Merge branch 'dev' into auth_token_support

.gitignore

@@ -225,3 +225,4 @@ cwl-tes/
 tests/tmp/*
 tests/output/*
 *.modified.yaml
+.netrc

Dockerfile

@@ -0,0 +1,52 @@
+##### BASE IMAGE #####
+FROM ubuntu:16.04
+
+##### METADATA #####
+LABEL base.image="ubuntu:16.04"
+LABEL version="1"
+LABEL software="WES-ELIXIR"
+LABEL software.version="1.0"
+LABEL software.description="Flask microservice implementing the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification."
+LABEL software.website="https://github.com/elixir-europe/WES-ELIXIR"
+LABEL software.documentation="https://github.com/elixir-europe/WES-ELIXIR"
+LABEL software.license="https://github.com/elixir-europe/WES-ELIXIR/blob/master/LICENSE"
+LABEL software.tags="General"
+LABEL maintainer="foivos.gypas@unibas.ch"
+LABEL maintainer.organisation="Biozentrum, University of Basel"
+LABEL maintainer.location="Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland"
+LABEL maintainer.lab="Zavolan Lab"
+LABEL maintainer.license="https://spdx.org/licenses/Apache-2.0"
+
+## install dependencies
+RUN apt-get update \
+  && apt-get install -y build-essential checkinstall libreadline-gplv2-dev libncursesw5-dev libssl-dev libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev zlib1g-dev openssl libffi-dev python3-dev python3-setuptools git wget curl
+
+## install python
+RUN wget https://www.python.org/ftp/python/3.6.0/Python-3.6.0.tar.xz \
+  && tar xJf Python-3.6.0.tar.xz \
+  && cd Python-3.6.0 \
+  && ./configure \
+  && make altinstall \
+  && ln -s /Python-3.6.0/python /usr/local/bin \
+  && cd ../ \
+  && python -m pip install --upgrade pip setuptools wheel virtualenv
+
+COPY ./ $HOME/WES-ELIXIR/
+
+## install WES-ELIXIR and cwl-tes
+#RUN git clone -b dockerize_app https://github.com/elixir-europe/WES-ELIXIR.git \
+
+RUN cd WES-ELIXIR \
+  && git clone https://github.com/common-workflow-language/cwl-tes.git \
+  && cd cwl-tes \
+  && git checkout ftp \
+  && git checkout ab58d1822a027eff2a456db9d712f5295ac42eac \
+  && python setup.py install \
+  && cd .. \
+  && pip install -r requirements.txt \
+  && python setup.py develop \
+  && cd ../
+
+ENV WES_CONFIG="/WES-ELIXIR/wes_elixir/config/app_config.yaml"
+
+COPY .netrc /root

docker-compose.yaml

@@ -0,0 +1,59 @@
+version: '3.6'
+services:
+
+  # nginx:
+  #   image: nginx:latest
+  #   restart: always
+  #   ports:
+  #     - "443:443"
+  #   links:
+  #     - wes-elixir
+  #   volumes:
+  #     - /docker/nginx/etc/ssl/:/etc/ssl/
+  #     - /docker/nginx/etc/nginx/conf.d/:/etc/nginx/conf.d
+
+  wes-elixir-celery:
+    image: wes-elixir:latest
+    build:
+      context: .
+      dockerfile: Dockerfile
+    restart: always
+    links:
+      - rabbit1
+    command: bash -c "cd /WES-ELIXIR/wes_elixir; celery worker -A celery_worker -E --loglevel=info"
+    volumes:
+      - ../data/tests:/WES-ELIXIR/tests
+
+
+  wes-elixir:
+    image: wes-elixir:latest
+    build:
+      context: .
+      dockerfile: Dockerfile
+    restart: always
+    ports:
+      - "7777:7777"
+    links:
+      - mongo
+    command: bash -c "cd /WES-ELIXIR/; python wes_elixir/app.py"
+    volumes:
+      - ../data/tests:/WES-ELIXIR/tests
+
+  rabbit1:
+    image: "rabbitmq:3-management"
+    hostname: "rabbit1"
+    ports:
+      - "15672:15672"
+      - "5672:5672"
+    links:
+      - mongo
+
+  mongo:
+    image: mongo:3.2
+    restart: always
+    ports:
+      - "27017:27017"
+    expose:
+      - "27017"
+    volumes:
+      - ../data/db:/data/db

requirements.txt

@@ -1,35 +1,65 @@
 amqp==2.3.2
 asn1crypto==0.24.0
 astroid==2.0.4
+attrs==18.2.0
+avro-cwl==1.8.4
+bagit==1.7.0
 billiard==3.5.0.4
+CacheControl==0.11.7
 celery==4.2.1
+certifi==2018.8.24
 cffi==1.11.5
+chardet==3.0.4
 click==6.7
 clickclick==1.2.2
 connexion==1.5.2
 cryptography==2.3.1
+decorator==4.3.0
 Flask==1.0.2
 Flask-Cors==3.0.6
 Flask-PyMongo==2.1.0
+future==0.16.0
 idna==2.7
 inflection==0.3.1
+isodate==0.6.0
 isort==4.3.4
 itsdangerous==0.24
 Jinja2==2.10
 jsonschema==2.6.0
 kombu==4.2.1
 lazy-object-proxy==1.3.1
+lockfile==0.12.2
+lxml==4.2.5
 MarkupSafe==1.0
 mccabe==0.6.1
+mistune==0.7.4
+mypy-extensions==0.4.1
+networkx==2.2
+prov==1.5.1
+psutil==5.4.7
+py-tes==0.2.1
 pycparser==2.19
 PyJWT==1.6.4
 pylint==2.1.1
 pymongo==3.7.1
+pyparsing==2.2.1
+python-dateutil==2.6.1
 pytz==2018.5
 PyYAML==3.13
+rdflib==4.2.2
+rdflib-jsonld==0.4.0
+requests==2.19.1
+ruamel.yaml==0.15.66
+scandir==1.9.0
+schema-salad==2.7.20180905124720
+shellescape==3.4.1
 six==1.11.0
+subprocess32==3.5.2
 swagger-spec-validator==2.3.1
 typed-ast==1.1.0
+typing==3.6.6
+typing-extensions==3.6.5
+urllib3==1.23
 vine==1.1.4
 Werkzeug==0.14.1
 wrapt==1.10.11

wes_elixir/app.py

@@ -41,9 +41,10 @@ def main():
 
     # Run app
     connexion_app.run(
+        host='0.0.0.0',
         use_reloader=get_conf(config, 'server', 'use_reloader')
     )
 
 
 if __name__ == '__main__':
-    main()
+    main()

wes_elixir/config/app_config.yaml

@@ -1,6 +1,6 @@
 # General server/service settings
 server:
-    host: localhost
+    host: '0.0.0.0'
     port: 7777
     debug: True
     environment: development
@@ -28,7 +28,7 @@ security:
 
 # Database settings
 database:
-    host: 'localhost'
+    host: 'mongo'
     port: 27017
     name: wes-elixir-db
     run_id:

wes_elixir/ga4gh/wes/utils_runs.py

@@ -128,6 +128,7 @@ def get_run_status(config, run_id, *args, **kwargs):
     collection_runs = get_conf(config, 'database', 'collections', 'runs')
 
     # Get document from database
+
     document = collection_runs.find_one(
         filter={'run_id': run_id},
         projection={
@@ -234,7 +235,7 @@ def run_workflow(config, form_data, *args, **kwargs):
     __run_workflow(config=config, document=document, **kwargs)
 
     # Build formatted response object
-    response = {"run_id": document['run_id']} 
+    response = {"run_id": document['run_id']}
 
     # Return response object
     return response
@@ -282,7 +283,7 @@ def __validate_run_workflow_request(data):
     #   required = False
     # workflow_url:
     #   type = str
-    #   required = True 
+    #   required = True
     # workflow_attachment:
     #   type = [str]
     #   required = False