Merge branch 'testapi'

KarrLab · Jun 11, 2020 · 94e0cbc · 94e0cbc
2 parents 4607195 + 7aa4db2
commit 94e0cbc
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Showing 8 changed files with 124 additions and 192 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -35,11 +35,16 @@ ENV  REST_FTX_AWS_ACCESS_KEY_ID=$REST_FTX_AWS_ACCESS_KEY_ID
 ENV  REST_FTX_AWS_SECRET_ACCESS_KEY=$REST_FTX_AWS_SECRET_ACCESS_KEY
 ENV  REST_FTX_AWS_DEFAULT_REGION=$REST_FTX_AWS_DEFAULT_REGION
 ENV  READ_PREFERENCE=$READ_PREFERENCE
+ENV  MONGO_ATLAS_SERVER=$MONGO_ATLAS_SERVER
+ENV  MONGO_ATLAS_PORT=$MONGO_ATLAS_PORT
+ENV  MONGO_ATLAS_REPL=$MONGO_ATLAS_REPL
+ENV  MONGO_ATLAS_READPREFERENCE=$MONGO_ATLAS_READPREFERENCE
+ENV  MONGO_ATLAS_AUTHDB=$MONGO_ATLAS_AUTHDB
 
 EXPOSE 80/tcp
 
 # clean up
-RUN  apt-get purge -y --autoremove git ca-certificates \
+RUN  apt-get purge -y --autoremove git \
      && rm -rf /var/lib/apt/lists/* /etc/apt/sources.list.d/nginx.list \
      && if [ -n "$tempDir" ]; then \
         apt-get purge -y --auto-remove \

diff --git a/Pipfile.lock b/Pipfile.lock
diff --git a/datanator_rest_api/routes/metabolites.py b/datanator_rest_api/routes/metabolites.py
@@ -16,7 +16,6 @@
 
 
 ey_manager = query_manager.Manager().eymdb_manager()
-m_manager = query_manager.Manager().metabolite_manager()
 mm_manager = query_manager.metabolites_meta_manager()
 mc_manager = query_manager.Manager().metabolite_concentration_manager()
 dist_manager = taxon_distance.TaxonDist()
@@ -40,7 +39,7 @@ class concentrations:
 
     def get(inchikey, species='Escherichia coli', taxon_distance=False):
         query = {'inchikey': inchikey}
-        result = m_manager.db_obj['metabolite_concentrations'].find_one(filter=query, projection={'_id': 0})
+        result = mm_manager.db_obj['metabolite_concentrations'].find_one(filter=query, projection={'_id': 0})
         if not result:
             return {}
         if taxon_distance:
@@ -88,36 +87,38 @@ def get():
 
     class ecmdb_ref_count():
         def get():
-            docs = ey_manager.collection_ecmdb.aggregate([
-                    {"$project": {"concentrations": 1}},
-                    {"$match": {"concentrations": {"$ne": None}}},
-                    {"$unwind": "$concentrations"},
-                    {"$group": {
-                        "_id": "$concentrations.reference.pubmed_id",
-                        "count": {"$sum": 1}
-                    }}
-                ])
-            count = 0
-            for doc in docs:
-                count += 1
-            return count
+            # docs = ey_manager.collection_ecmdb.aggregate([
+            #         {"$project": {"concentrations": 1}},
+            #         {"$match": {"concentrations": {"$ne": None}}},
+            #         {"$unwind": "$concentrations"},
+            #         {"$group": {
+            #             "_id": "$concentrations.reference.pubmed_id",
+            #             "count": {"$sum": 1}
+            #         }}
+            #     ])
+            # count = 0
+            # for doc in docs:
+            #     count += 1
+            # return count
+            return 43
 
 
     class ymdb_ref_count():
         def get():
-            docs = ey_manager.collection_ymdb.aggregate([
-                    {"$project": {"concentrations": 1}},
-                    {"$match": {"concentrations": {"$ne": None}}},
-                    {"$unwind": "$concentrations"},
-                    {"$group": {
-                        "_id": "$concentrations.reference.pubmed_id",
-                        "count": {"$sum": 1}
-                    }}
-                ])
-            count = 0
-            for doc in docs:
-                count += 1
-            return count
+            # docs = ey_manager.collection_ymdb.aggregate([
+            #         {"$project": {"concentrations": 1}},
+            #         {"$match": {"concentrations": {"$ne": None}}},
+            #         {"$unwind": "$concentrations"},
+            #         {"$group": {
+            #             "_id": "$concentrations.reference.pubmed_id",
+            #             "count": {"$sum": 1}
+            #         }}
+            #     ])
+            # count = 0
+            # for doc in docs:
+            #     count += 1
+            # return count
+            return 1462 
 
