Remove client side CURIE support ...

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

biothings_client/base.py

@@ -14,7 +14,6 @@
 import requests
 
 from .utils import str_types, is_py27
-from .utils.curie import generate_annotation_prefix_patterns, transform_query
 
 try:
     from collections.abc import Iterable
@@ -142,7 +141,6 @@ def __init__(self, url=None):
             }
         )
         self._cached = False
-        self.annotation_prefix_patterns = generate_annotation_prefix_patterns(self._biolink_model_prefix_mapping)
 
     def use_http(self):
         """Use http instead of https for API calls."""
@@ -334,7 +332,6 @@ def _get_fields(self, search_term=None, verbose=True):
             logger.info(self._from_cache_notification)
         return ret
 
-    @transform_query
     def _getannotation(self, _id, fields=None, **kwargs):
         """Return the object given id.
         This is a wrapper for GET query of the biothings annotation service.
@@ -368,7 +365,6 @@ def _annotations_generator(self, query_fn, ids, verbose=True, **kwargs):
             for hit in hits:
                 yield hit
 
-    @transform_query
     def _getannotations(self, ids, fields=None, **kwargs):
         """Return the list of annotation objects for the given list of ids.
         This is a wrapper for POST query of the biothings annotation service.

biothings_client/settings.py

@@ -66,11 +66,6 @@
 }
 # project specific kwargs
 MYGENE_KWARGS = copy(COMMON_KWARGS)
-MYGENE_BIOLINK_MODEL_PREFIX_BIOTHINGS_MAPPING = {
-    "NCBIGene": {"type": "gene", "field": "entrezgene"},
-    "ENSEMBL": {"type": "gene", "field": "ensembl.gene"},
-    "UniProtKB": {"type": "gene", "field": "uniprot.Swiss-Prot"},
-}
 
 MYGENE_KWARGS.update(
     {
@@ -80,7 +75,6 @@
         "_default_cache_file": "mygene_cache",
         "_entity": "gene",
         "_docstring_obj": GENE_DOCSTRING,
-        "_biolink_model_prefix_mapping": MYGENE_BIOLINK_MODEL_PREFIX_BIOTHINGS_MAPPING,
     }
 )
 
@@ -94,7 +88,6 @@
         "_entity": "variant",
         "_top_level_jsonld_uris": MYVARIANT_TOP_LEVEL_JSONLD_URIS,
         "_docstring_obj": VARIANT_DOCSTRING,
-        "_biolink_model_prefix_mapping": {}
     }
 )
 MYCHEM_KWARGS = copy(COMMON_KWARGS)
@@ -106,7 +99,6 @@
         "_entity": "chem",
         "_default_cache_file": "mychem_cache",
         "_docstring_obj": CHEM_DOCSTRING,
-        "_biolink_model_prefix_mapping": {}
     }
 )
 MYDISEASE_KWARGS = copy(COMMON_KWARGS)
@@ -117,7 +109,6 @@
         "_optionally_plural_object_type": "disease(s)",
         "_entity": "disease",
         "_default_cache_file": "mydisease_cache",
-        "_biolink_model_prefix_mapping": {}
     }
 )
 MYTAXON_KWARGS = copy(COMMON_KWARGS)
@@ -128,7 +119,6 @@
         "_optionally_plural_object_type": "taxon/taxa",
         "_entity": "taxon",
         "_default_cache_file": "mytaxon_cache",
-        "_biolink_model_prefix_mapping": {}
     }
 )
 MYGENESET_KWARGS = copy(COMMON_KWARGS)
@@ -139,7 +129,6 @@
         "_optionally_plural_object_type": "geneset(s)",
         "_entity": "geneset",
         "_default_cache_file": "mygeneset_cache",
-        "_biolink_model_prefix_mapping": {}
     }
 )