision = metadata_util.get_next_downloadable_changeset_revision( repository_dependency,
repo,
changeset_revision )
if new_changeset_revision != changeset_revision:
repository_dependency_repository_metadata = \
suc.get_repository_metadata_by_changeset_revision( trans.app,
repository_dependency_id,
new_changeset_revision )
metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
repository_dependency_id,
new_changeset_revision )
changeset_revision = new_changeset_revision
else:
decoded_repository_dependency_id = trans.security.decode_id( repository_dependency_id )
lib/galaxy/webapps/tool_shed/controllers/admin.py
+4 -4
View File
@@ -56,7 +56,7 @@ class AdminController( BaseUIController, Admin ):
# 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 = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
kwd[ 'f-email' ] = repository.user.email
elif operation == "repositories_by_category":
# Eliminate the current filters if any exist.
@@ -88,7 +88,7 @@ class AdminController( BaseUIController, Admin ):
changeset_revision_str = 'changeset_revision_'
if k.startswith( changeset_revision_str ):
repository_id = trans.security.encode_id( int( k.lstrip( changeset_revision_str ) ) )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
if repository.tip( trans.app ) != v:
return trans.response.send_redirect( web.url_for( controller='repository',
action='browse_repositories',
@@ -164,7 +164,7 @@ class AdminController( BaseUIController, Admin ):
count = 0
deleted_repositories = ""
for repository_id in ids:
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
if repository:
if not repository.deleted:
# Mark all installable repository_metadata records as not installable.
@@ -376,7 +376,7 @@ class AdminController( BaseUIController, Admin ):
count = 0
undeleted_repositories = ""
for repository_id in ids:
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
if repository:
if repository.deleted:
# Inspect all repository_metadata records to determine those that are installable, and mark
lib/galaxy/webapps/tool_shed/controllers/hg.py
+1 -1
View File
@@ -3,7 +3,7 @@ from galaxy import web
from galaxy.web.base.controller import BaseUIController
from tool_shed.util.common_util import generate_clone_url_for_repository_in_tool_shed
from tool_shed.util.shed_util_common import get_repository_by_name_and_owner
from tool_shed.util.repository_util import get_repository_by_name_and_owner
from tool_shed.util.hg_util import update_repository
from tool_shed.metadata import repository_metadata_manager
lib/galaxy/webapps/tool_shed/controllers/repository.py
+103 -103
View File
@@ -101,7 +101,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
# We'll try to get the desired encoded repository id to pass on.
try:
repository_name = kwd[ 'id' ]
repository = suc.get_repository_by_name( trans.app, repository_name )
repository = repository_util.get_repository_by_name( trans.app, repository_name )
kwd[ 'id' ] = trans.security.encode_id( repository.id )
except:
pass
@@ -280,7 +280,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
# The received id is the repository id, so we need to get the id of the user that owns the repository.
repository_id = kwd.get( 'id', None )
if repository_id:
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
user_id = trans.security.encode_id( repository.user.id )
kwd[ 'user_id' ] = user_id
else:
@@ -348,7 +348,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
# The received id is the repository id, so we need to get the id of the user that owns the repository.
repository_id = kwd.get( 'id', None )
if repository_id:
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
user_id = trans.security.encode_id( repository.user.id )
user = suc.get_user( trans.app, user_id )
self.repositories_by_user_grid.title = "Repositories owned by %s" % user.username
@@ -413,7 +413,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
commit_message = escape( kwd.get( 'commit_message', 'Deleted selected files' ) )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository = repository_util.get_repository_in_tool_shed( trans.app, id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
# Update repository files for browsing.
hg_util.update_repository( repo )
@@ -505,7 +505,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
# We'll try to get the desired encoded repository id to pass on.
try:
name = kwd[ 'id' ]
repository = suc.get_repository_by_name( trans.app, name )
repository = repository_util.get_repository_by_name( trans.app, name )
kwd[ 'id' ] = trans.security.encode_id( repository.id )
except:
pass
@@ -543,7 +543,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
if operation == "preview_tools_in_changeset":
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
repository_metadata = metadata_util.get_latest_repository_metadata( trans.app, repository.id, downloadable=True )
latest_installable_changeset_revision = repository_metadata.changeset_revision
return trans.response.send_redirect( web.url_for( controller='repository',
@@ -586,7 +586,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
# Default to the current changeset revision.
update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
@@ -612,9 +612,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
return no_update
# Return the same value for changeset_revision and latest_changeset_revision.
else:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
changeset_revision )
if repository_metadata:
# If changeset_revision is in the repository_metadata table for this repository, there are no
# additional updates.
@@ -635,9 +635,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
latest_changeset_revision = changeset_hash
break
else:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
changeset_hash )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
changeset_hash )
if repository_metadata:
# We found a RepositoryMetadata record.
update_to_ctx = hg_util.get_changectx_for_changeset( repo, changeset_hash )
@@ -662,7 +662,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def contact_owner( self, trans, id, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository = repository_util.get_repository_in_tool_shed( trans.app, id )
metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app,
id,
repository.tip( trans.app ),
@@ -688,7 +688,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
if operation == "include in docker image":
repository_tups = []
for repository_id in repository_ids:
repository = suc.get_repository_by_id( trans.app, repository_id )
repository = repository_util.get_repository_by_id( trans.app, repository_id )
repository_tups.append( ( str( repository.name ),
str( repository.user.username ),
str( repository.type ) ) )
@@ -709,7 +709,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
tool_shed_url = tool_shed_url = web.url_for( '/', qualified=True )
repository_string = ''
for repository_id in repository_ids:
repository = suc.get_repository_by_id( trans.app, repository_id )
repository = repository_util.get_repository_by_id( trans.app, repository_id )
template = basic_util.SELECTED_REPOSITORIES_TEMPLATE
repository_template = \
string.Template( template ).safe_substitute( tool_shed_url=tool_shed_url,
@@ -801,7 +801,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
mark_deprecated = util.string_as_bool( kwd.get( 'mark_deprecated', False ) )
repository.deprecated = mark_deprecated
trans.sa_session.add( repository )
@@ -835,10 +835,10 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
repository_id = kwd.get( 'repository_id', None )
relative_path_to_image_file = kwd.get( 'image_file', None )
if repository_id and relative_path_to_image_file:
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
if repository:
repo_files_dir = repository.repo_path( trans.app )
path_to_file = suc.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file )
path_to_file = repository_util.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file )
if os.path.exists( path_to_file ):
file_name = os.path.basename( relative_path_to_image_file )
try:
@@ -900,7 +900,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
"""Download an archive of the repository files compressed as zip, gz or bz2."""
# FIXME: thgis will currently only download the repository tip, no matter which installable changeset_revision is being viewed.
# This should be enhanced to use the export method below, which accounts for the currently viewed changeset_revision.
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
# Allow hgweb to handle the download. This requires the tool shed
# server account's .hgrc file to include the following setting:
# [web]
@@ -919,7 +919,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
export_repository_dependencies = kwd.get( 'export_repository_dependencies', '' )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
if kwd.get( 'export_repository_button', False ):
# We'll currently support only gzip-compressed tar archives.
export_repository_dependencies = CheckboxField.is_checked( export_repository_dependencies )
@@ -945,7 +945,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
repositories_archive_path, file_name = os.path.split( repositories_archive.name )
basic_util.remove_dir( repositories_archive_path )
return opened_archive
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
metadata = repository_metadata.metadata
toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
# Initialize the repository dependency RelationBuilder.
@@ -1007,7 +1007,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
# The received id is a RepositoryMetadata id, so we have to get the repository id.
repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, item_id )
repository_id = trans.security.encode_id( repository_metadata.repository.id )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
kwd[ 'id' ] = repository_id
kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
if trans.webapp.name == 'tool_shed' and ( is_admin or repository.user == trans.user ):
@@ -1098,7 +1098,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
# The received id is a RepositoryMetadata id, so we have to get the repository id.
repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, item_id )
repository_id = trans.security.encode_id( repository_metadata.repository.id )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
kwd[ 'id' ] = repository_id
kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
if trans.webapp.name == 'tool_shed' and ( is_admin or repository.user == trans.user ):
@@ -1205,7 +1205,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
repository_dependencies_dict = metadata.get( 'repository_dependencies', {} )
repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
suc.get_repository_dependency_types( repository_dependencies )
repository_util.get_repository_dependency_types( repository_dependencies )
has_galaxy_utilities_dict[ 'has_repository_dependencies' ] = has_repository_dependencies
has_galaxy_utilities_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = \
has_repository_dependencies_only_if_compiling_contained_td
@@ -1215,8 +1215,8 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
changeset_revision )
has_galaxy_utilities_dict = has_galaxy_utilities( repository_metadata )
@@ -1262,9 +1262,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
changeset_hash = str( repo.changectx( changeset ) )
hg_util.get_changectx_for_changeset( repo, changeset_hash )
if update_to_changeset_hash:
update_to_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
changeset_hash )
update_to_repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
changeset_hash )
if update_to_repository_metadata:
has_galaxy_utilities_dict = has_galaxy_utilities( repository_metadata )
includes_data_managers = has_galaxy_utilities_dict[ 'includes_data_managers' ]
@@ -1305,7 +1305,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
repository_name = kwd[ 'name' ]
repository_owner = kwd[ 'owner' ]
changeset_revision = kwd[ 'changeset_revision' ]
repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
if ctx:
@@ -1330,10 +1330,10 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
repository_name = kwd.get( 'name', None )
repository_owner = kwd.get( 'owner', None )
if repository_name is not None and repository_owner is not None:
repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
if repository:
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
return suc.get_latest_downloadable_changeset_revision( trans.app, repository, repo )
return metadata_util.get_latest_downloadable_changeset_revision( trans.app, repository, repo )
return hg_util.INITIAL_CHANGELOG_HASH
@web.json
@@ -1346,12 +1346,12 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
repository_owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
if repository_name is not None and repository_owner is not None and changeset_revision is not None:
repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
if repository:
repository_metadata = \
suc.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
changeset_revision )
metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
changeset_revision )
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
@@ -1370,7 +1370,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
# get_repository_dependencies( self, app, changeset, toolshed_url )
dependencies = repository.get_repository_dependencies( trans.app, changeset_revision, web.url_for( '/', qualified=True ) )
if dependencies:
@@ -1382,7 +1382,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
"""Given a repository name and owner, return the encoded repository id."""
repository_name = kwd[ 'name' ]
repository_owner = kwd[ 'owner' ]
repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
if repository:
return trans.security.encode_id( repository.id )
return ''
@@ -1427,7 +1427,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
"""Given a repository name and owner, return the type."""
repository_name = kwd[ 'name' ]
repository_owner = kwd[ 'owner' ]
repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
return str( repository.type )
@web.json
@@ -1448,7 +1448,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
for required_repository_tup in decoded_required_repository_tups:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( required_repository_tup )
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
encoded_repository_ids.append( trans.security.encode_id( repository.id ) )
changeset_revisions.append( changeset_revision )
if encoded_repository_ids and changeset_revisions:
@@ -1464,7 +1464,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
dependencies = repository.get_tool_dependencies( changeset_revision )
if dependencies is not None:
return encoding_util.tool_shed_encode( dependencies )
@@ -1478,7 +1478,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
"""
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
# TODO: We're currently returning the tool_dependencies.xml file that is available on disk. We need
# to enhance this process to retrieve older versions of the tool-dependencies.xml file from the repository
# manafest.
@@ -1501,12 +1501,12 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
"""
repository_name = kwd[ 'name' ]
repository_owner = kwd[ 'owner' ]
repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
encoded_id = trans.app.security.encode_id( repository.id )
repository_tip = repository.tip( trans.app )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
encoded_id,
repository_tip )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
encoded_id,
repository_tip )
return repository_metadata.metadata
@web.expose
@@ -1518,14 +1518,14 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
name = kwd[ 'name' ]
owner = kwd[ 'owner' ]
changeset_revision = kwd[ 'changeset_revision' ]
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
tool_version_dicts = []
for changeset in repo.changelog:
current_changeset_revision = str( repo.changectx( changeset ) )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
current_changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
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:
@@ -1540,18 +1540,18 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
Generate a dictionary that contains the information about a repository that is necessary for installing
it into a local Galaxy instance.
"""
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
repository_id = trans.security.encode_id( repository.id )
repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
if not repository_metadata:
# The received changeset_revision is no longer associated with metadata, so get the next changeset_revision in the repository
# changelog that is associated with metadata.
changeset_revision = suc.get_next_downloadable_changeset_revision( repository,
repo,
after_changeset_revision=changeset_revision )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
changeset_revision = metadata_util.get_next_downloadable_changeset_revision( repository,
repo,
after_changeset_revision=changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision )
repo_info_dict = repository_util.create_repo_info_dict( app=trans.app,
repository_clone_url=repository_clone_url,
@@ -1592,13 +1592,13 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
includes_tool_dependencies = False
for name, repo_info_tuple in repo_info_dict.items():
if not has_repository_dependencies or not has_repository_dependencies_only_if_compiling_contained_td or not includes_tool_dependencies:
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
description, reposectory_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
for rd_key, rd_tups in repository_dependencies.items():
if rd_key in [ 'root_key', 'description' ]:
continue
curr_has_repository_dependencies, curr_has_repository_dependencies_only_if_compiling_contained_td = \
suc.get_repository_dependency_types( rd_tups )
repository_util.get_repository_dependency_types( rd_tups )
if curr_has_repository_dependencies and not has_repository_dependencies:
has_repository_dependencies = True
if curr_has_repository_dependencies_only_if_compiling_contained_td and not has_repository_dependencies_only_if_compiling_contained_td:
@@ -1726,7 +1726,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
if not repository_ids:
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
repository_ids = trans.security.encode_id( repository.id )
galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
if galaxy_url:
@@ -1832,13 +1832,13 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def manage_repository( self, trans, id, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository = repository_util.get_repository_in_tool_shed( trans.app, id )
repository_type = kwd.get( 'repository_type', str( repository.type ) )
repo_dir = repository.repo_path( trans.app )
repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
repo_name = kwd.get( 'repo_name', repository.name )
changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) )
repository.share_url = suc.generate_sharable_link_for_repository_in_tool_shed( repository, changeset_revision=changeset_revision )
repository.share_url = repository_util.generate_sharable_link_for_repository_in_tool_shed( repository, changeset_revision=changeset_revision )
repository.clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository )
remote_repository_url = kwd.get( 'remote_repository_url', repository.remote_repository_url )
homepage_url = kwd.get( 'homepage_url', repository.homepage_url )
@@ -1939,7 +1939,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
is_malicious = False
repository_dependencies = None
if changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, id, changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, id, changeset_revision )
if repository_metadata:
revision_label = hg_util.get_revision_label( trans.app, repository, changeset_revision, include_date=False )
metadata = repository_metadata.metadata
@@ -1950,7 +1950,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
previous_changeset_revision = \
metadata_util.get_previous_metadata_changeset_revision( repository, repo, changeset_revision, downloadable=False )
if previous_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, id, previous_changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, id, previous_changeset_revision )
if repository_metadata:
revision_label = hg_util.get_revision_label( trans.app, repository, previous_changeset_revision, include_date=False )
metadata = repository_metadata.metadata
@@ -2037,11 +2037,11 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def manage_repository_admins( self, trans, id, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository = repository_util.get_repository_in_tool_shed( trans.app, id )
changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) )
metadata = None
if changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, id, changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, id, changeset_revision )
if repository_metadata:
metadata = repository_metadata.metadata
else:
@@ -2054,9 +2054,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
changeset_revision,
downloadable=False )
if previous_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
id,
previous_changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
id,
previous_changeset_revision )
if repository_metadata:
metadata = repository_metadata.metadata
role = repository.admin_role
@@ -2123,10 +2123,10 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
# Get the next installable changeset_revision beyond the received changeset_revision.
next_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
next_changeset_revision = metadata_util.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
if next_changeset_revision and next_changeset_revision != changeset_revision:
return next_changeset_revision
return ''
@@ -2143,9 +2143,9 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
if repository_metadata:
repository_metadata_id = trans.security.encode_id( repository_metadata.id ),
metadata = repository_metadata.metadata
@@ -2219,7 +2219,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
if name is not None and owner is not None:
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
from_tip = util.string_as_bool( from_tip )
if from_tip:
changeset_revision = repository.tip( trans.app )
@@ -2255,7 +2255,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
action='browse_repositories',
message='Select a repository to rate',
status='error' ) )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository = repository_util.get_repository_in_tool_shed( trans.app, id )
changeset_revision = repository.tip( trans.app )
if repository.user == trans.user:
return trans.response.send_redirect( web.url_for( controller='repository',
@@ -2291,7 +2291,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def reset_all_metadata( self, trans, id, **kwd ):
"""Reset all metadata on the complete changelog for a single repository in the tool shed."""
