Mercurial > repos > jjohnson > query_tabular

annotate query_tabular.py @ 4:9d73dca48178 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9893037a046e4f4c1e7ba859e05f49378c398cb1-dirty
author jjohnson
date Tue, 19 Apr 2016 16:46:18 -0400
parents 3e3b3c883bec
children 19ae309ec53c
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926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
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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
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2 """
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jjohnson
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3 """
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4 import sys
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5 import re
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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
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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
4
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17 index: ['c2','c4,c5']
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18 unique: ['c1']
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19 format: {
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20 c2 : re.sub('pat', 'sub', c2)
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21 c3 : len(c3)
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22 }
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23 def format(colname,val, expr):
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24
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25 - allow optional autoincrement id column - user supplied name?
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26 autoincrement : 'id'
0
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27 - column_defs dict of columns to create from tabular input
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28 column_defs : { 'name1' : 'expr', 'name2' : 'expr'}
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29 - allow multiple queries and outputs
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30 - add a --json input for table definitions (or yaml)
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31 JSON config:
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32 { tables : [
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33 { file_path : '/home/galaxy/dataset_101.dat',
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34 table_name : 't1',
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35 column_names : ['c1', 'c2', 'c3'],
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36 comment_lines : 1
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37 },
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38 { file_path : '/home/galaxy/dataset_102.dat',
3
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39 table_name : 'gff',
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40 column_names : ['seqname',,,'start','end']
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41 comment_lines : 1
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42 load_named_columns : True
0
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43 },
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44 { file_path : '/home/galaxy/dataset_103.dat',
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45 table_name : 'test',
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46 column_names : ['c1', 'c2', 'c3']
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47 }
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48 ]
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49 }
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50 """
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51
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52 tables_query = \
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53 "SELECT name, sql FROM sqlite_master WHERE type='table' ORDER BY name"
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54
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55
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56 def getValueType(val):
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57 if val or 0. == val:
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58 try:
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59 int(val)
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60 return 'INTEGER'
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61 except:
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62 try:
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63 float(val)
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64 return 'REAL'
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65 except:
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66 return 'TEXT'
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67 return None
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68
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69
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70 def get_column_def(file_path, table_name, skip=0, comment_char='#',
3
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71 column_names=None, max_lines=100,load_named_columns=False):
0
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72 col_pref = ['TEXT', 'REAL', 'INTEGER', None]
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73 col_types = []
3
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74 col_idx = None
0
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75 data_lines = 0
3
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76
0
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77 try:
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78 with open(file_path, "r") as fh:
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79 for linenum, line in enumerate(fh):
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80 if linenum < skip:
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81 continue
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82 if line.startswith(comment_char):
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83 continue
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84 data_lines += 1
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85 try:
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86 fields = line.split('\t')
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87 while len(col_types) < len(fields):
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88 col_types.append(None)
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89 for i, val in enumerate(fields):
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90 colType = getValueType(val)
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91 if col_pref.index(colType) < col_pref.index(col_types[i]):
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92 col_types[i] = colType
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93 except Exception, e:
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94 print >> sys.stderr, 'Failed at line: %d err: %s' % (linenum, e)
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95 except Exception, e:
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96 print >> sys.stderr, 'Failed: %s' % (e)
3
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97 for i,col_type in enumerate(col_types):
0
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98 if not col_type:
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99 col_types[i] = 'TEXT'
3
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100 if column_names:
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101 col_names = []
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102 if load_named_columns:
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103 col_idx = []
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104 for i, cname in enumerate([cn.strip() for cn in column_names.split(',')]):
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105 if cname != '':
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106 col_idx.append(i)
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107 col_names.append(cname)
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108 col_types = [col_types[i] for i in col_idx]
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109 else:
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110 col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
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111 for i, cname in enumerate([cn.strip() for cn in column_names.split(',')]):
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112 if cname and i < len(col_names):
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113 col_names[i] = cname
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114 else:
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115 col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
0
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116 col_def = []
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117 for i, col_name in enumerate(col_names):
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118 col_def.append('%s %s' % (col_names[i], col_types[i]))
3
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119 return col_names, col_types, col_def, col_idx
0
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120
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121
4
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122 def create_table(conn, file_path, table_name, skip=0, comment_char='#', column_names=None,load_named_columns=False,unique_indexes=[],indexes=[]):
3
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123 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)
0
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124 col_func = [float if t == 'REAL' else int if t == 'INTEGER' else str for t in col_types]
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125 table_def = 'CREATE TABLE %s (\n %s\n);' % (table_name, ', \n '.join(col_def))
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126 # print >> sys.stdout, table_def
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127 insert_stmt = 'INSERT INTO %s(%s) VALUES(%s)' % (table_name, ','.join(col_names), ','.join(["?" for x in col_names]))
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128 # print >> sys.stdout, insert_stmt
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129 data_lines = 0
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130 try:
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131 c = conn.cursor()
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132 c.execute(table_def)
4
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133 conn.commit()
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134 c.close()
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135 for i,index in enumerate(unique_indexes):
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136 index_name='idx_uniq_%s_%d' % (table_name,i)
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137 index_columns = index.split(',')
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138 create_index(conn, table_name, index_name, index_columns,unique=True)
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139 for i,index in enumerate(indexes):
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140 index_name='idx_%s_%d' % (table_name,i)
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141 index_columns = index.split(',')
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142 create_index(conn, table_name, index_name, index_columns)
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143 c = conn.cursor()
0
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144 with open(file_path, "r") as fh:
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145 for linenum, line in enumerate(fh):
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146 if linenum < skip or line.startswith(comment_char):
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147 continue
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148 data_lines += 1
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149 try:
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150 fields = line.rstrip('\r\n').split('\t')
3
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151 if col_idx:
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152 fields = [fields[i] for i in col_idx]
0
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153 vals = [col_func[i](x) if x else None for i, x in enumerate(fields)]
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154 c.execute(insert_stmt, vals)
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155 except Exception, e:
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156 print >> sys.stderr, 'Failed at line: %d err: %s' % (linenum, e)
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157 conn.commit()
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158 c.close()
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159 except Exception, e:
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160 print >> sys.stderr, 'Failed: %s' % (e)
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161 exit(1)
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162
4
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163 def create_index(conn, table_name, index_name, index_columns, unique=False):
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164 index_def = "CREATE %s INDEX %s on %s(%s)" % ('UNIQUE' if unique else '', index_name, table_name, ','.join(index_columns))
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165 c = conn.cursor()
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166 c.execute(index_def)
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167 conn.commit()
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168 c.close()
0
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169
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170 def regex_match(expr, item):
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171 return re.match(expr, item) is not None
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172
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173
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174 def regex_search(expr, item):
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175 return re.search(expr, item) is not None
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176
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177
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178 def regex_sub(expr, replace, item):
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179 return re.sub(expr, replace, item)
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180
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181
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182 def get_connection(sqlitedb_path, addfunctions=False):
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183 conn = sqlite.connect(sqlitedb_path)
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184 if addfunctions:
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185 conn.create_function("re_match", 2, regex_match)
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186 conn.create_function("re_search", 2, regex_search)
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187 conn.create_function("re_sub", 3, regex_sub)
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188 return conn
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189
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190
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191 def __main__():
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192 # Parse Command Line
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193 parser = optparse.OptionParser()
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194 parser.add_option('-s', '--sqlitedb', dest='sqlitedb', default=None, help='The SQLite Database')
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195 parser.add_option('-t', '--table', dest='tables', action="append", default=[], help='Tabular file: file_path[=table_name[:column_name, ...]')
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196 parser.add_option('-j', '--jsonfile', dest='jsonfile', default=None, help='Tabular file: file_path[=table_name[:column_name, ...]')
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197 parser.add_option('-q', '--query', dest='query', default=None, help='SQL query')
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198 parser.add_option('-Q', '--query_file', dest='query_file', default=None, help='SQL query file')
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199 parser.add_option('-n', '--no_header', dest='no_header', action='store_true', default=False, help='Include a column headers line')
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200 parser.add_option('-o', '--output', dest='output', default=None, help='Output file for query results')
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201 (options, args) = parser.parse_args()
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202
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203 # open sqlite connection
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204 conn = get_connection(options.sqlitedb)
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205 # determine output destination
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206 if options.output is not None:
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207 try:
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208 outputPath = os.path.abspath(options.output)
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209 outputFile = open(outputPath, 'w')
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210 except Exception, e:
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211 print >> sys.stderr, "failed: %s" % e
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212 exit(3)
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213 else:
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214 outputFile = sys.stdout
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215
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216 # get table defs
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217 if options.tables:
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218 for ti, table in enumerate(options.tables):
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219 table_name = 't%d' % (ti + 1)
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220 column_names = None
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221 fields = table.split('=')
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222 path = fields[0]
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223 if len(fields) > 1:
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224 names = fields[1].split(':')
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225 table_name = names[0] if names[0] else table_name
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226 if len(names) > 1:
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227 column_names = names[1]
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228 # print >> sys.stdout, '%s %s' % (table_name, path)
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229 create_table(conn, path, table_name, column_names=column_names)
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230 if options.jsonfile:
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231 try:
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232 fh = open(options.jsonfile)
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233 tdef = json.load(fh)
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234 if 'tables' in tdef:
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235 for ti, table in enumerate(tdef['tables']):
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236 path = table['file_path']
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237 table_name = table['table_name'] if 'table_name' in table else 't%d' % (ti + 1)
3
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238 comment_lines = table['comment_lines'] if 'comment_lines' in table else 0
0
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239 column_names = table['column_names'] if 'column_names' in table else None
3
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240 if column_names:
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241 load_named_columns = table['load_named_columns'] if 'load_named_columns' in table else False
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242 else:
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243 load_named_columns = False
4
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244 unique_indexes = table['unique'] if 'unique' in table else []
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245 indexes = table['index'] if 'index' in table else []
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246 create_table(conn, path, table_name, column_names=column_names,
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247 skip=comment_lines, load_named_columns=load_named_columns,
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248 unique_indexes=unique_indexes, indexes=indexes)
0
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249 except Exception, exc:
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250 print >> sys.stderr, "Error: %s" % exc
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251 conn.close()
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252
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253 query = None
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254 if (options.query_file is not None):
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255 with open(options.query_file, 'r') as fh:
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256 query = ''
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257 for line in fh:
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258 query += line
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259 elif (options.query is not None):
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260 query = options.query
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261
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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262 if (query is None):
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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263 try:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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264 conn = get_connection(options.sqlitedb)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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265 c = conn.cursor()
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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266 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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267 for table, sql in rslt:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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268 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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269 try:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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270 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
jjohnson
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271 cur = conn.cursor().execute(col_query)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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272 cols = [col[0] for col in cur.description]
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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273 print >> sys.stderr, " Columns: %s" % cols
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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274 except Exception, exc:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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275 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
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276 except Exception, exc:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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277 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
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278 exit(0)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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279 # if not sqlite.is_read_only_query(query):
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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280 # print >> sys.stderr, "Error: Must be a read only query"
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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281 # exit(2)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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282 try:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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283 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
jjohnson
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284 cur = conn.cursor()
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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285 results = cur.execute(query)
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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286 if not options.no_header:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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287 outputFile.write("#%s\n" % '\t'.join([str(col[0]) for col in cur.description]))
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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288 # yield [col[0] for col in cur.description]
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
parents:
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289 for i, row in enumerate(results):
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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290 # yield [val for val in row]
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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291 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:
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292 except Exception, exc:
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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293 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
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294 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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295
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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296 if __name__ == "__main__":
926c62f7fa09 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty
jjohnson
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297 __main__()