Details
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Type:
Task
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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:None
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Story Points:1.5
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Epic Link:
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Sprint:Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10
Description
Update:
https://bitbucket.org/lorainelab/2bit-reader/
To update the App:
- Add code to the POM to trigger building of an OBR index file "repository.xml"
- Ensure that repository.xml will get included with the jar file so that we can release the App on App Store
- Add a bitbucket pipelines YML file to trigger building and copying of the jar file and repository.xml file to Downloads
- Create an "md" file for display in the App Store and in IGB App Manager (not the current README.md file, which is for bitbucket users and developers)
- Create an image we can use as a logo (something with base letters or?)
- Contact Deepti Joshi (the author) to get her preferred contact information
Attachments
Issue Links
- relates to
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1908 [ 17998 ] |
| Rank | Ranked higher |
| Description |
Update:
https://bitbucket.org/lorainelab/biojava-example-app To update the App: * Add code to the POM to trigger building of an OBR index file "repository.xml" * Ensure that repository.xml will get included with the jar file so that we can release the App on App Store * Add a bitbucket pipelines YML file to trigger building and copying of the jar file and repository.xml file to Downloads * Create an "md" file for display in the App Store and in IGB App Manager (not the current README.md file, which is for bitbucket users and developers) * Create an image we can use as a logo (something with base letters or?) * Contact Deepti Joshi (the author) to get her preferred contact information |
Update:
https://bitbucket.org/lorainelab/2bit-reader/ To update the App: * Add code to the POM to trigger building of an OBR index file "repository.xml" * Ensure that repository.xml will get included with the jar file so that we can release the App on App Store * Add a bitbucket pipelines YML file to trigger building and copying of the jar file and repository.xml file to Downloads * Create an "md" file for display in the App Store and in IGB App Manager (not the current README.md file, which is for bitbucket users and developers) * Create an image we can use as a logo (something with base letters or?) * Contact Deepti Joshi (the author) to get her preferred contact information |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 2 : 20 Jan to 31 Jan [ 85 ] | Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb [ 85, 86 ] |
| Rank | Ranked higher |
Investigated the issue while uploading the app on dev-appstore-2 with the help of Sameer Shanbhag
The app upload fails due to export-package being mentioned in the manifest. This was used by Cytoscape to upload the package on one of their repository using Submit-API function which was removed by us in earlier sprints.
To allow the app to install, here are few suggestion:
1. Bring back submit api (Not Recommended)
2. Remove submit api from the code base as we are not using any other cloud service to store our packages differently. (Recommended - Can be done as a part of IGBF-2231)
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
Let's remove this now in a single commit because it will take some time before IGBF-2231 can be merged.
Please do it as part of this older ticket which I have re-opened: https://jira.transvar.org/browse/IGBF-1994
Maybe Noor Zahara or Sameer Shanbhag can do it quickly?
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
Prof. [~aloraine] I can take it up.
I'll do it as a part of https://jira.transvar.org/browse/IGBF-1994
The following changes have been made to the app.
1) OBR index file now gets generated and induced in the jar.
2) A bitbucket-pipelines.yml file has been added to trigger building and copying jar and repository.xml to Downloads.
3) An AppDescription.md file was added to display the description in App Manager.
4) A logo was added to the resources folder.
The changes are present in
https://bitbucket.org/skulka2710/shamika-2bit-reader/branch/IGBF-2238#diff
The app can be uploaded to Appstore after Sameer Shanbhag finishes his work on IGBF-1994.
Moving to first level review.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
Request for Shamika Gajanan Kulkarni
Can you investigate: Is it necessary to export packages from the bundle? There may be some weirdness related to how the biojava library is being handled which may require that the OSGi header includes an export packages statement. But if the biojava library is on the bundle's own classpath, that should not matter.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
Try unpacking the jar - looks like some things are being packaged with the jar that may should not be, including:
- guava-19.0.jar
- log4j-api-2.5.jar
- log4j-core-2.5.jar
- log4j-slf4j-impl-2.5.jar
$ jar xvf biojava-igb-app-0.0.1.jar
inflated: META-INF/MANIFEST.MF
created: META-INF/
created: META-INF/maven/
created: META-INF/maven/igb-app-examples/
created: META-INF/maven/igb-app-examples/biojava-igb-app/
inflated: META-INF/maven/igb-app-examples/biojava-igb-app/pom.properties
inflated: META-INF/maven/igb-app-examples/biojava-igb-app/pom.xml
created: OSGI-INF/
inflated: OSGI-INF/org.lorainelab.igb.sequencereader.TwoBitReaderApp.xml
inflated: biojava-alignment-4.2.8.jar
inflated: biojava-core-4.2.8.jar
inflated: biojava-genome-4.2.8.jar
inflated: biojava-phylo-4.2.8.jar
inflated: forester-1.038.jar
inflated: guava-19.0.jar
inflated: log4j-api-2.5.jar
inflated: log4j-core-2.5.jar
inflated: log4j-slf4j-impl-2.5.jar
inflated: logo.png
created: org/
created: org/biojava/
created: org/biojava/nbio/
created: org/biojava/nbio/genome/
created: org/biojava/nbio/genome/parsers/
created: org/biojava/nbio/genome/parsers/twobit/
inflated: org/biojava/nbio/genome/parsers/twobit/TwoBitParser.class
created: org/lorainelab/
created: org/lorainelab/igb/
created: org/lorainelab/igb/sequencereader/
inflated: org/lorainelab/igb/sequencereader/TwoBitFileSummarizer.class
inflated: org/lorainelab/igb/sequencereader/TwoBitReaderApp.class
inflated: repository.xml
inflated: slf4j-api-1.7.14.jar
inflated: summarize.png
There's a lot going on here – we might want to make an all-new ticket called "Re-factor biojava 2bit parser POM" to omit some of these things that are probably not needed.
I have a PDF that talks about how to transform 3rd party jars into OSGi bundles – I will add a link to it here. (I have to find it.)
Moving previous two comments to a new ticket and recommending PR.
| Status | To-Do [ 10305 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] | Ann Loraine [ aloraine ] |
Yes I found that many jars are being packaged in the target jar. I like the idea of making a separate ticket for it. I haven't submitted a pull request yet for this one.
| Sprint | Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb [ 85, 86 ] | Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 21 Feb [ 85, 86, 87 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] | Shamika Gajanan Kulkarni [ shamika ] |
Please resolve conflict with your branch and submit PR:
https://bitbucket.org/skulka2710/shamika-2bit-reader/branch/IGBF-2238#diff
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
Resolved the conflicts and submitted a PR.
https://bitbucket.org/lorainelab/2bit-reader/pull-requests/2/igbf-2238-update-pomxml/diff
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Sprint | Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb [ 85, 86, 87 ] | Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 85, 86, 87, 89 ] |
| Rank | Ranked higher |
| Sprint | Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 85, 86, 87, 89 ] | Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 85, 86, 87, 89, 90 ] |
| Rank | Ranked higher |
| Sprint | Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 85, 86, 87, 89, 90 ] | Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 85, 86, 87, 89, 90, 91 ] |
| Rank | Ranked higher |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Note: Just now added two Powerpoint presentations by Deepti Joshi to new folder in the repository.