Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
-
Story Points:0.5
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Epic Link:
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Sprint:Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct
Description
Our build process for integrated genome browser project is supposed to automatically build topic-branch specific installers for each major platform whenever a developer pushes a commit to a topic branch on their fork. Specifically, if a developer pushes a commit to a branch with a name that includes the string "IGBF" (e.g., IGBF-3001-Make-Me-A-Sandwich), a new installer named for the branch is supposed to get built and copied to the fork's Downloads section.
This is configured using the file "bitbucket_pipelines.yml" at the top-level of the IGB repository.
A few months ago, we made some improvements to the build process - see commit history on this file for details.
However, something about those improvements has broken the installer build. When something gets pushed, installers are indeed getting built, but the branch-specific pipeline does not appear to be getting triggered.
For this task, please look into why the topic branch build pipeline is not running as expected. First, confirm that this bug can be reproduced by creating an "IGBF" branch and pushing to your fork.
(Both Srishti Tiwari and myself ([~aloraine]) have observed this.)
Attachments
Activity
| Workflow | Fall 2019 Workflow Update [ 20784 ] | Revised Fall 2019 Workflow Update [ 22523 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | To-Do [ 10305 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Sure ma'am.
Submitted a PR for the same.
https://bitbucket.org/pkulka10/igb_prutha/pull-requests/1/igbf-2027-fix-branch-specific-installer/diff
Could you please merge it into the master?
Thanks.
I'm stumped.
Do you want to try this instead?
1) Use bitbucket web site GUI to create a branch from latest master (after updating fork)
2) Use the on-line editor to make the single edit (fix typo) on that branch
3) Submit a PR from that branch to master
I tried using eduroam as well as NCRCGuest. Still facing the same problem.
Maybe check the network you are using to connect? A lot of wifi networks block ssh for some reason. Eduroam should work OK.
There is some problem with my fork. It is not letting me push my commit to the origin repo. It is saying "Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
"
even when the ssh-keys are added.
I am not sure why this is happening.
Prof. [~aloraine] I wanted to know if you have any idea about it?
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Ann Loraine [ aloraine ] | Prutha Kulkarni [ prutha ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
I'm not sure why, but your most recently PR for IGBF-2027 is showing up as "DECLINED" when I visit it in Bitbucket.
Request:
Can you make edit the branch so that it only has one commit - fixing the typo - and then submit a new PR? Or, you could create an all-new branch.
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Steps for testing:
1) Go to "Branches" section of my fork:
https://bitbucket.org/pkulka10/igb_prutha/
2) Click on the "..." on the end of IGBF-2027 branch.
3) Select "Run pipeline for a branch".
4) Select "IGBF-*" pipeline configuration.
5) Once the pipeline is built successfully, check the downloads section for the branch specific installers.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
Prof. [~aloraine], I checked the configuration code for the same and found out that there was a typo in the branch configuration section.
It had "IBGF-" instead of "IGBF-" so, I fixed it and tried to trigger the pipeline build.
It is failing due to some error which says: install4j: compilation failed. Reason: java.io.FileNotFoundException: Could not find JRE bundle. Neither /opt/install4j7/jres/windows-amd64-1.8.0_212.tar.gz nor /root/.install4j7/jres/windows-amd64-1.8.0_212.tar.gz nor /opt/atlassian/pipelines/agent/build/distribution/windows-amd64-1.8.0_212.tar.gz exist.
Have you encountered anything like this before?
Branch code:
https://bitbucket.org/pkulka10/igb_prutha/src/IGBF-2027
| Rank | Ranked higher |
| Sprint | Fall 2019 Sprint 3 [ 74 ] | Fall 2019 Sprint 3, Fall 2019 Sprint 4 [ 74, 75 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Ann Loraine [ aloraine ] | Prutha Kulkarni [ prutha ] |
| Description |
Our build process for integrated genome browser project is supposed to automatically build topic-branch specific installers for each major platform whenever a developer pushes a commit to a topic branch on their fork. Specifically, if a developer pushes a commit to a branch with a name that includes the string "IGBF" (e.g., This is configured using the file "bitbucket_pipelines.yml" at the top-level of the IGB repository. A few months ago, we made some improvements to the build process - see commit history on this file for details. However, something about those improvements has broken the installer build. When something gets pushed, installers are indeed getting built, but the branch-specific pipeline does not appear to be getting triggered. For this task, please look into why the topic branch build pipeline is not running as expected. First, confirm that this bug can be reproduced by creating an "IGBF" branch and pushing to your fork. (Both [~stiwari8] and myself ([~aloraine]) have observed this.) |
Our build process for integrated genome browser project is supposed to automatically build topic-branch specific installers for each major platform whenever a developer pushes a commit to a topic branch on their fork. Specifically, if a developer pushes a commit to a branch with a name that includes the string "IGBF" (e.g., This is configured using the file "bitbucket_pipelines.yml" at the top-level of the IGB repository. A few months ago, we made some improvements to the build process - see commit history on this file for details. However, something about those improvements has broken the installer build. When something gets pushed, installers are indeed getting built, but the branch-specific pipeline does not appear to be getting triggered. For this task, please look into why the topic branch build pipeline is not running as expected. First, confirm that this bug can be reproduced by creating an "IGBF" branch and pushing to your fork. (Both [~stiwari8] and myself ([~aloraine]) have observed this.) |
| Status | Open [ 1 ] | To-Do [ 10305 ] |
| Rank | Ranked higher |
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1531 [ 17617 ] |
Prof. [~aloraine], please refer the new link mentioned below for the updated PR:
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/733/igbf-2027-fix-branch-specific-installer/diff