Note to implementer:

• Sign up for a free account at Docker Hub
• Ask Dr. Loraine to add your user to "installer" team within lorainelab organization

Prof. [~aloraine], could you please add 'pkulka10' to "installer" team within lorainelab organization?
Thanks.

Updates:
1) I have cloned and created a new branch for both genoviz-sdk & integrated-genome-browser-docker.
2) I have currently packed settings.xml file in the docker image.
3) Deployed the image on my docker-hub account repo.
4) Changed the image name to new image name in the bitbucket configuration file for genoviz-sdk.
5) Tried to build it normally just to check if there are any problems with the image which is newly built.
6) The build was successful.
7) Added environment variables for username and password in order to pass them as a command line argument.
8) Tried to incorporate maven deploy command in the bitbucket pipeline configuration file.

Results: It was failing to build the pipeline because of the maven deploy command.

Course of action:
1) I'll try to follow the steps which are mentioned on:
https://stackoverflow.com/questions/24830610/why-am-i-getting-a-401-unauthorized-error-in-maven
as the person was facing the same problem.
2) I will also try to post any local file to the test nexus repository just to make sure that there is no problem from repository side like access rights so that if we missed out on something then we could add it accordingly.
4) I will try to follow the same steps on local a project.

Questions:

• Are you able to use the credentials provided (separately) to log in to the nexus repository site?
• If you are able to do the above, can you use the Nexus Web UI to upload an artifact to the test repository?

If the answer to either of the above questions is "no" then it is possible the user created for your testing does not have the correct permissions set. If yes, please let me know and I will investigate.

Prof. [~aloraine], Yeah I was able to login into nexus repo.
I will try to upload an artifact manually and will let you know if that works out.

Prof. [~aloraine], there is nothing wrong with the credentials as I am able to login to the NEXUS repo.
But, when I am trying to upload any artifact, it is not allowing me to do so.
I have tried using the CURL command as well as mvn deploy command.
Below are the commands which were used to upload an artifact.
mvn deploy:deploy-file -DgeneratePom=false -DrepositoryId=nexus -Durl=https://nexus.bioviz.org/repository/test-maven2 -DpomFile=pom.xml -Dfile=target/genoviz-1.1.8.jar
curl -v -u pruthakulkarni:ndorwaedleo5883 --upload-file pom.xml https://nexus.bioviz.org/repository/test-maven2
Do you have any idea about it?

Probably the permissions are not properly set for your Nexus user. I would suggest setting this aside and helping with testing tasks for the rest of the day. (I won't be able to look at the permissions until later.)

Sure. I will go ahead and start testing a few tickets for today.

Prutha Kulkarni you should now be able to upload artifacts to test-maven2 repository. (I reconfigured permissions.) To test this, log in. You should now see an "upload" link on the left side of the page in "Browser Server Contents" view.

Updates:
I tried to upload artifacts using my local setup and the attempt was successful. When I tried to do the same this on my clone in bitbucket, the build was failing. I figured that the build is not picking up our customised settings.xml file so, I changed the docker image file a bit again and this time I copied the settings.xml to "/root/.m2/" instead of "/usr/share/maven/ref" folder to make settings.xml file accessible to all maven commands that are available in the bitbucket pipeline file. And the attempt was successful. Now we can deploy the artifacts to nexus repository with the help of bitbucket pipelines.

Steps taken:
1) Cloned my branch of integrated-genome-browser-docker to the local system.
2) Install docker application on system and started the docker daemon.
3) Logged into the docker hub and created one repository and given access of bitbucket to the repository.
4) Built the docker image using command :
"docker build -t pkula10/jre-1.8.0_212-mvn-deploy ."
5) Logged in to the docker hub with docker hub credentials using following command : "docker login iindex.docker.io"
6) Pushed the docker image to my account repository using following command:
"docker push pkula10/jre-1.8.0_212-mvn-deploy"
7) customized "distributionManagement" section in the parent pom of "genoviz sdk" project with :
id : test-maven2
name: test-maven2
url: https://nexus.bioviz.org/repository/test-maven2
8) Updated docker image in the bitbucket pipeline file.
9) Added custom pipeline for the mvn deploy command which refers our custom settings.xml.
Also, for this added two environment variables for the credentials of nexus repo.

