comparison planemo/lib/python3.7/site-packages/galaxy/util/dbkeys.py @ 1:56ad4e20f292 draft

"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"

1:56ad4e20f292

"""
Functionality for dealing with dbkeys.
"""
# dbkeys read from disk using builds.txt
from __future__ import absolute_import

import os.path
from json import loads

from galaxy.util import read_dbnames
from galaxy.util.object_wrapper import sanitize_lists_to_string


class GenomeBuilds(object):
    default_value = "?"
    default_name = "unspecified (?)"

    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 = []

    def get_genome_build_names(self, trans=None):
        # FIXME: how to deal with key duplicates?
        rval = []
        # 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, "%s (%s) [History]" % (dataset.name, dataset.dbkey)))
            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, "%s (%s) [Custom]" % (chrom_dict['name'], key)))
        # 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

    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, "%s.len" % sanitize_lists_to_string(dbkey))
        chrom_info = os.path.abspath(chrom_info)
        return (chrom_info, db_dataset)