# This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template.
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository = repository_util.get_repository_in_tool_shed( trans.app, id )
rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app,
user=trans.user,
repository=repository,
@@ -2336,7 +2336,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
commit_message = escape( kwd.get( 'commit_message', 'Deleted selected files' ) )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository = repository_util.get_repository_in_tool_shed( trans.app, id )
repo_dir = repository.repo_path( trans.app )
repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
selected_files_to_delete = kwd.get( 'selected_files_to_delete', '' )
@@ -2414,7 +2414,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
def send_to_owner( self, trans, id, message='' ):
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository = repository_util.get_repository_in_tool_shed( trans.app, id )
if not message:
message = 'Enter a message'
status = 'error'
@@ -2464,7 +2464,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
total_alerts_removed = 0
flush_needed = False
for repository_id in repository_ids:
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
if repository.email_alerts:
email_alerts = json.loads( repository.email_alerts )
else:
@@ -2496,7 +2496,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def set_malicious( self, trans, id, ctx_str, **kwd ):
malicious = kwd.get( 'malicious', '' )
if kwd.get( 'malicious_button', False ):
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, id, ctx_str )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, id, ctx_str )
malicious_checked = CheckboxField.is_checked( malicious )
repository_metadata.malicious = malicious_checked
trans.sa_session.add( repository_metadata )
@@ -2518,7 +2518,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def sharable_owner( self, trans, owner ):
"""Support for sharable URL for each repository owner's tools, e.g. http://example.org/view/owner."""
try:
user = suc.get_user_by_username( trans, owner )
user = common_util.get_user_by_username( trans, owner )
except:
user = None
if user:
@@ -2534,7 +2534,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def sharable_repository( self, trans, owner, name ):
"""Support for sharable URL for a specified repository, e.g. http://example.org/view/owner/name."""
try:
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
except:
repository = None
if repository:
@@ -2545,7 +2545,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
else:
# If the owner is valid, then show all of their repositories.
try:
user = suc.get_user_by_username( trans, owner )
user = common_util.get_user_by_username( trans, owner )
except:
user = None
if user:
@@ -2564,7 +2564,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def sharable_repository_revision( self, trans, owner, name, changeset_revision ):
"""Support for sharable URL for a specified repository revision, e.g. http://example.org/view/owner/name/changeset_revision."""
try:
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
except:
repository = None
if repository:
@@ -2575,7 +2575,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
if not repository_metadata:
# Get updates to the received changeset_revision if any exist.
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
upper_bound_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
upper_bound_changeset_revision = metadata_util.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
if upper_bound_changeset_revision and upper_bound_changeset_revision != changeset_revision:
changeset_revision = upper_bound_changeset_revision
repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app,
@@ -2610,11 +2610,11 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
if repository:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
trans.security.encode_id( repository.id ),
changeset_revision )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
tool_shed_status_dict = {}
# Handle repository deprecation.
@@ -2623,7 +2623,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
if changeset_revision == repository.tip( trans.app ):
tool_shed_status_dict[ 'latest_installable_revision' ] = 'True'
else:
next_installable_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
next_installable_revision = metadata_util.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
if repository_metadata is None:
if next_installable_revision and next_installable_revision != changeset_revision:
tool_shed_status_dict[ 'latest_installable_revision' ] = 'True'
@@ -2643,7 +2643,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
else:
tool_shed_status_dict[ 'revision_update' ] = 'False'
# Handle revision upgrades.
metadata_revisions = [ revision[ 1 ] for revision in suc.get_metadata_revisions( repository, repo ) ]
metadata_revisions = [ revision[ 1 ] for revision in metadata_util.get_metadata_revisions( repository, repo ) ]
num_metadata_revisions = len( metadata_revisions )
for index, metadata_revision in enumerate( metadata_revisions ):
if index == num_metadata_revisions:
@@ -2673,7 +2673,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
if name and owner and changeset_revision:
return suc.get_updated_changeset_revisions( trans.app, name, owner, changeset_revision )
return metadata_util.get_updated_changeset_revisions( trans.app, name, owner, changeset_revision )
return ''
@web.expose
@@ -2710,12 +2710,12 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def view_changelog( self, trans, id, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository = repository_util.get_repository_in_tool_shed( trans.app, id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
changesets = []
for changeset in repo.changelog:
ctx = repo.changectx( changeset )
if suc.get_repository_metadata_by_changeset_revision( trans.app, id, str( ctx ) ):
if metadata_util.get_repository_metadata_by_changeset_revision( trans.app, id, str( ctx ) ):
has_metadata = True
else:
has_metadata = False
@@ -2745,7 +2745,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def view_changeset( self, trans, id, ctx_str, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository = repository_util.get_repository_in_tool_shed( trans.app, id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
ctx = hg_util.get_changectx_for_changeset( repo, ctx_str )
if ctx is None:
@@ -2818,7 +2818,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def view_or_manage_repository( self, trans, **kwd ):
repository_id = kwd.get( 'id', None )
if repository_id:
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
user = trans.user
if repository:
if user is not None and ( trans.user_is_admin() or
@@ -2837,11 +2837,11 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
def view_repository( self, trans, id, **kwd ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, id )
repository = repository_util.get_repository_in_tool_shed( trans.app, id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model )
changeset_revision = kwd.get( 'changeset_revision', repository.tip( trans.app ) )
repository.share_url = suc.generate_sharable_link_for_repository_in_tool_shed( repository, changeset_revision=changeset_revision )
repository.share_url = repository_util.generate_sharable_link_for_repository_in_tool_shed( repository, changeset_revision=changeset_revision )
repository.clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans.user, repository )
display_reviews = kwd.get( 'display_reviews', False )
alerts = kwd.get( 'alerts', '' )
@@ -2875,7 +2875,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
add_id_to_name=False,
downloadable=False )
revision_label = hg_util.get_revision_label( trans.app, repository, changeset_revision, include_date=False )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, id, changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, id, changeset_revision )
if repository_metadata:
metadata = repository_metadata.metadata
# Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
@@ -2928,7 +2928,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
repo_files_dir = repository.repo_path( trans.app )
repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_files_dir, create=False )
tool_metadata_dict = {}
@@ -2937,7 +2937,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
guid = None
original_tool_data_path = trans.app.config.tool_data_path
revision_label = hg_util.get_revision_label( trans.app, repository, changeset_revision, include_date=False )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
if repository_metadata:
repository_metadata_id = trans.security.encode_id( repository_metadata.id )
metadata = repository_metadata.metadata
@@ -3012,7 +3012,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ):
if workflow_name:
workflow_name = encoding_util.tool_shed_decode( workflow_name )
repository_metadata = metadata_util.get_repository_metadata_by_id( trans.app, repository_metadata_id )
repository = suc.get_repository_in_tool_shed( trans.app, trans.security.encode_id( repository_metadata.repository_id ) )
repository = repository_util.get_repository_in_tool_shed( trans.app, trans.security.encode_id( repository_metadata.repository_id ) )
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
return trans.fill_template( "/webapps/tool_shed/repository/view_workflow.mako",
lib/galaxy/webapps/tool_shed/controllers/repository_review.py
+8 -6
View File
@@ -12,6 +12,8 @@ from galaxy.web.form_builder import CheckboxField
from galaxy.webapps.tool_shed.util import ratings_util
from tool_shed.util import hg_util
from tool_shed.util import review_util
from tool_shed.util import metadata_util
from tool_shed.util import repository_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util.container_util import STRSEP
from tool_shed.util.web_util import escape
@@ -139,7 +141,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
if repository_id:
if changeset_revision:
# Make sure there is not already a review of the revision by the user.
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
if review_util.get_review_by_repository_id_changeset_revision_user_id( app=trans.app,
repository_id=repository_id,
changeset_revision=changeset_revision,
@@ -156,7 +158,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
**kwd ) )
# A review can be initially performed only on an installable revision of a repository, so make sure we have metadata associated
# with the received changeset_revision.
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
@@ -489,7 +491,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
changeset_revision )
# Determine if the current user can add a review to this revision.
can_add_review = trans.user not in [ repository_review.user for repository_review in repository_reviews ]
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision )
if repository_metadata:
repository_metadata_reviews = util.listify( repository_metadata.reviews )
else:
@@ -520,7 +522,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
status = kwd.get( 'status', 'done' )
repository_id = kwd.get( 'id', None )
changeset_revision = kwd.get( 'changeset_revision', None )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ]
rev, changeset_revision_label = hg_util.get_rev_label_from_changeset_revision( repo, changeset_revision )
@@ -582,7 +584,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
# The value of the received id is the encoded repository id.
message = escape( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repository = suc.get_repository_in_tool_shed( trans.app, kwd[ 'id' ] )
repository = repository_util.get_repository_in_tool_shed( trans.app, kwd[ 'id' ] )
changeset_revision = kwd.get( 'changeset_revision', None )
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
previous_reviews_dict = review_util.get_previous_repository_reviews( trans.app,
@@ -600,7 +602,7 @@ class RepositoryReviewController( BaseUIController, ratings_util.ItemRatings ):
@web.expose
@web.require_login( "view or manage repository" )
def view_or_manage_repository( self, trans, **kwd ):
repository = suc.get_repository_in_tool_shed( trans.app, kwd[ 'id' ] )
repository = repository_util.get_repository_in_tool_shed( trans.app, kwd[ 'id' ] )
if trans.user_is_admin() or repository.user == trans.user:
return trans.response.send_redirect( web.url_for( controller='repository',
action='manage_repository',
lib/galaxy/webapps/tool_shed/controllers/upload.py
+2 -1
View File
@@ -20,6 +20,7 @@ from tool_shed.tools import data_table_manager
from tool_shed.util import basic_util
from tool_shed.util import commit_util
from tool_shed.util import hg_util
from tool_shed.util import repository_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import repository_content_util
from tool_shed.util import xml_util
@@ -38,7 +39,7 @@ class UploadController( BaseUIController ):
status = kwd.get( 'status', 'done' )
commit_message = escape( kwd.get( 'commit_message', 'Uploaded' ) )
repository_id = kwd.get( 'repository_id', '' )
repository = suc.get_repository_in_tool_shed( trans.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( trans.app, repository_id )
repo_dir = repository.repo_path( trans.app )
repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_dir, create=False )
uncompress_file = util.string_as_bool( kwd.get( 'uncompress_file', 'true' ) )
lib/galaxy/webapps/tool_shed/model/__init__.py
+7 -7
View File
@@ -10,7 +10,7 @@ from galaxy.util.hash_util import new_secure_hash
from galaxy.util.dictifiable import Dictifiable
import tool_shed.repository_types.util as rt_util
from tool_shed.dependencies.repository import relation_builder
from tool_shed.util import shed_util_common as suc
from tool_shed.util import metadata_util
from mercurial import hg
from mercurial import ui
@@ -230,9 +230,9 @@ class Repository( object, Dictifiable ):
# have repository dependencies. However, if a readme file is uploaded, or some other change
# is made that does not create a new downloadable changeset revision but updates the existing
# one, we still want to be able to get repository dependencies.
repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( app,
self,
changeset )
repository_metadata = metadata_util.get_current_repository_metadata_for_changeset_revision( app,
self,
changeset )
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
@@ -252,9 +252,9 @@ class Repository( object, Dictifiable ):
return []
def installable_revisions( self, app, sort_revisions=True ):
return suc.get_metadata_revisions( self,
hg.repository( ui.ui(), self.repo_path( app ) ),
sort_revisions=sort_revisions )
return metadata_util.get_metadata_revisions( self,
hg.repository( ui.ui(), self.repo_path( app ) ),
sort_revisions=sort_revisions )
def is_new( self, app ):
repo = hg.repository( ui.ui(), self.repo_path( app ) )
lib/tool_shed/capsule/capsule_manager.py
+30 -29
View File
@@ -27,6 +27,7 @@ from tool_shed.util import commit_util
from tool_shed.util import common_util
from tool_shed.util import encoding_util
from tool_shed.util import hg_util
from tool_shed.util import metadata_util
from tool_shed.util import repository_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import xml_util
@@ -68,9 +69,9 @@ class ExportRepositoryManager( object ):
ordered_changeset_revisions = []
if self.repository:
repository_metadata = \
suc.get_current_repository_metadata_for_changeset_revision( self.app,
self.repository,
self.changeset_revision )
metadata_util.get_current_repository_metadata_for_changeset_revision( self.app,
self.repository,
self.changeset_revision )
if repository_metadata:
ordered_repository_ids = [ self.repository_id ]
ordered_repositories = [ self.repository ]
@@ -214,11 +215,11 @@ class ExportRepositoryManager( object ):
# There should only be one entry in the received repo_info_dict.
description, repository_clone_url, changeset_revision, ctx_rev, \
repository_owner, repository_dependencies, tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tup )
repository = suc.get_repository_by_name_and_owner( self.app, repository_name, repository_owner )
repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( self.app,
repository,
changeset_revision )
repository_util.get_repo_info_tuple_contents( repo_info_tup )
repository = repository_util.get_repository_by_name_and_owner( self.app, repository_name, repository_owner )
repository_metadata = metadata_util.get_current_repository_metadata_for_changeset_revision( self.app,
repository,
changeset_revision )
if repository_metadata:
return repository, repository_metadata.changeset_revision
return None, None
@@ -242,10 +243,10 @@ class ExportRepositoryManager( object ):
associated with self.repository_id.
"""
rdim = RepositoryDependencyInstallManager( self.app )
repository = suc.get_repository_in_tool_shed( self.app, self.repository_id )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
self.repository_id,
self.changeset_revision )
repository = repository_util.get_repository_in_tool_shed( self.app, self.repository_id )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app,
self.repository_id,
self.changeset_revision )
# Get a dictionary of all repositories upon which the contents of the current
# repository_metadata record depend.
toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
@@ -305,8 +306,8 @@ class ExportRepositoryManager( object ):
description, repository_clone_url, changeset_revision, \
ctx_rev, repository_owner, repository_dependencies, \
tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tup )
repository = suc.get_repository_by_name_and_owner( self.app, repository_name, repository_owner )
repository_util.get_repo_info_tuple_contents( repo_info_tup )
repository = repository_util.get_repository_by_name_and_owner( self.app, repository_name, repository_owner )
repository_ids.append( self.app.security.encode_id( repository.id ) )
return repository_ids
@@ -328,9 +329,9 @@ class ExportRepositoryManager( object ):
# Create a dictionary whose keys are the received repository_ids and whose values are a list of
# repository_ids, each of which is contained in the received list of repository_ids and whose associated
# repository must be imported prior to the repository associated with the repository_id key.
prior_import_required_dict = suc.get_prior_import_or_install_required_dict( self.app,
repository_ids,
repo_info_dicts )
prior_import_required_dict = repository_util.get_prior_import_or_install_required_dict( self.app,
repository_ids,
repo_info_dicts )
processed_repository_ids = []
# Process the list of repository dependencies defined for the primary exported repository.
while len( processed_repository_ids ) != len( prior_import_required_dict.keys() ):
@@ -403,13 +404,13 @@ class ImportRepositoryManager( object ):
ok, name_owner, message = import_results_tup
name, owner = name_owner
if not ok:
repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( self.app, name, owner )
if repository is not None:
# Do not allow the repository to be automatically installed if population resulted in errors.
tip_changeset_revision = repository.tip( self.app )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
self.app.security.encode_id( repository.id ),
tip_changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app,
self.app.security.encode_id( repository.id ),
tip_changeset_revision )
if repository_metadata:
if repository_metadata.downloadable:
repository_metadata.downloadable = False
@@ -451,7 +452,7 @@ class ImportRepositoryManager( object ):
long_description = repository_archive_dict.get( 'long_description', '' )
# The owner entry in the repository_archive_dict is the public username of the user associated with
# the exported repository archive.
user = suc.get_user_by_username( self.app, username )
user = common_util.get_user_by_username( self.app, username )
if user is None:
ok = False
results_message += 'Import failed: repository owner <b>%s</b> does not have an account in this Tool Shed.' % \
@@ -595,15 +596,15 @@ class ImportRepositoryManager( object ):
if defined_repository_metadata is None:
# The defined changeset_revision is not associated with a repository_metadata
# record, so updates must be necessary.
defined_repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
defined_repository = repository_util.get_repository_by_name_and_owner( self.app, name, owner )
defined_repo = hg_util.get_repo_for_repository( self.app,
repository=defined_repository,
repo_path=None,
create=False )
updated_changeset_revision = \
suc.get_next_downloadable_changeset_revision( defined_repository,
defined_repo,
changeset_revision )
metadata_util.get_next_downloadable_changeset_revision( defined_repository,
defined_repo,
changeset_revision )
if updated_changeset_revision == rm_changeset_revision and updated_changeset_revision != changeset_revision:
dependent_downloadable_revisions.append( downloadable_revision )
return dependent_downloadable_revisions
@@ -691,9 +692,9 @@ class ImportRepositoryManager( object ):
"""
repository_status_info_dicts = []
for repository_info_dict in repository_info_dicts:
repository = suc.get_repository_by_name_and_owner( self.app,
repository_info_dict[ 'name' ],
repository_info_dict[ 'owner' ] )
repository = repository_util.get_repository_by_name_and_owner( self.app,
repository_info_dict[ 'name' ],
repository_info_dict[ 'owner' ] )
if repository:
if repository.deleted:
repository_info_dict[ 'status' ] = 'Exists, deleted'
lib/tool_shed/dependencies/attribute_handlers.py
+4 -3
View File
@@ -9,7 +9,8 @@ from tool_shed.dependencies.tool import tag_attribute_handler
from tool_shed.repository_types.util import REPOSITORY_DEPENDENCY_DEFINITION_FILENAME
from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION_FILENAME
from tool_shed.util import hg_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import metadata_util
from tool_shed.util import repository_util
from tool_shed.util import xml_util
log = logging.getLogger( __name__ )
@@ -106,14 +107,14 @@ class RepositoryDependencyAttributeHandler( object ):
# Populate the changeset_revision attribute with the latest installable metadata revision for
# the defined repository. We use the latest installable revision instead of the latest metadata
# revision to ensure that the contents of the revision are valid.
repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
repository = repository_util.get_repository_by_name_and_owner( self.app, name, owner )
if repository:
repo = hg_util.get_repo_for_repository( self.app,
repository=repository,
repo_path=None,
create=False )
lastest_installable_changeset_revision = \
suc.get_latest_downloadable_changeset_revision( self.app, repository, repo )
metadata_util.get_latest_downloadable_changeset_revision( self.app, repository, repo )
if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision
altered = True
lib/tool_shed/dependencies/repository/relation_builder.py
+10 -9
View File
@@ -2,6 +2,7 @@ import logging
from galaxy.util import asbool, listify
import tool_shed.util.repository_util
from tool_shed.util import common_util, container_util, hg_util, metadata_util
from tool_shed.util import shed_util_common as suc
@@ -80,10 +81,10 @@ class RelationBuilder( object ):
current_changeset_revision = str( self.repository_metadata.changeset_revision )
# Get the changeset revision to which the current value of required_repository_changeset_revision
# should be updated if it's not current.
text = suc.get_updated_changeset_revisions( self.app,
name=str( self.repository.name ),
owner=str( self.repository.user.username ),
changeset_revision=current_changeset_revision )
text = metadata_util.get_updated_changeset_revisions( self.app,
name=str( self.repository.name ),
owner=str( self.repository.user.username ),
changeset_revision=current_changeset_revision )
if text:
valid_changeset_revisions = listify( text )
if current_changeset_revision not in valid_changeset_revisions:
@@ -181,7 +182,7 @@ class RelationBuilder( object ):
rd_only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( repository_dependency )
if suc.tool_shed_is_this_tool_shed( rd_toolshed ):
repository = suc.get_repository_by_name_and_owner( self.app, rd_name, rd_owner )
repository = tool_shed.util.repository_util.get_repository_by_name_and_owner( self.app, rd_name, rd_owner )
if repository:
repository_id = self.app.security.encode_id( repository.id )
repository_metadata = \
@@ -196,7 +197,7 @@ class RelationBuilder( object ):
else:
# The repository changeset_revision is no longer installable, so see if there's been an update.
repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False )
changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision )
changeset_revision = metadata_util.get_next_downloadable_changeset_revision( repository, repo, rd_changeset_revision )
if changeset_revision != rd_changeset_revision:
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
@@ -215,7 +216,7 @@ class RelationBuilder( object ):
updated_key_rd_dicts.append( new_key_rd_dict )
else:
repository_components_tuple = container_util.get_components_from_key( key )
components_list = suc.extract_components_from_tuple( repository_components_tuple )
components_list = tool_shed.util.repository_util.extract_components_from_tuple( repository_components_tuple )
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[ 0:4 ]
# For backward compatibility to the 12/20/12 Galaxy release.
if len( components_list ) in (4, 5):
@@ -226,7 +227,7 @@ class RelationBuilder( object ):
log.debug( message )
else:
repository_components_tuple = container_util.get_components_from_key( key )
components_list = suc.extract_components_from_tuple( repository_components_tuple )
components_list = tool_shed.util.repository_util.extract_components_from_tuple( repository_components_tuple )
toolshed, repository_name, repository_owner, repository_changeset_revision = components_list[ 0:4 ]
message = "The revision %s defined for repository %s owned by %s is invalid, so repository " % \
( str( rd_changeset_revision ), str( rd_name ), str( rd_owner ) )
@@ -260,7 +261,7 @@ class RelationBuilder( object ):
toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( repository_dependency )
if suc.tool_shed_is_this_tool_shed( toolshed ):
required_repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
required_repository = tool_shed.util.repository_util.get_repository_by_name_and_owner( self.app, name, owner )
self.repository = required_repository
repository_id = self.app.security.encode_id( required_repository.id )
required_repository_metadata = \
lib/tool_shed/galaxy_install/dependency_display.py
+12 -9
View File
@@ -5,8 +5,11 @@ import threading
from galaxy import util
from tool_shed.galaxy_install.utility_containers import GalaxyUtilityContainerManager
from tool_shed.util import common_util, container_util, readme_util
from tool_shed.util import shed_util_common as suc, tool_dependency_util
from tool_shed.util import common_util
from tool_shed.util import container_util
from tool_shed.util import readme_util
from tool_shed.util import repository_util
from tool_shed.util import tool_dependency_util
from tool_shed.utility_containers import utility_container_manager
log = logging.getLogger( __name__ )
@@ -286,7 +289,7 @@ class DependencyDisplayer( object ):
folder_id += 1
repository_components_tuple = \
container_util.get_components_from_key( old_container_repository_dependencies_folder.key )
components_list = suc.extract_components_from_tuple( repository_components_tuple )
components_list = repository_util.extract_components_from_tuple( repository_components_tuple )
name = components_list[ 1 ]
# Generate the label by retrieving the repository name.
old_container_repository_dependencies_folder.label = str( name )
@@ -553,17 +556,17 @@ class DependencyDisplayer( object ):
description, repository_clone_url, changeset_revision, \
ctx_rev, repository_owner, repository_dependencies, \
tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
if tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
tool_dependencies = self.add_installation_directories_to_tool_dependencies( tool_dependencies )
# The required_repository may have been installed with a different changeset revision.
required_repository, installed_changeset_revision = \
suc.repository_was_previously_installed( self.app,
tool_shed_url,
name,
repo_info_tuple,
from_tip=False )
repository_util.repository_was_previously_installed( self.app,
tool_shed_url,
name,
repo_info_tuple,
from_tip=False )
if required_repository:
required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \
self.get_installed_and_missing_tool_dependencies_for_installed_repository( required_repository,
lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
+2 -2
View File
@@ -2,12 +2,12 @@ import logging
from sqlalchemy import false, or_
import tool_shed.util.shed_util_common as suc
from galaxy import util
from galaxy.model import tool_shed_install
from galaxy.web import url_for
from galaxy.web.framework.helpers import iff, grids
from tool_shed.util import tool_dependency_util
from tool_shed.util import repository_util
log = logging.getLogger( __name__ )
@@ -104,7 +104,7 @@ class InstalledRepositoryGrid( grids.Grid ):
class StatusColumn( grids.TextColumn ):
def get_value( self, trans, grid, tool_shed_repository ):
return suc.get_tool_shed_repository_status_label( trans.app, tool_shed_repository )
return repository_util.get_tool_shed_repository_status_label( trans.app, tool_shed_repository )
class ToolShedColumn( grids.TextColumn ):
lib/tool_shed/galaxy_install/install_manager.py
+14 -14
View File
@@ -10,7 +10,7 @@ from six import string_types
from sqlalchemy import or_
from galaxy import exceptions, util
from tool_shed.util import basic_util, common_util, encoding_util, hg_util
from tool_shed.util import basic_util, common_util, encoding_util, hg_util, repository_util
from tool_shed.util import shed_util_common as suc, tool_dependency_util
from tool_shed.util import tool_util, xml_util
@@ -517,7 +517,7 @@ class InstallRepositoryManager( object ):
irmm_metadata_dict = irmm.get_metadata_dict()
tool_shed_repository.metadata = irmm_metadata_dict
# Update the tool_shed_repository.tool_shed_status column in the database.
tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository )
tool_shed_status_dict = repository_util.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository )
if tool_shed_status_dict:
tool_shed_repository.tool_shed_status = tool_shed_status_dict
self.install_model.context.add( tool_shed_repository )
@@ -864,8 +864,8 @@ class InstallRepositoryManager( object ):
self.install_model.ToolShedRepository.installation_status.CLONING )
repo_info_tuple = repo_info_dict[ tool_shed_repository.name ]
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
relative_clone_dir = suc.generate_tool_shed_repository_install_dir( repository_clone_url,
tool_shed_repository.installed_changeset_revision )
relative_clone_dir = repository_util.generate_tool_shed_repository_install_dir( repository_clone_url,
tool_shed_repository.installed_changeset_revision )
relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name )
install_dir = os.path.join( tool_path, relative_install_dir )
cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
@@ -927,13 +927,13 @@ class InstallRepositoryManager( object ):
self.app.installed_repository_manager.handle_repository_install( tool_shed_repository )
else:
# An error occurred while cloning the repository, so reset everything necessary to enable another attempt.
suc.set_repository_attributes( self.app,
tool_shed_repository,
status=self.install_model.ToolShedRepository.installation_status.ERROR,
error_message=error_message,
deleted=False,
uninstalled=False,
remove_from_disk=True )
repository_util.set_repository_attributes( self.app,
tool_shed_repository,
status=self.install_model.ToolShedRepository.installation_status.ERROR,
error_message=error_message,
deleted=False,
uninstalled=False,
remove_from_disk=True )
def order_components_for_installation( self, tsr_ids, repo_info_dicts, tool_panel_section_keys ):
"""
@@ -952,9 +952,9 @@ class InstallRepositoryManager( object ):
# Create a dictionary whose keys are the received tsr_ids and whose values are a list of
# tsr_ids, each of which is contained in the received list of tsr_ids and whose associated
# repository must be installed prior to the repository associated with the tsr_id key.
prior_install_required_dict = suc.get_prior_import_or_install_required_dict( self.app,
tsr_ids,
repo_info_dicts )
prior_install_required_dict = repository_util.get_prior_import_or_install_required_dict( self.app,
tsr_ids,
repo_info_dicts )
processed_tsr_ids = []
while len( processed_tsr_ids ) != len( prior_install_required_dict.keys() ):
tsr_id = suc.get_next_prior_import_or_install_required_dict_entry( prior_install_required_dict,
lib/tool_shed/galaxy_install/installed_repository_manager.py
+14 -13
View File
@@ -10,6 +10,7 @@ from sqlalchemy import and_, false, true
from galaxy import util
from tool_shed.util import common_util
from tool_shed.util import container_util
from tool_shed.util import repository_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import tool_dependency_util
from tool_shed.util import xml_util
@@ -244,7 +245,7 @@ class InstalledRepositoryManager( object ):
name = repo_info_dict.keys()[ 0 ]
repo_info_tuple = repo_info_dict[ name ]
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
if tool_dependencies:
if not includes_tool_dependencies:
includes_tool_dependencies = True
@@ -256,11 +257,11 @@ class InstalledRepositoryManager( object ):
if repository_dependencies:
# We have a repository with one or more defined repository dependencies.
if not repository:
repository = suc.get_repository_for_dependency_relationship( self.app,
tool_shed_url,
name,
repository_owner,
changeset_revision )
repository = repository_util.get_repository_for_dependency_relationship( self.app,
tool_shed_url,
name,
repository_owner,
changeset_revision )
if not updating and repository and repository.metadata:
installed_rd, missing_rd = self.get_installed_and_missing_repository_dependencies( repository )
else:
@@ -282,7 +283,7 @@ class InstalledRepositoryManager( object ):
for name, repo_info_tuple in rid.items():
description, repository_clone_url, changeset_revision, ctx_rev, \
repository_owner, rid_repository_dependencies, rid_tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
if rid_tool_dependencies:
for td_key, td_dict in rid_tool_dependencies.items():
if td_key not in required_tool_dependencies:
@@ -403,7 +404,7 @@ class InstalledRepositoryManager( object ):
missing_rd_tups = []
installed_rd_tups = []
( description, repository_clone_url, changeset_revision, ctx_rev,
repository_owner, repository_dependencies, tool_dependencies ) = suc.get_repo_info_tuple_contents( repo_info_tuple )
repository_owner, repository_dependencies, tool_dependencies ) = repository_util.get_repo_info_tuple_contents( repo_info_tuple )
if repository_dependencies:
description = repository_dependencies[ 'description' ]
root_key = repository_dependencies[ 'root_key' ]
@@ -422,11 +423,11 @@ class InstalledRepositoryManager( object ):
# repository_dependencies, installed_td )
tmp_clone_url = common_util.generate_clone_url_from_repo_info_tup( self.app, rd_tup )
tmp_repo_info_tuple = ( None, tmp_clone_url, changeset_revision, None, owner, None, None )
repository, installed_changeset_revision = suc.repository_was_previously_installed( self.app,
tool_shed,
name,
tmp_repo_info_tuple,
from_tip=False )
repository, installed_changeset_revision = repository_util.repository_was_previously_installed( self.app,
tool_shed,
name,
tmp_repo_info_tuple,
from_tip=False )
if repository:
new_rd_tup = [ tool_shed,
name,
lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
+1 -2
View File
@@ -10,7 +10,6 @@ from tool_shed.galaxy_install.tools import tool_panel_manager
from tool_shed.metadata import metadata_generator
from tool_shed.util import common_util
from tool_shed.util import repository_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import tool_util
from tool_shed.util import xml_util
@@ -162,7 +161,7 @@ class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator )
owner = self.repository.owner
if not owner:
cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url )
owner = suc.get_repository_owner( cleaned_repository_clone_url )
owner = repository_util.get_repository_owner( cleaned_repository_clone_url )
guid_to_tool_elem_dict = {}
for tool_config_filename, guid, tool in repository_tools_tups:
guid_to_tool_elem_dict[ guid ] = self.tpm.generate_tool_elem( tool_shed,
lib/tool_shed/galaxy_install/repair_repository_manager.py
+18 -18
View File
@@ -30,22 +30,22 @@ class RepairRepositoryManager():
# rd_key is something like: 'http://localhost:9009__ESEP__package_rdkit_2012_12__ESEP__test__ESEP__d635ffb9c665__ESEP__True'
# rd_val is something like: [['http://localhost:9009', 'package_numpy_1_7', 'test', 'cddd64ecd985', 'True']]
repository_components_tuple = container_util.get_components_from_key( rd_key )
components_list = suc.extract_components_from_tuple( repository_components_tuple )
components_list = repository_util.extract_components_from_tuple( repository_components_tuple )
tool_shed, name, owner, changeset_revision = components_list[ 0:4 ]
installed_repository = suc.get_installed_repository( self.app,
tool_shed=tool_shed,
name=name,
owner=owner,
changeset_revision=changeset_revision )
installed_repository = repository_util.get_installed_repository( self.app,
tool_shed=tool_shed,
name=name,
owner=owner,
changeset_revision=changeset_revision )
if ( installed_repository ) and ( installed_repository not in installed_repositories ):
installed_repositories.append( installed_repository )
for rd_val in rd_vals:
tool_shed, name, owner, changeset_revision = rd_val[ 0:4 ]
installed_repository = suc.get_installed_repository( self.app,
tool_shed=tool_shed,
name=name,
owner=owner,
changeset_revision=changeset_revision )
installed_repository = repository_util.get_installed_repository( self.app,
tool_shed=tool_shed,
name=name,
owner=owner,
changeset_revision=changeset_revision )
if ( installed_repository ) and ( installed_repository not in installed_repositories ):
installed_repositories.append( installed_repository )
return installed_repositories
@@ -180,13 +180,13 @@ class RepairRepositoryManager():
else:
