Add curie query support (mychem version) (#34)

* Add the biolink prefix mapping to the settings ...

Also separate the settings into a separate file for isolating the
configuration from client construction methods

* Add work for supporting CURIE query support ...

Specifically targets _getannotation and _getannotations methods at the
moment and only for the mygene instance

* Update the tox configuration to use more modern python

* Change the default value for the prefix mapping

* Add proper list formatting for the fields support

* Add proper multiple id/query argument handling

* Add expectedFailure decorators to the chem tests

* Remove the default the regex pattern matching ...

Not all of the different sites will work with that. Ran into issues
with that default pattern with myvariant. Instead we should view this
feature as specifically targetting support for the biolink prefixes
and nothing else

* Remove client side CURIE support ...

Pivot to adding testing and verification that the API / server side
implementation supports the CURIE ID

* Add the CURIE ID query testing for the mygene instance

* Remove unused pytest import

* Add the curie id tests with mychem as the target

* Revert modifications to the settings configuration

* Update the pyproject file

---------

Co-authored-by: Johnathan Schaff <jschaff@scripps.edu>

biothings_client/base.py

@@ -1,6 +1,7 @@
 """
 Python Client for generic Biothings API services
 """
+
 from __future__ import print_function
 
 import logging

biothings_client/utils/gene.py

@@ -1,4 +1,5 @@
 """ Gene specific utils. """
+
 from collections import OrderedDict
 
 from biothings_client import get_client

pyproject.toml

@@ -7,7 +7,7 @@ name="biothings_client"
 authors = [
     {name = "Cyrus Afrasiabi"},
     {name = "Xinghua Zhou"},
-    {name = "Everaldo Rodolpho"},
+    {name = "Everaldo Rodolpho", email="erodolpho@scripps.edu"},
     {name = "Chunlei Wu", email = "cwu@scripps.edu"},
 ]
 requires-python = ">=2.7"

tests/chem.py

@@ -54,6 +54,121 @@ def test_getchem_with_fields(self):
         self.assertTrue("pubchem" in c)
         self.assertTrue("cid" in c["pubchem"])
 
+    def test_curie_id_query(self):
+        """
+        Tests the annotation endpoint support for the biolink CURIE ID.
+
+        If support is enabled then we should retrieve the exact same document for all the provided
+        queries
+        """
+        curie_id_testing_collection = [
+            ("57966", "CHEMBL.COMPOUND:57966", "chembl.molecule_chembl_id:57966"),
+            (57966, "chembl.compound:57966", "chembl.molecule_chembl_id:57966"),
+            (57966, "CheMBL.compOUND:57966", "chembl.molecule_chembl_id:57966"),
+            ("120933777", "PUBCHEM.COMPOUND:120933777", "pubchem.cid:120933777"),
+            (120933777, "pubchem.compound:120933777", "pubchem.cid:120933777"),
+            ("120933777", "PuBcHEm.COMPound:120933777", "pubchem.cid:120933777"),
+            (57966, "CHEBI:57966", "chebi.id:57966"),
+            ("57966", "chebi:57966", "chebi.id:57966"),
+            (57966, "CheBi:57966", "chebi.id:57966"),
+            ("11P2JDE17B", "UNII:11P2JDE17B", "unii.unii:11P2JDE17B"),
+            ("11P2JDE17B", "unii:11P2JDE17B", "unii.unii:11P2JDE17B"),
+            ("11P2JDE17B", "uNIi:11P2JDE17B", "unii.unii:11P2JDE17B"),
+            ("dB03107", "DRUGBANK:dB03107", "drugbank.id:dB03107"),
+            ("dB03107", "drugbank:dB03107", "drugbank.id:dB03107"),
+            ("dB03107", "DrugBaNK:dB03107", "drugbank.id:dB03107"),
+        ]
+
+        results_aggregation = []
+        for id_query, biothings_query, biolink_query in curie_id_testing_collection:
+            id_query_result = self.mc.getchem(_id=id_query)
+            biothings_term_query_result = self.mc.getchem(_id=biothings_query)
+            biolink_term_query_result = self.mc.getchem(_id=biolink_query)
+            results_aggregation.append(
+                (
+                    id_query_result == biothings_term_query_result,
+                    id_query_result == biolink_term_query_result,
+                    biothings_term_query_result == biolink_term_query_result,
+                )
+            )
+
+        results_validation = []
+        failure_messages = []
+        for result, test_query in zip(results_aggregation, curie_id_testing_collection):
+            cumulative_result = all(result)
+            if not cumulative_result:
+                failure_messages.append(f"Query Failure: {test_query} | Results: {result}")
+            results_validation.append(cumulative_result)
+
+        self.assertTrue(all(results_validation), msg="\n".join(failure_messages))
+
+    def test_multiple_curie_id_query(self):
+        """
+        Tests the annotations endpoint support for the biolink CURIE ID.
+
+        Batch query testing against the POST endpoint to verify that the CURIE ID can work with
+        multiple
+
+        If support is enabled then we should retrieve the exact same document for all the provided
+        queries
+        """
+        curie_id_testing_collection = [
+            ("57966", "CHEMBL.COMPOUND:57966", "chembl.molecule_chembl_id:57966"),
+            (57966, "chembl.compound:57966", "chembl.molecule_chembl_id:57966"),
+            (57966, "CheMBL.compOUND:57966", "chembl.molecule_chembl_id:57966"),
+            ("120933777", "PUBCHEM.COMPOUND:120933777", "pubchem.cid:120933777"),
+            (120933777, "pubchem.compound:120933777", "pubchem.cid:120933777"),
+            ("120933777", "PuBcHEm.COMPound:120933777", "pubchem.cid:120933777"),
+            (57966, "CHEBI:57966", "chebi.id:57966"),
+            ("57966", "chebi:57966", "chebi.id:57966"),
+            (57966, "CheBi:57966", "chebi.id:57966"),
+            ("11P2JDE17B", "UNII:11P2JDE17B", "unii.unii:11P2JDE17B"),
+            ("11P2JDE17B", "unii:11P2JDE17B", "unii.unii:11P2JDE17B"),
+            ("11P2JDE17B", "uNIi:11P2JDE17B", "unii.unii:11P2JDE17B"),
+            ("dB03107", "DRUGBANK:dB03107", "drugbank.id:dB03107"),
+            ("dB03107", "drugbank:dB03107", "drugbank.id:dB03107"),
+            ("dB03107", "DrugBaNK:dB03107", "drugbank.id:dB03107"),
+        ]
+
+        results_aggregation = []
+        for id_query, biothings_query, biolink_query in curie_id_testing_collection:
+            base_result = self.mc.getchem(_id=id_query)
+
+            batch_query = [id_query, biothings_query, biolink_query]
+            query_results = self.mc.getchems(ids=batch_query)
+            assert len(query_results) == len(batch_query)
+
+            batch_id_query = query_results[0]
+            batch_biothings_query = query_results[1]
+            batch_biolink_query = query_results[2]
+
+            batch_id_query_return_value = batch_id_query.pop("query")
+            assert batch_id_query_return_value == str(id_query)
+
+            batch_biothings_query_return_value = batch_biothings_query.pop("query")
+            assert batch_biothings_query_return_value == str(biothings_query)
+
+            batch_biolink_query_return_value = batch_biolink_query.pop("query")
+            assert batch_biolink_query_return_value == str(biolink_query)
+
+            batch_result = (
+                base_result == batch_id_query,
+                base_result == batch_biothings_query,
+                base_result == batch_biolink_query,
+            )
+            results_aggregation.append(batch_result)
+
+        results_validation = []
+        failure_messages = []
+        for result, test_query in zip(results_aggregation, curie_id_testing_collection):
+            cumulative_result = all(result)
+            if not cumulative_result:
+                failure_messages.append(f"Query Failure: {test_query} | Results: {result}")
+            results_validation.append(cumulative_result)
+
+        self.assertTrue(all(results_validation), msg="\n".join(failure_messages))
+
+    @unittest.expectedFailure
     def get_getdrug(self):
         c = self.mc.getdrug("CHEMBL1308")
         self.assertEqual(c["_id"], "ZRALSGWEFCBTJO-UHFFFAOYSA-N")
@@ -64,10 +179,10 @@ def get_getdrug(self):
 
         # PubChem CID
         # not working yet
-        # c = self.mc.getdrug("CID:1990")
-        # self.assertEqual(c['_id'], "ZRALSGWEFCBTJO-UHFFFAOYSA-N")
-        # c = self.mc.getdrug("1990")
-        # self.assertEqual(c['_id'], "ZRALSGWEFCBTJO-UHFFFAOYSA-N")
+        c = self.mc.getdrug("CID:1990")
+        self.assertEqual(c["_id"], "ZRALSGWEFCBTJO-UHFFFAOYSA-N")
+        c = self.mc.getdrug("1990")
+        self.assertEqual(c["_id"], "ZRALSGWEFCBTJO-UHFFFAOYSA-N")
 
     def test_getchems(self):
         c_li = self.mc.getchems(
@@ -102,16 +217,17 @@ def test_query_chembl(self):
         self.assertEqual(len(qres["hits"]), 1)
         self.assertEqual(qres["hits"][0]["_id"], "RRUDCFGSUDOHDG-UHFFFAOYSA-N")
 
+    @unittest.expectedFailure
     def test_query_drugcentral(self):
         qres = self.mc.query("drugcentral.drug_use.contraindication.umls_cui:C0023530", fields="drugcentral", size=50)
         self.assertTrue("hits" in qres)
         self.assertEqual(len(qres["hits"]), 50)
 
         # not working yet
-        # qres = self.mc.query('drugcentral.xrefs.kegg_drug:D00220')
-        # self.assertTrue('hits' in qres)
-        # self.assertEqual(len(qres['hits']), 1)
-        # self.assertEqual(qres['hits'][0]['_id'], 'ZRALSGWEFCBTJO-UHFFFAOYSA-N')
+        qres = self.mc.query("drugcentral.xrefs.kegg_drug:D00220")
+        self.assertTrue("hits" in qres)
+        self.assertEqual(len(qres["hits"]), 1)
+        self.assertEqual(qres["hits"][0]["_id"], "ZRALSGWEFCBTJO-UHFFFAOYSA-N")
 
     def test_query_pubchem(self):
         qres = self.mc.query("pubchem.molecular_formula:C2H5NO2", fields="pubchem", size=20)
@@ -139,15 +255,15 @@ def test_query_ndc(self):
         qres = self.mc.query('ndc.productndc:"27437-051"')
         self.assertTrue("hits" in qres)
         self.assertEqual(len(qres["hits"]), 1)
-        # Temp disable this check till we fix the data issue
-        # self.assertEqual(qres['hits'][0]['_id'], 'KPQZUUQMTUIKBP-UHFFFAOYSA-N')
+        self.assertEqual(qres["hits"][0]["_id"], "KPQZUUQMTUIKBP-UHFFFAOYSA-N")
 
+    @unittest.expectedFailure
     def test_query_sider(self):
         qres = self.mc.query("sider.meddra.umls_id:C0232487", fields="sider", size=5)
         self.assertTrue("hits" in qres)
         self.assertEqual(len(qres["hits"]), 5)
         # Temp disable this check till we fix the data issue
-        # self.assertEqual(qres['hits'][0]['_id'], 'ZRALSGWEFCBTJO-UHFFFAOYSA-N')
+        self.assertEqual(qres["hits"][0]["_id"], "ZRALSGWEFCBTJO-UHFFFAOYSA-N")
 
     def test_query_unii(self):
         qres = self.mc.query("unii.unii:JU58VJ6Y3B")