Source code for galaxy.util.dbkeys

"""
Functionality for dealing with dbkeys.
"""
import logging
import os.path
import re
from json import loads

from galaxy.util import (
    galaxy_directory,
    sanitize_lists_to_string,
    unicodify,
)

log = logging.getLogger(__name__)


[docs]def read_dbnames(filename): """Read build names from file""" db_names = [] try: ucsc_builds = {} man_builds = [] # assume these are integers name_to_db_base = {} if filename is None: # Should only be happening with the galaxy.tools.parameters.basic:GenomeBuildParameter docstring unit test filename = os.path.join(galaxy_directory(), "tool-data", "shared", "ucsc", "builds.txt.sample") for line in open(filename): try: if line[0:1] == "#": continue fields = line.replace("\r", "").replace("\n", "").split("\t") # Special case of unspecified build is at top of list if fields[0] == "?": db_names.insert(0, (fields[0], fields[1])) continue try: # manual build (i.e. microbes) int(fields[0]) man_builds.append((fields[1], fields[0])) except Exception: # UCSC build db_base = fields[0].rstrip("0123456789") if db_base not in ucsc_builds: ucsc_builds[db_base] = [] name_to_db_base[fields[1]] = db_base # we want to sort within a species numerically by revision number build_rev = re.compile(r"\d+$") try: build_rev = int(build_rev.findall(fields[0])[0]) except Exception: build_rev = 0 ucsc_builds[db_base].append((build_rev, fields[0], fields[1])) except Exception: continue sort_names = sorted(name_to_db_base.keys()) for name in sort_names: db_base = name_to_db_base[name] ucsc_builds[db_base].sort() ucsc_builds[db_base].reverse() ucsc_builds[db_base] = [(build, name) for _, build, name in ucsc_builds[db_base]] db_names = list(db_names + ucsc_builds[db_base]) man_builds.sort() man_builds = [(build, name) for name, build in man_builds] db_names = list(db_names + man_builds) except Exception as e: log.error("ERROR: Unable to read builds file: %s", unicodify(e)) return db_names
[docs]class GenomeBuilds: default_value = "?" default_name = "unspecified (?)"
[docs] def __init__(self, app, data_table_name="__dbkeys__", load_old_style=True): self._app = app self._data_table_name = data_table_name self._static_chrom_info_path = app.config.len_file_path # A dbkey can be listed multiple times, but with different names, so we can't use dictionaries for lookups if load_old_style: self._static_dbkeys = list(read_dbnames(app.config.builds_file_path)) else: self._static_dbkeys = []
[docs] def get_genome_build_names(self, trans=None): # FIXME: how to deal with key duplicates? rval = [(self.default_value, self.default_name)] # load user custom genome builds if trans is not None: if trans.history: # This is a little bit Odd. We are adding every .len file in the current history to dbkey list, # but this is previous behavior from trans.db_names, so we'll continue to do it. # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering, # so a len file will be listed twice (as the build name and again as dataset name), # if custom dbkey creation/conversion occurred within the current history. datasets = trans.sa_session.query(self._app.model.HistoryDatasetAssociation).filter_by( deleted=False, history_id=trans.history.id, extension="len" ) for dataset in datasets: rval.append((dataset.dbkey, f"{dataset.name} ({dataset.dbkey}) [History]")) user = trans.user if user and hasattr(user, "preferences") and "dbkeys" in user.preferences: user_keys = loads(user.preferences["dbkeys"]) for key, chrom_dict in user_keys.items(): rval.append((key, f"{chrom_dict['name']} ({key}) [Custom]")) # Load old builds.txt static keys rval.extend(self._static_dbkeys) # load dbkeys from dbkey data table dbkey_table = self._app.tool_data_tables.get(self._data_table_name, None) if dbkey_table is not None: for field_dict in dbkey_table.get_named_fields_list(): rval.append((field_dict["value"], field_dict["name"])) return rval
[docs] def get_chrom_info(self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True): # FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required chrom_info = None db_dataset = None # Collect chromInfo from custom builds if trans: db_dataset = trans.db_dataset_for(dbkey) if db_dataset: chrom_info = db_dataset.file_name else: # Do Custom Build handling if ( trans.user and ("dbkeys" in trans.user.preferences) and (dbkey in loads(trans.user.preferences["dbkeys"])) ): custom_build_dict = loads(trans.user.preferences["dbkeys"])[dbkey] # HACK: the attempt to get chrom_info below will trigger the # fasta-to-len converter if the dataset is not available or, # which will in turn create a recursive loop when # running the fasta-to-len tool. So, use a hack in the second # condition below to avoid getting chrom_info when running the # fasta-to-len converter. if "fasta" in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion: # Build is defined by fasta; get len file, which is obtained from converting fasta. build_fasta_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get( custom_build_dict["fasta"] ) chrom_info = build_fasta_dataset.get_converted_dataset(trans, "len").file_name elif "len" in custom_build_dict: # Build is defined by len file, so use it. chrom_info = ( trans.sa_session.query(trans.app.model.HistoryDatasetAssociation) .get(custom_build_dict["len"]) .file_name ) # Check Data table if not chrom_info: dbkey_table = self._app.tool_data_tables.get(self._data_table_name, None) if dbkey_table is not None: chrom_info = dbkey_table.get_entry("value", dbkey, "len_path", default=None) # use configured server len path if not chrom_info: # Default to built-in build. # Since we are using an unverified dbkey, we will sanitize the dbkey before use chrom_info = os.path.join(self._static_chrom_info_path, f"{sanitize_lists_to_string(dbkey)}.len") chrom_info = os.path.abspath(chrom_info) return (chrom_info, db_dataset)