docker fixes

src/DoresA/Dockerfile

@@ -1,7 +1,11 @@
-FROM python:3
-ENV PYTHONUNBUFFERED 1
+FROM python:3.6-alpine
+
+# numpy scipy spellchecking etc
+RUN apk add --no-cache mariadb-dev gcc gfortran musl-dev freetype-dev enchant
+
+#ENV PYTHONUNBUFFERED 1
 RUN mkdir /app
 WORKDIR /app
 ADD requirements.txt /app/
 RUN pip install -r requirements.txt
-ADD . /app/
+VOLUME /app

src/DoresA/db.py

@@ -10,6 +10,7 @@ mongodb_db_name = 'doresa'
 mongodb_collection_name = 'may'  # tmp TODO remove
 
 sql_host = 'localhost'
+sql_port = 3306
 sql_db_name = 'doresa'
 sql_user_name = 'doresa'
 sql_pw = '3qfACEZzbXY4b'
@@ -20,6 +21,9 @@ sql_table_name = 'pdns_logs_test'
 if 'MYSQL_HOST' in os.environ:
     sql_host = os.environ['MYSQL_HOST']
 
+if 'MYSQL_PORT' in os.environ:
+        sql_port = int(os.environ['MYSQL_PORT'])
+
 if 'MYSQL_DATABASE' in os.environ:
     sql_db_name = os.environ['MYSQL_DATABASE']
 
@@ -35,7 +39,7 @@ mongo_db = mongo_client[mongodb_db_name]
 pdns_logs_mongo = mongo_db[mongodb_collection_name]
 
 
-sql_connection = mariadb.connect(host=sql_host, user=sql_user_name, passwd=sql_pw, db=sql_db_name)
+sql_connection = mariadb.connect(host=sql_host, user=sql_user_name, passwd=sql_pw, db=sql_db_name, port=sql_port)
 sql_cursor = sql_connection.cursor()
 
 
@@ -61,7 +65,11 @@ def mariadb_insert_logs(csv_entries):
         values += [convert_timestamp_to_sql_datetime(float(csv_entry[0])), csv_entry[1],
                    csv_entry[2], csv_entry[3], csv_entry[4]]
 
+    try:
         sql_cursor.execute(inserts_sql, values)
+    except mariadb.OperationalError:
+        print('something happened')  # TODO proper error handling
+
     sql_connection.commit()
 
 
@@ -110,7 +118,7 @@ def close():
     mongo_client.close()
 
 
-mariadb_create_table()
+#mariadb_create_table()
 
 if __name__ == "__main__":
     exit()

src/DoresA/docker-compose.yml

@@ -1,10 +1,9 @@
 version: '3'
 
 services:
-  mariadb:
-    container_name: mariadb
+  doresa_mariadb:
+    container_name: doresa_mariadb
     image: mariadb
-    restart: unless-stopped
     ports: 
       - "3306:3306"
     environment:
@@ -13,19 +12,19 @@ services:
       MYSQL_USER: doresa
       MYSQL_PASSWORD: 3qfACEZzbXY4b
   
-  app:
+  doresa_app:
     build: .
-    container_name: app
-    restart: unless-stopped
+    container_name: doresa_app
     command: python3 serialize_logs_to_db.py
     volumes:
       - .:/app
-      - ./data:/data
+      - /media/backup/felix/uni/Mastersthesis/pDNS/2017.05:/data  # path to zipped pDNS logs
     environment:
-      MYSQL_HOST: mariadb
+      MYSQL_HOST: doresa_mariadb
+      MYSQL_PORT: 3306
       MYSQL_DATABASE: doresa
       MYSQL_USER: doresa
       MYSQL_PASSWORD: 3qfACEZzbXY4b
-      DATA_PATH: 
     depends_on:
-      - mariadb
+      - doresa_mariadb
+

src/DoresA/requirements.txt

@@ -2,7 +2,6 @@ maxminddb==1.3.0
 maxminddb-geolite2==2017.803
 mysqlclient==1.3.12
 numpy==1.13.1
-pandas==0.20.3
 progress==1.3
 pyenchant==1.6.11
 pymongo==3.5.1

src/DoresA/serialize_logs_to_db.py

@@ -3,16 +3,16 @@ import gzip
 import glob
 import time
 import datetime
-import pandas
 import os
 from progress.bar import Bar
 
 import db
 
+# TODO environment this
 analysis_start_date = datetime.date(2017, 5, 1)
 analysis_days_amount = 31
 # pdns_logs_path = 'data/'
-pdns_logs_path = '/run/media/felix/ext/2017.05/'  # tmp TODO remove
+pdns_logs_path = '/data/'
 
 # e.g. analysis_days = ['2017-04-07', '2017-04-08', '2017-04-09']
 analysis_days = [(analysis_start_date + datetime.timedelta(days=x)).strftime('%Y-%m-%d') for x in
@@ -38,8 +38,7 @@ def main():
             progress_bar.next()
             # everything[day][hour] = {}
             for hour_files in log_files_hour[hour]:
-
-                # a bit faster
+                # a bit faster, 10-15% (but pandas overhead)
                 # df = pandas.read_csv(log_file, compression='gzip', header=None)
                 # print(df.iloc[0])
                 with gzip.open(hour_files, 'rt', newline='') as file:
@@ -49,7 +48,7 @@ def main():
                     # batch mode (batches of 1000 entries)
                     for log_entries in batch(all_rows, 1000):
                         db.mariadb_insert_logs(log_entries)
-                        db.mongodb_insert_logs(log_entries)
+                        #db.mongodb_insert_logs(log_entries)
 
                         # single mode
                         # for log_entry in reader: