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Source code for galaxy.datatypes.registry
"""
Provides mapping between extensions and datatypes, mime-types, etc.
"""
import imp
import logging
import os
from collections import OrderedDict
from string import Template
import yaml
import galaxy.util
from galaxy.util import RW_R__R__
from galaxy.util.bunch import Bunch
from . import (
binary,
coverage,
data,
images,
interval,
qualityscore,
sequence,
tabular,
text,
tracks,
xml
)
from .display_applications.application import DisplayApplication
[docs]class Registry:
[docs] def __init__(self, config=None):
self.log = logging.getLogger(__name__)
self.log.addHandler(logging.NullHandler())
self.config = config
self.datatypes_by_extension = {}
self.mimetypes_by_extension = {}
self.datatype_converters = OrderedDict()
# Converters defined in local datatypes_conf.xml
self.converters = []
self.converter_tools = set()
# Converters defined in datatypes_conf.xml included in installed tool shed repositories.
self.proprietary_converters = []
self.converter_deps = {}
self.available_tracks = []
self.set_external_metadata_tool = None
self.sniff_order = []
self.upload_file_formats = []
# Datatype elements defined in local datatypes_conf.xml that contain display applications.
self.display_app_containers = []
# Datatype elements in datatypes_conf.xml included in installed
# tool shed repositories that contain display applications.
self.proprietary_display_app_containers = []
# Map a display application id to a display application
self.display_applications = OrderedDict()
# The following 2 attributes are used in the to_xml_file()
# method to persist the current state into an xml file.
self.display_path_attr = None
self.converters_path_attr = None
# The 'default' converters_path defined in local datatypes_conf.xml
self.converters_path = None
# The 'default' display_path defined in local datatypes_conf.xml
self.display_applications_path = None
self.inherit_display_application_by_class = []
# Keep a list of imported proprietary datatype class modules.
self.imported_modules = []
self.datatype_elems = []
self.datatype_info_dicts = []
self.sniffer_elems = []
self._registry_xml_string = None
self._edam_formats_mapping = None
self._edam_data_mapping = None
self._converters_by_datatype = {}
# Build sites
self.build_sites = {}
self.display_sites = {}
self.legacy_build_sites = {}
[docs] def load_datatypes(self, root_dir=None, config=None, deactivate=False, override=True, use_converters=True, use_display_applications=True, use_build_sites=True):
"""
Parse a datatypes XML file located at root_dir/config (if processing the Galaxy distributed config) or contained within
an installed Tool Shed repository. If deactivate is True, an installed Tool Shed repository that includes custom datatypes
is being deactivated or uninstalled, so appropriate loaded datatypes will be removed from the registry. The value of
override will be False when a Tool Shed repository is being installed. Since installation is occurring after the datatypes
registry has been initialized at server startup, its contents cannot be overridden by newly introduced conflicting data types.
"""
def __import_module(full_path, datatype_module, datatype_class_name):
open_file_obj, file_name, description = imp.find_module(datatype_module, [full_path])
imported_module = imp.load_module(datatype_class_name, open_file_obj, file_name, description)
return imported_module
if root_dir and config:
# If handling_proprietary_datatypes is determined as True below, we'll have an elem that looks something like this:
# <datatype display_in_upload="true"
# extension="blastxml"
# mimetype="application/xml"
# proprietary_datatype_module="blast"
# proprietary_path="[cloned repository path]"
# type="galaxy.datatypes.blast:BlastXml" />
compressed_sniffers = {}
handling_proprietary_datatypes = False
if isinstance(config, str):
# Parse datatypes_conf.xml
tree = galaxy.util.parse_xml(config)
root = tree.getroot()
# Load datatypes and converters from config
if deactivate:
self.log.debug('Deactivating datatypes from %s' % config)
else:
self.log.debug('Loading datatypes from %s' % config)
else:
root = config
registration = root.find('registration')
# Set default paths defined in local datatypes_conf.xml.
if use_converters:
if not self.converters_path:
self.converters_path_attr = registration.get('converters_path', 'lib/galaxy/datatypes/converters')
self.converters_path = os.path.join(root_dir, self.converters_path_attr)
if self.converters_path_attr == 'lib/galaxy/datatypes/converters' \
and not os.path.isdir(self.converters_path):
# Deal with the old default of this path being set in
# datatypes_conf.xml.sample (this path is not useful in an
# "installed Galaxy" world)
self.converters_path_attr = os.path.abspath(os.path.join(os.path.dirname(__file__), 'converters'))
self.converters_path = self.converters_path_attr
if not os.path.isdir(self.converters_path):
raise ConfigurationError("Directory does not exist: %s" % self.converters_path)
if use_display_applications:
if not self.display_applications_path:
self.display_path_attr = registration.get('display_path', 'display_applications')
self.display_applications_path = os.path.join(root_dir, self.display_path_attr)
if self.display_path_attr == 'display_applications' \
and not os.path.isdir('display_applications'):
# Ditto as with converters_path
self.display_path_attr = os.path.abspath(os.path.join(os.path.dirname(__file__), 'display_applications', 'configs'))
self.display_applications_path = self.display_path_attr
# Proprietary datatype's <registration> tag may have special attributes, proprietary_converter_path and proprietary_display_path.
