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  1. IGB
  2. IGBF-4081

Update SVG libraries used by IGB to export images

        Details

        • Type: Improvement
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: 10.2.0
        • Labels:
          None

          Description

          Situation: We've recently had several requests to export images in IGB as SVGs. While IGB does have the ability to export images as SVG, the libraries used are quite old and there are some weird artifacts that show up in the SVG images (see IGBF-2649).

          Task: Update the libraries used for SVG image export in IGB. This may require stripping out the current SVG library usage and using a newer one (something like this: https://github.com/jfree/jfreesvg).

            Attachments

            1. new_barbWire.png
              new_barbWire.png
              124 kB
            2. new.png
              new.png
              178 kB
            3. old_BarbWire.png
              old_BarbWire.png
              125 kB
            4. old.png
              old.png
              180 kB
            5. PranavTest.svg
              1.54 MB

              Issue Links

              blocks

              Bug - A problem which impairs or prevents the functions of the product. IGBF-2143 Fix exporting whole frame svg on windows

              • Major - Major loss of function.
              • Closed
              relates to

              Bug - A problem which impairs or prevents the functions of the product. HELP-311 Problem with exporting SVG from 9.0.1

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

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1106 Enhance Image Export ability to inlcude exporting of high-quality SVGs

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-2649 Investigate horizontal lines in IGB svg

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-3971 [ 14523 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2649 [ IGBF-2649 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-311 [ IGBF-311 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-311 [ IGBF-311 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to HELP-311 [ HELP-311 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pbhatia1 Pranav Bhatia (Inactive) made changes -
                Attachment PranavTest.svg [ 18630 ]
                Hide
                Permalink
                pbhatia1 Pranav Bhatia (Inactive) added a comment - - edited

                Replaced the freehep library to jfree.

                Attached is a screenshot of an SVG output using the newly integrated library.

                PranavTest.svg

                Link to branch - https://bitbucket.org/pranavbhatia1999/integrated-genome-browser/branch/IGBF-3971

                Please review.

                Show
                pbhatia1 Pranav Bhatia (Inactive) added a comment - - edited Replaced the freehep library to jfree. Attached is a screenshot of an SVG output using the newly integrated library. PranavTest.svg Link to branch - https://bitbucket.org/pranavbhatia1999/integrated-genome-browser/branch/IGBF-3971 Please review.
                pbhatia1 Pranav Bhatia (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                pbhatia1 Pranav Bhatia (Inactive) made changes -
                Assignee Pranav Bhatia [ pbhatia1 ] Ann Loraine [ aloraine ]
                pbhatia1 Pranav Bhatia (Inactive) made changes -
                Assignee Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 1 [ 210 ] Spring 1, Spring 2 [ 210, 211 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Attachment old.png [ 18633 ]
                nfreese Nowlan Freese made changes -
                Attachment new.png [ 18634 ]
                nfreese Nowlan Freese made changes -
                Attachment new.png [ 18635 ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment - - edited

                Tested Pranav's branch on Mac.

                Exported main view, main view with labels, whole frame, and sliced view images from Pranav's branch and IGB 10.1.0. I compared the images using inkscape. On Pranav's branch the images look much better as there are no longer overlapping parts.

                For example, here is the old version of IGB:

                Here is the new version:

                I would like to see a couple of changes in the commit before it is ready for a PR:

                • Set your IDE to not fix whitespace issues in files you are editing.
                  • I recommend creating a new branch off of main (name it IGBF-4081) and reimplement your changes as this will be easier than trying to fix the whitespaces.
                • Use the jfreesvg artifact for Java 11 and higher: <artifactId>org.jfree.svg</artifactId>
                • You should not need to add javax.xml.bind. We are using jakarta.xml.bind. See stackoverflow for more info.
                • Replace all imports of freehep with jfreesvg. If everything is working, commit, then see if you can identify if any of the imports of jfreesvg can be removed.
                • Remove unneeded freehep lines of code instead of commenting them out.
                Show
                nfreese Nowlan Freese added a comment - - edited Tested Pranav's branch on Mac. Exported main view, main view with labels, whole frame, and sliced view images from Pranav's branch and IGB 10.1.0. I compared the images using inkscape. On Pranav's branch the images look much better as there are no longer overlapping parts. For example, here is the old version of IGB: Here is the new version: I would like to see a couple of changes in the commit before it is ready for a PR: Set your IDE to not fix whitespace issues in files you are editing. I recommend creating a new branch off of main (name it IGBF-4081 ) and reimplement your changes as this will be easier than trying to fix the whitespaces. Use the jfreesvg artifact for Java 11 and higher: <artifactId>org.jfree.svg</artifactId> See the jfreesvg github for more info: https://github.com/jfree/jfreesvg MVN repository for jfreesvg: https://mvnrepository.com/artifact/org.jfree/org.jfree.svg You should not need to add javax.xml.bind. We are using jakarta.xml.bind. See stackoverflow for more info. Replace all imports of freehep with jfreesvg. If everything is working, commit, then see if you can identify if any of the imports of jfreesvg can be removed. Remove unneeded freehep lines of code instead of commenting them out.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Pranav Bhatia [ pbhatia1 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment - - edited

