Merge branch '91-browse-page-gene-list' into 'dev'

Browse trough pages on gene list

Closes #91

See merge request !51

.gitlab-ci.yml

@@ -40,10 +40,13 @@ test-backend:
   image: $CI_REGISTRY_IMAGE/backend:${CI_COMMIT_REF_NAME}
   services:
     - postgres:11.4
+    - redis:alpine
   stage: test
   variables:
     DATABASE_HOST: localhost
     DJANGO_SETTINGS_MODULE: "metagenedb.settings-gitlab-ci"
+    REDIS_HOST: "localhost"
+    CACHE_TTL: "0"
   script:
     - apt-get install -y postgresql-client
     - cd backend

backend/metagenedb/common/django_default/pagination.py

 from rest_framework.pagination import PageNumberPagination
 
+from metagenedb.common.django_default.paginator import CachedCountPaginator
+
 
 class DefaultPageNumberPagination(PageNumberPagination):
+    django_paginator_class = CachedCountPaginator
     page_size_query_param = 'page_size'
     max_page_size = 5000

backend/metagenedb/common/django_default/paginator.py

+import hashlib
+import inspect
+
+from django.conf import settings
+from django.core.cache import cache
+from django.core.cache.backends.base import DEFAULT_TIMEOUT
+from django.core.paginator import Paginator
+from django.utils.functional import cached_property
+from django.utils.inspect import method_has_no_args
+
+
+CACHE_TTL = getattr(settings, 'CACHE_TTL', DEFAULT_TIMEOUT)
+
+
+class CachedCountPaginator(Paginator):
+
+    @cached_property
+    def count(self):
+        """Return the total number of objects, across all pages."""
+        # Create has from SQL query for REDIS cache
+        hash_object = hashlib.md5(str(self.object_list.query).encode('utf-8'))
+        redis_key = hash_object.hexdigest()
+        if redis_key in cache:
+            return cache.get(redis_key)
+        else:
+            c = getattr(self.object_list, 'count', None)
+            if callable(c) and not inspect.isbuiltin(c) and method_has_no_args(c):
+                count = c()
+            else:
+                count = len(self.object_list)
+            cache.set(redis_key, count, timeout=CACHE_TTL)
+            return count

backend/metagenedb/settings/celery.py

@@ -21,6 +21,8 @@ CACHES = {
         "OPTIONS": {
             "CLIENT_CLASS": "django_redis.client.DefaultClient"
         },
-        "KEY_PREFIX": "example"
+        "KEY_PREFIX": "metagenedb"
     }
 }
+# Time in seconds for
+CACHE_TTL = int(os.getenv('CACHE_TTL', 600))

ci/deploy/deploy.sh

@@ -21,8 +21,8 @@ kubectl create secret generic backend-cron-credentials -n ${NAMESPACE} --from-li
 envsubst < ci/kubernetes/postgresql.yaml | kubectl apply -n ${NAMESPACE} -f -
 kubectl -n ${NAMESPACE} wait --for=condition=available --timeout=600s deployment/postgresql
 ## Redis
-# envsubst < ci/kubernetes/redis.yaml | kubectl apply -n ${NAMESPACE} -f -
-# kubectl -n ${NAMESPACE} wait --for=condition=available --timeout=600s deployment/redis
+envsubst < ci/kubernetes/redis.yaml | kubectl apply -n ${NAMESPACE} -f -
+kubectl -n ${NAMESPACE} wait --for=condition=available --timeout=600s deployment/redis
 ## Backend
 envsubst < ci/kubernetes/backend.yaml | kubectl apply -n ${NAMESPACE} -f -
 kubectl -n ${NAMESPACE} patch deployment backend -p "{\"spec\":{\"template\":{\"metadata\":{\"labels\":{\"date\":\"`date +'%s'`\"}}}}}"

ci/kubernetes/backend.yaml

@@ -45,6 +45,8 @@ spec:
               key: secret_key
         - name: REDIS_HOST
           value: redis
+        - name: REDIS_PORT
+          value: '6379'
         - name: PORT
           value: "8000"
         - name: DEBUG

docker-compose.yaml

@@ -64,6 +64,8 @@ services:
   redis:
     image: redis:alpine
     container_name: redis
+    ports:
+      - "6379:6379"
     networks:
       - main
 

frontend/src/views/genes/genes.html

@@ -179,7 +179,7 @@
               </v-btn>
               <v-btn
                 color="secondary lighten-1"
-                @click="runSearch"
+                @click="runNewSearch"
               >
                 Apply<v-icon right>far fa-check-square</v-icon>
               </v-btn>
@@ -231,8 +231,16 @@
         </template>
       </v-data-table>
       </v-list>
-      <v-card class="white" flat>
-      <v-subheader class="text-right">{{count}} genes found</v-subheader>
+      <v-card flat>
+            <div class="text-xs-center" v-if="count">
+              <v-pagination
+                v-model="pageNumber"
+                :length="pageTotalNumber"
+                :total-visible="7"
+                @input="getGenes"
+              ></v-pagination>
+            </div>
+            <v-subheader>{{count}} genes found</v-subheader>
       </v-card>
     </v-flex>
   </v-layout>

frontend/src/views/genes/genes.js

@@ -7,10 +7,11 @@ export default {
       genes: [],
       count: 0,
       page: 1,
-      page_size: 20,
+      // pagination
       pagination: {
         rowsPerPage: 20,
       },
+      pageNumber: 1,
       // Filters
       // - Gene info
       geneSource: 'all',
@@ -58,7 +59,10 @@ export default {
       return [this.page_size];
     },
     qParams() {
-      const qParams = { page_size: this.page_size };
+      const qParams = {
+        page_size: this.pagination.rowsPerPage,
+        page: this.pageNumber
+      };
       if (this.geneSource && this.geneSource != 'all') {
         qParams.source = this.geneSource
       }
@@ -86,6 +90,12 @@ export default {
     taxChoices() {
       return Object.keys(this.taxItems).sort();
     },
+    pageTotalNumber() {
+      if ((this.count % this.pagination.rowsPerPage) > 0) {
+        return Math.floor(this.count/this.pagination.rowsPerPage) + 1;
+      }
+      return Math.floor(this.count/this.pagination.rowsPerPage);
+    }
   },
   mounted() {
     this.getGenes();
@@ -176,8 +186,9 @@ export default {
       }
       this.getTaxoPresence();
     },
-    runSearch() {
+    runNewSearch() {
       this.requestDone = false;
+      this.pageNumber = 1;
       this.getGenes();
     },
   },