proprietary_converter_path = registration.get('proprietary_converter_path', None)
proprietary_display_path = registration.get('proprietary_display_path', None)
if proprietary_converter_path is not None or proprietary_display_path is not None and not handling_proprietary_datatypes:
handling_proprietary_datatypes = True
for elem in registration.findall('datatype'):
# Keep a status of the process steps to enable stopping the process of handling the datatype if necessary.
ok = True
extension = self.get_extension(elem)
dtype = elem.get('type', None)
type_extension = elem.get('type_extension', None)
auto_compressed_types = galaxy.util.listify(elem.get('auto_compressed_types', ''))
sniff_compressed_types = galaxy.util.string_as_bool_or_none(elem.get("sniff_compressed_types", "None"))
if sniff_compressed_types is None:
sniff_compressed_types = getattr(self.config, "sniff_compressed_dynamic_datatypes_default", True)
# Make sure this is set in the elems we write out so the config option is passed to the upload
# tool which does not have a config object.
elem.set("sniff_compressed_types", str(sniff_compressed_types))
mimetype = elem.get('mimetype', None)
display_in_upload = galaxy.util.string_as_bool(elem.get('display_in_upload', False))
# If make_subclass is True, it does not necessarily imply that we are subclassing a datatype that is contained
# in the distribution.
make_subclass = galaxy.util.string_as_bool(elem.get('subclass', False))
edam_format = elem.get('edam_format', None)
if edam_format and not make_subclass:
self.log.warning("Cannot specify edam_format without setting subclass to True, skipping datatype.")
continue
edam_data = elem.get('edam_data', None)
if edam_data and not make_subclass:
self.log.warning("Cannot specify edam_data without setting subclass to True, skipping datatype.")
continue
# Proprietary datatypes included in installed tool shed repositories will include two special attributes
# (proprietary_path and proprietary_datatype_module) if they depend on proprietary datatypes classes.
# The value of proprietary_path is the path to the cloned location of the tool shed repository's contained
# datatypes_conf.xml file.
proprietary_path = elem.get('proprietary_path', None)
proprietary_datatype_module = elem.get('proprietary_datatype_module', None)
if proprietary_path is not None or proprietary_datatype_module is not None and not handling_proprietary_datatypes:
handling_proprietary_datatypes = True
if deactivate:
# We are deactivating or uninstalling an installed tool shed repository, so eliminate the datatype
# elem from the in-memory list of datatype elems.
for in_memory_elem in self.datatype_elems:
in_memory_extension = in_memory_elem.get('extension', None)
if in_memory_extension == extension:
in_memory_dtype = elem.get('type', None)
in_memory_type_extension = elem.get('type_extension', None)
in_memory_mimetype = elem.get('mimetype', None)
in_memory_display_in_upload = galaxy.util.string_as_bool(elem.get('display_in_upload', False))
in_memory_make_subclass = galaxy.util.string_as_bool(elem.get('subclass', False))
if in_memory_dtype == dtype and \
in_memory_type_extension == type_extension and \
in_memory_mimetype == mimetype and \
in_memory_display_in_upload == display_in_upload and \
in_memory_make_subclass == make_subclass:
self.datatype_elems.remove(in_memory_elem)
if extension is not None and extension in self.datatypes_by_extension:
# We are deactivating or uninstalling an installed tool shed repository, so eliminate the datatype
# from the registry. TODO: Handle deactivating datatype converters, etc before removing from
# self.datatypes_by_extension.
del self.datatypes_by_extension[extension]
if extension in self.upload_file_formats:
self.upload_file_formats.remove(extension)
self.log.debug("Removed datatype with extension '%s' from the registry." % extension)
else:
# We are loading new datatype, so we'll make sure it is correctly defined before proceeding.
can_process_datatype = False
if extension is not None:
if dtype is not None or type_extension is not None:
if override or extension not in self.datatypes_by_extension:
can_process_datatype = True
if can_process_datatype:
if dtype is not None:
try:
fields = dtype.split(':')
datatype_module = fields[0]
datatype_class_name = fields[1]
except Exception:
self.log.exception('Error parsing datatype definition for dtype %s', str(dtype))
ok = False
if ok:
datatype_class = None
if proprietary_path and proprietary_datatype_module and datatype_class_name:
# TODO: previously comments suggested this needs to be locked because it modifys
# the sys.path, probably true but the previous lock wasn't doing that.
try:
imported_module = __import_module(proprietary_path,
proprietary_datatype_module,
datatype_class_name)
if imported_module not in self.imported_modules:
self.imported_modules.append(imported_module)
if hasattr(imported_module, datatype_class_name):
datatype_class = getattr(imported_module, datatype_class_name)
except Exception as e:
full_path = os.path.join(proprietary_path, proprietary_datatype_module)
self.log.debug("Exception importing proprietary code file %s: %s", full_path, galaxy.util.unicodify(e))
