mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-24 13:38:11 +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.
130 lines
5.4 KiB
Python
130 lines
5.4 KiB
Python
import json
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import unittest
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import unittest.mock
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from server.converters.schema import ontology
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class TestOntologyParsing(unittest.TestCase):
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def setUp(self):
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self.curies = ["UBERON:0002048", "HsapDv:0000174", "NCBITaxon:9606", "EFO:0008995"]
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self.names = ["UBERON", "HsapDv", "NCBITaxon", "EFO"]
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self.values = ["0002048", "0000174", "9606", "0008995"]
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self.iris = [
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"http://purl.obolibrary.org/obo/UBERON_0002048",
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"http://purl.obolibrary.org/obo/HsapDv_0000174",
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"http://purl.obolibrary.org/obo/NCBITaxon_9606",
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"http://www.ebi.ac.uk/efo/EFO_0008995",
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]
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URL_ROOT = "http://www.ebi.ac.uk/ols/api/ontologies/"
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self.urls = [
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URL_ROOT + "UBERON/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0002048",
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URL_ROOT + "HsapDv/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHsapDv_0000174",
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URL_ROOT + "NCBITaxon/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FNCBITaxon_9606",
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URL_ROOT + "EFO/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0008995",
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]
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self.responses = {
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"UBERON:0002048": {
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"iri": "http://purl.obolibrary.org/obo/UBERON_0002048",
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"description": ["Respiration organ that develops as an outpocketing of the esophagus."],
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"label": "lung",
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},
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"HsapDv:0000174": {
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"iri": "http://purl.obolibrary.org/obo/HsapDv_0000174",
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"description": ["Infant stage that refers to an infant who is over 1 and under 2 months old."],
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"label": "1-month-old human stage",
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},
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"NCBITaxon:9606": {
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"iri": "http://purl.obolibrary.org/obo/NCBITaxon_9606",
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"description": None,
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"label": "Homo sapiens",
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},
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"EFO:0008995": {
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"iri": "http://www.ebi.ac.uk/efo/EFO_0008995",
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"description": [
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(
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'10X is a "synthetic long-read" technology and works by capturing a barcoded oligo-coated '
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"gel-bead and 0.3x genome copies into a single emulsion droplet, processing the equivalent "
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"of 1 million pipetting steps. Successive versions of the 10x chemistry use different "
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"barcode locations to improve the sequencing yield and quality of 10x experiments."
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)
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],
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"label": "10X sequencing",
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},
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}
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def test_ontololgy_name(self):
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for curie, expected_name in zip(self.curies, self.names):
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self.assertEqual(ontology._ontology_name(curie), expected_name)
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def test_ontololgy_value(self):
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for curie, expected_value in zip(self.curies, self.values):
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self.assertEqual(ontology._ontology_value(curie), expected_value)
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def test_iri(self):
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for curie, expected_iri in zip(self.curies, self.iris):
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self.assertEqual(ontology._iri(curie), expected_iri)
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def test_ontology_info_url(self):
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for curie, expected_url in zip(self.curies, self.urls):
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self.assertEqual(ontology._ontology_info_url(curie), expected_url)
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def test_empty_ontology_info_url(self):
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self.assertEqual(ontology._ontology_info_url(""), "")
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class TestOntologyLookup(unittest.TestCase):
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def setUp(self):
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self.responses = {
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"UBERON:0002048": {
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"iri": "http://purl.obolibrary.org/obo/UBERON_0002048",
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"description": ["Respiration organ that develops as an outpocketing of the esophagus."],
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"label": "lung",
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},
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"HsapDv:0000174": {
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"iri": "http://purl.obolibrary.org/obo/HsapDv_0000174",
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"description": ["Infant stage that refers to an infant who is over 1 and under 2 months old."],
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"label": "1-month-old human stage",
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},
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"NCBITaxon:9606": {
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"iri": "http://purl.obolibrary.org/obo/NCBITaxon_9606",
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"description": None,
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"label": "Homo sapiens",
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},
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"EFO:0008995": {
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"iri": "http://www.ebi.ac.uk/efo/EFO_0008995",
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"description": [
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('10X is a "synthetic long-read" technology and works by capturing a barcoded oligo-coated '
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'gel-bead and 0.3x genome copies into a single emulsion droplet, processing the equivalent '
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'of 1 million pipetting steps. Successive versions of the 10x chemistry use different barcode '
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'locations to improve the sequencing yield and quality of 10x experiments.')
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],
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"label": "10X sequencing",
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},
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}
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self.labels = {
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"UBERON:0002048": "lung",
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"HsapDv:0000174": "1-month-old human stage",
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"NCBITaxon:9606": "Homo sapiens",
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"EFO:0008995": "10X sequencing",
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}
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@unittest.mock.patch("requests.get")
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def test_lookup_label(self, mock_get):
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for curie, response in self.responses.items():
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mock_get.return_value.content = json.dumps(response)
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mock_get.return_value.json.return_value = response
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mock_get.return_value.status_code = 200
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label = ontology.get_ontology_label(curie)
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self.assertEqual(label, self.labels[curie])
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