def sample(ctx, **kwargs):
ctx.obj.update(kwargs)
sample_set = SampleSet(
sample=Sample(alias=ctx.obj['alias'],
title=ctx.obj['title'],
taxon_id=ctx.obj['taxon_id'],
scientific_name=ctx.obj['scientific_name'],
common_name=ctx.obj['common_name'],
**ast.literal_eval(ctx.obj['attributes'])))
sample_set.write_xml(file=ctx.obj['sample_xml'])
if ctx.obj['verbose']:
print("Sample XML file created in " + ctx.obj['sample_xml'])
submission = Submission(**ctx.obj)
submission.write_xml(file=ctx.obj['submission_xml'])
if ctx.obj['verbose']:
print("Submission XML file created in " + ctx.obj['submission_xml'])
response = requests.post(ctx.obj['server_address'],
files={
'SUBMISSION':
(os.path.basename(ctx.obj['submission_xml']),
open(ctx.obj['submission_xml'], 'rb')),
'SAMPLE':
(os.path.basename(ctx.obj['sample_xml']),
open(ctx.obj['sample_xml'], 'rb')),
},
auth=(ctx.obj['user'], ctx.obj['password']))
print(response.content.decode())
return response
def run_set(ctx, **kwargs):
ctx.obj.update(kwargs)
run_set = RunSet(run=ctx.obj['table'], **kwargs)
run_set.write_xml(file=ctx.obj['run_xml'])
if ctx.obj['verbose']:
print("Run XML file created in " + ctx.obj['run_xml'])
submission = Submission(**ctx.obj)
submission.write_xml(file=ctx.obj['submission_xml'])
if ctx.obj['verbose']:
print("Submission XML file created in " + ctx.obj['submission_xml'])
response = requests.post(ctx.obj['server_address'],
files={
'SUBMISSION':
(os.path.basename(ctx.obj['submission_xml']),
open(ctx.obj['submission_xml'], 'rb')),
'RUN': (os.path.basename(ctx.obj['run_xml']),
open(ctx.obj['run_xml'], 'rb')),
},
auth=(ctx.obj['user'], ctx.obj['password']))
print(response.content.decode())
return response
def experiment(ctx, **kwargs):
ctx.obj.update(kwargs)
experiment_set = ExperimentSet(experiment=Experiment(**kwargs))
experiment_set.write_xml(file=ctx.obj['experiment_xml'])
if ctx.obj['verbose']:
print("Experiment XML file created in " + ctx.obj['experiment_xml'])
submission = Submission(**ctx.obj)
submission.write_xml(file=ctx.obj['submission_xml'])
if ctx.obj['verbose']:
print("Submission XML file created in " + ctx.obj['submission_xml'])
response = requests.post(ctx.obj['server_address'],
files={
'SUBMISSION':
(os.path.basename(ctx.obj['submission_xml']),
open(ctx.obj['submission_xml'], 'rb')),
'EXPERIMENT':
(os.path.basename(ctx.obj['experiment_xml']),
open(ctx.obj['experiment_xml'], 'rb')),
},
auth=(ctx.obj['user'], ctx.obj['password']))
print(response.content.decode())
return response
def study(ctx, **kwargs):
ctx.obj.update(kwargs)
project_set = ProjectSet(project=Project(**kwargs))
project_set.write_xml(file=ctx.obj['study_xml'])
if ctx.obj['verbose']:
print("Project XML file created in " + ctx.obj['study_xml'])
submission = Submission(**ctx.obj)
submission.write_xml(file=ctx.obj['submission_xml'])
if ctx.obj['verbose']:
print("Submission XML file created in " + ctx.obj['submission_xml'])
response = requests.post(ctx.obj['server_address'],
files={
'SUBMISSION':
(os.path.basename(ctx.obj['submission_xml']),
open(ctx.obj['submission_xml'], 'rb')),
'PROJECT':
(os.path.basename(ctx.obj['study_xml']),
open(ctx.obj['study_xml'], 'rb')),
},
auth=(ctx.obj['user'], ctx.obj['password']))
print(response.content.decode())
return response