Mercurial > repos > jjohnson > query_tabular

annotate query_tabular.py @ 5:19ae309ec53c draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 29288f94a382686e263623cf6ddcd235ed5f2310-dirty
author jjohnson
date Wed, 20 Apr 2016 15:46:04 -0400
parents 9d73dca48178
children 03842a4f71c6
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1 #!/usr/bin/env python
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2 """
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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
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 format: {
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18 c2 : re.sub('pat', 'sub', c2)
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19 c3 : len(c3)
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20 }
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21 def format(colname,val, expr):
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22 - column_defs dict of columns to create from tabular input
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23 column_defs : { 'name1' : 'expr', 'name2' : 'expr'}
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24 - allow multiple queries and outputs
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25 - add a --json input for table definitions (or yaml)
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26 JSON config:
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27 { tables : [
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28 { file_path : '/home/galaxy/dataset_101.dat',
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29 table_name : 't1',
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30 column_names : ['c1', 'c2', 'c3'],
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31 pkey_autoincr : 'id'
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32 comment_lines : 1
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33 unique: ['c1'],
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34 index: ['c2','c3']
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35 },
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36 { file_path : '/home/galaxy/dataset_102.dat',
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37 table_name : 'gff',
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38 column_names : ['seqname',,,'start','end']
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39 comment_lines : 1
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40 load_named_columns : True
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41 },
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42 { file_path : '/home/galaxy/dataset_103.dat',
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43 table_name : 'test',
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44 column_names : ['c1', 'c2', 'c3']
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45 }
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46 ]
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47 }
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48 """
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49
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50 tables_query = \
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51 "SELECT name, sql FROM sqlite_master WHERE type='table' ORDER BY name"
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52
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53
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54 def getValueType(val):
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55 if val or 0. == val:
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56 try:
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57 int(val)
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58 return 'INTEGER'
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59 except:
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60 try:
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61 float(val)
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62 return 'REAL'
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63 except:
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64 return 'TEXT'
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65 return None
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66
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67
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68 def get_column_def(file_path, table_name, skip=0, comment_char='#',
3
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69 column_names=None, max_lines=100,load_named_columns=False):
0
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70 col_pref = ['TEXT', 'REAL', 'INTEGER', None]
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71 col_types = []
3
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72 col_idx = None
0
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73 data_lines = 0
3
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74
0
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75 try:
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76 with open(file_path, "r") as fh:
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77 for linenum, line in enumerate(fh):
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78 if linenum < skip:
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79 continue
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80 if line.startswith(comment_char):
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81 continue
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82 data_lines += 1
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83 try:
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84 fields = line.split('\t')
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85 while len(col_types) < len(fields):
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86 col_types.append(None)
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87 for i, val in enumerate(fields):
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88 colType = getValueType(val)
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89 if col_pref.index(colType) < col_pref.index(col_types[i]):
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90 col_types[i] = colType
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91 except Exception, e:
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92 print >> sys.stderr, 'Failed at line: %d err: %s' % (linenum, e)
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93 except Exception, e:
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94 print >> sys.stderr, 'Failed: %s' % (e)
3
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95 for i,col_type in enumerate(col_types):
0
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96 if not col_type:
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97 col_types[i] = 'TEXT'
3
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98 if column_names:
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99 col_names = []
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100 if load_named_columns:
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101 col_idx = []
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102 for i, cname in enumerate([cn.strip() for cn in column_names.split(',')]):
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103 if cname != '':
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104 col_idx.append(i)
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105 col_names.append(cname)
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106 col_types = [col_types[i] for i in col_idx]
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107 else:
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108 col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
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109 for i, cname in enumerate([cn.strip() for cn in column_names.split(',')]):
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110 if cname and i < len(col_names):
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111 col_names[i] = cname
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112 else:
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113 col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
0
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114 col_def = []
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115 for i, col_name in enumerate(col_names):
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116 col_def.append('%s %s' % (col_names[i], col_types[i]))
3
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117 return col_names, col_types, col_def, col_idx
0
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118
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119
5
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120 def create_table(conn, file_path, table_name, skip=0, comment_char='#', pkey_autoincr=None, column_names=None,load_named_columns=False,unique_indexes=[],indexes=[]):
3
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121 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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122 col_func = [float if t == 'REAL' else int if t == 'INTEGER' else str for t in col_types]
5
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123 table_def = 'CREATE TABLE %s (\n %s%s\n);' % (
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124 table_name,
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125 '%s INTEGER PRIMARY KEY AUTOINCREMENT,' % pkey_autoincr if pkey_autoincr else '',
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126 ', \n '.join(col_def))
0
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127 # print >> sys.stdout, table_def
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128 insert_stmt = 'INSERT INTO %s(%s) VALUES(%s)' % (table_name, ','.join(col_names), ','.join(["?" for x in col_names]))
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129 # print >> sys.stdout, insert_stmt
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130 data_lines = 0
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131 try:
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132 c = conn.cursor()
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133 c.execute(table_def)
4
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134 conn.commit()
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135 c.close()
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136 for i,index in enumerate(unique_indexes):
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137 index_name='idx_uniq_%s_%d' % (table_name,i)
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138 index_columns = index.split(',')
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139 create_index(conn, table_name, index_name, index_columns,unique=True)
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140 for i,index in enumerate(indexes):
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141 index_name='idx_%s_%d' % (table_name,i)
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142 index_columns = index.split(',')
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143 create_index(conn, table_name, index_name, index_columns)
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144 c = conn.cursor()
0
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145 with open(file_path, "r") as fh:
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146 for linenum, line in enumerate(fh):
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147 if linenum < skip or line.startswith(comment_char):
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148 continue
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149 data_lines += 1
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150 try:
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151 fields = line.rstrip('\r\n').split('\t')
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152 if col_idx:
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153 fields = [fields[i] for i in col_idx]
0
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154 vals = [col_func[i](x) if x else None for i, x in enumerate(fields)]
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155 c.execute(insert_stmt, vals)
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156 except Exception, e:
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157 print >> sys.stderr, 'Failed at line: %d err: %s' % (linenum, e)
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158 conn.commit()
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159 c.close()
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160 except Exception, e:
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161 print >> sys.stderr, 'Failed: %s' % (e)
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162 exit(1)
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163
4
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164 def create_index(conn, table_name, index_name, index_columns, unique=False):
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165 index_def = "CREATE %s INDEX %s on %s(%s)" % ('UNIQUE' if unique else '', index_name, table_name, ','.join(index_columns))
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166 c = conn.cursor()
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167 c.execute(index_def)
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168 conn.commit()
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169 c.close()
0
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170
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171 def regex_match(expr, item):
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172 return re.match(expr, item) is not None
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173
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174
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175 def regex_search(expr, item):
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176 return re.search(expr, item) is not None
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177
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178
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179 def regex_sub(expr, replace, item):
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180 return re.sub(expr, replace, item)
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181
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182
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183 def get_connection(sqlitedb_path, addfunctions=False):
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184 conn = sqlite.connect(sqlitedb_path)
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185 if addfunctions:
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186 conn.create_function("re_match", 2, regex_match)
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187 conn.create_function("re_search", 2, regex_search)
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188 conn.create_function("re_sub", 3, regex_sub)
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189 return conn
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190
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191
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192 def __main__():
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193 # Parse Command Line
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194 parser = optparse.OptionParser()
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195 parser.add_option('-s', '--sqlitedb', dest='sqlitedb', default=None, help='The SQLite Database')
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196 parser.add_option('-t', '--table', dest='tables', action="append", default=[], help='Tabular file: file_path[=table_name[:column_name, ...]')
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197 parser.add_option('-j', '--jsonfile', dest='jsonfile', default=None, help='Tabular file: file_path[=table_name[:column_name, ...]')
