def get_ordered_installable_revisions(self, trans, name, owner, **kwd):
"""
GET /api/repositories/get_ordered_installable_revisions
:param name: the name of the Repository
:param owner: the owner of the Repository
Returns the ordered list of changeset revision hash strings that are associated with installable revisions.
As in the changelog, the list is ordered oldest to newest.
"""
# Example URL: http://localhost:9009/api/repositories/get_installable_revisions?name=add_column&owner=test
if name and owner:
# Get the repository information.
repository = suc.get_repository_by_name_and_owner(
trans.app, name, owner)
if repository is None:
error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
error_message += "cannot locate repository %s owned by %s." % (
str(name), str(owner))
log.debug(error_message)
return []
repo = hg_util.get_repo_for_repository(trans.app,
repository=repository,
repo_path=None,
create=False)
ordered_installable_revisions = suc.get_ordered_metadata_changeset_revisions(
repository, repo, downloadable=True)
return ordered_installable_revisions
else:
error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
error_message += "invalid name %s or owner %s received." % (
str(name), str(owner))
log.debug(error_message)
return []
def check_status_and_reset_downloadable( trans, import_results_tups ):
"""Check the status of each imported repository and set downloadable to False if errors."""
flush = False
for import_results_tup in import_results_tups:
ok, name_owner, message = import_results_tup
name, owner = name_owner
if not ok:
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
# Do not allow the repository to be automatically installed if population resulted in errors.
tip_changeset_revision = repository.tip( trans.app )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
trans.security.encode_id( repository.id ),
tip_changeset_revision )
if repository_metadata:
if repository_metadata.downloadable:
repository_metadata.downloadable = False
trans.sa_session.add( repository_metadata )
if not flush:
flush = True
# Do not allow dependent repository revisions to be automatically installed if population
# resulted in errors.
dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( trans, repository_metadata )
for dependent_downloadable_revision in dependent_downloadable_revisions:
if dependent_downloadable_revision.downloadable:
dependent_downloadable_revision.downloadable = False
trans.sa_session.add( dependent_downloadable_revision )
if not flush:
flush = True
if flush:
trans.sa_session.flush()
def handle_repository_dependency_elem(trans, elem):
# <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" />
error_message = ''
name = elem.get('name')
owner = elem.get('owner')
if not name or not owner:
error_message = handle_missing_repository_attribute(elem)
return False, elem, error_message
populated = False
toolshed = elem.get('toolshed')
if not toolshed:
# Default the setting to the current tool shed.
toolshed = str(url_for('/', qualified=True)).rstrip('/')
elem.attrib['toolshed'] = toolshed
populated = True
changeset_revision = elem.get('changeset_revision')
if not changeset_revision:
# 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(
trans.app, name, owner)
if repository:
repo_dir = repository.repo_path(trans.app)
repo = hg.repository(suc.get_configured_ui(), repo_dir)
lastest_installable_changeset_revision = suc.get_latest_downloadable_changeset_revision(
trans, repository, repo)
if lastest_installable_changeset_revision != suc.INITIAL_CHANGELOG_HASH:
elem.attrib[
'changeset_revision'] = lastest_installable_changeset_revision
populated = True
else:
error_message = 'Unable to locate repository with name %s and owner %s. ' % (
str(name), str(owner))
return populated, elem, error_message
def get_repository_dependency_tups_from_repository_metadata( app, repository_metadata, deprecated_only=False ):
"""
Return a list of of tuples defining repository objects required by the received repository. The returned
list defines the entire repository dependency tree. This method is called only from the Tool Shed.
"""
dependency_tups = []
if repository_metadata is not None:
metadata = repository_metadata.metadata
if metadata:
repository_dependencies_dict = metadata.get( 'repository_dependencies', None )
if repository_dependencies_dict is not None:
repository_dependency_tups = repository_dependencies_dict.get( 'repository_dependencies', None )
if repository_dependency_tups is not None:
# The value of repository_dependency_tups is a list of repository dependency tuples like this:
# ['http://localhost:9009', 'package_samtools_0_1_18', 'devteam', 'ef37fc635cb9', 'False', 'False']
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 )
if repository:
if deprecated_only:
if repository.deprecated:
dependency_tups.append( repository_dependency_tup )
else:
dependency_tups.append( repository_dependency_tup )
else:
log.debug( "Cannot locate repository %s owned by %s for inclusion in repository dependency tups." % \
( name, owner ) )
return dependency_tups
def handle_key_rd_dicts_for_repository( self, current_repository_key, repository_key_rd_dicts ):
key_rd_dict = repository_key_rd_dicts.pop( 0 )
repository_dependency = key_rd_dict[ current_repository_key ]
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 )
self.repository = required_repository
repository_id = self.app.security.encode_id( required_repository.id )
required_repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
repository_id,
changeset_revision )
self.repository_metadata = required_repository_metadata
if required_repository_metadata:
# The required_repository_metadata changeset_revision is installable.
required_metadata = required_repository_metadata.metadata
if required_metadata:
for current_repository_key_rd_dict in repository_key_rd_dicts:
if not self.in_key_rd_dicts( current_repository_key_rd_dict, self.key_rd_dicts_to_be_processed ):
# Add the current repository_dependency into self.key_rd_dicts_to_be_processed.
self.key_rd_dicts_to_be_processed.append( current_repository_key_rd_dict )
if not self.in_key_rd_dicts( key_rd_dict, self.handled_key_rd_dicts ):
# Add the current repository_dependency into self.handled_key_rd_dicts.
self.handled_key_rd_dicts.append( key_rd_dict )
if self.in_key_rd_dicts( key_rd_dict, self.key_rd_dicts_to_be_processed ):
# Remove the current repository from self.key_rd_dicts_to_be_processed.
self.key_rd_dicts_to_be_processed = self.remove_from_key_rd_dicts( key_rd_dict, self.key_rd_dicts_to_be_processed )
else:
# The repository is in a different tool shed, so build an url and send a request.
error_message = "Repository dependencies are currently supported only within the same Tool Shed. "
error_message += "Ignoring repository dependency definition for tool shed "
error_message += "%s, name %s, owner %s, changeset revision %s" % ( toolshed, name, owner, changeset_revision )
log.debug( error_message )
def handle_request( self, trans, **kwd ):
# The os command that results in this method being called will look something like:
# hg clone http://[email protected]:9009/repos/test/convert_characters1
hg_version = mercurial.__version__.version
cmd = kwd.get( 'cmd', None )
hgweb_config = trans.app.hgweb_config_manager.hgweb_config
def make_web_app():
hgwebapp = hgwebdir( hgweb_config )
return hgwebapp
wsgi_app = wsgiapplication( make_web_app )
if hg_version >= '2.2.3' and cmd == 'pushkey':
# When doing an "hg push" from the command line, the following commands, in order, will be retrieved from environ, depending
# upon the mercurial version being used. In mercurial version 2.2.3, section 15.2. Command changes includes a new feature:
# pushkey: add hooks for pushkey/listkeys (see http://mercurial.selenic.com/wiki/WhatsNew#Mercurial_2.2.3_.282012-07-01.29).
# We require version 2.2.3 since the pushkey hook was added in that version.
# If mercurial version >= '2.2.3': capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey
path_info = kwd.get( 'path_info', None )
if path_info:
owner, name = path_info.split( '/' )
repository = get_repository_by_name_and_owner( trans.app, name, owner )
if repository:
if hg_version >= '2.2.3':
# Set metadata using the repository files on disk.
error_message, status = set_repository_metadata( trans, repository )
if status == 'ok' and error_message:
log.debug( "Successfully reset metadata on repository %s, but encountered problem: %s" % ( repository.name, error_message ) )
elif status != 'ok' and error_message:
log.debug( "Error resetting metadata on repository %s: %s" % ( repository.name, error_message ) )
return wsgi_app
def validate_repository_name(app, name, user):
"""
Validate whether the given name qualifies as a new TS repo name.
Repository names must be unique for each user, must be at least two characters
in length and must contain only lower-case letters, numbers, and the '_' character.
"""
if name in ['None', None, '']:
return 'Enter the required repository name.'
if name in ['repos']:
return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name
check_existing = suc.get_repository_by_name_and_owner(
app, name, user.username)
if check_existing is not None:
if check_existing.deleted:
return 'You own a deleted repository named <b>%s</b>, please choose a different name.' % escape(
name)
else:
return "You already own a repository named <b>%s</b>, please choose a different name." % escape(
name)
if len(name) < 2:
return "Repository names must be at least 2 characters in length."
if len(name) > 80:
return "Repository names cannot be more than 80 characters in length."
if not (VALID_REPOSITORYNAME_RE.match(name)):
return "Repository names must contain only lower-case letters, numbers and underscore."
return ''
def get_ordered_installable_revisions(self, trans, name, owner, **kwd):
"""
GET /api/repositories/get_ordered_installable_revisions
:param name: the name of the Repository
:param owner: the owner of the Repository
Returns the ordered list of changeset revision hash strings that are associated with installable revisions. As in the changelog, the
list is ordered oldest to newest.
