def get_or_create_tool_shed_repository( self, tool_shed, name, owner, changeset_revision ):
"""
Return a tool shed repository database record defined by the combination of
tool shed, repository name, repository owner and changeset_revision or
installed_changeset_revision. A new tool shed repository record will be
created if one is not located.
"""
install_model = self.app.install_model
# We store the port in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
# This method is used only in Galaxy, not the tool shed.
repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed, name, owner, changeset_revision )
if not repository:
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed )
repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
ctx_rev = suc.get_ctx_rev( self.app, tool_shed_url, name, owner, changeset_revision )
repository = suc.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=None,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=None,
owner=owner,
dist_to_shed=False )
return repository
def create_or_update_tool_shed_repository_record(self,
name,
owner,
changeset_revision,
description=None):
# Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
relative_clone_dir = os.path.join(self.tool_shed, 'repos', owner, name,
changeset_revision)
clone_dir = os.path.join(self.tool_path, relative_clone_dir)
if not self.__iscloned(clone_dir):
repository_clone_url = os.path.join(self.tool_shed_url, 'repos',
owner, name)
ctx_rev = suc.get_ctx_rev(self.app, self.tool_shed_url, name,
owner, changeset_revision)
tool_shed_repository = repository_util.create_or_update_tool_shed_repository(
app=self.app,
name=name,
description=description,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=self.app.install_model.ToolShedRepository.
installation_status.NEW,
current_changeset_revision=None,
owner=self.repository_owner,
dist_to_shed=True)
return tool_shed_repository
return None
def get_or_create_tool_shed_repository( self, tool_shed, name, owner, changeset_revision ):
"""
Return a tool shed repository database record defined by the combination of
tool shed, repository name, repository owner and changeset_revision or
installed_changeset_revision. A new tool shed repository record will be
created if one is not located.
"""
install_model = self.app.install_model
# We store the port in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
# This method is used only in Galaxy, not the tool shed.
repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed, name, owner, changeset_revision )
if not repository:
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed )
repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
ctx_rev = suc.get_ctx_rev( self.app, tool_shed_url, name, owner, changeset_revision )
repository = suc.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=None,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=None,
owner=owner,
dist_to_shed=False )
return repository
def install_repository(self, repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=False):
"""Install a single repository, loading contained tools into the tool panel."""
# Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
relative_clone_dir = os.path.join(tool_shed_repository.tool_shed,
'repos',
tool_shed_repository.owner,
tool_shed_repository.name,
tool_shed_repository.installed_changeset_revision)
clone_dir = os.path.join(self.tool_path, relative_clone_dir)
cloned_ok = self.__iscloned(clone_dir)
is_installed = False
# Any of the following states should count as installed in this context.
if tool_shed_repository.status in [self.app.install_model.ToolShedRepository.installation_status.INSTALLED,
self.app.install_model.ToolShedRepository.installation_status.ERROR,
self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED,
self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED]:
is_installed = True
if cloned_ok and is_installed:
log.info("Skipping automatic install of repository '%s' because it has already been installed in location %s",
tool_shed_repository.name, clone_dir)
else:
irm = install_manager.InstallRepositoryManager(self.app, self.tpm)
repository_clone_url = os.path.join(self.tool_shed_url, 'repos', tool_shed_repository.owner, tool_shed_repository.name)
relative_install_dir = os.path.join(relative_clone_dir, tool_shed_repository.name)
install_dir = os.path.join(clone_dir, tool_shed_repository.name)
ctx_rev = suc.get_ctx_rev(self.app,
self.tool_shed_url,
tool_shed_repository.name,
tool_shed_repository.owner,
tool_shed_repository.installed_changeset_revision)
if not cloned_ok:
irm.update_tool_shed_repository_status(tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.CLONING)
cloned_ok, error_message = hg_util.clone_repository(repository_clone_url, os.path.abspath(install_dir), ctx_rev)
if cloned_ok and not is_installed:
self.handle_repository_contents(tool_shed_repository=tool_shed_repository,
repository_clone_url=repository_clone_url,
relative_install_dir=relative_install_dir,
repository_elem=repository_elem,
install_dependencies=install_dependencies,
is_repository_dependency=is_repository_dependency)
self.app.install_model.context.refresh(tool_shed_repository)
irm.update_tool_shed_repository_status(tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.INSTALLED)
else:
log.error('Error attempting to clone repository %s: %s', str(tool_shed_repository.name), str(error_message))
irm.update_tool_shed_repository_status(tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.ERROR,
error_message=error_message)
def create_or_update_tool_shed_repository_record( self, name, owner, changeset_revision, description=None ):
# Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
relative_clone_dir = os.path.join( self.tool_shed, 'repos', owner, name, changeset_revision )
clone_dir = os.path.join( self.tool_path, relative_clone_dir )
if not self.__iscloned( clone_dir ):
repository_clone_url = os.path.join( self.tool_shed_url, 'repos', owner, name )
ctx_rev = suc.get_ctx_rev( self.app, self.tool_shed_url, name, owner, changeset_revision )
tool_shed_repository = suc.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=description,
installed_changeset_revision=changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=self.app.install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=None,
owner=self.repository_owner,
dist_to_shed=True )
return tool_shed_repository
return None
def install_repository( self, repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=False ):
"""Install a single repository, loading contained tools into the tool panel."""
# Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
relative_clone_dir = os.path.join( tool_shed_repository.tool_shed,
'repos',
tool_shed_repository.owner,
tool_shed_repository.name,
tool_shed_repository.installed_changeset_revision )
clone_dir = os.path.join( self.tool_path, relative_clone_dir )
cloned_ok = self.__iscloned( clone_dir )
is_installed = False
# Any of the following states should count as installed in this context.
if tool_shed_repository.status in [ self.app.install_model.ToolShedRepository.installation_status.INSTALLED,
self.app.install_model.ToolShedRepository.installation_status.ERROR,
self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED,
self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED ]:
is_installed = True
if cloned_ok and is_installed:
print "Skipping automatic install of repository '", tool_shed_repository.name, "' because it has already been installed in location ", clone_dir
else:
irm = install_manager.InstallRepositoryManager( self.app, self.tpm )
repository_clone_url = os.path.join( self.tool_shed_url, 'repos', tool_shed_repository.owner, tool_shed_repository.name )
relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name )
install_dir = os.path.join( clone_dir, tool_shed_repository.name )
ctx_rev = suc.get_ctx_rev( self.app,
self.tool_shed_url,
tool_shed_repository.name,
tool_shed_repository.owner,
tool_shed_repository.installed_changeset_revision )
if not cloned_ok:
irm.update_tool_shed_repository_status( tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.CLONING )
cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
if cloned_ok and not is_installed:
self.handle_repository_contents( tool_shed_repository=tool_shed_repository,
repository_clone_url=repository_clone_url,
relative_install_dir=relative_install_dir,
repository_elem=repository_elem,
install_dependencies=install_dependencies,
is_repository_dependency=is_repository_dependency )
self.app.install_model.context.refresh( tool_shed_repository )
metadata_dict = tool_shed_repository.metadata
if 'tools' in metadata_dict:
# Initialize the ToolVersionManager.
tvm = tool_version_manager.ToolVersionManager( self.app )
irm.update_tool_shed_repository_status( tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
# Get the tool_versions from the tool shed for each tool in the installed change set.
url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
( self.tool_shed_url, tool_shed_repository.name, self.repository_owner, tool_shed_repository.installed_changeset_revision )
text = common_util.tool_shed_get( self.app, self.tool_shed_url, url )
if text:
tool_version_dicts = json.loads( text )
tvm.handle_tool_versions( tool_version_dicts, tool_shed_repository )
else:
