def get_readme_files_dict_for_display(app, tool_shed_url, repo_info_dict):
"""
Return a dictionary of README files contained in the single repository being installed so they can be displayed on the tool panel section
selection page.
"""
name = next(iter(repo_info_dict))
repo_info_tuple = repo_info_dict[name]
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \
repository_util.get_repo_info_tuple_contents(repo_info_tuple)
# Handle changing HTTP protocols over time.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(app, tool_shed_url)
params = dict(name=name, owner=repository_owner, changeset_revision=changeset_revision)
pathspec = ['repository', 'get_readme_files']
raw_text = url_get(tool_shed_url, auth=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params)
readme_files_dict = json.loads(raw_text)
return readme_files_dict
def get_readme_files_dict_for_display( app, tool_shed_url, repo_info_dict ):
"""
Return a dictionary of README files contained in the single repository being installed so they can be displayed on the tool panel section
selection page.
"""
name = next(iter(repo_info_dict))
repo_info_tuple = repo_info_dict[ name ]
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
# Handle changing HTTP protocols over time.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
params = dict( name=name, owner=repository_owner, changeset_revision=changeset_revision )
pathspec = [ 'repository', 'get_readme_files' ]
raw_text = url_get( tool_shed_url, password_mgr=app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params )
readme_files_dict = json.loads( raw_text )
return readme_files_dict
def get_required_repo_info_dicts(self, tool_shed_url, repo_info_dicts):
"""
Inspect the list of repo_info_dicts for repository dependencies and append a repo_info_dict for each of
them to the list. All repository_dependency entries in each of the received repo_info_dicts includes
all required repositories, so only one pass through this method is required to retrieve all repository
dependencies.
"""
all_required_repo_info_dict = {}
all_repo_info_dicts = []
if repo_info_dicts:
# We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool
# shed to discover repository ids.
required_repository_tups = []
for repo_info_dict in repo_info_dicts:
if repo_info_dict not in all_repo_info_dicts:
all_repo_info_dicts.append(repo_info_dict)
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 = \
repository_util.get_repo_info_tuple_contents(repo_info_tup)
if repository_dependencies:
for key, val in repository_dependencies.items():
if key in ['root_key', 'description']:
continue
repository_components_tuple = container_util.get_components_from_key(key)
components_list = repository_util.extract_components_from_tuple(repository_components_tuple)
# Skip listing a repository dependency if it is required only to compile a tool dependency
# defined for the dependent repository since in this case, the repository dependency is really
# a dependency of the dependent repository's contained tool dependency, and only if that
# tool dependency requires compilation.
# For backward compatibility to the 12/20/12 Galaxy release.
only_if_compiling_contained_td = 'False'
if len(components_list) == 4:
only_if_compiling_contained_td = 'False'
elif len(components_list) == 5:
only_if_compiling_contained_td = 'False'
if not asbool(only_if_compiling_contained_td):
if components_list not in required_repository_tups:
required_repository_tups.append(components_list)
for components_list in val:
try:
only_if_compiling_contained_td = components_list[5]
except:
only_if_compiling_contained_td = 'False'
# Skip listing a repository dependency if it is required only to compile a tool dependency
# defined for the dependent repository (see above comment).
if not asbool(only_if_compiling_contained_td):
if components_list not in required_repository_tups:
required_repository_tups.append(components_list)
else:
# We have a single repository with no dependencies.
components_list = [tool_shed_url, repository_name, repository_owner, changeset_revision]
required_repository_tups.append(components_list)
if required_repository_tups:
# The value of required_repository_tups is a list of tuples, so we need to encode it.
encoded_required_repository_tups = []
for required_repository_tup in required_repository_tups:
# Convert every item in required_repository_tup to a string.
required_repository_tup = [str(item) for item in required_repository_tup]
encoded_required_repository_tups.append(encoding_util.encoding_sep.join(required_repository_tup))
encoded_required_repository_str = encoding_util.encoding_sep2.join(encoded_required_repository_tups)
encoded_required_repository_str = encoding_util.tool_shed_encode(encoded_required_repository_str)
if repository_util.is_tool_shed_client(self.app):
# Handle secure / insecure Tool Shed URL protocol changes and port changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_shed_url)
pathspec = ['repository', 'get_required_repo_info_dict']
url = build_url(tool_shed_url, pathspec=pathspec)
# Fix for handling 307 redirect not being handled nicely by urlopen() when the Request() has data provided
url = _urlopen(url).geturl()
response = _urlopen(url, urlencode(dict(encoded_str=encoded_required_repository_str))).read()
if response:
try:
required_repo_info_dict = json.loads(response)
except Exception as e:
log.exception(e)
return all_repo_info_dicts
required_repo_info_dicts = []
for k, v in required_repo_info_dict.items():
if k == 'repo_info_dicts':
encoded_dict_strings = required_repo_info_dict['repo_info_dicts']
for encoded_dict_str in encoded_dict_strings:
decoded_dict = encoding_util.tool_shed_decode(encoded_dict_str)
required_repo_info_dicts.append(decoded_dict)
else:
if k not in all_required_repo_info_dict:
all_required_repo_info_dict[k] = v
else:
if v and not all_required_repo_info_dict[k]:
all_required_repo_info_dict[k] = v
if required_repo_info_dicts:
for required_repo_info_dict in required_repo_info_dicts:
