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Fix 1493 #1495

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merged 7 commits into from
Oct 10, 2015
Merged

Fix 1493 #1495

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9e6c7f5
solving conflicts
antgonza Oct 9, 2015
fbe3cb2
Merge branch 'next-joy-list' of https://github.com/antgonza/qiita int…
antgonza Oct 9, 2015
1b07926
Merge branch 'next-joy-list' of https://github.com/antgonza/qiita int…
antgonza Oct 10, 2015
a68f09d
Merge branch 'ebi-improvements'
antgonza Oct 10, 2015
7279e74
Merge branch 'ebi-improvements' of https://github.com/biocore/qiita
antgonza Oct 10, 2015
e6dd1be
fix #1493
antgonza Oct 10, 2015
a4d9810
fix error
antgonza Oct 10, 2015
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5 changes: 4 additions & 1 deletion qiita_db/meta_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -189,7 +189,10 @@ def get_lat_longs():
AND SPLIT_PART(table_name, '_', 2)::int IN %s;"""
TRN.add(sql, [tuple(portal_table_ids)])

sql = "SELECT latitude, longitude FROM qiita.{0}"
sql = """SELECT latitude, longitude
FROM qiita.{0}
WHERE latitude IS NOT NULL
AND longitude IS NOT NULL"""
idx = TRN.index

portal_tables = TRN.execute_fetchflatten()
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4 changes: 2 additions & 2 deletions qiita_db/support_files/populate_test_db.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -168,8 +168,8 @@ INSERT INTO qiita.sample_1 (sample_id, season_environment, assigned_from_geo, te
('1.SKM8.640201', 'winter', 'n', '63.1 sand, 17.7 silt, 19.2 clay', '1118232', 0.15, '3483', 'root metagenome', 0.101, 114, 15, 1.3, 7.44, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.82, 'SKM8', 3.31, 'Bucu Roots', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:D8', 'Cannabis Soil Microbiome', 3.21190859967, 26.8138925876, '1118232'),
('1.SKB8.640193', 'winter', 'n', '64.6 sand, 17.6 silt, 17.8 clay', '1118232', 0.15, '3483', 'root metagenome', 0.164, 114, 15, 1.41, 7.15, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.94, 'SKB8', 5, 'Burmese root', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:M7', 'Cannabis Soil Microbiome', 74.0894932572, 65.3283470202, '1118232'),
('1.SKD2.640178', 'winter', 'n', '66 sand, 16.3 silt, 17.7 clay', '410658', 0.15, '3483', 'soil metagenome', 0.178, 114, 15, 1.51, 7.1, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.8, 'SKD2', 4.32, 'Diesel bulk', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:B5', 'Cannabis Soil Microbiome', 53.5050692395, 31.6056761814, '1118232'),
('1.SKM3.640197', 'winter', 'n', '63.1 sand, 17.7 silt, 19.2 clay', '410658', 0.15, '3483', 'soil metagenome', 0.101, 114, 15, 1.3, 7.44, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.82, 'SKM3', 3.31, 'Bucu bulk', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:B7', 'Cannabis Soil Microbiome', 63.6505562766, 31.2003474585, '1118232'),
('1.SKM4.640180', 'winter', 'n', '63.1 sand, 17.7 silt, 19.2 clay', '939928', 0.15, '3483', 'rhizosphere metagenome', 0.101, 114, 15, 1.3, 7.44, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.82, 'SKM4', 3.31, 'Bucu Rhizo', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:D2', 'Cannabis Soil Microbiome', 31.7167821863, 95.5088566087, '1118232'),
('1.SKM3.640197', 'winter', 'n', '63.1 sand, 17.7 silt, 19.2 clay', '410658', 0.15, '3483', 'soil metagenome', 0.101, 114, 15, 1.3, 7.44, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.82, 'SKM3', 3.31, 'Bucu bulk', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:B7', 'Cannabis Soil Microbiome', NULL, 31.2003474585, '1118232'),
('1.SKM4.640180', 'winter', 'n', '63.1 sand, 17.7 silt, 19.2 clay', '939928', 0.15, '3483', 'rhizosphere metagenome', 0.101, 114, 15, 1.3, 7.44, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.82, 'SKM4', 3.31, 'Bucu Rhizo', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:D2', 'Cannabis Soil Microbiome', NULL, NULL, '1118232'),
('1.SKB9.640200', 'winter', 'n', '64.6 sand, 17.6 silt, 17.8 clay', '1118232', 0.15, '3483', 'root metagenome', 0.164, 114, 15, 1.41, 7.15, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.8, 'SKB9', 5, 'Burmese root', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:B3', 'Cannabis Soil Microbiome', 12.6245524972, 96.0693176066, '1118232'),
('1.SKB4.640189', 'winter', 'n', '64.6 sand, 17.6 silt, 17.8 clay', '939928', 0.15, '3483', 'rhizosphere metagenome', 0.164, 114, 15, 1.41, 7.15, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.94, 'SKB4', 5, 'Burmese Rhizo', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:D7', 'Cannabis Soil Microbiome', 43.9614715197, 82.8516734159, '1118232'),
('1.SKB5.640181', 'winter', 'n', '64.6 sand, 17.6 silt, 17.8 clay', '939928', 0.15, '3483', 'rhizosphere metagenome', 0.164, 114, 15, 1.41, 7.15, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.94, 'SKB5', 5, 'Burmese Rhizo', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:M4', 'Cannabis Soil Microbiome', 10.6655599093, 70.784770579, '1118232'),
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2 changes: 0 additions & 2 deletions qiita_db/test/test_meta_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,6 @@ def test_get_lat_longs(self):
[57.571893782, 32.5563076447],
[13.089194595, 92.5274472082],
[12.7065957714, 84.9722975792],
[31.7167821863, 95.5088566087],
[44.9725384282, 66.1920014699],
[10.6655599093, 70.784770579],
[29.1499460692, 82.1270418227],
Expand All @@ -121,7 +120,6 @@ def test_get_lat_longs(self):
[82.8302905615, 86.3615778099],
[12.6245524972, 96.0693176066],
[85.4121476399, 15.6526750776],
[63.6505562766, 31.2003474585],
[23.1218032799, 42.838497795],
[43.9614715197, 82.8516734159],
[68.51099627, 2.35063674718],
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5 changes: 1 addition & 4 deletions qiita_ware/test/test_util.py
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Expand Up @@ -80,7 +80,7 @@ def test_per_sample_sequences_complex(self):
def test_stats_from_df(self):
obs = stats_from_df(SampleTemplate(1).to_dataframe())
for k in obs:
self.assertEqual(obs[k], SUMMARY_STATS[k])
self.assertItemsEqual(obs[k], SUMMARY_STATS[k])

def test_dataframe_from_template(self):
template = PrepTemplate(1)
Expand Down Expand Up @@ -327,7 +327,6 @@ def test_hdf5IO_open(self):
('13.089194595', 1),
('23.1218032799', 1),
('29.1499460692', 1),
('31.7167821863', 1),
('35.2374368957', 1),
('38.2627021402', 1),
('40.8623799474', 1),
Expand All @@ -336,7 +335,6 @@ def test_hdf5IO_open(self):
('53.5050692395', 1),
('57.571893782', 1),
('60.1102854322', 1),
('63.6505562766', 1),
('68.0991287718', 1),
('68.51099627', 1),
('74.0894932572', 1),
Expand Down Expand Up @@ -392,7 +390,6 @@ def test_hdf5IO_open(self):
('84.9722975792', 1),
('86.3615778099', 1),
('92.5274472082', 1),
('95.5088566087', 1),
('96.0693176066', 1)],
'pcr_primers': [('FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT', 27)],
'ph': [('6.8', 9), ('6.82', 10), ('6.94', 8)],
Expand Down