[IGBF-4108] Implement logic to load the genomes for GenArk - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
2
Epic Link:
Add UCSC GenArk to IGB
Sprint:
Spring 4, Spring 5, Spring 6

Description

Implement logic to load the GenArk genomes to IGB when the user clicks the Load button.

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Jaya Sravani Sirigineedi (Inactive) created issue - 25/Feb/25 10:25 AM

Jaya Sravani Sirigineedi (Inactive) made changes - 25/Feb/25 10:25 AM

Field	Original Value	New Value
Epic Link		IGBF-4086 [ 23382 ]

Jaya Sravani Sirigineedi (Inactive) made changes - 25/Feb/25 10:35 AM

Description

Jaya Sravani Sirigineedi (Inactive) made changes - 25/Feb/25 10:36 AM

Description

Implement logic to load the GenArk genomes to IGB when the user clicks the Load button.

Jaya Sravani Sirigineedi (Inactive) made changes - 25/Feb/25 10:37 AM

Story Points

Jaya Sravani Sirigineedi (Inactive) made changes - 25/Feb/25 10:37 AM

Story Points

Jaya Sravani Sirigineedi (Inactive) made changes - 25/Feb/25 10:38 AM

Sprint

Spring 3 [ 212 ]

Jaya Sravani Sirigineedi (Inactive) made changes - 27/Feb/25 1:38 PM

Sprint

Spring 3 [ 212 ]

Spring 4 [ 213 ]

Ann Loraine made changes - 31/Mar/25 9:30 AM

Sprint

Spring 4 [ 213 ]

Spring 4, Spring 5 [ 213, 214 ]

Ann Loraine made changes - 31/Mar/25 9:30 AM

Rank

Ranked higher

Jaya Sravani Sirigineedi (Inactive) made changes - 01/Apr/25 9:48 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Jaya Sravani Sirigineedi (Inactive) added a comment - 08/Apr/25 2:39 PM - edited

Completed the implementation and made a few changes that we discussed after the initial review. Here is the updated code:
https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-4108
https://bitbucket.org/jaya-sravani/ucsc-genark-data-provider/branch/IGBF-4108
To test:

Pull both the branches into your local.
Build and run IGB from the given branch.
Build the ucsc-genark-data-provider service as well using "mvn clean install"
Now add the data provder as a plugin in IGB, while choosing the folder choose the generated target folder of the ucsc-genark-data-provider service.
Load any of the genomes from the table.
Review the pop-up window and the message it shows.
Check whether the genome is added as a Quickload with a prefix "GenArk_" in its name.
Check whether the genome is loaded into IGB. (there won't be any default dataset that will load but all the datasets should be shown under Available data and chromosomes should be loaded.)

Please review the changes and let me know if there's any issue.

Note: This ticket can be tested along with https://jira.bioviz.org/browse/IGBF-4167. PR for this is raised along with that ticket: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1069

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Jaya Sravani Sirigineedi (Inactive) added a comment - 08/Apr/25 2:39 PM - edited Completed the implementation and made a few changes that we discussed after the initial review. Here is the updated code: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-4108 https://bitbucket.org/jaya-sravani/ucsc-genark-data-provider/branch/IGBF-4108 To test: Pull both the branches into your local. Build and run IGB from the given branch. Build the ucsc-genark-data-provider service as well using "mvn clean install" Now add the data provder as a plugin in IGB, while choosing the folder choose the generated target folder of the ucsc-genark-data-provider service. Load any of the genomes from the table. Review the pop-up window and the message it shows. Check whether the genome is added as a Quickload with a prefix "GenArk_" in its name. Check whether the genome is loaded into IGB. (there won't be any default dataset that will load but all the datasets should be shown under Available data and chromosomes should be loaded.) Please review the changes and let me know if there's any issue. Note: This ticket can be tested along with https://jira.bioviz.org/browse/IGBF-4167 . PR for this is raised along with that ticket: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1069

Jaya Sravani Sirigineedi (Inactive) made changes - 08/Apr/25 2:39 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Jaya Sravani Sirigineedi (Inactive) made changes - 08/Apr/25 2:39 PM

Assignee

Jaya Sravani Sirigineedi [ jsirigin ]

Ann Loraine made changes - 15/Apr/25 10:05 AM

Sprint

Spring 4, Spring 5 [ 213, 214 ]

Spring 4, Spring 5, Spring 6 [ 213, 214, 215 ]

Ann Loraine made changes - 15/Apr/25 10:05 AM

Rank

Ranked higher

Nowlan Freese made changes - 23/Apr/25 2:19 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

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Nowlan Freese added a comment - 23/Apr/25 3:41 PM - edited

Tested on Sravani's branch 4123 on Mac.

Popup appears when the "Load" button is clicked
The genome is added to the data provider with GenArk
IGB switches to the new genome
I can load data and sequence for the genome

Ready for PR

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Nowlan Freese added a comment - 23/Apr/25 3:41 PM - edited Tested on Sravani's branch 4123 on Mac. Popup appears when the "Load" button is clicked The genome is added to the data provider with GenArk IGB switches to the new genome I can load data and sequence for the genome Ready for PR

Nowlan Freese made changes - 23/Apr/25 3:45 PM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

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Jaya Sravani Sirigineedi (Inactive) added a comment - 24/Apr/25 2:15 PM

Raised a new PR for this as part of https://jira.bioviz.org/browse/IGBF-4123.

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Jaya Sravani Sirigineedi (Inactive) added a comment - 24/Apr/25 2:15 PM Raised a new PR for this as part of https://jira.bioviz.org/browse/IGBF-4123 .

Jaya Sravani Sirigineedi (Inactive) made changes - 24/Apr/25 2:15 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Ann Loraine made changes - 25/Apr/25 10:38 AM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

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Ann Loraine added a comment - 25/Apr/25 10:39 AM

Merged PR, built installers and deployed to Early Access section of BioViz.org.

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Ann Loraine added a comment - 25/Apr/25 10:39 AM Merged PR, built installers and deployed to Early Access section of BioViz.org.

Ann Loraine made changes - 25/Apr/25 10:39 AM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

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Nowlan Freese added a comment - 25/Apr/25 4:06 PM

Tested main branch on Mac:

Popup appears when the "Load" button is clicked
The genome is added to the data provider with GenArk
IGB switches to the new genome
I can load data and sequence for the genome

Closing ticket.

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Nowlan Freese added a comment - 25/Apr/25 4:06 PM Tested main branch on Mac: Popup appears when the "Load" button is clicked The genome is added to the data provider with GenArk IGB switches to the new genome I can load data and sequence for the genome Closing ticket.

Nowlan Freese made changes - 25/Apr/25 4:06 PM

Assignee

Jaya Sravani Sirigineedi [ jsirigin ]

Nowlan Freese made changes - 25/Apr/25 4:06 PM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

Nowlan Freese made changes - 25/Apr/25 4:06 PM

Resolution		Done [ 10000 ]
Status	Post-merge Testing In Progress [ 10003 ]	Closed [ 6 ]

People

Assignee:

Jaya Sravani Sirigineedi (Inactive)

Reporter:

Jaya Sravani Sirigineedi (Inactive)

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Watchers:

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Dates

Created:

25/Feb/25 10:25 AM

Updated:

25/Apr/25 4:06 PM

Resolved:

25/Apr/25 4:06 PM