Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/util/dbkeys.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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 import logging |
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5 import os.path |
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6 import re |
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7 from json import loads |
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8 |
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9 from galaxy.util import ( |
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10 galaxy_directory, |
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11 unicodify, |
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12 ) |
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13 from galaxy.util.object_wrapper import sanitize_lists_to_string |
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14 |
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15 log = logging.getLogger(__name__) |
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16 |
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17 |
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18 def read_dbnames(filename): |
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19 """ Read build names from file """ |
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20 db_names = [] |
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21 try: |
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22 ucsc_builds = {} |
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23 man_builds = [] # assume these are integers |
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24 name_to_db_base = {} |
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25 if filename is None: |
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26 # Should only be happening with the galaxy.tools.parameters.basic:GenomeBuildParameter docstring unit test |
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27 filename = os.path.join(galaxy_directory(), 'tool-data', 'shared', 'ucsc', 'builds.txt.sample') |
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28 for line in open(filename): |
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29 try: |
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30 if line[0:1] == "#": |
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31 continue |
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32 fields = line.replace("\r", "").replace("\n", "").split("\t") |
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33 # Special case of unspecified build is at top of list |
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34 if fields[0] == "?": |
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35 db_names.insert(0, (fields[0], fields[1])) |
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36 continue |
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37 try: # manual build (i.e. microbes) |
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38 int(fields[0]) |
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39 man_builds.append((fields[1], fields[0])) |
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40 except Exception: # UCSC build |
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41 db_base = fields[0].rstrip('0123456789') |
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42 if db_base not in ucsc_builds: |
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43 ucsc_builds[db_base] = [] |
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44 name_to_db_base[fields[1]] = db_base |
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45 # we want to sort within a species numerically by revision number |
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46 build_rev = re.compile(r'\d+$') |
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47 try: |
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48 build_rev = int(build_rev.findall(fields[0])[0]) |
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49 except Exception: |
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50 build_rev = 0 |
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51 ucsc_builds[db_base].append((build_rev, fields[0], fields[1])) |
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52 except Exception: |
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53 continue |
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54 sort_names = sorted(name_to_db_base.keys()) |
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55 for name in sort_names: |
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56 db_base = name_to_db_base[name] |
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57 ucsc_builds[db_base].sort() |
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58 ucsc_builds[db_base].reverse() |
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59 ucsc_builds[db_base] = [(build, name) for _, build, name in ucsc_builds[db_base]] |
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60 db_names = list(db_names + ucsc_builds[db_base]) |
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61 if len(db_names) > 1 and len(man_builds) > 0: |
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62 db_names.append((GenomeBuilds.default_value, '----- Additional Species Are Below -----')) |
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63 man_builds.sort() |
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64 man_builds = [(build, name) for name, build in man_builds] |
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65 db_names = list(db_names + man_builds) |
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66 except Exception as e: |
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67 log.error("ERROR: Unable to read builds file: %s", unicodify(e)) |
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68 return db_names |
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69 |
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70 |
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71 class GenomeBuilds: |
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72 default_value = "?" |
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73 default_name = "unspecified (?)" |
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74 |
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75 def __init__(self, app, data_table_name="__dbkeys__", load_old_style=True): |
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76 self._app = app |
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77 self._data_table_name = data_table_name |
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78 self._static_chrom_info_path = app.config.len_file_path |
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79 # A dbkey can be listed multiple times, but with different names, so we can't use dictionaries for lookups |
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80 if load_old_style: |
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81 self._static_dbkeys = list(read_dbnames(app.config.builds_file_path)) |
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82 else: |
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83 self._static_dbkeys = [] |
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84 |
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85 def get_genome_build_names(self, trans=None): |
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86 # FIXME: how to deal with key duplicates? |
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87 rval = [(self.default_value, self.default_name)] |
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88 # load user custom genome builds |
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89 if trans is not None: |
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90 if trans.history: |
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91 # This is a little bit Odd. We are adding every .len file in the current history to dbkey list, |
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92 # but this is previous behavior from trans.db_names, so we'll continue to do it. |
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93 # It does allow one-off, history specific dbkeys to be created by a user. But we are not filtering, |
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94 # so a len file will be listed twice (as the build name and again as dataset name), |
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95 # if custom dbkey creation/conversion occurred within the current history. |
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96 datasets = trans.sa_session.query(self._app.model.HistoryDatasetAssociation) \ |
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97 .filter_by(deleted=False, history_id=trans.history.id, extension="len") |
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98 for dataset in datasets: |
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99 rval.append((dataset.dbkey, f"{dataset.name} ({dataset.dbkey}) [History]")) |
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100 user = trans.user |
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101 if user and hasattr(user, 'preferences') and 'dbkeys' in user.preferences: |
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102 user_keys = loads(user.preferences['dbkeys']) |
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103 for key, chrom_dict in user_keys.items(): |
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104 rval.append((key, "{} ({}) [Custom]".format(chrom_dict['name'], key))) |
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105 # Load old builds.txt static keys |
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106 rval.extend(self._static_dbkeys) |
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107 # load dbkeys from dbkey data table |
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108 dbkey_table = self._app.tool_data_tables.get(self._data_table_name, None) |
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109 if dbkey_table is not None: |
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110 for field_dict in dbkey_table.get_named_fields_list(): |
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111 rval.append((field_dict['value'], field_dict['name'])) |
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112 return rval |
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113 |
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114 def get_chrom_info(self, dbkey, trans=None, custom_build_hack_get_len_from_fasta_conversion=True): |
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115 # FIXME: flag to turn off custom_build_hack_get_len_from_fasta_conversion should not be required |
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116 chrom_info = None |
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117 db_dataset = None |
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118 # Collect chromInfo from custom builds |
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119 if trans: |
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120 db_dataset = trans.db_dataset_for(dbkey) |
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121 if db_dataset: |
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122 chrom_info = db_dataset.file_name |
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123 else: |
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124 # Do Custom Build handling |
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125 if trans.user and ('dbkeys' in trans.user.preferences) and (dbkey in loads(trans.user.preferences['dbkeys'])): |
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126 custom_build_dict = loads(trans.user.preferences['dbkeys'])[dbkey] |
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127 # HACK: the attempt to get chrom_info below will trigger the |
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128 # fasta-to-len converter if the dataset is not available or, |
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129 # which will in turn create a recursive loop when |
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130 # running the fasta-to-len tool. So, use a hack in the second |
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131 # condition below to avoid getting chrom_info when running the |
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132 # fasta-to-len converter. |
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133 if 'fasta' in custom_build_dict and custom_build_hack_get_len_from_fasta_conversion: |
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134 # Build is defined by fasta; get len file, which is obtained from converting fasta. |
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135 build_fasta_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(custom_build_dict['fasta']) |
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136 chrom_info = build_fasta_dataset.get_converted_dataset(trans, 'len').file_name |
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137 elif 'len' in custom_build_dict: |
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138 # Build is defined by len file, so use it. |
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139 chrom_info = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(custom_build_dict['len']).file_name |
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140 # Check Data table |
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141 if not chrom_info: |
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142 dbkey_table = self._app.tool_data_tables.get(self._data_table_name, None) |
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143 if dbkey_table is not None: |
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144 chrom_info = dbkey_table.get_entry('value', dbkey, 'len_path', default=None) |
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145 # use configured server len path |
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146 if not chrom_info: |
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147 # Default to built-in build. |
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148 # Since we are using an unverified dbkey, we will sanitize the dbkey before use |
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149 chrom_info = os.path.join(self._static_chrom_info_path, "%s.len" % sanitize_lists_to_string(dbkey)) |
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150 chrom_info = os.path.abspath(chrom_info) |
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151 return (chrom_info, db_dataset) |