Details
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Type:
New Feature
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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: None
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Labels:
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Story Points:2
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Epic Link:
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Sprint:Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20
Description
When a user clicks "Load Sequence" button, IGB asks whether the user would like to download the entire sequence for faster access in future.
This is great for smaller-sized files (e.g., human genome size or smaller), but for very large genomes such as wheat, which is 3+ Gb in size, this should not be done.
We need to add some logic that checks the size of the genome sequence file to be cached and then only shows the message when the genome size is smaller than a configurable maximum.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Sprint | Fall 4 Oct 26 - Nov 6 [ 107 ] | |
| Labels | Advanced |
| Description |
When a user clicks "Load Sequence" button, IGB asks whether the user would like to download the entire sequence for faster access in future.
This is great for smaller-sized files (e.g., human genome size or smaller), but for very large genomes such as wheat, which is many Gb in size, this should not be done. We need to add some logic that checks the size of the genome sequence file to be cached and then only shows the message when the genome size is small. The maximum size for a cache-able file should be something we can set in IGB's preferences file. |
When a user clicks "Load Sequence" button, IGB asks whether the user would like to download the entire sequence for faster access in future.
This is great for smaller-sized files (e.g., human genome size or smaller), but for very large genomes such as wheat, which is 3+ Gb in size, this should not be done. We need to add some logic that checks the size of the genome sequence file to be cached and then only shows the message when the genome size is smaller than a configurable maximum. |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Let's go with 0.8 Gb for now.
Code diff - https://bitbucket.org/noorzahara/integrated-genome-browser-local1/branch/IGBF-2565#diff
Testing Steps -
1. Load genome of any species
2. Load the sequence by clicking on. 'Load Sequence' button. A message pop up appears asking to cache the 2bit file.
3. Load genome whose sequence file is greater than 0.8 gb (wheat). In this case, the pop-up box shouldn't appear when the sequence is loaded.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Everything looks good to me. Please submit pull request
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] | 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 ] |
To test:
1-
- Visit the Wheat genome (which is huge)
- Click "Load Sequence" button
- No message should appear inviting you to download the entire file for faster future access
2-
- Visit the Arabidopsis genome (which is small)
- Click "Load Sequence" button
- A message should appear inviting you to download the entire file for faster future access.
- Click "yes"
3-
- Repeat 2.
- The message should not appear a second time.
Plus anything else you can think of – add instructions here.
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Sprint | Fall 4 Oct 26 - Nov 6 [ 107 ] | Fall 4 Oct 26 - Nov 6, Fall 5 Nov 9 - Nov 20 [ 107, 108 ] |
| Rank | Ranked higher |
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Everything looks good to me. Closing the ticket
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] | Noor Zahara [ noor91zahara ] |
What should be the threshold genome sequence file size be?