cwl-conformance-tests.md

DISCLAIMER: CWL conformance testing on REANA is in progress, please ask for clarifications if things go wrong.

Instructions

To run CWL conformance tests on REANA follow the next steps:

1. Install and launch REANA according to instructions

2. Replace the following REANA components with latest images that support CWL execution:

• reana-server

    1. git clone https://github.com/reanahub/reana-server
    2. git checkout reana-cwl-runner
    3. eval $(minikube docker-env)
    4. docker build . -t reana-server:v0.0.1
    5. kubectl get pods 
    6. kubectl delete pods <reana-server-container-id>
 

• reana-workflow-controller

    
    1. git clone https://github.com/anton-khodak/reana-workflow-controller
    2. git checkout reana-cwl-runner
    3. eval $(minikube docker-env)
    4. docker build . -t reana-workflow-controller:v0.0.1
    5. minikube ssh
    6. cd /reana/default
    7. curl https://transfer.sh/x0OfE/reana.db --output reana.db
    8. kubectl get pods 
    9. kubectl delete pods <reana-workflow-controller-container-id

• reana-workflow-engine-cwl

    1. git clone https://github.com/anton-khodak/reana-workflow-engine-cwl
    2. git checkout reana-cwl-runner
    3. eval $(minikube docker-env)
    4. docker build . -t reana-workflow-engine-cwl:v0.0.1

• reana-resources-k8s

   1. git clone https://github.com/anton-khodak/reana-resources-k8s
   2. git checkout cwl-support
   3. cd /path/to/reana-installation
   4. rm -r configuration-manifests
   5. cp /path/to/anton-khodak/reana-resources-k8s/configuration-manifests .
   6. kubectl create -Rf configuration-manifests
  

After these steps cwl-default-worker must be visible in kubectl get pods

3. Checkout reana-client with reana-cwl-runner interface

   • reana-client

    1. git clone https://github.com/anton-khodak/reana-client
    2. git checkout reana-cwl-runner
    3. source /path/to/reana-virtualenv/bin/activate
    4. reana get reana-server // here you get reana-server URL
    5. export REANA_SERVER_URL=server_url_from_previous_step
    6. python setup.py install
    7. cd /path/to/cwltool/cwltool/schemas
    8. ./run_test.sh RUNNER=reana-cwl-runner

Warnings:

• currently, sometimes reana-cwl-runner might not process exceptions from the server right, and tests fall in the infinite loop. If the tool takes a suspiciously long time to execute, terminate the execution and relaunch ./run_test.sh with -n option, specifying the order number of a test following to the failing one. However, if a tool runs first the first time, it will always take time to pull the necessary docker images.

• if reana-cwl-runner cannot reach http host of reana-server, check whether you ran eval $(minikube docker-env) in the shell where minikube was launched

Useful links:

• development instructions for REANA components

Log of my setup on Linux so far

curl -Lo kubectl https://storage.googleapis.com/kubernetes-release/release/v1.8.0/bin/linux/amd64/kubectl && chmod +x kubectl && sudo mv kubectl /usr/local/bin/
curl -Lo minikube https://storage.googleapis.com/minikube/releases/latest/minikube-linux-amd64 && chmod +x minikube && sudo mv minikube /usr/local/bin/
sudo minikube start --vm-driver=none
virtualenv env
. env/bin/activate
pip install \
     -e 'git+https://github.com/reanahub/reana.git@master#egg=reana'
bash env/bin/reana  init

wget https://transfer.sh/x0OfE/reana.db does not work inside the minikube, the busbox wget doesn't support https.