Details
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Type:
New Plugin
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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: 9.1.8 Major Release
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Labels:
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Story Points:3
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Epic Link:
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Sprint:Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2
Description
IGB makes it possible for users to visualize "custom genomes," which are genomes where they have used their own reference genome and visualized their own data files.
Please see this User's Guide page for guidance on how this features works from the user's perspective:
https://wiki.transvar.org/pages/viewpage.action?pageId=23200542
Unfortunately, each time a user needs to use their "custom genome," they have to repeat the entire process described in the wiki.
Instead of making them do this every time, let's implement a way for them to save their custom genome between sessions.
How this could work:
- Users will do the same thing as now when opening their custom genome.
- We will create a new submenu option under the "File" menu that says "Save Custom Genome to Local Quickload Site"
- When they choose that option, a popup will appear that asks the user to select a folder in the file system
- Once they do that, IGB creates a quickload site consisting of meta-data files only - contents.txt, genome.txt, annots.xml
- The annots.xml file tag "file" attribute will point to the local (or remote) files the user has loaded into IGB
Note that thanks to the new "reference" file tag implemented in IGB 9.1.6, the reference sequence no longer has to reside in the same folder as the Quickload site, as was previously the case.
Attachments
Issue Links
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IGBF-2805 Describe how to test the feature of adding and using a local quickload on Windows, Mac, Linux to Release Testing.
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IGBF-2783 Improve Open Genome from File UI
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Show 4 more links (4 relates to)
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-440 [ 15498 ] |
| Rank | Ranked higher |
| Rank | Ranked lower |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Rank | Ranked lower |
| Epic Link | IGBF-440 [ 15498 ] |
| Workflow | Loraine Lab Workflow [ 15776 ] | Fall 2019 Workflow Update [ 18756 ] |
| Workflow | Fall 2019 Workflow Update [ 18756 ] | Revised Fall 2019 Workflow Update [ 20878 ] |
| Status | Open [ 1 ] | To-Do [ 10305 ] |
| Link | This issue relates to IGBF-409 [ IGBF-409 ] |
| Epic Link | IGBF-1765 [ 17855 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Fall 6 Nov 30 - Dec 11 [ 109 ] |
| Rank | Ranked lower |
| Story Points | 2 |
| Description |
This story has been created as a reminder for the task of implementing the ability for IGB to Preserve Custom Genomes between IGB Sessions.
This would be a big usability enhancement. |
IGB makes it possible for users to visualize "custom genomes," which are genomes where they have |
| Description | IGB makes it possible for users to visualize "custom genomes," which are genomes where they have |
IGB makes it possible for users to visualize "custom genomes," which are genomes where they have used their own reference genome and visualized their own data files.
Please see this User's Guide page for guidance on how this features works from the user's perspective: https://wiki.transvar.org/pages/viewpage.action?pageId=23200542 Unfortunately, each time a user needs to use their "custom genome," they have to repeat the entire process described in the wiki. Instead of making them do this every time, let's implement a way for them to save their custom genome between sessions. How this could work: * Users will do the same thing as now when opening their custom genome. * We will create a new submenu option under the "File" menu that says "Save Custom Genome to Local Quickload Site" * When they choose that option, a popup will appear that asks the user to select a folder in the file system * Once they do that, IGB creates a quickload site consisting of meta-data files only - contents.txt, genome.txt, annots.xml * The annots.xml file tag "file" attribute will point to the local files the users has loaded into IGB |
| Story Points | 2 | 3 |
| Labels | Advanced |
| Issue Type | Improvement [ 4 ] | New Feature [ 2 ] |
| Fix Version/s | 9.1.8 Major Release [ 10605 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Comment | [ Yes, we could do that. I was trying to figure out a way to access genome version object but no luck as of now. Will try debugging more on this. ] |
| Sprint | Fall 6 Nov 30 - Dec 11 [ 109 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 109, 110 ] |
| Rank | Ranked higher |
| Comment | [ [~aloraine] - Thanks for the clarification. Should I also be creating 2bit and species file? ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
IGB makes it possible for users to visualize "custom genomes," which are genomes where they have used their own reference genome and visualized their own data files.
Please see this User's Guide page for guidance on how this features works from the user's perspective: https://wiki.transvar.org/pages/viewpage.action?pageId=23200542 Unfortunately, each time a user needs to use their "custom genome," they have to repeat the entire process described in the wiki. Instead of making them do this every time, let's implement a way for them to save their custom genome between sessions. How this could work: * Users will do the same thing as now when opening their custom genome. * We will create a new submenu option under the "File" menu that says "Save Custom Genome to Local Quickload Site" * When they choose that option, a popup will appear that asks the user to select a folder in the file system * Once they do that, IGB creates a quickload site consisting of meta-data files only - contents.txt, genome.txt, annots.xml * The annots.xml file tag "file" attribute will point to the local files the users has loaded into IGB |
IGB makes it possible for users to visualize "custom genomes," which are genomes where they have used their own reference genome and visualized their own data files.
Please see this User's Guide page for guidance on how this features works from the user's perspective: https://wiki.transvar.org/pages/viewpage.action?pageId=23200542 Unfortunately, each time a user needs to use their "custom genome," they have to repeat the entire process described in the wiki. Instead of making them do this every time, let's implement a way for them to save their custom genome between sessions. How this could work: * Users will do the same thing as now when opening their custom genome. * We will create a new submenu option under the "File" menu that says "Save Custom Genome to Local Quickload Site" * When they choose that option, a popup will appear that asks the user to select a folder in the file system * Once they do that, IGB creates a quickload site consisting of meta-data files only - contents.txt, genome.txt, annots.xml * The annots.xml file tag "file" attribute will point to the local (or remote) files the user has loaded into IGB Note that thanks to the new "reference" file tag implemented in IGB 9.1.6, the reference sequence no longer has to reside in the same folder as the Quickload site, as was previously the case. |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Attachment | annots.xml [ 15057 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Attachment | annots.xml [ 15058 ] |
| Attachment | annots.xml [ 15057 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 109, 110 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 109, 110, 111 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| 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 | Noor Zahara [ noor91zahara ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| 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 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Comment |
[ Thanks.
When will the load strategy be set to Whole Sequence? Is there a way I can reproduce? ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 109, 110, 111 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 109, 110, 111, 112 ] |
| Rank | Ranked higher |
| Assignee | Nowlan Freese [ nfreese ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 109, 110, 111, 112 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5 [ 109, 110, 111, 112, 113 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5 [ 109, 110, 111, 112, 113 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19 [ 109, 110, 111, 112, 113, 114 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| 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 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19 [ 109, 110, 111, 112, 113, 114 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 109, 110, 111, 112, 113, 114, 115 ] |
| Rank | Ranked higher |
| Assignee | Rachel Weidenhammer [ rweidenh ] |
| Assignee | Rachel Weidenhammer [ rweidenh ] | Nowlan Freese [ nfreese ] |
| 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 ] |
| Summary | Preserve Custom Genomes between IGB Sessions | Create Quickload Saver IGB app |
| Issue Type | New Feature [ 2 ] | New Plugin [ 10 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5 [ 109, 110, 111, 112, 113, 114, 115 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Winter 6 Mar 8 - Mar 19 [ 109, 110, 111, 112, 113, 114, 115, 116 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| 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 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] |
| 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 ] |
| Sprint | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Winter 6 Mar 8 - Mar 19 [ 109, 110, 111, 112, 113, 114, 115, 116 ] | Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Winter 6 Mar 8 - Mar 19, Spring 1 Mar 22 - Apr 2 [ 109, 110, 111, 112, 113, 114, 115, 116, 117 ] |
| Rank | Ranked higher |
| Assignee | Chester Dias [ cdias1 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Chester Dias [ cdias1 ] | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] | Noor Zahara [ noor91zahara ] |
| Fix Version/s | 9.1.8 Major Release [ 10605 ] |
| Fix Version/s | 9.1.8 Major Release [ 10605 ] |