Wait for an output readiness before downloading it. Fails if download…

[pkrog]

…ed file is empty.

I've added these lines in order to be on the safe side. Tell me if the "file empty" test could cause issues with some workflow test. Maybe we can make it an option on the command line or better: test if an expected output is also empty.

[ilveroluca]

Hi @pierrickrogermele. An error on an empty file wouldn't work in the general case. It's plausible that some tools may in some cases generate an empty dataset.

Has the addition of output.wait() solved the issue for you?

[pkrog]

Unfortunately the error disappeared. I can't see it anymore. However, in order to be on the safe side, I was looking for some improvements. I don't think output.wait() can do any harm, so better call it than not call it, I guess. About the file size, I will add a check on the expected output (if it's also empty or not). Is it ok with you?

[pkrog]

Hi @ilveroluca , There has been a failure with python 3.6 tests:

Installing dependencies
fetch http://dl-cdn.alpinelinux.org/alpine/v3.6/main/x86_64/APKINDEX.tar.gz
ERROR: http://dl-cdn.alpinelinux.org/alpine/v3.6/main: IO ERROR
WARNING: Ignoring APKINDEX.84815163.tar.gz: No such file or directory
fetch http://dl-cdn.alpinelinux.org/alpine/v3.6/community/x86_64/APKINDEX.tar.gz
v3.6.1-4-g94d0fc53b2 [http://dl-cdn.alpinelinux.org/alpine/v3.6/community]
1 errors; 2891 distinct packages available
The command '/bin/sh -c echo "Installing dependencies" >&2     && apk update && apk add         build-base         gcc         make         git         py-pip         bash         python         py-setuptools         python-dev         py-lxml     && pip install --upgrade pip     && echo "Cloning wft4galaxy: branch=${WFT4GALAXY_BRANCH} url=${WFT4GALAXY_REPOSITORY_URL}" >&2     && git clone --single-branch --depth 1 -b ${WFT4GALAXY_BRANCH} ${WFT4GALAXY_REPOSITORY_URL} ${WFT4GALAXY_PATH}     && cd ${WFT4GALAXY_PATH}     && pip install -r requirements.txt     && echo "Building and installing wft4galaxy" >&2     && python setup.py install     && echo "Removing build-time dependencies" >&2     && apk del         build-base         gcc         make         git         py-pip         python-dev     && rm -rf ${WFT4GALAXY_PATH}     && rm -rf /var/cache/apk/*' returned a non-zero code: 1
CMD: ./wft4galaxy-docker --repository crs4/wft4galaxy --skip-update  --tag feature-output-download-check --network galaxy --server http://172.18.0.22 --api-key 172d1ecbe8f98cf889166e5431ad675f -f examples/change_case/workflow-test.yml
Unable to find image 'crs4/wft4galaxy:feature-output-download-check' locally
Pulling repository docker.io/crs4/wft4galaxy
docker: Tag feature-output-download-check not found in repository docker.io/crs4/wft4galaxy.
See 'docker run --help'.
Test failed (exit code: 125
The command "tests/docker/run-all.sh --branch ${branch} --server ${GALAXY_URL} --api-key ${GALAXY_API_KEY} --network ${GALAXY_NETWORK}" exited with 125.

Any idea about the reason?

[kikkomep]

Hi @pierrickrogermele. The failure was because your feature branch was not rebased wrt the latest version of the develop branch.