Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-2565

Investigate and modify cache code to not download very large sequence files

        Details

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

          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

              Ascending order - Click to sort in descending order
              Hide
              Permalink
              noor91zahara Noor Zahara (Inactive) added a comment -

              What should be the threshold genome sequence file size be?

              Show
              noor91zahara Noor Zahara (Inactive) added a comment - What should be the threshold genome sequence file size be?
              Hide
              Permalink
              ann.loraine Ann Loraine added a comment -

              Let's go with 0.8 Gb for now.

              Show
              ann.loraine Ann Loraine added a comment - Let's go with 0.8 Gb for now.
              Hide
              Permalink
              noor91zahara Noor Zahara (Inactive) added a comment - - edited

              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.

              Show
              noor91zahara Noor Zahara (Inactive) added a comment - - edited 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.
              Hide
              Permalink
              ssegu Sai Supreeth Segu (Inactive) added a comment -

              Everything looks good to me. Please submit pull request

              Show
              ssegu Sai Supreeth Segu (Inactive) added a comment - Everything looks good to me. Please submit pull request
              Hide
              Permalink
              noor91zahara Noor Zahara (Inactive) added a comment -

              PR submitted - https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/845/igbf-2565-investigate-and-modify-cache/diff

              Show
              noor91zahara Noor Zahara (Inactive) added a comment - PR submitted - https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/845/igbf-2565-investigate-and-modify-cache/diff
              Hide
              Permalink
              ann.loraine Ann Loraine added a comment -

              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.

              Show
              ann.loraine Ann Loraine added a comment - 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.
              Hide
              Permalink
              ssegu Sai Supreeth Segu (Inactive) added a comment -

              Everything looks good to me. Closing the ticket

              Show
              ssegu Sai Supreeth Segu (Inactive) added a comment - Everything looks good to me. Closing the ticket

                People

                • Assignee:
                  noor91zahara Noor Zahara (Inactive)
                  Reporter:
                  ann.loraine Ann Loraine
                • Votes:
                  0 Vote for this issue
                  Watchers:
                  3 Start watching this issue

                  Dates

                  • Created:
                    Updated:
                    Resolved: