Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Minor
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:1
-
Epic Link:
-
Sprint:Fall 7 Dec 14 - Dec 23, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16, Spring 6 2022 Mar 14 - Mar 25
Description
A lot of Web sites are configured to redirect http to https for most URLs.
However, it is not clear how IGB handles this when accessing Quickload URLs.
For example, what happens if IGB tries to contact a site added to IGB as Quickload URL "http://example.com/quickload" and the server is configured to redirect request to "https://example.com/quickload" ?
Can IGB properly handle the redirect?
Please investigate.
Possible strategy:
- Add an all-new testing Quickload site to BioViz.org (e.g., http://bioviz.org/example_quickload), submit PR for the example and wait for it to merged and deployed
- Confirm that the redirection is working by opening the "contents.txt" URL in a browser (http://bioviz.org/example_quickload/contents.txt)
- Deactivate all current Quickload sites in IGB and then re-start IGB
- Next, add this new Quickload testing URL to IGB using protocol "http" as the quickload address
- Then try to open the genome from the testing site in IGB
- Report any errors observed.
Does IGB appear to be reading and using the testing quickload meta-data files to configure the genome?
Report on any errors.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Sprint | Fall 6 Nov 30 - Dec 11 [ 109 ] | Fall 7 Dec 14 - Dec 23 [ 110 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Description |
BioViz.org sites are configured to redirect http to https for most URLs.
Currently, IGB does not handle it very well when a site redirects a Quickload URL. Until we can fix this, let's modify the bioviz.org site so that no redirect to https happens for any directories at or below /quickload Note: IGB release 9.1.6 specifies a bioviz.org address for "bar" quickload site. We do this to more easily demonstrate to users how to create a quickload site for sharing data in IGB. |
BioViz.org sites are configured to redirect http to https for most URLs.
Currently, IGB does not handle it very well when a site redirects a Quickload URL. Until we can fix this, let's modify the bioviz.org site so that no redirect to https happens for any directories at or below /quickload |
| Sprint | Fall 7 Dec 14 - Dec 23 [ 110 ] | Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 110, 111 ] |
| Rank | Ranked higher |
| Sprint | Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 110, 111 ] | Fall 7 Dec 14 - Dec 23 [ 110 ] |
| Sprint | Fall 7 Dec 14 - Dec 23 [ 110 ] | Fall 7 Dec 14 - Dec 23, Spring 1 Mar 22 - Apr 2 [ 110, 117 ] |
| Description |
BioViz.org sites are configured to redirect http to https for most URLs.
Currently, IGB does not handle it very well when a site redirects a Quickload URL. Until we can fix this, let's modify the bioviz.org site so that no redirect to https happens for any directories at or below /quickload |
BioViz.org sites are configured to redirect http to https for most URLs.
This may not be working well in conjunction with IGB's ability to fetch data using URLs configured in annots.xml annotation file listings. Please investigate. |
| Summary | Allow http for /quickload URLs on BioViz.org | Investigate: Allow http for /quickload URLs on BioViz.org |
| Rank | Ranked higher |
| Sprint | Fall 7 Dec 14 - Dec 23, Spring 1 2021 Mar 22 - Apr 2 [ 110, 117 ] | Fall 7 Dec 14 - Dec 23, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16 [ 110, 117, 118 ] |
| Rank | Ranked higher |
| Sprint | Fall 7 Dec 14 - Dec 23, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16 [ 110, 117, 118 ] | Fall 7 Dec 14 - Dec 23, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30 [ 110, 117, 118, 119 ] |
| Rank | Ranked higher |
| Summary | Investigate: Allow http for /quickload URLs on BioViz.org | Quickload URLs on BioViz.org |
| Description |
BioViz.org sites are configured to redirect http to https for most URLs.
This may not be working well in conjunction with IGB's ability to fetch data using URLs configured in annots.xml annotation file listings. Please investigate. |
BioViz.org sites are configured to redirect http to https for most URLs.
What happens if IGB tries to contact a site added to IGB as "http://bioviz.org/quickload" and then the server redirects request to https://bioviz.org/quickload Can IGB properly handle the direct? Please investigate. |
| Priority | Major [ 3 ] | Minor [ 4 ] |
| Issue Type | Bug [ 1 ] | Task [ 3 ] |
| Description |
BioViz.org sites are configured to redirect http to https for most URLs.
What happens if IGB tries to contact a site added to IGB as "http://bioviz.org/quickload" and then the server redirects request to https://bioviz.org/quickload Can IGB properly handle the direct? Please investigate. |
BioViz.org sites are configured to redirect http to https for most URLs.
