def test_add_sample_stage(ws):
models.add_project(name='Manhattan', sample_mask='man-###')
models.add_sample(project_id='PqrX9', name='sample 1')
models.add_method(name='X-ray tomography', description='Placeholder description.')
t = models._sample_stage_token_hashid().encode(0)
m = models.add_sample_stage(
sample_id='OQn6Q', method_id='XZOQ0', token=t, annotation='Annotation')
assert 1 == m.id
assert 'Drn1Q' == m.obfuscated_id
assert None == m.alt_id
assert 'Annotation' == m.annotation
assert 1 == m._sample_id
assert 'OQn6Q' == m.sample_id
assert 1 == m._method_id
assert 'XZOQ0' == m.method_id
def test_add_sample(ws):
models.add_project(name='Manhattan', sample_mask='man-###')
m = models.add_sample(project_id='PqrX9', name='sample 1')
assert 1 == m.id
assert 'OQn6Q' == m.obfuscated_id
assert 'sample 1' == m.name
assert 1 == m._project_id
assert 'PqrX9' == m.project_id
def sample(ws):
project = models.add_project(name='Manhattan', sample_mask='man-###')
sample = models.add_sample(project_id='PqrX9', name='sample 1')
method = models.add_method(name='X-ray tomography', description='Placeholder description.')
return {'app' : ws,
'project' : project,
'sample' : sample,
'method' : method}
def test_add_sample(ws):
models.add_project(name='Manhattan', sample_mask='man-###')
m = models.add_sample(project_id='PqrX9', name='sample 1')
assert 1 == m.id
assert 'OQn6Q' == m.obfuscated_id
assert 'sample 1' == m.name
assert 1 == m._project_id
assert 'PqrX9' == m.project_id
def test_add_sample_stage(ws):
models.add_project(name='Manhattan', sample_mask='man-###')
models.add_sample(project_id='PqrX9', name='sample 1')
models.add_method(name='X-ray tomography',
description='Placeholder description.')
t = models._sample_stage_token_hashid().encode(0)
m = models.add_sample_stage(sample_id='OQn6Q',
method_id='XZOQ0',
token=t,
annotation='Annotation')
assert 1 == m.id
assert 'Drn1Q' == m.obfuscated_id
assert None == m.alt_id
assert 'Annotation' == m.annotation
assert 1 == m._sample_id
assert 'OQn6Q' == m.sample_id
assert 1 == m._method_id
assert 'XZOQ0' == m.method_id
root = '/mnt/adapt/analysis/inconel/versa-data/P001-B001/Uncompressed'
project = 'PqrX9'
method = 'XZOQ0'
labelled = collect(
lambda m: m['label'],
map(
parse_fpath,
find(root,
'^((?!.*Multiple_Images).)*\.(xrm|txm|txrm|tar|tif|avi)$')))
errors = []
for s in map(lambda x: x.split('-')[0], labelled.keys()):
try:
m.add_sample(project, s)
except Exception as e:
errors.append(e)
upload_root = config.UPLOAD_PATH
builders = [
stage_builder(method, label, map(lambda m: m['path'], labelled[label]))
for label in labelled.keys()
]
errors = []
for builderfn in builders:
try:
builderfn()
except Exception as e:
errors.append(e)
def sample(ws):
project = models.add_project(name='Manhattan', sample_mask='man-###')
sample = models.add_sample(project_id='PqrX9', name='sample 1')
method = models.add_method(name='X-ray tomography',
description='Placeholder description.')
return {'app': ws, 'project': project, 'sample': sample, 'method': method}
st.with_files(files)
return st.to_sample(sample(parts[0]).obfuscated_id)
if __name__ == "__example__":
import app
import app.models as m
import config
import os
root = '/mnt/adapt/analysis/inconel/versa-data/P001-B001/Uncompressed'
project = 'PqrX9'
method = 'XZOQ0'
labelled = collect(lambda m: m['label'], map(parse_fpath, find(root, '^((?!.*Multiple_Images).)*\.(xrm|txm|txrm|tar|tif|avi)$')))
errors = []
for s in map(lambda x: x.split('-')[0], labelled.keys()):
try:
m.add_sample(project, s)
except Exception as e:
errors.append(e)
upload_root = config.UPLOAD_PATH
builders = [stage_builder(method, label, map(lambda m: m['path'], labelled[label])) for label in labelled.keys()]
errors = []
for builderfn in builders:
try:
builderfn()
except Exception as e:
errors.append(e)