# The tools will be loaded outside of any sections in the tool panel.
tool_panel_section_key = None
suc.set_repository_attributes( self.app,
repository,
status=self.app.install_model.ToolShedRepository.installation_status.NEW,
error_message=None,
deleted=False,
uninstalled=False,
remove_from_disk=True )
repository_util.set_repository_attributes( self.app,
repository,
status=self.app.install_model.ToolShedRepository.installation_status.NEW,
error_message=None,
deleted=False,
uninstalled=False,
remove_from_disk=True )
irm = install_manager.InstallRepositoryManager( self.app, tpm )
irm.install_tool_shed_repository( repository,
repo_info_dict,
lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
+32 -31
View File
@@ -15,6 +15,7 @@ from tool_shed.galaxy_install.tools import tool_panel_manager
from tool_shed.util import common_util
from tool_shed.util import container_util
from tool_shed.util import encoding_util
from tool_shed.util import repository_util
from tool_shed.util import shed_util_common as suc
log = logging.getLogger( __name__ )
@@ -44,14 +45,14 @@ class RepositoryDependencyInstallManager( object ):
repository_owner, \
repository_dependencies, \
tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
if repository_dependencies:
for key, val in repository_dependencies.items():
if key in [ 'root_key', 'description' ]:
continue
d_repository = None
repository_components_tuple = container_util.get_components_from_key( key )
components_list = suc.extract_components_from_tuple( repository_components_tuple )
components_list = repository_util.extract_components_from_tuple( repository_components_tuple )
d_toolshed, d_name, d_owner, d_changeset_revision = components_list[ 0:4 ]
for tsr in tool_shed_repositories:
# Get the the tool_shed_repository defined by name, owner and changeset_revision. This is
@@ -165,10 +166,10 @@ class RepositoryDependencyInstallManager( object ):
repository_owner, \
repository_dependencies, \
tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
# See if the repository has an existing record in the database.
repository_db_record, installed_changeset_revision = \
suc.repository_was_previously_installed( self.app, tool_shed_url, name, repo_info_tuple, from_tip=False )
repository_util.repository_was_previously_installed( self.app, tool_shed_url, name, repo_info_tuple, from_tip=False )
if repository_db_record:
if repository_db_record.status in [ install_model.ToolShedRepository.installation_status.INSTALLED,
install_model.ToolShedRepository.installation_status.CLONING,
@@ -199,7 +200,7 @@ class RepositoryDependencyInstallManager( object ):
# No additional updates to the database record are necessary.
can_update_db_record = False
elif repository_db_record.status not in [ install_model.ToolShedRepository.installation_status.NEW ]:
# Set changeset_revision here so suc.create_or_update_tool_shed_repository will find
# Set changeset_revision here so repository_util.create_or_update_tool_shed_repository will find
# the previously installed and uninstalled repository instead of creating a new record.
changeset_revision = repository_db_record.installed_changeset_revision
self.reset_previously_installed_repository( repository_db_record )
@@ -226,17 +227,17 @@ class RepositoryDependencyInstallManager( object ):
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=new_tool_panel_section_label )
tool_shed_repository = \
suc.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=description,
installed_changeset_revision=installed_changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=changeset_revision,
owner=repository_owner,
dist_to_shed=False )
repository_util.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=description,
installed_changeset_revision=installed_changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=changeset_revision,
owner=repository_owner,
dist_to_shed=False )
if tool_shed_repository not in all_created_or_updated_tool_shed_repositories:
all_created_or_updated_tool_shed_repositories.append( tool_shed_repository )
# Only append the tool shed repository to the list of created_or_updated_tool_shed_repositories if
@@ -262,22 +263,22 @@ class RepositoryDependencyInstallManager( object ):
# We store the port in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
# This method is used only in Galaxy, not the tool shed.
repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed, name, owner, changeset_revision )
repository = repository_util.get_repository_for_dependency_relationship( self.app, tool_shed, name, owner, changeset_revision )
if not repository:
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed )
repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
ctx_rev = suc.get_ctx_rev( self.app, tool_shed_url, name, owner, changeset_revision )
repository = suc.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=None,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=None,
owner=owner,
dist_to_shed=False )
repository = repository_util.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=None,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=None,
owner=owner,
dist_to_shed=False )
return repository
def get_repository_dependencies_for_installed_tool_shed_repository( self, app, repository ):
@@ -331,13 +332,13 @@ class RepositoryDependencyInstallManager( object ):
repository_owner, \
repository_dependencies, \
tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tup )
repository_util.get_repo_info_tuple_contents( repo_info_tup )
if repository_dependencies:
for key, val in repository_dependencies.items():
if key in [ 'root_key', 'description' ]:
continue
repository_components_tuple = container_util.get_components_from_key( key )
components_list = suc.extract_components_from_tuple( repository_components_tuple )
components_list = repository_util.extract_components_from_tuple( repository_components_tuple )
# Skip listing a repository dependency if it is required only to compile a tool dependency
# defined for the dependent repository since in this case, the repository dependency is really
# a dependency of the dependent repository's contained tool dependency, and only if that
@@ -374,7 +375,7 @@ class RepositoryDependencyInstallManager( object ):
encoded_required_repository_tups.append( encoding_util.encoding_sep.join( required_repository_tup ) )
encoded_required_repository_str = encoding_util.encoding_sep2.join( encoded_required_repository_tups )
encoded_required_repository_str = encoding_util.tool_shed_encode( encoded_required_repository_str )
if suc.is_tool_shed_client( self.app ):
if repository_util.is_tool_shed_client( self.app ):
# Handle secure / insecure Tool Shed URL protocol changes and port changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed_url )
pathspec = [ 'repository', 'get_required_repo_info_dict' ]
lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
+6 -6
View File
@@ -1,8 +1,8 @@
import logging
import os
import tool_shed.util.shed_util_common as suc
from tool_shed.util import common_util
from tool_shed.util import repository_util
log = logging.getLogger( __name__ )
@@ -67,11 +67,11 @@ class EnvManager( object ):
if toolshed and repository_name and repository_owner and changeset_revision:
# The protocol is not stored, but the port is if it exists.
toolshed = common_util.remove_protocol_from_tool_shed_url( toolshed )
repository = suc.get_repository_for_dependency_relationship( self.app,
toolshed,
repository_name,
repository_owner,
changeset_revision )
repository = repository_util.get_repository_for_dependency_relationship( self.app,
toolshed,
repository_name,
repository_owner,
changeset_revision )
if repository:
for sub_elem in elem:
tool_dependency_type = sub_elem.tag
lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
+12 -11
View File
@@ -6,7 +6,8 @@ from galaxy.tools.deps.resolvers import INDETERMINATE_DEPENDENCY
from galaxy.util import listify, url_get
from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import metadata_util
from tool_shed.util import repository_util
from tool_shed.util import tool_dependency_util
from tool_shed.util import xml_util
@@ -372,10 +373,10 @@ class Repository( RecipeTag, SyncDatabase ):
required_repository_name = elem.attrib[ 'name' ]
required_repository_owner = elem.attrib[ 'owner' ]
default_required_repository_changeset_revision = elem.attrib[ 'changeset_revision' ]
required_repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed_url,
required_repository_name,
required_repository_owner,
default_required_repository_changeset_revision )
required_repository = repository_util.get_repository_for_dependency_relationship( self.app, tool_shed_url,
required_repository_name,
required_repository_owner,
default_required_repository_changeset_revision )
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
tmp_filename = None
if required_repository:
@@ -436,7 +437,7 @@ class Repository( RecipeTag, SyncDatabase ):
message = "Unable to locate the repository directory for revision %s of installed repository %s owned by %s." % \
( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) )
raise Exception( message )
tool_dependencies_config = suc.get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
tool_dependencies_config = repository_util.get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
if tool_dependencies_config:
config_to_use = tool_dependencies_config
else:
@@ -446,11 +447,11 @@ class Repository( RecipeTag, SyncDatabase ):
else:
# Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision
# should be updated if it's not current.
text = suc.get_updated_changeset_revisions_from_tool_shed( app=self.app,
tool_shed_url=tool_shed,
name=required_repository_name,
owner=required_repository_owner,
changeset_revision=required_repository_changeset_revision )
text = metadata_util.get_updated_changeset_revisions_from_tool_shed( app=self.app,
tool_shed_url=tool_shed,
name=required_repository_name,
owner=required_repository_owner,
changeset_revision=required_repository_changeset_revision )
if text:
updated_changeset_revisions = listify( text )
# The list of changeset revisions is in reverse order, so the newest will be first.
lib/tool_shed/galaxy_install/tool_migration_manager.py
+12 -11
View File
@@ -25,6 +25,7 @@ from tool_shed.tools import tool_version_manager
from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import hg_util
from tool_shed.util import repository_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import tool_dependency_util
from tool_shed.util import tool_util
@@ -173,17 +174,17 @@ class ToolMigrationManager( object ):
if not self.__iscloned( clone_dir ):
repository_clone_url = os.path.join( self.tool_shed_url, 'repos', owner, name )
ctx_rev = suc.get_ctx_rev( self.app, self.tool_shed_url, name, owner, changeset_revision )
tool_shed_repository = suc.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=description,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=self.app.install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=None,
owner=self.repository_owner,
dist_to_shed=True )
tool_shed_repository = repository_util.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=description,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=self.app.install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=None,
owner=self.repository_owner,
dist_to_shed=True )
return tool_shed_repository
return None
lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
+2 -1
View File
@@ -5,6 +5,7 @@ from xml.etree import ElementTree as XmlET
from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import repository_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import xml_util
@@ -220,7 +221,7 @@ class ToolPanelManager( object ):
tool_elem = None
cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url )
if not owner:
owner = suc.get_repository_owner( cleaned_repository_clone_url )
owner = repository_util.get_repository_owner( cleaned_repository_clone_url )
tool_shed = cleaned_repository_clone_url.split( '/repos/' )[ 0 ].rstrip( '/' )
for guid, tool_section_dicts in tool_panel_dict.items():
for tool_section_dict in tool_section_dicts:
lib/tool_shed/galaxy_install/update_repository_manager.py
+3 -2
View File
@@ -9,6 +9,7 @@ from sqlalchemy import false
import tool_shed.util.shed_util_common as suc
from tool_shed.util import common_util
from tool_shed.util import encoding_util
from tool_shed.util import repository_util
from galaxy import util
log = logging.getLogger( __name__ )
@@ -84,7 +85,7 @@ class UpdateRepositoryManager( object ):
# has been deprecated in the Tool Shed.
for repository in self.context.query( self.app.install_model.ToolShedRepository ) \
.filter( self.app.install_model.ToolShedRepository.table.c.deleted == false() ):
tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository )
tool_shed_status_dict = repository_util.get_tool_shed_status_for_installed_repository( self.app, repository )
if tool_shed_status_dict:
if tool_shed_status_dict != repository.tool_shed_status:
repository.tool_shed_status = tool_shed_status_dict
@@ -115,7 +116,7 @@ class UpdateRepositoryManager( object ):
repository.changeset_revision = updated_changeset_revision
repository.ctx_rev = updated_ctx_rev
# Update the repository.tool_shed_status column in the database.
tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository )
tool_shed_status_dict = repository_util.get_tool_shed_status_for_installed_repository( self.app, repository )
if tool_shed_status_dict:
repository.tool_shed_status = tool_shed_status_dict
else:
lib/tool_shed/grids/repository_grids.py
+5 -5
View File
@@ -9,7 +9,7 @@ import tool_shed.repository_types.util as rt_util
import tool_shed.util.shed_util_common as suc
from galaxy.web.framework.helpers import grids
from galaxy.webapps.tool_shed import model
from tool_shed.util import hg_util, metadata_util
from tool_shed.util import hg_util, metadata_util, repository_util
log = logging.getLogger( __name__ )
@@ -1007,7 +1007,7 @@ class RepositoryDependenciesGrid( RepositoryMetadataGrid ):
for rd_tup in sorted_rd_tups:
name, owner, changeset_revision = rd_tup[1:4]
rd_line = ''
required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
required_repository = repository_util.get_repository_by_name_and_owner( trans.app, name, owner )
if required_repository and not required_repository.deleted:
required_repository_id = trans.security.encode_id( required_repository.id )
required_repository_metadata = \
@@ -1020,9 +1020,9 @@ class RepositoryDependenciesGrid( RepositoryMetadataGrid ):
repo_path=None,
create=False )
updated_changeset_revision = \
suc.get_next_downloadable_changeset_revision( required_repository,
repo,
changeset_revision )
metadata_util.get_next_downloadable_changeset_revision( required_repository,
repo,
changeset_revision )
required_repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans.app,
required_repository_id,
lib/tool_shed/grids/util.py
+9 -9
View File
@@ -1,7 +1,7 @@
import logging
from galaxy.web.form_builder import SelectField
from tool_shed.util import hg_util, metadata_util, shed_util_common as suc
from tool_shed.util import hg_util, metadata_util
log = logging.getLogger( __name__ )
@@ -118,7 +118,7 @@ def get_latest_downloadable_repository_metadata( trans, repository ):
tip_ctx = str( repo.changectx( repo.changelog.tip() ) )
repository_metadata = None
try:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, encoded_repository_id, tip_ctx )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, encoded_repository_id, tip_ctx )
if repository_metadata is not None and repository_metadata.downloadable:
return repository_metadata
return None
@@ -129,9 +129,9 @@ def get_latest_downloadable_repository_metadata( trans, repository ):
downloadable=True )
if latest_downloadable_revision == hg_util.INITIAL_CHANGELOG_HASH:
return None
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
encoded_repository_id,
latest_downloadable_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
encoded_repository_id,
latest_downloadable_revision )
if repository_metadata is not None and repository_metadata.downloadable:
return repository_metadata
return None
@@ -159,7 +159,7 @@ def get_latest_repository_metadata( trans, repository ):
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
tip_ctx = str( repo.changectx( repo.changelog.tip() ) )
try:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, encoded_repository_id, tip_ctx )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app, encoded_repository_id, tip_ctx )
return repository_metadata
except:
latest_downloadable_revision = metadata_util.get_previous_metadata_changeset_revision( repository,
@@ -168,9 +168,9 @@ def get_latest_repository_metadata( trans, repository ):
downloadable=False )
if latest_downloadable_revision == hg_util.INITIAL_CHANGELOG_HASH:
return None
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app,
encoded_repository_id,
latest_downloadable_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( trans.app,
encoded_repository_id,
latest_downloadable_revision )
return repository_metadata
lib/tool_shed/metadata/metadata_generator.py
+17 -15
View File
@@ -16,6 +16,8 @@ from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import hg_util
from tool_shed.util import readme_util
from tool_shed.util import metadata_util
from tool_shed.util import repository_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import tool_dependency_util
from tool_shed.util import tool_util
@@ -903,30 +905,30 @@ class MetadataGenerator( object ):
# the changeset_revision defined in the repository_elem (it may be outdated). If
# we're successful in locating an installed repository with the attributes defined
# in the repository_elem, we know it is valid.
repository = suc.get_repository_for_dependency_relationship( self.app,
toolshed,
name,
owner,
changeset_revision )
repository = repository_util.get_repository_for_dependency_relationship( self.app,
toolshed,
name,
owner,
changeset_revision )
if repository:
return repository_dependency_tup, is_valid, error_message
else:
# Send a request to the tool shed to retrieve appropriate additional changeset
# revisions with which the repository
# may have been installed.
text = suc.get_updated_changeset_revisions_from_tool_shed( self.app,
toolshed,
name,
owner,
changeset_revision )
if text:
updated_changeset_revisions = util.listify( text )
for updated_changeset_revision in updated_changeset_revisions:
repository = suc.get_repository_for_dependency_relationship( self.app,
text = metadata_util.get_updated_changeset_revisions_from_tool_shed( self.app,
toolshed,
name,
owner,
updated_changeset_revision )
changeset_revision )
if text:
updated_changeset_revisions = util.listify( text )
for updated_changeset_revision in updated_changeset_revisions:
repository = repository_util.get_repository_for_dependency_relationship( self.app,
toolshed,
name,
owner,
updated_changeset_revision )
if repository:
return repository_dependency_tup, is_valid, error_message
if self.updating_installed_repository:
lib/tool_shed/metadata/repository_metadata_manager.py
+16 -15
View File
@@ -14,6 +14,7 @@ from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import hg_util
from tool_shed.util import metadata_util
from tool_shed.util import repository_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import tool_util
@@ -340,7 +341,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ):
repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} )
repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
suc.get_repository_dependency_types( repository_dependencies )
repository_util.get_repository_dependency_types( repository_dependencies )
if 'datatypes' in metadata_dict:
includes_datatypes = True
if 'tools' in metadata_dict:
@@ -356,9 +357,9 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ):
downloadable = True
else:
downloadable = False
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
self.app.security.encode_id( self.repository.id ),
changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app,
self.app.security.encode_id( self.repository.id ),
changeset_revision )
if repository_metadata:
repository_metadata.metadata = metadata_dict
repository_metadata.downloadable = downloadable
@@ -400,7 +401,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ):
cleaned_tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
if cleaned_rd_tool_shed == cleaned_tool_shed and rd_name == name and rd_owner == owner:
# Determine if the repository represented by the dependency tuple is an instance of the repository type TipOnly.
required_repository = suc.get_repository_by_name_and_owner( self.app, name, owner )
required_repository = repository_util.get_repository_by_name_and_owner( self.app, name, owner )
repository_type_class = self.app.repository_types_registry.get_class_by_label( required_repository.type )
return isinstance( repository_type_class, TipOnly )
return False
@@ -410,7 +411,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ):
# Compare from most recent to oldest.
changeset_revisions.reverse()
for changeset_revision in changeset_revisions:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision )
metadata = repository_metadata.metadata
tools_dicts = metadata.get( 'tools', [] )
for tool_dict in tools_dicts:
@@ -823,9 +824,9 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ):
changeset_revisions_that_contain_tools = []
for changeset in repo.changelog:
changeset_revision = str( repo.changectx( changeset ) )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
changeset_revision )
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
@@ -836,9 +837,9 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ):
# { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision.
for index, changeset_revision in enumerate( changeset_revisions_that_contain_tools ):
tool_versions_dict = {}
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
changeset_revision )
metadata = repository_metadata.metadata
tool_dicts = metadata[ 'tools' ]
if index == 0:
@@ -873,7 +874,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ):
unsuccessful_count = 0
for repository_id in repository_ids:
try:
repository = suc.get_repository_in_tool_shed( self.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( self.app, repository_id )
self.set_repository( repository )
self.resetting_all_metadata_on_repository = True
self.reset_all_metadata_on_repository_in_tool_shed()
@@ -953,7 +954,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ):
repository_dependencies_dict = self.metadata_dict.get( 'repository_dependencies', {} )
repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \
suc.get_repository_dependency_types( repository_dependencies )
repository_util.get_repository_dependency_types( repository_dependencies )
repository_metadata.has_repository_dependencies = has_repository_dependencies
if 'tool_dependencies' in self.metadata_dict:
repository_metadata.includes_tool_dependencies = True
@@ -980,7 +981,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ):
changeset_revisions = []
for changeset in repo.changelog:
changeset_revision = str( repo.changectx( changeset ) )
if suc.get_repository_metadata_by_changeset_revision( self.app, encoded_id, changeset_revision ):
if metadata_util.get_repository_metadata_by_changeset_revision( self.app, encoded_id, changeset_revision ):
changeset_revisions.append( changeset_revision )
self.add_tool_versions( encoded_id, repository_metadata, changeset_revisions )
elif len( repo ) == 1 and not self.invalid_file_tups:
lib/tool_shed/repository_registry.py
+8 -8
View File
@@ -5,7 +5,7 @@ from sqlalchemy import and_, false, or_
import tool_shed.repository_types.util as rt_util
from galaxy.webapps.tool_shed import model
from tool_shed.util import hg_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import metadata_util
log = logging.getLogger( __name__ )
@@ -163,12 +163,12 @@ class Registry( object ):
return ( None, False )
repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False )
# Get the latest installable changeset revision since that is all that is currently configured for testing.
latest_installable_changeset_revision = suc.get_latest_downloadable_changeset_revision( self.app, repository, repo )
latest_installable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision( self.app, repository, repo )
if latest_installable_changeset_revision not in [ None, hg_util.INITIAL_CHANGELOG_HASH ]:
encoded_repository_id = self.app.security.encode_id( repository.id )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
latest_installable_changeset_revision )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
latest_installable_changeset_revision )
if repository_metadata:
# No repository_metadata.
return ( latest_installable_changeset_revision, True )
@@ -264,9 +264,9 @@ class Registry( object ):
is_valid = self.is_valid( repository )
encoded_repository_id = self.app.security.encode_id( repository.id )
tip_changeset_hash = repository.tip( self.app )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
tip_changeset_hash )
repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision( self.app,
encoded_repository_id,
tip_changeset_hash )
self.viewable_repositories_and_suites_by_category[ category_name ] += 1
if is_valid:
self.viewable_valid_repositories_and_suites_by_category[ category_name ] += 1
lib/tool_shed/tools/tool_validator.py
+3 -3
View File
@@ -11,7 +11,7 @@ from tool_shed.tools import data_table_manager
from tool_shed.util import basic_util
from tool_shed.util import hg_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import repository_util
from tool_shed.util import tool_util
from tool_shed.util import xml_util
@@ -244,13 +244,13 @@ class ToolValidator( object ):
searching backwards.
"""
original_tool_data_path = self.app.config.tool_data_path
repository = suc.get_repository_in_tool_shed( self.app, repository_id )
repository = repository_util.get_repository_in_tool_shed( self.app, repository_id )
repo_files_dir = repository.repo_path( self.app )
repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_files_dir, create=False )
message = ''
tool = None
can_use_disk_file = False
tool_config_filepath = suc.get_absolute_path_to_file_in_repository( repo_files_dir, tool_config_filename )
tool_config_filepath = repository_util.get_absolute_path_to_file_in_repository( repo_files_dir, tool_config_filename )
work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ltfcr" )
can_use_disk_file = self.can_use_tool_config_disk_file( repository,
repo,
lib/tool_shed/tools/tool_version_manager.py
+5 -4
View File
@@ -3,7 +3,8 @@ import logging
from sqlalchemy import and_, or_
from tool_shed.util import hg_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import metadata_util
from tool_shed.util import repository_util
log = logging.getLogger( __name__ )
@@ -36,7 +37,7 @@ class ToolVersionManager( object ):
guid contained in the received repsitory_metadata.tool_versions. This function
is called only from the Tool Shed.
"""
repository = suc.get_repository_by_id( self.app, repository_id )
repository = repository_util.get_repository_by_id( self.app, repository_id )
repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False )
# Initialize the tool lineage
version_lineage = [ guid ]
@@ -44,7 +45,7 @@ class ToolVersionManager( object ):
current_child_guid = guid
for changeset in hg_util.reversed_upper_bounded_changelog( repo, repository_metadata.changeset_revision ):
ctx = repo.changectx( changeset )
rm = suc.get_repository_metadata_by_changeset_revision( self.app, repository_id, str( ctx ) )
rm = metadata_util.get_repository_metadata_by_changeset_revision( self.app, repository_id, str( ctx ) )
if rm:
parent_guid = rm.tool_versions.get( current_child_guid, None )
if parent_guid:
@@ -56,7 +57,7 @@ class ToolVersionManager( object ):
repository_metadata.changeset_revision,
repository.tip( self.app ) ):
ctx = repo.changectx( changeset )
rm = suc.get_repository_metadata_by_changeset_revision( self.app, repository_id, str( ctx ) )
rm = metadata_util.get_repository_metadata_by_changeset_revision( self.app, repository_id, str( ctx ) )
if rm:
tool_versions = rm.tool_versions
for child_guid, parent_guid in tool_versions.items():
lib/tool_shed/util/common_util.py
+12
View File
@@ -242,6 +242,18 @@ def get_tool_shed_url_from_tool_shed_registry( app, tool_shed ):
return None
def get_user_by_username( app, username ):
"""Get a user from the database by username."""
sa_session = app.model.context.current
try:
user = sa_session.query( app.model.User ) \
.filter( app.model.User.table.c.username == username ) \
.one()
return user
except Exception:
return None
def handle_galaxy_url( trans, **kwd ):
galaxy_url = kwd.get( 'galaxy_url', None )
if galaxy_url:
lib/tool_shed/util/metadata_util.py
+159 -17
View File
@@ -1,6 +1,10 @@
import logging
from tool_shed.util import common_util, hg_util, shed_util_common as suc
from tool_shed.util import common_util
from tool_shed.util import hg_util
from sqlalchemy import and_
from operator import itemgetter
import tool_shed.util.repository_util
log = logging.getLogger( __name__ )
@@ -35,27 +39,62 @@ def get_all_dependencies( app, metadata_entry, processed_dependency_links=[] ):
return returned_dependencies
def get_current_repository_metadata_for_changeset_revision( app, repository, changeset_revision ):
encoded_repository_id = app.security.encode_id( repository.id )
repository_metadata = get_repository_metadata_by_changeset_revision( app,
encoded_repository_id,
changeset_revision )
if repository_metadata:
return repository_metadata
# The installable changeset_revision may have been changed because it was "moved ahead"
# in the repository changelog.
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
updated_changeset_revision = get_next_downloadable_changeset_revision( repository,
repo,
after_changeset_revision=changeset_revision )
if updated_changeset_revision and updated_changeset_revision != changeset_revision:
repository_metadata = get_repository_metadata_by_changeset_revision( app,
encoded_repository_id,
updated_changeset_revision )
if repository_metadata:
return repository_metadata
return None
def get_dependencies_for_metadata_revision( app, metadata ):
dependencies = []
for shed, name, owner, changeset, prior, _ in metadata[ 'repository_dependencies' ]:
required_repository = suc.get_repository_by_name_and_owner( app, name, owner )
required_repository = tool_shed.util.repository_util.get_repository_by_name_and_owner( app, name, owner )
repo = hg_util.get_repo_for_repository( app, repository=required_repository, repo_path=None, create=False )
updated_changeset = suc.get_next_downloadable_changeset_revision( required_repository, repo, changeset )
updated_changeset = get_next_downloadable_changeset_revision( required_repository, repo, changeset )
if updated_changeset is None:
continue
metadata_entry = suc.get_repository_metadata_by_changeset_revision( app, app.security.encode_id( required_repository.id ), updated_changeset )
metadata_entry = get_repository_metadata_by_changeset_revision( app, app.security.encode_id( required_repository.id ), updated_changeset )
dependencies.append( metadata_entry )
return dependencies
def get_latest_changeset_revision( app, repository, repo ):
repository_tip = repository.tip( app )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( app,
app.security.encode_id( repository.id ),
repository_tip )
repository_metadata = get_repository_metadata_by_changeset_revision( app,
app.security.encode_id( repository.id ),
repository_tip )
if repository_metadata and repository_metadata.downloadable:
return repository_tip
changeset_revisions = [ revision[ 1 ] for revision in suc.get_metadata_revisions( repository, repo ) ]
changeset_revisions = [ revision[ 1 ] for revision in get_metadata_revisions( repository, repo ) ]
if changeset_revisions:
return changeset_revisions[ -1 ]
return hg_util.INITIAL_CHANGELOG_HASH
def get_latest_downloadable_changeset_revision( app, repository, repo=None ):
if repo is None:
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
repository_tip = repository.tip( app )
repository_metadata = get_repository_metadata_by_changeset_revision( app, app.security.encode_id( repository.id ), repository_tip )
if repository_metadata and repository_metadata.downloadable:
return repository_tip
changeset_revisions = [ revision[ 1 ] for revision in get_metadata_revisions( repository, repo ) ]
if changeset_revisions:
return changeset_revisions[ -1 ]
return hg_util.INITIAL_CHANGELOG_HASH
@@ -67,12 +106,12 @@ def get_latest_repository_metadata( app, decoded_repository_id, downloadable=Fal
repository = sa_session.query( app.model.Repository ).get( decoded_repository_id )
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
if downloadable:
changeset_revision = suc.get_latest_downloadable_changeset_revision( app, repository, repo )
changeset_revision = get_latest_downloadable_changeset_revision( app, repository, repo )
else:
changeset_revision = get_latest_changeset_revision( app, repository, repo )
return suc.get_repository_metadata_by_changeset_revision( app,
app.security.encode_id( repository.id ),
changeset_revision )
return get_repository_metadata_by_changeset_revision( app,
app.security.encode_id( repository.id ),
changeset_revision )
def get_metadata_by_id( app, metadata_id ):
@@ -80,13 +119,72 @@ def get_metadata_by_id( app, metadata_id ):
return sa_session.query( app.model.RepositoryMetadata ).filter( app.model.RepositoryMetadata.table.c.id == metadata_id ).one()
def get_metadata_changeset_revisions( repository, repo ):
"""
Return an unordered list of changeset_revisions and changeset numbers that are defined as installable.
"""
changeset_tups = []
for repository_metadata in repository.downloadable_revisions:
ctx = hg_util.get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
if ctx:
rev = ctx.rev()
else:
rev = -1
changeset_tups.append( ( rev, repository_metadata.changeset_revision ) )
return sorted( changeset_tups )
def get_metadata_revisions( repository, repo, sort_revisions=True, reverse=False, downloadable=True ):
"""
Return a list of changesets for the provided repository.
"""
if downloadable:
metadata_revisions = repository.downloadable_revisions
else:
metadata_revisions = repository.metadata_revisions
changeset_tups = []
for repository_metadata in metadata_revisions:
ctx = hg_util.get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
if ctx:
rev = '%04d' % ctx.rev()
else:
rev = -1
changeset_tups.append( ( rev, repository_metadata.changeset_revision ) )
if sort_revisions:
changeset_tups.sort( key=itemgetter( 0 ), reverse=reverse )
return changeset_tups
def get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision ):
"""
Return the installable changeset_revision in the repository changelog after the changeset to which
after_changeset_revision refers. If there isn't one, return None. If there is only one installable
changeset, and that matches the requested revision, return it.
"""
changeset_revisions = [ revision[ 1 ] for revision in get_metadata_revisions( repository, repo ) ]
if len( changeset_revisions ) == 1:
changeset_revision = changeset_revisions[ 0 ]
if changeset_revision == after_changeset_revision:
return after_changeset_revision
found_after_changeset_revision = False
for changeset in repo.changelog:
changeset_revision = str( repo.changectx( changeset ) )
if found_after_changeset_revision:
if changeset_revision in changeset_revisions:
return changeset_revision
elif not found_after_changeset_revision and changeset_revision == after_changeset_revision:
# We've found the changeset in the changelog for which we need to get the next downloadable changeset.
found_after_changeset_revision = True
return None
def get_previous_metadata_changeset_revision( repository, repo, before_changeset_revision, downloadable=True ):
"""
Return the changeset_revision in the repository changelog that has associated metadata prior to
the changeset to which before_changeset_revision refers. If there isn't one, return the hash value
of an empty repository changelog, hg_util.INITIAL_CHANGELOG_HASH.
"""
changeset_revisions = [ revision[ 1 ] for revision in suc.get_metadata_revisions( repository, repo ) ]
changeset_revisions = [ revision[ 1 ] for revision in get_metadata_revisions( repository, repo ) ]
if len( changeset_revisions ) == 1:
changeset_revision = changeset_revisions[ 0 ]
if changeset_revision == before_changeset_revision:
@@ -128,7 +226,7 @@ def get_repository_dependency_tups_from_repository_metadata( app, repository_met
for repository_dependency_tup in repository_dependency_tups:
toolshed, name, owner, changeset_revision, pir, oicct = \
common_util.parse_repository_dependency_tuple( repository_dependency_tup )
repository = suc.get_repository_by_name_and_owner( app, name, owner )
repository = tool_shed.util.repository_util.get_repository_by_name_and_owner( app, name, owner )
if repository:
if deprecated_only:
if repository.deprecated:
@@ -141,6 +239,28 @@ def get_repository_dependency_tups_from_repository_metadata( app, repository_met
return dependency_tups
def get_repository_metadata_by_changeset_revision( app, id, changeset_revision ):
"""Get metadata for a specified repository change set from the database."""
