Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Critical
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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
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Sprint:Fall 2018 Sprint 3, Fall 2018 Sprint 4
Description
We are now using packages from htsjdk artifact in the IGB project. However, there is a problem. It is not an OSGi bundle. To handle this, we are now importing the htsjdk into the "shared-lib-wrapper" module of IGB project. The pom.xml file of this module uses the BND-tool maven plug-in to packages htsjdk along with many other completely unrelated artifacts into one large bundle, which then gets loaded into the OSGi run-time along with all the other bundles that make up the IGB application.
This is not ideal. Maintaining the "shared-lib-wrapper" module is made extra complicated by this approach. For example, if some of these libraries rely on different versions of the same artifact, the approach won't work.
To simplify our codebase, we should transform these 3rd-party jar artifacts into proper OSGi bundles.
To do this, let's "fork" the htsjdk library and modify/enhance their build process to create a proper OSGi bundle.
Following this, we should add it to our nexus maven repository (https://nexus.bioviz.org) so that the new htsjdk OSGi bundle is available to IGB developers.
Attachments
Issue Links
- relates to
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IGBF-1457 Startup Error in Console (ERROR com.affymetrix.main.OSGiHandler)
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- Closed
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- Closed
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- Closed
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IGBF-1417 Create new artifact with bigbed and bigwig parsing code from IGV codebase
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- Closed
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Sprint | Fall 2018 Sprint 3 [ 53 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Status | In Progress [ 3 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Needs Testing [ 10002 ] |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Rank | Ranked higher |
| Sprint | Fall 2018 Sprint 3 [ 53 ] | Fall 2018 Sprint 3, Fall 2018 Sprint 4 [ 53, 54 ] |
| Rank | Ranked higher |
| Assignee | Kiran Korey [ kkorey ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Status | Testing In Progress [ 10003 ] | Open [ 1 ] |
| Assignee | Kiran Korey [ kkorey ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Needs 1st Level Review [ 10005 ] |
| Resolution | Done [ 10000 ] | |
| Status | Needs 1st Level Review [ 10005 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 18124 ] | Fall 2019 Workflow Update [ 19950 ] |
| Workflow | Fall 2019 Workflow Update [ 19950 ] | Revised Fall 2019 Workflow Update [ 22071 ] |