# Each required_repo_info_dict has a single entry, and all_repo_info_dicts is a list
# of dictionaries, each of which has a single entry. We'll check keys here rather than
# the entire dictionary because a dictionary entry in all_repo_info_dicts will include
# lists of discovered repository dependencies, but these lists will be empty in the
# required_repo_info_dict since dependency discovery has not yet been performed for these
# dictionaries.
required_repo_info_dict_key = next(iter(required_repo_info_dict))
all_repo_info_dicts_keys = [next(iter(d)) for d in all_repo_info_dicts]
if required_repo_info_dict_key not in all_repo_info_dicts_keys:
all_repo_info_dicts.append(required_repo_info_dict)
else:
# required_repo_info_dict_key corresponds to the repo name.
# A single install transaction might require the installation of 2 or more repos
# with the same repo name but different owners or versions.
# Therefore, if required_repo_info_dict_key is already in all_repo_info_dicts,
# check that the tool id is already present. If it is not, we are dealing with the same repo name,
# but a different owner/changeset revision or version and we add the repo to the list of repos to be installed.
tool_id = required_repo_info_dict[required_repo_info_dict_key][1]
is_present = False
for repo_info_dict in all_repo_info_dicts:
for k, v in repo_info_dict.items():
if required_repo_info_dict_key == k:
if tool_id == v[1]:
is_present = True
break
if not is_present:
all_repo_info_dicts.append(required_repo_info_dict)
all_required_repo_info_dict['all_repo_info_dicts'] = all_repo_info_dicts
return all_required_repo_info_dict
def create_repository_dependency_objects(self, tool_path, tool_shed_url, repo_info_dicts, install_repository_dependencies=False,
no_changes_checked=False, tool_panel_section_id=None, new_tool_panel_section_label=None):
"""
Discover all repository dependencies and make sure all tool_shed_repository and
associated repository_dependency records exist as well as the dependency relationships
between installed repositories. This method is called when uninstalled repositories
are being reinstalled. If the user elected to install repository dependencies, all
items in the all_repo_info_dicts list will be processed. However, if repository
dependencies are not to be installed, only those items contained in the received
repo_info_dicts list will be processed.
"""
install_model = self.app.install_model
log.debug("Creating repository dependency objects...")
# The following list will be maintained within this method to contain all created
# or updated tool shed repositories, including repository dependencies that may not
# be installed.
all_created_or_updated_tool_shed_repositories = []
# There will be a one-to-one mapping between items in 3 lists:
# created_or_updated_tool_shed_repositories, tool_panel_section_keys
# and filtered_repo_info_dicts. The 3 lists will filter out repository
# dependencies that are not to be installed.
created_or_updated_tool_shed_repositories = []
tool_panel_section_keys = []
# Repositories will be filtered (e.g., if already installed, if elected
# to not be installed, etc), so filter the associated repo_info_dicts accordingly.
filtered_repo_info_dicts = []
# Discover all repository dependencies and retrieve information for installing
# them. Even if the user elected to not install repository dependencies we have
# to make sure all repository dependency objects exist so that the appropriate
# repository dependency relationships can be built.
all_required_repo_info_dict = self.get_required_repo_info_dicts(tool_shed_url, repo_info_dicts)
all_repo_info_dicts = all_required_repo_info_dict.get('all_repo_info_dicts', [])
if not all_repo_info_dicts:
# No repository dependencies were discovered so process the received repositories.
all_repo_info_dicts = [rid for rid in repo_info_dicts]
for repo_info_dict in all_repo_info_dicts:
# If the user elected to install repository dependencies, all items in the
# all_repo_info_dicts list will be processed. However, if repository dependencies
# are not to be installed, only those items contained in the received repo_info_dicts
# list will be processed but the all_repo_info_dicts list will be used to create all
# defined repository dependency relationships.
if self.is_in_repo_info_dicts(repo_info_dict, repo_info_dicts) or install_repository_dependencies:
for name, repo_info_tuple in repo_info_dict.items():
can_update_db_record = False
description, \
repository_clone_url, \
changeset_revision, \
ctx_rev, \
repository_owner, \
repository_dependencies, \
tool_dependencies = \
repository_util.get_repo_info_tuple_contents(repo_info_tuple)
# See if the repository has an existing record in the database.
repository_db_record, installed_changeset_revision = \
repository_util.repository_was_previously_installed(self.app, tool_shed_url, name, repo_info_tuple, from_tip=False)
if repository_db_record:
if repository_db_record.status in [install_model.ToolShedRepository.installation_status.INSTALLED,
install_model.ToolShedRepository.installation_status.CLONING,
install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES]:
debug_msg = "Skipping installation of revision %s of repository '%s' because it was installed " % \
(str(changeset_revision), str(repository_db_record.name))
debug_msg += "with the (possibly updated) revision %s and its current installation status is '%s'." % \
(str(installed_changeset_revision), str(repository_db_record.status))
log.debug(debug_msg)
can_update_db_record = False
else:
if repository_db_record.status in [install_model.ToolShedRepository.installation_status.ERROR,
install_model.ToolShedRepository.installation_status.NEW,
install_model.ToolShedRepository.installation_status.UNINSTALLED]:
# The current tool shed repository is not currently installed, so we can update its
# record in the database.
name = repository_db_record.name
installed_changeset_revision = repository_db_record.installed_changeset_revision
can_update_db_record = True
elif repository_db_record.status in [install_model.ToolShedRepository.installation_status.DEACTIVATED]:
# The current tool shed repository is deactivated, so updating its database record
# is not necessary - just activate it.
log.debug("Reactivating deactivated tool_shed_repository '%s'." % str(repository_db_record.name))
self.app.installed_repository_manager.activate_repository(repository_db_record)
# No additional updates to the database record are necessary.
can_update_db_record = False
elif repository_db_record.status not in [install_model.ToolShedRepository.installation_status.NEW]:
# Set changeset_revision here so repository_util.create_or_update_tool_shed_repository will find
# the previously installed and uninstalled repository instead of creating a new record.
changeset_revision = repository_db_record.installed_changeset_revision
self.reset_previously_installed_repository(repository_db_record)
can_update_db_record = True
else:
# No record exists in the database for the repository currently being processed.
installed_changeset_revision = changeset_revision
can_update_db_record = True
if can_update_db_record:
# The database record for the tool shed repository currently being processed can be updated.
# Get the repository metadata to see where it was previously located in the tool panel.
tpm = tool_panel_manager.ToolPanelManager(self.app)
if repository_db_record and repository_db_record.metadata:
_, tool_panel_section_key = \
tpm.handle_tool_panel_selection(toolbox=self.app.toolbox,
metadata=repository_db_record.metadata,
no_changes_checked=no_changes_checked,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=new_tool_panel_section_label)
else:
# We're installing a new tool shed repository that does not yet have a database record.
tool_panel_section_key, _ = \
tpm.handle_tool_panel_section(self.app.toolbox,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=new_tool_panel_section_label)
tool_shed_repository = \
repository_util.create_or_update_tool_shed_repository(app=self.app,
name=name,
description=description,
installed_changeset_revision=installed_changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=changeset_revision,
owner=repository_owner,
dist_to_shed=False)
if tool_shed_repository not in all_created_or_updated_tool_shed_repositories:
all_created_or_updated_tool_shed_repositories.append(tool_shed_repository)
# Only append the tool shed repository to the list of created_or_updated_tool_shed_repositories if
# it is supposed to be installed.
if install_repository_dependencies or self.is_in_repo_info_dicts(repo_info_dict, repo_info_dicts):
if tool_shed_repository not in created_or_updated_tool_shed_repositories:
# Keep the one-to-one mapping between items in 3 lists.
created_or_updated_tool_shed_repositories.append(tool_shed_repository)
tool_panel_section_keys.append(tool_panel_section_key)
filtered_repo_info_dicts.append(repo_info_dict)
# Build repository dependency relationships even if the user chose to not install repository dependencies.
self.build_repository_dependency_relationships(all_repo_info_dicts, all_created_or_updated_tool_shed_repositories)
return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts
def build_repository_dependency_relationships(self, repo_info_dicts, tool_shed_repositories):
"""
Build relationships between installed tool shed repositories and other installed
tool shed repositories upon which they depend. These relationships are defined in
the repository_dependencies entry for each dictionary in the received list of repo_info_dicts.
Each of these dictionaries is associated with a repository in the received tool_shed_repositories
list.
"""
install_model = self.app.install_model
log.debug("Building repository dependency relationships...")
for repo_info_dict in repo_info_dicts:
for name, repo_info_tuple in repo_info_dict.items():
description, \
repository_clone_url, \
changeset_revision, \
ctx_rev, \
repository_owner, \
repository_dependencies, \
tool_dependencies = \
repository_util.get_repo_info_tuple_contents(repo_info_tuple)
if repository_dependencies:
for key, val in repository_dependencies.items():
if key in ['root_key', 'description']:
continue
d_repository = None
repository_components_tuple = container_util.get_components_from_key(key)
components_list = repository_util.extract_components_from_tuple(repository_components_tuple)
d_toolshed, d_name, d_owner, d_changeset_revision = components_list[0:4]
for tsr in tool_shed_repositories:
# Get the the tool_shed_repository defined by name, owner and changeset_revision. This is
# the repository that will be dependent upon each of the tool shed repositories contained in
# val. We'll need to check tool_shed_repository.tool_shed as well if/when repository dependencies
# across tool sheds is supported.
if tsr.name == d_name and tsr.owner == d_owner and tsr.changeset_revision == d_changeset_revision:
d_repository = tsr
break
if d_repository is None:
# The dependent repository is not in the received list so look in the database.
d_repository = self.get_or_create_tool_shed_repository(d_toolshed,
d_name,
d_owner,
d_changeset_revision)
# Process each repository_dependency defined for the current dependent repository.
for repository_dependency_components_list in val:
required_repository = None
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_components_list)
# Get the the tool_shed_repository defined by rd_name, rd_owner and rd_changeset_revision. This
# is the repository that will be required by the current d_repository.
# TODO: Check tool_shed_repository.tool_shed as well when repository dependencies across tool sheds is supported.
for tsr in tool_shed_repositories:
if tsr.name == rd_name and tsr.owner == rd_owner and tsr.changeset_revision == rd_changeset_revision:
required_repository = tsr
break
if required_repository is None:
# The required repository is not in the received list so look in the database.
required_repository = self.get_or_create_tool_shed_repository(rd_toolshed,
rd_name,
rd_owner,
rd_changeset_revision)
# Ensure there is a repository_dependency relationship between d_repository and required_repository.
rrda = None
for rd in d_repository.repository_dependencies:
if rd.id == required_repository.id:
rrda = rd
break
if not rrda:
# Make sure required_repository is in the repository_dependency table.
repository_dependency = self.get_repository_dependency_by_repository_id(install_model,
required_repository.id)
if not repository_dependency:
log.debug('Creating new repository_dependency record for installed revision %s of repository: %s owned by %s.' %
(str(required_repository.installed_changeset_revision),
str(required_repository.name),
str(required_repository.owner)))
repository_dependency = install_model.RepositoryDependency(tool_shed_repository_id=required_repository.id)
install_model.context.add(repository_dependency)
install_model.context.flush()
# Build the relationship between the d_repository and the required_repository.
rrda = install_model.RepositoryRepositoryDependencyAssociation(tool_shed_repository_id=d_repository.id,
repository_dependency_id=repository_dependency.id)
install_model.context.add(rrda)
install_model.context.flush()
def populate_tool_dependencies_dicts(
self, tool_shed_url, tool_path,
repository_installed_tool_dependencies,
repository_missing_tool_dependencies, required_repo_info_dicts):
"""
Return the populated installed_tool_dependencies and missing_tool_dependencies dictionaries
for all repositories defined by entries in the received required_repo_info_dicts.
"""
installed_tool_dependencies = None
missing_tool_dependencies = None
if repository_installed_tool_dependencies is None:
repository_installed_tool_dependencies = {}
else:
# Add the install_dir attribute to the tool_dependencies.
repository_installed_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( repository_installed_tool_dependencies )
if repository_missing_tool_dependencies is None:
repository_missing_tool_dependencies = {}
else:
# Add the install_dir attribute to the tool_dependencies.
repository_missing_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( repository_missing_tool_dependencies )
if required_repo_info_dicts:
# Handle the tool dependencies defined for each of the repository's repository dependencies.
for rid in required_repo_info_dicts:
for name, repo_info_tuple in rid.items():
description, repository_clone_url, changeset_revision, \
ctx_rev, repository_owner, repository_dependencies, \
tool_dependencies = \
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
if tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
tool_dependencies = self.add_installation_directories_to_tool_dependencies(
tool_dependencies)