# Either the above exception was thrown because the proprietary_datatype_module is not derived from a class
# in the repository, or we are loading Galaxy's datatypes. In either case we'll look in the registry.
if datatype_class is None:
try:
# The datatype class name must be contained in one of the datatype modules in the Galaxy distribution.
fields = datatype_module.split('.')[1:]
module = __import__(datatype_module)
for mod in fields:
module = getattr(module, mod)
datatype_class = getattr(module, datatype_class_name)
self.log.debug('Retrieved datatype module {}:{} from the datatype registry for extension {}.'.format(str(datatype_module), datatype_class_name, extension))
except Exception:
self.log.exception('Error importing datatype module %s', str(datatype_module))
ok = False
elif type_extension is not None:
try:
datatype_class = self.datatypes_by_extension[type_extension].__class__
self.log.debug('Retrieved datatype module {} from type_extension {} for extension {}.'.format(str(datatype_class.__name__), type_extension, extension))
except Exception:
self.log.exception('Error determining datatype_class for type_extension %s', str(type_extension))
ok = False
if ok:
if not deactivate:
# A new tool shed repository that contains custom datatypes is being installed, and since installation is
# occurring after the datatypes registry has been initialized at server startup, its contents cannot be
# overridden by new introduced conflicting data types unless the value of override is True.
if extension in self.datatypes_by_extension:
# Because of the way that the value of can_process_datatype was set above, we know that the value of
# override is True.
self.log.debug("Overriding conflicting datatype with extension '%s', using datatype from %s." %
(str(extension), str(config)))
if make_subclass:
datatype_class = type(datatype_class_name, (datatype_class, ), {})
if edam_format:
datatype_class.edam_format = edam_format
if edam_data:
datatype_class.edam_data = edam_data
datatype_class.is_subclass = make_subclass
description = elem.get("description", None)
description_url = elem.get("description_url", None)
datatype_instance = datatype_class()
self.datatypes_by_extension[extension] = datatype_instance
if mimetype is None:
# Use default mimetype per datatype specification.
mimetype = self.datatypes_by_extension[extension].get_mime()
self.mimetypes_by_extension[extension] = mimetype
if datatype_class.track_type:
self.available_tracks.append(extension)
if display_in_upload and extension not in self.upload_file_formats:
self.upload_file_formats.append(extension)
# Max file size cut off for setting optional metadata.
self.datatypes_by_extension[extension].max_optional_metadata_filesize = elem.get('max_optional_metadata_filesize', None)
for converter in elem.findall('converter'):
# Build the list of datatype converters which will later be loaded into the calling app's toolbox.
converter_config = converter.get('file', None)
target_datatype = converter.get('target_datatype', None)
depends_on = converter.get('depends_on', None)
if depends_on is not None and target_datatype is not None:
if extension not in self.converter_deps:
self.converter_deps[extension] = {}
self.converter_deps[extension][target_datatype] = depends_on.split(',')
if converter_config and target_datatype:
if proprietary_converter_path:
self.proprietary_converters.append((converter_config, extension, target_datatype))
else:
self.converters.append((converter_config, extension, target_datatype))
# Add composite files.
for composite_file in elem.findall('composite_file'):
name = composite_file.get('name', None)
if name is None:
self.log.warning("You must provide a name for your composite_file (%s)." % composite_file)
optional = composite_file.get('optional', False)
mimetype = composite_file.get('mimetype', None)
self.datatypes_by_extension[extension].add_composite_file(name, optional=optional, mimetype=mimetype)
for display_app in elem.findall('display'):
if proprietary_display_path:
if elem not in self.proprietary_display_app_containers:
self.proprietary_display_app_containers.append(elem)
else:
if elem not in self.display_app_containers:
self.display_app_containers.append(elem)
datatype_info_dict = {
"display_in_upload": display_in_upload,
"extension": extension,
"description": description,
"description_url": description_url,
}
composite_files = datatype_instance.composite_files
if composite_files:
datatype_info_dict['composite_files'] = [_.dict() for _ in composite_files.values()]
self.datatype_info_dicts.append(datatype_info_dict)
for auto_compressed_type in auto_compressed_types:
compressed_extension = "{}.{}".format(extension, auto_compressed_type)
upper_compressed_type = auto_compressed_type[0].upper() + auto_compressed_type[1:]
auto_compressed_type_name = datatype_class_name + upper_compressed_type
attributes = {}
if auto_compressed_type == "gz":
dynamic_parent = binary.GzDynamicCompressedArchive
elif auto_compressed_type == "bz2":
dynamic_parent = binary.Bz2DynamicCompressedArchive
else:
raise Exception("Unknown auto compression type [%s]" % auto_compressed_type)
attributes["file_ext"] = compressed_extension
attributes["uncompressed_datatype_instance"] = datatype_instance
compressed_datatype_class = type(auto_compressed_type_name, (datatype_class, dynamic_parent, ), attributes)
if edam_format:
compressed_datatype_class.edam_format = edam_format
if edam_data:
compressed_datatype_class.edam_data = edam_data
compressed_datatype_instance = compressed_datatype_class()
self.datatypes_by_extension[compressed_extension] = compressed_datatype_instance
if display_in_upload and compressed_extension not in self.upload_file_formats:
self.upload_file_formats.append(compressed_extension)
self.datatype_info_dicts.append({
"display_in_upload": display_in_upload,
"extension": compressed_extension,
"description": description,
"description_url": description_url,
})
self.converters.append(("%s_to_uncompressed.xml" % auto_compressed_type, compressed_extension, extension))
if datatype_class not in compressed_sniffers:
compressed_sniffers[datatype_class] = []
if sniff_compressed_types:
compressed_sniffers[datatype_class].append(compressed_datatype_instance)