# Make sure there are no duplicate records, and return the single unique record for the changeset_revision.
# Duplicate records were somehow created in the past. The cause of this issue has been resolved, but we'll
# leave this method as is for a while longer to ensure all duplicate records are removed.
sa_session = app.model.context.current
all_metadata_records = sa_session.query( app.model.RepositoryMetadata ) \
.filter( and_( app.model.RepositoryMetadata.table.c.repository_id == app.security.decode_id( id ),
app.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \
.order_by( app.model.RepositoryMetadata.table.c.update_time.desc() ) \
.all()
if len( all_metadata_records ) > 1:
# Delete all records older than the last one updated.
for repository_metadata in all_metadata_records[ 1: ]:
sa_session.delete( repository_metadata )
sa_session.flush()
return all_metadata_records[ 0 ]
elif all_metadata_records:
return all_metadata_records[ 0 ]
return None
def get_repository_metadata_by_id( app, id ):
"""Get repository metadata from the database"""
sa_session = app.model.context.current
@@ -150,11 +270,11 @@ def get_repository_metadata_by_id( app, id ):
def get_repository_metadata_by_repository_id_changeset_revision( app, id, changeset_revision, metadata_only=False ):
"""Get a specified metadata record for a specified repository in the tool shed."""
if metadata_only:
repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, id, changeset_revision )
repository_metadata = get_repository_metadata_by_changeset_revision( app, id, changeset_revision )
if repository_metadata and repository_metadata.metadata:
return repository_metadata.metadata
return None
return suc.get_repository_metadata_by_changeset_revision( app, id, changeset_revision )
return get_repository_metadata_by_changeset_revision( app, id, changeset_revision )
def get_repository_metadata_revisions_for_review( repository, reviewed=True ):
@@ -178,6 +298,28 @@ def get_repository_metadata_revisions_for_review( repository, reviewed=True ):
return repository_metadata_revisions
def get_updated_changeset_revisions( app, name, owner, changeset_revision ):
"""
Return a string of comma-separated changeset revision hashes for all available updates to the received changeset
revision for the repository defined by the received name and owner.
"""
repository = tool_shed.util.repository_util.get_repository_by_name_and_owner( app, name, owner )
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
# Get the upper bound changeset revision.
upper_bound_changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
# Build the list of changeset revision hashes defining each available update up to, but excluding
# upper_bound_changeset_revision.
changeset_hashes = []
for changeset in hg_util.reversed_lower_upper_bounded_changelog( repo, changeset_revision, upper_bound_changeset_revision ):
# Make sure to exclude upper_bound_changeset_revision.
if changeset != upper_bound_changeset_revision:
changeset_hashes.append( str( repo.changectx( changeset ) ) )
if changeset_hashes:
changeset_hashes_str = ','.join( changeset_hashes )
return changeset_hashes_str
return ''
def is_downloadable( metadata_dict ):
# NOTE: although repository README files are considered Galaxy utilities, they have no
# effect on determining if a revision is installable. See the comments in the
@@ -202,7 +344,7 @@ def is_downloadable( metadata_dict ):
def is_malicious( app, id, changeset_revision, **kwd ):
"""Check the malicious flag in repository metadata for a specified change set revision."""
repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, id, changeset_revision )
repository_metadata = get_repository_metadata_by_changeset_revision( app, id, changeset_revision )
if repository_metadata:
return repository_metadata.malicious
return False
lib/tool_shed/util/readme_util.py
+7 -3
View File
@@ -8,7 +8,11 @@ from mako.template import Template
import tool_shed.util.shed_util_common as suc
from galaxy import web
from galaxy.util import rst_to_html, unicodify, url_get
from tool_shed.util import basic_util, common_util, hg_util
from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import hg_util
from tool_shed.util import metadata_util
from tool_shed.util import repository_util
log = logging.getLogger( __name__ )
@@ -23,7 +27,7 @@ def build_readme_files_dict( app, repository, changeset_revision, metadata, tool
can_use_disk_files = True
else:
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
latest_downloadable_changeset_revision = suc.get_latest_downloadable_changeset_revision( app, repository, repo )
latest_downloadable_changeset_revision = metadata_util.get_latest_downloadable_changeset_revision( app, repository, repo )
can_use_disk_files = changeset_revision == latest_downloadable_changeset_revision
readme_files_dict = {}
if metadata:
@@ -92,7 +96,7 @@ def get_readme_files_dict_for_display( app, tool_shed_url, repo_info_dict ):
name = repo_info_dict.keys()[ 0 ]
repo_info_tuple = repo_info_dict[ name ]
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
# Handle changing HTTP protocols over time.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
params = dict( name=name, owner=repository_owner, changeset_revision=changeset_revision )
lib/tool_shed/util/repository_util.py
+780 -203
View File
File diff suppressed because it is too large Load Diff
lib/tool_shed/util/shed_util_common.py
+53 -798
View File
@@ -2,21 +2,18 @@ import json
import logging
import os
import re
import shutil
import socket
import string
from urllib2 import HTTPError
from operator import itemgetter
import sqlalchemy.orm.exc
from sqlalchemy import and_, false, or_, true
from sqlalchemy import and_, false, true
import tool_shed.util.repository_util
from galaxy import util
from galaxy.web import url_for
from galaxy.util import checkers
from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import encoding_util
from tool_shed.util import hg_util
log = logging.getLogger( __name__ )
@@ -149,97 +146,6 @@ def clean_dependency_relationships(trans, metadata_dict, tool_shed_repository, t
trans.install_model.context.flush()
def create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url,
metadata_dict, status, current_changeset_revision=None, owner='', dist_to_shed=False ):
"""
Update a tool shed repository record in the Galaxy database with the new information received.
If a record defined by the received tool shed, repository name and owner does not exist, create
a new record with the received information.
"""
# The received value for dist_to_shed will be True if the ToolMigrationManager is installing a repository
# that contains tools or datatypes that used to be in the Galaxy distribution, but have been moved
# to the main Galaxy tool shed.
if current_changeset_revision is None:
# The current_changeset_revision is not passed if a repository is being installed for the first
# time. If a previously installed repository was later uninstalled, this value should be received
# as the value of that change set to which the repository had been updated just prior to it being
# uninstalled.
current_changeset_revision = installed_changeset_revision
context = app.install_model.context
tool_shed = get_tool_shed_from_clone_url( repository_clone_url )
if not owner:
owner = get_repository_owner_from_clone_url( repository_clone_url )
includes_datatypes = 'datatypes' in metadata_dict
if status in [ app.install_model.ToolShedRepository.installation_status.DEACTIVATED ]:
deleted = True
uninstalled = False
elif status in [ app.install_model.ToolShedRepository.installation_status.UNINSTALLED ]:
deleted = True
uninstalled = True
else:
deleted = False
uninstalled = False
tool_shed_repository = \
get_installed_repository( app, tool_shed=tool_shed, name=name, owner=owner, installed_changeset_revision=installed_changeset_revision )
if tool_shed_repository:
log.debug( "Updating an existing row for repository '%s' in the tool_shed_repository table, status set to '%s'." %
( str( name ), str( status ) ) )
tool_shed_repository.description = description
tool_shed_repository.changeset_revision = current_changeset_revision
tool_shed_repository.ctx_rev = ctx_rev
tool_shed_repository.metadata = metadata_dict
tool_shed_repository.includes_datatypes = includes_datatypes
tool_shed_repository.deleted = deleted
tool_shed_repository.uninstalled = uninstalled
tool_shed_repository.status = status
else:
log.debug( "Adding new row for repository '%s' in the tool_shed_repository table, status set to '%s'." %
( str( name ), str( status ) ) )
tool_shed_repository = \
app.install_model.ToolShedRepository( tool_shed=tool_shed,
name=name,
description=description,
owner=owner,
installed_changeset_revision=installed_changeset_revision,
changeset_revision=current_changeset_revision,
ctx_rev=ctx_rev,
metadata=metadata_dict,
includes_datatypes=includes_datatypes,
dist_to_shed=dist_to_shed,
deleted=deleted,
uninstalled=uninstalled,
status=status )
context.add( tool_shed_repository )
context.flush()
return tool_shed_repository
def extract_components_from_tuple( repository_components_tuple ):
'''Extract the repository components from the provided tuple in a backward-compatible manner.'''
toolshed = repository_components_tuple[ 0 ]
name = repository_components_tuple[ 1 ]
owner = repository_components_tuple[ 2 ]
changeset_revision = repository_components_tuple[ 3 ]
components_list = [ toolshed, name, owner, changeset_revision ]
if len( repository_components_tuple ) == 5:
toolshed, name, owner, changeset_revision, prior_installation_required = repository_components_tuple
components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required ]
elif len( repository_components_tuple ) == 6:
toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = repository_components_tuple
components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td ]
return components_list
def generate_sharable_link_for_repository_in_tool_shed( repository, changeset_revision=None ):
"""Generate the URL for sharing a repository that is in the tool shed."""
base_url = url_for( '/', qualified=True ).rstrip( '/' )
protocol, base = base_url.split( '://' )
sharable_url = '%s://%s/view/%s/%s' % ( protocol, base, repository.user.username, repository.name )
if changeset_revision:
sharable_url += '/%s' % changeset_revision
return sharable_url
def generate_tool_guid( repository_clone_url, tool ):
"""
Generate a guid for the installed tool. It is critical that this guid matches the guid for
@@ -250,33 +156,6 @@ def generate_tool_guid( repository_clone_url, tool ):
return '%s/%s/%s' % ( tmp_url, tool.id, tool.version )
def generate_tool_shed_repository_install_dir( repository_clone_url, changeset_revision ):
"""
Generate a repository installation directory that guarantees repositories with the same
name will always be installed in different directories. The tool path will be of the form:
<tool shed url>/repos/<repository owner>/<repository name>/<installed changeset revision>
"""
tmp_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url )
# Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column
items = tmp_url.split( '/repos/' )
tool_shed_url = items[ 0 ]
repo_path = items[ 1 ]
tool_shed_url = common_util.remove_port_from_tool_shed_url( tool_shed_url )
return '/'.join( [ tool_shed_url, 'repos', repo_path, changeset_revision ] )
def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ):
"""Return the absolute path to a specified disk file contained in a repository."""
stripped_file_name = basic_util.strip_path( file_name )
file_path = None
for root, dirs, files in os.walk( repo_files_dir ):
if root.find( '.hg' ) < 0:
for name in files:
if name == stripped_file_name:
return os.path.abspath( os.path.join( root, name ) )
return file_path
def get_categories( app ):
"""Get all categories from the database."""
sa_session = app.model.context.current
@@ -313,112 +192,6 @@ def get_ctx_rev( app, tool_shed_url, name, owner, changeset_revision ):
return ctx_rev
def get_current_repository_metadata_for_changeset_revision( app, repository, changeset_revision ):
encoded_repository_id = app.security.encode_id( repository.id )
repository_metadata = get_repository_metadata_by_changeset_revision( app,
encoded_repository_id,
changeset_revision )
if repository_metadata:
return repository_metadata
# The installable changeset_revision may have been changed because it was "moved ahead"
# in the repository changelog.
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
updated_changeset_revision = get_next_downloadable_changeset_revision( repository,
repo,
after_changeset_revision=changeset_revision )
if updated_changeset_revision and updated_changeset_revision != changeset_revision:
repository_metadata = get_repository_metadata_by_changeset_revision( app,
encoded_repository_id,
updated_changeset_revision )
if repository_metadata:
return repository_metadata
return None
def get_ids_of_tool_shed_repositories_being_installed( app, as_string=False ):
installing_repository_ids = []
new_status = app.install_model.ToolShedRepository.installation_status.NEW
cloning_status = app.install_model.ToolShedRepository.installation_status.CLONING
setting_tool_versions_status = app.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS
installing_dependencies_status = app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES
loading_datatypes_status = app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
for tool_shed_repository in \
app.install_model.context.query( app.install_model.ToolShedRepository ) \
.filter( or_( app.install_model.ToolShedRepository.status == new_status,
app.install_model.ToolShedRepository.status == cloning_status,
app.install_model.ToolShedRepository.status == setting_tool_versions_status,
app.install_model.ToolShedRepository.status == installing_dependencies_status,
app.install_model.ToolShedRepository.status == loading_datatypes_status ) ):
installing_repository_ids.append( app.security.encode_id( tool_shed_repository.id ) )
if as_string:
return ','.join( installing_repository_ids )
return installing_repository_ids
def get_latest_downloadable_changeset_revision( app, repository, repo=None ):
if repo is None:
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
repository_tip = repository.tip( app )
repository_metadata = get_repository_metadata_by_changeset_revision( app, app.security.encode_id( repository.id ), repository_tip )
if repository_metadata and repository_metadata.downloadable:
return repository_tip
changeset_revisions = [ revision[ 1 ] for revision in get_metadata_revisions( repository, repo ) ]
if changeset_revisions:
return changeset_revisions[ -1 ]
return hg_util.INITIAL_CHANGELOG_HASH
def get_tool_dependency_definition_metadata_from_tool_shed( app, tool_shed_url, name, owner ):
"""
Send a request to the tool shed to retrieve the current metadata for a
repository of type tool_dependency_definition defined by the combination
of a name and owner.
"""
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
params = dict( name=name, owner=owner )
pathspec = [ 'repository', 'get_tool_dependency_definition_metadata' ]
metadata = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
return metadata
def get_metadata_changeset_revisions( repository, repo ):
"""
Return an unordered list of changeset_revisions and changeset numbers that are defined as installable.
"""
changeset_tups = []
for repository_metadata in repository.downloadable_revisions:
ctx = hg_util.get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
if ctx:
rev = ctx.rev()
else:
rev = -1
changeset_tups.append( ( rev, repository_metadata.changeset_revision ) )
return sorted( changeset_tups )
def get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision ):
"""
Return the installable changeset_revision in the repository changelog after the changeset to which
after_changeset_revision refers. If there isn't one, return None. If there is only one installable
changeset, and that matches the requested revision, return it.
"""
changeset_revisions = [ revision[ 1 ] for revision in get_metadata_revisions( repository, repo ) ]
if len( changeset_revisions ) == 1:
changeset_revision = changeset_revisions[ 0 ]
if changeset_revision == after_changeset_revision:
return after_changeset_revision
found_after_changeset_revision = False
for changeset in repo.changelog:
changeset_revision = str( repo.changectx( changeset ) )
if found_after_changeset_revision:
if changeset_revision in changeset_revisions:
return changeset_revision
elif not found_after_changeset_revision and changeset_revision == after_changeset_revision:
# We've found the changeset in the changelog for which we need to get the next downloadable changeset.
found_after_changeset_revision = True
return None
def get_next_prior_import_or_install_required_dict_entry( prior_required_dict, processed_tsr_ids ):
"""
This method is used in the Tool Shed when exporting a repository and its dependencies, and in Galaxy
@@ -453,196 +226,11 @@ def get_next_prior_import_or_install_required_dict_entry( prior_required_dict, p
return key
def get_metadata_revisions( repository, repo, sort_revisions=True, reverse=False, downloadable=True ):
"""
Return a list of changesets for the provided repository.
"""
if downloadable:
metadata_revisions = repository.downloadable_revisions
else:
metadata_revisions = repository.metadata_revisions
changeset_tups = []
for repository_metadata in metadata_revisions:
ctx = hg_util.get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
if ctx:
rev = '%04d' % ctx.rev()
else:
rev = -1
changeset_tups.append( ( rev, repository_metadata.changeset_revision ) )
if sort_revisions:
changeset_tups.sort( key=itemgetter( 0 ), reverse=reverse )
return changeset_tups
def get_prior_import_or_install_required_dict( app, tsr_ids, repo_info_dicts ):
"""
This method is used in the Tool Shed when exporting a repository and its dependencies,
and in Galaxy when a repository and its dependencies are being installed. Return a
dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids,
each of which is contained in the received list of tsr_ids and whose associated repository
must be imported or installed prior to the repository associated with the tsr_id key.
