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: 9.1.6 Major Release
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Fall 5 Nov 9 - Nov 20
Description
Situation: Quickloads that point to files stored in ftp are unable to be loaded in IGB. This feature was last working in version 8.3.4, indicating a change in 8.4.0 broke some of the functionality.
The issue may be several issues. For example, in FeatureTreeView.java actionPerformed there is a check to see if the data is reachable. In 9.1.6 attempting to load an ftp via quickload causes the isReachable(dataset) to return false. If this is hardcoded to true, then the file will be added to IGB, however, when the data are loaded a bai index file not found error is then thrown.
Note that loading ftp data directly through IGB works, it is only when the ftp data are attempted to load through the quickload that it fails.
Task: Implement a fix so that ftp files can be loaded via quickload.
Attachments
Issue Links
- blocks
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IGBF-1217 add Genome in a Bottle data sets to IGB Quickload
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
Situation: Quickloads that point to files stored in ftp are unable to be loaded in IGB. This feature was last working in version 8.3.4, indicating a change in 8.4.0 broke some of the functionality. The issue may be several issues. For example, in FeatureTreeView.java actionPerformed there is a check to see if the data is reachable. In 9.1.6 attempting to load an ftp via quickload causes the isReachable(dataset) to return false. If this is hardcoded to true, then the file will be added to IGB, however, when the data are loaded a bai index file not found error is then thrown. Note that loading ftp data directly through IGB works, it is only when the ftp data are attempted to load through the quickload that it fails.
Task: Implement a fix so that ftp files can be loaded via quickload. |
Situation: Quickloads that point to files stored in ftp are unable to be loaded in IGB. This feature was last working in version 8.3.4, indicating a change in 8.4.0 broke some of the functionality.
The issue may be several issues. For example, in FeatureTreeView.java actionPerformed there is a check to see if the data is reachable. In 9.1.6 attempting to load an ftp via quickload causes the isReachable(dataset) to return false. If this is hardcoded to true, then the file will be added to IGB, however, when the data are loaded a bai index file not found error is then thrown. Note that loading ftp data directly through IGB works, it is only when the ftp data are attempted to load through the quickload that it fails. Task: Implement a fix so that ftp files can be loaded via quickload. |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
Fixed the errors and updated the changes. Please review my changes.
Link for the branch: https://bitbucket.org/supreeth27/integrated-genome-browser/branch/IGBF-2589#diff
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
I have a request for clarification:
It looks like there is some logic intended to handle all the protocols - http, etc.
FTP was not handled & now it is.
Should we also address https? I am not seeing where it is handled, but I may be missing it.
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
[~aloraine] (!file.getName().startsWith("http") handles https as well because https also starts with http. I have already tested https request as well.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Tested IGBF-2589 installer on Mac from Supreeth's branch.
Able to load ftp and http remotely hosted files as specified through the quickload.
Sai Supreeth Segu please create a pull request.
| Assignee | Nowlan Freese [ nfreese ] | Sai Supreeth Segu [ ssegu ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Please review my pull request.
Link for pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/847/igbf-2589-fixing-ftp-quickload
| Assignee | Sai Supreeth Segu [ ssegu ] |
| Comment | [ Pull request https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/847 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Merged and master branch installers built.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Story Points | 3 | 2 |
Tested master dmg installer on Mac.
Able to view remote ftp and http data from local quickload.
Closing issue.
| Assignee | Nowlan Freese [ nfreese ] | Sai Supreeth Segu [ ssegu ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Fix Version/s | 9.1.6 Major Release [ 10604 ] |
I have attached an example quickload (zip file) for the human genome that includes links to two bam files. The Illumina_2x250 points to an ftp file.