Merge pull request #523 from NBISweden/feature/postgres-database

Feature/postgres database

.gitignore

@@ -15,3 +15,13 @@ tornado/static/js/app.min.js
 backend/static
 backend/templates
 static
+# importer and config stuff
+mysql-data*
+scripts/importer/downloaded_files
+# docker stuff
+postgres-data
+# local personal things
+personal
+# travis test remnants
+master-schema.sql
+settings.json.tmp

.travis.yml

@@ -10,3 +10,8 @@ install:
     - pip install coverage coveralls
 script:
     - test/travis_script.sh
+addons:
+  postgresql: "10"
+  apt:
+    packages:
+    - postgresql-client-10

Dockerfile-backend

@@ -1,13 +1,14 @@
-FROM ubuntu:16.04
+FROM ubuntu:18.04
 
 RUN apt-get update && apt-get install -y \
         python3 \
-        python3-pip \
-        libmysqlclient-dev
+        python3-pip
 
 ADD . /code
+COPY settings_sample.json /settings.json
+RUN sed -i 's/"postgresHost"\s*:.*,/"postgresHost" : "db",/' /settings.json
 WORKDIR /code
 
 RUN pip3 install -r backend/requirements.txt
 
-CMD ["python3", "backend/route.py", "--develop"]
+CMD ["python3", "backend/route.py", "--develop", "--settings_file", "/settings.json"]

Dockerfile-database

@@ -0,0 +1,6 @@
+FROM postgres:10
+
+ENV POSTGRES_DB swefreq
+COPY sql/data_schema.sql /docker-entrypoint-initdb.d/01_data_schema.sql
+COPY sql/user_schema.sql /docker-entrypoint-initdb.d/02_user_schema.sql
+COPY sql/beacon_schema.sql /docker-entrypoint-initdb.d/03_beacon_schema.sql

Dockerfile-frontend-rebuilder

@@ -1,4 +1,4 @@
-FROM ubuntu:16.04
+FROM ubuntu:18.04
 
 RUN apt-get update && \
     apt-get install -y \
@@ -7,12 +7,12 @@ RUN apt-get update && \
         python3 \
         python3-pip \
         python3-pyinotify \
-        inotify-tools \
-        libmysqlclient-dev && \
+        inotify-tools && \
     update-alternatives --install /usr/bin/python python /usr/bin/python3 5
 
-RUN curl -sL https://deb.nodesource.com/setup_6.x | bash - && \
-    apt-get install -y nodejs
+RUN apt-get install -y \
+        nodejs \
+        npm
 
 ADD . /code
 WORKDIR /code

backend/application.py

@@ -259,7 +259,7 @@ def get(self, dataset, version=None):
         for f in dataset_version.files:
             d = db.build_dict_from_row(f)
             d['dirname'] = path.dirname(d['uri'])
-            d['human_size'] = format_bytes(d['bytes'])
+            d['human_size'] = format_bytes(d['file_size'])
             ret.append(d)
 
         self.finish({'files': ret})
@@ -576,7 +576,7 @@ def get(self, dataset):
             return
 
         self.set_header("Content-Type", logo_entry.mimetype)
-        self.write(logo_entry.data)
+        self.write(logo_entry.data.tobytes())
         self.finish()