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annotate lemuriformes/csv2sqlite.py @ 11:afc259799019

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[CSV] add script to convert to SQL
author Jeff Hammel <k0scist@gmail.com>
date Sun, 10 Dec 2017 13:58:55 -0800
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11
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1 #!/usr/bin/env python
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2
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3 """
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4 convert CSV files to a SQLite DB file
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5 """
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6
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7 # For SQLite types see
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8 # http://www.sqlite.org/datatype3.html
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9
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10 import argparse
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11 import csv
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12 import os
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13 import sqlite3
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14 import sys
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15 from collections import OrderedDict
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16 from .cast import string
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17 from .sql import SQLConnection
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18
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19
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20 def read_csv(csv_file):
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21 """read csv file with header and return list of dicts"""
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22
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23 reader = csv.DictReader(csv_file)
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24 return [row for row in reader]
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25
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26
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27 def path_root(path):
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28 """return basename file root sans extension"""
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29
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30 return os.path.splitext(os.path.basename(path))[0]
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31
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32
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33 class SQLiteConnection(SQLConnection):
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34 """connection class to SQLite database"""
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35
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36 # mapping of python types to SQLite types
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37 types = {int: "INTEGER",
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38 float: "REAL",
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39 str: "TEXT"}
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40
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41 def __init__(self, db_file):
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42 if not os.path.exists(db_file):
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43 with open(db_file, 'wb') as f:
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44 # touch file
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45 pass
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46 self.db_file = db_file
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47 self.conn = sqlite3.connect(self.db_file)
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48
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49 def __call__(self, sql, *args):
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50 c = self.conn.cursor()
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51 c.execute(sql, args)
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52 retval = c.fetchall()
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53 self.conn.commit()
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54 return retval
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55
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56 def __del__(self):
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57 self.conn.close()
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58
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59 def tables(self):
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60 """
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61 return tables in the SQLite database
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62 Ref: https://stackoverflow.com/questions/82875/how-to-list-the-tables-in-an-sqlite-database-file-that-was-opened-with-attach
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63 """
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64 sql = "SELECT name FROM sqlite_master WHERE type='table';"
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65 results = self(sql)
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66 return [row[0] for row in results]
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67
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68 def create_table(self, table, **columns):
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69 """add a table to the database"""
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70
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71 columns = ', '.join(["{key} {value}".format(key=key, value=value)
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72 for key, value in columns.items()])
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73 self("CREATE TABLE IF NOT EXISTS {table} ({columns});".format(table=table,
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74 columns=columns))
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75
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76 def schema(self, table):
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77 """get dictionary of typing for a table"""
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78 # http://www.sqlite.org/pragma.html#pragma_table_info
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79
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80 sql = "PRAGMA table_info('{}')".format(table)
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81 results = self(sql)
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82 # TODO: get data types from e.g.
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83 # [(0, u'how', u'', 0, None, 0), (1, u'are', u'', 0, None, 0), (2, u'you', u'', 0, None, 0)]
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84 # ... now
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85 # [(0, u'how', u'TEXT', 0, None, 0), (1, u'you', u'TEXT', 0, None, 0), (2, u'are', u'TEXT', 0, None, 0)]
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86 return OrderedDict([(result[1], result[2])
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87 for result in results])
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88
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89 def columns(self, table):
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90 """return ordered list of column names"""
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91
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92 return self.schema(table).keys()
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93
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94 def select(self, table):
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95 """just `select *` for now"""
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96
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97 sql = "SELECT * FROM {table};"
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98 sql = sql.format(table=table)
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99 data = self(sql)
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100 columns = self.columns(table)
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101 return [OrderedDict(zip(columns, row))
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102 for row in data]
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103
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104 select_all = select
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105
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106
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107 class CSV2SQLite(object):
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108 """
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109 convert Comma Separated Value input to SQLite
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110 """
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111 # TODO: allow conversion to arbitrary SQL
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112
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113 def __init__(self, output):
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114 self.conn = SQLiteConnection(output)
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115
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116 def __call__(self, *csv_files, **csv_dict):
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117
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118 # allow tables of default(ing) name
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119 csv_dict.update({csv_file: None
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120 for csv_file in csv_files})
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121
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122 for csv_file, tablename in csv_dict.items():
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123 self.csv2table(csv_file, tablename=tablename)
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124
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125 def csv2table(self, csv_file, tablename=None):
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126 if isinstance(csv_file, string):
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127 with open(csv_file) as f:
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128 return self.csv2table(f, tablename=tablename)
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129 if tablename is None:
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130 # TODO: allow lookup from scheme
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131 tablename = path_root(csv_file.name)
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132 # read csv
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133 data = read_csv(csv_file)
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134 assert data
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135
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136 # infer schema from data
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137 # TODO: allow lookup from scheme
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138 columns = {column: "TEXT" for column in data[0].keys()}
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139
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140 # create table
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141 self.conn.create_table(tablename, **columns)
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142
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143 # inseert data
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144 for row in data:
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145 self.conn.insert_row(tablename, **row)
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146
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147
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148 def main(args=sys.argv[1:]):
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149 """CLI"""
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150
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151 # parse command line
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152 parser = argparse.ArgumentParser(description=__doc__)
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153 parser.add_argument('input', nargs='+',
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154 type=argparse.FileType('r'),
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155 help="input CSV files; table names taken from file names")
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156 parser.add_argument('-o', '--output', dest='output',
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157 required=True,
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158 help="output SQLite file")
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159 options = parser.parse_args(args)
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160
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161 # overwrite the file
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162 # TODO: deprecate and allow appending
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163 with open(options.output, 'w') as f:
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164 pass
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165
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166 # instantiate converter
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167 conn = CSV2SQLite(options.output)
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168
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169 # convert input CSV to SQLite tables
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170 conn(*options.input)
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171
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172
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173 if __name__ == '__main__':
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174 main()