                Note from Paige on tickets we may be able to close after testing with the new SVG library:

                IGBF-1106 - Make sure saved SVG files can be opened in popular image editing tools (e.g., Adobe Illustrator) on Mac
                IGBF-2649 - This can be completed once Pranav’s ticket is closed.
                DB-84 - “”
                IGBD-437 - “”

                Show
                nfreese Nowlan Freese added a comment - - edited Note from Paige on tickets we may be able to close after testing with the new SVG library: IGBF-1106 - Make sure saved SVG files can be opened in popular image editing tools (e.g., Adobe Illustrator) on Mac IGBF-2649 - This can be completed once Pranav’s ticket is closed. DB-84 - “” IGBD-437 - “”
                Hide
                Permalink
                pbhatia1 Pranav Bhatia (Inactive) added a comment - - edited

                Worked on the suggested improvements.

                Link to branch - https://bitbucket.org/pranavbhatia1999/integrated-genome-browser/branch/IGBF-4081

                Show
                pbhatia1 Pranav Bhatia (Inactive) added a comment - - edited Worked on the suggested improvements. Link to branch - https://bitbucket.org/pranavbhatia1999/integrated-genome-browser/branch/IGBF-4081
                pbhatia1 Pranav Bhatia (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pbhatia1 Pranav Bhatia (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                pbhatia1 Pranav Bhatia (Inactive) made changes -
                Assignee Pranav Bhatia [ pbhatia1 ] Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Attachment new.png [ 18635 ]
                Hide
                Permalink
                pbhatia1 Pranav Bhatia (Inactive) added a comment -

                PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1060

                Show
                pbhatia1 Pranav Bhatia (Inactive) added a comment - PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1060
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                Tested on Mac and Windows using the main branch installer. SVG files look good on both systems.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Tested on Mac and Windows using the main branch installer. SVG files look good on both systems. Closing ticket.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Pranav Bhatia [ pbhatia1 ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-1106 [ IGBF-1106 ]
                nfreese Nowlan Freese made changes -
                Attachment mainViewWithLabelsOLD.svg [ 18637 ]
                nfreese Nowlan Freese made changes -
                Attachment mainViewWithLabelsNEW.svg [ 18638 ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment - - edited

                Note that there are some visual differences between the old SVG library and the new SVG library. For example, the "barb wire" in IGB does not always appear correctly with the new SVG library, though I do not see this as an issue.
                Old:

                New:

                Show
                nfreese Nowlan Freese added a comment - - edited Note that there are some visual differences between the old SVG library and the new SVG library. For example, the "barb wire" in IGB does not always appear correctly with the new SVG library, though I do not see this as an issue. Old: New:
                nfreese Nowlan Freese made changes -
                Attachment mainViewWithLabelsOLD.svg [ 18637 ]
                nfreese Nowlan Freese made changes -
                Attachment mainViewWithLabelsNEW.svg [ 18638 ]
                nfreese Nowlan Freese made changes -
                Attachment old_BarbWire.png [ 18639 ]
                Attachment new_barbWire.png [ 18640 ]
                nfreese Nowlan Freese made changes -
                Link This issue blocks IGBF-2143 [ IGBF-2143 ]
                pkulzer Paige Kulzer (Inactive) made changes -
                Fix Version/s 10.2.0 [ 11100 ]

                  People

                  • Assignee:
                    pbhatia1 Pranav Bhatia (Inactive)
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: