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https://github.com/chanzuckerberg/cellxgene.git
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Madison Dunitz
78c9d24ed4
* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
87 lines
2.8 KiB
Python
87 lines
2.8 KiB
Python
"""Methods for working with ontologies and the OLS."""
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from urllib.parse import quote_plus
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import requests
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OLS_API_ROOT = "http://www.ebi.ac.uk/ols/api"
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# Curie means something like CL:0000001
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def _ontology_name(curie):
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"""Get the name of the ontology from the curie, CL or UBERON for example."""
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return curie.split(":")[0]
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def _ontology_value(curie):
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"""Get the id component of the curie, 0000001 from CL:0000001 for example."""
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return curie.split(":")[1]
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def _double_encode(url):
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"""Double url encode a url. This is required by the OLS API."""
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return quote_plus(quote_plus(url))
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def _iri(curie):
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"""Get the iri from a curie. This is a bit hopeful that they all map to purl.obolibrary.org"""
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if _ontology_name(curie) == "EFO":
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return f"http://www.ebi.ac.uk/efo/EFO_{_ontology_value(curie)}"
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return f"http://purl.obolibrary.org/obo/{_ontology_name(curie)}_{_ontology_value(curie)}"
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class OntologyLookupError(Exception):
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"""Exception for some problem with looking up ontology information."""
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def _ontology_info_url(curie):
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"""Get the to make a GET to to get information about an ontology term."""
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# If the curie is empty, just return an empty string. This happens when there is no
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# valid ontology value.
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if not curie:
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return ""
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else:
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return f"{OLS_API_ROOT}/ontologies/{_ontology_name(curie)}/terms/{_double_encode(_iri(curie))}"
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def get_ontology_label(curie):
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"""For a given curie like 'CL:1000413', get the label like 'endothelial cell of artery'"""
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url = _ontology_info_url(curie)
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if not url:
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return ""
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response = requests.get(url)
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if not response.ok:
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raise OntologyLookupError(
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f"Curie {curie} lookup failed, got status code {response.status_code}: {response.text}"
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)
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return response.json()["label"]
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def lookup_candidate_term(label, ontology="cl", method="select"):
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"""Lookup candidate terms for a label. This is useful when there is an existing label in a
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submitted dataset, and you want to find an appropriate ontology term.
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Args:
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label: the label to find ontology terms for
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ontology: the ontology to search in, cl or uberon or efo for example
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method: select or search. search provides much broader results
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Returns:
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list of (curie, label) tuples returned by OLS
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"""
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# using OLS REST API [https://www.ebi.ac.uk/ols/docs/api]
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url = f"{OLS_API_ROOT}/{method}?q={quote_plus(label)}&ontology={ontology.lower()}"
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response = requests.get(url)
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if not response.ok:
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raise OntologyLookupError(
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f"Label {label} lookup failed, got status code {response.status_code}: {response.text}"
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)
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return [(r["obo_id"], r["label"]) for r in response.json()["response"]["docs"]]
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