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

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