[IGBF-2213] Fix NCBI Primer design App - JIRA UNCC

Details

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

Story Points:
2
Epic Link:
Build & maintain IGB Apps
Sprint:
Spring 1 : 25 Dec to 17 Jan

Description

Update the code for NCBI Primer Blast to use declarative services to add new item to context menu that appears when users right-click an item in the IGB display.

Attachments

Issue Links

relates to

IGBF-2241 Re-factor NCBI Primer design App

Closed

IGBF-2212 Simplify development (experimental) apps build and deployment system

Closed

Activity

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Ann Loraine created issue - 04/Jan/20 5:35 PM

Ann Loraine made changes - 04/Jan/20 5:35 PM

Field	Original Value	New Value
Epic Link		IGBF-1908 [ 17998 ]

Ann Loraine made changes - 04/Jan/20 5:35 PM

Link

This issue relates to ~~IGBF-2212~~ [ ~~IGBF-2212~~ ]

Ann Loraine made changes - 04/Jan/20 5:35 PM

Rank

Ranked higher

Ann Loraine made changes - 04/Jan/20 5:36 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Ann Loraine added a comment - 04/Jan/20 5:43 PM

For developer convenience, working on topic branch and pushing topic branch to team repository:
https://bitbucket.org/lorainelab/experimental-apps-for-igb/branch/IGBF-2213

Note: When topic branch is merged, will close it.

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Ann Loraine added a comment - 04/Jan/20 5:43 PM For developer convenience, working on topic branch and pushing topic branch to team repository: https://bitbucket.org/lorainelab/experimental-apps-for-igb/branch/IGBF-2213 Note : When topic branch is merged, will close it.

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Ann Loraine added a comment - 05/Jan/20 9:17 PM

Made some progress, but it still does not work.
Call to NCBI service is being made incorrectly somehow. I added some notes on this to the code. Also, I moved some testing code from "main" into "test" and add junit imports and Test annotations. Also added notes as to what I think needs to be done next.
I am not sure if the App can be fixed. The next step would be to find out why it is not working. Once we know that, we can determine if it is possible to fix it. One concern I have is that the code seems to assume that the primer design will happen quickly, which may have been the case in the past but does not appear to be currently. What happens is that that a job gets submitted and then you have to wait 30 seconds to a minute or more for it to complete. In the meantime, you get back a URL with a job ID. This is similar to how the InterproScan web service works (see ProtAnnot App). If the waiting period is long, then we need to run the search in a separate thread so that IGB does not block. Also, we might want to change the UI so that a user can observe the progress, similar to how ProtAnnot works. Last but not least, we should probably use more modern tooling to send the POST request to the NCBI server.
That's all I've got for now! Closing this issue for the moment.

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Ann Loraine added a comment - 05/Jan/20 9:17 PM Made some progress, but it still does not work. Call to NCBI service is being made incorrectly somehow. I added some notes on this to the code. Also, I moved some testing code from "main" into "test" and add junit imports and Test annotations. Also added notes as to what I think needs to be done next. I am not sure if the App can be fixed. The next step would be to find out why it is not working. Once we know that, we can determine if it is possible to fix it. One concern I have is that the code seems to assume that the primer design will happen quickly, which may have been the case in the past but does not appear to be currently. What happens is that that a job gets submitted and then you have to wait 30 seconds to a minute or more for it to complete. In the meantime, you get back a URL with a job ID. This is similar to how the InterproScan web service works (see ProtAnnot App). If the waiting period is long, then we need to run the search in a separate thread so that IGB does not block. Also, we might want to change the UI so that a user can observe the progress, similar to how ProtAnnot works. Last but not least, we should probably use more modern tooling to send the POST request to the NCBI server. That's all I've got for now! Closing this issue for the moment.