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  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

          Hide
          noor91zahara Noor Zahara added a comment -

          What should be the threshold genome sequence file size be?

          Show
          noor91zahara Noor Zahara added a comment - What should be the threshold genome sequence file size be?
          Hide
          aloraine Ann Loraine added a comment -

          Let's go with 0.8 Gb for now.

          Show
          aloraine Ann Loraine added a comment - Let's go with 0.8 Gb for now.
          Hide
          noor91zahara Noor Zahara 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 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
          ssegu Sai Supreeth Segu added a comment -

          Everything looks good to me. Please submit pull request

          Show
          ssegu Sai Supreeth Segu added a comment - Everything looks good to me. Please submit pull request
          Show
          noor91zahara Noor Zahara added a comment - PR submitted - https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/845/igbf-2565-investigate-and-modify-cache/diff
          Hide
          aloraine 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
          aloraine 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
          ssegu Sai Supreeth Segu added a comment -

          Everything looks good to me. Closing the ticket

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

            People

            • Assignee:
              noor91zahara Noor Zahara
              Reporter:
              aloraine Ann Loraine
            • Votes:
              0 Vote for this issue
              Watchers:
              3 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: