mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-24 01:08:11 +08:00
Marcus Kinsella
78176f9711
Add the `cellxgene schema apply` and `cellxgene schema validate` subcommands. The first takes an h5ad file and a yaml with config information and produces a new h5ad that follows the cellxgene data integration schema. The second takes an h5ad and checks if it follows the schema version written into its metadata. Both are currently marked as "experimental" as the primary intended users are still at CZI.
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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