Mercurial > repos > iuc > query_tabular

annotate query_tabular.py @ 8:0c95a3f1654f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"
author iuc
date Thu, 23 Jan 2020 07:36:39 -0500
parents 973f03d82c86
children
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3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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1 #!/usr/bin/env python
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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2
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3 from __future__ import print_function
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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4
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5 import json
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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6 import optparse
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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7 import os.path
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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8 import sys
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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9
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10 from load_db import create_table
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11 from query_db import describe_tables, get_connection, run_query
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12
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13
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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14 """
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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15 JSON config:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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16 { tables : [
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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17 { file_path : '/home/galaxy/dataset_101.dat',
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18 table_name : 't1',
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19 column_names : ['c1','c2','c3'],
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20 pkey_autoincr : 'id'
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21 comment_lines : 1
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22 unique: ['c1'],
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23 index: ['c2', 'c3']
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24 },
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25 { file_path : '/home/galaxy/dataset_102.dat',
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26 table_name : 'gff',
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27 column_names : ['seqname',,'date','start','end']
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28 comment_lines : 1
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29 load_named_columns : True
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30 filters : [{'filter': 'regex', 'pattern': '#peptide',
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31 'action': 'exclude_match'},
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32 {'filter': 'replace', 'column': 3,
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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33 'replace': 'gi[|]', 'pattern': ''}]
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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34 },
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35 { file_path : '/home/galaxy/dataset_103.dat',
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36 table_name : 'test',
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37 column_names : ['c1', 'c2', 'c3']
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38 }
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39 ]
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40 }
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41 """
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42
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43
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44 def __main__():
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45 # Parse Command Line
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46 parser = optparse.OptionParser()
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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47 parser.add_option('-s', '--sqlitedb', dest='sqlitedb', default=None,
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48 help='The SQLite Database')
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49 parser.add_option('-j', '--jsonfile', dest='jsonfile', default=None,
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50 help='JSON dict of table specifications')
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51 parser.add_option('-q', '--query', dest='query', default=None,
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52 help='SQL query')
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53 parser.add_option('-Q', '--query_file', dest='query_file', default=None,
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54 help='SQL query file')
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55 parser.add_option('-n', '--no_header', dest='no_header', default=False,
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56 action='store_true',
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57 help='Include a column headers line')
1
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58 parser.add_option('-c', '--comment_char', dest='comment_char', default='',
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59 help='comment character to prefix column header line')
0
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60 parser.add_option('-o', '--output', dest='output', default=None,
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61 help='Output file for query results')
4
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62 parser.add_option('-d', '--debug', dest='debug', default=False,
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63 action='store_true',
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64 help='Output info to stderr')
0
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65 (options, args) = parser.parse_args()
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66
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67 # determine output destination
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68 if options.output is not None:
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69 try:
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70 outputPath = os.path.abspath(options.output)
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71 outputFile = open(outputPath, 'w')
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72 except Exception as e:
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73 exit('Error: %s' % (e))
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74 else:
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75 outputFile = sys.stdout
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76
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77 def _create_table(ti, table):
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78 path = table['file_path']
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79 table_name =\
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80 table['table_name'] if 'table_name' in table else 't%d' % (ti + 1)
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81 comment_lines =\
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82 table['comment_lines'] if 'comment_lines' in table else 0
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83 comment_char =\
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84 table['comment_char'] if 'comment_char' in table else None
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85 column_names =\
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86 table['column_names'] if 'column_names' in table else None
1
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87 firstlinenames =\
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88 table['firstlinenames'] if 'firstlinenames' in table else False
0
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89 if column_names:
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90 load_named_columns =\
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
91 table['load_named_columns']\
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff changeset
92 if 'load_named_columns' in table else False
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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diff changeset
93 else:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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diff changeset
94 load_named_columns = False
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff changeset
95 unique_indexes = table['unique'] if 'unique' in table else []
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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96 indexes = table['index'] if 'index' in table else []
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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97 filters = table['filters'] if 'filters' in table else None
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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98 pkey_autoincr = \
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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99 table['pkey_autoincr'] if 'pkey_autoincr' in table else None
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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100 create_table(get_connection(options.sqlitedb), path, table_name,
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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101 pkey_autoincr=pkey_autoincr,
1
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102 firstlinenames=firstlinenames,
0
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103 column_names=column_names,
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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104 skip=comment_lines,
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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105 comment_char=comment_char,
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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106 load_named_columns=load_named_columns,
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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107 filters=filters,
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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108 unique_indexes=unique_indexes,
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diff changeset
109 indexes=indexes)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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110
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111 if options.jsonfile:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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112 try:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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113 with open(options.jsonfile) as fh:
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114 tdef = json.load(fh)
4
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115 if options.debug:
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116 print('JSON: %s' % tdef, file=sys.stderr)
0
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117 if 'tables' in tdef:
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118 for ti, table in enumerate(tdef['tables']):
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119 _create_table(ti, table)
4
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120 if 'sql_stmts' in tdef:
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121 for si, stmt in enumerate(tdef['sql_stmts']):
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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122 rowcount = run_query(get_connection(options.sqlitedb), stmt, None)
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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123 if options.debug:
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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124 print('\nDB modification: %s \nrowcount: %s' %
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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125 (stmt, rowcount), file=sys.stderr)
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126 if 'queries' in tdef:
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127 for qi, qstmt in enumerate(tdef['queries']):
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128 if 'header' in qstmt:
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129 no_header = False
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130 comment_char = qstmt['header']
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131 else:
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132 no_header = True
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133 comment_char = None
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134 with open(qstmt['result_file'], 'w') as fh:
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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135 query = qstmt['query']
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136 rowcount = run_query(get_connection(options.sqlitedb),
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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diff changeset
137 query,
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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diff changeset
138 fh,
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139 no_header=no_header,
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140 comment_char=comment_char)
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141 if options.debug:
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142 print('\nSQL: %s \nrowcount: %s' %
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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143 (query, rowcount), file=sys.stderr)
0
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144 except Exception as e:
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145 exit('Error: %s' % (e))
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146
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147 query = None
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148 if options.query_file is not None:
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149 with open(options.query_file, 'r') as fh:
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150 query = ''
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151 for line in fh:
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152 query += line
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153 elif options.query is not None:
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154 query = options.query
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155
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156 if query is None:
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diff changeset
157 try:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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158 describe_tables(get_connection(options.sqlitedb), outputFile)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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diff changeset
159 except Exception as e:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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160 exit('Error: %s' % (e))
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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161 else:
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162 try:
4
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diff changeset
163 rowcount = run_query(get_connection(options.sqlitedb),
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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diff changeset
164 query, outputFile,
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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165 no_header=options.no_header,
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166 comment_char=options.comment_char)
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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diff changeset
167 if options.debug:
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168 print('\nSQL: %s \nrowcount: %s' %
973f03d82c86 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 6a362345c31764c28bb6328da1f0d81ef8f35d40
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diff changeset
169 (query, rowcount), file=sys.stderr)
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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170 except Exception as e:
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diff changeset
171 exit('Error: %s' % (e))
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diff changeset
172
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173
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174 if __name__ == "__main__":
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175 __main__()