[IGBF-3032] Change default name for bookmarks - JIRA UNCC

Details

Type: Improvement
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 9.1.10 Major Release
Labels:
None

Story Points:
0.25
Epic Link:
Improve IGB for users
Sprint:
Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28

Description

Currently, bookmark "default name" looks like:

H_sapiens_Dec_2013, chr1 : 0 - 248,956,422

The "default name" is getting constructed from the genome name (e.g., H_sapiens_Dec_2013), the currently viewed chromosome (e.g., chr1), and the currently visible region (e.g., 0 - 248,956,422).

The format of the default name is OK, but it would be more useful if it used a format accepted by the "samtools view" command. (Samtools is a very popular program in bioinformatics.)

Samtools view accepts a region string that looks like:

chr1:0-248,956,422

Note it is very similar to our current "default" name, but ours contains space characters.

Let's modify our "default" name to look like what samtools view accepts, by removing the space characters in the region string part.

For example:

H_sapiens_Dec_2013, chr1 : 0 - 248,956,422

will be instead:

H_sapiens_Dec_2013, chr1:0-248,956,422

Please change the format so that the "default name" is

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conflict.png
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13/Jan/22 2:03 PM
New Bookmark name format.png
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13/Jan/22 11:17 AM

Issue Links

relates to

IGBF-3008 Improve bookmark interface

Closed

Activity

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Ann Loraine created issue - 16/Dec/21 9:44 AM

Ann Loraine made changes - 16/Dec/21 9:44 AM

Field	Original Value	New Value
Epic Link		IGBF-1765 [ 17855 ]

Ann Loraine made changes - 16/Dec/21 9:44 AM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 16/Dec/21 9:44 AM

Link

This issue relates to ~~IGBF-3008~~ [ ~~IGBF-3008~~ ]

Ann Loraine made changes - 12/Jan/22 10:22 AM

Rank

Ranked higher

Omkar Marne (Inactive) made changes - 12/Jan/22 10:23 AM

Assignee

Omkar Marne [ omarne ]

Omkar Marne (Inactive) made changes - 13/Jan/22 10:50 AM

Attachment

New bookmark name format.png [ 17062 ]

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Omkar Marne (Inactive) added a comment - 13/Jan/22 10:51 AM - edited

I edited the default bookmark name format in BookmarkController.java file. Spaces in the name are no longer visible. Please see attached screenshot.

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Omkar Marne (Inactive) added a comment - 13/Jan/22 10:51 AM - edited I edited the default bookmark name format in BookmarkController.java file. Spaces in the name are no longer visible. Please see attached screenshot.

Omkar Marne (Inactive) made changes - 13/Jan/22 11:17 AM

Attachment

New bookmark name format.png [ 17062 ]

Omkar Marne (Inactive) made changes - 13/Jan/22 11:17 AM

Attachment

New Bookmark name format.png [ 17064 ]

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Omkar Marne (Inactive) added a comment - 13/Jan/22 11:30 AM

Dr. [~aloraine] Please see my changes here

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Omkar Marne (Inactive) added a comment - 13/Jan/22 11:30 AM Dr. [~aloraine] Please see my changes here

Omkar Marne (Inactive) made changes - 13/Jan/22 11:31 AM

Assignee

Omkar Marne [ omarne ]

Ann Loraine [ aloraine ]

Omkar Marne (Inactive) made changes - 13/Jan/22 11:31 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Omkar Marne (Inactive) made changes - 13/Jan/22 11:31 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

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Ann Loraine added a comment - 13/Jan/22 11:34 AM - edited

Please squash the commits into one so that when you submit the PR, there will be only one committed change to the codebase. Other than this, the changes are fine. When that is done, submit the PR for merging.

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Ann Loraine added a comment - 13/Jan/22 11:34 AM - edited Please squash the commits into one so that when you submit the PR, there will be only one committed change to the codebase. Other than this, the changes are fine. When that is done, submit the PR for merging.

Ann Loraine made changes - 13/Jan/22 11:34 AM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Ann Loraine made changes - 13/Jan/22 11:34 AM

Status

First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

Ann Loraine made changes - 13/Jan/22 11:35 AM

Assignee

Ann Loraine [ aloraine ]

Omkar Marne [ omarne ]

Omkar Marne (Inactive) made changes - 13/Jan/22 11:35 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Omkar Marne (Inactive) added a comment - 13/Jan/22 1:26 PM

Dr. [~aloraine] Please find my pull requests. https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/894/igbf-3032

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Omkar Marne (Inactive) added a comment - 13/Jan/22 1:26 PM Dr. [~aloraine] Please find my pull requests. https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/894/igbf-3032

Ann Loraine made changes - 13/Jan/22 2:03 PM

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conflict.png [ 17067 ]

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Ann Loraine added a comment - 13/Jan/22 2:04 PM

I am not able to merge the PR due to a conflict. Please see attached.
attn: Omkar Marne

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Ann Loraine added a comment - 13/Jan/22 2:04 PM I am not able to merge the PR due to a conflict. Please see attached. attn: Omkar Marne

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Omkar Marne (Inactive) added a comment - 13/Jan/22 2:53 PM - edited

Dr. [~aloraine] Please find my new pull request : https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/895/igbf-3032-new-name-format-for-bookmark

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Omkar Marne (Inactive) added a comment - 13/Jan/22 2:53 PM - edited Dr. [~aloraine] Please find my new pull request : https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/895/igbf-3032-new-name-format-for-bookmark

Omkar Marne (Inactive) made changes - 13/Jan/22 3:06 PM

Assignee

Omkar Marne [ omarne ]

Ann Loraine [ aloraine ]

Omkar Marne (Inactive) made changes - 13/Jan/22 3:06 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Omkar Marne (Inactive) made changes - 13/Jan/22 3:06 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Omkar Marne (Inactive) made changes - 13/Jan/22 3:06 PM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

Omkar Marne (Inactive) made changes - 13/Jan/22 3:06 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Ann Loraine made changes - 17/Jan/22 11:09 PM

Sprint

Spring 1 2022 Jan 3 - Jan 14 [ 136 ]

Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28 [ 136, 137 ]

Ann Loraine made changes - 17/Jan/22 11:09 PM

Rank

Ranked higher

Ann Loraine made changes - 18/Jan/22 12:30 PM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

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Ann Loraine added a comment - 18/Jan/22 12:31 PM

PR is merged. Building master branch installers.

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Ann Loraine added a comment - 18/Jan/22 12:31 PM PR is merged. Building master branch installers.

Ann Loraine made changes - 18/Jan/22 1:11 PM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

Ann Loraine made changes - 18/Jan/22 1:11 PM

Assignee

Ann Loraine [ aloraine ]

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Ann Loraine added a comment - 18/Jan/22 1:12 PM

Master branch installers are deployed to the IGB early access section of bioviz main Web site. Ready for testing.

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Ann Loraine added a comment - 18/Jan/22 1:12 PM Master branch installers are deployed to the IGB early access section of bioviz main Web site. Ready for testing.

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Omkar Marne (Inactive) added a comment - 18/Jan/22 4:38 PM - edited

Testing protocol:

Please pull the latest changes made in the IGB code.
Open IGB local environment and select any genome
Open the bookmark menu.
The format of the default bookmark name should be like H_sapiens_Dec_2013, chr1:0-248,956,422 instead of H_sapiens_Dec_2013, chr1 : 0 - 248,956,422.
The spaces between the numbers and before and after colon have been removed.

Show

Omkar Marne (Inactive) added a comment - 18/Jan/22 4:38 PM - edited Testing protocol: Please pull the latest changes made in the IGB code. Open IGB local environment and select any genome Open the bookmark menu. The format of the default bookmark name should be like H_sapiens_Dec_2013, chr1:0-248,956,422 instead of H_sapiens_Dec_2013, chr1 : 0 - 248,956,422. The spaces between the numbers and before and after colon have been removed.

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Nowlan Freese added a comment - 20/Jan/22 4:20 PM

Tested on Mac, working correctly, no errors in log.

Closing ticket.

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Nowlan Freese added a comment - 20/Jan/22 4:20 PM Tested on Mac, working correctly, no errors in log. Closing ticket.

Nowlan Freese made changes - 20/Jan/22 4:20 PM

Assignee

Omkar Marne [ omarne ]

Nowlan Freese made changes - 20/Jan/22 4:20 PM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

Nowlan Freese made changes - 20/Jan/22 4:20 PM

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

Nowlan Freese made changes - 04/Aug/22 3:12 PM

Fix Version/s

9.1.10 Major Release [ 10700 ]

People

Assignee:

Omkar Marne (Inactive)

Reporter:

Ann Loraine

Votes:

0 Vote for this issue

Watchers:

3 Start watching this issue

Dates

Created:

16/Dec/21 9:44 AM

Updated:

04/Aug/22 3:12 PM

Resolved:

20/Jan/22 4:20 PM