def get_bibtex(this):
from galaxy.managers.citations import CitationsManager
citations = []
for e in this.history.contents_iter():
if e.creating_job.any_output_dataset_deleted is True or e.creating_job.any_output_dataset_collection_instances_deleted is True:
continue
b = CitationsManager(this.trans.app).citations_for_tool_ids([e.creating_job.tool_id])
if b:
bib = b[0].to_bibtex()
if b[0].has_doi and re.search(r'title\s*=\s*\{.+', bib) is None:
try:
if isinstance(b[0], DoiCitation):
tmp = CitationsManager(this.trans.app).doi_cache.get_bibtex(b[0].doi())
bib = tmp
else:
doi = re.search(r'doi\s*=\s*\{(.+)\}', b).group(1)
tmp = CitationsManager(this.trans.app).doi_cache.get_bibtex(doi)
bib = tmp
except:
pass
bib = bib.lstrip()
if not bib in citations:
citations.append(bib)
this.bibtex = this.bibtex + "\n\n" + bib
return {
'bibtex': this.bibtex
}
def __init__(self, **kwd):
log.debug("python path is: %s", ", ".join(sys.path))
self.name = "tool_shed"
# Read the tool_shed.ini configuration file and check for errors.
self.config = config.Configuration(**kwd)
self.config.check()
configure_logging(self.config)
self.application_stack = application_stack_instance()
# Initialize the Galaxy datatypes registry.
self.datatypes_registry = galaxy.datatypes.registry.Registry()
self.datatypes_registry.load_datatypes(self.config.root,
self.config.datatypes_config)
# Initialize the Tool Shed repository_types registry.
self.repository_types_registry = tool_shed.repository_types.registry.Registry(
)
# Initialize the RepositoryGridFilterManager.
self.repository_grid_filter_manager = RepositoryGridFilterManager()
# Determine the Tool Shed database connection string.
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
# Initialize the Tool Shed database and check for appropriate schema version.
from galaxy.webapps.tool_shed.model.migrate.check import create_or_verify_database
create_or_verify_database(db_url, self.config.database_engine_options)
# Set up the Tool Shed database engine and ORM.
from galaxy.webapps.tool_shed.model import mapping
self.model = mapping.init(self.config.file_path, db_url,
self.config.database_engine_options)
self.security = idencoding.IdEncodingHelper(
id_secret=self.config.id_secret)
# initialize the Tool Shed tag handler.
self.tag_handler = CommunityTagHandler(self)
# Initialize the Tool Shed tool data tables. Never pass a configuration file here
# because the Tool Shed should always have an empty dictionary!
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(
self.config.tool_data_path)
self.genome_builds = GenomeBuilds(self)
from galaxy import auth
self.auth_manager = auth.AuthManager(self)
# Citation manager needed to load tools.
from galaxy.managers.citations import CitationsManager
self.citations_manager = CitationsManager(self)
# The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required.
self.toolbox = tools.ToolBox([], self.config.tool_path, self)
# Initialize the Tool Shed security agent.
self.security_agent = self.model.security_agent
# The Tool Shed makes no use of a quota, but this attribute is still required.
self.quota_agent = galaxy.quota.NoQuotaAgent(self.model)
# Initialize the baseline Tool Shed statistics component.
self.shed_counter = self.model.shed_counter
# Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located.
self.hgweb_config_manager = self.model.hgweb_config_manager
self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
# Initialize the repository registry.
self.repository_registry = tool_shed.repository_registry.Registry(self)
# used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
self.server_starttime = int(time.time())
log.debug("Tool shed hgweb.config file is: %s",
self.hgweb_config_manager.hgweb_config)
def __init__(self, **kwd):
print >> sys.stderr, "python path is: " + ", ".join(sys.path)
self.name = "tool_shed"
# Read the tool_shed_wsgi.ini configuration file and check for errors.
self.config = config.Configuration(**kwd)
self.config.check()
config.configure_logging(self.config)
# Initialize the Galaxy datatypes registry.
self.datatypes_registry = galaxy.datatypes.registry.Registry()
self.datatypes_registry.load_datatypes(self.config.root,
self.config.datatypes_config)
# Initialize the Tool Shed repository_types registry.
self.repository_types_registry = tool_shed.repository_types.registry.Registry(
)
# Initialize the RepositoryGridFilterManager.
self.repository_grid_filter_manager = RepositoryGridFilterManager()
# Determine the Tool Shed database connection string.
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
# Initialize the Tool Shed database and check for appropriate schema version.
from galaxy.webapps.tool_shed.model.migrate.check import create_or_verify_database
create_or_verify_database(db_url, self.config.database_engine_options)
# Set up the Tool Shed database engine and ORM.
from galaxy.webapps.tool_shed.model import mapping
self.model = mapping.init(self.config.file_path, db_url,
self.config.database_engine_options)
# Initialize the Tool SHed security helper.
self.security = security.SecurityHelper(
id_secret=self.config.id_secret)
# initialize the Tool Shed tag handler.
self.tag_handler = CommunityTagHandler()
# Initialize the Tool Shed tool data tables. Never pass a configuration file here
# because the Tool Shed should always have an empty dictionary!
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(
self.config.tool_data_path)
self.genome_builds = GenomeBuilds(self)
# Citation manager needed to load tools.
from galaxy.managers.citations import CitationsManager
self.citations_manager = CitationsManager(self)
# The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required.
self.toolbox = tools.ToolBox([], self.config.tool_path, self)
# Initialize the Tool Shed security agent.
self.security_agent = self.model.security_agent
# The Tool Shed makes no use of a quota, but this attribute is still required.
self.quota_agent = galaxy.quota.NoQuotaAgent(self.model)
# TODO: Add OpenID support
self.openid_providers = OpenIDProviders()
# Initialize the baseline Tool Shed statistics component.
self.shed_counter = self.model.shed_counter
# Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located.
self.hgweb_config_manager = self.model.hgweb_config_manager
self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
# Initialize the repository registry.
self.repository_registry = tool_shed.repository_registry.Registry(self)
print >> sys.stderr, "Tool shed hgweb.config file is: ", self.hgweb_config_manager.hgweb_config
def _configure_toolbox(self):
if not isinstance(self, BasicSharedApp):
raise Exception("Must inherit from BasicSharedApp")
self.citations_manager = CitationsManager(self)
self.biotools_metadata_source = get_galaxy_biotools_metadata_source(
self.config)
self.dynamic_tools_manager = DynamicToolManager(self)
self._toolbox_lock = threading.RLock()
self.toolbox = tools.ToolBox(self.config.tool_configs,
self.config.tool_path, self)
galaxy_root_dir = os.path.abspath(self.config.root)
file_path = os.path.abspath(self.config.file_path)
app_info = AppInfo(
galaxy_root_dir=galaxy_root_dir,
default_file_path=file_path,
tool_data_path=self.config.tool_data_path,
shed_tool_data_path=self.config.shed_tool_data_path,
outputs_to_working_directory=self.config.
outputs_to_working_directory,
container_image_cache_path=self.config.container_image_cache_path,
library_import_dir=self.config.library_import_dir,
enable_mulled_containers=self.config.enable_mulled_containers,
container_resolvers_config_file=self.config.
container_resolvers_config_file,
container_resolvers_config_dict=self.config.container_resolvers,
involucro_path=self.config.involucro_path,
involucro_auto_init=self.config.involucro_auto_init,
mulled_channels=self.config.mulled_channels,
)
mulled_resolution_cache = None
if self.config.mulled_resolution_cache_type:
cache_opts = {
"cache.type": self.config.mulled_resolution_cache_type,
"cache.data_dir": self.config.mulled_resolution_cache_data_dir,
"cache.lock_dir": self.config.mulled_resolution_cache_lock_dir,
"cache.expire": self.config.mulled_resolution_cache_expire,
}
mulled_resolution_cache = CacheManager(
**parse_cache_config_options(cache_opts)).get_cache(
'mulled_resolution')
self.container_finder = containers.ContainerFinder(
app_info, mulled_resolution_cache=mulled_resolution_cache)
self._set_enabled_container_types()
index_help = getattr(self.config, "index_tool_help", True)
self.toolbox_search = ToolBoxSearch(
self.toolbox,
index_dir=self.config.tool_search_index_dir,
index_help=index_help)
def _configure_toolbox( self ):
# Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file.
tool_configs = self.config.tool_configs
if self.config.migrated_tools_config not in tool_configs:
tool_configs.append( self.config.migrated_tools_config )
from galaxy.managers.citations import CitationsManager
self.citations_manager = CitationsManager( self )
from galaxy import tools
self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self )
self.reindex_tool_search()
from galaxy.tools.deps import containers
galaxy_root_dir = os.path.abspath(self.config.root)
file_path = os.path.abspath(getattr(self.config, "file_path"))
app_info = containers.AppInfo(
galaxy_root_dir,
default_file_path=file_path,
outputs_to_working_directory=self.config.outputs_to_working_directory,
container_image_cache_path=self.config.container_image_cache_path,
)
self.container_finder = containers.ContainerFinder(app_info)
def __init__(self, **kwd) -> None:
super().__init__()
self[BasicApp] = self
log.debug("python path is: %s", ", ".join(sys.path))
self.name = "tool_shed"
# will be overwritten when building WSGI app
self.is_webapp = False
# Read the tool_shed.ini configuration file and check for errors.
self.config: Any = config.Configuration(**kwd)
self.config.check()
configure_logging(self.config)
self.application_stack = application_stack_instance()
# Initialize the Galaxy datatypes registry.
self.datatypes_registry = galaxy.datatypes.registry.Registry()
self.datatypes_registry.load_datatypes(self.config.root,
self.config.datatypes_config)
# Initialize the Tool Shed repository_types registry.
self.repository_types_registry = tool_shed.repository_types.registry.Registry(
)
# Initialize the RepositoryGridFilterManager.
self.repository_grid_filter_manager = RepositoryGridFilterManager()
# Determine the Tool Shed database connection string.
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = f"sqlite:///{self.config.database}?isolation_level=IMMEDIATE"
# Initialize the Tool Shed database and check for appropriate schema version.
from tool_shed.webapp.model.migrate.check import create_or_verify_database
create_or_verify_database(db_url, self.config.database_engine_options)
# Set up the Tool Shed database engine and ORM.
from tool_shed.webapp.model import mapping
model: mapping.ToolShedModelMapping = mapping.init(
self.config.file_path, db_url, self.config.database_engine_options)
self.model = model
self.security = idencoding.IdEncodingHelper(
id_secret=self.config.id_secret)
self._register_singleton(idencoding.IdEncodingHelper, self.security)
self._register_singleton(SharedModelMapping, model)
self._register_singleton(mapping.ToolShedModelMapping, model)
self._register_singleton(scoped_session, self.model.context)
self._register_singleton(UserManager, UserManager)
# initialize the Tool Shed tag handler.
self.tag_handler = CommunityTagHandler(self)
# Initialize the Tool Shed tool data tables. Never pass a configuration file here
# because the Tool Shed should always have an empty dictionary!
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(
self.config.tool_data_path)
self.genome_builds = GenomeBuilds(self)
self.auth_manager = self._register_singleton(
auth.AuthManager, auth.AuthManager(self.config))
# Citation manager needed to load tools.
self.citations_manager = self._register_singleton(
CitationsManager, CitationsManager(self))
self.use_tool_dependency_resolution = False
# Initialize the Tool Shed security agent.
self.security_agent = model.security_agent
# The Tool Shed makes no use of a quota, but this attribute is still required.
self.quota_agent = self._register_singleton(QuotaAgent, NoQuotaAgent())
# Initialize the baseline Tool Shed statistics component.
self.shed_counter = model.shed_counter
# Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located.
self.hgweb_config_manager = hgweb_config_manager
self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
# Initialize the repository registry.
self.repository_registry = tool_shed.repository_registry.Registry(self)
# used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
self.server_starttime = int(time.time())
log.debug("Tool shed hgweb.config file is: %s",
self.hgweb_config_manager.hgweb_config)