"""
# Initialize the dictionary.
prior_import_or_install_required_dict = {}
for tsr_id in tsr_ids:
prior_import_or_install_required_dict[ tsr_id ] = []
# Inspect the repository dependencies for each repository about to be installed and populate the dictionary.
for repo_info_dict in repo_info_dicts:
repository, repository_dependencies = get_repository_and_repository_dependencies_from_repo_info_dict( app, repo_info_dict )
if repository:
encoded_repository_id = app.security.encode_id( repository.id )
if encoded_repository_id in tsr_ids:
# We've located the database table record for one of the repositories we're about to install, so find out if it has any repository
# dependencies that require prior installation.
prior_import_or_install_ids = get_repository_ids_requiring_prior_import_or_install( app, tsr_ids, repository_dependencies )
prior_import_or_install_required_dict[ encoded_repository_id ] = prior_import_or_install_ids
return prior_import_or_install_required_dict
def get_repo_info_tuple_contents( repo_info_tuple ):
"""Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced."""
if len( repo_info_tuple ) == 6:
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
repository_dependencies = None
elif len( repo_info_tuple ) == 7:
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
return description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies
def get_repositories_by_category( app, category_id ):
def get_repository_categories( app, id ):
"""Get categories of a repository on the tool shed side from the database via id"""
sa_session = app.model.context.current
resultset = sa_session.query( app.model.Category ).get( category_id )
repositories = []
default_value_mapper = { 'id': app.security.encode_id, 'user_id': app.security.encode_id }
for row in resultset.repositories:
repository_dict = row.repository.to_dict( value_mapper=default_value_mapper )
repository_dict[ 'metadata' ] = {}
for changeset, changehash in row.repository.installable_revisions( app ):
encoded_id = app.security.encode_id( row.repository.id )
metadata = get_repository_metadata_by_changeset_revision( app, encoded_id, changehash )
repository_dict[ 'metadata' ][ '%s:%s' % ( changeset, changehash ) ] = metadata.to_dict( value_mapper=default_value_mapper )
repositories.append( repository_dict )
return repositories
def get_repository_and_repository_dependencies_from_repo_info_dict( app, repo_info_dict ):
"""Return a tool_shed_repository or repository record defined by the information in the received repo_info_dict."""
repository_name = repo_info_dict.keys()[ 0 ]
repo_info_tuple = repo_info_dict[ repository_name ]
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
get_repo_info_tuple_contents( repo_info_tuple )
if hasattr( app, "install_model" ):
# In a tool shed client (Galaxy, or something install repositories like Galaxy)
tool_shed = get_tool_shed_from_clone_url( repository_clone_url )
repository = get_repository_for_dependency_relationship( app, tool_shed, repository_name, repository_owner, changeset_revision )
else:
# We're in the tool shed.
repository = get_repository_by_name_and_owner( app, repository_name, repository_owner )
return repository, repository_dependencies
def get_repository_by_id( app, id ):
"""Get a repository from the database via id."""
if is_tool_shed_client( app ):
return app.install_model.context.query( app.install_model.ToolShedRepository ).get( app.security.decode_id( id ) )
else:
sa_session = app.model.context.current
return sa_session.query( app.model.Repository ).get( app.security.decode_id( id ) )
def get_repository_by_name( app, name ):
"""Get a repository from the database via name."""
repository_query = get_repository_query( app )
return repository_query.filter_by( name=name ).first()
def get_repository_by_name_and_owner( app, name, owner ):
"""Get a repository from the database via name and owner"""
repository_query = get_repository_query( app )
if is_tool_shed_client( app ):
return repository_query \
.filter( and_( app.install_model.ToolShedRepository.table.c.name == name,
app.install_model.ToolShedRepository.table.c.owner == owner ) ) \
.first()
# We're in the tool shed.
user = get_user_by_username( app, owner )
if user:
return repository_query \
.filter( and_( app.model.Repository.table.c.name == name,
app.model.Repository.table.c.user_id == user.id ) ) \
.first()
return None
def get_repository_dependency_types( repository_dependencies ):
"""
Inspect the received list of repository_dependencies tuples and return boolean values
for has_repository_dependencies and has_repository_dependencies_only_if_compiling_contained_td.
"""
# Set has_repository_dependencies, which will be True only if at least one repository_dependency
# is defined with the value of
# only_if_compiling_contained_td as False.
has_repository_dependencies = False
for rd_tup in repository_dependencies:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( rd_tup )
if not util.asbool( only_if_compiling_contained_td ):
has_repository_dependencies = True
break
# Set has_repository_dependencies_only_if_compiling_contained_td, which will be True only if at
# least one repository_dependency is defined with the value of only_if_compiling_contained_td as True.
has_repository_dependencies_only_if_compiling_contained_td = False
for rd_tup in repository_dependencies:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( rd_tup )
if util.asbool( only_if_compiling_contained_td ):
has_repository_dependencies_only_if_compiling_contained_td = True
break
return has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td
def get_repository_for_dependency_relationship( app, tool_shed, name, owner, changeset_revision ):
"""
Return an installed tool_shed_repository database record that is defined by either the current changeset
revision or the installed_changeset_revision.
"""
# This method is used only in Galaxy, not the Tool Shed. We store the port (if one exists) in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
if tool_shed is None or name is None or owner is None or changeset_revision is None:
message = "Unable to retrieve the repository record from the database because one or more of the following "
message += "required parameters is None: tool_shed: %s, name: %s, owner: %s, changeset_revision: %s " % \
( str( tool_shed ), str( name ), str( owner ), str( changeset_revision ) )
raise Exception( message )
repository = get_installed_repository( app=app,
tool_shed=tool_shed,
name=name,
owner=owner,
installed_changeset_revision=changeset_revision )
if not repository:
repository = get_installed_repository( app=app,
tool_shed=tool_shed,
name=name,
owner=owner,
changeset_revision=changeset_revision )
if not repository:
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed )
repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
repo_info_tuple = (None, repository_clone_url, changeset_revision, None, owner, None, None)
repository, pcr = repository_was_previously_installed( app, tool_shed_url, name, repo_info_tuple )
if not repository:
# The received changeset_revision is no longer installable, so get the next changeset_revision
# in the repository's changelog in the tool shed that is associated with repository_metadata.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed )
params = dict( name=name, owner=owner, changeset_revision=changeset_revision )
pathspec = [ 'repository', 'next_installable_changeset_revision' ]
text = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
if text:
repository = get_installed_repository( app=app,
tool_shed=tool_shed,
name=name,
owner=owner,
changeset_revision=text )
return repository
return sa_session.query( app.model.RepositoryCategoryAssociation ) \
.filter(app.model.RepositoryCategoryAssociation.table.c.repository_id == app.security.decode_id( id ))
def get_repository_file_contents( app, file_path, repository_id, is_admin=False ):
@@ -712,123 +300,13 @@ def get_repository_from_refresh_on_change( app, **kwd ):
changeset_revision_str = 'changeset_revision_'
if k.startswith( changeset_revision_str ):
repository_id = app.security.encode_id( int( k.lstrip( changeset_revision_str ) ) )
repository = get_repository_in_tool_shed( app, repository_id )
repository = tool_shed.util.repository_util.get_repository_in_tool_shed( app, repository_id )
if repository.tip( app ) != v:
return v, repository
# This should never be reached - raise an exception?
return v, None
def get_repository_ids_requiring_prior_import_or_install( app, tsr_ids, repository_dependencies ):
"""
This method is used in the Tool Shed when exporting a repository and its dependencies,
and in Galaxy when a repository and its dependencies are being installed. Inspect the
received repository_dependencies and determine if the encoded id of each required
repository is in the received tsr_ids. If so, then determine whether that required
repository should be imported / installed prior to its dependent repository. Return a
list of encoded repository ids, each of which is contained in the received list of tsr_ids,
and whose associated repositories must be imported / installed prior to the dependent
repository associated with the received repository_dependencies.
"""
prior_tsr_ids = []
if repository_dependencies:
for key, rd_tups in repository_dependencies.items():
if key in [ 'description', 'root_key' ]:
continue
for rd_tup in rd_tups:
tool_shed, \
name, \
owner, \
changeset_revision, \
prior_installation_required, \
only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( rd_tup )
# If only_if_compiling_contained_td is False, then the repository dependency
# is not required to be installed prior to the dependent repository even if
# prior_installation_required is True. This is because the only meaningful
# content of the repository dependency is its contained tool dependency, which
# is required in order to compile the dependent repository's tool dependency.
# In the scenario where the repository dependency is not installed prior to the
# dependent repository's tool dependency compilation process, the tool dependency
# compilation framework will install the repository dependency prior to compilation
# of the dependent repository's tool dependency.
if not util.asbool( only_if_compiling_contained_td ):
if util.asbool( prior_installation_required ):
if is_tool_shed_client( app ):
# We store the port, if one exists, in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
repository = get_repository_for_dependency_relationship( app,
tool_shed,
name,
owner,
changeset_revision )
else:
repository = get_repository_by_name_and_owner( app, name, owner )
if repository:
encoded_repository_id = app.security.encode_id( repository.id )
if encoded_repository_id in tsr_ids:
prior_tsr_ids.append( encoded_repository_id )
return prior_tsr_ids
def get_repository_in_tool_shed( app, id ):
"""Get a repository on the tool shed side from the database via id."""
sa_session = app.model.context.current
return sa_session.query( app.model.Repository ).get( app.security.decode_id( id ) )
def get_repository_categories( app, id ):
"""Get categories of a repository on the tool shed side from the database via id"""
sa_session = app.model.context.current
return sa_session.query( app.model.RepositoryCategoryAssociation ) \
.filter(app.model.RepositoryCategoryAssociation.table.c.repository_id == app.security.decode_id( id ))
def get_repository_metadata_by_changeset_revision( app, id, changeset_revision ):
"""Get metadata for a specified repository change set from the database."""
# Make sure there are no duplicate records, and return the single unique record for the changeset_revision.
# Duplicate records were somehow created in the past. The cause of this issue has been resolved, but we'll
# leave this method as is for a while longer to ensure all duplicate records are removed.
sa_session = app.model.context.current
all_metadata_records = sa_session.query( app.model.RepositoryMetadata ) \
.filter( and_( app.model.RepositoryMetadata.table.c.repository_id == app.security.decode_id( id ),
app.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \
.order_by( app.model.RepositoryMetadata.table.c.update_time.desc() ) \
.all()
if len( all_metadata_records ) > 1:
# Delete all records older than the last one updated.
for repository_metadata in all_metadata_records[ 1: ]:
sa_session.delete( repository_metadata )
sa_session.flush()
return all_metadata_records[ 0 ]
elif all_metadata_records:
return all_metadata_records[ 0 ]
return None
def get_repository_owner( cleaned_repository_url ):
"""Gvien a "cleaned" repository clone URL, return the owner of the repository."""
items = cleaned_repository_url.split( '/repos/' )
repo_path = items[ 1 ]
if repo_path.startswith( '/' ):
repo_path = repo_path.replace( '/', '', 1 )
return repo_path.lstrip( '/' ).split( '/' )[ 0 ]
def get_repository_owner_from_clone_url( repository_clone_url ):
"""Given a repository clone URL, return the owner of the repository."""
tmp_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url )
return get_repository_owner( tmp_url )
def get_repository_query( app ):
if is_tool_shed_client( app ):
query = app.install_model.context.query( app.install_model.ToolShedRepository )
else:
query = app.model.context.query( app.model.Repository )
return query
def get_repository_type_from_tool_shed( app, tool_shed_url, name, owner ):
"""
Send a request to the tool shed to retrieve the type for a repository defined by the
@@ -841,6 +319,19 @@ def get_repository_type_from_tool_shed( app, tool_shed_url, name, owner ):
return repository_type
def get_tool_dependency_definition_metadata_from_tool_shed( app, tool_shed_url, name, owner ):
"""
Send a request to the tool shed to retrieve the current metadata for a
repository of type tool_dependency_definition defined by the combination
of a name and owner.
"""
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
params = dict( name=name, owner=owner )
pathspec = [ 'repository', 'get_tool_dependency_definition_metadata' ]
metadata = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
return metadata
def get_tool_panel_config_tool_path_install_dir( app, repository ):
"""
Return shed-related tool panel config, the tool_path configured in it, and the relative path to
@@ -881,177 +372,12 @@ def get_tool_path_by_shed_tool_conf_filename( app, shed_tool_conf ):
return None
def get_tool_shed_from_clone_url( repository_clone_url ):
tmp_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url )
return tmp_url.split( '/repos/' )[ 0 ].rstrip( '/' )
def get_installed_repository( app, tool_shed, name, owner, changeset_revision=None, installed_changeset_revision=None ):
"""
Return a tool shed repository database record defined by the combination of a toolshed, repository name,
repository owner and either current or originally installed changeset_revision.
"""
query = app.install_model.context.query( app.install_model.ToolShedRepository )
# We store the port, if one exists, in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
clause_list = [ app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
app.install_model.ToolShedRepository.table.c.name == name,
app.install_model.ToolShedRepository.table.c.owner == owner ]
if changeset_revision is not None:
clause_list.append( app.install_model.ToolShedRepository.table.c.changeset_revision == changeset_revision )
if installed_changeset_revision is not None:
clause_list.append( app.install_model.ToolShedRepository.table.c.installed_changeset_revision == installed_changeset_revision )
return query.filter( and_( *clause_list ) ).first()
def get_tool_shed_repository_by_id( app, repository_id ):
"""Return a tool shed repository database record defined by the id."""
# This method is used only in Galaxy, not the tool shed.
return app.install_model.context.query( app.install_model.ToolShedRepository ) \
.filter( app.install_model.ToolShedRepository.table.c.id == app.security.decode_id( repository_id ) ) \
.first()
def get_tool_shed_status_for_installed_repository( app, repository ):
"""
Send a request to the tool shed to retrieve information about newer installable repository revisions,
current revision updates, whether the repository revision is the latest downloadable revision, and
whether the repository has been deprecated in the tool shed. The received repository is a ToolShedRepository
object from Galaxy.
"""
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, str( repository.tool_shed ) )
params = dict( name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision )
pathspec = [ 'repository', 'status_for_installed_repository' ]
try:
encoded_tool_shed_status_dict = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
tool_shed_status_dict = encoding_util.tool_shed_decode( encoded_tool_shed_status_dict )
return tool_shed_status_dict
except HTTPError as e:
# This should handle backward compatility to the Galaxy 12/20/12 release. We used to only handle updates for an installed revision
# using a boolean value.
log.debug( "Error attempting to get tool shed status for installed repository %s: %s\nAttempting older 'check_for_updates' method.\n" %
( str( repository.name ), str( e ) ) )
pathspec = [ 'repository', 'check_for_updates' ]
params[ 'from_update_manager' ] = True
try:
# The value of text will be 'true' or 'false', depending upon whether there is an update available for the installed revision.
text = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
return dict( revision_update=text )
except Exception as e:
# The required tool shed may be unavailable, so default the revision_update value to 'false'.
return dict( revision_update='false' )
except Exception as e:
log.exception( "Error attempting to get tool shed status for installed repository %s: %s" % ( str( repository.name ), str( e ) ) )
return {}
def get_tool_shed_repository_status_label( app, tool_shed_repository=None, name=None, owner=None, changeset_revision=None, repository_clone_url=None ):
"""Return a color-coded label for the status of the received tool-shed_repository installed into Galaxy."""
if tool_shed_repository is None:
if name is not None and owner is not None and repository_clone_url is not None:
tool_shed = get_tool_shed_from_clone_url( repository_clone_url )
tool_shed_repository = get_installed_repository( app,
tool_shed=tool_shed,
name=name,
owner=owner,
installed_changeset_revision=changeset_revision )
if tool_shed_repository:
status_label = tool_shed_repository.status
if tool_shed_repository.status in [ app.install_model.ToolShedRepository.installation_status.CLONING,
app.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
app.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ]:
bgcolor = app.install_model.ToolShedRepository.states.INSTALLING
elif tool_shed_repository.status in [ app.install_model.ToolShedRepository.installation_status.NEW,
app.install_model.ToolShedRepository.installation_status.UNINSTALLED ]:
bgcolor = app.install_model.ToolShedRepository.states.UNINSTALLED
elif tool_shed_repository.status in [ app.install_model.ToolShedRepository.installation_status.ERROR ]:
bgcolor = app.install_model.ToolShedRepository.states.ERROR
elif tool_shed_repository.status in [ app.install_model.ToolShedRepository.installation_status.DEACTIVATED ]:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
elif tool_shed_repository.status in [ app.install_model.ToolShedRepository.installation_status.INSTALLED ]:
if tool_shed_repository.repository_dependencies_being_installed:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
status_label = '%s, %s' % ( status_label,
app.install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES )
elif tool_shed_repository.missing_repository_dependencies:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
status_label = '%s, missing repository dependencies' % status_label
elif tool_shed_repository.tool_dependencies_being_installed:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
status_label = '%s, %s' % ( status_label,
app.install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
elif tool_shed_repository.missing_tool_dependencies:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
status_label = '%s, missing tool dependencies' % status_label
else:
bgcolor = app.install_model.ToolShedRepository.states.OK
else:
bgcolor = app.install_model.ToolShedRepository.states.ERROR
else:
bgcolor = app.install_model.ToolShedRepository.states.WARNING
status_label = 'unknown status'
return '<div class="count-box state-color-%s">%s</div>' % ( bgcolor, status_label )
def get_updated_changeset_revisions( app, name, owner, changeset_revision ):
"""
Return a string of comma-separated changeset revision hashes for all available updates to the received changeset
revision for the repository defined by the received name and owner.
