Mercurial > repos > iuc > query_tabular

annotate load_db.py @ 8:0c95a3f1654f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"
author iuc
date Thu, 23 Jan 2020 07:36:39 -0500
parents 33d61c89fb8d
children a3aab6045663
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rev   line source
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff changeset
1 #!/usr/bin/env python
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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2
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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3 from __future__ import print_function
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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4
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
5 import re
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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6 import sys
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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7
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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8 from filters import TabularReader
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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9
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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10
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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11 SQLITE_KEYWORDS = [
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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12 'ABORT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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13 'ACTION',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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14 'ADD',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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15 'AFTER',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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16 'ALL',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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17 'ALTER',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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18 'ANALYZE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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19 'AND',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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20 'AS',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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21 'ASC',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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22 'ATTACH',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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23 'AUTOINCREMENT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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24 'BEFORE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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25 'BEGIN',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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26 'BETWEEN',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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27 'BY',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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28 'CASCADE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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29 'CASE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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30 'CAST',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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31 'CHECK',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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32 'COLLATE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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33 'COLUMN',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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34 'COMMIT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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35 'CONFLICT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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36 'CONSTRAINT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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37 'CREATE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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38 'CROSS',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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39 'CURRENT_DATE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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40 'CURRENT_TIME',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
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41 'CURRENT_TIMESTAMP',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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42 'DATABASE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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43 'DEFAULT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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44 'DEFERRABLE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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45 'DEFERRED',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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46 'DELETE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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47 'DESC',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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48 'DETACH',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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49 'DISTINCT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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50 'DROP',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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51 'EACH',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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52 'ELSE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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53 'END',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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54 'ESCAPE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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55 'EXCEPT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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56 'EXCLUSIVE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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57 'EXISTS',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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58 'EXPLAIN',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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diff changeset
59 'FAIL',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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diff changeset
60 'FOR',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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61 'FOREIGN',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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62 'FROM',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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63 'FULL',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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64 'GLOB',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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65 'GROUP',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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66 'HAVING',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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67 'IF',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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68 'IGNORE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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69 'IMMEDIATE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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70 'IN',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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71 'INDEX',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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72 'INDEXED',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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73 'INITIALLY',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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74 'INNER',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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75 'INSERT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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76 'INSTEAD',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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77 'INTERSECT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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78 'INTO',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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79 'IS',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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80 'ISNULL',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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81 'JOIN',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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82 'KEY',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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83 'LEFT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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84 'LIKE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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85 'LIMIT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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86 'MATCH',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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87 'NATURAL',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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88 'NO',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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89 'NOT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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90 'NOTNULL',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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91 'NULL',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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92 'OF',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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diff changeset
93 'OFFSET',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
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diff changeset
94 'ON',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
95 'OR',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
96 'ORDER',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
97 'OUTER',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
98 'PLAN',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
99 'PRAGMA',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
100 'PRIMARY',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
101 'QUERY',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
102 'RAISE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
103 'RECURSIVE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
104 'REFERENCES',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
105 'REGEXP',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
106 'REINDEX',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
107 'RELEASE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
108 'RENAME',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
109 'REPLACE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
110 'RESTRICT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
111 'RIGHT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
112 'ROLLBACK',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
113 'ROW',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
114 'SAVEPOINT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
115 'SELECT',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
116 'SET',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
117 'TABLE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
118 'TEMP',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
119 'TEMPORARY',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
120 'THEN',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
121 'TO',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
122 'TRANSACTION',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
123 'TRIGGER',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
124 'UNION',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
125 'UNIQUE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
126 'UPDATE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
127 'USING',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
128 'VACUUM',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
129 'VALUES',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
130 'VIEW',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
131 'VIRTUAL',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
132 'WHEN',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
133 'WHERE',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
134 'WITH',
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
135 'WITHOUT'
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
136 ]
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
137
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
138
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
139 def get_valid_column_name(name):
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
140 valid_name = name
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
141 if not name or not name.strip():
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
142 return None
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
143 elif name.upper() in SQLITE_KEYWORDS:
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
144 valid_name = '"%s"' % name
7
33d61c89fb8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 2
diff changeset
145 elif re.match(r'^[a-zA-Z]\w*$', name):
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
146 pass
7
33d61c89fb8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 2
diff changeset
147 elif re.match(r'^"[^"]+"$', name):
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
148 pass
7
33d61c89fb8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 2
diff changeset
149 elif re.match(r'^\[[^\[\]]*\]$', name):
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
150 pass
7
33d61c89fb8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents: 2
diff changeset
151 elif re.match(r"^`[^`]+`$", name):
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
152 pass
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
153 elif name.find('"') < 0:
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
154 valid_name = '"%s"' % name
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
155 elif name.find('[') < 0 and name.find(']') < 0:
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
156 valid_name = '[%s]' % name
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
157 elif name.find('`') < 0:
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
158 valid_name = '`%s`' % name
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
159 elif name.find("'") < 0:
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
160 valid_name = "'%s'" % name
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
161 return valid_name
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
162
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
163
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
164 def getValueType(val):
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
165 if val or 0. == val:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
166 try:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
167 int(val)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
168 return 'INTEGER'
2
fb8484ee54d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
169 except ValueError:
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
170 try:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
171 float(val)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
172 return 'REAL'
2
fb8484ee54d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 1
diff changeset
173 except ValueError:
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
174 return 'TEXT'
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
175 return None
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
176
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
177
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
178 def get_column_def(file_path, table_name, skip=0, comment_char='#',
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
179 column_names=None, max_lines=100, load_named_columns=False,
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
180 firstlinenames=False, filters=None):
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
181 col_pref = ['TEXT', 'REAL', 'INTEGER', None]
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
182 col_types = []
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
183 col_idx = None
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
184 col_names = []
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
185 try:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
186 tr = TabularReader(file_path, skip=skip, comment_char=comment_char,
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
187 col_idx=None, filters=filters)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
188 for linenum, fields in enumerate(tr):
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
189 if linenum == 0 and firstlinenames:
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
190 col_names = [get_valid_column_name(name) or 'c%d' % (i + 1)
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
191 for i, name in enumerate(fields)]
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
192 continue
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
193 if linenum > max_lines:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
194 break
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
195 try:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
196 while len(col_types) < len(fields):
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
197 col_types.append(None)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
198 for i, val in enumerate(fields):
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
199 colType = getValueType(val)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
200 if col_pref.index(colType) < col_pref.index(col_types[i]):
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
201 col_types[i] = colType
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
202 except Exception as e:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
203 print('Failed at line: %d err: %s' % (linenum, e),
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
204 file=sys.stderr)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
205 except Exception as e:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
206 print('Failed: %s' % (e), file=sys.stderr)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
207 for i, col_type in enumerate(col_types):
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
208 if not col_type:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
209 col_types[i] = 'TEXT'
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
210 if not col_names:
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
211 col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
212 if column_names:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
213 if load_named_columns:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
214 col_idx = []
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
215 cnames = []
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
216 for i, cname in enumerate(
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
217 [cn.strip() for cn in column_names.split(',')]):
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
218 if cname != '':
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
219 col_idx.append(i)
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
220 cnames.append(cname)
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
221 col_types = [col_types[i] for i in col_idx]
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
222 col_names = cnames
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
223 else:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
224 for i, cname in enumerate(
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
225 [cn.strip() for cn in column_names.split(',')]):
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
226 if cname and i < len(col_names):
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
227 col_names[i] = cname
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
228 col_def = []
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
229 for i, col_name in enumerate(col_names):
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
230 col_def.append('%s %s' % (col_names[i], col_types[i]))
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
231 return col_names, col_types, col_def, col_idx
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
232
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
233
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
234 def create_table(conn, file_path, table_name, skip=0, comment_char='#',
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff changeset
235 pkey_autoincr=None, column_names=None,
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
236 load_named_columns=False, firstlinenames=False,
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
237 filters=None, unique_indexes=[], indexes=[]):
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
238 col_names, col_types, col_def, col_idx = \
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
239 get_column_def(file_path, table_name, skip=skip,
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff changeset
240 comment_char=comment_char, column_names=column_names,
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
241 load_named_columns=load_named_columns,
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
242 firstlinenames=firstlinenames,
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
243 filters=filters)
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
244 col_func = [float if t == 'REAL' else int
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
245 if t == 'INTEGER' else str for t in col_types]
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
246 table_def = 'CREATE TABLE %s (\n %s%s\n);' % (
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
247 table_name,
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
248 '%s INTEGER PRIMARY KEY AUTOINCREMENT,' %
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff changeset
249 pkey_autoincr if pkey_autoincr else '',
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
250 ', \n '.join(col_def))
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
251 # print >> sys.stdout, table_def
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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diff changeset
252 insert_stmt = 'INSERT INTO %s(%s) VALUES(%s)' % (
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
253 table_name, ','.join(col_names),
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
254 ','.join(["?" for x in col_names]))
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
255 # print >> sys.stdout, insert_stmt
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
256 data_lines = 0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
257 try:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
258 c = conn.cursor()
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
259 c.execute(table_def)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
260 conn.commit()
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
261 c.close()
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
262
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
263 c = conn.cursor()
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
264 tr = TabularReader(file_path, skip=skip, comment_char=comment_char,
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
265 col_idx=col_idx, filters=filters)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
266 for linenum, fields in enumerate(tr):
1
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
267 if linenum == 0 and firstlinenames:
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
iuc
parents: 0
diff changeset
268 continue
0
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
269 data_lines += 1
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
270 try:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
271 vals = [col_func[i](x)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
272 if x else None for i, x in enumerate(fields)]
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
273 c.execute(insert_stmt, vals)
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
274 except Exception as e:
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
diff changeset
275 print('Failed at line: %d err: %s' % (linenum, e),
3708ff0198b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
parents:
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276 file=sys.stderr)
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277 conn.commit()
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278 c.close()
1
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279 for i, index in enumerate(unique_indexes):
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280 index_name = 'idx_uniq_%s_%d' % (table_name, i)
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281 index_columns = index.split(',')
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282 create_index(conn, table_name, index_name, index_columns,
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283 unique=True)
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284 for i, index in enumerate(indexes):
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285 index_name = 'idx_%s_%d' % (table_name, i)
8a33b442ecd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 81f69ad5f39223059c40501e55ac777d3feca845
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286 index_columns = index.split(',')
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287 create_index(conn, table_name, index_name, index_columns)
0
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288 except Exception as e:
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289 exit('Error: %s' % (e))
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290
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291
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292 def create_index(conn, table_name, index_name, index_columns, unique=False):
1
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293 index_def = 'CREATE %s INDEX %s on %s(%s)' % (
0
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294 'UNIQUE' if unique else '', index_name,
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295 table_name, ','.join(index_columns))
1
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296 try:
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297 c = conn.cursor()
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298 c.execute(index_def)
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299 conn.commit()
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300 c.close()
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301 except Exception as e:
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302 print('Failed: %s err: %s' % (index_def, e), file=sys.stderr)
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303 raise(e)