Details
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Type:
Improvement
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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:
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Story Points:4
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Epic Link:
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Sprint:Summer 2019 Sprint 8, Summer 2019 Sprint 9, Summer 2019 Sprint 10, Summer 2019 Sprint 11
Description
Now that we are moving ahead with deploying IGB Apps using the new App Store, let's separate the Apps currently version-controlled and built as part of the integrated-genome-browser platform repository into their own repositories and build systems.
Doing this will make understanding the platform code easier for users (less to look through) and will also allow each App to become a first-class project with independent versioning, build, and distribution system.
Moving the Apps into their own separate repositories will not take long, but once this is done, we need to modify their respective pom.xml files to enable compilation.
Tasks - for each optionalPlugin IGB App:
- Create new repos for each IGB App currently in optionalPlugins
- Re-configure pom.xml to enable local compilation of jar and OBR index file (parent pom no longer available)
- Bundle artifact should include a properties file with last git commit hash, origin repository. Ask NZ for details and/or see related issue below.
Attachments
Issue Links
- relates to
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IGBF-1907 Move developmentPlugins Apps to new repository
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- Closed
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- Closed
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- Closed
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- Closed
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IGBF-1772 Add code repo for current Apps
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- Closed
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1. |
Configure build for new 23andMe SNP Converter app repository |
|
Closed | Prutha Kulkarni (Inactive) | |
2. |
Create repo for Merge Annotation Operator |
|
Closed | Unassigned | |
3. |
Create repo for Command Socket |
|
Closed | Unassigned | |
4. |
Create repo for Geometric Mean Graph Operator |
|
Closed | Prutha Kulkarni (Inactive) | |
5. |
Create repo for ProtAnnot |
|
Closed | Prutha Kulkarni (Inactive) | |
6. |
Figure out how to set up bitbucket pipeline build for App repositories |
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Closed | Unassigned | |
7. |
Assist devs to set up bb pipelines for Apps |
|
Closed | Prutha Kulkarni (Inactive) | |
8. |
Add logos to repositories for each App |
|
Closed | Prutha Kulkarni (Inactive) | |
9. |
Check pipelines and POM for all optional Apps |
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Closed | Unassigned |
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1388 [ 17463 ] |
| Description |
Don't start this without talking to me (Ann).
Tasks: * Create new repos for each IGB App currently in optionalPlugins * Set up bitbucket pipeline for each * Bitbucket pipeline should build the jar and repository.xml for the App and copy to Downloads section |
Review code & related issues then confer with Dr. Loraine for the next steps.
Tasks: * Create new repos for each IGB App currently in optionalPlugins * Set up bitbucket pipeline for each * Bitbucket pipeline should build the jar and repository.xml for the App and copy to Downloads section |
| Sprint | Summer 2019 Sprint 9 [ 68 ] | Summer 2019 Sprint 8 [ 67 ] |
| Rank | Ranked lower |
| Assignee | Ann Loraine [ aloraine ] |
| Rank | Ranked lower |
| Sprint | Summer 2019 Sprint 8 [ 67 ] | Summer 2019 Sprint 9 [ 68 ] |
| Rank | Ranked higher |
| Summary | Create new repositories in bitbucket or github for the optional plugins | Create new repositories in bitbucket for the optional plugins |
How I did this for the 23andMe SNP converter
Step 0: Set-up:
- Created an all-new fork of integrated-genome-browser team repository. This was: https://bitbucket.org/lorainelab/23andme-snp-converter/src/master/
Note: Another developer would need to make their own fork. I recommend not using the one you are using for regular IGB development.
Step 1: Cloned above fork to my local
- git clone git@bitbucket.org:aloraine/for-filtering-optionalplugins.git
Step 2: Inside my local clone, pruned all commits and files except for 23andMe SNP converter code in optionalPlugins
- git filter-branch --prune-empty --subdirectory-filter optionalPlugins/23andMe-snp-converter master
Step 3: Created a new empty repo in bitbucket, renamed origin in my local clone to use the new empty repo
- git remote set-url origin git@bitbucket.org:lorainelab/23andme-snp-converter.git
Note: My bitbucket user can create and configure repositories owned by team lorainelab. Another developer would create the new empty repo under their own account and then later transfer of ownership to lorainelab group to make it the team repository for this App project.
Step 4: Pushed the new master branch to the new origin.
- git push origin master
| Description |
Review code & related issues then confer with Dr. Loraine for the next steps.
Tasks: * Create new repos for each IGB App currently in optionalPlugins * Set up bitbucket pipeline for each * Bitbucket pipeline should build the jar and repository.xml for the App and copy to Downloads section |
Review code & related issues then confer with Dr. Loraine for the next steps.
Tasks: * Create new repos for each IGB App currently in optionalPlugins * Set up bitbucket pipeline for each * Bitbucket pipeline should build the jar and repository.xml for the App and copy to Downloads section * Bundle artifact should include a properties file with last git commit hash, origin repository |
| Story Points | 3 | 2 |
| Story Points | 2 | 4 |
| Description |
Review code & related issues then confer with Dr. Loraine for the next steps.
Tasks: * Create new repos for each IGB App currently in optionalPlugins * Set up bitbucket pipeline for each * Bitbucket pipeline should build the jar and repository.xml for the App and copy to Downloads section * Bundle artifact should include a properties file with last git commit hash, origin repository |
Now that we are moving ahead with deploying IGB Apps using the new App Store, let's separate the Apps currently version-controlled and built as part of the integrated-genome-browser platform repository into their own repositories and build systems.
Doing this will make understanding the platform code easier for users (less to look through) and will also allow each App to become a first-class project with independent versioning, build, and distribution system. Moving the Apps into their own separate repositories will not take long, but once this is done, we need to modify their respective pom.xml files to enable compilation. Tasks: * Create new repos for each IGB App currently in optionalPlugins * Re-configure pom.xml to enable compiling (parent pom no longer available) * Set up bitbucket pipeline - should build the jar and OBR index file, copy both to Downloads section * Bundle artifact should include a properties file with last git commit hash, origin repository |
| Description |
Now that we are moving ahead with deploying IGB Apps using the new App Store, let's separate the Apps currently version-controlled and built as part of the integrated-genome-browser platform repository into their own repositories and build systems.
Doing this will make understanding the platform code easier for users (less to look through) and will also allow each App to become a first-class project with independent versioning, build, and distribution system. Moving the Apps into their own separate repositories will not take long, but once this is done, we need to modify their respective pom.xml files to enable compilation. Tasks: * Create new repos for each IGB App currently in optionalPlugins * Re-configure pom.xml to enable compiling (parent pom no longer available) * Set up bitbucket pipeline - should build the jar and OBR index file, copy both to Downloads section * Bundle artifact should include a properties file with last git commit hash, origin repository |
Now that we are moving ahead with deploying IGB Apps using the new App Store, let's separate the Apps currently version-controlled and built as part of the integrated-genome-browser platform repository into their own repositories and build systems.
Doing this will make understanding the platform code easier for users (less to look through) and will also allow each App to become a first-class project with independent versioning, build, and distribution system. Moving the Apps into their own separate repositories will not take long, but once this is done, we need to modify their respective pom.xml files to enable compilation. Tasks: * Create new repos for each IGB App currently in optionalPlugins * Re-configure pom.xml to enable compiling (parent pom no longer available) * Set up bitbucket pipeline - should build the jar and OBR index file, copy both to Downloads section * Bundle artifact should include a properties file with last git commit hash, origin repository. Ask NZ for details and/or see related issue below. |
Progress thus far:
- Created a new repository for the 23andMe SNP converter as described above.
https://bitbucket.org/lorainelab/23andme-snp-converter/src/master/
| Sprint | Summer 2019 Sprint 9 [ 68 ] | Summer 2019 Sprint 8 [ 67 ] |
| Rank | Ranked lower |
| Sprint | Summer 2019 Sprint 8 [ 67 ] | Summer 2019 Sprint 8, Summer 2019 Sprint 9 [ 67, 68 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Summary | Create new repositories in bitbucket for the optional plugins | Create and configure new repos for optionalPlugins |
| Rank | Ranked higher |
| Description |
Now that we are moving ahead with deploying IGB Apps using the new App Store, let's separate the Apps currently version-controlled and built as part of the integrated-genome-browser platform repository into their own repositories and build systems.
Doing this will make understanding the platform code easier for users (less to look through) and will also allow each App to become a first-class project with independent versioning, build, and distribution system. Moving the Apps into their own separate repositories will not take long, but once this is done, we need to modify their respective pom.xml files to enable compilation. Tasks: * Create new repos for each IGB App currently in optionalPlugins * Re-configure pom.xml to enable compiling (parent pom no longer available) * Set up bitbucket pipeline - should build the jar and OBR index file, copy both to Downloads section * Bundle artifact should include a properties file with last git commit hash, origin repository. Ask NZ for details and/or see related issue below. |
Now that we are moving ahead with deploying IGB Apps using the new App Store, let's separate the Apps currently version-controlled and built as part of the integrated-genome-browser platform repository into their own repositories and build systems.
Doing this will make understanding the platform code easier for users (less to look through) and will also allow each App to become a first-class project with independent versioning, build, and distribution system. Moving the Apps into their own separate repositories will not take long, but once this is done, we need to modify their respective pom.xml files to enable compilation. Tasks - for each optionalPlugin IGB App: * Create new repos for each IGB App currently in optionalPlugins * Re-configure pom.xml to enable local compilation of jar and OBR index file (parent pom no longer available) * Bundle artifact should include a properties file with last git commit hash, origin repository. Ask NZ for details and/or see related issue below. |
| Summary | Create and configure new repos for optionalPlugins | Create new repos for optionalPlugins |
| Sprint | Summer 2019 Sprint 8, Summer 2019 Sprint 9 [ 67, 68 ] | Summer 2019 Sprint 8, Summer 2019 Sprint 9, Summer 2019 Sprint 10 [ 67, 68, 69 ] |
| Rank | Ranked higher |
| Sprint | Summer 2019 Sprint 8, Summer 2019 Sprint 9, Summer 2019 Sprint 10 [ 67, 68, 69 ] | Summer 2019 Sprint 8, Summer 2019 Sprint 9, Summer 2019 Sprint 10, Summer 2019 Sprint 11 [ 67, 68, 69, 70 ] |
| Rank | Ranked higher |
New repositories have all been created, jars are being built, and each downloads location can function as an App repository.
| Resolution | Done [ 10000 ] | |
| Status | Open [ 1 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 18495 ] | Fall 2019 Workflow Update [ 20197 ] |
| Workflow | Fall 2019 Workflow Update [ 20197 ] | Revised Fall 2019 Workflow Update [ 22334 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
How to create a new repository from a sub-folder of an existing repository: