Split out the local backend (#2052)

This splits the backend into two parts: the local backend for desktop cellxgene and the AWS backend for hosted cellxgene. The local backend is in local_server while the hosted remains in server. The general idea is to copy everything from server to local_server, pull unneeded stuff out of local_server, and keep server as-is for this PR. Not touching server means all the infra and deployment code will continue working just as it did before so we can make those changes incrementally.
2026-10-08 18:18:11 +08:00 · 2021-02-18 12:58:22 -08:00
parent 036b5f8c0f
commit fb61bd6e9c
153 changed files with 14027 additions and 46 deletions
@@ -0,0 +1,129 @@
+import json
+
+import unittest
+import unittest.mock
+
+from local_server.converters.schema import ontology
+
+
+class TestOntologyParsing(unittest.TestCase):
+    def setUp(self):
+
+        self.curies = ["UBERON:0002048", "HsapDv:0000174", "NCBITaxon:9606", "EFO:0008995"]
+
+        self.names = ["UBERON", "HsapDv", "NCBITaxon", "EFO"]
+
+        self.values = ["0002048", "0000174", "9606", "0008995"]
+
+        self.iris = [
+            "http://purl.obolibrary.org/obo/UBERON_0002048",
+            "http://purl.obolibrary.org/obo/HsapDv_0000174",
+            "http://purl.obolibrary.org/obo/NCBITaxon_9606",
+            "http://www.ebi.ac.uk/efo/EFO_0008995",
+        ]
+
+        URL_ROOT = "http://www.ebi.ac.uk/ols/api/ontologies/"
+        self.urls = [
+            URL_ROOT + "UBERON/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0002048",
+            URL_ROOT + "HsapDv/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FHsapDv_0000174",
+            URL_ROOT + "NCBITaxon/terms/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FNCBITaxon_9606",
+            URL_ROOT + "EFO/terms/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0008995",
+        ]
+
+        self.responses = {
+            "UBERON:0002048": {
+                "iri": "http://purl.obolibrary.org/obo/UBERON_0002048",
+                "description": ["Respiration organ that develops as an outpocketing of the esophagus."],
+                "label": "lung",
+            },
+            "HsapDv:0000174": {
+                "iri": "http://purl.obolibrary.org/obo/HsapDv_0000174",
+                "description": ["Infant stage that refers to an infant who is over 1 and under 2 months old."],
+                "label": "1-month-old human stage",
+            },
+            "NCBITaxon:9606": {
+                "iri": "http://purl.obolibrary.org/obo/NCBITaxon_9606",
+                "description": None,
+                "label": "Homo sapiens",
+            },
+            "EFO:0008995": {
+                "iri": "http://www.ebi.ac.uk/efo/EFO_0008995",
+                "description": [
+                    (
+                        '10X is a "synthetic long-read" technology and works by capturing a barcoded oligo-coated '
+                        "gel-bead and 0.3x genome copies into a single emulsion droplet, processing the equivalent "
+                        "of 1 million pipetting steps. Successive versions of the 10x chemistry use different "
+                        "barcode locations to improve the sequencing yield and quality of 10x experiments."
+                    )
+                ],
+                "label": "10X sequencing",
+            },
+        }
+
+    def test_ontololgy_name(self):
+        for curie, expected_name in zip(self.curies, self.names):
+            self.assertEqual(ontology._ontology_name(curie), expected_name)
+
+    def test_ontololgy_value(self):
+        for curie, expected_value in zip(self.curies, self.values):
+            self.assertEqual(ontology._ontology_value(curie), expected_value)
+
+    def test_iri(self):
+        for curie, expected_iri in zip(self.curies, self.iris):
+            self.assertEqual(ontology._iri(curie), expected_iri)
+
+    def test_ontology_info_url(self):
+        for curie, expected_url in zip(self.curies, self.urls):
+            self.assertEqual(ontology._ontology_info_url(curie), expected_url)
+
+    def test_empty_ontology_info_url(self):
+        self.assertEqual(ontology._ontology_info_url(""), "")
+
+
+class TestOntologyLookup(unittest.TestCase):
+    def setUp(self):
+        self.responses = {
+            "UBERON:0002048": {
+                "iri": "http://purl.obolibrary.org/obo/UBERON_0002048",
+                "description": ["Respiration organ that develops as an outpocketing of the esophagus."],
+                "label": "lung",
+            },
+            "HsapDv:0000174": {
+                "iri": "http://purl.obolibrary.org/obo/HsapDv_0000174",
+                "description": ["Infant stage that refers to an infant who is over 1 and under 2 months old."],
+                "label": "1-month-old human stage",
+            },
+            "NCBITaxon:9606": {
+                "iri": "http://purl.obolibrary.org/obo/NCBITaxon_9606",
+                "description": None,
+                "label": "Homo sapiens",
+            },
+            "EFO:0008995": {
+                "iri": "http://www.ebi.ac.uk/efo/EFO_0008995",
+                "description": [
+                    ('10X is a "synthetic long-read" technology and works by capturing a barcoded oligo-coated '
+                     'gel-bead and 0.3x genome copies into a single emulsion droplet, processing the equivalent '
+                     'of 1 million pipetting steps. Successive versions of the 10x chemistry use different barcode '
+                     'locations to improve the sequencing yield and quality of 10x experiments.')
+                ],
+                "label": "10X sequencing",
+            },
+        }
+
+        self.labels = {
+            "UBERON:0002048": "lung",
+            "HsapDv:0000174": "1-month-old human stage",
+            "NCBITaxon:9606": "Homo sapiens",
+            "EFO:0008995": "10X sequencing",
+        }
+
+    @unittest.mock.patch("requests.get")
+    def test_lookup_label(self, mock_get):
+
+        for curie, response in self.responses.items():
+            mock_get.return_value.content = json.dumps(response)
+            mock_get.return_value.json.return_value = response
+            mock_get.return_value.status_code = 200
+
+            label = ontology.get_ontology_label(curie)
+            self.assertEqual(label, self.labels[curie])