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: 9.1.10 Major Release
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Summer 4 2022 July 4, Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15
Description
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.
See:
core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java
Note that "Runtime" lines are incompatible with Java 18. See this commit for invocation of Runtime obsolete stack trace setting method.
Attachments
Issue Links
- relates to
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- To-Do
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1531 [ 17617 ] |
| Description | The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid the need to update it for newer versions of Java. |
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid the need to update it for newer versions of Java.
See: core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java Note that "Runtime" lines are incompatible with Java 18. |
| Description |
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid the need to update it for newer versions of Java.
See: core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java Note that "Runtime" lines are incompatible with Java 18. |
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.
See: core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java Note that "Runtime" lines are incompatible with Java 18. |
| Description |
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.
See: core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java Note that "Runtime" lines are incompatible with Java 18. |
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.
See: core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java Note that "Runtime" lines are incompatible with Java 18. See [this commit for details|https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f]. |
| Description |
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.
See: core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java Note that "Runtime" lines are incompatible with Java 18. See [this commit for details|https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f]. |
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.
See: core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java Note that "Runtime" lines are incompatible with Java 18. See [this commit |https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f] for obsolete (as of Java 11?) Runtime method invocation. |
| Description |
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.
See: core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java Note that "Runtime" lines are incompatible with Java 18. See [this commit |https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f] for obsolete (as of Java 11?) Runtime method invocation. |
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.
See: core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java Note that "Runtime" lines are incompatible with Java 18. See [this commit |https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f] for invocation of Runtime obsolete stack trace setting method invocation. |
| Description |
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.
See: core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java Note that "Runtime" lines are incompatible with Java 18. See [this commit |https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f] for invocation of Runtime obsolete stack trace setting method invocation. |
The "useq" format is no longer being used, so far as I know. If possible, we should remove this code from the code base to avoid having to update the code to compile / run under newer JDK versions.
See: core/genometry/src/main/java/com/affymetrix/genometry/parsers/useq/USeqUtilities.java Note that "Runtime" lines are incompatible with Java 18. See [this commit |https://bitbucket.org/aloraine/integrated-genome-browser/commits/253e525b8c214ac68b2581486452cc9c7c24ee1f] for invocation of Runtime obsolete stack trace setting method. |
| Story Points | 1 | 0.25 |
| Sprint | Summer 4 2022 July 4 [ 150 ] | Summer 4 2022 July 4, Summer 5 2022 July 18 [ 150, 151 ] |
| Rank | Ranked higher |
| Sprint | Summer 4 2022 July 4, Summer 5 2022 July 18 [ 150, 151 ] | Summer 4 2022 July 4, Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 150, 151, 152 ] |
| Rank | Ranked higher |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] | Nowlan Freese [ nfreese ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
- Remove the following comment in GeneralLoadUtils.java
Get GenomeVersion for USEQ file format.
- Check line 54 of TrackDefaultView.java for use of "useq".
- Should we remove the following useq test files?
core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_Graph.useq core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_Region.useq core/genometry/src/test/resources/data/useq/chr17_H_sapiens_Mar_2006_StrandedReadCoverage_Graph.useq
- I'm also seeing a lot of imports being replaced with "". This seems like the IDE automatically making the change and I think we should not change them to "".
I removed the above useq references in addition to Karthik's changes and pushed my branch (https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3146).
| Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Fix Version/s | 9.1.10 Major Release [ 10700 ] |
Add the additional changes and removed import errors. Commit
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
We have fixed the issue with Karthik's branch, here is the new commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/70b1c45edfb1f1169ebdef6bcc85844a94d73f5a
| Attachment | chr17_H_sapiens_Mar_2006_Graph.useq [ 17257 ] |
Testing on Mac OS 12.5
Reset preferences to default and delete the .igb folder.
Attempting to load the attached useq file into the H_sapiens_Mar_2006 genome resulted in a "Format not recognized" error. This is the appropriate behavior.
In the A_thaliana_Jun_2009 genome, loaded the RNA-Seq > Auxin arf19 > Graph - Scaled > Col-0 control scaled coverage graph file successfully.
In the Graph tab, used Single-Graph Operations to successfully copy and divide the graph.
In the Graph tab, used Multi-Graph Operations to successfully Sum two graphs.
Since I can find no files in IGB that include mention of useq and the other IGB graph functionality does not appear to be affected, ready for pull request.
| Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | Reviewing Pull Request [ 10303 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Karthik Raveendran [ karthik ] |
Merged.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Sprint | Summer 4 2022 July 4, Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 150, 151, 152 ] | Summer 4 2022 July 4, Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15 [ 150, 151, 152, 153 ] |
| Rank | Ranked higher |
Master branch is built and ready for testing.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Post-merge Testing In Progress [ 10003 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Summary | Investigate: Remove "useq" packages from genometry bundle in IGB | Remove "useq" packages from genometry bundle in IGB |
| Story Points | 0.25 | 1 |
Testing master branch installer on Mac OS 12.5
Reset preferences to default and delete the .igb folder.
Attempting to load the attached useq file into the H_sapiens_Mar_2006 genome resulted in a "Format not recognized" error. This is the appropriate behavior.
In the A_thaliana_Jun_2009 genome, loaded the RNA-Seq > Auxin arf19 > Graph - Scaled > Col-0 control scaled coverage graph file successfully.
Closing ticket.
| Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
The code parsing and supporting "useq" files in IGB has been removed from the codebase. Commit