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198 parser.add_option('-q', '--query', dest='query', default=None, help='SQL query')
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199 parser.add_option('-Q', '--query_file', dest='query_file', default=None, help='SQL query file')
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200 parser.add_option('-n', '--no_header', dest='no_header', action='store_true', default=False, help='Include a column headers line')
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201 parser.add_option('-o', '--output', dest='output', default=None, help='Output file for query results')
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202 (options, args) = parser.parse_args()
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203
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204 # open sqlite connection
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205 conn = get_connection(options.sqlitedb)
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206 # determine output destination
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207 if options.output is not None:
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208 try:
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209 outputPath = os.path.abspath(options.output)
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210 outputFile = open(outputPath, 'w')
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211 except Exception, e:
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212 print >> sys.stderr, "failed: %s" % e
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213 exit(3)
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214 else:
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215 outputFile = sys.stdout
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216
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217 # get table defs
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218 if options.tables:
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219 for ti, table in enumerate(options.tables):
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220 table_name = 't%d' % (ti + 1)
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221 column_names = None
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222 fields = table.split('=')
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223 path = fields[0]
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224 if len(fields) > 1:
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225 names = fields[1].split(':')
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226 table_name = names[0] if names[0] else table_name
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227 if len(names) > 1:
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228 column_names = names[1]
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229 # print >> sys.stdout, '%s %s' % (table_name, path)
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230 create_table(conn, path, table_name, column_names=column_names)
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231 if options.jsonfile:
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232 try:
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233 fh = open(options.jsonfile)
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234 tdef = json.load(fh)
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235 if 'tables' in tdef:
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236 for ti, table in enumerate(tdef['tables']):
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237 path = table['file_path']
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238 table_name = table['table_name'] if 'table_name' in table else 't%d' % (ti + 1)
3
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239 comment_lines = table['comment_lines'] if 'comment_lines' in table else 0
0
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240 column_names = table['column_names'] if 'column_names' in table else None
3
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241 if column_names:
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242 load_named_columns = table['load_named_columns'] if 'load_named_columns' in table else False
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243 else:
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244 load_named_columns = False
4
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245 unique_indexes = table['unique'] if 'unique' in table else []
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246 indexes = table['index'] if 'index' in table else []
5
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247 pkey_autoincr = table['pkey_autoincr'] if 'pkey_autoincr' in table else None
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248 create_table(conn, path, table_name, pkey_autoincr=pkey_autoincr, column_names=column_names,
4
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249 skip=comment_lines, load_named_columns=load_named_columns,
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250 unique_indexes=unique_indexes, indexes=indexes)
0
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251 except Exception, exc:
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252 print >> sys.stderr, "Error: %s" % exc
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253 conn.close()
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254
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255 query = None
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256 if (options.query_file is not None):
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257 with open(options.query_file, 'r') as fh:
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258 query = ''
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259 for line in fh:
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260 query += line
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261 elif (options.query is not None):
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262 query = options.query
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263
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jjohnson
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264 if (query is None):
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265 try:
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jjohnson
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266 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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267 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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268 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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269 for table, sql in rslt:
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jjohnson
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270 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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271 try:
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272 col_query = 'SELECT * FROM %s LIMIT 0' % table
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jjohnson
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273 cur = conn.cursor().execute(col_query)
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jjohnson
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274 cols = [col[0] for col in cur.description]
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jjohnson
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275 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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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
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jjohnson
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278 except Exception, exc:
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jjohnson
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279 print >> sys.stderr, "Error: %s" % exc
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jjohnson
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280 exit(0)
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jjohnson
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281 # 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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282 # print >> sys.stderr, "Error: Must be a read only query"
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283 # exit(2)
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jjohnson
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284 try:
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jjohnson
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285 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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286 cur = conn.cursor()
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jjohnson
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287 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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288 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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289 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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290 # yield [col[0] for col in cur.description]
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jjohnson
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291 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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292 # yield [val for val in row]
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jjohnson
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293 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
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294 except Exception, exc:
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jjohnson
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295 print >> sys.stderr, "Error: %s" % exc
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jjohnson
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296 exit(1)
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297
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jjohnson
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298 if __name__ == "__main__":
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299 __main__()