total number of abundance observations #98

KarrLab · May 26, 2020 · e66140e · e66140e
1 parent 8dfd546
commit e66140e
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diff --git a/datanator_rest_api/routes/proteins.py b/datanator_rest_api/routes/proteins.py
@@ -9,6 +9,7 @@
 
 
 from datanator_query_python.config import query_manager
+from datanator_query_python.aggregate import pipelines
 from datanator_rest_api.util import taxon_distance
 
 
@@ -96,6 +97,13 @@ def get():
             return p_manager.collection.count_documents({'abundances': {"$exists": True}})
 
 
+    class num_obs_abundances():
+        def get():
+            pipeline = pipelines.Pipeline().aggregate_total_array_length("observation")
+            for doc in p_manager.db_obj['pax'].aggregate(pipeline):
+                return doc['total'] 
+
+
     class num_publications():
 
         def get():

diff --git a/datanator_rest_api/spec/DatanatorAPI.yaml b/datanator_rest_api/spec/DatanatorAPI.yaml
@@ -961,6 +961,19 @@ paths:
       summary: Get number of proteins with abundance values
       tags:
       - Proteins
+  /proteins/summary/num_obs_abundances/:
+    get:
+      description: For about page
+      responses:
+        '200':
+          content:
+            application/json:
+              schema:
+                type: integer
+          description: OK
+      summary: Get number of observed abundance values
+      tags:
+      - Proteins
   /proteins/summary/num_organism/:
     get:
       description: For about page

diff --git a/datanator_rest_api/spec/paths/proteins.yaml b/datanator_rest_api/spec/paths/proteins.yaml
@@ -216,6 +216,20 @@ summary:
             application/json:
               schema:
                 type: integer
+
+  num_obs_abundances:
+    get:
+      tags:
+        - Proteins
+      summary: Get number of observed abundance values
+      description: For about page
+      responses:
+        "200":
+          description: OK
+          content:
+            application/json:
+              schema:
+                type: integer
 
   num_publications:
     get:

diff --git a/datanator_rest_api/spec/root.yaml b/datanator_rest_api/spec/root.yaml
@@ -79,6 +79,8 @@ paths:
     $ref: paths/proteins.yaml#/summary/num_abundances
   /proteins/summary/num_publications/:
     $ref: paths/proteins.yaml#/summary/num_publications
+  /proteins/summary/num_obs_abundances/:
+    $ref: paths/proteins.yaml#/summary/num_obs_abundances
   /proteins/similar_protein/refseq/:
     $ref: paths/proteins.yaml#/similar_protein/refseq
   /proteins/related/related_reactions_by_kegg/:

diff --git a/tests/routes/test_proteins.py b/tests/routes/test_proteins.py
@@ -74,6 +74,10 @@ def test_summary_num_publications(self):
         result = self.client.get('/proteins/summary/num_publications/')
         self.assertEqual(result.status_code, 200)
 
+    def test_summary_num_obs_abundances(self):
+        result = self.client.get('/proteins/summary/num_obs_abundances/')
+        self.assertEqual(result.status_code, 200)
+
     def test_similar_protein_refseq(self):
         result = self.client.get('/proteins/similar_protein/refseq/?uniprot_id=q9vb24&identity=90')
         self.assertEqual(result.status_code, 200)