def setUpClass(self):
super(TestSampling_Event, self).setUpClass()
sd = Uploader(self._config_file)
sd.use_message_buffer = True
json_data = json.loads('''{
"values": {
"sample_oxford_id": {
"column": 0,
"type": "string"
},
"study_id": {
"column": 1,
"type": "string"
},
"latitude": {
"column": 2,
"type": "string"
},
"longitude": {
"column": 3,
"type": "string"
},
"location_name": {
"column": 4,
"type": "string"
}
}
}''')
sd.load_data_file(json_data, 'multiple_study.tsv')
self._messages = sd.message_buffer
def setUpClass(self):
super(TestDate, self).setUpClass()
sd = Uploader(self._config_file)
sd.use_message_buffer = True
json_data = json.loads('''{
"values": {
"sample_oxford_id": {
"column": 0,
"type": "string"
},
"study_id": {
"column": 1,
"type": "string"
},
"doc": {
"column": 2,
"type": "datetime",
"date_format": "%Y-%m-%d"
},
"doc_accuracy": {
"column": 3,
"type": "string"
}
}
}''')
sd.load_data_file(json_data, 'dates.tsv')
self._messages = sd.message_buffer
def setUpClass(self):
super(TestLocation, self).setUpClass()
sd = Uploader(self._config_file)
sd.use_message_buffer = True
json_data = json.loads('''{
"values": {
"sample_oxford_id": {
"column": 0,
"type": "string"
},
"study_id": {
"column": 1,
"type": "string"
},
"latitude": {
"column": 2,
"type": "float"
},
"longitude": {
"column": 3,
"type": "float"
},
"location_name": {
"column": 4,
"type": "string"
},
"country": {
"column": 5,
"type": "string"
},
"proxy_latitude": {
"column": 6,
"type": "float"
},
"proxy_longitude": {
"column": 7,
"type": "float"
},
"proxy_location_name": {
"column": 8,
"type": "string"
}
}
}''')
sd.load_data_file(json_data, 'locations.tsv')
self._messages = sd.message_buffer
self.setUpSSR()
sd = Uploader(self._config_file)
# sd.use_message_buffer = True
json_data = json.loads(self._ag_json)
sd.load_data_file(json_data, 'loc_no_study.tsv')
def setUpClass(self):
super(TestIndividual, self).setUpClass()
sd = Uploader(self._config_file)
sd.use_message_buffer = True
json_data = json.loads('''{
"values": {
"unique_id": {
"column": 2,
"type": "string"
},
"unique_os_id": {
"column": 2,
"type": "string"
},
"sample_oxford_id": {
"column": 3,
"type": "string"
},
"sample_alternate_oxford_id": {
"column": 4,
"type": "string"
},
"sample_source_id": {
"column": 6,
"type": "string"
},
"donor_source_code": {
"column": 7,
"type": "string"
},
"sample_source_type": {
"column": 8,
"type": "string"
},
"species": {
"column": 11,
"type": "string"
}
}
}''')
sd.load_data_file(json_data, 'individual.tsv')
self._messages = sd.message_buffer
def setUpClass(self):
super(TestMerge, self).setUpClass()
sd = Uploader(self._config_file)
sd.use_message_buffer = True
json_data = json.loads(self._oxford_config)
sd.load_data_file(json_data, 'oxford_merge.tsv')
self._messages = sd.message_buffer
self.setUpSSR()
sd = Uploader(self._config_file)
sd.use_message_buffer = True
json_data = json.loads('''{
"values":
{
"sample_oxford_id": {
"column": 0,
"type": "string",
"id": true
},
"sample_partner_id": {
"column": 1,
"type": "string"
},
"study_id": {
"column": 4,
"type": "string"
},
"type": {
"column": 5,
"type": "string"
},
"location_name": {
"column": 6,
"type": "string"
},
"latitude": {
"column": 7,
"type": "float"
},
"longitude": {
"column": 8,
"type": "float"
},
"doc": {
"column": 9,
"type": "datetime",
"date_format": "%Y-%m-%d",
"comment": "inconsistent date format"
},
"year": {
"column": 10,
"type": "datetime",
"date_format": "%Y"
}
}
}''')
sd.load_data_file(json_data, 'pf6_merge.tsv')
sd1 = Uploader(self._config_file)
sd1.use_message_buffer = True
json_data = json.loads(self._pv_3_config)
sd1.load_data_file(json_data, 'pv3_merge.tsv')
el = Upload_ROMA(self._config_file)
el.use_message_buffer = True
el.load_data_file('roma_dump.20180116103346.json')
sd = Uploader(self._config_file)
sd.use_message_buffer = True
json_data = json.loads(self._sanger_lims_config)
sd.load_data_file(json_data, 'sanger-lims_merge.tsv')
def setUpClass(self):
super(TestCountry, self).setUpClass()
sd = Uploader(self._config_file)
json_data = json.loads('''
{
"values": {
"unique_id": {
"column": 2,
"type": "string"
},
"sample_oxford_id": {
"column": 3,
"type": "string"
},
"sample_alternate_oxford_id": {
"column": 4,
"type": "string"
},
"sample_source_id": {
"column": 6,
"type": "string"
},
"sample_source_type": {
"column": 8,
"type": "string"
},
"species": {
"column": 11,
"type": "string"
}
}
}
''')
sd.load_data_file(json_data, 'oxford_country.tsv')
self.setUpSSR()
sd = Uploader(self._config_file)
json_data = json.loads('''{
"values":
{
"sample_oxford_id": {
"column": 0,
"type": "string",
"id": true
},
"study_id": {
"column": 1,
"type": "string"
},
"sample_partner_id": {
"column": 2,
"type": "string"
},
"location_name": {
"column": 13,
"type": "string"
},
"latitude": {
"column": 14,
"type": "float",
"regex": "^\\\\s*([-0-9]*\\\\.?\\\\d{0,7})"
},
"longitude": {
"column": 14,
"type": "float",
"regex": "([-0-9]*\\\\.?\\\\d{0,7})(\\\\d*)$"
},
"country": {
"column": 5,
"type": "string",
"replace": [
[ "Madagascar", "MDG" ]
]
},
"proxy_country": {
"column": 5,
"type": "string",
"replace": [
[ "Madagascar", "MDG" ]
]
},
"proxy_location_name": {
"column": 6,
"type": "string"
},
"proxy_latitude": {
"column": 7,
"type": "float",
"regex": "^\\\\s*([-0-9]*\\\\.?\\\\d{0,7})"
},
"proxy_longitude": {
"column": 7,
"type": "float",
"regex": "([-0-9]*\\\\.?\\\\d{0,7})\\\\d*$"
},
"doc": {
"column": 8,
"type": "datetime",
"date_format": "%Y-%m-%d"
}
}
}''')
sd.load_data_file(json_data, 'countries.tsv')
sd = SetCountry(self._config_file)
sd.use_message_buffer = True
sd._countries_file = '../' + sd._countries_file
id_type = 'oxford_id'
input_file = 'oxford_country.tsv'
id_column = 3
country_column = 10
ssr = 'TestSSR.xls'
sd.load_location_cache()
sd.set_countries(input_file, id_type, id_column, country_column)
sheets = None
sd.load_data_file(ssr, sheets)
self._messages = sd.message_buffer