# Processing the new datatype elem is now complete, so make sure the element defining it is retained by appending
# the new datatype to the in-memory list of datatype elems to enable persistence.
self.datatype_elems.append(elem)
else:
if extension is not None:
if dtype is not None or type_extension is not None:
if extension in self.datatypes_by_extension:
if not override:
# Do not load the datatype since it conflicts with an existing datatype which we are not supposed
# to override.
self.log.debug("Ignoring conflicting datatype with extension '{}' from {}.".format(extension, config))
# Load datatype sniffers from the config - we'll do this even if one or more datatypes were not properly processed in the config
# since sniffers are not tightly coupled with datatypes.
self.load_datatype_sniffers(root,
deactivate=deactivate,
handling_proprietary_datatypes=handling_proprietary_datatypes,
override=override,
compressed_sniffers=compressed_sniffers)
self.upload_file_formats.sort()
# Load build sites
if use_build_sites:
self._load_build_sites(root)
self.set_default_values()
def append_to_sniff_order():
sniff_order_classes = {type(_) for _ in self.sniff_order}
for datatype in self.datatypes_by_extension.values():
# Add a datatype only if it is not already in sniff_order, it
# has a sniff() method and was not defined with subclass="true".
# Do not add dynamic compressed types - these were carefully added or not
# to the sniff order in the proper position above.
if type(datatype) not in sniff_order_classes and \
hasattr(datatype, 'sniff') and not datatype.is_subclass and \
not hasattr(datatype, "uncompressed_datatype_instance"):
self.sniff_order.append(datatype)
append_to_sniff_order()
def _load_build_sites(self, root):
def load_build_site(build_site_config):
# Take in either an XML element or simple dictionary from YAML and add build site for this.
if not (build_site_config.get('type') and build_site_config.get('file')):
self.log.exception("Site is missing required 'type' and 'file' attributes")
return
site_type = build_site_config.get('type')
path = build_site_config.get('file')
if not os.path.exists(path):
sample_path = "%s.sample" % path
if os.path.exists(sample_path):
self.log.debug("Build site file [{}] not found using sample [{}].".format(path, sample_path))
path = sample_path
self.build_sites[site_type] = path
if site_type in ('ucsc', 'gbrowse'):
self.legacy_build_sites[site_type] = galaxy.util.read_build_sites(path)
if build_site_config.get('display', None):
display = build_site_config.get('display')
if not isinstance(display, list):
display = [x.strip() for x in display.lower().split(',')]
self.display_sites[site_type] = display
self.log.debug("Loaded build site '%s': %s with display sites: %s", site_type, path, display)
else:
self.log.debug("Loaded build site '%s': %s", site_type, path)
if root.find('build_sites') is not None:
for elem in root.find('build_sites').findall('site'):
load_build_site(elem)
else:
build_sites_config_file = getattr(self.config, "build_sites_config_file", None)
if build_sites_config_file and os.path.exists(build_sites_config_file):
with open(build_sites_config_file) as f:
build_sites_config = yaml.safe_load(f)
if not isinstance(build_sites_config, list):
self.log.exception("Build sites configuration YAML file does not declare list of sites.")
return
for build_site_config in build_sites_config:
load_build_site(build_site_config)
else:
self.log.debug("No build sites source located.")
[docs] def get_legacy_sites_by_build(self, site_type, build):
sites = []
for site in self.legacy_build_sites.get(site_type, []):
if build in site['builds']:
sites.append((site['name'], site['url']))
return sites
[docs] def load_datatype_sniffers(self, root, deactivate=False, handling_proprietary_datatypes=False, override=False, compressed_sniffers=None):
"""
Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy
distributed config) or contained within an installed Tool Shed repository. If deactivate is True, an installed Tool
Shed repository that includes custom sniffers is being deactivated or uninstalled, so appropriate loaded sniffers will
be removed from the registry. The value of override will be False when a Tool Shed repository is being installed.
Since installation is occurring after the datatypes registry has been initialized at server startup, its contents
cannot be overridden by newly introduced conflicting sniffers.
"""
sniffer_elem_classes = [e.attrib['type'] for e in self.sniffer_elems]
sniffers = root.find('sniffers')
if sniffers is not None:
for elem in sniffers.findall('sniffer'):
# Keep a status of the process steps to enable stopping the process of handling the sniffer if necessary.
ok = True
dtype = elem.get('type', None)
if dtype is not None:
try:
fields = dtype.split(":")
datatype_module = fields[0]
datatype_class_name = fields[1]
module = None
except Exception:
self.log.exception('Error determining datatype class or module for dtype %s', str(dtype))
ok = False
if ok:
if handling_proprietary_datatypes:
