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Merged
merged 13 commits into from
Apr 29, 2015
Merged

Join using instead on db issues #1126

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dbf7ad5
ENH: Meta Analysis -> Analysis
ElDeveloper Apr 27, 2015
af5423c
ENH: ✨ the magic of grep✨
ElDeveloper Apr 27, 2015
33e5404
Merge pull request #1112 from ElDeveloper/minor-wording
josenavas Apr 28, 2015
13fa06e
BUG: Fix bug in moi.init
ElDeveloper Apr 29, 2015
9cdc4c5
BUG: Update code using moi.init
ElDeveloper Apr 29, 2015
a546233
Reverting the comment from @squirrelo on search for JOIN...ON -> USIN…
josenavas Apr 29, 2015
402003a
Removing the ambiguity
josenavas Apr 29, 2015
d87890b
Removing join as now all the columns are in the dynamic table...
josenavas Apr 29, 2015
7ed5b1f
Merge pull request #1123 from ElDeveloper/moi-bug
antgonza Apr 29, 2015
f73887f
Execute the tests even if you change the format... there might be a s…
josenavas Apr 29, 2015
4830b24
Merge branch 'master' of https://github.com/biocore/qiita into join-u…
josenavas Apr 29, 2015
7a29adc
Fixing bug in _build_mapping_file and create a test for it
josenavas Apr 29, 2015
fa2392c
Adding tests for test_build_biom_tables
josenavas Apr 29, 2015
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Reverting the comment from @squirrelo on search for JOIN...ON -> USIN… 
…G cause it currently breaks
  • Loading branch information
@josenavas
josenavas committed Apr 29, 2015
commit a546233f1af8b43458aab65a63c302a6224c066f
4 changes: 2 additions & 2 deletions qiita_db/search.py
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Original file line number Diff line number Diff line change
Expand Up @@ -343,8 +343,8 @@ def _parse_study_search_string(self, searchstr,

sample_sql = ("SELECT ss.sample_id,%s "
"FROM qiita.study_sample ss "
"JOIN qiita.sample_{0} sa USING (sample_id) "
"JOIN qiita.study st USING (study_id) "
"JOIN qiita.sample_{0} sa ON ss.sample_id = sa.sample_id"
" JOIN qiita.study st ON st.study_id = ss.study_id "
"WHERE %s" %
(','.join(header_info), sql_where))
return study_sql, sample_sql, meta_header_type_lookup.keys()
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35 changes: 21 additions & 14 deletions qiita_db/test/test_search.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,8 +29,9 @@ def test_parse_study_search_string(self):
"in ('integer', 'float8')")
exp_samp_sql = ("SELECT ss.sample_id,sa.altitude "
"FROM qiita.study_sample ss "
"JOIN qiita.sample_{0} sa USING (sample_id) "
"JOIN qiita.study st USING (study_id) "
"JOIN qiita.sample_{0} sa "
"ON ss.sample_id = sa.sample_id "
"JOIN qiita.study st ON st.study_id = ss.study_id "
"WHERE sa.altitude > 0")
self.assertEqual(st_sql, exp_st_sql)
self.assertEqual(samp_sql, exp_samp_sql)
Expand All @@ -44,8 +45,9 @@ def test_parse_study_search_string(self):
"in ('integer', 'float8')")
exp_samp_sql = ("SELECT ss.sample_id,sa.altitude "
"FROM qiita.study_sample ss "
"JOIN qiita.sample_{0} sa USING (sample_id) "
"JOIN qiita.study st USING (study_id) "
"JOIN qiita.sample_{0} sa "
"ON ss.sample_id = sa.sample_id "
"JOIN qiita.study st ON st.study_id = ss.study_id "
"WHERE NOT sa.altitude > 0")
self.assertEqual(st_sql, exp_st_sql)
self.assertEqual(samp_sql, exp_samp_sql)
Expand All @@ -59,8 +61,9 @@ def test_parse_study_search_string(self):
"('integer', 'float8')")
exp_samp_sql = ("SELECT ss.sample_id,sa.ph "
"FROM qiita.study_sample ss "
"JOIN qiita.sample_{0} sa USING (sample_id) "
"JOIN qiita.study st USING (study_id) "
"JOIN qiita.sample_{0} sa "
"ON ss.sample_id = sa.sample_id "
"JOIN qiita.study st ON st.study_id = ss.study_id "
"WHERE (sa.ph > 7 AND sa.ph < 9)")
self.assertEqual(st_sql, exp_st_sql)
self.assertEqual(samp_sql, exp_samp_sql)
Expand All @@ -74,8 +77,9 @@ def test_parse_study_search_string(self):
"('integer', 'float8')")
exp_samp_sql = ("SELECT ss.sample_id,sa.ph "
"FROM qiita.study_sample ss "
"JOIN qiita.sample_{0} sa USING (sample_id) "
"JOIN qiita.study st USING (study_id) "
"JOIN qiita.sample_{0} sa "
"ON ss.sample_id = sa.sample_id "
"JOIN qiita.study st ON st.study_id = ss.study_id "
"WHERE (sa.ph > 7 OR sa.ph < 9)")
self.assertEqual(st_sql, exp_st_sql)
self.assertEqual(samp_sql, exp_samp_sql)
Expand All @@ -90,8 +94,9 @@ def test_parse_study_search_string(self):
"and column_type in ('varchar')")
exp_samp_sql = ("SELECT ss.sample_id,sa.host_subject_id "
"FROM qiita.study_sample ss "
"JOIN qiita.sample_{0} sa USING (sample_id) "
"JOIN qiita.study st USING (study_id) "
"JOIN qiita.sample_{0} sa "
"ON ss.sample_id = sa.sample_id "
"JOIN qiita.study st ON st.study_id = ss.study_id "
"WHERE LOWER(sa.host_subject_id) "
"LIKE '%chicken little%'")
self.assertEqual(st_sql, exp_st_sql)
Expand All @@ -110,8 +115,9 @@ def test_parse_study_search_string(self):
exp_samp_sql = (
"SELECT ss.sample_id,sa.name "
"FROM qiita.study_sample ss "
"JOIN qiita.sample_{0} sa USING (sample_id) "
"JOIN qiita.study st USING (study_id) "
"JOIN qiita.sample_{0} sa "
"ON ss.sample_id = sa.sample_id "
"JOIN qiita.study st ON st.study_id = ss.study_id "
"WHERE (sa.name = 'Billy Bob' OR sa.name = 'Timmy' OR "
"(sa.name = 'Jimbo' AND sa.name > 25) OR sa.name < 5)")
self.assertEqual(st_sql, exp_st_sql)
Expand All @@ -131,8 +137,9 @@ def test_parse_study_search_string(self):
"lower('ph') and column_type in ('integer', 'float8')"]
exp_samp_sql = ("SELECT ss.sample_id,sa.pH,sa.ph "
"FROM qiita.study_sample ss "
"JOIN qiita.sample_{0} sa USING (sample_id) "
"JOIN qiita.study st USING (study_id) "
"JOIN qiita.sample_{0} sa "
"ON ss.sample_id = sa.sample_id "
"JOIN qiita.study st ON st.study_id = ss.study_id "
"WHERE (sa.ph > 7 OR sa.ph < 9)")
# use the split list to make sure the SQL is properly formed
self.assertEqual(len(st_sql), 2)
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