# Set the tool versions since they seem to be missing for this repository in the tool shed.
# CRITICAL NOTE: These default settings may not properly handle all parent/child associations.
for tool_dict in metadata_dict[ 'tools' ]:
flush_needed = False
tool_id = tool_dict[ 'guid' ]
old_tool_id = tool_dict[ 'id' ]
tool_version = tool_dict[ 'version' ]
tool_version_using_old_id = tvm.get_tool_version( old_tool_id )
tool_version_using_guid = tvm.get_tool_version( tool_id )
if not tool_version_using_old_id:
tool_version_using_old_id = self.app.install_model.ToolVersion( tool_id=old_tool_id,
tool_shed_repository=tool_shed_repository )
self.app.install_model.context.add( tool_version_using_old_id )
self.app.install_model.context.flush()
if not tool_version_using_guid:
tool_version_using_guid = self.app.install_model.ToolVersion( tool_id=tool_id,
tool_shed_repository=tool_shed_repository )
self.app.install_model.context.add( tool_version_using_guid )
self.app.install_model.context.flush()
# Associate the two versions as parent / child.
tool_version_association = tvm.get_tool_version_association( tool_version_using_old_id,
tool_version_using_guid )
if not tool_version_association:
tool_version_association = \
self.app.install_model.ToolVersionAssociation( tool_id=tool_version_using_guid.id,
parent_id=tool_version_using_old_id.id )
self.app.install_model.context.add( tool_version_association )
self.app.install_model.context.flush()
irm.update_tool_shed_repository_status( tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.INSTALLED )
else:
print 'Error attempting to clone repository %s: %s' % ( str( tool_shed_repository.name ), str( error_message ) )
irm.update_tool_shed_repository_status( tool_shed_repository,
self.app.install_model.ToolShedRepository.installation_status.ERROR,
error_message=error_message )
def install_repository(self,
repository_elem,
tool_shed_repository,
install_dependencies,
is_repository_dependency=False):
"""Install a single repository, loading contained tools into the tool panel."""
# Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
relative_clone_dir = os.path.join(
tool_shed_repository.tool_shed, 'repos',
tool_shed_repository.owner, tool_shed_repository.name,
tool_shed_repository.installed_changeset_revision)
clone_dir = os.path.join(self.tool_path, relative_clone_dir)
cloned_ok = self.__iscloned(clone_dir)
is_installed = False
# Any of the following states should count as installed in this context.
if tool_shed_repository.status in [
self.app.install_model.ToolShedRepository.installation_status.
INSTALLED, self.app.install_model.ToolShedRepository.
installation_status.ERROR, self.app.install_model.
ToolShedRepository.installation_status.UNINSTALLED,
self.app.install_model.ToolShedRepository.installation_status.
DEACTIVATED
]:
is_installed = True
if cloned_ok and is_installed:
log.info(
"Skipping automatic install of repository '%s' because it has already been installed in location %s",
tool_shed_repository.name, clone_dir)
else:
irm = install_manager.InstallRepositoryManager(self.app, self.tpm)
repository_clone_url = os.path.join(self.tool_shed_url, 'repos',
tool_shed_repository.owner,
tool_shed_repository.name)
relative_install_dir = os.path.join(relative_clone_dir,
tool_shed_repository.name)
install_dir = os.path.join(clone_dir, tool_shed_repository.name)
ctx_rev = suc.get_ctx_rev(
self.app, self.tool_shed_url, tool_shed_repository.name,
tool_shed_repository.owner,
tool_shed_repository.installed_changeset_revision)
if not cloned_ok:
irm.update_tool_shed_repository_status(
tool_shed_repository, self.app.install_model.
ToolShedRepository.installation_status.CLONING)
cloned_ok, error_message = hg_util.clone_repository(
repository_clone_url, os.path.abspath(install_dir),
ctx_rev)
if cloned_ok and not is_installed:
self.handle_repository_contents(
tool_shed_repository=tool_shed_repository,
repository_clone_url=repository_clone_url,
relative_install_dir=relative_install_dir,
repository_elem=repository_elem,
install_dependencies=install_dependencies,
is_repository_dependency=is_repository_dependency)
self.app.install_model.context.refresh(tool_shed_repository)
irm.update_tool_shed_repository_status(
tool_shed_repository, self.app.install_model.
ToolShedRepository.installation_status.INSTALLED)
else:
log.error('Error attempting to clone repository %s: %s',
str(tool_shed_repository.name), str(error_message))
irm.update_tool_shed_repository_status(
tool_shed_repository,
self.app.install_model.ToolShedRepository.
installation_status.ERROR,
error_message=error_message)
def install_repository(self,
repository_elem,
tool_shed_repository,
install_dependencies,
is_repository_dependency=False):
"""Install a single repository, loading contained tools into the tool panel."""
# Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
relative_clone_dir = os.path.join(
tool_shed_repository.tool_shed, 'repos',
tool_shed_repository.owner, tool_shed_repository.name,
tool_shed_repository.installed_changeset_revision)
clone_dir = os.path.join(self.tool_path, relative_clone_dir)
cloned_ok = self.__iscloned(clone_dir)
is_installed = False
# Any of the following states should count as installed in this context.
if tool_shed_repository.status in [
self.app.install_model.ToolShedRepository.installation_status.
INSTALLED, self.app.install_model.ToolShedRepository.
installation_status.ERROR, self.app.install_model.
ToolShedRepository.installation_status.UNINSTALLED,
self.app.install_model.ToolShedRepository.installation_status.
DEACTIVATED
]:
is_installed = True
if cloned_ok and is_installed:
log.info(
"Skipping automatic install of repository '%s' because it has already been installed in location %s",
tool_shed_repository.name, clone_dir)
else:
irm = install_manager.InstallRepositoryManager(self.app, self.tpm)
repository_clone_url = os.path.join(self.tool_shed_url, 'repos',
tool_shed_repository.owner,
tool_shed_repository.name)
relative_install_dir = os.path.join(relative_clone_dir,
tool_shed_repository.name)
install_dir = os.path.join(clone_dir, tool_shed_repository.name)
ctx_rev = suc.get_ctx_rev(
self.app, self.tool_shed_url, tool_shed_repository.name,
tool_shed_repository.owner,
tool_shed_repository.installed_changeset_revision)
if not cloned_ok:
irm.update_tool_shed_repository_status(
tool_shed_repository, self.app.install_model.
ToolShedRepository.installation_status.CLONING)
cloned_ok, error_message = hg_util.clone_repository(
repository_clone_url, os.path.abspath(install_dir),
ctx_rev)
if cloned_ok and not is_installed:
self.handle_repository_contents(
tool_shed_repository=tool_shed_repository,
repository_clone_url=repository_clone_url,
relative_install_dir=relative_install_dir,
repository_elem=repository_elem,
install_dependencies=install_dependencies,
is_repository_dependency=is_repository_dependency)
self.app.install_model.context.refresh(tool_shed_repository)
metadata_dict = tool_shed_repository.metadata
if 'tools' in metadata_dict:
# Initialize the ToolVersionManager.
tvm = tool_version_manager.ToolVersionManager(self.app)
irm.update_tool_shed_repository_status(
tool_shed_repository,
self.app.install_model.ToolShedRepository.
installation_status.SETTING_TOOL_VERSIONS)
# Get the tool_versions from the tool shed for each tool in the installed change set.
params = dict(name=tool_shed_repository.name,
owner=self.repository_owner,
changeset_revision=tool_shed_repository.
installed_changeset_revision)
pathspec = ['repository', 'get_tool_versions']
text = util.url_get(
self.tool_shed_url,
password_mgr=self.app.tool_shed_registry.url_auth(
self.tool_shed_url),
pathspec=pathspec,
params=params)
if text:
tool_version_dicts = json.loads(text)
tvm.handle_tool_versions(tool_version_dicts,
tool_shed_repository)
else:
# Set the tool versions since they seem to be missing
# for this repository in the tool shed. CRITICAL NOTE:
# These default settings may not properly handle all
# parent/child associations.
for tool_dict in metadata_dict['tools']:
tool_id = tool_dict['guid']
old_tool_id = tool_dict['id']
tool_version_using_old_id = tvm.get_tool_version(
old_tool_id)
tool_version_using_guid = tvm.get_tool_version(
tool_id)
if not tool_version_using_old_id:
tool_version_using_old_id = self.app.install_model.ToolVersion(
tool_id=old_tool_id,
tool_shed_repository=tool_shed_repository)
self.app.install_model.context.add(
tool_version_using_old_id)
self.app.install_model.context.flush()
if not tool_version_using_guid:
tool_version_using_guid = self.app.install_model.ToolVersion(
tool_id=tool_id,
tool_shed_repository=tool_shed_repository)
self.app.install_model.context.add(
tool_version_using_guid)
self.app.install_model.context.flush()
# Associate the two versions as parent / child.
tool_version_association = tvm.get_tool_version_association(
tool_version_using_old_id,
tool_version_using_guid)
if not tool_version_association:
tool_version_association = \
self.app.install_model.ToolVersionAssociation( tool_id=tool_version_using_guid.id,
parent_id=tool_version_using_old_id.id )
self.app.install_model.context.add(
tool_version_association)
self.app.install_model.context.flush()
irm.update_tool_shed_repository_status(
tool_shed_repository, self.app.install_model.
ToolShedRepository.installation_status.INSTALLED)
else:
log.error('Error attempting to clone repository %s: %s',
str(tool_shed_repository.name), str(error_message))
irm.update_tool_shed_repository_status(
tool_shed_repository,
self.app.install_model.ToolShedRepository.
installation_status.ERROR,
error_message=error_message)
def install_repository( self, repository_elem, install_dependencies ):
# Install a single repository, loading contained tools into the tool panel.
name = repository_elem.get( 'name' )
description = repository_elem.get( 'description' )
installed_changeset_revision = repository_elem.get( 'changeset_revision' )
# Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision>
relative_clone_dir = os.path.join( self.tool_shed, 'repos', self.repository_owner, name, installed_changeset_revision )
clone_dir = os.path.join( self.tool_path, relative_clone_dir )
if self.__isinstalled( clone_dir ):
print "Skipping automatic install of repository '", name, "' because it has already been installed in location ", clone_dir
else:
tool_shed_url = suc.get_url_from_tool_shed( self.app, self.tool_shed )
repository_clone_url = os.path.join( tool_shed_url, 'repos', self.repository_owner, name )
relative_install_dir = os.path.join( relative_clone_dir, name )
install_dir = os.path.join( clone_dir, name )
ctx_rev = suc.get_ctx_rev( self.app, tool_shed_url, name, self.repository_owner, installed_changeset_revision )
tool_shed_repository = suc.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=description,
installed_changeset_revision=installed_changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=self.app.model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=None,
owner=self.repository_owner,
dist_to_shed=True )
suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING )
cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
if cloned_ok:
self.handle_repository_contents( tool_shed_repository=tool_shed_repository,
repository_clone_url=repository_clone_url,
relative_install_dir=relative_install_dir,
repository_elem=repository_elem,
install_dependencies=install_dependencies )
self.app.sa_session.refresh( tool_shed_repository )
metadata_dict = tool_shed_repository.metadata
if 'tools' in metadata_dict:
suc.update_tool_shed_repository_status( self.app,
tool_shed_repository,
self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
# Get the tool_versions from the tool shed for each tool in the installed change set.
url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
( tool_shed_url, tool_shed_repository.name, self.repository_owner, installed_changeset_revision )
text = common_util.tool_shed_get( self.app, tool_shed_url, url )
if text:
tool_version_dicts = from_json_string( text )
tool_util.handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository )
else:
# Set the tool versions since they seem to be missing for this repository in the tool shed.
# CRITICAL NOTE: These default settings may not properly handle all parent/child associations.
for tool_dict in metadata_dict[ 'tools' ]:
flush_needed = False
tool_id = tool_dict[ 'guid' ]
old_tool_id = tool_dict[ 'id' ]
tool_version = tool_dict[ 'version' ]
tool_version_using_old_id = tool_util.get_tool_version( self.app, old_tool_id )
tool_version_using_guid = tool_util.get_tool_version( self.app, tool_id )
if not tool_version_using_old_id:
tool_version_using_old_id = self.app.model.ToolVersion( tool_id=old_tool_id,
tool_shed_repository=tool_shed_repository )
self.app.sa_session.add( tool_version_using_old_id )
self.app.sa_session.flush()
if not tool_version_using_guid:
tool_version_using_guid = self.app.model.ToolVersion( tool_id=tool_id,
tool_shed_repository=tool_shed_repository )
self.app.sa_session.add( tool_version_using_guid )
self.app.sa_session.flush()
# Associate the two versions as parent / child.
tool_version_association = tool_util.get_tool_version_association( self.app,
tool_version_using_old_id,
tool_version_using_guid )
if not tool_version_association:
tool_version_association = self.app.model.ToolVersionAssociation( tool_id=tool_version_using_guid.id,
parent_id=tool_version_using_old_id.id )
self.app.sa_session.add( tool_version_association )
self.app.sa_session.flush()
suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.INSTALLED )
