Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/galaxy/util/dbkeys.py @ 0:26e78fe6e8c4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:26e78fe6e8c4
1 """
2 Functionality for dealing with dbkeys.
3 """
4 # dbkeys read from disk using builds.txt
5 from __future__ import absolute_import
6
7 import os.path
8 from json import loads
9
10 from galaxy.util import read_dbnames
11 from galaxy.util.object_wrapper import sanitize_lists_to_string
12
13
14 class GenomeBuilds(object):
15 default_value = "?"
16 default_name = "unspecified (?)"
17
18 def __init__(self, app, data_table_name="__dbkeys__", load_old_style=True):
19 self._app = app
20 self._data_table_name = data_table_name
21 self._static_chrom_info_path = app.config.len_file_path
22 # A dbkey can be listed multiple times, but with different names, so we can't use dictionaries for lookups
23 if load_old_style:
24 self._static_dbkeys = list(read_dbnames(app.config.builds_file_path))
25 else:
26 self._static_dbkeys = []
27
28 def get_genome_build_names(self, trans=None):
29 # FIXME: how to deal with key duplicates?
30 rval = []
31 # load user custom genome builds
32 if trans is not None:
33 if trans.history:
34 # This is a little bit Odd. We are adding every .len file in the current history to dbkey list,
35 # but this is previous behavior from trans.db_names, so we'll continue to do it.
36 # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering,
37 # so a len file will be listed twice (as the build name and again as dataset name),
38 # if custom dbkey creation/conversion occurred within the current history.
39 datasets = trans.sa_session.query(self._app.model.HistoryDatasetAssociation) \
40 .filter_by(deleted=False, history_id=trans.history.id, extension="len")
41 for dataset in datasets:
42 rval.append((dataset.dbkey, "%s (%s) [History]" % (dataset.name, dataset.dbkey)))
43 user = trans.user
44 if user and hasattr(user, 'preferences') and 'dbkeys' in user.preferences:
45 user_keys = loads(user.preferences['dbkeys'])
46 for key, chrom_dict in user_keys.items():
47 rval.append((key, "%s (%s) [Custom]" % (chrom_dict['name'], key)))
48 # Load old builds.txt static keys
49 rval.extend(self._static_dbkeys)
50 # load dbkeys from dbkey data table
51 dbkey_table = self._app.tool_data_tables.get(self._data_table_name, None)
52 if dbkey_table is not None:
53 for field_dict in dbkey_table.get_named_fields_list():
54 rval.append((field_dict['value'], field_dict['name']))
55 return rval
56
57 def get_chrom_info(self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True):
58 # FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required
59 chrom_info = None
60 db_dataset = None
61 # Collect chromInfo from custom builds
62 if trans:
63 db_dataset = trans.db_dataset_for(dbkey)
64 if db_dataset:
65 chrom_info = db_dataset.file_name
66 else:
67 # Do Custom Build handling
68 if trans.user and ('dbkeys' in trans.user.preferences) and (dbkey in loads(trans.user.preferences['dbkeys'])):
69 custom_build_dict = loads(trans.user.preferences['dbkeys'])[dbkey]
70 # HACK: the attempt to get chrom_info below will trigger the
71 # fasta-to-len converter if the dataset is not available or,
72 # which will in turn create a recursive loop when
73 # running the fasta-to-len tool. So, use a hack in the second
74 # condition below to avoid getting chrom_info when running the
75 # fasta-to-len converter.
76 if 'fasta' in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion:
77 # Build is defined by fasta; get len file, which is obtained from converting fasta.
78 build_fasta_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(custom_build_dict['fasta'])
79 chrom_info = build_fasta_dataset.get_converted_dataset(trans, 'len').file_name
80 elif 'len' in custom_build_dict:
81 # Build is defined by len file, so use it.
82 chrom_info = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(custom_build_dict['len']).file_name
83 # Check Data table
84 if not chrom_info:
85 dbkey_table = self._app.tool_data_tables.get(self._data_table_name, None)
86 if dbkey_table is not None:
87 chrom_info = dbkey_table.get_entry('value', dbkey, 'len_path', default=None)
88 # use configured server len path
89 if not chrom_info:
90 # Default to built-in build.
91 # Since we are using an unverified dbkey, we will sanitize the dbkey before use
92 chrom_info = os.path.join(self._static_chrom_info_path, "%s.len" % sanitize_lists_to_string(dbkey))
93 chrom_info = os.path.abspath(chrom_info)
94 return (chrom_info, db_dataset)