What happens if IGB tries to contact a site added to IGB as "http://bioviz.org/quickload" and then the server redirects request to https://bioviz.org/quickload Can IGB properly handle the redirect? Please investigate. |
| Assignee | Rachel Weidenhammer [ rweidenh ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Assignee | Rachel Weidenhammer [ rweidenh ] |
| Description |
BioViz.org sites are configured to redirect http to https for most URLs.
What happens if IGB tries to contact a site added to IGB as "http://bioviz.org/quickload" and then the server redirects request to https://bioviz.org/quickload Can IGB properly handle the redirect? Please investigate. |
BioViz.org sites are configured to redirect http to https for most URLs.
What happens if IGB tries to contact a site added to IGB as "http://bioviz.org/quickload" and then the server redirects request to https://bioviz.org/quickload Can IGB properly handle the redirect? Please investigate. |
| Link | This issue relates to IGBF-2814 [ IGBF-2814 ] |
| Assignee | Rachel Weidenhammer [ rweidenh ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
BioViz.org sites are configured to redirect http to https for most URLs.
What happens if IGB tries to contact a site added to IGB as "http://bioviz.org/quickload" and then the server redirects request to https://bioviz.org/quickload Can IGB properly handle the redirect? Please investigate. |
BioViz.org sites are configured to redirect http to https for most URLs.
What happens if IGB tries to contact a site added to IGB as "http://bioviz.org/quickload" and then the server redirects request to https://bioviz.org/quickload Can IGB properly handle the redirect? Please investigate. Add an http remote quickload as a data source, whose site will redirect to https. Then open the genome and version in IGB. Check to see that the remote quickload is available in the Data Access panel. Check that the quickload files can be opened and loaded in IGB. |
| Description |
BioViz.org sites are configured to redirect http to https for most URLs.
What happens if IGB tries to contact a site added to IGB as "http://bioviz.org/quickload" and then the server redirects request to https://bioviz.org/quickload Can IGB properly handle the redirect? Please investigate. Add an http remote quickload as a data source, whose site will redirect to https. Then open the genome and version in IGB. Check to see that the remote quickload is available in the Data Access panel. Check that the quickload files can be opened and loaded in IGB. |
BioViz.org sites are configured to redirect http to https for most URLs.
What happens if IGB tries to contact a site added to IGB as "http://bioviz.org/quickload" and then the server redirects request to https://bioviz.org/quickload Can IGB properly handle the redirect? Please investigate. Add a http remote quickload as a data source, whose site will redirect to https. Then open the genome and version in IGB. Check to see that the remote quickload is available in the Data Access panel. Check that the quickload files can be opened and loaded in IGB. |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Assignee | Rachel Weidenhammer [ rweidenh ] |
| Sprint | Fall 7 Dec 14 - Dec 23, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30 [ 110, 117, 118, 119 ] | Fall 7 Dec 14 - Dec 23, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16 [ 110, 117, 118 ] |
| Rank | Ranked higher |
| Description |
BioViz.org sites are configured to redirect http to https for most URLs.
What happens if IGB tries to contact a site added to IGB as "http://bioviz.org/quickload" and then the server redirects request to https://bioviz.org/quickload Can IGB properly handle the redirect? Please investigate. Add a http remote quickload as a data source, whose site will redirect to https. Then open the genome and version in IGB. Check to see that the remote quickload is available in the Data Access panel. Check that the quickload files can be opened and loaded in IGB. |
A lot of Web sites are configured to redirect http to https for most URLs.
However, it is not clear how IGB handles this when accessing Quickload URLs. For example, what happens if IGB tries to contact a site added to IGB as "http://example.com/quickload" and then the server redirects request to https://example.com/quickload Can IGB properly handle the redirect? Please investigate. Add a http remote quickload as a data source, whose site will redirect to https. Then open the genome and version in IGB. Check to see that the remote quickload is available in the Data Access panel. Check that the quickload files can be opened and loaded in IGB. |
| Summary | Quickload URLs on BioViz.org | Investigate: How does IGB handle Quickload URL redirection from http to https |
| Description |
A lot of Web sites are configured to redirect http to https for most URLs.
However, it is not clear how IGB handles this when accessing Quickload URLs. For example, what happens if IGB tries to contact a site added to IGB as "http://example.com/quickload" and then the server redirects request to https://example.com/quickload Can IGB properly handle the redirect? Please investigate. Add a http remote quickload as a data source, whose site will redirect to https. Then open the genome and version in IGB. Check to see that the remote quickload is available in the Data Access panel. Check that the quickload files can be opened and loaded in IGB. |
A lot of Web sites are configured to redirect http to https for most URLs.
However, it is not clear how IGB handles this when accessing Quickload URLs. For example, what happens if IGB tries to contact a site added to IGB as Quickload URL "http://example.com/quickload" and the server is configured to redirect request to https://example.com/quickload? Can IGB properly handle the redirect? Please investigate. Possible strategy: * Add an all-new testing Quickload site to BioViz.org (e.g., http://bioviz.org/example_quickload), submit PR for the example and wait for it to merged and deployed * Confirm that the redirection is working by opening the "contents.txt" URL in a browser (http://bioviz.org/example_quickload/contents.txt) * Deactivate all current Quickload sites in IGB and then re-start IGB * Next, add this new Quickload testing URL to IGB using protocol "http" as the quickload address * Then try to open the genome from the testing site in IGB * Report any errors observed. Does IGB appear to be reading and using the testing quickload meta-data files to configure the genome? Report on any errors. |
| Comment |
[ It looks like per the related issue [code changes|https://bitbucket.org/pbadzuh/bioviz-playbooks_pbdev/commits/a9083860d12ee60458013c39b91b110b44a9ebf4] that only a user coming from galaxy will be redirected to the http site, otherwise a user will be redirected to the https site.
So, https redirection is turned on for IGB. When I use http://bioviz.org/quickload/bar/ as a quickload, it is accepted by IGB as an available data source. Both the http and https version of this link appear to work per the Data Sources tab in Preferences window. I haven't yet been able to figure out how to load them in IGB because the genome version from the remote site is the same as one already available on IGB, and it will automatically load that one even when another source is available. ] |
| Comment |
[ The sites: http://bioviz.org/quickload/bar/ and http://bioviz.org/quickload/test/
fail to redirect from http to https and so cannot be used for testing this issue. I have connected via Cisco AnyConnect vpn.uncc.edu. The site https://cci-igbquickload-dev.dyn.uncc.edu/quickload/ fails to load for me so cannot be used for testing at this time. ] |
| Comment |
[ It may be possible to test this issue by testing the server specified in IGBF-2814.
Note that you will need to be signed in to the UNCC VPN to be able to access the site: https://cci-igbquickload-dev.dyn.uncc.edu/quickload/ ] |
| Rank | Ranked higher |
| Sprint | Fall 7 Dec 14 - Dec 23, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16 [ 110, 117, 118 ] | Fall 7 Dec 14 - Dec 23, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16, Spring 6 2022 Mar 14 - Mar 25 [ 110, 117, 118, 141 ] |
| Story Points | 0.25 | 1 |
| Description |
A lot of Web sites are configured to redirect http to https for most URLs.
However, it is not clear how IGB handles this when accessing Quickload URLs. For example, what happens if IGB tries to contact a site added to IGB as Quickload URL "http://example.com/quickload" and the server is configured to redirect request to https://example.com/quickload? Can IGB properly handle the redirect? Please investigate. Possible strategy: * Add an all-new testing Quickload site to BioViz.org (e.g., http://bioviz.org/example_quickload), submit PR for the example and wait for it to merged and deployed * Confirm that the redirection is working by opening the "contents.txt" URL in a browser (http://bioviz.org/example_quickload/contents.txt) * Deactivate all current Quickload sites in IGB and then re-start IGB * Next, add this new Quickload testing URL to IGB using protocol "http" as the quickload address * Then try to open the genome from the testing site in IGB * Report any errors observed. Does IGB appear to be reading and using the testing quickload meta-data files to configure the genome? Report on any errors. |
A lot of Web sites are configured to redirect http to https for most URLs.
However, it is not clear how IGB handles this when accessing Quickload URLs. For example, what happens if IGB tries to contact a site added to IGB as Quickload URL "http://example.com/quickload" and the server is configured to redirect request to https://example.com/quickload ? Can IGB properly handle the redirect? Please investigate. Possible strategy: * Add an all-new testing Quickload site to BioViz.org (e.g., http://bioviz.org/example_quickload), submit PR for the example and wait for it to merged and deployed * Confirm that the redirection is working by opening the "contents.txt" URL in a browser (http://bioviz.org/example_quickload/contents.txt) * Deactivate all current Quickload sites in IGB and then re-start IGB * Next, add this new Quickload testing URL to IGB using protocol "http" as the quickload address * Then try to open the genome from the testing site in IGB * Report any errors observed. Does IGB appear to be reading and using the testing quickload meta-data files to configure the genome? Report on any errors. |
| Description |
A lot of Web sites are configured to redirect http to https for most URLs.
However, it is not clear how IGB handles this when accessing Quickload URLs. For example, what happens if IGB tries to contact a site added to IGB as Quickload URL "http://example.com/quickload" and the server is configured to redirect request to https://example.com/quickload ? Can IGB properly handle the redirect? Please investigate. Possible strategy: * Add an all-new testing Quickload site to BioViz.org (e.g., http://bioviz.org/example_quickload), submit PR for the example and wait for it to merged and deployed * Confirm that the redirection is working by opening the "contents.txt" URL in a browser (http://bioviz.org/example_quickload/contents.txt) * Deactivate all current Quickload sites in IGB and then re-start IGB * Next, add this new Quickload testing URL to IGB using protocol "http" as the quickload address * Then try to open the genome from the testing site in IGB * Report any errors observed. Does IGB appear to be reading and using the testing quickload meta-data files to configure the genome? Report on any errors. |
A lot of Web sites are configured to redirect http to https for most URLs.
However, it is not clear how IGB handles this when accessing Quickload URLs. For example, what happens if IGB tries to contact a site added to IGB as Quickload URL "http://example.com/quickload" and the server is configured to redirect request to "https://example.com/quickload" ? Can IGB properly handle the redirect? Please investigate. Possible strategy: * Add an all-new testing Quickload site to BioViz.org (e.g., http://bioviz.org/example_quickload), submit PR for the example and wait for it to merged and deployed * Confirm that the redirection is working by opening the "contents.txt" URL in a browser (http://bioviz.org/example_quickload/contents.txt) * Deactivate all current Quickload sites in IGB and then re-start IGB * Next, add this new Quickload testing URL to IGB using protocol "http" as the quickload address * Then try to open the genome from the testing site in IGB * Report any errors observed. Does IGB appear to be reading and using the testing quickload meta-data files to configure the genome? Report on any errors. |
| Assignee | Omkar Marne [ omarne ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Please review or search the commit history of the bioviz.org git repository: https://bitbucket.org/lorainelab/bioviz/src/master/
Hello Dr. Loraine, I have created a sample example_quickload. Please find my PR : https://bitbucket.org/lorainelab/bioviz/pull-requests/86/igbf-2669-example-quicload
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| 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 ] |
| Assignee | Omkar Marne [ omarne ] | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Change requests:
1) Change "example_genome" directory name to A_thaliana_Jun_2009
2) Move "example_quickload" to "htdocs/quickload"
3) Change name of "example_quickload" to "example"
4) Edit "annots.xml" to include only one file tag
5) Squash commits on the branch so that only the smaller version of annots.xml file does will get merged in
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Omkar Marne [ omarne ] |
Hello Dr. [~aloraine] Please see the requested changes below.
https://bitbucket.org/lorainelab/bioviz/pull-requests/86/igbf-2669
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Omkar Marne [ omarne ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
Please get rid of initial commit that added enormous xml file to repo.
Hello Dr. Loraine
Please find my new pull request : https://bitbucket.org/lorainelab/bioviz/pull-requests/87/igbf-2669-new-sample-quickload
| Status | To-Do [ 10305 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Ann Loraine [ aloraine ] |
Thanks - looks good. Proceeding to merge.
New example quickload is deployed to https://www.bioviz.org/quickload/example/
Moving back to "to-do" for Omkar Marne to use the new quickload to test as noted in the Description.
New example quickload is deployed to https://www.bioviz.org/quickload/example/
Moving back to "to-do" for Omkar Marne to use the new quickload to test as noted in the Description.
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Omkar Marne [ omarne ] |
| Attachment | example.png [ 17210 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | http.png [ 17211 ] |
| Attachment | https.png [ 17212 ] |
Test results after adding above quickload as data source:
IGB won't allow http protocol as data source as the server is set to automatically redirect from http to https. If the user uses the http quickload url then IGB won't follow the redirect and the quickload will not be added.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| 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 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Testing on a quickload hosted on bitbucket (which redirects from http to https as tested using Google Chrome and the contents.txt file) also fails to work in IGB if the quickload URL is set to http. Along with Omkar's testing it would appear that IGB does not follow the redirect from http to https for Quickloads.
Console logs:
10:18:29.900 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://bitbucket.org/nfreese/quickload-genome-in-a-bottle/raw/release-v1.0.0/
10:18:30.036 WARN o.l.i.quickload.util.QuickloadUtils - Could not read contents.txt from: http://bitbucket.org/nfreese/quickload-genome-in-a-bottle/raw/release-v1.0.0/contents.txt
10:18:30.037 WARN o.l.i.q.QuickloadDataProvider - Missing required quickload file, or could not reach source. This quickloak source will be disabled for this session.
10:18:30.069 WARN o.l.i.quickload.util.QuickloadUtils - Optional quickload synonyms.txt file could not be loaded from http://bitbucket.org/nfreese/quickload-genome-in-a-bottle/raw/release-v1.0.0/synonyms.txt
10:18:30.101 WARN o.l.i.quickload.util.QuickloadUtils - Optional species.txt could not be loaded from: http://bitbucket.org/nfreese/quickload-genome-in-a-bottle/raw/release-v1.0.0/species.txt
I have created a new ticket (IGBF-3103) to address the redirect issue.
Closing ticket.
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Dr. [~aloraine] Do you have the reference links or previous tickets of adding new quickload site to bioviz.org?