The code changes can be found at:
https://bitbucket.org/pkulka10/igb_docker/src/IGBF-1993/
https://bitbucket.org/pkulka10/new_genoviz/src/IGBF-1945/

For testing:
1) Go to the Branches section of my fork and click on the "..." present at the end of IGBF-1945 branch row.
2) Click on Run pipeline for a branch option and select custom pipeline "deployToNEXUSRepo".
3) Click on Run and wait for the pipeline to build.
4) After the build you can log into my https://nexus.bioviz.org/ account
Please ask the credentials whenever you are testing it.
5) Go to test-maven2 repository. you will find the uploaded artifact directory there.
You can also compare the content of the directory of maven-release repository with the test-maven2 repository just to be sure if the artifact is uploaded properly.

Note: The image value is changed in bitbucket pipeline for genoviz sdk and it is pointing to the latest docker image in my account. I have changed it for the code review and testing purpose. Let me know once the review is finished. I will change it back to the original one and will submit a pull request for the same.

Prof. [~aloraine], I have made the changed that were suggested by you.
Please check the latest commits for the same.
Links are given below:
https://bitbucket.org/pkulka10/igb_docker/commits/9564f6e05be82e895c80b59f0a5c88b9c65d739b
https://bitbucket.org/pkulka10/new_genoviz/commits/4d2ad88ea59022ed65b29dc221d8323190beefc6

Thank you Prutha Kulkarni!

When you get a moment, please push the newest Docker image to the LoraineLab Team Docker Hub account.

HOWEVER - please be careful! The Loraine Lab production image needs two coordinates: image name AND tag. In your Docker Hub account (pkula10), you are not using using tags. For production, however, we need BOTH*.

To publish the Docker image to the production Docker Hub account, you need to push to

• https://cloud.docker.com/u/lorainelab/repository/docker/lorainelab/igb-maven-install4j

using this command (from above):

• docker push lorainelab/igb-maven-install4j:tagname

With "tagname" as "jre-1.8.0-212-mvn-deploy"

Note that in the above docker repository, every image has the same name with DIFFERENT tags. This allows us to easily track down JRE-specific errors and other such problems, while also retaining our ability to build older release branches as needed.

This can wait until next week – don't worry about doing this today if you are not in Kannapolis. Take your time and don't rush.

Prof. [~aloraine], I have noted the things mentioned above. Whenever I am in Kannapolis next week, I will push the changes to production docker hub account carefully.
Thanks.

Prof. [~aloraine], I have deployed the latest docker image to lorainlab account with name "lorainelab/igb-maven-install4j:jre-1.8.0-212-mvn-deploy".
Also, I have tested it on my genoviz sdk fork. Since, I was using the changed bitbucket configuration of genoviz sdk to test the changes in the docker image. So I wanted to know if I can submit a pull request for genoviz repository also (with changed docker image name as well as new bitbucket configuration)?
I am confused because we were using its pipeline configuration for testing even though there is a different ticket related to genoviz sdk which is IGBF-1945.
Please let me know the same.

Thank you Prutha Kulkarni

Please submit 2 PRs:

• to genoviz sdk repository (to master)
• to igb docker repository (if not already merged - new settings.xml file and Docker file as required)

Update:

• igb docker PR merged

Prof. [~aloraine], I have also submitted a PR for genoviz sdk.
code changes are present at: https://bitbucket.org/lorainelab/genoviz-sdk/pull-requests/17/igbf-1945/diff

I am able to build Genoviz SDK using the new Docker and configured as in above. The new Docker image appears to be working great. Marking this as "closed".