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add_test_data.py
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import argparse
import requests
import random
from json import loads
def rand_percentage():
return random.randint(0, 100)
def rand_float():
return round(random.random(), 2)
def rand_int():
return random.randint(1000, 4000)
def rand_barcode():
ret_string = ''
for x in range(8):
ret_string += random.choice(['A', 'T', 'G', 'C'])
return ret_string
def rand_file_path():
parts = (random.choice(['this', 'that', 'other', 'another', 'more']) for _ in range(3))
return '/'.join(parts)
def _around(base_num):
return base_num * random.triangular(0.8, 1.2)
def sample_element(sample_id, run_element_ids):
bam_file_reads = random.randint(8000, 10000)
return {
'library_id': 'lib_' + sample_id,
'project': sample_id.split('_sample')[0],
'sample_id': sample_id,
'user_sample_id': 'user_' + sample_id,
'bam_file_reads': bam_file_reads,
'mapped_reads': bam_file_reads * _around(0.8),
'properly_mapped_reads': bam_file_reads * _around(0.78),
'duplicate_reads': bam_file_reads * _around(0.1),
'median_coverage': rand_float(),
'pc_callable': rand_percentage(),
'run_elements': run_element_ids,
'reviewed': random.choice(['not reviewed', 'pass', 'fail'])
}
def run_element(run_id, lane_nb, barcode, sample_id, incomplete=False):
run_element_id = '_'.join([run_id, lane_nb, barcode])
total_reads = random.randint(8000, 10000)
bases_r1 = random.randint(1200000000, 1800000000)
bases_r2 = random.randint(1200000000, 1800000000)
if incomplete:
return {
'run_element_id': run_element_id,
'run_id': run_id,
'lane': lane_nb,
'barcode': barcode,
'project': sample_id.split('_')[0],
'library_id': 'lib_' + sample_id,
'sample_id': sample_id
}
else:
return {
'run_element_id': run_element_id,
'run_id': run_id,
'lane': lane_nb,
'barcode': barcode,
'project': sample_id.split('_')[0],
'library_id': 'lib_' + sample_id,
'sample_id': sample_id,
'total_reads': total_reads,
'passing_filter_reads': total_reads * _around(0.79),
'pc_reads_in_lane': rand_percentage(),
'bases_r1': bases_r1,
'q30_bases_r1': bases_r1 * _around(0.81),
'bases_r2': bases_r2,
'q30_bases_r2': bases_r2 * _around(0.81),
'fastqc_report_r1': rand_file_path(),
'fastqc_report_r2': rand_file_path(),
'reviewed': random.choice(['not reviewed', 'pass', 'fail'])
}
def unexpected_barcode(run_id, lane_nb, barcode):
return {
'run_element_id': '_'.join([run_id, lane_nb, barcode]),
'run_id': run_id,
'lane': lane_nb,
'barcode': barcode,
'passing_filter_reads': rand_int(),
'pc_reads_in_lane': rand_percentage()
}
def run(run_id, nlanes):
return {
'run_id': run_id,
'number_of_lanes': nlanes
}
def lane(run_id, lane_number, run_element_ids):
return {
'lane_id': '_'.join((run_id, lane_number)),
'run_id': run_id,
'lane_number': lane_number,
'run_elements': run_element_ids
}
def project(name, sample_ids):
return {
'project_id': name,
'samples': sample_ids
}
ext_api = 'http://egclaritydev.mvm.ed.ac.uk:4999/api/0.1/'
int_api = 'http://localhost:4999/api/0.1/'
api_url = int_api
class RESTError(Exception):
pass
def push(resource, json):
response = requests.post(api_url + resource, json=json)
content = loads(response.content.decode('utf-8'))
if content['_status'] != 'OK':
raise RESTError('oh noes! problem pushing to ' + resource + '\n' + str(json) + '\n' + str(content))
def multi_push(run_ids_and_samples, elements_per_run=6, lanes_per_run=8):
runs = []
projects = []
for project_id, run_ids in run_ids_and_samples:
r_e_ids = []
for run_id in run_ids:
print(run_id)
lanes = []
for lane_number in (range(lanes_per_run)):
lane_number = str(lane_number + 1)
run_elements = []
barcodes = []
_sample_id = project_id + '_sample_' + lane_number
for e in range(elements_per_run):
b = rand_barcode()
while b in barcodes:
b = rand_barcode()
run_elements.append(
run_element(
run_id,
lane_number,
b,
_sample_id,
incomplete=random.choice([True, False])
)
)
l = lane(
run_id,
lane_number,
[e['run_element_id'] for e in run_elements]
)
lanes.append(l)
r_e_ids.extend([e['run_element_id'] for e in run_elements])
push('run_elements', json=run_elements)
r = run(run_id, len(lanes))
runs.append(r)
push('lanes', json=lanes)
samples = []
for s in range(lanes_per_run):
s = str(s + 1)
sample_id = project_id + '_sample_' + s
s = sample_element(sample_id, r_e_ids)
samples.append(s)
p = project(project_id, [e['sample_id'] for e in samples])
projects.append(p)
push('samples', json=samples)
push('runs', json=runs)
push('projects', json=projects)
if __name__ == '__main__':
p = argparse.ArgumentParser()
p.add_argument('--nruns', type=int, help='number of runs to add to the database')
p.add_argument('--nsamples', type=int, help='number of samples to add. this must divide nruns cleanly.')
args = p.parse_args()
nruns = args.nruns
nsamples = args.nsamples
run_ids = ['run_' + str(x + 1) for x in range(nruns)]
projects = ['test_project_' + str(y + 1) for y in range(nsamples)]
assert nruns > nsamples, 'must have more runs than samples'
runs_per_sample = int(nruns / nsamples)
input_data = ((p, (run_ids.pop(0) for _ in range(runs_per_sample))) for p in projects)
multi_push(input_data)