# The required_repository may have been installed with a different changeset revision.
required_repository, installed_changeset_revision = \
repository_util.repository_was_previously_installed( self.app,
tool_shed_url,
name,
repo_info_tuple,
from_tip=False )
if required_repository:
required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \
self.get_installed_and_missing_tool_dependencies_for_installed_repository( required_repository,
tool_dependencies )
if required_repository_installed_tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
required_repository_installed_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( required_repository_installed_tool_dependencies )
for td_key, td_dict in required_repository_installed_tool_dependencies.items(
):
if td_key not in repository_installed_tool_dependencies:
repository_installed_tool_dependencies[
td_key] = td_dict
if required_repository_missing_tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
required_repository_missing_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( required_repository_missing_tool_dependencies )
for td_key, td_dict in required_repository_missing_tool_dependencies.items(
):
if td_key not in repository_missing_tool_dependencies:
repository_missing_tool_dependencies[
td_key] = td_dict
if repository_installed_tool_dependencies:
installed_tool_dependencies = repository_installed_tool_dependencies
if repository_missing_tool_dependencies:
missing_tool_dependencies = repository_missing_tool_dependencies
return installed_tool_dependencies, missing_tool_dependencies
def populate_tool_dependencies_dicts( self, tool_shed_url, tool_path, repository_installed_tool_dependencies,
repository_missing_tool_dependencies, required_repo_info_dicts ):
"""
Return the populated installed_tool_dependencies and missing_tool_dependencies dictionaries
for all repositories defined by entries in the received required_repo_info_dicts.
"""
installed_tool_dependencies = None
missing_tool_dependencies = None
if repository_installed_tool_dependencies is None:
repository_installed_tool_dependencies = {}
else:
# Add the install_dir attribute to the tool_dependencies.
repository_installed_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( repository_installed_tool_dependencies )
if repository_missing_tool_dependencies is None:
repository_missing_tool_dependencies = {}
else:
# Add the install_dir attribute to the tool_dependencies.
repository_missing_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( repository_missing_tool_dependencies )
if required_repo_info_dicts:
# Handle the tool dependencies defined for each of the repository's repository dependencies.
for rid in required_repo_info_dicts:
for name, repo_info_tuple in rid.items():
description, repository_clone_url, changeset_revision, \
ctx_rev, repository_owner, repository_dependencies, \
tool_dependencies = \
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
if tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
tool_dependencies = self.add_installation_directories_to_tool_dependencies( tool_dependencies )
# The required_repository may have been installed with a different changeset revision.
required_repository, installed_changeset_revision = \
repository_util.repository_was_previously_installed( self.app,
tool_shed_url,
name,
repo_info_tuple,
from_tip=False )
if required_repository:
required_repository_installed_tool_dependencies, required_repository_missing_tool_dependencies = \
self.get_installed_and_missing_tool_dependencies_for_installed_repository( required_repository,
tool_dependencies )
if required_repository_installed_tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
required_repository_installed_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( required_repository_installed_tool_dependencies )
for td_key, td_dict in required_repository_installed_tool_dependencies.items():
if td_key not in repository_installed_tool_dependencies:
repository_installed_tool_dependencies[ td_key ] = td_dict
if required_repository_missing_tool_dependencies:
# Add the install_dir attribute to the tool_dependencies.
required_repository_missing_tool_dependencies = \
self.add_installation_directories_to_tool_dependencies( required_repository_missing_tool_dependencies )
for td_key, td_dict in required_repository_missing_tool_dependencies.items():
if td_key not in repository_missing_tool_dependencies:
repository_missing_tool_dependencies[ td_key ] = td_dict
if repository_installed_tool_dependencies:
installed_tool_dependencies = repository_installed_tool_dependencies
if repository_missing_tool_dependencies:
missing_tool_dependencies = repository_missing_tool_dependencies
return installed_tool_dependencies, missing_tool_dependencies
def get_required_repo_info_dicts( self, tool_shed_url, repo_info_dicts ):
"""
Inspect the list of repo_info_dicts for repository dependencies and append a repo_info_dict for each of
them to the list. All repository_dependency entries in each of the received repo_info_dicts includes
all required repositories, so only one pass through this method is required to retrieve all repository
dependencies.
"""
all_required_repo_info_dict = {}
all_repo_info_dicts = []
if repo_info_dicts:
# We'll send tuples of ( tool_shed, repository_name, repository_owner, changeset_revision ) to the tool
# shed to discover repository ids.
required_repository_tups = []
for repo_info_dict in repo_info_dicts:
if repo_info_dict not in all_repo_info_dicts:
all_repo_info_dicts.append( repo_info_dict )
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 = \
repository_util.get_repo_info_tuple_contents( repo_info_tup )
if repository_dependencies:
for key, val in repository_dependencies.items():
if key in [ 'root_key', 'description' ]:
continue
repository_components_tuple = container_util.get_components_from_key( key )
components_list = repository_util.extract_components_from_tuple( repository_components_tuple )
