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: 10.0.0 Major Release
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Labels:None
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Story Points:4
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Epic Link:
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Sprint:Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21
Description
In previous work, we observed that updating SCR syntax to match the OSGI SCR R6 coincided with inability to run IGB using JDK 11.
We do not know why this occurred.
To get a better understanding of how SCR annotations are used in IGB, update the annotations to use R6 instead of R5 syntax, using the master branch of the team repository, version 9.1.12.
Hopefully, we will see how the changes affect IGB and in what way. For example, if we observe wiring errors, we would like to know why these wiring errors would occur if there is only a change in the Component syntax.
This task emerged from work on a different ticket. See this comment from that ticket.
Attachments
Issue Links
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- Closed
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- relates to
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IGBF-3422 Investigate Test Failure that is occurring in QuickloadUtilsTest class.
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- Closed
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- Closed
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- Closed
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- Closed
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- Closed
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Show 1 more links (1 relates to)
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3142 [ 21688 ] |
| Description |
In previous work, we observed that updating SCR syntax to match the OSGI SCR R6 coincided with inability to run IGB using JDK 11.
We do not know why this occurred. To get a better understanding of how SCR annotations are used in IGB, update the annotations to use R6 instead of R5 syntax. Hopefully, we will see how the changes affect IGB and in what way. For example, if we observe wiring errors, we would like to know why these wiring errors would occur if there is only a change in the Component syntax. |
In previous work, we observed that updating SCR syntax to match the OSGI SCR R6 coincided with inability to run IGB using JDK 11.
We do not know why this occurred. To get a better understanding of how SCR annotations are used in IGB, update the annotations to use R6 instead of R5 syntax, using the master branch of the team repository, version 9.1.12. Hopefully, we will see how the changes affect IGB and in what way. For example, if we observe wiring errors, we would like to know why these wiring errors would occur if there is only a change in the Component syntax. |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
In previous work, we observed that updating SCR syntax to match the OSGI SCR R6 coincided with inability to run IGB using JDK 11.
We do not know why this occurred. To get a better understanding of how SCR annotations are used in IGB, update the annotations to use R6 instead of R5 syntax, using the master branch of the team repository, version 9.1.12. Hopefully, we will see how the changes affect IGB and in what way. For example, if we observe wiring errors, we would like to know why these wiring errors would occur if there is only a change in the Component syntax. |
In previous work, we observed that updating SCR syntax to match the OSGI SCR R6 coincided with inability to run IGB using JDK 11.
We do not know why this occurred. To get a better understanding of how SCR annotations are used in IGB, update the annotations to use R6 instead of R5 syntax, using the master branch of the team repository, version 9.1.12. Hopefully, we will see how the changes affect IGB and in what way. For example, if we observe wiring errors, we would like to know why these wiring errors would occur if there is only a change in the Component syntax. This task emerged from work on a different ticket. See [this comment | https://jira.bioviz.org/browse/IGBF-3371?focusedCommentId=37842&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-37842] from that ticket. |
| Sprint | Summer 4 2023 June 26 [ 173 ] | Summer 4 2023 June 26, Summer 5 2023 July 10 [ 173, 174 ] |
| Rank | Ranked higher |
| Assignee | Karthik Raveendran [ karthik ] | Nowlan Freese [ nfreese ] |
| Sprint | Summer 4 2023 June 26, Summer 5 2023 July 10 [ 173, 174 ] | Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24 [ 173, 174, 175 ] |