"""
# Example URL: http://localhost:9009/api/repositories/get_installable_revisions?name=add_column&owner=test
try:
# Get the repository information.
repository = suc.get_repository_by_name_and_owner(
trans.app, name, owner)
encoded_repository_id = trans.security.encode_id(repository.id)
repo_dir = repository.repo_path(trans.app)
repo = hg.repository(suc.get_configured_ui(), repo_dir)
ordered_installable_revisions = suc.get_ordered_metadata_changeset_revisions(
repository, repo, downloadable=True)
return ordered_installable_revisions
except Exception, e:
message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: %s" % str(
e)
log.error(message, exc_info=True)
trans.response.status = 500
return message
def get_repository_status_from_tool_shed( trans, repository_info_dicts ):
"""
For each exported repository archive contained in the capsule, inspect the Tool Shed to see if that repository already
exists or if the current user is authorized to create the repository, and set a status appropriately. If repository
dependencies are included in the capsule, repositories may have various owners. We will keep repositories associated
with owners, so we need to restrict created repositories to those the current user can create. If the current user is
an admin or a member of the IUC, all repositories will be created no matter the owner. Otherwise, only repositories
whose associated owner is the current user will be created.
"""
repository_status_info_dicts = []
for repository_info_dict in repository_info_dicts:
repository = suc.get_repository_by_name_and_owner( trans.app, repository_info_dict[ 'name' ], repository_info_dict[ 'owner' ] )
if repository:
if repository.deleted:
repository_info_dict[ 'status' ] = 'Exists, deleted'
elif repository.deprecated:
repository_info_dict[ 'status' ] = 'Exists, deprecated'
else:
repository_info_dict[ 'status' ] = 'Exists'
else:
# No repository with the specified name and owner currently exists, so make sure the current user can create one.
if trans.user_is_admin():
repository_info_dict[ 'status' ] = None
elif trans.app.security_agent.user_can_import_repository_archive( trans.user, repository_info_dict[ 'owner' ] ):
repository_info_dict[ 'status' ] = None
else:
repository_info_dict[ 'status' ] = 'Not authorized to import'
repository_status_info_dicts.append( repository_info_dict )
return repository_status_info_dicts
def handle_key_rd_dicts_for_repository( self, current_repository_key, repository_key_rd_dicts ):
key_rd_dict = repository_key_rd_dicts.pop( 0 )
repository_dependency = key_rd_dict[ current_repository_key ]
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 )
self.repository = required_repository
repository_id = self.app.security.encode_id( required_repository.id )
required_repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
repository_id,
changeset_revision )
self.repository_metadata = required_repository_metadata
if required_repository_metadata:
# The required_repository_metadata changeset_revision is installable.
required_metadata = required_repository_metadata.metadata
if required_metadata:
for current_repository_key_rd_dict in repository_key_rd_dicts:
if not self.in_key_rd_dicts( current_repository_key_rd_dict, self.key_rd_dicts_to_be_processed ):
# Add the current repository_dependency into self.key_rd_dicts_to_be_processed.
self.key_rd_dicts_to_be_processed.append( current_repository_key_rd_dict )
if not self.in_key_rd_dicts( key_rd_dict, self.handled_key_rd_dicts ):
# Add the current repository_dependency into self.handled_key_rd_dicts.
self.handled_key_rd_dicts.append( key_rd_dict )
if self.in_key_rd_dicts( key_rd_dict, self.key_rd_dicts_to_be_processed ):
# Remove the current repository from self.key_rd_dicts_to_be_processed.
self.key_rd_dicts_to_be_processed = self.remove_from_key_rd_dicts( key_rd_dict, self.key_rd_dicts_to_be_processed )
else:
# The repository is in a different tool shed, so build an url and send a request.
error_message = "Repository dependencies are currently supported only within the same Tool Shed. "
error_message += "Ignoring repository dependency definition for tool shed "
error_message += "%s, name %s, owner %s, changeset revision %s" % ( toolshed, name, owner, changeset_revision )
log.debug( error_message )
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 )
metadata_entry = suc.get_repository_metadata_by_changeset_revision( app, app.security.encode_id( required_repository.id ), changeset )
dependencies.append( metadata_entry )
return dependencies
def get_ordered_installable_revisions( self, trans, name, owner, **kwd ):
"""
GET /api/repositories/get_ordered_installable_revisions
:param name: the name of the Repository
:param owner: the owner of the Repository
Returns the ordered list of changeset revision hash strings that are associated with installable revisions.
As in the changelog, the list is ordered oldest to newest.
"""
# Example URL: http://localhost:9009/api/repositories/get_installable_revisions?name=add_column&owner=test
if name and owner:
# Get the repository information.
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
if repository is None:
error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
error_message += "cannot locate repository %s owned by %s." % ( str( name ), str( owner ) )
log.debug( error_message )
return []
repo = hg_util.get_repo_for_repository( trans.app, repository=repository, repo_path=None, create=False )
ordered_installable_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True )
return ordered_installable_revisions
else:
error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
error_message += "invalid name %s or owner %s received." % ( str( name ), str( owner ) )
log.debug( error_message )
return []
def validate_repository_name(app, name, user):
"""
Validate whether the given name qualifies as a new TS repo name.
Repository names must be unique for each user, must be at least two characters
in length and must contain only lower-case letters, numbers, and the '_' character.
"""
if name in ["None", None, ""]:
return "Enter the required repository name."
if name in ["repos"]:
return (
"The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name
)
check_existing = suc.get_repository_by_name_and_owner(app, name, user.username)
if check_existing is not None:
if check_existing.deleted:
return "You own a deleted repository named <b>%s</b>, please choose a different name." % escape(name)
else:
return "You already own a repository named <b>%s</b>, please choose a different name." % escape(name)
if len(name) < 2:
return "Repository names must be at least 2 characters in length."
if len(name) > 80:
return "Repository names cannot be more than 80 characters in length."
if not (VALID_REPOSITORYNAME_RE.match(name)):
return "Repository names must contain only lower-case letters, numbers and underscore."
return ""
def handle_request(self, trans, **kwd):
# The os command that results in this method being called will look something like:
# hg clone http://[email protected]:9009/repos/test/convert_characters1
hg_version = mercurial.__version__.version
cmd = kwd.get('cmd', None)
hgweb_config = trans.app.hgweb_config_manager.hgweb_config
def make_web_app():
hgwebapp = hgwebdir(hgweb_config)
return hgwebapp
wsgi_app = wsgiapplication(make_web_app)
if hg_version >= '2.2.3' and cmd == 'pushkey':
# When doing an "hg push" from the command line, the following commands, in order, will be
# retrieved from environ, depending upon the mercurial version being used. In mercurial
# version 2.2.3, section 15.2. Command changes includes a new feature:
# pushkey: add hooks for pushkey/listkeys
# (see http://mercurial.selenic.com/wiki/WhatsNew#Mercurial_2.2.3_.282012-07-01.29).
# We require version 2.2.3 since the pushkey hook was added in that version.
# If mercurial version >= '2.2.3': capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey
path_info = kwd.get('path_info', None)
if path_info:
owner, name = path_info.split('/')
repository = get_repository_by_name_and_owner(
trans.app, name, owner)
if repository:
if hg_version >= '2.2.3':
# Update the repository on disk to the tip revision, because the web upload
# form uses the on-disk working directory. If the repository is not updated
# on disk, pushing from the command line and then uploading via the web
# interface will result in a new head being created.
repo = hg.repository(ui.ui(),
repository.repo_path(trans.app))
update_repository(repo, ctx_rev=None)
repository_clone_url = generate_clone_url_for_repository_in_tool_shed(
trans.user, repository)
# Set metadata using the repository files on disk.
rmm = repository_metadata_manager.RepositoryMetadataManager(
app=trans.app,
user=trans.user,
repository=repository,
changeset_revision=repository.tip(trans.app),
repository_clone_url=repository_clone_url,
relative_install_dir=repository.repo_path(
trans.app),
repository_files_dir=None,
resetting_all_metadata_on_repository=False,
updating_installed_repository=False,
persist=False)
error_message, status = rmm.set_repository_metadata(
trans.request.host)
if status == 'ok' and error_message:
log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \
( str( repository.name ), str( repository.user.username ), error_message ) )
elif status != 'ok' and error_message:
log.debug( "Error resetting metadata on repository %s owned by %s: %s" % \
( str( repository.name ), str( repository.user.username ), error_message ) )
return wsgi_app
def get_repository_ids( trans, repo_info_dicts ):
repository_ids = []
for repo_info_dict in repo_info_dicts:
for repository_name, repo_info_tup in repo_info_dict.items():
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( trans.app, repository_name, repository_owner )
repository_ids.append( trans.security.encode_id( repository.id ) )
return repository_ids
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)
metadata_entry = suc.get_repository_metadata_by_changeset_revision(
app, app.security.encode_id(required_repository.id), changeset)
dependencies.append(metadata_entry)
return dependencies
def get_repository_ids(trans, repo_info_dicts):
"""Return a list of repository ids associated with each dictionary in the received repo_info_dicts."""