# See if one of the imported modules contains the datatype class name.
for imported_module in self.imported_modules:
if hasattr(imported_module, datatype_class_name):
module = imported_module
break
if module is None:
try:
# The datatype class name must be contained in one of the datatype modules in the Galaxy distribution.
module = __import__(datatype_module)
for comp in datatype_module.split('.')[1:]:
module = getattr(module, comp)
except Exception:
self.log.exception("Error importing datatype class for '%s'", str(dtype))
ok = False
if ok:
try:
aclass = getattr(module, datatype_class_name)()
except Exception:
self.log.exception('Error calling method %s from class %s', str(datatype_class_name), str(module))
ok = False
if ok:
if deactivate:
# We are deactivating or uninstalling an installed Tool Shed repository, so eliminate the appropriate sniffers.
sniffer_class = elem.get('type', None)
if sniffer_class is not None:
for index, s_e_c in enumerate(sniffer_elem_classes):
if sniffer_class == s_e_c:
del self.sniffer_elems[index]
sniffer_elem_classes = [elem.attrib['type'] for elem in self.sniffer_elems]
self.log.debug("Removed sniffer element for datatype '%s'" % str(dtype))
break
for sniffer_class in self.sniff_order:
if sniffer_class.__class__ == aclass.__class__:
self.sniff_order.remove(sniffer_class)
self.log.debug("Removed sniffer class for datatype '%s' from sniff order" % str(dtype))
break
else:
# We are loading new sniffer, so see if we have a conflicting sniffer already loaded.
conflict = False
for conflict_loc, sniffer_class in enumerate(self.sniff_order):
if sniffer_class.__class__ == aclass.__class__:
# We have a conflicting sniffer, so replace the one previously loaded.
conflict = True
if override:
del self.sniff_order[conflict_loc]
self.log.debug("Removed conflicting sniffer for datatype '%s'" % dtype)
break
if not conflict or override:
if compressed_sniffers and aclass.__class__ in compressed_sniffers:
for compressed_sniffer in compressed_sniffers[aclass.__class__]:
self.sniff_order.append(compressed_sniffer)
self.sniff_order.append(aclass)
self.log.debug("Loaded sniffer for datatype '%s'" % dtype)
# Processing the new sniffer elem is now complete, so make sure the element defining it is loaded if necessary.
sniffer_class = elem.get('type', None)
if sniffer_class is not None:
if sniffer_class not in sniffer_elem_classes:
self.sniffer_elems.append(elem)
[docs] def is_extension_unsniffable_binary(self, ext):
datatype = self.get_datatype_by_extension(ext)
return datatype is not None and isinstance(datatype, binary.Binary) and not hasattr(datatype, 'sniff')
[docs] def get_datatype_class_by_name(self, name):
"""
Return the datatype class where the datatype's `type` attribute
(as defined in the datatype_conf.xml file) contains `name`.
"""
# TODO: obviously not ideal but some of these base classes that are useful for testing datatypes
# aren't loaded into the datatypes registry, so we'd need to test for them here
if name == 'images.Image':
return images.Image
# TODO: too inefficient - would be better to generate this once as a map and store in this object
for ext, datatype_obj in self.datatypes_by_extension.items():
datatype_obj_class = datatype_obj.__class__
datatype_obj_class_str = str(datatype_obj_class)
if name in datatype_obj_class_str:
return datatype_obj_class
return None
[docs] def get_mimetype_by_extension(self, ext, default='application/octet-stream'):
"""Returns a mimetype based on an extension"""
try:
mimetype = self.mimetypes_by_extension[ext]
except KeyError:
# datatype was never declared
mimetype = default
self.log.warning('unknown mimetype in data factory %s' % str(ext))
return mimetype
[docs] def get_datatype_by_extension(self, ext):
"""Returns a datatype object based on an extension"""
return self.datatypes_by_extension.get(ext, None)
[docs] def change_datatype(self, data, ext):
data.extension = ext
# call init_meta and copy metadata from itself. The datatype
# being converted *to* will handle any metadata copying and
# initialization.
if data.has_data():
data.set_size()
data.init_meta(copy_from=data)
return data
[docs] def load_datatype_converters(self, toolbox, installed_repository_dict=None, deactivate=False, use_cached=False):
"""
If deactivate is False, add datatype converters from self.converters or self.proprietary_converters
to the calling app's toolbox. If deactivate is True, eliminates relevant converters from the calling
app's toolbox.
"""
if installed_repository_dict:
# Load converters defined by datatypes_conf.xml included in installed tool shed repository.
converters = self.proprietary_converters
else:
# Load converters defined by local datatypes_conf.xml.
converters = self.converters
for elem in converters:
tool_config = elem[0]
source_datatype = elem[1]
target_datatype = elem[2]
if installed_repository_dict:
converter_path = installed_repository_dict['converter_path']
else:
converter_path = self.converters_path
try:
config_path = os.path.join(converter_path, tool_config)
converter = toolbox.load_tool(config_path, use_cached=use_cached)
self.converter_tools.add(converter)
if installed_repository_dict:
# If the converter is included in an installed tool shed repository, set the tool
# shed related tool attributes.
converter.tool_shed = installed_repository_dict['tool_shed']
converter.repository_name = installed_repository_dict['repository_name']
converter.repository_owner = installed_repository_dict['repository_owner']
converter.installed_changeset_revision = installed_repository_dict['installed_changeset_revision']
converter.old_id = converter.id
# The converter should be included in the list of tools defined in tool_dicts.
tool_dicts = installed_repository_dict['tool_dicts']
for tool_dict in tool_dicts:
if tool_dict['id'] == converter.id:
converter.guid = tool_dict['guid']
converter.id = tool_dict['guid']
break
if deactivate:
toolbox.remove_tool_by_id(converter.id, remove_from_panel=False)
if source_datatype in self.datatype_converters:
if target_datatype in self.datatype_converters[source_datatype]:
del self.datatype_converters[source_datatype][target_datatype]
self.log.debug("Deactivated converter: %s", converter.id)
else:
toolbox.register_tool(converter)
if source_datatype not in self.datatype_converters:
self.datatype_converters[source_datatype] = OrderedDict()
self.datatype_converters[source_datatype][target_datatype] = converter
if not hasattr(toolbox.app, 'tool_cache') or converter.id in toolbox.app.tool_cache._new_tool_ids:
self.log.debug("Loaded converter: %s", converter.id)
except Exception:
if deactivate:
self.log.exception("Error deactivating converter from (%s)" % converter_path)
else:
self.log.exception("Error loading converter (%s)" % converter_path)
[docs] def load_display_applications(self, app, installed_repository_dict=None, deactivate=False):
"""
If deactivate is False, add display applications from self.display_app_containers or
self.proprietary_display_app_containers to appropriate datatypes. If deactivate is
True, eliminates relevant display applications from appropriate datatypes.
"""
if installed_repository_dict:
# Load display applications defined by datatypes_conf.xml included in installed tool shed repository.
datatype_elems = self.proprietary_display_app_containers
else:
# Load display applications defined by local datatypes_conf.xml.
datatype_elems = self.display_app_containers
for elem in datatype_elems:
extension = self.get_extension(elem)
for display_app in elem.findall('display'):
display_file = display_app.get('file', None)
if installed_repository_dict:
display_path = installed_repository_dict['display_path']
display_file_head, display_file_tail = os.path.split(display_file)
config_path = os.path.join(display_path, display_file_tail)
else:
config_path = os.path.join(self.display_applications_path, display_file)
try:
inherit = galaxy.util.string_as_bool(display_app.get('inherit', 'False'))
display_app = DisplayApplication.from_file(config_path, app)
if display_app:
if display_app.id in self.display_applications:
if deactivate:
del self.display_applications[display_app.id]
else:
# If we already loaded this display application, we'll use the first one loaded.
display_app = self.display_applications[display_app.id]
elif installed_repository_dict:
# If the display application is included in an installed tool shed repository,
# set the tool shed related tool attributes.
display_app.tool_shed = installed_repository_dict['tool_shed']
display_app.repository_name = installed_repository_dict['repository_name']
display_app.repository_owner = installed_repository_dict['repository_owner']
display_app.installed_changeset_revision = installed_repository_dict['installed_changeset_revision']
display_app.old_id = display_app.id
# The display application should be included in the list of tools defined in tool_dicts.
tool_dicts = installed_repository_dict['tool_dicts']
for tool_dict in tool_dicts:
if tool_dict['id'] == display_app.id:
display_app.guid = tool_dict['guid']
display_app.id = tool_dict['guid']
break
if deactivate:
if display_app.id in self.display_applications:
del self.display_applications[display_app.id]
if extension in self.datatypes_by_extension:
if display_app.id in self.datatypes_by_extension[extension].display_applications:
del self.datatypes_by_extension[extension].display_applications[display_app.id]
if inherit and (self.datatypes_by_extension[extension], display_app) in self.inherit_display_application_by_class:
self.inherit_display_application_by_class.remove((self.datatypes_by_extension[extension], display_app))
self.log.debug("Deactivated display application '{}' for datatype '{}'.".format(display_app.id, extension))
else:
self.display_applications[display_app.id] = display_app
self.datatypes_by_extension[extension].add_display_application(display_app)
if inherit and (self.datatypes_by_extension[extension], display_app) not in self.inherit_display_application_by_class:
self.inherit_display_application_by_class.append((self.datatypes_by_extension[extension], display_app))
self.log.debug("Loaded display application '{}' for datatype '{}', inherit={}.".format(display_app.id, extension, inherit))
except Exception:
if deactivate:
self.log.exception("Error deactivating display application (%s)" % config_path)
else:
self.log.exception("Error loading display application (%s)" % config_path)
# Handle display_application subclass inheritance.
for extension, d_type1 in self.datatypes_by_extension.items():
for d_type2, display_app in self.inherit_display_application_by_class:
current_app = d_type1.get_display_application(display_app.id, None)
if current_app is None and isinstance(d_type1, type(d_type2)):
self.log.debug("Adding inherited display application '{}' to datatype '{}'".format(display_app.id, extension))
d_type1.add_display_application(display_app)
[docs] def reload_display_applications(self, display_application_ids=None):
"""
Reloads display applications: by id, or all if no ids provided
Returns tuple( [reloaded_ids], [failed_ids] )
"""
if not display_application_ids:
display_application_ids = self.display_applications.keys()
elif not isinstance(display_application_ids, list):
display_application_ids = [display_application_ids]
reloaded = []
failed = []
for display_application_id in display_application_ids:
try:
self.display_applications[display_application_id].reload()
reloaded.append(display_application_id)
except Exception as e:
self.log.debug('Requested to reload display application "%s", but failed: %s.', display_application_id, e)
failed.append(display_application_id)
return (reloaded, failed)
[docs] def load_external_metadata_tool(self, toolbox):
"""Adds a tool which is used to set external metadata"""
# We need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated
# tool. We'll load a special tool to be used for Auto-Detecting metadata; this is less than ideal, but effective
# Properly building a tool without relying on parsing an XML file is near difficult...so we bundle with Galaxy.
set_meta_tool = toolbox.load_hidden_lib_tool(os.path.abspath(os.path.join(os.path.dirname(__file__), "set_metadata_tool.xml")))
self.set_external_metadata_tool = set_meta_tool
self.log.debug("Loaded external metadata tool: %s", self.set_external_metadata_tool.id)
[docs] def set_default_values(self):
# Default values.
if not self.datatypes_by_extension:
self.datatypes_by_extension = {
'ab1' : binary.Ab1(),
'axt' : sequence.Axt(),
'bam' : binary.Bam(),
'bed' : interval.Bed(),
'coverage' : coverage.LastzCoverage(),
'customtrack' : interval.CustomTrack(),
'csfasta' : sequence.csFasta(),
'fasta' : sequence.Fasta(),
'eland' : tabular.Eland(),
'fastq' : sequence.Fastq(),
'fastqsanger' : sequence.FastqSanger(),
'gtf' : interval.Gtf(),
'gff' : interval.Gff(),
'gff3' : interval.Gff3(),
'genetrack' : tracks.GeneTrack(),
'h5' : binary.H5(),
'interval' : interval.Interval(),
'laj' : images.Laj(),
'lav' : sequence.Lav(),
'maf' : sequence.Maf(),
'pileup' : tabular.Pileup(),
'qualsolid' : qualityscore.QualityScoreSOLiD(),
'qualsolexa' : qualityscore.QualityScoreSolexa(),
'qual454' : qualityscore.QualityScore454(),
'sam' : tabular.Sam(),
'scf' : binary.Scf(),
'sff' : binary.Sff(),
'tabular' : tabular.Tabular(),
'csv' : tabular.CSV(),
'taxonomy' : tabular.Taxonomy(),
'txt' : data.Text(),
'wig' : interval.Wiggle(),
'xml' : xml.GenericXml(),
}
self.mimetypes_by_extension = {
'ab1' : 'application/octet-stream',
'axt' : 'text/plain',
'bam' : 'application/octet-stream',
'bed' : 'text/plain',
'customtrack' : 'text/plain',
'csfasta' : 'text/plain',
'eland' : 'application/octet-stream',
'fasta' : 'text/plain',
'fastq' : 'text/plain',
'fastqsanger' : 'text/plain',
'gtf' : 'text/plain',
'gff' : 'text/plain',
'gff3' : 'text/plain',
'h5' : 'application/octet-stream',
'interval' : 'text/plain',
'laj' : 'text/plain',
'lav' : 'text/plain',
'maf' : 'text/plain',
'memexml' : 'application/xml',
'pileup' : 'text/plain',
'qualsolid' : 'text/plain',
'qualsolexa' : 'text/plain',
'qual454' : 'text/plain',
'sam' : 'text/plain',
'scf' : 'application/octet-stream',
'sff' : 'application/octet-stream',
'tabular' : 'text/plain',
'csv' : 'text/plain',
'taxonomy' : 'text/plain',
'txt' : 'text/plain',
'wig' : 'text/plain',
'xml' : 'application/xml',
}
# super supertype fix for input steps in workflows.
if 'data' not in self.datatypes_by_extension:
self.datatypes_by_extension['data'] = data.Data()
self.mimetypes_by_extension['data'] = 'application/octet-stream'
# Default values - the order in which we attempt to determine data types is critical
# because some formats are much more flexibly defined than others.
if len(self.sniff_order) < 1:
self.sniff_order = [
binary.Bam(),
binary.Sff(),
binary.H5(),
xml.GenericXml(),
sequence.Maf(),
sequence.Lav(),
sequence.csFasta(),
qualityscore.QualityScoreSOLiD(),
qualityscore.QualityScore454(),
sequence.Fasta(),
sequence.FastqSanger(),
sequence.FastqCSSanger(),
sequence.Fastq(),
interval.Wiggle(),
text.Html(),
sequence.Axt(),
interval.Bed(),
interval.CustomTrack(),
interval.Gtf(),
interval.Gff(),
interval.Gff3(),
tabular.Pileup(),
interval.Interval(),
tabular.Sam(),
tabular.Eland(),
tabular.CSV()
]
[docs] def get_converters_by_datatype(self, ext):
"""Returns available converters by source type"""
if ext not in self._converters_by_datatype:
converters = OrderedDict()
source_datatype = type(self.get_datatype_by_extension(ext))
for ext2, converters_dict in self.datatype_converters.items():
converter_datatype = type(self.get_datatype_by_extension(ext2))
if issubclass(source_datatype, converter_datatype):
converters.update(converters_dict)
# Ensure ext-level converters are present
if ext in self.datatype_converters.keys():
converters.update(self.datatype_converters[ext])
self._converters_by_datatype[ext] = converters
return self._converters_by_datatype[ext]
[docs] def get_converter_by_target_type(self, source_ext, target_ext):
"""Returns a converter based on source and target datatypes"""
converters = self.get_converters_by_datatype(source_ext)
if target_ext in converters.keys():
return converters[target_ext]
return None
[docs] def find_conversion_destination_for_dataset_by_extensions(self, dataset_or_ext, accepted_formats, converter_safe=True):
"""
returns (direct_match, converted_ext, converted_dataset)
- direct match is True iff no the data set already has an accepted format
- target_ext becomes None if conversion is not possible (or necesary)
"""
if hasattr(dataset_or_ext, "ext"):
ext = dataset_or_ext.ext
dataset = dataset_or_ext
else:
ext = dataset_or_ext
dataset = None
if self.get_datatype_by_extension(ext) is not None and self.get_datatype_by_extension(ext).matches_any(accepted_formats):
return True, None, None
for convert_ext in self.get_converters_by_datatype(ext):
convert_ext_datatype = self.get_datatype_by_extension(convert_ext)
if convert_ext_datatype is None:
self.log.warning("Datatype class not found for extension '{}', which is used as target for conversion from datatype '{}'".format(convert_ext, dataset.ext))
elif convert_ext_datatype.matches_any(accepted_formats):
converted_dataset = dataset and dataset.get_converted_files_by_type(convert_ext)
if converted_dataset:
ret_data = converted_dataset
elif not converter_safe:
continue
else:
ret_data = None
return False, convert_ext, ret_data
return False, None, None
[docs] def get_composite_extensions(self):
return [ext for (ext, d_type) in self.datatypes_by_extension.items() if d_type.composite_type is not None]
[docs] def get_upload_metadata_params(self, context, group, tool):
"""Returns dict of case value:inputs for metadata conditional for upload tool"""
rval = {}
for ext, d_type in self.datatypes_by_extension.items():
inputs = []
for meta_name, meta_spec in d_type.metadata_spec.items():
if meta_spec.set_in_upload:
help_txt = meta_spec.desc
if not help_txt or help_txt == meta_name:
help_txt = ""
inputs.append('<param type="text" name="{}" label="Set metadata value for "{}"" value="{}" help="{}"/>'.format(meta_name, meta_name, meta_spec.default, help_txt))
rval[ext] = "\n".join(inputs)
if 'auto' not in rval and 'txt' in rval: # need to manually add 'auto' datatype
rval['auto'] = rval['txt']
return rval
@property
def edam_formats(self):
"""
"""
if not self._edam_formats_mapping:
self._edam_formats_mapping = {k: v.edam_format for k, v in self.datatypes_by_extension.items()}
return self._edam_formats_mapping
@property
def edam_data(self):
"""
"""
if not self._edam_data_mapping:
self._edam_data_mapping = {k: v.edam_data for k, v in self.datatypes_by_extension.items()}
return self._edam_data_mapping
[docs] def to_xml_file(self, path):
if not self._registry_xml_string:
registry_string_template = Template("""<?xml version="1.0"?>
<datatypes>
<registration converters_path="$converters_path" display_path="$display_path">
$datatype_elems
</registration>
<sniffers>
$sniffer_elems
</sniffers>
</datatypes>
""")
converters_path = self.converters_path_attr or ''
display_path = self.display_path_attr or ''
datatype_elems = "".join(galaxy.util.xml_to_string(elem) for elem in self.datatype_elems)
sniffer_elems = "".join(galaxy.util.xml_to_string(elem) for elem in self.sniffer_elems)
self._registry_xml_string = registry_string_template.substitute(converters_path=converters_path,
display_path=display_path,
datatype_elems=datatype_elems,
sniffer_elems=sniffer_elems)
with open(os.path.abspath(path), 'w') as registry_xml:
os.chmod(path, RW_R__R__)
registry_xml.write(self._registry_xml_string)
[docs] def get_extension(self, elem):
"""
Function which returns the extension lowercased
:param elem:
:return extension:
"""
extension = elem.get('extension', None)
# If extension is not None and is uppercase or mixed case, we need to lowercase it
if extension is not None and not extension.islower():
self.log.debug("%s is not lower case, that could cause troubles in the future. \
Please change it to lower case" % extension)
extension = extension.lower()
return extension
[docs]def example_datatype_registry_for_sample(sniff_compressed_dynamic_datatypes_default=True):
galaxy_dir = galaxy.util.galaxy_directory()
sample_conf = os.path.join(galaxy_dir, "lib", "galaxy", "config", "sample", "datatypes_conf.xml.sample")
config = Bunch(sniff_compressed_dynamic_datatypes_default=sniff_compressed_dynamic_datatypes_default)
datatypes_registry = Registry(config)
datatypes_registry.load_datatypes(root_dir=galaxy_dir, config=sample_conf)
return datatypes_registry