Add basic search implementation for OLS (#163)

src/oaklib/implementations/ols/ols_implementation.py

@@ -9,7 +9,7 @@
 
 from oaklib.datamodels import oxo
 from oaklib.datamodels.oxo import ScopeEnum
-from oaklib.datamodels.search import SearchConfiguration
+from oaklib.datamodels.search import SearchConfiguration, SearchProperty
 from oaklib.datamodels.text_annotator import TextAnnotation
 from oaklib.datamodels.vocabulary import IS_A
 from oaklib.implementations.ols import SEARCH_CONFIG
@@ -21,6 +21,7 @@
 from oaklib.types import CURIE, PRED_CURIE
 
 ANNOTATION = Dict[str, Any]
+SEARCH_ROWS = 50
 
 oxo_pred_mappings = {
     ScopeEnum.EXACT.text: "skos:exactMatch",
@@ -43,7 +44,7 @@ class OlsImplementation(TextAnnotatorInterface, SearchInterface, MappingProvider
     ols_api_key: str = None
     label_cache: Dict[CURIE, str] = field(default_factory=lambda: {})
     base_url = "https://www.ebi.ac.uk/spot/oxo/api/mappings"
-    ols_base_url = "https://www.ebi.ac.uk/ols/api/ontologies/"
+    ols_base_url = "https://www.ebi.ac.uk/ols/api"
     prefix_map: Dict[str, str] = field(default_factory=lambda: {})
     focus_ontology: str = None
 
@@ -61,7 +62,8 @@ def get_prefix_map(self) -> PREFIX_MAP:
         return self.prefix_map
 
     def get_labels_for_curies(self, curies: Iterable[CURIE]) -> Iterable[Tuple[CURIE, str]]:
-        raise NotImplementedError
+        for curie in curies:
+            yield curie, self.label_cache[curie]
 
     def annotate_text(self, text: str) -> Iterator[TextAnnotation]:
         raise NotImplementedError
@@ -88,7 +90,7 @@ def ancestors(
             # must be double encoded https://www.ebi.ac.uk/ols/docs/api
             term_id_quoted = urllib.parse.quote(term_id, safe="")
             term_id_quoted = urllib.parse.quote(term_id_quoted, safe="")
-            url = f"{self.ols_base_url}{ontology}/terms/{term_id_quoted}/{query}"
+            url = f"{self.ols_base_url}/ontologies/{ontology}/terms/{term_id_quoted}/{query}"
             logging.debug(f"URL={url}")
             result = requests.get(url)
             obj = result.json()
@@ -106,7 +108,49 @@ def ancestors(
     def basic_search(
         self, search_term: str, config: SearchConfiguration = SEARCH_CONFIG
     ) -> Iterable[CURIE]:
-        raise NotImplementedError
+        query_fields = set()
+        # Anything not covered by these conditions (i.e. query_fields set remains empty)
+        # will cause the queryFields query param to be left off and all fields to be queried
+        if SearchProperty(SearchProperty.IDENTIFIER) in config.properties:
+            query_fields.update(["iri", "obo_id"])
+        if SearchProperty(SearchProperty.LABEL) in config.properties:
+            query_fields.update(["label"])
+        if SearchProperty(SearchProperty.ALIAS) in config.properties:
+            query_fields.update(["synonym"])
+        if SearchProperty(SearchProperty.DEFINITION) in config.properties:
+            query_fields.update(["description"])
+        if SearchProperty(SearchProperty.INFORMATIVE_TEXT) in config.properties:
+            query_fields.update(["description"])
+
+        params = {
+            "q": search_term,
+            "type": "class",
+            "local": "true",
+            "fieldList": "iri,label",
+            "rows": config.limit if config.limit is not None else SEARCH_ROWS,
+            "start": 0,
+            "exact": "true"
+            if (config.is_complete is True or config.is_partial is False)
+            else "false",
+        }
+        if len(query_fields) > 0:
+            params["queryFields"] = ",".join(query_fields)
+        if self.focus_ontology:
+            params["ontology"] = self.focus_ontology.lower()
+
+        finished = False
+        while not finished:
+            response = requests.get(f"{self.ols_base_url}/search", params=params)
+            logging.debug(f"URL={response.url}")
+            body = response.json()
+            params["start"] += params["rows"]
+            if params["start"] > body["response"]["numFound"]:
+                finished = True
+            for doc in body["response"]["docs"]:
+                curie = self.uri_to_curie(doc["iri"])
+                label = doc["label"]
+                self.label_cache[curie] = label
+                yield curie
 
     # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
     # Implements: MappingsInterface

tests/test_implementations/test_ols.py

@@ -1,7 +1,9 @@
+import itertools
 import unittest
 
 from linkml_runtime.dumpers import yaml_dumper
 
+from oaklib.datamodels.search import SearchConfiguration, SearchProperty
 from oaklib.datamodels.vocabulary import IS_A
 from oaklib.implementations.ols.ols_implementation import OlsImplementation
 from oaklib.resource import OntologyResource
@@ -32,3 +34,27 @@ def test_ancestors(self):
         #    print(a)
         assert CYTOPLASM not in ancs
         assert CELLULAR_COMPONENT in ancs
+
+    def test_basic_search(self):
+        self.oi.focus_ontology = None
+        results = list(itertools.islice(self.oi.basic_search("epilepsy"), 20))
+        self.assertIn("MONDO:0005027", results)
+
+    def test_focus_ontology_search(self):
+        self.oi.focus_ontology = "MONDO"
+        results = list(itertools.islice(self.oi.basic_search("epilepsy"), 20))
+        for result in results:
+            self.assertRegex(result, "^MONDO:")
+
+    def test_search_configuration(self):
+        self.oi.focus_ontology = None
+
+        config = SearchConfiguration(properties=[SearchProperty.LABEL])
+        results = list(itertools.islice(self.oi.basic_search("swimming", config), 20))
+        self.assertIn("GO:0036268", results)  # GO:0036268 == swimming
+        self.assertNotIn("NBO:0000371", results)  # NBO:0000371 == aquatic locomotion
+
+        config = SearchConfiguration(is_complete=True)
+        results = list(itertools.islice(self.oi.basic_search("swimming", config), 20))
+        self.assertIn("OMIT:0014415", results)  # OMIT:0014415 == Swimming
+        self.assertNotIn("OMIT:0014416", results)  # OMIT:0014416 == Swimming Pools