# Skip listing a repository dependency if it is required only to compile a tool dependency
# defined for the dependent repository since in this case, the repository dependency is really
# a dependency of the dependent repository's contained tool dependency, and only if that
# tool dependency requires compilation.
# For backward compatibility to the 12/20/12 Galaxy release.
only_if_compiling_contained_td = 'False'
if len( components_list ) == 4:
only_if_compiling_contained_td = 'False'
elif len( components_list ) == 5:
only_if_compiling_contained_td = 'False'
if not asbool( only_if_compiling_contained_td ):
if components_list not in required_repository_tups:
required_repository_tups.append( components_list )
for components_list in val:
try:
only_if_compiling_contained_td = components_list[ 5 ]
except:
only_if_compiling_contained_td = 'False'
# Skip listing a repository dependency if it is required only to compile a tool dependency
# defined for the dependent repository (see above comment).
if not asbool( only_if_compiling_contained_td ):
if components_list not in required_repository_tups:
required_repository_tups.append( components_list )
else:
# We have a single repository with no dependencies.
components_list = [ tool_shed_url, repository_name, repository_owner, changeset_revision ]
required_repository_tups.append( components_list )
if required_repository_tups:
# The value of required_repository_tups is a list of tuples, so we need to encode it.
encoded_required_repository_tups = []
for required_repository_tup in required_repository_tups:
# Convert every item in required_repository_tup to a string.
required_repository_tup = [ str( item ) for item in required_repository_tup ]
encoded_required_repository_tups.append( encoding_util.encoding_sep.join( required_repository_tup ) )
encoded_required_repository_str = encoding_util.encoding_sep2.join( encoded_required_repository_tups )
encoded_required_repository_str = encoding_util.tool_shed_encode( encoded_required_repository_str )
if repository_util.is_tool_shed_client( self.app ):
# Handle secure / insecure Tool Shed URL protocol changes and port changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed_url )
pathspec = [ 'repository', 'get_required_repo_info_dict' ]
url = build_url( tool_shed_url, pathspec=pathspec )
# Fix for handling 307 redirect not being handled nicely by urlopen() when the Request() has data provided
url = urlopen( Request( url ) ).geturl()
request = Request( url, data=urlencode( dict( encoded_str=encoded_required_repository_str ) ) )
response = urlopen( request ).read()
if response:
try:
required_repo_info_dict = json.loads( response )
except Exception as e:
log.exception( e )
return all_repo_info_dicts
required_repo_info_dicts = []
for k, v in required_repo_info_dict.items():
if k == 'repo_info_dicts':
encoded_dict_strings = required_repo_info_dict[ 'repo_info_dicts' ]
for encoded_dict_str in encoded_dict_strings:
decoded_dict = encoding_util.tool_shed_decode( encoded_dict_str )
required_repo_info_dicts.append( decoded_dict )
else:
if k not in all_required_repo_info_dict:
all_required_repo_info_dict[ k ] = v
else:
if v and not all_required_repo_info_dict[ k ]:
all_required_repo_info_dict[ k ] = v
if required_repo_info_dicts:
for required_repo_info_dict in required_repo_info_dicts:
# Each required_repo_info_dict has a single entry, and all_repo_info_dicts is a list
# of dictionaries, each of which has a single entry. We'll check keys here rather than
# the entire dictionary because a dictionary entry in all_repo_info_dicts will include
# lists of discovered repository dependencies, but these lists will be empty in the
# required_repo_info_dict since dependency discovery has not yet been performed for these
# dictionaries.
required_repo_info_dict_key = next(iter(required_repo_info_dict))
all_repo_info_dicts_keys = [ next(iter(d)) for d in all_repo_info_dicts ]
if required_repo_info_dict_key not in all_repo_info_dicts_keys:
all_repo_info_dicts.append( required_repo_info_dict )
else:
# required_repo_info_dict_key corresponds to the repo name.
# A single install transaction might require the installation of 2 or more repos
# with the same repo name but different owners or versions.
# Therefore, if required_repo_info_dict_key is already in all_repo_info_dicts,
# check that the tool id is already present. If it is not, we are dealing with the same repo name,
# but a different owner/changeset revision or version and we add the repo to the list of repos to be installed.
tool_id = required_repo_info_dict[ required_repo_info_dict_key ][ 1 ]
is_present = False
for repo_info_dict in all_repo_info_dicts:
for k, v in repo_info_dict.items():
if required_repo_info_dict_key == k:
if tool_id == v[1]:
is_present = True
break
if not is_present:
all_repo_info_dicts.append( required_repo_info_dict )
all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts
return all_required_repo_info_dict
def build_repository_dependency_relationships( self, repo_info_dicts, tool_shed_repositories ):
"""
Build relationships between installed tool shed repositories and other installed
tool shed repositories upon which they depend. These relationships are defined in
the repository_dependencies entry for each dictionary in the received list of repo_info_dicts.
Each of these dictionaries is associated with a repository in the received tool_shed_repositories
list.
"""
install_model = self.app.install_model
log.debug( "Building repository dependency relationships..." )
for repo_info_dict in repo_info_dicts:
for name, repo_info_tuple in repo_info_dict.items():
description, \
repository_clone_url, \
changeset_revision, \
ctx_rev, \
repository_owner, \
repository_dependencies, \
tool_dependencies = \
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
if repository_dependencies:
for key, val in repository_dependencies.items():
if key in [ 'root_key', 'description' ]:
continue
d_repository = None
repository_components_tuple = container_util.get_components_from_key( key )
components_list = repository_util.extract_components_from_tuple( repository_components_tuple )
d_toolshed, d_name, d_owner, d_changeset_revision = components_list[ 0:4 ]
for tsr in tool_shed_repositories:
# Get the the tool_shed_repository defined by name, owner and changeset_revision. This is
# the repository that will be dependent upon each of the tool shed repositories contained in
# val. We'll need to check tool_shed_repository.tool_shed as well if/when repository dependencies
# across tool sheds is supported.
if tsr.name == d_name and tsr.owner == d_owner and tsr.changeset_revision == d_changeset_revision:
d_repository = tsr
break
if d_repository is None:
# The dependent repository is not in the received list so look in the database.
d_repository = self.get_or_create_tool_shed_repository( d_toolshed,
d_name,
d_owner,
d_changeset_revision )
# Process each repository_dependency defined for the current dependent repository.
for repository_dependency_components_list in val:
required_repository = None
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_components_list )
# Get the the tool_shed_repository defined by rd_name, rd_owner and rd_changeset_revision. This
# is the repository that will be required by the current d_repository.
# TODO: Check tool_shed_repository.tool_shed as well when repository dependencies across tool sheds is supported.
for tsr in tool_shed_repositories:
if tsr.name == rd_name and tsr.owner == rd_owner and tsr.changeset_revision == rd_changeset_revision:
required_repository = tsr
break
if required_repository is None:
# The required repository is not in the received list so look in the database.
required_repository = self.get_or_create_tool_shed_repository( rd_toolshed,
rd_name,
rd_owner,
rd_changeset_revision )
# Ensure there is a repository_dependency relationship between d_repository and required_repository.
rrda = None
for rd in d_repository.repository_dependencies:
if rd.id == required_repository.id:
rrda = rd
break
if not rrda:
# Make sure required_repository is in the repository_dependency table.
repository_dependency = self.get_repository_dependency_by_repository_id( install_model,
required_repository.id )
if not repository_dependency:
log.debug( 'Creating new repository_dependency record for installed revision %s of repository: %s owned by %s.' %
( str( required_repository.installed_changeset_revision ),
str( required_repository.name ),
str( required_repository.owner ) ) )
repository_dependency = install_model.RepositoryDependency( tool_shed_repository_id=required_repository.id )
install_model.context.add( repository_dependency )
install_model.context.flush()
# Build the relationship between the d_repository and the required_repository.
rrda = install_model.RepositoryRepositoryDependencyAssociation( tool_shed_repository_id=d_repository.id,
repository_dependency_id=repository_dependency.id )
install_model.context.add( rrda )
install_model.context.flush()
def create_repository_dependency_objects( self, tool_path, tool_shed_url, repo_info_dicts, install_repository_dependencies=False,
no_changes_checked=False, tool_panel_section_id=None, new_tool_panel_section_label=None ):
"""
Discover all repository dependencies and make sure all tool_shed_repository and
associated repository_dependency records exist as well as the dependency relationships
between installed repositories. This method is called when uninstalled repositories
are being reinstalled. If the user elected to install repository dependencies, all
items in the all_repo_info_dicts list will be processed. However, if repository
dependencies are not to be installed, only those items contained in the received
repo_info_dicts list will be processed.
"""
install_model = self.app.install_model
log.debug( "Creating repository dependency objects..." )
# The following list will be maintained within this method to contain all created
# or updated tool shed repositories, including repository dependencies that may not
# be installed.
all_created_or_updated_tool_shed_repositories = []
# There will be a one-to-one mapping between items in 3 lists:
# created_or_updated_tool_shed_repositories, tool_panel_section_keys
# and filtered_repo_info_dicts. The 3 lists will filter out repository
# dependencies that are not to be installed.
created_or_updated_tool_shed_repositories = []
tool_panel_section_keys = []
# Repositories will be filtered (e.g., if already installed, if elected
# to not be installed, etc), so filter the associated repo_info_dicts accordingly.
filtered_repo_info_dicts = []
# Discover all repository dependencies and retrieve information for installing
# them. Even if the user elected to not install repository dependencies we have
# to make sure all repository dependency objects exist so that the appropriate
# repository dependency relationships can be built.
all_required_repo_info_dict = self.get_required_repo_info_dicts( tool_shed_url, repo_info_dicts )
all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] )
if not all_repo_info_dicts:
# No repository dependencies were discovered so process the received repositories.
all_repo_info_dicts = [ rid for rid in repo_info_dicts ]
for repo_info_dict in all_repo_info_dicts:
# If the user elected to install repository dependencies, all items in the
# all_repo_info_dicts list will be processed. However, if repository dependencies
# are not to be installed, only those items contained in the received repo_info_dicts
# list will be processed but the all_repo_info_dicts list will be used to create all
# defined repository dependency relationships.
if self.is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ) or install_repository_dependencies:
for name, repo_info_tuple in repo_info_dict.items():
can_update_db_record = False
description, \
repository_clone_url, \
changeset_revision, \
ctx_rev, \
repository_owner, \
repository_dependencies, \
tool_dependencies = \
repository_util.get_repo_info_tuple_contents( repo_info_tuple )
# See if the repository has an existing record in the database.
repository_db_record, installed_changeset_revision = \
repository_util.repository_was_previously_installed( self.app, tool_shed_url, name, repo_info_tuple, from_tip=False )
if repository_db_record:
if repository_db_record.status in [ install_model.ToolShedRepository.installation_status.INSTALLED,
install_model.ToolShedRepository.installation_status.CLONING,
install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS,
install_model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES,
install_model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES,
install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ]:
debug_msg = "Skipping installation of revision %s of repository '%s' because it was installed " % \
( str( changeset_revision ), str( repository_db_record.name ) )
debug_msg += "with the (possibly updated) revision %s and its current installation status is '%s'." % \
( str( installed_changeset_revision ), str( repository_db_record.status ) )
log.debug( debug_msg )
can_update_db_record = False
else:
if repository_db_record.status in [ install_model.ToolShedRepository.installation_status.ERROR,
install_model.ToolShedRepository.installation_status.NEW,
install_model.ToolShedRepository.installation_status.UNINSTALLED ]:
# The current tool shed repository is not currently installed, so we can update its
# record in the database.
name = repository_db_record.name
installed_changeset_revision = repository_db_record.installed_changeset_revision
can_update_db_record = True
elif repository_db_record.status in [ install_model.ToolShedRepository.installation_status.DEACTIVATED ]:
# The current tool shed repository is deactivated, so updating its database record
# is not necessary - just activate it.
log.debug( "Reactivating deactivated tool_shed_repository '%s'." % str( repository_db_record.name ) )
self.app.installed_repository_manager.activate_repository( repository_db_record )
# No additional updates to the database record are necessary.
can_update_db_record = False
elif repository_db_record.status not in [ install_model.ToolShedRepository.installation_status.NEW ]:
# Set changeset_revision here so repository_util.create_or_update_tool_shed_repository will find
# the previously installed and uninstalled repository instead of creating a new record.
changeset_revision = repository_db_record.installed_changeset_revision
self.reset_previously_installed_repository( repository_db_record )
can_update_db_record = True
else:
# No record exists in the database for the repository currently being processed.
installed_changeset_revision = changeset_revision
can_update_db_record = True
if can_update_db_record:
# The database record for the tool shed repository currently being processed can be updated.
# Get the repository metadata to see where it was previously located in the tool panel.
tpm = tool_panel_manager.ToolPanelManager( self.app )
if repository_db_record and repository_db_record.metadata:
_, tool_panel_section_key = \
tpm.handle_tool_panel_selection( toolbox=self.app.toolbox,
metadata=repository_db_record.metadata,
no_changes_checked=no_changes_checked,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=new_tool_panel_section_label )
else:
# We're installing a new tool shed repository that does not yet have a database record.
tool_panel_section_key, _ = \
tpm.handle_tool_panel_section( self.app.toolbox,
tool_panel_section_id=tool_panel_section_id,
new_tool_panel_section_label=new_tool_panel_section_label )
tool_shed_repository = \
repository_util.create_or_update_tool_shed_repository( app=self.app,
name=name,
description=description,
installed_changeset_revision=installed_changeset_revision,
ctx_rev=ctx_rev,
repository_clone_url=repository_clone_url,
metadata_dict={},
status=install_model.ToolShedRepository.installation_status.NEW,
current_changeset_revision=changeset_revision,
owner=repository_owner,
dist_to_shed=False )
if tool_shed_repository not in all_created_or_updated_tool_shed_repositories:
all_created_or_updated_tool_shed_repositories.append( tool_shed_repository )
# Only append the tool shed repository to the list of created_or_updated_tool_shed_repositories if
# it is supposed to be installed.
if install_repository_dependencies or self.is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ):
if tool_shed_repository not in created_or_updated_tool_shed_repositories:
# Keep the one-to-one mapping between items in 3 lists.
created_or_updated_tool_shed_repositories.append( tool_shed_repository )
tool_panel_section_keys.append( tool_panel_section_key )
filtered_repo_info_dicts.append( repo_info_dict )
# Build repository dependency relationships even if the user chose to not install repository dependencies.
self.build_repository_dependency_relationships( all_repo_info_dicts, all_created_or_updated_tool_shed_repositories )
return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts
