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Source code for galaxy.datatypes.registry

Provides mapping between extensions and datatypes, mime-types, etc.

import importlib.util
import logging
import os
import pkgutil
from pathlib import Path
from string import Template
from typing import (

import yaml

import galaxy.util
from galaxy.datatypes.protocols import DatasetProtocol
from galaxy.tool_util.edam_util import load_edam_tree
from galaxy.util import RW_R__R__
from galaxy.util.bunch import Bunch
from . import (
from .display_applications.application import DisplayApplication

[docs]class ConfigurationError(Exception): pass
[docs]class Registry:
[docs] def __init__(self, config=None): edam_ontology_path = config.get("edam_toolbox_ontology_path", None) if config is not None else None edam = load_edam_tree( None if not edam_ontology_path or not os.path.exists(edam_ontology_path) else edam_ontology_path, "format_", "data_", "operation_", "topic_", ) self.log = logging.getLogger(__name__) self.log.addHandler(logging.NullHandler()) self.config = config self.edam = edam self.datatypes_by_extension = {} self.datatypes_by_suffix_inferences = {} self.mimetypes_by_extension = {} self.datatype_converters = {} # Converters defined in local datatypes_conf.xml self.converters = [] self.converter_tools = set() 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 = [] # Map a display application id to a display application self.display_applications: Dict[str, DisplayApplication] = {} # 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 = [] 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, 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. """ def __import_module(full_path: str, datatype_module: str): path_entry_finder = pkgutil.get_importer(full_path) assert path_entry_finder, "path_entry_finder is None" spec = path_entry_finder.find_spec(datatype_module) assert spec, "spec is None" module = importlib.util.module_from_spec(spec) assert spec.loader, "spec.loader is None" spec.loader.exec_module(module) return module if root_dir and config: compressed_sniffers = {} if isinstance(config, (str, Path)): # Parse datatypes_conf.xml tree = galaxy.util.parse_xml(config) root = tree.getroot() # Load datatypes and converters from config self.log.debug(f"Loading datatypes from {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(f"Directory does not exist: {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 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 # 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 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( f"Retrieved datatype module {str(datatype_module)}:{datatype_class_name} from the datatype registry for extension {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( f"Retrieved datatype module {str(datatype_class.__name__)} from type_extension {type_extension} for extension {extension}." ) except Exception: self.log.exception( "Error determining datatype_class for type_extension %s", str(type_extension) ) ok = False if ok: # 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.", extension, 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) # process as a list, in the future handle grabbing extensions here upload_warning_els = elem.findall("upload_warning") upload_warning_template = None for upload_warning_el in upload_warning_els: if upload_warning_template is not None: raise NotImplementedError("Multiple upload_warnings not implemented") upload_warning_template = Template(upload_warning_el.text) 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 ) infer_from_suffixes = [] # read from element instead of attribute so we can customize references to # compressed files in the future (e.g. maybe some day faz will be a compressed fasta # or something along those lines) for infer_from in elem.findall("infer_from"): suffix = infer_from.get("suffix", None) if suffix is None: raise Exception("Failed to parse infer_from datatype element") infer_from_suffixes.append(suffix) self.datatypes_by_suffix_inferences[suffix] = datatype_instance 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: 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(f"You must provide a name for your composite_file ({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 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, "upload_warning": upload_warning(upload_warning_template), } composite_files = datatype_instance.get_composite_files() if composite_files: _composite_files = [] for name, composite_file in composite_files.items(): _composite_file = composite_file.dict() _composite_file["name"] = name _composite_files.append(_composite_file) datatype_info_dict["composite_files"] = _composite_files self.datatype_info_dicts.append(datatype_info_dict) for auto_compressed_type in auto_compressed_types: compressed_extension = f"{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(f"Unknown auto compression type [{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 for suffix in infer_from_suffixes: self.datatypes_by_suffix_inferences[ f"{suffix}.{auto_compressed_type}" ] = 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, "upload_warning": upload_warning(upload_warning_template, auto_compressed_type), } ) if auto_compressed_type == "gz": self.converters.append( ( f"uncompressed_to_{auto_compressed_type}.xml", extension, compressed_extension, ) ) self.converters.append( (f"{auto_compressed_type}_to_uncompressed.xml", 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( f"Ignoring conflicting datatype with extension '{extension}' from {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, 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 = f"{path}.sample" if os.path.exists(sample_path): self.log.debug(f"Build site file [{path}] not found using sample [{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 get_display_sites(self, site_type): return self.display_sites.get(site_type, [])
[docs] def load_datatype_sniffers(self, root, 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. """ sniffer_elem_classes = [e.attrib["type"] for e in self.sniffer_elems] if (sniffers := root.find("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 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: # 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(f"Removed conflicting sniffer for datatype '{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(f"Loaded sniffer for datatype '{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 get_datatype_from_filename(self, name): max_extension_parts = 3 generic_datatype_instance = self.get_datatype_by_extension("data") if "." not in name: return generic_datatype_instance extension_parts = name.rsplit(".", max_extension_parts)[1:] possible_extensions = [] for n, _ in enumerate(extension_parts): possible_extensions.append(".".join(extension_parts[n:])) infer_from = self.datatypes_by_suffix_inferences for possible_extension in possible_extensions: if possible_extension in infer_from: return infer_from[possible_extension] for possible_extension in possible_extensions: if possible_extension in self.datatypes_by_extension: return self.datatypes_by_extension[possible_extension] return generic_datatype_instance
[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 datatype_obj in self.datatypes_by_extension.values(): 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_available_tracks(self): return self.available_tracks
[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(f"unknown mimetype in data factory {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): if data.extension != 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, use_cached=False): """ Add datatype converters from self.converters to the calling app's toolbox. """ # 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] 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) toolbox.register_tool(converter) if source_datatype not in self.datatype_converters: self.datatype_converters[source_datatype] = {} 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: self.log.exception(f"Error loading converter ({converter_path})")
[docs] def load_display_applications(self, app): """ Add display applications from self.display_app_containers or to appropriate datatypes. """ # 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) 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 we already loaded this display application, we'll use the first one loaded. display_app = self.display_applications[display_app.id] 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( f"Loaded display application '{display_app.id}' for datatype '{extension}', inherit={inherit}." ) except Exception: self.log.exception(f"Error loading display application ({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(f"Adding inherited display application '{display_app.id}' to datatype '{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(), "jp2": binary.JP2(), "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", "jp2": "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.JP2(), 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 = {} 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({k: v for k, v in converters_dict.items() if k != ext}) # 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: Union[str, DatasetProtocol], accepted_formats: List[str], converter_safe: bool = True ) -> Tuple[bool, Optional[str], Optional[DatasetProtocol]]: """ 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 = cast(DatasetProtocol, dataset_or_ext) else: ext = dataset_or_ext dataset = None datatype_by_extension = self.get_datatype_by_extension(ext) if datatype_by_extension and datatype_by_extension.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( f"Datatype class not found for extension '{convert_ext}', which is used as target for conversion from datatype '{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( f'<param type="text" name="{meta_name}" label="Set metadata value for &quot;{meta_name}&quot;" value="{meta_spec.default}" help="{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
def __getstate__(self): state = self.__dict__.copy() # Don't pickle xml elements unpickleable_attributes = [ "converter_tools", "datatype_converters", "datatype_elems", "display_app_containers", "display_applications", "inherit_display_application_by_class", "set_external_metadata_tool", "sniffer_elems", ] for unpicklable in unpickleable_attributes: state[unpicklable] = [] return state
[docs]def upload_warning(template: Optional[Template], auto_compressed_type: Optional[str] = None) -> Optional[str]: if template is None: return None template_args = {"auto_compressed_type": "" if auto_compressed_type is None else f".{auto_compressed_type}"} return template.safe_substitute(template_args)
[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