Merge branch 'testapi'

Author: Zhouyang Lian

.circleci/requirements.txt

@@ -1,3 +1,3 @@
 # Karr Lab packages
 git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils
-prance
+prance

Pipfile.lock

@@ -59,6 +59,6 @@ def get(query_message, indices, size, fields, from_=0):
     class gene_ranked_by_ko:
 
         def get(query_message, from_, size, fields=['*']):
-            r = f_manager.get_genes_ko_count(query_message, size,
-                                             fields=fields, from_=from_)
+            r = f_manager.get_genes_orthodb_count(query_message, size,
+                                                  fields=fields, from_=from_)
             return r

datanator_rest_api/routes/ftx.py

@@ -17,6 +17,6 @@
 class get_meta:
 
     def get(kegg_ids, _from=0, size=10):
-        docs, count = k_manager.get_meta_by_kegg_ids(kegg_ids)
+        docs, count = k_manager.get_meta_by_ortho_ids(kegg_ids, limit=size)
         manager = paginator.Paginator(count, list(docs))
         return manager.page(_from=_from, size=size)

datanator_rest_api/routes/kegg.py

@@ -15,6 +15,7 @@
 
 
 p_manager = query_manager.Manager().protein_manager()
+p_manager_new = query_manager.Manager().protein_manager(database="datanator-test")
 dist_manager = taxon_distance.TaxonDist()
 
 
@@ -53,7 +54,7 @@ def get(uniprot_id, distance, depth):
     class proximity_abundance_kegg:
 
         def get(kegg_id, distance, anchor='homo sapiens'):
-            return p_manager.get_all_kegg(kegg_id, anchor, distance)
+            return p_manager_new.get_all_ortho(kegg_id, anchor, distance)
 
 
 class meta:
@@ -62,7 +63,7 @@ class meta_combo:
 
         def get(uniprot_id=None, ncbi_taxon_id=None, species_name=None, name=None):
             if uniprot_id is not None:   # uniprot_id
-                return p_manager.get_meta_by_id(uniprot_id)
+                return p_manager_new.get_ortho_by_id(uniprot_id[0])
             elif name is not None and ncbi_taxon_id is not None and species_name is None:  # name + taxon_id
                 return p_manager.get_meta_by_name_taxon(name, ncbi_taxon_id)
             elif name is not None and species_name is not None:   # name + species_name
@@ -134,7 +135,7 @@ class related:
 
     class related_reactions_by_kegg:
         def get(ko):
-            lists = p_manager.get_info_by_ko(ko)
+            lists = p_manager_new.get_info_by_orthodb(ko)
             uniprot_ids = lists[0]['uniprot_ids']
             kinlaw_ids = query_manager.RxnManager().rxn_manager().get_reaction_by_subunit(uniprot_ids)
             return list(kinlaw_ids)

datanator_rest_api/routes/proteins.py

@@ -56,8 +56,8 @@ class get_info_by_ko:
         def get(ko_number, _from=0, size=10, 
                 taxon_distance=True, species='homo sapiens'):
             result = []
-            docs, _ = rna_manager.get_doc_by_ko(ko_number, _from=_from,
-                                                size=size)
+            docs, _ = rna_manager.get_doc_by_orthodb(ko_number, _from=_from,
+                                                    size=size)
             if not docs:
                 return result
             for doc in docs:
@@ -94,7 +94,7 @@ class modification:
     class get_modifications_by_ko:
         def get(ko_number, _from=0, size=10, target_organism='Escherichia coli', taxon_distance=False):
             result = []
-            query = {"kegg_orthology_id": ko_number}
+            query = {"orthodb_id": ko_number}
             docs = rna_manager.db_obj['rna_modification'].find(filter=query, skip=_from,
                                                                 limit=size, projection={'_id': 0})
             if not docs:

datanator_rest_api/routes/rna.py

@@ -0,0 +1,20 @@
+""" Full text search
+perform full text search
+
+:Author: Zhouyang Lian < zhouyang.lian@familian.life >
+:Date: 2020-08-10
+:Copyright: 2019, Karr Lab
+:License: MIT
+"""
+from datanator_query_python.query_schema_2 import query_entity
+
+e_manager = query_entity.QueryEn()
+
+class get_entity_meta:
+    def get(identifier, datatype="metabolite", limit=10, skip=0):
+        identifier = {"namespace": identifier["namespace"],
+                      "value": identifier["value"]}
+        return e_manager.query_entity(identifier,
+                                    datatype=datatype,
+                                    limit=limit,
+                                    skip=skip)

datanator_rest_api/routes/v2/entity.py

@@ -0,0 +1,21 @@
+""" Full text search
+perform full text search
+
+:Author: Zhouyang Lian < zhouyang.lian@familian.life >
+:Date: 2020-08-05
+:Copyright: 2019, Karr Lab
+:License: MIT
+"""
+from datanator_query_python.query_schema_2 import query_observation
+
+o_manager = query_observation.QueryObs()
+
+class get_entity_value:
+    def get(identifier, entity="protein", datatype="half-life", limit=10, skip=0):
+        identifier = {"namespace": identifier["namespace"],
+                      "value": identifier["value"]}
+        return o_manager.get_entity_datatype(identifier,
+                                             entity=entity,
+                                             datatype=datatype,
+                                             limit=limit,
+                                             skip=skip)