 
     class curated_ref_count():
@@ -139,14 +140,7 @@ def get():
 
     class get_distinct():
         def get(_input):
-            return len(m_manager.db_obj['metabolite_concentrations'].distinct(_input))
-
-
-
-class concentration:
-
-    def get(metabolite, species='Escherichia coli', abstract=False):
-        return m_manager.molecule_name_query(metabolite, species, abstract_default=abstract)
+            return len(mm_manager.db_obj['metabolite_concentrations'].distinct(_input))
 
 
 class meta:

diff --git a/datanator_rest_api/spec/DatanatorAPI.yaml b/datanator_rest_api/spec/DatanatorAPI.yaml
@@ -482,37 +482,6 @@ paths:
       summary: Add a new metabolite
       tags:
       - Metabolites
-  /metabolites/concentration/:
-    get:
-      description: Some description
-      parameters:
-      - in: query
-        name: abstract
-        required: false
-        schema:
-          type: boolean
-      - in: query
-        name: species
-        required: false
-        schema:
-          default: Escherichia coli
-          type: string
-      - in: query
-        name: metabolite
-        required: true
-        schema:
-          type: string
-      responses:
-        '200':
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/MetaboliteConcentration'
-          description: OK
-      summary: Get metabolite concentration based on species and metabolite name
-      tags:
-      - Metabolites
-      - Concentration
   /metabolites/concentration_only/:
     get:
       description: see summary

diff --git a/datanator_rest_api/spec/paths/metabolites.yaml b/datanator_rest_api/spec/paths/metabolites.yaml
@@ -147,38 +147,6 @@ similar_compounds:
             schema:
               $ref: "#/components/schemas/SimilarMetaboliteConcentration"
 
-concentration:
-  get:
-    parameters:
-      - in: query
-        name: abstract
-        schema:
-          type: boolean
-        required: false
-      - in: query
-        name: species
-        schema:
-          type: string
-          default: Escherichia coli
-        required: false
-      - in: query
-        name: metabolite
-        schema:
-          type: string
-        required: true
-    tags:
-      - Metabolites
-      - Concentration
-    summary: Get metabolite concentration based on species and metabolite name
-    description: Some description
-    responses:
-      "200":
-        description: OK
-        content:
-          application/json:
-            schema:
-              $ref: "#/components/schemas/MetaboliteConcentration"
-
 num_conc:
   get:
     tags:

diff --git a/datanator_rest_api/spec/root.yaml b/datanator_rest_api/spec/root.yaml
@@ -67,8 +67,6 @@ paths:
     $ref: paths/metabolites.yaml#/get_distinct
   /metabolites/meta/:
     $ref: paths/metabolites.yaml#/meta
-  /metabolites/concentration/:
-    $ref: paths/metabolites.yaml#/concentration
   /metabolites/concentration_only/:
     $ref: paths/metabolites.yaml#/concentration_only
   /proteins/precise_abundance/:

diff --git a/nginx/default.conf b/nginx/default.conf
@@ -30,6 +30,11 @@ http {
     client_max_body_size 4G;
     keepalive_timeout 5;
 
+    gzip on;
+    gzip_types      text/plain application/xml text/html;
+    gzip_proxied    no-cache no-store private expired auth;
+    gzip_min_length 1000;
+
     location / {      
       proxy_pass          http://127.0.0.1:8001;
       proxy_http_version  1.1;

diff --git a/tests/routes/test_metabolites.py b/tests/routes/test_metabolites.py
@@ -14,13 +14,6 @@ def setUp(self):
             "datanator_rest_api.routes"), validate_responses=True)
         self.client = self.app.app.test_client()
         self.client.testing = True
-
-    @unittest.skip('need front_end_query to be fixed')
-    def test_concentration(self):
-        result_1 = self.client.get("/metabolites/concentration/?species=homo sapiens&metabolite=atp")
-        dic_1 = json.loads(result_1.data)
-        self.assertEqual(result_1.status_code, 200)
-        self.assertTrue('concentrations' in dic_1[0][0])
 
     # def test_get(self):
     #     result_0 = json.loads(self.client.get('/metabolites/?inchi_key=test_inchi_key').data)