Mercurial > repos > jjohnson > query_tabular

annotate query_tabular.py @ 3:3e3b3c883bec draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty
author jjohnson
date Tue, 16 Feb 2016 09:34:30 -0500
parents 926c62f7fa09
children 9d73dca48178
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926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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1 #!/usr/bin/env python
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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2 """
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jjohnson
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3 """
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jjohnson
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4 import sys
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jjohnson
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5 import re
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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6 import os.path
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7 import json
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8 import sqlite3 as sqlite
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9 import optparse
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10 from optparse import OptionParser
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11
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12 """
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13 TODO:
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14 - could read column names from comment lines, but issues with legal names
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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15 - could add some transformations on tabular columns,
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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16 e.g. a regex to format date/time strings
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17 c2 : re.sub('pat', 'sub', c2)
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18 c3 :
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19 - column_defs dict of columns to create from tabular input
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20 column_defs : { 'name1' : 'expr', 'name2' : 'expr'}
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21 - allow multiple queries and outputs
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22 - add a --json input for table definitions (or yaml)
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23 JSON config:
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24 { tables : [
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25 { file_path : '/home/galaxy/dataset_101.dat',
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26 table_name : 't1',
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27 column_names : ['c1', 'c2', 'c3'],
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28 comment_lines : 1
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29 },
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30 { file_path : '/home/galaxy/dataset_102.dat',
3
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31 table_name : 'gff',
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32 column_names : ['seqname',,,'start','end']
3e3b3c883bec planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty
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33 comment_lines : 1
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34 load_named_columns : True
0
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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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43
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44 tables_query = \
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45 "SELECT name, sql FROM sqlite_master WHERE type='table' ORDER BY name"
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46
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47
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48 def getValueType(val):
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49 if val or 0. == val:
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50 try:
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51 int(val)
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52 return 'INTEGER'
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53 except:
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54 try:
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55 float(val)
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56 return 'REAL'
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57 except:
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58 return 'TEXT'
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59 return None
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60
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61
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62 def get_column_def(file_path, table_name, skip=0, comment_char='#',
3
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63 column_names=None, max_lines=100,load_named_columns=False):
0
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64 col_pref = ['TEXT', 'REAL', 'INTEGER', None]
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65 col_types = []
3
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66 col_idx = None
0
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67 data_lines = 0
3
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68
0
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69 try:
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70 with open(file_path, "r") as fh:
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71 for linenum, line in enumerate(fh):
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72 if linenum < skip:
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73 continue
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74 if line.startswith(comment_char):
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75 continue
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76 data_lines += 1
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77 try:
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78 fields = line.split('\t')
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79 while len(col_types) < len(fields):
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80 col_types.append(None)
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81 for i, val in enumerate(fields):
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82 colType = getValueType(val)
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83 if col_pref.index(colType) < col_pref.index(col_types[i]):
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84 col_types[i] = colType
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85 except Exception, e:
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86 print >> sys.stderr, 'Failed at line: %d err: %s' % (linenum, e)
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87 except Exception, e:
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88 print >> sys.stderr, 'Failed: %s' % (e)
3
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89 for i,col_type in enumerate(col_types):
0
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90 if not col_type:
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91 col_types[i] = 'TEXT'
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92 if column_names:
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93 col_names = []
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94 if load_named_columns:
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95 col_idx = []
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96 for i, cname in enumerate([cn.strip() for cn in column_names.split(',')]):
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97 if cname != '':
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98 col_idx.append(i)
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99 col_names.append(cname)
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100 col_types = [col_types[i] for i in col_idx]
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101 else:
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102 col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
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103 for i, cname in enumerate([cn.strip() for cn in column_names.split(',')]):
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104 if cname and i < len(col_names):
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105 col_names[i] = cname
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106 else:
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107 col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
0
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108 col_def = []
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109 for i, col_name in enumerate(col_names):
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110 col_def.append('%s %s' % (col_names[i], col_types[i]))
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111 return col_names, col_types, col_def, col_idx
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112
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113
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114 def create_table(conn, file_path, table_name, skip=0, comment_char='#', column_names=None,load_named_columns=False):
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115 col_names, col_types, col_def, col_idx = get_column_def(file_path, table_name, skip=skip, comment_char=comment_char, column_names=column_names,load_named_columns=load_named_columns)
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116 col_func = [float if t == 'REAL' else int if t == 'INTEGER' else str for t in col_types]
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117 table_def = 'CREATE TABLE %s (\n %s\n);' % (table_name, ', \n '.join(col_def))
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118 # print >> sys.stdout, table_def
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119 insert_stmt = 'INSERT INTO %s(%s) VALUES(%s)' % (table_name, ','.join(col_names), ','.join(["?" for x in col_names]))
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120 # print >> sys.stdout, insert_stmt
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121 data_lines = 0
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122 try:
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123 c = conn.cursor()
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124 c.execute(table_def)
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125 with open(file_path, "r") as fh:
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126 for linenum, line in enumerate(fh):
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127 if linenum < skip or line.startswith(comment_char):
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128 continue
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129 data_lines += 1
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130 try:
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131 fields = line.rstrip('\r\n').split('\t')
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132 if col_idx:
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133 fields = [fields[i] for i in col_idx]
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134 vals = [col_func[i](x) if x else None for i, x in enumerate(fields)]
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135 c.execute(insert_stmt, vals)
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136 except Exception, e:
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137 print >> sys.stderr, 'Failed at line: %d err: %s' % (linenum, e)
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138 conn.commit()
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139 c.close()
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140 except Exception, e:
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141 print >> sys.stderr, 'Failed: %s' % (e)
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142 exit(1)
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143
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144
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145 def regex_match(expr, item):
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146 return re.match(expr, item) is not None
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147
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148
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149 def regex_search(expr, item):
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150 return re.search(expr, item) is not None
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151
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152
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153 def regex_sub(expr, replace, item):
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154 return re.sub(expr, replace, item)
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155
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156
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157 def get_connection(sqlitedb_path, addfunctions=False):
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158 conn = sqlite.connect(sqlitedb_path)
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159 if addfunctions:
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160 conn.create_function("re_match", 2, regex_match)
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161 conn.create_function("re_search", 2, regex_search)
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162 conn.create_function("re_sub", 3, regex_sub)
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163 return conn
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164
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165
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166 def __main__():
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167 # Parse Command Line
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168 parser = optparse.OptionParser()
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169 parser.add_option('-s', '--sqlitedb', dest='sqlitedb', default=None, help='The SQLite Database')
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170 parser.add_option('-t', '--table', dest='tables', action="append", default=[], help='Tabular file: file_path[=table_name[:column_name, ...]')
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171 parser.add_option('-j', '--jsonfile', dest='jsonfile', default=None, help='Tabular file: file_path[=table_name[:column_name, ...]')
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172 parser.add_option('-q', '--query', dest='query', default=None, help='SQL query')
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173 parser.add_option('-Q', '--query_file', dest='query_file', default=None, help='SQL query file')
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174 parser.add_option('-n', '--no_header', dest='no_header', action='store_true', default=False, help='Include a column headers line')
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parents:
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175 parser.add_option('-o', '--output', dest='output', default=None, help='Output file for query results')
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176 (options, args) = parser.parse_args()
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177
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178 # open sqlite connection
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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179 conn = get_connection(options.sqlitedb)
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180 # determine output destination
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181 if options.output is not None:
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jjohnson
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182 try:
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jjohnson
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183 outputPath = os.path.abspath(options.output)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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184 outputFile = open(outputPath, 'w')
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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185 except Exception, e:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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186 print >> sys.stderr, "failed: %s" % e
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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187 exit(3)
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188 else:
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189 outputFile = sys.stdout
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190
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jjohnson
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191 # get table defs
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192 if options.tables:
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193 for ti, table in enumerate(options.tables):
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194 table_name = 't%d' % (ti + 1)
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195 column_names = None
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196 fields = table.split('=')
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197 path = fields[0]
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jjohnson
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198 if len(fields) > 1:
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199 names = fields[1].split(':')
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200 table_name = names[0] if names[0] else table_name
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201 if len(names) > 1:
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202 column_names = names[1]
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203 # print >> sys.stdout, '%s %s' % (table_name, path)
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204 create_table(conn, path, table_name, column_names=column_names)
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205 if options.jsonfile:
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jjohnson
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206 try:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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207 fh = open(options.jsonfile)
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jjohnson
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208 tdef = json.load(fh)
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jjohnson
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209 if 'tables' in tdef:
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210 for ti, table in enumerate(tdef['tables']):
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211 path = table['file_path']
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jjohnson
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212 table_name = table['table_name'] if 'table_name' in table else 't%d' % (ti + 1)
3
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213 comment_lines = table['comment_lines'] if 'comment_lines' in table else 0
0
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214 column_names = table['column_names'] if 'column_names' in table else None
3
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215 if column_names:
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216 load_named_columns = table['load_named_columns'] if 'load_named_columns' in table else False
3e3b3c883bec planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 60d1a49c09f87c1c1ec6fecbe54aa226bdc695a7-dirty
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diff changeset
217 else:
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218 load_named_columns = False
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219 create_table(conn, path, table_name, column_names=column_names, skip=comment_lines,load_named_columns=load_named_columns)
0
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220 except Exception, exc:
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221 print >> sys.stderr, "Error: %s" % exc
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222 conn.close()
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223
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224 query = None
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225 if (options.query_file is not None):
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226 with open(options.query_file, 'r') as fh:
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227 query = ''
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228 for line in fh:
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229 query += line
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230 elif (options.query is not None):
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231 query = options.query
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232
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233 if (query is None):
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jjohnson
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234 try:
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jjohnson
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235 conn = get_connection(options.sqlitedb)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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236 c = conn.cursor()
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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237 rslt = c.execute(tables_query).fetchall()
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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238 for table, sql in rslt:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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239 print >> sys.stderr, "Table %s:" % table
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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240 try:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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241 col_query = 'SELECT * FROM %s LIMIT 0' % table
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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242 cur = conn.cursor().execute(col_query)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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243 cols = [col[0] for col in cur.description]
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244 print >> sys.stderr, " Columns: %s" % cols
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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245 except Exception, exc:
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246 print >> sys.stderr, "Error: %s" % exc
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diff changeset
247 except Exception, exc:
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248 print >> sys.stderr, "Error: %s" % exc
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249 exit(0)
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250 # if not sqlite.is_read_only_query(query):
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251 # print >> sys.stderr, "Error: Must be a read only query"
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252 # exit(2)
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253 try:
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jjohnson
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254 conn = get_connection(options.sqlitedb, addfunctions=True)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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255 cur = conn.cursor()
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256 results = cur.execute(query)
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257 if not options.no_header:
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258 outputFile.write("#%s\n" % '\t'.join([str(col[0]) for col in cur.description]))
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259 # yield [col[0] for col in cur.description]
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260 for i, row in enumerate(results):
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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261 # yield [val for val in row]
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262 outputFile.write("%s\n" % '\t'.join([str(val) for val in row]))
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
diff changeset
263 except Exception, exc:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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264 print >> sys.stderr, "Error: %s" % exc
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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265 exit(1)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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266
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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267 if __name__ == "__main__":
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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268 __main__()