def LoadOp(line, succ):
pr = Genotype(
name=line['rs#'], study=Import.study, datasource=Import.ds,
)
SaveKVs(pr, line)
pr.save()
return True
def LoadOp(line, succ):
pr = Genotype(
name=line['rs#'],
study=Import.study,
datasource=Import.ds,
)
SaveKVs(pr, line)
pr.save()
return True
def test_query_csv_to_rows_different_fields(self):
"""
Tests that query_csv_to_rows creates the correct csv strings when given a query
set of Genotype models that have different fields to each other
"""
expected_experi_model.switch_db(TEST_DB_ALIAS)
expected_experi_model.save()
expected_ds_model.switch_db(TEST_DB_ALIAS)
expected_ds_model.save()
date = datetime.datetime(2015, 11, 20, 11, 14, 40, round(386012, -2))
date_string = str(date)
xreflsid = "Helge what even is this field anyway?"
gen_1 = Genotype(
name="foo", statuscode=3, obs={"chicken": "pie"}, study=expected_experi_model,
datasource=expected_ds_model, xreflsid=xreflsid, createddate=date, dtt=date,
lastupdateddate=date
)
gen_1.switch_db(TEST_DB_ALIAS)
gen_1.save()
gen_2 = Genotype(
name="bar", description="baz", obs={"chicken": "snitchel"}, study=expected_experi_model,
datasource=expected_ds_model, lastupdatedby="Badi", createddate=date, dtt=date,
lastupdateddate=date
)
gen_2.switch_db(TEST_DB_ALIAS)
gen_2.save()
expected_rows = [
"alias,createddate,datasource__name,description,dtt,lastupdatedby,lastupdateddate,name,"
+ "obs,statuscode,study__name,xreflsid",
str.format(
"unknown,{0},What is up,baz,{0},Badi,{0},bar,\"{{'chicken':'snitchel'}}\",1,What is up,",
date_string
),
str.format(
"unknown,{0},What is up,,{0},,{0},foo,\"{{'chicken':'pie'}}\",3,What is up,{1}",
date_string, xreflsid
)
]
with switch_db(Genotype, TEST_DB_ALIAS) as TestGen:
query = TestGen.objects.all()
actual_rows = query_to_csv_rows_list(query, testing=True)
self.assertEqual(len(expected_rows), len(actual_rows))
self.assertEqual(actual_rows[0], expected_rows[0]) # Checks header rows are equal
# Checks csv representations of genotype docs are in actual_rows
for row in expected_rows:
with self.subTest(row=row):
self.assertIn(row, actual_rows)
def test_query_csv_to_rows_different_fields(self):
"""
Tests that query_csv_to_rows creates the correct csv strings when given a query
set of Genotype models that have different fields to each other
"""
expected_experi_model.switch_db(TEST_DB_ALIAS)
expected_experi_model.save()
expected_ds_model.switch_db(TEST_DB_ALIAS)
expected_ds_model.save()
date = datetime.datetime(2015, 11, 20, 11, 14, 40, round(386012, -2))
date_string = str(date)
xreflsid = "Helge what even is this field anyway?"
gen_1 = Genotype(name="foo",
statuscode=3,
obs={"chicken": "pie"},
study=expected_experi_model,
datasource=expected_ds_model,
xreflsid=xreflsid,
createddate=date,
dtt=date,
lastupdateddate=date)
gen_1.switch_db(TEST_DB_ALIAS)
gen_1.save()
gen_2 = Genotype(name="bar",
description="baz",
obs={"chicken": "snitchel"},
study=expected_experi_model,
datasource=expected_ds_model,
lastupdatedby="Badi",
createddate=date,
dtt=date,
lastupdateddate=date)
gen_2.switch_db(TEST_DB_ALIAS)
gen_2.save()
expected_rows = [
"alias,createddate,datasource__name,description,dtt,lastupdatedby,lastupdateddate,name,"
+ "obs,statuscode,study__name,xreflsid",
str.format(
"unknown,{0},What is up,baz,{0},Badi,{0},bar,\"{{'chicken':'snitchel'}}\",1,What is up,",
date_string),
str.format(
"unknown,{0},What is up,,{0},,{0},foo,\"{{'chicken':'pie'}}\",3,What is up,{1}",
date_string, xreflsid)
]
with switch_db(Genotype, TEST_DB_ALIAS) as TestGen:
query = TestGen.objects.all()
actual_rows = query_to_csv_rows_list(query, testing=True)
self.assertEqual(len(expected_rows), len(actual_rows))
self.assertEqual(actual_rows[0],
expected_rows[0]) # Checks header rows are equal
# Checks csv representations of genotype docs are in actual_rows
for row in expected_rows:
with self.subTest(row=row):
self.assertIn(row, actual_rows)
)
expected_experiment_yaml = Experiment(
name='Bar', description="Test experiment configuration for Kaka",
pi="Badi James", createddate=datetime(2016, 1, 7)
)
expected_datasource_json = DataSource(
name='Foo', source=path_string_json + "/a_test_source.hmp.txt.gz",
supplieddate=datetime(2016, 1, 8, 11, 7, 33),
)
expected_datasource_yaml = DataSource(
name='Bar', source=path_string_yaml + "/a_test_source.hmp.txt.gz",
supplieddate=datetime(2016, 1, 8, 11, 7, 33),
)
expected_genotype_json = Genotype(
name='Test source', description="Test json configuration for kaka",
createddate=datetime(2016, 1, 7), obs={'foo': '1', 'bar': '2', 'baz': '3', 'rs#': 'Test source'},
study=expected_experiment_json, datasource=expected_datasource_json
)
expected_genotype_yaml = Genotype(
name='Test source', description="Test experiment configuration for Kaka",
createddate=datetime(2016, 1, 7), obs={'foo': '1', 'bar': '2', 'baz': '3', 'rs#': 'Test source'},
study=expected_experiment_yaml, datasource=expected_datasource_yaml
)
yaml_config_string = """---
Data Creator : Badi James
Experiment Description : >-
Test experiment configuration
for Kaka
Experiment Code : 123456
Upload Date : dt(2016-01-08T11:07:33Z)
Experiment Date : dt(2016-01-07)