| Rank | Ranked higher |
| Attachment | IGBF-3379_coreIGB-bundle.txt [ 17917 ] | |
| Attachment | main-JDK8_coreIGB-bundle.txt [ 17918 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Sprint | Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24 [ 173, 174, 175 ] | Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24, Summer 7 2023 Aug 7 [ 173, 174, 175, 176 ] |
| Rank | Ranked higher |
| Assignee | Karthik Raveendran [ karthik ] | Kaushik Gopu [ kgopu ] |
| Comment |
[ Core - Heatmap Editor
Core - Affymetrix Common Core - Genometry (Data Models) Core - IGB Core - IGB Swing Extensions Core - IGB Services API Core - Window Service Core - Bundle wrapper, deployer Core - Logging Config Core - Genoviz Extensions Core - Preferences Core - Web Links Core - Quickload (data source) Core - DAS (data source) Core - Frame Manager Core - Synonym Lookup Core - JavaFX Utilities Core - Menu API Core - Context Menu Service ] |
| Comment |
[ Plugin - Apollo Library
(COMPLETE) Plugin - Annotation Tab (COMPLETE) Plugin - Console Tab Plugin - Track Operations API, GUI Plugin - Bigbed data format handler Plugin - Bigwig data format handler Plugin - Bookmarks and REST API Plugin - External View (COMPLETE) Plugin - Graph Tab Plugin - Script handler Plugin - Keyword Search Plugin - NCBI Blast (COMPLETE) Plugin - Selection Info tab (COMPLETE) Plugin - Restriction Sites tab Plugin - Search Id or Props (COMPLETE) Plugin - Advanced Search Tab Plugin - Sequence Viewer GUI Plugin - Survey GUI Plugin - Graph thresholding visual analytics Plugin - Update Plugin - App Manager GUI Plugin - Paired-end Read Preprocessor (COMPLETE) Plugin - Save Image GUI (COMPLETE) Plugin - Save Session Manager Plugin - Toolbar Preferences GUI Plugin - Data caching GUI Plugin - Data caching API Plugin - Feedback Plugin - Sorting API and Impl Plugin - Narrowpeak data format handler Plugin - File Handler - Genotyping Results Plugin - BED file format handler Plugin - BAM data format handler Plugin - BAI index visualization handler Plugin - App Store REST API ] |
| Comment |
[ Initial testing steps:
# Delete the .m2 folder # Delete the .igb folder (appData/igb folder on Windows). # Run mvn clean install (Do not skip tests). # If any test fails, make a new ticket, do not commit changes to branch. # Start IGB, check log/standard output for any warnings/errors. If there are relevant warnings/errors make a new ticket, do not commit changes to branch. # Check the Felix Web Console in your browser (http://localhost:7080/system/console/bundles#). If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch. # Click on the Arabidopsis genome. # Test the individual module functionality. # Reset preferences to default when closing IGB. ] |
| Comment | [ [~kgopu] - my most recent/updated branch rebased on top of Karthik's changes: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3379-updateModule ] |
| 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 | Kaushik Gopu [ kgopu ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| 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 | Karthik Raveendran [ karthik ] |
| Assignee | Molly Davis [ molly ] |
| Assignee | Molly Davis [ molly ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Comment |
[ *+Subsystems Test on MAC+*:
*File used*: main-JDK8-r6.jar Review resource: https://wiki.bioviz.org/confluence/display/ITD/Add+Data+Source+endpoint 1) Add Data Source endpoint - Tested well, 'dataSourceEndpointTest QuickLoad' now called 'Genome in a bottle'? 2) App Manager - 3) BioViz Connect - 4) Bookmarks - 5) Cache - 6) Data Provider - 7) eFP-Seq Browser - 8) External View - 9) FileChooser - 10) File Formats - 11) Galaxy - 12) Image Export - 13) Installer - 14) Local Quickload - 15) Navigation - 16) ProtAnnot - 17) Quickload Saver - 18) Search - 19) Soft-Clipping - 20) Synonyms - 21) Tabbed Panels - 22) Toolbar - 23) Track Operators: Annotation Tracks - 24) Track Operators: Graph Tracks - 25) Track View - ] |
| Sprint | Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24, Summer 7 2023 Aug 7 [ 173, 174, 175, 176 ] | Summer 4 2023 June 26, Summer 5 2023 July 10, Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21 [ 173, 174, 175, 176, 177 ] |
| Rank | Ranked higher |
| Assignee | Karthik Raveendran [ karthik ] |
| Assignee | Molly Davis [ molly ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Molly Davis [ molly ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Link | This issue relates to IGBF-3426 [ IGBF-3426 ] |
| Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Fix Version/s | 10.0.0 Major Release [ 10900 ] |