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.

local_server/converters/schema/ontology.py

@@ -0,0 +1,86 @@
+"""Methods for working with ontologies and the OLS."""
+from urllib.parse import quote_plus
+
+import requests
+
+OLS_API_ROOT = "http://www.ebi.ac.uk/ols/api"
+
+# Curie means something like CL:0000001
+
+
+def _ontology_name(curie):
+    """Get the name of the ontology from the curie, CL or UBERON for example."""
+    return curie.split(":")[0]
+
+
+def _ontology_value(curie):
+    """Get the id component of the curie, 0000001 from CL:0000001 for example."""
+    return curie.split(":")[1]
+
+
+def _double_encode(url):
+    """Double url encode a url. This is required by the OLS API."""
+    return quote_plus(quote_plus(url))
+
+
+def _iri(curie):
+    """Get the iri from a curie. This is a bit hopeful that they all map to purl.obolibrary.org"""
+    if _ontology_name(curie) == "EFO":
+        return f"http://www.ebi.ac.uk/efo/EFO_{_ontology_value(curie)}"
+    return f"http://purl.obolibrary.org/obo/{_ontology_name(curie)}_{_ontology_value(curie)}"
+
+
+class OntologyLookupError(Exception):
+    """Exception for some problem with looking up ontology information."""
+
+
+def _ontology_info_url(curie):
+    """Get the to make a GET to to get information about an ontology term."""
+
+    # If the curie is empty, just return an empty string. This happens when there is no
+    # valid ontology value.
+    if not curie:
+        return ""
+    else:
+        return f"{OLS_API_ROOT}/ontologies/{_ontology_name(curie)}/terms/{_double_encode(_iri(curie))}"
+
+
+def get_ontology_label(curie):
+    """For a given curie like 'CL:1000413', get the label like 'endothelial cell of artery'"""
+
+    url = _ontology_info_url(curie)
+
+    if not url:
+        return ""
+
+    response = requests.get(url)
+
+    if not response.ok:
+        raise OntologyLookupError(
+            f"Curie {curie} lookup failed, got status code {response.status_code}: {response.text}"
+        )
+    return response.json()["label"]
+
+
+def lookup_candidate_term(label, ontology="cl", method="select"):
+    """Lookup candidate terms for a label. This is useful when there is an existing label in a
+    submitted dataset, and you want to find an appropriate ontology term.
+
+    Args:
+      label: the label to find ontology terms for
+      ontology: the ontology to search in, cl or uberon or efo for example
+      method: select or search. search provides much broader results
+
+    Returns:
+      list of (curie, label) tuples returned by OLS
+    """
+    # using OLS REST API [https://www.ebi.ac.uk/ols/docs/api]
+    url = f"{OLS_API_ROOT}/{method}?q={quote_plus(label)}&ontology={ontology.lower()}"
+    response = requests.get(url)
+
+    if not response.ok:
+        raise OntologyLookupError(
+            f"Label {label} lookup failed, got status code {response.status_code}: {response.text}"
+        )
+
+    return [(r["obo_id"], r["label"]) for r in response.json()["response"]["docs"]]