Mercurial > repos > jjohnson > query_tabular

annotate query_tabular.py @ 23:5bb148ee644a draft default tip

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author jjohnson
date Mon, 17 Jul 2017 15:22:38 -0400
parents bed5018e7ae3
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1 #!/usr/bin/env python
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2
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3 from __future__ import print_function
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4
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5 import json
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6 import optparse
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7 import os.path
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8 import sys
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9
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10 from load_db import create_table
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11
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12 from query_db import describe_tables, get_connection, run_query
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13
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15 """
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16 JSON config:
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17 { tables : [
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18 { file_path : '/home/galaxy/dataset_101.dat',
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19 table_name : 't1',
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20 column_names : ['c1','c2','c3'],
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21 pkey_autoincr : 'id'
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22 comment_lines : 1
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23 unique: ['c1'],
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24 index: ['c2', 'c3']
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25 },
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26 { file_path : '/home/galaxy/dataset_102.dat',
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27 table_name : 'gff',
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28 column_names : ['seqname',,'date','start','end']
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29 comment_lines : 1
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30 load_named_columns : True
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31 filters : [{'filter': 'regex', 'pattern': '#peptide',
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32 'action': 'exclude_match'},
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33 {'filter': 'replace', 'column': 3,
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34 'replace': 'gi[|]', 'pattern': ''}]
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35 },
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36 { file_path : '/home/galaxy/dataset_103.dat',
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37 table_name : 'test',
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38 column_names : ['c1', 'c2', 'c3']
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39 }
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40 ]
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41 }
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42 """
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45 def __main__():
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46 # Parse Command Line
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47 parser = optparse.OptionParser()
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48 parser.add_option('-s', '--sqlitedb', dest='sqlitedb', default=None,
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49 help='The SQLite Database')
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50 parser.add_option('-j', '--jsonfile', dest='jsonfile', default=None,
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51 help='JSON dict of table specifications')
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52 parser.add_option('-q', '--query', dest='query', default=None,
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53 help='SQL query')
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54 parser.add_option('-Q', '--query_file', dest='query_file', default=None,
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55 help='SQL query file')
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56 parser.add_option('-n', '--no_header', dest='no_header', default=False,
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57 action='store_true',
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58 help='Include a column headers line')
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59 parser.add_option('-o', '--output', dest='output', default=None,
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60 help='Output file for query results')
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61 (options, args) = parser.parse_args()
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62
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63 # determine output destination
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64 if options.output is not None:
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65 try:
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66 outputPath = os.path.abspath(options.output)
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67 outputFile = open(outputPath, 'w')
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68 except Exception as e:
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69 exit('Error: %s' % (e))
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70 else:
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71 outputFile = sys.stdout
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72
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73 def _create_table(ti, table):
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74 path = table['file_path']
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75 table_name =\
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76 table['table_name'] if 'table_name' in table else 't%d' % (ti + 1)
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77 comment_lines =\
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78 table['comment_lines'] if 'comment_lines' in table else 0
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79 comment_char =\
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80 table['comment_char'] if 'comment_char' in table else None
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81 column_names =\
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82 table['column_names'] if 'column_names' in table else None
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83 if column_names:
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84 load_named_columns =\
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85 table['load_named_columns']\
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86 if 'load_named_columns' in table else False
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87 else:
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88 load_named_columns = False
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89 unique_indexes = table['unique'] if 'unique' in table else []
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90 indexes = table['index'] if 'index' in table else []
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91 filters = table['filters'] if 'filters' in table else None
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92 pkey_autoincr = \
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93 table['pkey_autoincr'] if 'pkey_autoincr' in table else None
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94 create_table(get_connection(options.sqlitedb), path, table_name,
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95 pkey_autoincr=pkey_autoincr,
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96 column_names=column_names,
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97 skip=comment_lines,
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98 comment_char=comment_char,
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99 load_named_columns=load_named_columns,
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100 filters=filters,
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101 unique_indexes=unique_indexes,
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102 indexes=indexes)
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103
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104 if options.jsonfile:
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105 try:
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106 fh = open(options.jsonfile)
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107 tdef = json.load(fh)
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108 if 'tables' in tdef:
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109 for ti, table in enumerate(tdef['tables']):
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110 _create_table(ti, table)
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111 except Exception as e:
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112 exit('Error: %s' % (e))
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113
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114 query = None
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115 if (options.query_file is not None):
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116 with open(options.query_file, 'r') as fh:
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117 query = ''
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118 for line in fh:
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119 query += line
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120 elif (options.query is not None):
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121 query = options.query
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122
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123 if (query is None):
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124 try:
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125 describe_tables(get_connection(options.sqlitedb), outputFile)
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126 except Exception as e:
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127 exit('Error: %s' % (e))
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128 else:
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129 try:
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130 run_query(get_connection(options.sqlitedb), query, outputFile,
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131 no_header=options.no_header)
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132 except Exception as e:
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133 exit('Error: %s' % (e))
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134
0
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135
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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136 if __name__ == "__main__":
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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137 __main__()