Merge pull request #5 from OpenKBC/dev-branch

Version up

README.md

@@ -9,15 +9,17 @@
 * Current version has a problem with CSRF token. If you have BAD REQUEST error, click refresh button on your browser(Sorry!)
 
 ### Version history (Development phase)
+* version(v1.0.4) Updated log process
+* version(v1.0.3) bug fix
 * version(v1.0.2) docker-compose
-* version(v1.0.1) imported celery-redis for workers and communication
-* version(v1.0.0) does not have loading spinner, please wait for browser spinne instead of it
+* version(v1.0.1) imported celery-redis for workers and communication, loading spinner
+* version(v1.0.0) Initial launch
 
 ### Requirements
 - The controller should be located to same root folder with pipeline folders
 - All pipelines should have same snakefile name(Snakemake) and configuration(config.yaml)
 - Don't change Dockerfile in pipelines
-- Requirements of pipeline(requirements.txt) needs to be copied to pipelines/ folder
+- Requirements of pipeline(requirements.txt) needs to be copied to pipelines/ folder(copy to requirements.txt inside pipelines/ folder)
 - Structure example:
 ```
 (root)

docker-compose.yaml

@@ -12,7 +12,7 @@ services:
     depends_on:
       - redis
     working_dir: /pipeline_controller
-    command: conda run -n pipeline_controller_base gunicorn --bind 0.0.0.0:5000 --workers 2 --threads 4 --worker-class gthread connector:app
+    command: conda run -vv -n pipeline_controller_base gunicorn --bind 0.0.0.0:5000 --workers 2 --threads 4 --worker-class gthread connector:app
     #command: tail -f /dev/null #(Testing purpose)
     container_name: snakemakeController
 
@@ -35,7 +35,7 @@ services:
         limits:
           memory: 8000m
     working_dir: /pipeline_controller
-    command: conda run -n pipeline_controller_base celery -A app.celery worker --loglevel=info
+    command: conda run -vv -n pipeline_controller_base celery -A app.celery worker --loglevel=info
     #command: tail -f /dev/null #(Testing purpose)
     depends_on:
       - redis

pipelines/Dockerfile

@@ -1,4 +1,4 @@
-FROM swiri021/snakemake-gui-controller:v1.0.3
+FROM swiri021/snakemake-gui-controller:v1.0.4
 
 COPY . .
 RUN pip install -r requirements.txt

pipelines/test-pipeline-1/import_files/put_string.py

@@ -1,8 +1,12 @@
 from sys import argv
 import pandas as pd
+import time
 
 count_start = 0
 with open(argv[1], "r") as f:
     data = f.read()
+
+time.sleep(3)
+
 with open(argv[2], "w") as rw:
     rw.write(data+("-this is test result"))

pipelines/test-pipeline-1/import_files/sum.py

@@ -1,9 +1,12 @@
 from sys import argv
+import time
 
 count_start = 0
 with open(argv[1], "r") as f:
     for line in f.readlines():
         count_start+=int(line)
 
+time.sleep(3)
+
 with open(argv[2], "w") as rw:
     rw.write(str(count_start))