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sampleset_domain_example.py
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64 lines (53 loc) · 2.13 KB
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from labkey.api_wrapper import APIWrapper
labkey_server = "localhost:8080"
container_path = "Tutorials/MySamples" # Full project/folder container path
context_path = "labkey"
api = APIWrapper(labkey_server, container_path, context_path, use_ssl=False)
###################
# Create a SampleSet domain
###################
sampleset_domain_definition = {
"kind": "SampleSet",
"domainDesign": {
"name": "BloodSamples",
"description": "Human blood samples.",
"fields": [
{"name": "Name", "rangeURI": "string"},
{"name": "volume_mL", "rangeURI": "int"},
{"name": "Project", "rangeURI": "string"},
{"name": "DrawDate", "rangeURI": "dateTime"},
{"name": "ReceivedDate", "rangeURI": "dateTime"},
{"name": "ReceivedFrom", "rangeURI": "string"},
{"name": "ReceivingOperator", "rangeURI": "string"},
{"name": "TubeColor", "rangeURI": "string"},
{"name": "TubeType", "rangeURI": "string"},
{"name": "ProblemWithTube", "rangeURI": "boolean"},
{"name": "Comments", "rangeURI": "string"},
],
},
}
# domain.create returns the full Domain definition
created_sampleset_domain = api.domain.create(sampleset_domain_definition)
###################
# Get a domain
###################
sampleset_domain = api.domain.get("samples", "BloodSamples")
# examine different fields from the domain
print(sampleset_domain.name)
print(sampleset_domain.fields[0].name)
###################
# Save a domain
###################
sampleset_domain.add_field({"name": "canTransfuse", "rangeURI": "boolean"})
# Use infer fields to define additional fields
fields_file = open("data/infer.tsv", "rb")
inferred_fields = api.domain.infer_fields(fields_file)
for field in inferred_fields:
sampleset_domain.add_field(field)
api.domain.save("samples", "BloodSamples", sampleset_domain)
###################
# Drop a domain
###################
drop_response = api.domain.drop("samples", "BloodSamples")
if "success" in drop_response:
print("The SampleSet domain was deleted.")