"""
repository = get_repository_by_name_and_owner( app, name, owner )
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
# Get the upper bound changeset revision.
upper_bound_changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
# Build the list of changeset revision hashes defining each available update up to, but excluding
# upper_bound_changeset_revision.
changeset_hashes = []
for changeset in hg_util.reversed_lower_upper_bounded_changelog( repo, changeset_revision, upper_bound_changeset_revision ):
# Make sure to exclude upper_bound_changeset_revision.
if changeset != upper_bound_changeset_revision:
changeset_hashes.append( str( repo.changectx( changeset ) ) )
if changeset_hashes:
changeset_hashes_str = ','.join( changeset_hashes )
return changeset_hashes_str
return ''
def get_updated_changeset_revisions_from_tool_shed( app, tool_shed_url, name, owner, changeset_revision ):
"""
Get all appropriate newer changeset revisions for the repository defined by
the received tool_shed_url / name / owner combination.
"""
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
if tool_shed_url is None or name is None or owner is None or changeset_revision is None:
message = "Unable to get updated changeset revisions from the Tool Shed because one or more of the following "
message += "required parameters is None: tool_shed_url: %s, name: %s, owner: %s, changeset_revision: %s " % \
( str( tool_shed_url ), str( name ), str( owner ), str( changeset_revision ) )
raise Exception( message )
params = dict( name=name, owner=owner, changeset_revision=changeset_revision )
pathspec = [ 'repository', 'updated_changeset_revisions' ]
text = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
return text
def get_user( app, id ):
"""Get a user from the database by id."""
sa_session = app.model.context.current
return sa_session.query( app.model.User ).get( app.security.decode_id( id ) )
def get_user_by_username( app, username ):
"""Get a user from the database by username."""
sa_session = app.model.context.current
try:
user = sa_session.query( app.model.User ) \
.filter( app.model.User.table.c.username == username ) \
.one()
return user
except Exception:
return None
def handle_email_alerts( app, host, repository, content_alert_str='', new_repo_alert=False, admin_only=False ):
"""
There are 2 complementary features that enable a tool shed user to receive email notification:
@@ -1077,7 +403,7 @@ def handle_email_alerts( app, host, repository, content_alert_str='', new_repo_a
"""
sa_session = app.model.context.current
repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False )
sharable_link = generate_sharable_link_for_repository_in_tool_shed( repository, changeset_revision=None )
sharable_link = tool_shed.util.repository_util.generate_sharable_link_for_repository_in_tool_shed( repository, changeset_revision=None )
smtp_server = app.config.smtp_server
if smtp_server and ( new_repo_alert or repository.email_alerts ):
# Send email alert to users that want them.
@@ -1149,14 +475,39 @@ def have_shed_tool_conf_for_install( app ):
return bool( app.toolbox.dynamic_confs( include_migrated_tool_conf=False ) )
def is_tool_shed_client( app ):
def is_path_browsable( app, path, repository_id, is_admin=False ):
"""
The tool shed and clients to the tool (i.e. Galaxy) require a lot
of similar functionality in this file but with small differences. This
method should determine if the app performing the action is the tool shed
or a client of the tool shed.
Detects whether the given path is browsable i.e. is within the
allowed repository folders. Admins can additionaly browse folders
with tool dependencies.
"""
return hasattr( app, "install_model" )
if is_admin and is_path_within_dependency_dir( app, path ):
return True
return is_path_within_repo( app, path, repository_id)
def is_path_within_dependency_dir( app, path ):
"""
Detect whether the given path is within the tool_dependency_dir folder on the disk.
(Specified by the config option). Use to filter malicious symlinks targeting outside paths.
"""
allowed = False
resolved_path = os.path.realpath( path )
tool_dependency_dir = app.config.get( 'tool_dependency_dir', None )
if tool_dependency_dir:
dependency_path = os.path.abspath( tool_dependency_dir )
allowed = os.path.commonprefix( [ dependency_path, resolved_path ] ) == dependency_path
return allowed
def is_path_within_repo( app, path, repository_id ):
"""
Detect whether the given path is within the repository folder on the disk.
Use to filter malicious symlinks targeting outside paths.
"""
repo_path = os.path.abspath( tool_shed.util.repository_util.get_repository_by_id( app, repository_id ).repo_path( app ) )
resolved_path = os.path.realpath( path )
return os.path.commonprefix( [ repo_path, resolved_path ] ) == repo_path
def open_repository_files_folder( app, folder_path, repository_id, is_admin=False ):
@@ -1196,84 +547,6 @@ def open_repository_files_folder( app, folder_path, repository_id, is_admin=Fals
return folder_contents
def is_path_browsable( app, path, repository_id, is_admin=False ):
"""
Detects whether the given path is browsable i.e. is within the
allowed repository folders. Admins can additionaly browse folders
with tool dependencies.
"""
if is_admin and is_path_within_dependency_dir( app, path ):
return True
return is_path_within_repo( app, path, repository_id)
def is_path_within_repo( app, path, repository_id ):
"""
Detect whether the given path is within the repository folder on the disk.
Use to filter malicious symlinks targeting outside paths.
"""
repo_path = os.path.abspath( get_repository_by_id( app, repository_id ).repo_path( app ) )
resolved_path = os.path.realpath( path )
return os.path.commonprefix( [ repo_path, resolved_path ] ) == repo_path
def is_path_within_dependency_dir( app, path ):
"""
Detect whether the given path is within the tool_dependency_dir folder on the disk.
(Specified by the config option). Use to filter malicious symlinks targeting outside paths.
"""
allowed = False
resolved_path = os.path.realpath( path )
tool_dependency_dir = app.config.get( 'tool_dependency_dir', None )
if tool_dependency_dir:
dependency_path = os.path.abspath( tool_dependency_dir )
allowed = os.path.commonprefix( [ dependency_path, resolved_path ] ) == dependency_path
return allowed
def repository_was_previously_installed( app, tool_shed_url, repository_name, repo_info_tuple, from_tip=False ):
"""
Find out if a repository is already installed into Galaxy - there are several scenarios where this
is necessary. For example, this method will handle the case where the repository was previously
installed using an older changeset_revsion, but later the repository was updated in the tool shed
and now we're trying to install the latest changeset revision of the same repository instead of
updating the one that was previously installed. We'll look in the database instead of on disk since
the repository may be currently uninstalled.
"""
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \
get_repo_info_tuple_contents( repo_info_tuple )
tool_shed = get_tool_shed_from_clone_url( repository_clone_url )
# See if we can locate the repository using the value of changeset_revision.
tool_shed_repository = get_installed_repository( app,
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=changeset_revision )
if tool_shed_repository:
return tool_shed_repository, changeset_revision
# Get all previous changeset revisions from the tool shed for the repository back to, but excluding,
# the previous valid changeset revision to see if it was previously installed using one of them.
params = dict( galaxy_url=url_for( '/', qualified=True ),
name=repository_name,
owner=repository_owner,
changeset_revision=changeset_revision,
from_tip=str( from_tip ) )
pathspec = [ 'repository', 'previous_changeset_revisions' ]
text = util.url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
if text:
changeset_revisions = util.listify( text )
for previous_changeset_revision in changeset_revisions:
tool_shed_repository = get_installed_repository( app,
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=previous_changeset_revision )
if tool_shed_repository:
return tool_shed_repository, previous_changeset_revision
return None, None
def set_image_paths( app, encoded_repository_id, text ):
"""
Handle tool help image display for tools that are contained in repositories in
@@ -1282,7 +555,7 @@ def set_image_paths( app, encoded_repository_id, text ):
return the path to it that will enable the caller to open the file.
"""
if text:
if is_tool_shed_client( app ):
if tool_shed.util.repository_util.is_tool_shed_client( app ):
route_to_images = 'admin_toolshed/static/images/%s' % encoded_repository_id
else:
# We're in the tool shed.
@@ -1300,24 +573,6 @@ def set_image_paths( app, encoded_repository_id, text ):
return text
def set_repository_attributes( app, repository, status, error_message, deleted, uninstalled, remove_from_disk=False ):
if remove_from_disk:
relative_install_dir = repository.repo_path( app )
if relative_install_dir:
clone_dir = os.path.abspath( relative_install_dir )
try:
shutil.rmtree( clone_dir )
log.debug( "Removed repository installation directory: %s" % str( clone_dir ) )
except Exception as e:
log.debug( "Error removing repository installation directory %s: %s" % ( str( clone_dir ), str( e ) ) )
repository.error_message = error_message
repository.status = status
repository.deleted = deleted
repository.uninstalled = uninstalled
app.install_model.context.add( repository )
app.install_model.context.flush()
def tool_shed_is_this_tool_shed( toolshed_base_url ):
"""Determine if a tool shed is the current tool shed."""
cleaned_toolshed_base_url = common_util.remove_protocol_from_tool_shed_url( toolshed_base_url )
lib/tool_shed/util/workflow_util.py
+2 -2
View File
@@ -18,7 +18,7 @@ from tool_shed.tools import tool_validator
from tool_shed.util import encoding_util
from tool_shed.util import metadata_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import repository_util
log = logging.getLogger( __name__ )
@@ -164,7 +164,7 @@ def generate_workflow_image( trans, workflow_name, repository_metadata_id=None,
metadata = repository_metadata.metadata
else:
# We're in Galaxy.
repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id )
repository = repository_util.get_tool_shed_repository_by_id( trans.app, repository_id )
changeset_revision = repository.changeset_revision
metadata = repository.metadata
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
lib/tool_shed/utility_containers/utility_container_manager.py
+5 -5
View File
@@ -3,7 +3,7 @@ import logging
from galaxy import util
from tool_shed.util import common_util
from tool_shed.util import container_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import repository_util
log = logging.getLogger( __name__ )
@@ -701,8 +701,8 @@ class UtilityContainerManager( object ):
tool_shed_repository_id = None
installation_status = 'unknown'
if tool_shed_repository_id:
tool_shed_repository = suc.get_tool_shed_repository_by_id( self.app,
self.app.security.encode_id( tool_shed_repository_id ) )
tool_shed_repository = repository_util.get_tool_shed_repository_by_id( self.app,
self.app.security.encode_id( tool_shed_repository_id ) )
if tool_shed_repository:
if tool_shed_repository.missing_repository_dependencies:
installation_status = '%s, missing repository dependencies' % installation_status
@@ -720,7 +720,7 @@ class UtilityContainerManager( object ):
def handle_repository_dependencies_container_entry( self, repository_dependencies_folder, rd_key, rd_value, folder_id,
repository_dependency_id, folder_keys ):
repository_components_tuple = container_util.get_components_from_key( rd_key )
components_list = suc.extract_components_from_tuple( repository_components_tuple )
components_list = repository_util.extract_components_from_tuple( repository_components_tuple )
toolshed, repository_name, repository_owner, changeset_revision = components_list[ 0:4 ]
# For backward compatibility to the 12/20/12 Galaxy release.
if len( components_list ) == 4:
@@ -802,7 +802,7 @@ class UtilityContainerManager( object ):
def key_is_current_repositorys_key( self, repository_name, repository_owner, changeset_revision,
prior_installation_required, only_if_compiling_contained_td, key ):
repository_components_tuple = container_util.get_components_from_key( key )
components_list = suc.extract_components_from_tuple( repository_components_tuple )
components_list = repository_util.extract_components_from_tuple( repository_components_tuple )
toolshed, key_name, key_owner, key_changeset_revision = components_list[ 0:4 ]
# For backward compatibility to the 12/20/12 Galaxy release.
if len( components_list ) == 4:
templates/admin/tool_shed_repository/repair_repository.mako
+1 -1
View File
@@ -41,7 +41,7 @@ ${render_galaxy_repository_actions( repository )}
<form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ) )}" method="post" >
<input type="hidden" name="repair_dict" value="${encoded_repair_dict|h}"/>
<%
from tool_shed.util.shed_util_common import get_tool_shed_repository_status_label
from tool_shed.util.repository_util import get_tool_shed_repository_status_label
ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] )
%>
<table class="grid">
templates/webapps/tool_shed/repository/common.mako
+2 -2
View File
@@ -219,7 +219,7 @@
<%def name="render_sharable_str( repository, changeset_revision=None )">
<%
from tool_shed.util.shed_util_common import generate_sharable_link_for_repository_in_tool_shed
from tool_shed.util.repository_util import generate_sharable_link_for_repository_in_tool_shed
sharable_link = generate_sharable_link_for_repository_in_tool_shed( repository, changeset_revision=changeset_revision )
%>
<a href="${ sharable_link }" target="_blank">${ sharable_link }</a>
@@ -575,7 +575,7 @@
<%def name="render_repository_dependency( repository_dependency, pad, parent, row_counter, row_is_header=False, render_repository_actions_for='tool_shed' )">
<%
from galaxy.util import asbool
from tool_shed.util.shed_util_common import get_repository_by_name_and_owner
from tool_shed.util.repository_util import get_repository_by_name_and_owner
encoded_id = trans.security.encode_id( repository_dependency.id )
if trans.webapp.name == 'galaxy':
if repository_dependency.tool_shed_repository_id:
test/shed_functional/base/twilltestcase.py
+6
View File
@@ -700,6 +700,12 @@ class ShedTwillTestCase( TwillTestCase ):
last_review = None
return last_review
def get_repositories_category_api( self, categories, strings_displayed=None, strings_not_displayed=None ):
for category in categories:
url = '/api/categories/%s/repositories' % self.security.encode_id( category.id )
self.visit_url( url )
self.check_for_strings( strings_displayed, strings_not_displayed )
def get_tool_dependency_path( self, tool_dependency_name, tool_dependency_version, repository ):
'''Return the absolute path for an installed tool dependency.'''
return os.path.join( self.galaxy_tool_dependency_dir,
test/shed_functional/functional/test_0000_basic_repository_features.py
+7
View File
@@ -349,3 +349,10 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
strings_displayed = [ '%d:%s' % ( revision_number, revision_hash ), 'filtering_0000', 'user1', 'repos', 'added:',
'+These&nbsp;characters&nbsp;should&nbsp;not' ]
self.load_changeset_in_tool_shed( repository_id, changeset_revision, strings_displayed=strings_displayed )
def test_0135_api_get_repositories_in_category( self ):
'''Load the api endpoint for repositories in a category.'''
categories = []
categories.append( self.test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' ) )
categories.append( self.test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 2' ) )
self.get_repositories_category_api( categories )
test/shed_functional/functional/test_1000_install_basic_repository.py
+3 -2
View File
@@ -21,8 +21,9 @@ class BasicToolShedFeatures( ShedTwillTestCase ):
def test_0005_ensure_repositories_and_categories_exist( self ):
'''Create the 0000 category and upload the filtering repository to it, if necessary.'''
category = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' )
self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' )
self.login( email=common.admin_email, username=common.admin_username )
category = self.create_category( name='Test 0000 Basic Repository Features 2', description='Test Description 0000 Basic Repository Features 2' )
category = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test Description 0000 Basic Repository Features 1' )
self.login( email=common.test_user_1_email, username=common.test_user_1_name )
repository = self.get_or_create_repository( name='filtering_0000',
description="Galaxy's filtering tool",