repository_ids = []
for repo_info_dict in repo_info_dicts:
for repository_name, repo_info_tup in repo_info_dict.items():
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(trans.app, repository_name, repository_owner)
repository_ids.append(trans.security.encode_id(repository.id))
return repository_ids
def export(self, trans, payload, **kwd):
"""
POST /api/repository_revisions/export
Creates and saves a gzip compressed tar archive of a repository and optionally all of its repository dependencies.
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed from which the Repository is to be exported
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
:param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository
:param export_repository_dependencies (optional): whether to export repository dependencies - defaults to False
:param download_dir (optional): the local directory to which to download the archive - defaults to /tmp
"""
tool_shed_url = payload.get('tool_shed_url', '')
if not tool_shed_url:
raise HTTPBadRequest(
detail="Missing required parameter 'tool_shed_url'.")
tool_shed_url = tool_shed_url.rstrip('/')
name = payload.get('name', '')
if not name:
raise HTTPBadRequest(detail="Missing required parameter 'name'.")
owner = payload.get('owner', '')
if not owner:
raise HTTPBadRequest(detail="Missing required parameter 'owner'.")
changeset_revision = payload.get('changeset_revision', '')
if not changeset_revision:
raise HTTPBadRequest(
detail="Missing required parameter 'changeset_revision'.")
export_repository_dependencies = payload.get(
'export_repository_dependencies', False)
# We'll currently support only gzip-compressed tar archives.
file_type = 'gz'
export_repository_dependencies = util.asbool(
export_repository_dependencies)
# Get the repository information.
repository = suc.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)
return None, error_message
repository_id = trans.security.encode_id(repository.id)
erm = capsule_manager.ExportRepositoryManager(
app=trans.app,
user=trans.user,
tool_shed_url=tool_shed_url,
repository=repository,
changeset_revision=changeset_revision,
export_repository_dependencies=export_repository_dependencies,
using_api=True)
return erm.export_repository()
def handle_request( self, trans, **kwd ):
# The os command that results in this method being called will look something like:
# hg clone http://[email protected]:9009/repos/test/convert_characters1
hg_version = mercurial.__version__.version
cmd = kwd.get( 'cmd', None )
hgweb_config = trans.app.hgweb_config_manager.hgweb_config
def make_web_app():
hgwebapp = hgwebdir( hgweb_config )
return hgwebapp
wsgi_app = wsgiapplication( make_web_app )
if hg_version >= '2.2.3' and cmd == 'pushkey':
# When doing an "hg push" from the command line, the following commands, in order, will be
# retrieved from environ, depending upon the mercurial version being used. In mercurial
# version 2.2.3, section 15.2. Command changes includes a new feature:
# pushkey: add hooks for pushkey/listkeys
# (see http://mercurial.selenic.com/wiki/WhatsNew#Mercurial_2.2.3_.282012-07-01.29).
# We require version 2.2.3 since the pushkey hook was added in that version.
# If mercurial version >= '2.2.3': capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey
path_info = kwd.get( 'path_info', None )
if path_info:
owner, name = path_info.split( '/' )
repository = get_repository_by_name_and_owner( trans.app, name, owner )
if repository:
if hg_version >= '2.2.3':
# Update the repository on disk to the tip revision, because the web upload
# form uses the on-disk working directory. If the repository is not updated
# on disk, pushing from the command line and then uploading via the web
# interface will result in a new head being created.
repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) )
update_repository( repo, ctx_rev=None )
repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans.user, repository )
# Set metadata using the repository files on disk.
rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app,
user=trans.user,
repository=repository,
changeset_revision=repository.tip( trans.app ),
repository_clone_url=repository_clone_url,
relative_install_dir=repository.repo_path( trans.app ),
repository_files_dir=None,
resetting_all_metadata_on_repository=False,
updating_installed_repository=False,
persist=False )
error_message, status = rmm.set_repository_metadata( trans.request.host )
if status == 'ok' and error_message:
log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" %
( str( repository.name ), str( repository.user.username ), error_message ) )
elif status != 'ok' and error_message:
log.debug( "Error resetting metadata on repository %s owned by %s: %s" %
( str( repository.name ), str( repository.user.username ), error_message ) )
return wsgi_app
def get_components_from_repo_info_dict( trans, repo_info_dict ):
"""
Return the repository and the associated latest installable changeset_revision (including updates) for the repository defined by the received
repo_info_dict.
"""
for repository_name, repo_info_tup in repo_info_dict.items():
# 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( trans.app, repository_name, repository_owner )
repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( trans, repository, changeset_revision )
if repository_metadata:
return repository, repository_metadata.changeset_revision
return None, None
def export( self, trans, payload, **kwd ):
"""
POST /api/repository_revisions/export
Creates and saves a gzip compressed tar archive of a repository and optionally all of it's repository dependencies.
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed from which the Repository was installed
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
:param changset_revision (required): the changset_revision of the RepositoryMetadata object associated with the Repository
:param export_repository_dependencies (optional): whether to export repository dependencies - defaults to False
:param download_dir (optional): the local directory to which to download the archive - defaults to /tmp
"""
tool_shed_url = payload.get( 'tool_shed_url', '' )
if not tool_shed_url:
raise HTTPBadRequest( detail="Missing required parameter 'tool_shed_url'." )
tool_shed_url = tool_shed_url.rstrip( '/' )
name = payload.get( 'name', '' )
if not name:
raise HTTPBadRequest( detail="Missing required parameter 'name'." )
owner = payload.get( 'owner', '' )
if not owner:
raise HTTPBadRequest( detail="Missing required parameter 'owner'." )
changeset_revision = payload.get( 'changeset_revision', '' )
if not changeset_revision:
raise HTTPBadRequest( detail="Missing required parameter 'changeset_revision'." )
export_repository_dependencies = payload.get( 'export_repository_dependencies', False )
try:
# We'll currently support only gzip-compressed tar archives.
file_type = 'gz'
export_repository_dependencies = util.string_as_bool( export_repository_dependencies )
# Get the repository information.
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository_id = trans.security.encode_id( repository.id )
response = export_util.export_repository( trans,
tool_shed_url,
repository_id,
str( repository.name ),
changeset_revision,
file_type,
export_repository_dependencies,
api=True )
return response
except Exception, e:
message = "Error in the Tool Shed repository_revisions API in export: %s" % str( e )
log.error( message, exc_info=True )
trans.response.status = 500
return message
def handle_repository_dependency_elem( trans, elem, unpopulate=False ):
# <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" />
error_message = ''
name = elem.get( 'name' )
owner = elem.get( 'owner' )
# The name and owner attributes are always required, so if either are missing, return the error message.
if not name or not owner:
error_message = handle_missing_repository_attribute( elem )
return False, elem, error_message
revised = False
toolshed = elem.get( 'toolshed' )
changeset_revision = elem.get( 'changeset_revision' )
if unpopulate:
# We're exporting the repository, so eliminate all toolshed and changeset_revision attributes from the <repository> tag.
if toolshed or changeset_revision:
attributes = odict()
attributes[ 'name' ] = name
attributes[ 'owner' ] = owner
attributes[ 'prior_installation_required' ] = elem.get( 'prior_installation_required', 'False' )
elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=None )
revised = True
return revised, elem, error_message
# From here on we're populating the toolshed and changeset_revisions if necessary.
if not toolshed:
# Default the setting to the current tool shed.
toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' )
elem.attrib[ 'toolshed' ] = toolshed
revised = True
if not changeset_revision:
# 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( trans.app, name, owner )
if repository:
repo_dir = repository.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
lastest_installable_changeset_revision = suc.get_latest_downloadable_changeset_revision( trans, repository, repo )
if lastest_installable_changeset_revision != suc.INITIAL_CHANGELOG_HASH:
elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision
revised = True
else:
error_message = 'Invalid latest installable changeset_revision %s ' % str( lastest_installable_changeset_revision )
error_message += 'retrieved for repository %s owned by %s. ' % ( str( name ), str( owner ) )
else:
error_message = 'Unable to locate repository with name %s and owner %s. ' % ( str( name ), str( owner ) )
return revised, elem, error_message
def export( self, trans, payload, **kwd ):
"""
POST /api/repository_revisions/export
Creates and saves a gzip compressed tar archive of a repository and optionally all of its repository dependencies.
