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  1. IGB
  2. IGBF-1635

Develop a strategy to refactor REST endpoint code used by Galaxy/BAR/CyVerse (maybe AppStore)

        Details

        • Type: Improvement
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          3
        • Epic Link:
        • Sprint:
          Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec

          Description

          IGB implements REST endpoints that trigger loading of genomes and data files. This code is supporting IGB bookmarks, Galaxy and CyVerse bridges, and BAR connectivity.

          Currently all the code is written in one place and is handled based on conditions. It makes the code highly complicated, hard to read, and hard/risky to modify.

          Goal: Develop a strategy to re-architect this code to make it easier to understand and modify.

          Files to look at:
          IGB:

          • BookmarkUnibrowControlServlet.java
          • BookmarkHttpRequestHandler.java

          BioViz:

          • bar.js
          • galaxy.js
          • cyversetoigb.js

          Important Urls for testing:
          BAR:

          Galaxy:

          CyVerse (You can use testing environment for Bioviz. Take credentials from Cyverse Team):

          • bioviz.org/cyverseData.html

          Also, you should look at the REST endpoint we wrote to trigger installation of IGB Apps. Ask Riddhi and Charan.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2133 Implement CyVerse metadata bridge with IGB bookmarks

              • Critical - Crashes, loss of data, severe memory leak.
              • Closed

              Task - A task that needs to be done. IGBF-1666 Design new services based architecture for handling REST requests

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2066 Define CyVerse REST calls to be handled by IGB REST endpoint(s)

              • Major - Major loss of function.
              • Closed

              New Feature - A new feature of the product, which has yet to be developed. IGBF-1632 IGB-CyVerse load data without genome

              • Blocker - Blocks development and/or testing work, production could not run.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                stiwari8 Srishti Tiwari (Inactive) created issue -
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Field Original Value New Value
                Link This issue relates to IGBF-1632 [ IGBF-1632 ]
                srishteeM Srishtee Marotkar (Inactive) made changes -
                Description Task: To refactor and segregate code for handling data from Galaxy, Bar and CyVerse. Currently all the code is written in one place and is handled based on conditions. It makes the code highly complicated and unreadable.

                Files to look at:
                BookmarkUnibrowControlServlet.java
                BookmarkHttpRequestHandler.java
                bar.js
                galaxy.js
                cyversetoigb.js
                 
                Important Urls for testing:
                BAR:
                https://bar.utoronto.ca/eFP-Seq_Browser/

                Galaxy:
                https://usegalaxy.org/u/nfreese/h/visualization-of-whole-genome-dna-methylation-data-in-igb-focus-on-a-feature

                CyVerse (You can use testing environment for Bioviz. Take credentials from Cyverse Team):
                bioviz.org/cyverseData.html                 		Task: To refactor and segregate code for handling data from Galaxy, Bar and CyVerse. Currently all the code is written in one place and is handled based on conditions. It makes the code highly complicated and unreadable.

                Files to look at:
                IGB:
                BookmarkUnibrowControlServlet.java
                BookmarkHttpRequestHandler.java

                BioViz:
                bar.js
                galaxy.js
                cyversetoigb.js
                 
                Important Urls for testing:
                BAR:
                https://bar.utoronto.ca/eFP-Seq_Browser/

                Galaxy:
                https://usegalaxy.org/u/nfreese/h/visualization-of-whole-genome-dna-methylation-data-in-igb-focus-on-a-feature

                CyVerse (You can use testing environment for Bioviz. Take credentials from Cyverse Team):
                bioviz.org/cyverseData.html
                srishteeM Srishtee Marotkar (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4 [ 62 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 62, 63 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                srishteeM Srishtee Marotkar (Inactive) made changes -
                Status In Progress [ 3 ] Open [ 1 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 62, 63 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6 [ 62, 63, 64 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6 [ 62, 63, 64 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 62, 63 ]
                ann.loraine Ann Loraine made changes -
                Assignee Srishtee Marotkar [ srishteem ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-1666 [ IGBF-1666 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 62, 63 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Summer 2019 Sprint 9 [ 62, 63, 68 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked lower
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-1531 [ 17617 ]
                ann.loraine Ann Loraine made changes -
                Labels Advanced
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5, Summer 2019 Sprint 9 [ 62, 63, 68 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 62, 63 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 62, 63 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Summer 2019 Sprint 11 [ 62, 63, 70 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5, Summer 2019 Sprint 11 [ 62, 63, 70 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Summer 2019 Sprint 12 [ 62, 63, 71 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5, Summer 2019 Sprint 12 [ 62, 63, 71 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Summer 2019 Sprint 13 [ 62, 63, 72 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 1 [ 62, 63, 72 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2 [ 62, 63, 73 ]
                ann.loraine Ann Loraine made changes -
                Fix Version/s 9.1.0 Major Release [ 10601 ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18356 ] Fall 2019 Workflow Update [ 18963 ]
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ] Srishti Tiwari [ stiwari8 ]
                ann.loraine Ann Loraine made changes -
                Description Task: To refactor and segregate code for handling data from Galaxy, Bar and CyVerse. Currently all the code is written in one place and is handled based on conditions. It makes the code highly complicated and unreadable.

                Files to look at:
                IGB:
                BookmarkUnibrowControlServlet.java
                BookmarkHttpRequestHandler.java

                BioViz:
                bar.js
                galaxy.js
                cyversetoigb.js
                 
                Important Urls for testing:
                BAR:
                https://bar.utoronto.ca/eFP-Seq_Browser/

                Galaxy:
                https://usegalaxy.org/u/nfreese/h/visualization-of-whole-genome-dna-methylation-data-in-igb-focus-on-a-feature

                CyVerse (You can use testing environment for Bioviz. Take credentials from Cyverse Team):
                bioviz.org/cyverseData.html                 		Currently all the code is written in one place and is handled based on conditions. It makes the code highly complicated and unreadable.


                Goal: Rfactor and segregate code for handling data from Galaxy, Bar and CyVerse.
                Files to look at:
                IGB:
                BookmarkUnibrowControlServlet.java
                BookmarkHttpRequestHandler.java

                BioViz:
                bar.js
                galaxy.js
                cyversetoigb.js
                 
                Important Urls for testing:
                BAR:
                https://bar.utoronto.ca/eFP-Seq_Browser/

                Galaxy:
                https://usegalaxy.org/u/nfreese/h/visualization-of-whole-genome-dna-methylation-data-in-igb-focus-on-a-feature

                CyVerse (You can use testing environment for Bioviz. Take credentials from Cyverse Team):
                bioviz.org/cyverseData.html
                ann.loraine Ann Loraine made changes -
                Status Open [ 1 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Description Currently all the code is written in one place and is handled based on conditions. It makes the code highly complicated and unreadable.


                Goal: Rfactor and segregate code for handling data from Galaxy, Bar and CyVerse.
                Files to look at:
                IGB:
                BookmarkUnibrowControlServlet.java
                BookmarkHttpRequestHandler.java

                BioViz:
                bar.js
                galaxy.js
                cyversetoigb.js
                 
                Important Urls for testing:
                BAR:
                https://bar.utoronto.ca/eFP-Seq_Browser/

                Galaxy:
                https://usegalaxy.org/u/nfreese/h/visualization-of-whole-genome-dna-methylation-data-in-igb-focus-on-a-feature

                CyVerse (You can use testing environment for Bioviz. Take credentials from Cyverse Team):
                bioviz.org/cyverseData.html                 		IGB implements REST endpoints that trigger loading of genomes and data files. This code is supporting IGB bookmarks, Galaxy and CyVerse bridges, and BAR connectivity.

                Currently all the code is written in one place and is handled based on conditions. It makes the code highly complicated, hard to read, and hard/risky to modify.

                Goal: Develop a strategy to re-architect this code to make it easier to understand and modify.

                Files to look at:
                IGB:
                * BookmarkUnibrowControlServlet.java
                * BookmarkHttpRequestHandler.java

                BioViz:
                * bar.js
                * galaxy.js
                * cyversetoigb.js
                 
                Important Urls for testing:
                BAR:
                * https://bar.utoronto.ca/eFP-Seq_Browser/

                Galaxy:
                * https://usegalaxy.org/u/nfreese/h/visualization-of-whole-genome-dna-methylation-data-in-igb-focus-on-a-feature

                CyVerse (You can use testing environment for Bioviz. Take credentials from Cyverse Team):
                * bioviz.org/cyverseData.html

                Also, you should look at the REST endpoint we wrote to trigger installation of IGB Apps. Ask Riddhi and Charan.
                ann.loraine Ann Loraine made changes -
                Summary Refactor servlet code used by Galaxy/BAR/CyVerse Develop a strategy to refactor REST endpoint code used by Galaxy/BAR/CyVerse (maybe AppStore)
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2 [ 62, 63, 73 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 4 [ 62, 63, 73, 74 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Srishti Tiwari [ stiwari8 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3 [ 62, 63, 73, 74 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 2019 Sprint 4 [ 62, 63, 73, 74, 75 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2066 [ IGBF-2066 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct [ 62, 63, 73, 74, 75 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct [ 62, 63, 73, 74, 75, 76 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 18963 ] Revised Fall 2019 Workflow Update [ 21188 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct [ 62, 63, 73, 74, 75, 76 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov [ 62, 63, 73, 74, 75, 76, 77 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov [ 62, 63, 73, 74, 75, 76, 77 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov [ 62, 63, 73, 74, 75, 76, 77, 78 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2133 [ IGBF-2133 ]
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-1531 [ 17617 ] IGBF-1880 [ 17970 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov [ 62, 63, 73, 74, 75, 76, 77, 78 ] Spring 2019 Sprint 4, Spring 2019 Sprint 5, Fall 2019 Sprint 2, Fall 2019 Sprint 3, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec [ 62, 63, 73, 74, 75, 76, 77, 78, 79 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Fix Version/s 9.1.0 Major Release [ 10601 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    stiwari8 Srishti Tiwari (Inactive)
                    Reporter:
                    stiwari8 Srishti Tiwari (Inactive)
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                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: