Remove the deprecated methods (#62)

Co-authored-by: jschaff <[email protected]>

biothings_annotator/annotator/annotator.py

@@ -224,76 +224,3 @@ def annotate_trapi(
                 node_d[node_id]["attributes"] = [res]
 
         return node_d
-
-    def annotate_trapi_0(
-        self, trapi_input: Dict, append: bool = False, raw: bool = False, fields: list = None, limit: int = None
-    ):
-        """
-        Deprecated! Kept here for reference for now, pending to be deleted soon.
-        Annotate a TRAPI input message with node annotator annotations
-        """
-        try:
-            node_d = get_dotfield_value("message.knowledge_graph.nodes", trapi_input)
-            assert isinstance(node_d, dict)
-        except (KeyError, ValueError, AssertionError):
-            raise TRAPIInputError(trapi_input)
-
-        # if limit is set, we truncate the node_d to that size
-        if limit:
-            _node_d = {}
-            i = 0
-            for node_id in node_d:
-                i += 1
-                if i > limit:
-                    break
-                _node_d[node_id] = node_d[node_id]
-            node_d = _node_d
-            del i, _node_d
-
-        node_list_by_type = {}
-        for node_id in node_d:
-            node_type = parse_curie(node_id, return_type=True, return_id=False)
-            if node_type:
-                if node_type not in node_list_by_type:
-                    node_list_by_type[node_type] = [node_id]
-                else:
-                    node_list_by_type[node_type].append(node_id)
-            else:
-                logger.warning("Unsupported Curie prefix: %s. Skipped!", node_id)
-
-        for node_type, node_list in node_list_by_type.items():
-            if node_type not in ANNOTATOR_CLIENTS or not node_list_by_type[node_type]:
-                # skip for now
-                continue
-
-            # this is the list of original node ids like NCBIGene:1017, should be a unique list
-            node_list = node_list_by_type[node_type]
-
-            # this is the list of query ids like 1017
-            query_list = [parse_curie(_id, return_type=False, return_id=True) for _id in node_list_by_type[node_type]]
-            # query_id to original id mapping
-            node_id_d = dict(zip(query_list, node_list))
-            res_by_id = self.query_biothings(node_type, query_list, fields=fields)
-            if not raw:
-                res_by_id = self.transform(res_by_id, node_type)
-            for node_id in res_by_id:
-                orig_node_id = node_id_d[node_id]
-                res = res_by_id[node_id]
-                # if not raw:
-                #     if isinstance(res, list):
-                #         # TODO: handle multiple results here
-                #         res = [self.transform(r) for r in res]
-                #     else:
-                #         res = self.transform(res)
-                res = {
-                    "attribute_type_id": "biothings_annotations",
-                    "value": res,
-                }
-                if append:
-                    # append annotations to existing "attributes" field
-                    node_d[orig_node_id]["attributes"].append(res)
-                else:
-                    # return annotations only
-                    node_d[orig_node_id]["attributes"] = [res]
-
-        return node_d

biothings_annotator/annotator/transformer.py

@@ -165,37 +165,6 @@ def caching_ncit_descriptions(self):
             if ncit_def_d:
                 self.data_cache["ncit"] = ncit_def_d
 
-    def deprecated_transform_add_ncit_description(self, doc):
-        """
-        add ncit_description field to unii object based on unii.ncit field
-        deprecated now, as ncit_description is now returned directly from mychem.info
-        """
-        if self.node_type != "chem":
-            return doc
-
-        if "ncit" not in self.data_cache:
-            self.caching_ncit_descriptions()
-
-        ncit_def_d = self.data_cache.get("ncit", {})
-
-        def _add_ncit_description(unii):
-            ncit = unii.get("ncit")
-            ncit = f"NCIT:{ncit}"
-            if ncit:
-                ncit_def = ncit_def_d.get(ncit)
-                if ncit_def:
-                    unii["ncit_description"] = ncit_def
-
-        unii = doc.get("unii", {})
-        if unii:
-            if isinstance(unii, list):
-                # in case returned chembl is a list, rare but still possible
-                for u in unii:
-                    _add_ncit_description(u)
-            else:
-                _add_ncit_description(unii)
-        return doc
-
     def transform_one_doc(self, doc):
         """transform the response from biothings client"""
         for fn_name, fn in inspect.getmembers(self, predicate=inspect.ismethod):