Details
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Type:
Task
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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:None
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Story Points:2
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Epic Link:
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Sprint:Spring 3, Spring 5
Description
Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.
Task: Update BioViz Connect so that CRAM is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions.
Attachments
Issue Links
- is blocked by
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IGBF-3478 Add CRAM support to IGB
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2376 [ 18533 ] |
| Description |
Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.
Task: Update BioViz Connect so that cram is an accepted file format. |
Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.
Task: Update BioViz Connect so that cram is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions. |
| Assignee | Karthik Raveendran [ karthik ] |
| Summary | Add Cram to list of supported files for BioViz Connect | Add CRAM to list of supported files for BioViz Connect |
| Description |
Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.
Task: Update BioViz Connect so that cram is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions. |
Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.
Task: Update BioViz Connect so that CRAM is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions. |
| Description |
Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.
Task: Update BioViz Connect so that CRAM is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions. |
Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.
Task: Update BioViz Connect so that CRAM is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions. |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Added cram to IGB supported file format. See commit
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Karthik Raveendran - how do we want to tackle version checking for cram?
Option 1: Do nothing, any user who is using an older version of IGB will see the View in IGB button for a CRAM file, but when clicked it will throw an error in IGB.
Option 2: Update logic in BioViz Connect to check the IGB version (major/minor/patch) and anything less than 10.0.0 will not show the View in IGB button for CRAM files.
Option 3: Update logic in BioViz Connect to check the IGB version (major/minor/patch) and anything less than 10.0.0 will show a modal informing the user "To view a CRAM file in IGB, please update your IGB to the most recent version".
I think we are checking IGB version in cyverse.js and there is a popup_modals.html warning for older versions of IGB.
| Assignee | Karthik Raveendran [ karthik ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Implemented Option 3 from the prev comment by Dr. Nowlan Freese. See commit
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| 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 ] |
| Sprint | Spring 3 [ 187 ] | Spring 3, Spring 4 [ 187, 188 ] |
| Rank | Ranked higher |
| Sprint | Spring 3, Spring 4 [ 187, 188 ] | Spring 3, Spring 5 [ 187, 189 ] |
To deploy testing and new versions using code in bioviz connect playbooks repository.
AL request: Karthik Raveendran to take over deploying new versions of bioviz connect code, using playbooks.
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Merged and deployed to connect.bioviz.org/
Deployed following instructions from bioviz-connect-playbooks repo with:
ansible-playbook -i inventory.ini setup.yml
Once the playbook was completed I had to hit the SyncAppDataToBioViz endpoint to see the change:
https://connect.bioviz.org/SyncAppDataToBioViz/?accesstoken=<validKeyCloakAccessToken>
I first tested the changes on bvctest7 (Nowlan has access to start/stop the instance).
Note that you will need to proper crt files and key. You will also need to have a properly filled out inventory.ini and group_vars > setup_vars.yml files. I also specify my repo in the roles > clone > defaults > main.yml file:
repo: https://bitbucket.org/nfreese/bioviz-connect.git
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
I uploaded a folder with matching cram/bam/sam files. I was able to modify the metadata to specify the Arabidopsis genome for the CRAM file. Once the CRAM file and its index were made public I was able to click View in IGB and view the files in IGB. If I tried to load a CRAM file into a version of IGB less than 10.0.0 I saw a warning from BioViz Connect that I should upgrade my version of IGB.
Closing ticket.
| Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Here is some additional information on the CRAM file format if anyone would like to better familiarize themselves: https://academic.oup.com/bioinformatics/article/38/6/1497/6499262