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: 9.0.2 Minor Release
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Labels:
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Story Points:1
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Sprint:B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2
Description
IGB appears hard-coded to request resources from BioViz.org and a few other sites.
This makes testing and developing IGB challenging for developers because they need access to the access_logs of BioViz to add new features or fix bugs. It also makes updating URLs difficult and may slow down startup if IGB tries to access resources that no longer exist.
Task is:
Identify all places in IGB code base with URLs. Document these:
- Report name of file with hard-coded URL (.java or other resources)
- Report URL
Request BioViz.org access_log from Dr. Loraine. Do not attach here to respect users' privacy.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Description |
IGB appears hard-coded to request resources from BioViz.org.
This makes testing and developing IGB challenging for developers because they need access to the access_logs of BioViz to add new features or fix bugs. * Identify all places in IGB code bas with hard-coded URLs. Document here. Ideas for how to fix/improve: * IGB installer Install4J uses codeBaseUrl setting in its configuration file to configure future updates. Use this to determine IGB code base URL. * Create a new IGB Service (new module) that provides URLs on demand for key IGB functions, e.g., IGB Help Page, IGB Code Base, etc. |
IGB appears hard-coded to request resources from BioViz.org and others.
This makes testing and developing IGB challenging for developers because they need access to the access_logs of BioViz to add new features or fix bugs. It also makes updating URLs difficult and may slow down startup if IGB tries to access resources that no longer exist. * Identify all places in IGB code base with hard-coded URLs. Document these here. * Develop a plan for how to improve the situation. Thought for how to fix/improve: * IGB installer Install4J uses codeBaseUrl setting in its configuration file to configure future updates. Use this to determine IGB BioViz code base URL. * Create a new IGB Service (new module) that provides URLs on demand for key IGB functions, e.g., IGB Help Page, IGB Code Base, etc. |
| Description |
IGB appears hard-coded to request resources from BioViz.org and others.
This makes testing and developing IGB challenging for developers because they need access to the access_logs of BioViz to add new features or fix bugs. It also makes updating URLs difficult and may slow down startup if IGB tries to access resources that no longer exist. * Identify all places in IGB code base with hard-coded URLs. Document these here. * Develop a plan for how to improve the situation. Thought for how to fix/improve: * IGB installer Install4J uses codeBaseUrl setting in its configuration file to configure future updates. Use this to determine IGB BioViz code base URL. * Create a new IGB Service (new module) that provides URLs on demand for key IGB functions, e.g., IGB Help Page, IGB Code Base, etc. |
IGB appears hard-coded to request resources from BioViz.org and others.
This makes testing and developing IGB challenging for developers because they need access to the access_logs of BioViz to add new features or fix bugs. It also makes updating URLs difficult and may slow down startup if IGB tries to access resources that no longer exist. * Identify all places in IGB code base with hard-coded URLs. Document these here. * Develop & implement solution. Thought for how to fix/improve: * IGB installer Install4J uses codeBaseUrl setting in its configuration file to configure future updates. Use this to determine IGB BioViz code base URL. * Create a new IGB Service (new module) that provides URLs on demand for key IGB functions, e.g., IGB Help Page, IGB Code Base, etc. |
| Description |
IGB appears hard-coded to request resources from BioViz.org and others.
This makes testing and developing IGB challenging for developers because they need access to the access_logs of BioViz to add new features or fix bugs. It also makes updating URLs difficult and may slow down startup if IGB tries to access resources that no longer exist. * Identify all places in IGB code base with hard-coded URLs. Document these here. * Develop & implement solution. Thought for how to fix/improve: * IGB installer Install4J uses codeBaseUrl setting in its configuration file to configure future updates. Use this to determine IGB BioViz code base URL. * Create a new IGB Service (new module) that provides URLs on demand for key IGB functions, e.g., IGB Help Page, IGB Code Base, etc. |
IGB appears hard-coded to request resources from BioViz.org and others.
This makes testing and developing IGB challenging for developers because they need access to the access_logs of BioViz to add new features or fix bugs. It also makes updating URLs difficult and may slow down startup if IGB tries to access resources that no longer exist. * Identify all places in IGB code base with hard-coded URLs. Document these here. * Develop & implement solution. Thought for how to fix/improve: * IGB installer Install4J uses codeBaseUrl setting in its configuration file to configure future updates. Use this to determine IGB BioViz code base URL. * Create a new IGB Service (new module) that provides URLs on demand for key IGB functions, e.g., IGB Help Page, IGB Code Base, etc. |
| Rank | Ranked higher |
| Sprint | B - Summer 2018 [ 48 ] | B - Summer 2018, Summer 2018 Part 2 [ 48, 49 ] |
| Rank | Ranked higher |
| Summary | identify and parameterize all references to BioViz.org in IGB code base | identify hard-coded URLs in IGB code base |
| Description |
IGB appears hard-coded to request resources from BioViz.org and others.
This makes testing and developing IGB challenging for developers because they need access to the access_logs of BioViz to add new features or fix bugs. It also makes updating URLs difficult and may slow down startup if IGB tries to access resources that no longer exist. * Identify all places in IGB code base with hard-coded URLs. Document these here. * Develop & implement solution. Thought for how to fix/improve: * IGB installer Install4J uses codeBaseUrl setting in its configuration file to configure future updates. Use this to determine IGB BioViz code base URL. * Create a new IGB Service (new module) that provides URLs on demand for key IGB functions, e.g., IGB Help Page, IGB Code Base, etc. |
IGB appears hard-coded to request resources from BioViz.org and a few other sites.
This makes testing and developing IGB challenging for developers because they need access to the access_logs of BioViz to add new features or fix bugs. It also makes updating URLs difficult and may slow down startup if IGB tries to access resources that no longer exist. Task is: Identify all places in IGB code base with URLs. Document these: * Report name of file with hard-coded URL (.java or other resources) * Report URL Request BioViz.org access_log from Dr. Loraine. Do not attach here to respect users' privacy. |
| Assignee | Ann Loraine [ aloraine ] | Sneha Ramesh Watharkar [ jdaly ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] |
| Rank | Ranked higher |
| Summary | identify hard-coded URLs in IGB code base | Identify hard-coded URLs in IGB code base |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Kiran Korey [ kkorey ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Attachment | hard_coded_urls_formatted.txt [ 14123 ] | |
| Attachment | hard_coded_urls_original.txt [ 14124 ] |
Please find the attached hard_coded_urls_formatted.txt
file which contains references to the hardcoded URLs which are relevant and hard_coded_urls_original.txt which contains all references to the string "http://".
| Attachment | hard_coded_https_urls.txt [ 14125 ] |
| Assignee | Kiran Korey [ kkorey ] | Sneha Ramesh Watharkar [ jdaly ] |
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
Followed the recommendations provided by Professor [~aloraine] and made changes to the files which contains hard coded URLs.
Moving it to 1st Level review column.
| Assignee | Sneha Ramesh Watharkar [ jdaly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Add link to branch.
| Assignee | Sneha Ramesh Watharkar [ jdaly ] |
You can find the work in this branch : https://bitbucket.org/swathark/integrated-genome-browser/branch/IGBF-1348#diff
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Ann Loraine [ aloraine ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2 [ 48, 49 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3 [ 48, 49, 50 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
Following change is needed before pull request can be merged:
- Change: "updates=http://bioviz.org/igb/releases/igb-9.0.1/updates.xml" to "updates=http://bioviz.org/igb/releases/current/updates.xml" in plugins/Update/src/main/resources/updates.properties
| Status | Reviewing [ 10301 ] | Open [ 1 ] |
| Assignee | Ann Loraine [ aloraine ] | Sneha Ramesh Watharkar [ jdaly ] |
Done with the above fix.
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Ann Loraine [ aloraine ] |
| Status | Open [ 1 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
Ready for pull request.
| Assignee | Ann Loraine [ aloraine ] | Sneha Ramesh Watharkar [ jdaly ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
PR submitted.
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3 [ 48, 49, 50 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1 [ 48, 49, 50, 51 ] |
| Rank | Ranked lower |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1 [ 48, 49, 50, 51 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2 [ 48, 49, 50, 51, 52 ] |
| Rank | Ranked lower |
I don't know how to test this issue.
In the changes that were made for this issue, we removed things that we were sure were not used.
So I am moving it to done.
Reassigning to Sneha because she did the work.
| Resolution | Done [ 10000 ] | |
| Status | Needs Testing [ 10002 ] | Closed [ 6 ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] |
| Workflow | Loraine Lab Workflow [ 18040 ] | Fall 2019 Workflow Update [ 19915 ] |
| Workflow | Fall 2019 Workflow Update [ 19915 ] | Revised Fall 2019 Workflow Update [ 22034 ] |
Tip:
IGB already is designed to request specific files from Quickload hosts (these are "baked in" and less likely to be optimizable). For example, IGB will try to retrieve a file called synonyms.txt from a Quickload site. This file is optional. If it not there, it's not considered an error.