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Fixed failing gatk-nightly Docker builds. #5759

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Merged
merged 7 commits into from
Mar 7, 2019
Merged

Fixed failing gatk-nightly Docker builds. #5759

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0236eb2
Changed the travis cron job configuration to support uploading prebui…
jamesemery Mar 5, 2019
b18d937
responded to comments
jamesemery Mar 5, 2019
e464b16
removing the sudo
jamesemery Mar 6, 2019
f7da4eb
trying something that should hopefully fail for the sake
jamesemery Mar 7, 2019
7524e0b
travis.yml not being parsable
jamesemery Mar 7, 2019
e123081
i hate travis .yml
jamesemery Mar 7, 2019
ca1f92d
moved the task so it will properly fail if there is a problem uploadi…
jamesemery Mar 7, 2019
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16 changes: 12 additions & 4 deletions .travis.yml
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Expand Up @@ -175,16 +175,24 @@ after_success:
fi;

# This creates and uploads the gatk zip file to the nightly build bucket, only keeping the 10 newest entries
# This also pokes the Dockerhub web api which is securely stored in the travis API with the variable "DOCKERHUB_URL"
# This also constructs the Docker image and uploads it to https://cloud.docker.com/u/broadinstitute/repository/docker/broadinstitute/gatk-nightly/
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Can we mention the nightly dockerhub repo in our README (if we don't already)?

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Its already mentioned. I added a line about the nightly zip folder in there.

- if [[ $TRAVIS_BRANCH == master && $TRAVIS_EVENT_TYPE == cron && $UPLOAD == true ]]; then
docker login --username=$DOCKER_SERVICE_LOGIN --password=$DOCKER_SERVICE_PASS;
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Are the values of these variables properly secured in travis?

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Yes, if you go into settings on travis you can see them. There is no way to extract the plaintext for the password (louis entered the username as unsecured). Furthermore perusing the logs it doesn't expose it when I type that command. Travis internally hides these variable names from the logs through some magic as well.

$GCLOUD_HOME/gcloud components -q update gsutil;
gsutil ls -l gs://gatk-nightly-builds | grep gatk | sort -r -k 2 | grep -o '\S\+$' | tail -n +11 | xargs -I {} gsutil rm {};
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Do we currently mention the gs://gatk-nightly-builds bucket anywhere in our README? If not can we mention it?

./gradlew bundle;
ZIP_FILE="$(ls build/ | grep .zip)";
ZIP_FILE="$(ls build/ | grep SNAPSHOT.zip)";
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I think this grep will fail if we happen to be on a commit in master with a tag (eg., we are on version 4.1.0.0 exactly). Can you just grep for a zip file that starts with "gatk" instead?

echo "Uploading zip to gs://gatk-nightly-builds/";
$GCLOUD_HOME/gsutil -m cp build/$ZIP_FILE gs://gatk-nightly-builds/"$(date +%Y-%m-%d)"-$ZIP_FILE;
echo "Triggering an automatic build on dockerhub";
curl -H "Content-Type:application/json" --data '{"build":true}' -X POST ${DOCKERHUB_URL};

sudo bash build_docker.sh -e ${TRAVIS_COMMIT} -s -u;
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Does this need to be run as root? If not, can you change this?

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Also, should you be specifying a staging dir via -d, or did you deliberately want to use the working dir?

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The working dir in this case saves us having to pull from lfs again. The travis environment is also essentially an untouched gatk repo at this point anyway.

DOCKER_TAG=$(docker images -q | head -n 1);
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Is this guaranteed to be in the right order?

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Yes. It only builds one docker image on this machine (it will have downloaded the base image but its in descending order by newest)

DATE=`date +%Y-%m-%d`;
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Be consistent in your command substitution convention (backticks vs. $() )

DOCKER_UPLOAD=broadinstitute/gatk-nightly:$DATE-$(git describe)-SNAPSHOT;
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Perhaps this should end in -NIGHTLY-SNAPSHOT?

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Also, rename DOCKER_UPLOAD to DOCKER_NIGHTLY_TAG

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Okay, its inconsistent with the previous syntax but only a handful of people use these so its probably fine chaning things up


echo "Pushing Docker image";
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Pushing nightly docker image

docker tag $DOCKER_TAG $DOCKER_UPLOAD;
docker push $DOCKER_UPLOAD;
fi;
after_failure:
- dmesg | tail -100
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4 changes: 0 additions & 4 deletions hooks/README.md
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4 changes: 0 additions & 4 deletions hooks/post_checkout
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19 changes: 0 additions & 19 deletions hooks/post_push
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