[IGBF-4263] Investigate: Workflow implemented in galaxy bridge page is not working as expected - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Critical
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
2
Epic Link:
Improve Galaxy integration
Sprint:
Summer 4, Summer 5

Description

The workflow implemented in the Galaxy Bridge page - with URL https://bioviz.org/galaxy.html - is not working as expected. A re-design of the code may be needed!

Here is what should happen:

If a user clicks a "display in IGB ( View )" link for a Galaxy dataset and IGB is not yet running, a message is supposed to appear letting the user know that they need to start IGB to see the data. This works fine if a dataset dbkey is set.

However, if a dataset is lacking a dbkey and IGB is not running, then another message appears that does not make a lot of sense if IGB is not running. That message says:

The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.

Thus, the business logic of the page appears to be messed up. Here is what ideally should happen whenever a user clicks the "view in IGB" link for a Galaxy History dataset:

First, the page code should check: Is IGB running?

Yes -> go to A
No -> go to B

A: Check: is there a "dbkey" for the dataset?

Yes -> go to C
No -> go to D

B: Display a message that tells the user to start IGB and then refresh the page. Upon refresh, do A.

C: At this point, we know that Galaxy History dataset dbkey value is set and also that IGB is running. Now tell the user to check IGB. IGB should have opened a new empty track for the dataset. They should zoom in on a gene or a group of genes, and click Load Data button to load the Galaxy History dataset's data into the new track.

D. At this point, we know that Galaxy History dataset dbkey value is NOT set and also that IGB is running. This means that IGB may or may not be showing a genome version appropriate for the dataset to be shown on top of. Tell the user that if they have not already done so, go to IGB and open the genome of corresponding to the Galaxy History dataset they are trying to view. Let them know that once they do that, they can refresh the page to send the data to a new track in IGB.

Note that we have set up Google Analytics for this page. We are tracking a number of the steps in the workflow, and we need to take this into account when making any changes. Ideally, we would not lose our ability to track any of these key "milestones" when viewing data from Galaxy History data files.

For this task, please:

Attempt to reproduce the bug, e.g., when IGB is not running and you click a "view in IGB" link from a Galaxy History dataset, you see the message from above:

The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.

Propose a new structure for the underlying code that will correctly guide an astute user through the steps they need to perform in order to view the data from a Galaxy History dataset in IGB.

Attachments

Issue Links

relates to

IGBF-4111 Create a storyboard showing the Galaxy-to-IGB workflow

To-Do

IGBF-3960 Test and improve Galaxy page on BioViz.org

Closed

Activity

Ascending order - Click to sort in descending order

Ann Loraine created issue - 09/Jul/25 10:55 AM

Ann Loraine made changes - 09/Jul/25 10:55 AM

Field	Original Value	New Value
Epic Link		IGBF-1880 [ 17970 ]

Ann Loraine made changes - 09/Jul/25 10:55 AM

Description

The workflow implemented in the Galaxy Bridge page - with URL https://bioviz.org/galaxy.html - is not working as expected. A re-design of the code may be needed!

Here is what should happen:

If a user clicks a "view in IGB" link for a Galaxy dataset *and* IGB is not yet running, a message is supposed to appear letting the user know that they need to start IGB to see the data. This works fine if a dataset dbkey is set. It does not work if the dbkey is not set.

If a dataset is lacking a dbkey and IGB is not running, then another message appears that does not make a lot of sense if IGB is not running. That message says:

{quote}
The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.
{quote}

The business logic of the page appears to be messed up. Here is what ideally should happen whenever a user clicks the "view in IGB" link for a Galaxy History dataset:

First, the page code should check: Is IGB running?
* Yes -> go to A
* No -> go to B

A: Check: is there a "dbkey" for the dataset?
* Yes -> go to C
* No -> go to D

B: Display a message that tells the user to start IGB and then refresh the page. Upon refresh, do A.

C: At this point, we know that Galaxy History dataset dbkey value is set and also that IGB is running. Now tell the user to check IGB. IGB should have opened a new empty track for the dataset. They should zoom in on a gene or a group of genes, and click Load Data button to load the Galaxy History dataset's data into the new track.

D. At this point, we know that Galaxy History dataset dbkey value is NOT set and also that IGB is running. This means that IGB may or may not be showing a genome version appropriate for the dataset to be shown on top of. Tell the user that if they have not already done so, go to IGB and open the genome of corresponding to the Galaxy History dataset they are trying to view. Let them know that once they do that, they can refresh the page to send the data to a new track in IGB.

Note that we have set up Google Analytics for this page. We are tracking a number of the steps in the workflow, and we need to take this into account when making any changes. Ideally, we would not lose our ability to track any of these key "milestones" when viewing data from Galaxy History data files.

For this task, please:

* Attempt to reproduce the bug, e.g., when IGB is not running and you click a "view in IGB" link from a Galaxy History dataset, you see the message from above:

{quote}
The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.
{quote}

* Propose a new structure for the underlying code that will correctly guide an astute user through the steps they need to perform in order to view the data from a Galaxy History dataset in IGB.

The workflow implemented in the Galaxy Bridge page - with URL https://bioviz.org/galaxy.html - is not working as expected. A re-design of the code may be needed!

Here is what should happen:

If a user clicks a "view in IGB" link for a Galaxy dataset *and* IGB is not yet running, a message is supposed to appear letting the user know that they need to start IGB to see the data. This works fine if a dataset dbkey is set. It does not work if the dbkey is not set.

If a dataset is lacking a dbkey and IGB is not running, then another message appears that does not make a lot of sense if IGB is not running. That message says:

{quote}
The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.
{quote}

Thus, the business logic of the page appears to be messed up. Here is what ideally should happen whenever a user clicks the "view in IGB" link for a Galaxy History dataset:

First, the page code should check: Is IGB running?
* Yes -> go to A
* No -> go to B

A: Check: is there a "dbkey" for the dataset?
* Yes -> go to C
* No -> go to D

B: Display a message that tells the user to start IGB and then refresh the page. Upon refresh, do A.

C: At this point, we know that Galaxy History dataset dbkey value is set and also that IGB is running. Now tell the user to check IGB. IGB should have opened a new empty track for the dataset. They should zoom in on a gene or a group of genes, and click Load Data button to load the Galaxy History dataset's data into the new track.

D. At this point, we know that Galaxy History dataset dbkey value is NOT set and also that IGB is running. This means that IGB may or may not be showing a genome version appropriate for the dataset to be shown on top of. Tell the user that if they have not already done so, go to IGB and open the genome of corresponding to the Galaxy History dataset they are trying to view. Let them know that once they do that, they can refresh the page to send the data to a new track in IGB.

Note that we have set up Google Analytics for this page. We are tracking a number of the steps in the workflow, and we need to take this into account when making any changes. Ideally, we would not lose our ability to track any of these key "milestones" when viewing data from Galaxy History data files.

For this task, please:

* Attempt to reproduce the bug, e.g., when IGB is not running and you click a "view in IGB" link from a Galaxy History dataset, you see the message from above:

{quote}
The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.
{quote}

* Propose a new structure for the underlying code that will correctly guide an astute user through the steps they need to perform in order to view the data from a Galaxy History dataset in IGB.

Ann Loraine made changes - 09/Jul/25 11:19 AM

Description

The workflow implemented in the Galaxy Bridge page - with URL https://bioviz.org/galaxy.html - is not working as expected. A re-design of the code may be needed!

Here is what should happen:

If a user clicks a "view in IGB" link for a Galaxy dataset *and* IGB is not yet running, a message is supposed to appear letting the user know that they need to start IGB to see the data. This works fine if a dataset dbkey is set. It does not work if the dbkey is not set.

If a dataset is lacking a dbkey and IGB is not running, then another message appears that does not make a lot of sense if IGB is not running. That message says:

{quote}
The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.
{quote}

Thus, the business logic of the page appears to be messed up. Here is what ideally should happen whenever a user clicks the "view in IGB" link for a Galaxy History dataset:

First, the page code should check: Is IGB running?
* Yes -> go to A
* No -> go to B

A: Check: is there a "dbkey" for the dataset?
* Yes -> go to C
* No -> go to D

B: Display a message that tells the user to start IGB and then refresh the page. Upon refresh, do A.

C: At this point, we know that Galaxy History dataset dbkey value is set and also that IGB is running. Now tell the user to check IGB. IGB should have opened a new empty track for the dataset. They should zoom in on a gene or a group of genes, and click Load Data button to load the Galaxy History dataset's data into the new track.

D. At this point, we know that Galaxy History dataset dbkey value is NOT set and also that IGB is running. This means that IGB may or may not be showing a genome version appropriate for the dataset to be shown on top of. Tell the user that if they have not already done so, go to IGB and open the genome of corresponding to the Galaxy History dataset they are trying to view. Let them know that once they do that, they can refresh the page to send the data to a new track in IGB.

Note that we have set up Google Analytics for this page. We are tracking a number of the steps in the workflow, and we need to take this into account when making any changes. Ideally, we would not lose our ability to track any of these key "milestones" when viewing data from Galaxy History data files.

For this task, please:

* Attempt to reproduce the bug, e.g., when IGB is not running and you click a "view in IGB" link from a Galaxy History dataset, you see the message from above:

{quote}
The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.
{quote}

* Propose a new structure for the underlying code that will correctly guide an astute user through the steps they need to perform in order to view the data from a Galaxy History dataset in IGB.

The workflow implemented in the Galaxy Bridge page - with URL https://bioviz.org/galaxy.html - is not working as expected. A re-design of the code may be needed!

Here is what should happen:

If a user clicks a "display in IGB ( View )" link for a Galaxy dataset *and* IGB is not yet running, a message is supposed to appear letting the user know that they need to start IGB to see the data. This works fine if a dataset dbkey is set.

However, if a dataset is lacking a dbkey and IGB is not running, then another message appears that does not make a lot of sense if IGB is not running. That message says:

{quote}
The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.
{quote}

Thus, the business logic of the page appears to be messed up. Here is what ideally should happen whenever a user clicks the "view in IGB" link for a Galaxy History dataset:

First, the page code should check: Is IGB running?
* Yes -> go to A
* No -> go to B

A: Check: is there a "dbkey" for the dataset?
* Yes -> go to C
* No -> go to D

B: Display a message that tells the user to start IGB and then refresh the page. Upon refresh, do A.

C: At this point, we know that Galaxy History dataset dbkey value is set and also that IGB is running. Now tell the user to check IGB. IGB should have opened a new empty track for the dataset. They should zoom in on a gene or a group of genes, and click Load Data button to load the Galaxy History dataset's data into the new track.

D. At this point, we know that Galaxy History dataset dbkey value is NOT set and also that IGB is running. This means that IGB may or may not be showing a genome version appropriate for the dataset to be shown on top of. Tell the user that if they have not already done so, go to IGB and open the genome of corresponding to the Galaxy History dataset they are trying to view. Let them know that once they do that, they can refresh the page to send the data to a new track in IGB.

Note that we have set up Google Analytics for this page. We are tracking a number of the steps in the workflow, and we need to take this into account when making any changes. Ideally, we would not lose our ability to track any of these key "milestones" when viewing data from Galaxy History data files.

For this task, please:

* Attempt to reproduce the bug, e.g., when IGB is not running and you click a "view in IGB" link from a Galaxy History dataset, you see the message from above:

{quote}
The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.
{quote}

* Propose a new structure for the underlying code that will correctly guide an astute user through the steps they need to perform in order to view the data from a Galaxy History dataset in IGB.

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Ann Loraine added a comment - 10/Jul/25 10:20 AM - edited

Nowlan Freese and Ann Loraine discussed this in depth yesterday. We are planning to dedicate the remainder of July to investigating how to improve the code and the workflow.

Next steps:

Develop a Powerpoint showing screens in Bioviz for a more user-friendly workflow.

Show

Ann Loraine added a comment - 10/Jul/25 10:20 AM - edited Nowlan Freese and Ann Loraine discussed this in depth yesterday. We are planning to dedicate the remainder of July to investigating how to improve the code and the workflow. Next steps: Develop a Powerpoint showing screens in Bioviz for a more user-friendly workflow.

Nowlan Freese made changes - 10/Jul/25 10:28 AM

Link

This issue relates to ~~IGBF-3960~~ [ ~~IGBF-3960~~ ]

Nowlan Freese made changes - 10/Jul/25 10:28 AM

Link

This issue relates to IGBF-4111 [ IGBF-4111 ]

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Permalink

Nowlan Freese added a comment - 10/Jul/25 10:31 AM

See ~~IGBF-3960~~ for a powerpoint exploring the Galaxy bridge.

Show

Nowlan Freese added a comment - 10/Jul/25 10:31 AM See IGBF-3960 for a powerpoint exploring the Galaxy bridge.

Nowlan Freese made changes - 11/Jul/25 3:00 PM

Sprint

Summer 5 [ 222 ]

Summer 4 [ 221 ]

Nowlan Freese made changes - 11/Jul/25 3:00 PM

Rank

Ranked lower

Nowlan Freese made changes - 11/Jul/25 3:00 PM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 11/Jul/25 3:00 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Nowlan Freese made changes - 18/Jul/25 9:59 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 21/Jul/25 10:04 AM

Sprint

Summer 4 [ 221 ]

Summer 4, Summer 5 [ 221, 222 ]

Ann Loraine made changes - 21/Jul/25 10:04 AM

Rank

Ranked higher

Nowlan Freese made changes - 22/Jul/25 11:54 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Hide

Permalink

Ann Loraine added a comment - 23/Jul/25 11:00 AM

Replace the "you don't have a dbkey" message with:

"Go to Integrated Genome Browser to view your data."

Show

Ann Loraine added a comment - 23/Jul/25 11:00 AM Replace the "you don't have a dbkey" message with: "Go to Integrated Genome Browser to view your data."

Hide

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Nowlan Freese added a comment - 25/Jul/25 1:51 PM - edited

I made two commits, the first is to improve the wording of the message when no genome/dbkey is associated with a file. The second is to improve the logic for when the genome/dbkey warning is shown to the user if IGB is or is not open.

Branch with both commits: https://bitbucket.org/nfreese/bioviz/branch/IGBF-4263

To test assuming testing local branch and using Webstorm:

Fetch my branch
Close IGB
This link has a version attached. You should see the warning page that IGB is closed.
This link has no version attached. You should see the warning page that IGB is closed and that no genome version is attached.
Start IGB
Repeat loading the above two files.

The first file should only show the file loading successfully in IGB page.
The second file (with no genome version) should show the file loading successfully page along with a warning that no genome version is attached.

If testing post-merge and release, the test file URLs should be:

Genome version attached link
No genome version link

Pull request that includes BOTH commits: https://bitbucket.org/lorainelab/bioviz/pull-requests/180

Pull request that ONLY includes the text change commit: https://bitbucket.org/lorainelab/bioviz/pull-requests/181

Show

Nowlan Freese added a comment - 25/Jul/25 1:51 PM - edited I made two commits, the first is to improve the wording of the message when no genome/dbkey is associated with a file. The second is to improve the logic for when the genome/dbkey warning is shown to the user if IGB is or is not open. Branch with both commits: https://bitbucket.org/nfreese/bioviz/branch/IGBF-4263 To test assuming testing local branch and using Webstorm: Fetch my branch Close IGB This link has a version attached. You should see the warning page that IGB is closed. This link has no version attached. You should see the warning page that IGB is closed and that no genome version is attached. Start IGB Repeat loading the above two files. The first file should only show the file loading successfully in IGB page. The second file (with no genome version) should show the file loading successfully page along with a warning that no genome version is attached. If testing post-merge and release, the test file URLs should be: Genome version attached link No genome version link Pull request that includes BOTH commits: https://bitbucket.org/lorainelab/bioviz/pull-requests/180 Pull request that ONLY includes the text change commit: https://bitbucket.org/lorainelab/bioviz/pull-requests/181

Nowlan Freese made changes - 25/Jul/25 2:48 PM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 25/Jul/25 2:48 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Nowlan Freese made changes - 25/Jul/25 2:49 PM

Assignee

Ann Loraine [ aloraine ]

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Ann Loraine added a comment - 25/Jul/25 3:09 PM

The changes look good and I am going to go ahead and merge the PR that contains both commits and then deploy onto bioviz.org.

Show

Ann Loraine added a comment - 25/Jul/25 3:09 PM The changes look good and I am going to go ahead and merge the PR that contains both commits and then deploy onto bioviz.org.

Ann Loraine made changes - 25/Jul/25 3:09 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Ann Loraine made changes - 25/Jul/25 3:09 PM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

Ann Loraine made changes - 25/Jul/25 3:09 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

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Ann Loraine added a comment - 25/Jul/25 3:18 PM

PR is merged and deployed to bioviz.org. Ready for testing.
I went ahead and tested the workflow with a dataset that has no dbkey (SL5 from tomato), without IGB running and with IGB running. In the case of IGB running, I checked how it works with and without the correct genome loaded. In all cases, I observed the expected behavior.

I really like the yellow banner below the "Welcome Galaxy user" box. It is a big improvement over the previous design, in my opinion.

Close this issue. Thank you Nowlan Freese!

Show

Ann Loraine added a comment - 25/Jul/25 3:18 PM PR is merged and deployed to bioviz.org. Ready for testing. I went ahead and tested the workflow with a dataset that has no dbkey (SL5 from tomato), without IGB running and with IGB running. In the case of IGB running, I checked how it works with and without the correct genome loaded. In all cases, I observed the expected behavior. I really like the yellow banner below the "Welcome Galaxy user" box. It is a big improvement over the previous design, in my opinion. Close this issue. Thank you Nowlan Freese !