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Removing any instance of required_sample_info and common_prep_info. … #1168

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Merged
merged 1 commit into from
May 8, 2015
Merged

Removing any instance of required_sample_info and common_prep_info. … #1168

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2 changes: 1 addition & 1 deletion qiita_db/metadata_template/prep_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -232,7 +232,7 @@ def delete(cls, id_):
conn_handler.execute(
"DROP TABLE qiita.{0}".format(table_name))

# Remove the rows from common_prep_info
# Remove the rows from prep_template_samples
conn_handler.execute(
"DELETE FROM qiita.{0} where {1} = %s".format(cls._table,
cls._id_column),
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2 changes: 0 additions & 2 deletions qiita_db/metadata_template/sample_template.py
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Expand Up @@ -84,8 +84,6 @@ def metadata_headers():
return [x[0] for x in
conn_handler.execute_fetchall(
"SELECT DISTINCT column_name FROM qiita.study_sample_columns "
"UNION SELECT column_name FROM information_schema.columns "
"WHERE table_name = 'required_sample_info' "
"ORDER BY column_name")]

@classmethod
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15 changes: 14 additions & 1 deletion qiita_db/metadata_template/test/test_sample_template.py
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Expand Up @@ -574,6 +574,19 @@ class TestSampleTemplateReadOnly(BaseTestSampleTemplate):
def setUp(self):
self._set_up()

def test_metadata_headers(self):
obs = SampleTemplate.metadata_headers()
exp = {'physical_specimen_location', 'physical_specimen_remaining',
'dna_extracted', 'sample_type', 'collection_timestamp',
'host_subject_id', 'description', 'season_environment',
'assigned_from_geo', 'texture', 'taxon_id', 'depth',
'host_taxid', 'common_name', 'water_content_soil', 'elevation',
'temp', 'tot_nitro', 'samp_salinity', 'altitude', 'env_biome',
'country', 'ph', 'anonymized_name', 'tot_org_carb',
'description_duplicate', 'env_feature', 'latitude', 'longitude',
'sample_id'}
self.assertEqual(set(obs), exp)

def test_study_id(self):
"""Ensure that the correct study ID is returned"""
self.assertEqual(self.tester.study_id, 1)
Expand Down Expand Up @@ -1111,7 +1124,7 @@ def test_create_int_prefix(self):
# The returned object has the correct id
self.assertEqual(st.id, new_id)

# The relevant rows to required_sample_info have been added.
# The relevant rows to study_sample have been added.
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study_sample WHERE study_id=%s", (new_id,))
exp = [["%s.12.Sample1" % new_id, new_id],
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4 changes: 2 additions & 2 deletions qiita_db/metadata_template/util.py
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Expand Up @@ -221,13 +221,13 @@ def load_template_to_dataframe(fn, strip_whitespace=True):
parse_dates=True, index_col=False, comment='\t',
mangle_dupe_cols=False, converters={
'sample_name': lambda x: str(x).strip(),
# required_sample_info
# required sample template information
'physical_location': str,
'sample_type': str,
# collection_timestamp is not added here
'host_subject_id': str,
'description': str,
# common_prep_info
# common prep template information
'center_name': str,
'center_projct_name': str})

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82 changes: 41 additions & 41 deletions qiita_db/support_files/populate_test_db.sql
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Expand Up @@ -107,26 +107,26 @@ INSERT INTO qiita.study_sample (study_id, sample_id) VALUES
-- Add the study sample columns for study 1
INSERT INTO qiita.study_sample_columns (study_id, column_name, column_type) VALUES
(1, 'sample_id', 'varchar'),
(1, 'SEASON_ENVIRONMENT', 'varchar'),
(1, 'ASSIGNED_FROM_GEO', 'varchar'),
(1, 'TEXTURE', 'varchar'),
(1, 'TAXON_ID', 'varchar'),
(1, 'DEPTH', 'float8'),
(1, 'HOST_TAXID', 'varchar'),
(1, 'COMMON_NAME', 'varchar'),
(1, 'WATER_CONTENT_SOIL', 'float8'),
(1, 'ELEVATION', 'float8'),
(1, 'TEMP', 'float8'),
(1, 'TOT_NITRO', 'float8'),
(1, 'SAMP_SALINITY', 'float8'),
(1, 'ALTITUDE', 'float8'),
(1, 'ENV_BIOME', 'varchar'),
(1, 'COUNTRY', 'varchar'),
(1, 'PH', 'float8'),
(1, 'ANONYMIZED_NAME', 'varchar'),
(1, 'TOT_ORG_CARB', 'float8'),
(1, 'Description_duplicate', 'varchar'),
(1, 'ENV_FEATURE', 'varchar'),
(1, 'season_environment', 'varchar'),
(1, 'assigned_from_geo', 'varchar'),
(1, 'texture', 'varchar'),
(1, 'taxon_id', 'varchar'),
(1, 'depth', 'float8'),
(1, 'host_taxid', 'varchar'),
(1, 'common_name', 'varchar'),
(1, 'water_content_soil', 'float8'),
(1, 'elevation', 'float8'),
(1, 'temp', 'float8'),
(1, 'tot_nitro', 'float8'),
(1, 'samp_salinity', 'float8'),
(1, 'altitude', 'float8'),
(1, 'env_biome', 'varchar'),
(1, 'country', 'varchar'),
(1, 'ph', 'float8'),
(1, 'anonymized_name', 'varchar'),
(1, 'tot_org_carb', 'float8'),
(1, 'description_duplicate', 'varchar'),
(1, 'env_feature', 'varchar'),
(1, 'physical_specimen_location', 'varchar'),
(1, 'physical_specimen_remaining', 'bool'),
(1, 'dna_extracted', 'bool'),
Expand All @@ -140,26 +140,26 @@ INSERT INTO qiita.study_sample_columns (study_id, column_name, column_type) VALU
-- Crate the sample_1 dynamic table
CREATE TABLE qiita.sample_1 (
sample_id varchar,
SEASON_ENVIRONMENT varchar,
ASSIGNED_FROM_GEO varchar,
TEXTURE varchar,
TAXON_ID varchar,
DEPTH float8,
HOST_TAXID varchar,
COMMON_NAME varchar,
WATER_CONTENT_SOIL float8,
ELEVATION float8,
TEMP float8,
TOT_NITRO float8,
SAMP_SALINITY float8,
ALTITUDE float8,
ENV_BIOME varchar,
COUNTRY varchar,
PH float8,
ANONYMIZED_NAME varchar,
TOT_ORG_CARB float8,
Description_duplicate varchar,
ENV_FEATURE varchar,
season_environment varchar,
assigned_from_geo varchar,
texture varchar,
taxon_id varchar,
depth float8,
host_taxid varchar,
common_name varchar,
water_content_soil float8,
elevation float8,
temp float8,
tot_nitro float8,
samp_salinity float8,
altitude float8,
env_biome varchar,
country varchar,
ph float8,
anonymized_name varchar,
tot_org_carb float8,
description_duplicate varchar,
env_feature varchar,
physical_specimen_location varchar,
physical_specimen_remaining bool,
dna_extracted bool,
Expand All @@ -173,7 +173,7 @@ CREATE TABLE qiita.sample_1 (
);

-- Populates the sample_1 dynamic table
INSERT INTO qiita.sample_1 (sample_id, SEASON_ENVIRONMENT, ASSIGNED_FROM_GEO, TEXTURE, TAXON_ID, DEPTH, HOST_TAXID, COMMON_NAME, WATER_CONTENT_SOIL, ELEVATION, TEMP, TOT_NITRO, SAMP_SALINITY, ALTITUDE, ENV_BIOME, COUNTRY, PH, ANONYMIZED_NAME, TOT_ORG_CARB, Description_duplicate, ENV_FEATURE, physical_specimen_location, physical_specimen_remaining, dna_extracted, sample_type, collection_timestamp, host_subject_id, description, latitude, longitude) VALUES
INSERT INTO qiita.sample_1 (sample_id, season_environment, assigned_from_geo, texture, taxon_id, depth, host_taxid, common_name, water_content_soil, elevation, temp, tot_nitro, samp_salinity, altitude, env_biome, country, ph, anonymized_name, tot_org_carb, description_duplicate, env_feature, physical_specimen_location, physical_specimen_remaining, dna_extracted, sample_type, collection_timestamp, host_subject_id, description, latitude, longitude) VALUES
('1.SKM7.640188', '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, 'SKM7', 3.31, 'Bucu Roots', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:B6', 'Cannabis Soil Microbiome', 60.1102854322, 74.7123248382),
('1.SKD9.640182', 'winter', 'n', '66 sand, 16.3 silt, 17.7 clay', '1118232', 0.15, '3483', 'root metagenome', 0.178, 114, 15, 1.51, 7.1, 0, 'ENVO:Temperate grasslands, savannas, and shrubland biome', 'GAZ:United States of America', 6.82, 'SKD9', 4.32, 'Diesel Root', 'ENVO:plant-associated habitat', 'ANL', TRUE, TRUE, 'ENVO:soil', '2011-11-11 13:00', '1001:D3', 'Cannabis Soil Microbiome', 23.1218032799, 42.838497795),
('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),
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2 changes: 1 addition & 1 deletion qiita_db/test/test_setup.py
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Expand Up @@ -65,7 +65,7 @@ def test_sample_1(self):
def test_prep_template(self):
self.assertEqual(get_count("qiita.prep_template"), 1)

def test_common_prep_info(self):
def test_prep_template_sample(self):
self.assertEqual(get_count("qiita.prep_template_sample"), 27)

def test_prep_columns(self):
Expand Down