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Handle new repository_metadata columns when resetting metadata on repositories in the tool shed.

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This commit is contained in:
Greg Von Kuster
2013-02-25 16:30:40 -05:00
parent ec65dc585a
commit ae11991ffb
3 changed files with 29 additions and 20 deletions
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lib/galaxy/util/shed_util_common.py
+27 -16
View File
@@ -34,8 +34,6 @@ INITIAL_CHANGELOG_HASH = '000000000000'
REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = "data_manager_conf.xml"
MAX_CONTENT_SIZE = 32768
NOT_TOOL_CONFIGS = [ 'datatypes_conf.xml', 'repository_dependencies.xml', 'tool_dependencies.xml', REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ]
GALAXY_ADMIN_TOOL_SHED_CONTROLLER = 'GALAXY_ADMIN_TOOL_SHED_CONTROLLER'
TOOL_SHED_ADMIN_CONTROLLER = 'TOOL_SHED_ADMIN_CONTROLLER'
TOOL_TYPES_NOT_IN_TOOL_PANEL = [ 'manage_data' ]
VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}&<>" )
@@ -484,10 +482,11 @@ def build_repository_dependency_relationships( trans, repo_info_dicts, tool_shed
repository_dependency_id=repository_dependency.id )
trans.sa_session.add( rrda )
trans.sa_session.flush()
def build_repository_ids_select_field( trans, cntrller, name='repository_ids', multiple=True, display='checkboxes' ):
def build_repository_ids_select_field( trans, name='repository_ids', multiple=True, display='checkboxes' ):
"""Method called from both Galaxy and the Tool Shed to generate the current list of repositories for resetting metadata."""
repositories_select_field = SelectField( name=name, multiple=multiple, display=display )
if cntrller == TOOL_SHED_ADMIN_CONTROLLER:
if trans.webapp.name == 'community':
# We're in the tool shed.
for repository in trans.sa_session.query( trans.model.Repository ) \
.filter( trans.model.Repository.table.c.deleted == False ) \
.order_by( trans.model.Repository.table.c.name,
@@ -496,7 +495,8 @@ def build_repository_ids_select_field( trans, cntrller, name='repository_ids', m
option_label = '%s (%s)' % ( repository.name, owner )
option_value = '%s' % trans.security.encode_id( repository.id )
repositories_select_field.add_option( option_label, option_value )
elif cntrller == GALAXY_ADMIN_TOOL_SHED_CONTROLLER:
else:
# We're in Galaxy.
for repository in trans.sa_session.query( trans.model.ToolShedRepository ) \
.filter( trans.model.ToolShedRepository.table.c.uninstalled == False ) \
.order_by( trans.model.ToolShedRepository.table.c.name,
@@ -899,6 +899,7 @@ def copy_sample_file( app, filename, dest_path=None ):
if not os.path.exists( os.path.join( dest_path, copied_file ) ):
shutil.copy( full_source_path, os.path.join( dest_path, copied_file ) )
def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ):
"""Create or update a repository_metadatqa record in the tool shed."""
downloadable = is_downloadable( metadata_dict )
repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
if repository_metadata:
@@ -909,6 +910,11 @@ def create_or_update_repository_metadata( trans, id, repository, changeset_revis
changeset_revision=changeset_revision,
metadata=metadata_dict,
downloadable=downloadable )
# Always set the default values for the following columns. When resetting all metadata on a repository, this will reset the values.
repository_metadata.tools_functionally_correct = False
repository_metadata.do_not_test = False
repository_metadata.time_last_tested = None
repository_metadata.tool_test_errors = None
trans.sa_session.add( repository_metadata )
trans.sa_session.flush()
return repository_metadata
@@ -2949,7 +2955,7 @@ def is_circular_repository_dependency( repository_key, repository_dependency, al
return True
return False
def is_downloadable( metadata_dict ):
# NOTE: although repository README files are considered Galaxy utilities, they have no effect on determining if a revision is instakllable.
# 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 compare_readme_files() method.
if 'datatypes' in metadata_dict:
# We have proprietary datatypes.
@@ -3503,7 +3509,8 @@ def reset_all_metadata_on_installed_repository( trans, id ):
def reset_all_metadata_on_repository_in_tool_shed( trans, id ):
"""Reset all metadata on a single repository in a tool shed."""
def reset_all_tool_versions( trans, id, repo ):
changeset_revisions = []
"""Reset tool version lineage for those changeset revisions that include valid tools."""
changeset_revisions_that_contain_tools = []
for changeset in repo.changelog:
changeset_revision = str( repo.changectx( changeset ) )
repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
@@ -3511,10 +3518,10 @@ def reset_all_metadata_on_repository_in_tool_shed( trans, id ):
metadata = repository_metadata.metadata
if metadata:
if metadata.get( 'tools', None ):
changeset_revisions.append( changeset_revision )
# The list of changeset_revisions is now filtered to contain only those that are downloadable and contain tools.
changeset_revisions_that_contain_tools.append( changeset_revision )
# The list of changeset_revisions_that_contain_tools is now filtered to contain only those that are downloadable and contain tools.
# If a repository includes tools, build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision.
for index, changeset_revision in enumerate( changeset_revisions ):
for index, changeset_revision in enumerate( changeset_revisions_that_contain_tools ):
tool_versions_dict = {}
repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
metadata = repository_metadata.metadata
@@ -3531,7 +3538,7 @@ def reset_all_metadata_on_repository_in_tool_shed( trans, id ):
tool_dict[ 'id' ],
tool_dict[ 'version' ],
tool_dict[ 'guid' ],
changeset_revisions[ 0:index ] )
changeset_revisions_that_contain_tools[ 0:index ] )
tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id
if tool_versions_dict:
repository_metadata.tool_versions = tool_versions_dict
@@ -3556,7 +3563,7 @@ def reset_all_metadata_on_repository_in_tool_shed( trans, id ):
work_dir = tempfile.mkdtemp()
current_changeset_revision = str( repo.changectx( changeset ) )
ctx = repo.changectx( changeset )
log.debug( "Cloning repository revision: %s", str( ctx.rev() ) )
log.debug( "Cloning repository changeset revision: %s", str( ctx.rev() ) )
cloned_ok, error_message = clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) )
if cloned_ok:
log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) )
@@ -3626,9 +3633,11 @@ def reset_all_metadata_on_repository_in_tool_shed( trans, id ):
reset_tool_data_tables( trans.app )
return invalid_file_tups, metadata_dict
def reset_metadata_on_selected_repositories( trans, **kwd ):
# This method is called from both Galaxy and the Tool Shed, so the cntrller param is required.
"""
Inspect the repository changelog to reset metadata for all appropriate changeset revisions. This method is called from both Galaxy and the
Tool Shed.
"""
repository_ids = util.listify( kwd.get( 'repository_ids', None ) )
CONTROLLER = kwd[ 'CONTROLLER' ]
message = ''
status = 'done'
if repository_ids:
@@ -3636,10 +3645,12 @@ def reset_metadata_on_selected_repositories( trans, **kwd ):
unsuccessful_count = 0
for repository_id in repository_ids:
try:
if CONTROLLER == 'TOOL_SHED_ADMIN_CONTROLLER':
if trans.webapp.name == 'community':
# We're in the tool shed.
repository = get_repository_in_tool_shed( trans, repository_id )
invalid_file_tups, metadata_dict = reset_all_metadata_on_repository_in_tool_shed( trans, repository_id )
elif CONTROLLER == 'GALAXY_ADMIN_TOOL_SHED_CONTROLLER':
else:
# We're in Galaxy.
repository = get_installed_tool_shed_repository( trans, repository_id )
invalid_file_tups, metadata_dict = reset_all_metadata_on_installed_repository( trans, repository_id )
if invalid_file_tups:
lib/galaxy/webapps/community/controllers/admin.py
+1 -2
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@@ -721,12 +721,11 @@ class AdminController( BaseUIController, Admin ):
@web.require_admin
def reset_metadata_on_selected_repositories_in_tool_shed( self, trans, **kwd ):
if 'reset_metadata_on_selected_repositories_button' in kwd:
kwd[ 'CONTROLLER' ] = suc.TOOL_SHED_ADMIN_CONTROLLER
message, status = suc.reset_metadata_on_selected_repositories( trans, **kwd )
else:
message = util.restore_text( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repositories_select_field = suc.build_repository_ids_select_field( trans, suc.TOOL_SHED_ADMIN_CONTROLLER )
repositories_select_field = suc.build_repository_ids_select_field( trans )
return trans.fill_template( '/webapps/community/admin/reset_metadata_on_selected_repositories.mako',
repositories_select_field=repositories_select_field,
message=message,
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+1 -2
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@@ -1711,12 +1711,11 @@ class AdminToolshed( AdminGalaxy ):
@web.require_admin
def reset_metadata_on_selected_installed_repositories( self, trans, **kwd ):
if 'reset_metadata_on_selected_repositories_button' in kwd:
kwd[ 'CONTROLLER' ] = suc.GALAXY_ADMIN_TOOL_SHED_CONTROLLER
message, status = suc.reset_metadata_on_selected_repositories( trans, **kwd )
else:
message = util.restore_text( kwd.get( 'message', '' ) )
status = kwd.get( 'status', 'done' )
repositories_select_field = suc.build_repository_ids_select_field( trans, suc.GALAXY_ADMIN_TOOL_SHED_CONTROLLER )
repositories_select_field = suc.build_repository_ids_select_field( trans )
return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako',
repositories_select_field=repositories_select_field,
message=message,