Details
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Type:
Bug
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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:
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Story Points:0.25
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Epic Link:
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Sprint:Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2
Description
This issue calls for improving the Galaxy-to-IGB bridge javascript code galaxy.js.
The Galaxy-to-IGB workflow works like this:
1. User visits usegalaxy.org and uses the site to create some files, which get added to their History.
2. User clicks a file in their History and sees a link to view the file in IGB
3. Users clicks the link, which goes to the Galaxy-to-IGB bridge page on Bioviz.org
4. The page contains some javascript code that detects whether or not IGB is running by hitting an IGB REST endpoint on localhost
5. If IGB is running, the javascript code then hits another REST endpoint in IGB, passing it the location of the file stored on Galaxy that the user wants to load
6. IGB then accesses the file and creates a new track for it
7. User can then load data by clicking the Load Data button in IGB
Once number 5 (above) happens, the javascript code displays a poorly worded message: "Data loading takes a while. If it doesn't load in a minute then, Please go back to galaxy and try again!"
Change this message to:
"Your data will appear in IGB as a new (empty) track. When you see the new track, zoom in and click Load Data."
Note: "Load Data" should be in bold font.
Also note:
To do this task, you will need to deploy a local copy of BioViz.org on your machine or onto a cloud VM, such as EC2. Code and instructions on how to deploy the BioViz Web site code are here: https://bitbucket.org/lorainelab/bioviz
Use the same workflow for developing BioViz.org as you use for developing IGB itself: make a fork, clone your fork, make a branch, develop on your branch, push to your fork, etc
Once you have deployed bioviz on EC2 or on your local host, you will need to test with Galaxy itself. The links coming from Galaxy all go to the production server at http://bioviz.org, not your local computer or EC2 instances. However, you can "trick" your computer into think your local machine or your EC2 instance is actually Bioviz.org by editing some local configuration files. The files you edit will depend on your OS. If you set this up correctly, then you can click links in Galaxy and they will go to your own development site and not the main production site.
See:
- https://wiki.transvar.org/display/ITD/Galaxy - for directions on how to load data files from a Galaxy "history" we use for testing
- https://jira.transvar.org/browse/IGBF-1406 - for tips on how to "trick" your computer into thinking your development deployment of BioViz is the main BioViz production server
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Fall 2018 Sprint 5 [ 55 ] | Fall 2018 Sprint 5, Winter 2018 Sprint 1 [ 55, 56 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Description |
Galaxy landing page shows this message:
Data loading takes a while. If it doesn't load in a minute then, Please go back to galaxy and try again! Replace with: Your data will appear in IGB as a new (empty) track. When you see the new track, click Load Data to add your data. Note: Load Data should be bold. Add link to user's guide. |
This issue calls for improving the Galaxy-to-IGB bridge javascript code galaxy.js.
To test, you'll need to deploy a copy of the BioViz Web site to your local machine or to an EC2 instance. Then, to test the flow from Galaxy to your local BioViz instance, you will need to "spoof" bioviz by editing your /etc/hosts file to make it appear that your local host is actually bioviz.org. Galaxy landing page shows this message: Data loading takes a while. If it doesn't load in a minute then, Please go back to galaxy and try again! Replace with: Your data will appear in IGB as a new (empty) track. When you see the new track, click Load Data to add your data. Note: Load Data should be bold. Add link to user's guide. |
| Description |
This issue calls for improving the Galaxy-to-IGB bridge javascript code galaxy.js.
To test, you'll need to deploy a copy of the BioViz Web site to your local machine or to an EC2 instance. Then, to test the flow from Galaxy to your local BioViz instance, you will need to "spoof" bioviz by editing your /etc/hosts file to make it appear that your local host is actually bioviz.org. Galaxy landing page shows this message: Data loading takes a while. If it doesn't load in a minute then, Please go back to galaxy and try again! Replace with: Your data will appear in IGB as a new (empty) track. When you see the new track, click Load Data to add your data. Note: Load Data should be bold. Add link to user's guide. |
This issue calls for improving the Galaxy-to-IGB bridge javascript code galaxy.js.
The Galaxy-to-IGB workflow works like this: 1. User visits usegalaxy.org and uses the site to create some files, which get added to their history. 2. User clicks the file in the History and sees a link to view the file in IGB 3. Users clicks the link, which goes to the Galaxy-to-IGB bridge page on Bioviz.org 4. The page contains some javascript code that detects whether or not IGB is running by hitting an IGB REST endpoint on localhost 5. The javascript code then hits another REST endpoint in IGB, passing it the location of the file stored on Galaxy that the user wants to load 6. IGB then loads the file Once number 5 (above) happens, the javascript code displays a poorly worded message: "Data loading takes a while. If it doesn't load in a minute then, Please go back to galaxy and try again!" Change this message to: Your data will appear in IGB as a new (empty) track. When you see the new track, click Load Data to add your data. Note: "Load Data" should be in bold font. Also note: To do this task, you will need to deploy a local copy of BioViz.org on your machine or on a cloud VM, such as EC2. Code and instructions on how to deploy the BioViz Web site code is here: https://bitbucket.org/lorainelab/bioviz Once you have set it up, you will need to test with Galaxy itself. The links coming from Galaxy all go to the production server at http://bioviz.org, not your local computer or EC2 instances. However, you can "trick" your computer into think your local machine or your EC2 instance is actually Bioviz.org by editing some local configuration files. The files you edit will depend on your OS. See: * https://wiki.transvar.org/display/ITD/Galaxy - for directions on how to load data files from a Galaxy "history" we use for testing * https://jira.transvar.org/browse/IGBF-1406 - for tips on how to "trick" your computer into thinking your development deployment of BioViz is the main BioViz production server |
| Description |
This issue calls for improving the Galaxy-to-IGB bridge javascript code galaxy.js.
The Galaxy-to-IGB workflow works like this: 1. User visits usegalaxy.org and uses the site to create some files, which get added to their history. 2. User clicks the file in the History and sees a link to view the file in IGB 3. Users clicks the link, which goes to the Galaxy-to-IGB bridge page on Bioviz.org 4. The page contains some javascript code that detects whether or not IGB is running by hitting an IGB REST endpoint on localhost 5. The javascript code then hits another REST endpoint in IGB, passing it the location of the file stored on Galaxy that the user wants to load 6. IGB then loads the file Once number 5 (above) happens, the javascript code displays a poorly worded message: "Data loading takes a while. If it doesn't load in a minute then, Please go back to galaxy and try again!" Change this message to: Your data will appear in IGB as a new (empty) track. When you see the new track, click Load Data to add your data. Note: "Load Data" should be in bold font. Also note: To do this task, you will need to deploy a local copy of BioViz.org on your machine or on a cloud VM, such as EC2. Code and instructions on how to deploy the BioViz Web site code is here: https://bitbucket.org/lorainelab/bioviz Once you have set it up, you will need to test with Galaxy itself. The links coming from Galaxy all go to the production server at http://bioviz.org, not your local computer or EC2 instances. However, you can "trick" your computer into think your local machine or your EC2 instance is actually Bioviz.org by editing some local configuration files. The files you edit will depend on your OS. See: * https://wiki.transvar.org/display/ITD/Galaxy - for directions on how to load data files from a Galaxy "history" we use for testing * https://jira.transvar.org/browse/IGBF-1406 - for tips on how to "trick" your computer into thinking your development deployment of BioViz is the main BioViz production server |
This issue calls for improving the Galaxy-to-IGB bridge javascript code galaxy.js.
The Galaxy-to-IGB workflow works like this: 1. User visits usegalaxy.org and uses the site to create some files, which get added to their history. 2. User clicks the file in the History and sees a link to view the file in IGB 3. Users clicks the link, which goes to the Galaxy-to-IGB bridge page on Bioviz.org 4. The page contains some javascript code that detects whether or not IGB is running by hitting an IGB REST endpoint on localhost 5. The javascript code then hits another REST endpoint in IGB, passing it the location of the file stored on Galaxy that the user wants to load 6. IGB then loads the file Once number 5 (above) happens, the javascript code displays a poorly worded message: "Data loading takes a while. If it doesn't load in a minute then, Please go back to galaxy and try again!" Change this message to: "Your data will appear in IGB as a new (empty) track. When you see the new track, zoom in and click Load Data." Note: "Load Data" should be in bold font. Also note: To do this task, you will need to deploy a local copy of BioViz.org on your machine or on a cloud VM, such as EC2. Code and instructions on how to deploy the BioViz Web site code is here: https://bitbucket.org/lorainelab/bioviz Once you have set it up, you will need to test with Galaxy itself. The links coming from Galaxy all go to the production server at http://bioviz.org, not your local computer or EC2 instances. However, you can "trick" your computer into think your local machine or your EC2 instance is actually Bioviz.org by editing some local configuration files. The files you edit will depend on your OS. See: * https://wiki.transvar.org/display/ITD/Galaxy - for directions on how to load data files from a Galaxy "history" we use for testing * https://jira.transvar.org/browse/IGBF-1406 - for tips on how to "trick" your computer into thinking your development deployment of BioViz is the main BioViz production server |
| Description |
This issue calls for improving the Galaxy-to-IGB bridge javascript code galaxy.js.
The Galaxy-to-IGB workflow works like this: 1. User visits usegalaxy.org and uses the site to create some files, which get added to their history. 2. User clicks the file in the History and sees a link to view the file in IGB 3. Users clicks the link, which goes to the Galaxy-to-IGB bridge page on Bioviz.org 4. The page contains some javascript code that detects whether or not IGB is running by hitting an IGB REST endpoint on localhost 5. The javascript code then hits another REST endpoint in IGB, passing it the location of the file stored on Galaxy that the user wants to load 6. IGB then loads the file Once number 5 (above) happens, the javascript code displays a poorly worded message: "Data loading takes a while. If it doesn't load in a minute then, Please go back to galaxy and try again!" Change this message to: "Your data will appear in IGB as a new (empty) track. When you see the new track, zoom in and click Load Data." Note: "Load Data" should be in bold font. Also note: To do this task, you will need to deploy a local copy of BioViz.org on your machine or on a cloud VM, such as EC2. Code and instructions on how to deploy the BioViz Web site code is here: https://bitbucket.org/lorainelab/bioviz Once you have set it up, you will need to test with Galaxy itself. The links coming from Galaxy all go to the production server at http://bioviz.org, not your local computer or EC2 instances. However, you can "trick" your computer into think your local machine or your EC2 instance is actually Bioviz.org by editing some local configuration files. The files you edit will depend on your OS. See: * https://wiki.transvar.org/display/ITD/Galaxy - for directions on how to load data files from a Galaxy "history" we use for testing * https://jira.transvar.org/browse/IGBF-1406 - for tips on how to "trick" your computer into thinking your development deployment of BioViz is the main BioViz production server |
This issue calls for improving the Galaxy-to-IGB bridge javascript code galaxy.js.
The Galaxy-to-IGB workflow works like this: 1. User visits usegalaxy.org and uses the site to create some files, which get added to their History. 2. User clicks a file in their History and sees a link to view the file in IGB 3. Users clicks the link, which goes to the Galaxy-to-IGB bridge page on Bioviz.org 4. The page contains some javascript code that detects whether or not IGB is running by hitting an IGB REST endpoint on localhost 5. If IGB is running, the javascript code then hits another REST endpoint in IGB, passing it the location of the file stored on Galaxy that the user wants to load 6. IGB then accesses the file and creates a new track for it 7. User can then load data by clicking the Load Data button in IGB Once number 5 (above) happens, the javascript code displays a poorly worded message: "Data loading takes a while. If it doesn't load in a minute then, Please go back to galaxy and try again!" Change this message to: "Your data will appear in IGB as a new (empty) track. When you see the new track, zoom in and click Load Data." Note: "Load Data" should be in bold font. Also note: To do this task, you will need to deploy a local copy of BioViz.org on your machine or onto a cloud VM, such as EC2. Code and instructions on how to deploy the BioViz Web site code are here: https://bitbucket.org/lorainelab/bioviz Use the same workflow for developing BioViz.org as you use for developing IGB itself: make a fork, clone your fork, make a branch, develop on your branch, push to your fork, etc Once you have deployed bioviz on EC2 or on your local host, you will need to test with Galaxy itself. The links coming from Galaxy all go to the production server at http://bioviz.org, not your local computer or EC2 instances. However, you can "trick" your computer into think your local machine or your EC2 instance is actually Bioviz.org by editing some local configuration files. The files you edit will depend on your OS. If you set this up correctly, then you can click links in Galaxy and they will go to your own development site and not the main production site. See: * https://wiki.transvar.org/display/ITD/Galaxy - for directions on how to load data files from a Galaxy "history" we use for testing * https://jira.transvar.org/browse/IGBF-1406 - for tips on how to "trick" your computer into thinking your development deployment of BioViz is the main BioViz production server |
| Assignee | Pawan Bole [ pbole ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Rank | Ranked higher |
| Sprint | Fall 2018 Sprint 5, Winter 2018 Sprint 1 [ 55, 56 ] | Fall 2018 Sprint 5, Winter 2018 Sprint 1, Winter 2018 Sprint 2 [ 55, 56, 57 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Pawan Bole [ pbole ] |
| Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
Ready for pull request.
| Assignee | Pawan Bole [ pbole ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Submitted the pull request
| Assignee | Pawan Bole [ pbole ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Testing In Progress [ 10003 ] |
| Assignee | Ann Loraine [ aloraine ] |
Pull request merged.
Tested on Dr. Loraine's BioViz mirror.
Typo in "igb not running" message is fixed.
Message upon loading data into IGB is corrected.
Deployed on BioViz Main
Re-assigning to original developer as this issue is now complete.
| Assignee | Ann Loraine [ aloraine ] | Pawan Bole [ pbole ] |
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 18176 ] | Fall 2019 Workflow Update [ 19982 ] |
| Workflow | Fall 2019 Workflow Update [ 19982 ] | Revised Fall 2019 Workflow Update [ 22104 ] |
| Epic Link | IGBF-1880 [ 17970 ] |
Changed the message for the users when IGB is running in the background and also corrected typo when IGB is not running.
Please review the changes :
https://bitbucket.org/pawanbole/pawansfork-bioviz/commits/ab8ac28e88a9d5b0c327eb68e2e03594406daa0a