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed from which the Repository is to be exported
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
:param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository
:param export_repository_dependencies (optional): whether to export repository dependencies - defaults to False
:param download_dir (optional): the local directory to which to download the archive - defaults to /tmp
"""
tool_shed_url = payload.get( 'tool_shed_url', '' )
if not tool_shed_url:
raise HTTPBadRequest( detail="Missing required parameter 'tool_shed_url'." )
tool_shed_url = tool_shed_url.rstrip( '/' )
name = payload.get( 'name', '' )
if not name:
raise HTTPBadRequest( detail="Missing required parameter 'name'." )
owner = payload.get( 'owner', '' )
if not owner:
raise HTTPBadRequest( detail="Missing required parameter 'owner'." )
changeset_revision = payload.get( 'changeset_revision', '' )
if not changeset_revision:
raise HTTPBadRequest( detail="Missing required parameter 'changeset_revision'." )
export_repository_dependencies = payload.get( 'export_repository_dependencies', False )
# We'll currently support only gzip-compressed tar archives.
file_type = 'gz'
export_repository_dependencies = util.asbool( export_repository_dependencies )
# Get the repository information.
repository = suc.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 )
return None, error_message
repository_id = trans.security.encode_id( repository.id )
erm = capsule_manager.ExportRepositoryManager( app=trans.app,
user=trans.user,
tool_shed_url=tool_shed_url,
repository=repository,
changeset_revision=changeset_revision,
export_repository_dependencies=export_repository_dependencies,
using_api=True )
return erm.export_repository()
def add_repository_registry_entry(self, trans, payload, **kwd):
"""
POST /api/repositories/add_repository_registry_entry
Adds appropriate entries to the repository registry for the repository defined by the received name and owner.
:param key: the user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed containing the Repository
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
"""
response_dict = {}
if not trans.user_is_admin():
response_dict['status'] = 'error'
response_dict[
'message'] = "You are not authorized to add entries to this Tool Shed's repository registry."
return response_dict
tool_shed_url = payload.get('tool_shed_url', '')
if not tool_shed_url:
raise HTTPBadRequest(
detail="Missing required parameter 'tool_shed_url'.")
tool_shed_url = tool_shed_url.rstrip('/')
name = payload.get('name', '')
if not name:
raise HTTPBadRequest(detail="Missing required parameter 'name'.")
owner = payload.get('owner', '')
if not owner:
raise HTTPBadRequest(detail="Missing required parameter 'owner'.")
repository = suc.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)
response_dict['status'] = 'error'
response_dict['message'] = error_message
return response_dict
# Update the repository registry.
trans.app.repository_registry.add_entry(repository)
response_dict['status'] = 'ok'
response_dict[ 'message' ] = 'Entries for repository %s owned by %s have been added to the Tool Shed repository registry.' \
% ( name, owner )
return response_dict
def remove_repository_registry_entry(self, trans, payload, **kwd):
"""
POST /api/repositories/remove_repository_registry_entry
Removes appropriate entries from the repository registry for the repository defined by the received name and owner.
:param key: the user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed containing the Repository
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
"""
response_dict = {}
if not trans.user_is_admin():
response_dict["status"] = "error"
response_dict[
"message"
] = "You are not authorized to remove entries from this Tool Shed's repository registry."
return response_dict
tool_shed_url = payload.get("tool_shed_url", "")
if not tool_shed_url:
raise HTTPBadRequest(detail="Missing required parameter 'tool_shed_url'.")
tool_shed_url = tool_shed_url.rstrip("/")
name = payload.get("name", "")
if not name:
raise HTTPBadRequest(detail="Missing required parameter 'name'.")
owner = payload.get("owner", "")
if not owner:
raise HTTPBadRequest(detail="Missing required parameter 'owner'.")
repository = suc.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)
response_dict["status"] = "error"
response_dict["message"] = error_message
return response_dict
# Update the repository registry.
trans.app.repository_registry.remove_entry(repository)
response_dict["status"] = "ok"
response_dict["message"] = (
"Entries for repository %s owned by %s have been removed from the Tool Shed repository registry."
% (name, owner)
)
return response_dict
def validate_repository_name( app, name, user ):
# Repository names must be unique for each user, must be at least four characters
# in length and must contain only lower-case letters, numbers, and the '_' character.
if name in [ 'None', None, '' ]:
return 'Enter the required repository name.'
if name in [ 'repos' ]:
return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name
check_existing = suc.get_repository_by_name_and_owner( app, name, user.username )
if check_existing is not None:
if check_existing.deleted:
return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name
else:
return "You already have a repository named <b>%s</b>, so choose a different name." % name
if len( name ) < 4:
return "Repository names must be at least 4 characters in length."
if len( name ) > 80:
return "Repository names cannot be more than 80 characters in length."
if not( VALID_REPOSITORYNAME_RE.match( name ) ):
return "Repository names must contain only lower-case letters, numbers and underscore <b>_</b>."
return ''
def validate_repository_name( app, name, user ):
# Repository names must be unique for each user, must be at least four characters
# in length and must contain only lower-case letters, numbers, and the '_' character.
if name in [ 'None', None, '' ]:
return 'Enter the required repository name.'
if name in [ 'repos' ]:
return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name
check_existing = suc.get_repository_by_name_and_owner( app, name, user.username )
if check_existing is not None:
if check_existing.deleted:
return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name
else:
return "You already have a repository named <b>%s</b>, so choose a different name." % name
if len( name ) < 4:
return "Repository names must be at least 4 characters in length."
if len( name ) > 80:
return "Repository names cannot be more than 80 characters in length."
if not( VALID_REPOSITORYNAME_RE.match( name ) ):
return "Repository names must contain only lower-case letters, numbers and underscore <b>_</b>."
return ''
def add_repository_registry_entry( self, trans, payload, **kwd ):
"""
POST /api/repositories/add_repository_registry_entry
Adds appropriate entries to the repository registry for the repository defined by the received name and owner.
:param key: the user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed containing the Repository
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
"""
response_dict = {}
if not trans.user_is_admin():
response_dict[ 'status' ] = 'error'
response_dict[ 'message' ] = "You are not authorized to add entries to this Tool Shed's repository registry."
return response_dict
tool_shed_url = payload.get( 'tool_shed_url', '' )
if not tool_shed_url:
raise HTTPBadRequest( detail="Missing required parameter 'tool_shed_url'." )
tool_shed_url = tool_shed_url.rstrip( '/' )
name = payload.get( 'name', '' )
if not name:
raise HTTPBadRequest( detail="Missing required parameter 'name'." )
owner = payload.get( 'owner', '' )
if not owner:
raise HTTPBadRequest( detail="Missing required parameter 'owner'." )
repository = suc.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 )
response_dict[ 'status' ] = 'error'
response_dict[ 'message' ] = error_message
return response_dict
# Update the repository registry.
trans.app.repository_registry.add_entry( repository )
response_dict[ 'status' ] = 'ok'
response_dict[ 'message' ] = 'Entries for repository %s owned by %s have been added to the Tool Shed repository registry.' \
% ( name, owner )
return response_dict
def get_ordered_installable_revisions( self, trans, name, owner, **kwd ):
"""
GET /api/repositories/get_ordered_installable_revisions
:param name: the name of the Repository
:param owner: the owner of the Repository
Returns the ordered list of changeset revision hash strings that are associated with installable revisions. As in the changelog, the
list is ordered oldest to newest.
"""
# Example URL: http://localhost:9009/api/repositories/get_installable_revisions?name=add_column&owner=test
try:
# Get the repository information.
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repo_dir = repository.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
ordered_installable_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True )
return ordered_installable_revisions
except Exception, e:
message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: %s" % str( e )
log.error( message, exc_info=True )
trans.response.status = 500
return message
def handle_request(self, trans, **kwd):
# The os command that results in this method being called will look something like:
# hg clone http://[email protected]:9009/repos/test/convert_characters1
hg_version = mercurial.__version__.version
cmd = kwd.get('cmd', None)
hgweb_config = trans.app.hgweb_config_manager.hgweb_config
def make_web_app():
hgwebapp = hgwebdir(hgweb_config)
return hgwebapp
wsgi_app = wsgiapplication(make_web_app)
if hg_version >= '2.2.3' and cmd == 'pushkey':
# When doing an "hg push" from the command line, the following commands, in order, will be retrieved from environ, depending
# upon the mercurial version being used. In mercurial version 2.2.3, section 15.2. Command changes includes a new feature:
# pushkey: add hooks for pushkey/listkeys (see http://mercurial.selenic.com/wiki/WhatsNew#Mercurial_2.2.3_.282012-07-01.29).
# We require version 2.2.3 since the pushkey hook was added in that version.
# If mercurial version >= '2.2.3': capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey
path_info = kwd.get('path_info', None)
if path_info:
owner, name = path_info.split('/')
repository = get_repository_by_name_and_owner(
trans.app, name, owner)
if repository:
if hg_version >= '2.2.3':
# Set metadata using the repository files on disk.
error_message, status = set_repository_metadata(
trans, repository)
if status == 'ok' and error_message:
log.debug(
"Successfully reset metadata on repository %s, but encountered problem: %s"
% (repository.name, error_message))
elif status != 'ok' and error_message:
log.debug(
"Error resetting metadata on repository %s: %s"
% (repository.name, error_message))
return wsgi_app
def get_updated_changeset_revisions_for_repository_dependencies(
self, key_rd_dicts):
updated_key_rd_dicts = []
for key_rd_dict in key_rd_dicts:
key = key_rd_dict.keys()[0]
repository_dependency = key_rd_dict[key]
rd_toolshed, \
rd_name, \
rd_owner, \
rd_changeset_revision, \
rd_prior_installation_required, \
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)
if repository:
repository_id = self.app.security.encode_id(repository.id)
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
repository_id,
rd_changeset_revision )
if repository_metadata:
# The repository changeset_revision is installable, so no updates are available.
new_key_rd_dict = {}
new_key_rd_dict[key] = repository_dependency
updated_key_rd_dicts.append(key_rd_dict)
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)
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
repository_id,
changeset_revision )
if repository_metadata:
new_key_rd_dict = {}
new_key_rd_dict[ key ] = \
[ rd_toolshed, \
rd_name, \
rd_owner, \
repository_metadata.changeset_revision, \
rd_prior_installation_required, \
rd_only_if_compiling_contained_td ]
# We have the updated changset revision.
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)
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) == 4:
prior_installation_required = 'False'
rd_only_if_compiling_contained_td = 'False'
elif len(components_list) == 5:
rd_only_if_compiling_contained_td = 'False'
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 ) )
message += "dependencies defined for repository %s will be ignored." % str(
repository_name)
log.debug(message)
else:
repository_components_tuple = container_util.get_components_from_key(
key)
components_list = suc.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 ) )
message += "dependencies defined for repository %s will be ignored." % str(
repository_name)
log.debug(message)
return updated_key_rd_dicts
def get_updated_changeset_revisions_for_repository_dependencies( self, key_rd_dicts ):
updated_key_rd_dicts = []
for key_rd_dict in key_rd_dicts:
key = key_rd_dict.keys()[ 0 ]
repository_dependency = key_rd_dict[ key ]
rd_toolshed, rd_name, rd_owner, rd_changeset_revision, \
rd_prior_installation_required, \
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 )
if repository:
repository_id = self.app.security.encode_id( repository.id )
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
repository_id,
rd_changeset_revision )
if repository_metadata:
# The repository changeset_revision is installable, so no updates are available.
new_key_rd_dict = {}
new_key_rd_dict[ key ] = repository_dependency
updated_key_rd_dicts.append( key_rd_dict )
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 )
repository_metadata = \
metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
repository_id,
changeset_revision )
if repository_metadata:
new_key_rd_dict = {}
new_key_rd_dict[ key ] = \
[ rd_toolshed,
rd_name,
rd_owner,
repository_metadata.changeset_revision,
rd_prior_installation_required,
rd_only_if_compiling_contained_td ]
# We have the updated changeset revision.
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 )
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):
rd_only_if_compiling_contained_td = 'False'
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 ) )
message += "dependencies defined for repository %s will be ignored." % str( repository_name )
log.debug( message )
else:
repository_components_tuple = container_util.get_components_from_key( key )
components_list = suc.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 ) )
message += "dependencies defined for repository %s will be ignored." % str( repository_name )
log.debug( message )
return updated_key_rd_dicts
def handle_elem(self, elem):
"""Populate or unpopulate the changeset_revision and toolshed attributes of repository tags."""
# <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" />
# <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy">
# <package name="xorg_macros" version="1.17.1" />
# </repository>
error_message = ''
name = elem.get('name')
owner = elem.get('owner')
# The name and owner attributes are always required, so if either are missing, return the error message.
if not name or not owner:
error_message = self.check_tag_attributes(elem)
return False, elem, error_message
altered = False
toolshed = elem.get('toolshed')
changeset_revision = elem.get('changeset_revision')
# Over a short period of time a bug existed which caused the prior_installation_required attribute
# to be set to False and included in the <repository> tag when a repository was exported along with
# its dependencies. The following will eliminate this problematic attribute upon import.
prior_installation_required = elem.get('prior_installation_required')
if prior_installation_required is not None and not asbool(
prior_installation_required):
del elem.attrib['prior_installation_required']
sub_elems = [child_elem for child_elem in list(elem)]
if len(sub_elems) > 0:
# At this point, a <repository> tag will point only to a package.
# <package name="xorg_macros" version="1.17.1" />
# Coerce the list to an odict().
sub_elements = odict()
packages = []
for sub_elem in sub_elems:
sub_elem_type = sub_elem.tag
sub_elem_name = sub_elem.get('name')
sub_elem_version = sub_elem.get('version')
if sub_elem_type and sub_elem_name and sub_elem_version:
packages.append((sub_elem_name, sub_elem_version))
sub_elements['packages'] = packages
else:
# Set to None.
sub_elements = None
if self.unpopulate:
# We're exporting the repository, so eliminate all toolshed and changeset_revision attributes
# from the <repository> tag.
if toolshed or changeset_revision:
attributes = odict()
attributes['name'] = name
attributes['owner'] = owner
prior_installation_required = elem.get(
'prior_installation_required')
if asbool(prior_installation_required):
attributes['prior_installation_required'] = 'True'
new_elem = xml_util.create_element('repository',
attributes=attributes,
sub_elements=sub_elements)
altered = True
return altered, new_elem, error_message
# From here on we're populating the toolshed and changeset_revision attributes if necessary.
if not toolshed:
# Default the setting to the current tool shed.
toolshed = str(url_for('/', qualified=True)).rstrip('/')
elem.attrib['toolshed'] = toolshed
altered = True
if not changeset_revision:
# 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)
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 )
if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
elem.attrib[
'changeset_revision'] = lastest_installable_changeset_revision
altered = True
else:
error_message = 'Invalid latest installable changeset_revision %s ' % \
str( lastest_installable_changeset_revision )
error_message += 'retrieved for repository %s owned by %s. ' % (
str(name), str(owner))
else:
error_message = 'Unable to locate repository with name %s and owner %s. ' % (
str(name), str(owner))
return altered, elem, error_message
def create_repo_info_dict(app,
repository_clone_url,
changeset_revision,
ctx_rev,
repository_owner,
repository_name=None,
repository=None,
repository_metadata=None,
tool_dependencies=None,
repository_dependencies=None):
"""
Return a dictionary that includes all of the information needed to install a repository into a local
Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined
for the repository, as well as the defined tool dependencies.
This method is called from Galaxy under four scenarios:
1. During the tool shed repository installation process via the tool shed's get_repository_information()
method. In this case both the received repository and repository_metadata will be objects, but
tool_dependencies and repository_dependencies will be None.
2. When getting updates for an installed repository where the updates include newly defined repository
dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information()
method is the caller, and both the received repository and repository_metadata will be objects, but
tool_dependencies and repository_dependencies will be None.
3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no
updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies
and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes
definitions for them.
4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates
available. In this case, this method is reached via the tool shed's get_updated_repository_information()
method, and both repository and repository_metadata will be objects but tool_dependencies and
repository_dependencies will be None.
"""
repo_info_dict = {}
repository = suc.get_repository_by_name_and_owner(app, repository_name,
repository_owner)
if app.name == 'tool_shed':
# We're in the tool shed.
repository_metadata = suc.get_repository_metadata_by_changeset_revision(
app, app.security.encode_id(repository.id), changeset_revision)
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
tool_shed_url = str(web.url_for('/',
qualified=True)).rstrip('/')
rb = relation_builder.RelationBuilder(app, repository,
repository_metadata,
tool_shed_url)
# Get a dictionary of all repositories upon which the contents of the received repository depends.
repository_dependencies = rb.get_repository_dependencies_for_changeset_revision(
)
tool_dependencies = metadata.get('tool_dependencies', {})
if tool_dependencies:
new_tool_dependencies = {}
for dependency_key, requirements_dict in tool_dependencies.items():
if dependency_key in ['set_environment']:
new_set_environment_dict_list = []
for set_environment_dict in requirements_dict:
set_environment_dict['repository_name'] = repository_name
set_environment_dict['repository_owner'] = repository_owner
set_environment_dict[
'changeset_revision'] = changeset_revision
new_set_environment_dict_list.append(set_environment_dict)
new_tool_dependencies[
dependency_key] = new_set_environment_dict_list
else:
requirements_dict['repository_name'] = repository_name
requirements_dict['repository_owner'] = repository_owner
requirements_dict['changeset_revision'] = changeset_revision
new_tool_dependencies[dependency_key] = requirements_dict
tool_dependencies = new_tool_dependencies
# Cast unicode to string, with the exception of description, since it is free text and can contain special characters.
repo_info_dict[str(
repository.name)] = (repository.description, str(repository_clone_url),
str(changeset_revision), str(ctx_rev),
str(repository_owner), repository_dependencies,
tool_dependencies)
return repo_info_dict
def get_repository_revision_install_info( self, trans, name, owner, changeset_revision, **kwd ):
"""
GET /api/repositories/get_repository_revision_install_info
:param name: the name of the Repository
:param owner: the owner of the Repository
:param changeset_revision: the changeset_revision of the RepositoryMetadata object associated with the Repository
Returns a list of the following dictionaries::
- a dictionary defining the Repository. For example:
{
"deleted": false,
"deprecated": false,
"description": "add_column hello",
"id": "f9cad7b01a472135",
"long_description": "add_column hello",
"name": "add_column",
"owner": "test",
"private": false,
"times_downloaded": 6,
"url": "/api/repositories/f9cad7b01a472135",
"user_id": "f9cad7b01a472135"
}
- a dictionary defining the Repository revision (RepositoryMetadata). For example:
{
"changeset_revision": "3a08cc21466f",
"downloadable": true,
"has_repository_dependencies": false,
"has_repository_dependencies_only_if_compiling_contained_td": false,
"id": "f9cad7b01a472135",
"includes_datatypes": false,
"includes_tool_dependencies": false,
"includes_tools": true,
"includes_tools_for_display_in_tool_panel": true,
"includes_workflows": false,
"malicious": false,
"repository_id": "f9cad7b01a472135",
"url": "/api/repository_revisions/f9cad7b01a472135"
}
- a dictionary including the additional information required to install the repository. For example:
{
"add_column": [
"add_column hello",
"http://test@localhost:9009/repos/test/add_column",
"3a08cc21466f",
"1",
"test",
{},
{}
]
}
"""
# Example URL:
# 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( trans.app, name, owner )
if repository is None:
log.debug( 'Cannot locate repository %s owned by %s' % ( str( name ), str( owner ) ) )
return {}, {}, {}
encoded_repository_id = trans.security.encode_id( repository.id )
repository_dict = repository.to_dict( view='element',
value_mapper=self.__get_value_mapper( trans ) )
repository_dict[ 'url' ] = web.url_for( controller='repositories',
action='show',
id=encoded_repository_id )
# Get the repository_metadata information.
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.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( trans.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( trans.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 )
repository_metadata_dict = repository_metadata.to_dict( view='collection',
value_mapper=self.__get_value_mapper( trans ) )
repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions',
action='show',
id=encoded_repository_metadata_id )
# Get the repo_info_dict for installing the repository.
repo_info_dict, \
includes_tools, \
includes_tool_dependencies, \
includes_tools_for_display_in_tool_panel, \
has_repository_dependencies, \
has_repository_dependencies_only_if_compiling_contained_td = \
repository_util.get_repo_info_dict( trans.app,
trans.user,
encoded_repository_id,
changeset_revision )
return repository_dict, repository_metadata_dict, repo_info_dict
else:
log.debug( "Unable to locate repository_metadata record for repository id %s and changeset_revision %s" % \
( str( repository.id ), str( changeset_revision ) ) )
return repository_dict, {}, {}
else:
debug_msg = "Error in the Tool Shed repositories API in get_repository_revision_install_info: "
debug_msg += "Invalid name %s or owner %s or changeset_revision %s received." % \
( str( name ), str( owner ), str( changeset_revision ) )
log.debug( debug_msg )
return {}, {}, {}
def get_repository_revision_install_info( self, trans, name, owner, changeset_revision, **kwd ):
"""
GET /api/repositories/get_repository_revision_install_info
:param name: the name of the Repository
:param owner: the owner of the Repository
:param changset_revision: the changset_revision of the RepositoryMetadata object associated with the Repository
Returns a list of the following dictionaries::
- a dictionary defining the Repository. For example:
{
"deleted": false,
"deprecated": false,
"description": "add_column hello",
"id": "f9cad7b01a472135",
"long_description": "add_column hello",
"name": "add_column",
"owner": "test",
"private": false,
"times_downloaded": 6,
"url": "/api/repositories/f9cad7b01a472135",
"user_id": "f9cad7b01a472135"
}
- a dictionary defining the Repository revision (RepositoryMetadata). For example:
{
"changeset_revision": "3a08cc21466f",
"downloadable": true,
"has_repository_dependencies": false,
"id": "f9cad7b01a472135",
"includes_datatypes": false,
"includes_tool_dependencies": false,
"includes_tools": true,
"includes_tools_for_display_in_tool_panel": true,
"includes_workflows": false,
"malicious": false,
"repository_id": "f9cad7b01a472135",
"url": "/api/repository_revisions/f9cad7b01a472135"
}
- a dictionary including the additional information required to install the repository. For example:
{
"add_column": [
"add_column hello",
"http://test@localhost:9009/repos/test/add_column",
"3a08cc21466f",
"1",
"test",
{},
{}
]
}
"""
# Example URL: http://localhost:9009/api/repositories/get_repository_revision_install_info?name=add_column&owner=test&changeset_revision=3a08cc21466f
try:
# Get the repository information.
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
encoded_repository_id = trans.security.encode_id( repository.id )
repository_dict = repository.get_api_value( view='element', value_mapper=default_repository_value_mapper( trans, repository ) )
repository_dict[ 'url' ] = web.url_for( controller='repositories',
action='show',
id=encoded_repository_id )
# Get the repository_metadata information.
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, changeset_revision )
if not repository_metadata:
# 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_dir = repository.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, new_changeset_revision )
changeset_revision = new_changeset_revision
if repository_metadata:
encoded_repository_metadata_id = trans.security.encode_id( repository_metadata.id )
repository_metadata_dict = repository_metadata.get_api_value( view='collection',
value_mapper=default_repository_metadata_value_mapper( trans, repository_metadata ) )
repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions',
action='show',
id=encoded_repository_metadata_id )
# Get the repo_info_dict for installing the repository.
repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, has_repository_dependencies = \
repository_util.get_repo_info_dict( trans, encoded_repository_id, changeset_revision )
return repository_dict, repository_metadata_dict, repo_info_dict
else:
message = "Unable to locate repository_metadata record for repository id %d and changeset_revision %s" % ( repository.id, changeset_revision )
log.error( message, exc_info=True )
trans.response.status = 500
return repository_dict, {}, {}
except Exception, e:
message = "Error in the Tool Shed repositories API in get_repository_revision_install_info: %s" % str( e )
log.error( message, exc_info=True )
trans.response.status = 500
return message
def create_repo_info_dict( app, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None,
repository=None, repository_metadata=None, tool_dependencies=None, repository_dependencies=None ):
"""
Return a dictionary that includes all of the information needed to install a repository into a local
Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined
for the repository, as well as the defined tool dependencies.
This method is called from Galaxy under four scenarios:
1. During the tool shed repository installation process via the tool shed's get_repository_information()
method. In this case both the received repository and repository_metadata will be objects, but
tool_dependencies and repository_dependencies will be None.
2. When getting updates for an installed repository where the updates include newly defined repository
dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information()
method is the caller, and both the received repository and repository_metadata will be objects, but
tool_dependencies and repository_dependencies will be None.
3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no
updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies
and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes
definitions for them.
4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates
available. In this case, this method is reached via the tool shed's get_updated_repository_information()
method, and both repository and repository_metadata will be objects but tool_dependencies and
repository_dependencies will be None.
"""
repo_info_dict = {}
repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner )
if app.name == 'tool_shed':
# We're in the tool shed.
repository_metadata = suc.get_repository_metadata_by_changeset_revision( app,
app.security.encode_id( repository.id ),
changeset_revision )
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
tool_shed_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
rb = relation_builder.RelationBuilder( app, repository, repository_metadata, tool_shed_url )
# Get a dictionary of all repositories upon which the contents of the received repository depends.
repository_dependencies = rb.get_repository_dependencies_for_changeset_revision()
tool_dependencies = metadata.get( 'tool_dependencies', {} )
if tool_dependencies:
new_tool_dependencies = {}
for dependency_key, requirements_dict in tool_dependencies.items():
if dependency_key in [ 'set_environment' ]:
new_set_environment_dict_list = []
for set_environment_dict in requirements_dict:
set_environment_dict[ 'repository_name' ] = repository_name
set_environment_dict[ 'repository_owner' ] = repository_owner
set_environment_dict[ 'changeset_revision' ] = changeset_revision
new_set_environment_dict_list.append( set_environment_dict )
new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list
else:
requirements_dict[ 'repository_name' ] = repository_name
requirements_dict[ 'repository_owner' ] = repository_owner
requirements_dict[ 'changeset_revision' ] = changeset_revision
new_tool_dependencies[ dependency_key ] = requirements_dict
tool_dependencies = new_tool_dependencies
# Cast unicode to string, with the exception of description, since it is free text and can contain special characters.
repo_info_dict[ str( repository.name ) ] = ( repository.description,
str( repository_clone_url ),
str( changeset_revision ),
str( ctx_rev ),
str( repository_owner ),
repository_dependencies,
tool_dependencies )
return repo_info_dict
def get_repository_revision_install_info(self, trans, name, owner,
changeset_revision, **kwd):
"""
GET /api/repositories/get_repository_revision_install_info
:param name: the name of the Repository
:param owner: the owner of the Repository
:param changset_revision: the changset_revision of the RepositoryMetadata object associated with the Repository
Returns a list of the following dictionaries::
- a dictionary defining the Repository. For example:
{
"deleted": false,
"deprecated": false,
"description": "add_column hello",
"id": "f9cad7b01a472135",
"long_description": "add_column hello",
"name": "add_column",
"owner": "test",
"private": false,
"times_downloaded": 6,
"url": "/api/repositories/f9cad7b01a472135",
"user_id": "f9cad7b01a472135"
}
- a dictionary defining the Repository revision (RepositoryMetadata). For example:
{
"changeset_revision": "3a08cc21466f",
"downloadable": true,
"has_repository_dependencies": false,
"id": "f9cad7b01a472135",
"includes_datatypes": false,
"includes_tool_dependencies": false,
"includes_tools": true,
"includes_tools_for_display_in_tool_panel": true,
"includes_workflows": false,
"malicious": false,
"repository_id": "f9cad7b01a472135",
"url": "/api/repository_revisions/f9cad7b01a472135"
}
- a dictionary including the additional information required to install the repository. For example:
{
"add_column": [
"add_column hello",
"http://test@localhost:9009/repos/test/add_column",
"3a08cc21466f",
"1",
"test",
{},
{}
]
}
"""
# Example URL: http://localhost:9009/api/repositories/get_repository_revision_install_info?name=add_column&owner=test&changeset_revision=3a08cc21466f
try:
# Get the repository information.
repository = suc.get_repository_by_name_and_owner(
trans.app, name, owner)
encoded_repository_id = trans.security.encode_id(repository.id)
repository_dict = repository.get_api_value(
view='element',
value_mapper=default_repository_value_mapper(
trans, repository))
repository_dict['url'] = web.url_for(controller='repositories',
action='show',
id=encoded_repository_id)
# Get the repository_metadata information.
repository_metadata = suc.get_repository_metadata_by_changeset_revision(
trans, encoded_repository_id, changeset_revision)
if not repository_metadata:
# 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_dir = repository.repo_path(trans.app)
repo = hg.repository(suc.get_configured_ui(), repo_dir)
new_changeset_revision = suc.get_next_downloadable_changeset_revision(
repository, repo, changeset_revision)
repository_metadata = suc.get_repository_metadata_by_changeset_revision(
trans, encoded_repository_id, new_changeset_revision)
changeset_revision = new_changeset_revision
if repository_metadata:
encoded_repository_metadata_id = trans.security.encode_id(
repository_metadata.id)
repository_metadata_dict = repository_metadata.get_api_value(
view='collection',
value_mapper=default_repository_metadata_value_mapper(
trans, repository_metadata))
repository_metadata_dict['url'] = web.url_for(
controller='repository_revisions',
action='show',
id=encoded_repository_metadata_id)
# Get the repo_info_dict for installing the repository.
repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, has_repository_dependencies = \
repository_util.get_repo_info_dict( trans, encoded_repository_id, changeset_revision )
return repository_dict, repository_metadata_dict, repo_info_dict
else:
message = "Unable to locate repository_metadata record for repository id %d and changeset_revision %s" % (
repository.id, changeset_revision)
log.error(message, exc_info=True)
trans.response.status = 500
return repository_dict, {}, {}
except Exception, e:
message = "Error in the Tool Shed repositories API in get_repository_revision_install_info: %s" % str(
e)
log.error(message, exc_info=True)
trans.response.status = 500
return message
def get_repository_revision_install_info(self, trans, name, owner,
changeset_revision, **kwd):
"""
GET /api/repositories/get_repository_revision_install_info
:param name: the name of the Repository
:param owner: the owner of the Repository
:param changeset_revision: the changeset_revision of the RepositoryMetadata object associated with the Repository
Returns a list of the following dictionaries::
- a dictionary defining the Repository. For example:
{
"deleted": false,
"deprecated": false,
"description": "add_column hello",
"id": "f9cad7b01a472135",
"long_description": "add_column hello",
"name": "add_column",
"owner": "test",
"private": false,
"times_downloaded": 6,
"url": "/api/repositories/f9cad7b01a472135",
"user_id": "f9cad7b01a472135"
}
- a dictionary defining the Repository revision (RepositoryMetadata). For example:
{
"changeset_revision": "3a08cc21466f",
"downloadable": true,
"has_repository_dependencies": false,
"has_repository_dependencies_only_if_compiling_contained_td": false,
"id": "f9cad7b01a472135",
"includes_datatypes": false,
"includes_tool_dependencies": false,
"includes_tools": true,
"includes_tools_for_display_in_tool_panel": true,
"includes_workflows": false,
"malicious": false,
"repository_id": "f9cad7b01a472135",
"url": "/api/repository_revisions/f9cad7b01a472135"
}
- a dictionary including the additional information required to install the repository. For example:
{
"add_column": [
"add_column hello",
"http://test@localhost:9009/repos/test/add_column",
"3a08cc21466f",
"1",
"test",
{},
{}
]
}
"""
# Example URL:
# 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(
trans.app, name, owner)
if repository is None:
log.debug('Cannot locate repository %s owned by %s' %
(str(name), str(owner)))
return {}, {}, {}
encoded_repository_id = trans.security.encode_id(repository.id)
repository_dict = repository.to_dict(
view='element', value_mapper=self.__get_value_mapper(trans))
repository_dict['url'] = web.url_for(controller='repositories',
action='show',
id=encoded_repository_id)
# Get the repository_metadata information.
repository_metadata = suc.get_repository_metadata_by_changeset_revision(
trans.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(trans.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(
trans.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)
repository_metadata_dict = repository_metadata.to_dict(
view='collection',
value_mapper=self.__get_value_mapper(trans))
repository_metadata_dict['url'] = web.url_for(
controller='repository_revisions',
action='show',
id=encoded_repository_metadata_id)
# Get the repo_info_dict for installing the repository.
repo_info_dict, \
includes_tools, \
includes_tool_dependencies, \
includes_tools_for_display_in_tool_panel, \
has_repository_dependencies, \
has_repository_dependencies_only_if_compiling_contained_td = \
repository_util.get_repo_info_dict( trans.app,
trans.user,
encoded_repository_id,
changeset_revision )
return repository_dict, repository_metadata_dict, repo_info_dict
else:
log.debug( "Unable to locate repository_metadata record for repository id %s and changeset_revision %s" % \
( str( repository.id ), str( changeset_revision ) ) )
return repository_dict, {}, {}
else:
debug_msg = "Error in the Tool Shed repositories API in get_repository_revision_install_info: "
debug_msg += "Invalid name %s or owner %s or changeset_revision %s received." % \
( str( name ), str( owner ), str( changeset_revision ) )
log.debug(debug_msg)
return {}, {}, {}
def repository_dependencies(self, trans, id, **kwd):
"""
GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies
Returns a list of dictionaries that each define a specific downloadable revision of a
repository in the Tool Shed. This method returns dictionaries with more information in
them than other methods in this controller. The information about repository_metdata is
enhanced to include information about the repository (e.g., name, owner, etc) associated
with the repository_metadata record.
:param id: the encoded id of the `RepositoryMetadata` object
"""
# Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb125606ff9ea620
repository_dependencies_dicts = []
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans.app, id)
if repository_metadata is None:
log.debug('Invalid repository_metadata id received: %s' % str(id))
return repository_dependencies_dicts
metadata = repository_metadata.metadata
if metadata is None:
log.debug(
'The repository_metadata record with id %s has no metadata.' %
str(id))
return repository_dependencies_dicts
if 'repository_dependencies' in metadata:
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)
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 )
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.
repo = hg_util.get_repo_for_repository(
trans.app,
repository=repository_dependency,
repo_path=None,
create=False)
new_changeset_revision = suc.get_next_downloadable_changeset_revision(
repository_dependency, repo, changeset_revision)
repository_dependency_repository_metadata = \
suc.get_repository_metadata_by_changeset_revision( trans.app,
repository_dependency_id,
new_changeset_revision )
if repository_dependency_repository_metadata is None:
decoded_repository_dependency_id = trans.security.decode_id(
repository_dependency_id)
debug_msg = 'Cannot locate repository_metadata with id %d for repository dependency %s owned by %s ' % \
( decoded_repository_dependency_id, str( name ), str( owner ) )
debug_msg += 'using either of these changeset_revisions: %s, %s.' % \
( str( changeset_revision ), str( new_changeset_revision ) )
log.debug(debug_msg)
continue
else:
changeset_revision = new_changeset_revision
repository_dependency_metadata_dict = \
repository_dependency_repository_metadata.to_dict( view='element',
value_mapper=self.__get_value_mapper( trans ) )
repository_dependency_dict = repository_dependency.to_dict(
view='element',
value_mapper=self.__get_value_mapper(trans))
# We need to be careful with the entries in our repository_dependency_dict here since this Tool Shed API
# controller is working with repository_metadata records. The above to_dict() method returns a dictionary
# with an id entry for the repository record. However, all of the other methods in this controller have
# the id entry associated with a repository_metadata record id. To avoid confusion, we'll update the
# repository_dependency_metadata_dict with entries from the repository_dependency_dict without using the
# Python dictionary update() method because we do not want to overwrite existing entries.
for k, v in repository_dependency_dict.items():
if k not in repository_dependency_metadata_dict:
repository_dependency_metadata_dict[k] = v
repository_dependency_metadata_dict['url'] = web.url_for(
controller='repositories',
action='show',
id=repository_dependency_id)
repository_dependencies_dicts.append(
repository_dependency_metadata_dict)
return repository_dependencies_dicts
def handle_elem( self, elem ):
"""Populate or unpopulate the changeset_revision and toolshed attributes of repository tags."""
# <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" />
# <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy">
# <package name="xorg_macros" version="1.17.1" />
# </repository>
error_message = ''
name = elem.get( 'name' )
owner = elem.get( 'owner' )
# The name and owner attributes are always required, so if either are missing, return the error message.
if not name or not owner:
error_message = self.check_tag_attributes( elem )
return False, elem, error_message
altered = False
toolshed = elem.get( 'toolshed' )
changeset_revision = elem.get( 'changeset_revision' )
# Over a short period of time a bug existed which caused the prior_installation_required attribute
# to be set to False and included in the <repository> tag when a repository was exported along with
# its dependencies. The following will eliminate this problematic attribute upon import.
prior_installation_required = elem.get( 'prior_installation_required' )
if prior_installation_required is not None and not asbool( prior_installation_required ):
del elem.attrib[ 'prior_installation_required' ]
sub_elems = [ child_elem for child_elem in list( elem ) ]
if len( sub_elems ) > 0:
# At this point, a <repository> tag will point only to a package.
# <package name="xorg_macros" version="1.17.1" />
# Coerce the list to an odict().
sub_elements = odict()
packages = []
for sub_elem in sub_elems:
sub_elem_type = sub_elem.tag
sub_elem_name = sub_elem.get( 'name' )
sub_elem_version = sub_elem.get( 'version' )
if sub_elem_type and sub_elem_name and sub_elem_version:
packages.append( ( sub_elem_name, sub_elem_version ) )
sub_elements[ 'packages' ] = packages
else:
# Set to None.
sub_elements = None
if self.unpopulate:
# We're exporting the repository, so eliminate all toolshed and changeset_revision attributes
# from the <repository> tag.
if toolshed or changeset_revision:
attributes = odict()
attributes[ 'name' ] = name
attributes[ 'owner' ] = owner
prior_installation_required = elem.get( 'prior_installation_required' )
if asbool( prior_installation_required ):
attributes[ 'prior_installation_required' ] = 'True'
new_elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements )
altered = True
return altered, new_elem, error_message
# From here on we're populating the toolshed and changeset_revision attributes if necessary.
if not toolshed:
# Default the setting to the current tool shed.
toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' )
elem.attrib[ 'toolshed' ] = toolshed
altered = True
if not changeset_revision:
# 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 )
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 )
if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision
altered = True
else:
error_message = 'Invalid latest installable changeset_revision %s ' % \
str( lastest_installable_changeset_revision )
error_message += 'retrieved for repository %s owned by %s. ' % ( str( name ), str( owner ) )
else:
error_message = 'Unable to locate repository with name %s and owner %s. ' % ( str( name ), str( owner ) )
return altered, elem, error_message
def repository_dependencies( self, trans, id, **kwd ):
"""
GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies
Returns a list of dictionaries that each define a specific downloadable revision of a
repository in the Tool Shed. This method returns dictionaries with more information in
them than other methods in this controller. The information about repository_metdata is
enhanced to include information about the repository (e.g., name, owner, etc) associated
with the repository_metadata record.
:param id: the encoded id of the `RepositoryMetadata` object
"""
# Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb125606ff9ea620
repository_dependencies_dicts = []
repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id )
if repository_metadata is None:
log.debug( 'Invalid repository_metadata id received: %s' % str( id ) )
return repository_dependencies_dicts
metadata = repository_metadata.metadata
if metadata is None:
log.debug( 'The repository_metadata record with id %s has no metadata.' % str ( id ) )
return repository_dependencies_dicts
if 'repository_dependencies' in metadata:
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 )
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, 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.
repo_dir = repository_dependency.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository_dependency,
repo,
changeset_revision )
repository_dependency_repository_metadata = \
suc.get_repository_metadata_by_changeset_revision( trans,
repository_dependency_id,
new_changeset_revision )
if repository_dependency_repository_metadata is None:
decoded_repository_dependency_id = trans.security.decode_id( repository_dependency_id )
debug_msg = 'Cannot locate repository_metadata with id %d for repository dependency %s owned by %s ' % \
( decoded_repository_dependency_id, str( name ), str( owner ) )
debug_msg += 'using either of these changeset_revisions: %s, %s.' % \
( str( changeset_revision ), str( new_changeset_revision ) )
log.debug( debug_msg )
continue
else:
changeset_revision = new_changeset_revision
repository_dependency_repository_metadata_id = trans.security.encode_id( repository_dependency_repository_metadata.id )
repository_dependency_metadata_dict = \
repository_dependency_repository_metadata.to_dict( view='element',
value_mapper=self.__get_value_mapper( trans ) )
repository_dependency_dict = repository_dependency.to_dict( view='element',
value_mapper=self.__get_value_mapper( trans ) )
# We need to be careful with the entries in our repository_dependency_dict here since this Tool Shed API
# controller is working with repository_metadata records. The above to_dict() method returns a dictionary
# with an id entry for the repository record. However, all of the other methods in this controller have
# the id entry associated with a repository_metadata record id. To avoid confusion, we'll update the
# repository_dependency_metadata_dict with entries from the repository_dependency_dict without using the
# Python dictionary update() method because we do not want to overwrite existing entries.
for k, v in repository_dependency_dict.items():
if k not in repository_dependency_metadata_dict:
repository_dependency_metadata_dict[ k ] = v
repository_dependency_metadata_dict[ 'url' ] = web.url_for( controller='repositories',
action='show',
id=repository_dependency_id )
repository_dependencies_dicts.append( repository_dependency_metadata_dict )
return repository_dependencies_dicts
