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  1. Jalview
  2. JAL-4059

Upgrade to SwingJS 5.0.x for for jalviewJS 2.12

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    Details

    • Type: Improvement
    • Status: In Progress
    • Priority: Blocker
    • Resolution: Unresolved
    • Affects Version/s: 2.11.2.4, 2.11.2.5, 2.11.2.6, 2.11.2.7, 2.11.3.0, 2.11.3.1, 2.11.3.2, 2.11.3.3
    • Fix Version/s: 2.11.4, 2.12.0
    • Component/s: jalview-j2s
    • Labels:
      None

      Description

      For 2.12 - this is now a catch all issue. Work to do:
       - make sure we have a baseline working JalviewJS with SwingJS/JSmol/JSVARNA 5.0 + AptX experimental support ([~jprocter] and [~kjvdheide])
       - incorporate patches/improvements from [~soares] 2.11.x branches


      JalviewJS build from 2.11.2.4 crashes when opening the example file (or other structures) because the StructureViewerBase class requires Random.nextLong() in startProgressBar:

      jalview.gui.StructureViewerBase.startProgressBar$S(msg)
      at clazz.eval [as nextLong$] (swingjs/j2s/java/util/Random.js:95:8)
       

        Attachments

          Issue Links

          blocks

          Bug - A problem which impairs or prevents the functions of the product. JAL-4369 Uniprot record retrieval not working in JalviewJS

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2275 Cannot view local structures imported via direct network mount (e.g. cifs/samba, onedrive, etc)

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

          Bug - A problem which impairs or prevents the functions of the product. JAL-4239 java.util.Random.NextLong not implemented

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

          Bug - A problem which impairs or prevents the functions of the product. JAL-4240 sequence ID tooltip in JalviewJS has double line spacing

          • Critical - Crashes, loss of data, severe memory leak.
          • Ready for testing

          Improvement - An improvement or enhancement to an existing feature or task. JAL-4395 Allow local_eclipse.properties to be read by buildship

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Ready for testing
          depends on

          Bug - A problem which impairs or prevents the functions of the product. JAL-4235 Gradle task jalviewjsTranspile does not fail on eclipse error

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Ready for testing

          Task - A task that needs to be done. JAL-4359 patch JalviewJS to correctly handle relative and absolute paths from page rather than j2s directory

          • Major - Major loss of function.
          • Open
          mentioned on

          GitLab Commit - JAL-4059 Added some more Platform.addJ2SDirectDatabaseCall web service URLs in...

          GitLab Commit - JAL-4059 added test for <br/> break

          GitLab Commit - JAL-4059 Allow form-created querystring style values for boolean values

          GitLab Commit - JAL-4059 Attempts to set JalviewJS desktop geometry from Info hash

          GitLab Commit - JAL-4059 Big improvements to jalviewjsProjectImport dependencies avoiding more...

          GitLab Commit - JAL-4059 Change long querystringnamespace to namespace as it's being used for...

          GitLab Commit - JAL-4059 Checked through and fixed build tasks

          GitLab Commit - JAL-4059 Fix jalviewjsLaunchTest for non-macos

          GitLab Commit - JAL-4059 fix not merging html files to the final site from libs

          GitLab Commit - JAL-4059 fix other PopupMenuTest

          GitLab Commit - JAL-4059 fix that boolean for non-value query string args

          GitLab Commit - JAL-4059 Fix the tooltip formatting for when, e.g. enclose=false

          GitLab Commit - JAL-4059 Fix up Jsmol calls and delete html files from JS zips in...

          GitLab Commit - JAL-4059 Fixed a test for adding jalview.bin.JalviewJS

          GitLab Commit - JAL-4059 fixed a test that is now working as expected due to <br/>. Better...

          GitLab Commit - JAL-4059 Fixed Copy tasks merging site

          GitLab Commit - JAL-4059 Fixed macOS timeoutscheduler and revert to --timeout for other OSes

          GitLab Commit - JAL-4059 Improvement to launch indicator

          GitLab Commit - JAL-4059 JAL-4395 Updated closure-compiler. Added local_eclipse.properties for buildship

          GitLab Commit - JAL-4059 Made jalview.bin.JalviewJS to use new command-line args in...

          GitLab Commit - JAL-4059 minor CSS fix

          GitLab Commit - JAL-4059 Only run this once

          GitLab Commit - JAL-4059 redo these tests as TestNG asserts to add message

          GitLab Commit - JAL-4059 rename files from jsmol j2s zip from jsmol to swingjs

          GitLab Commit - JAL-4059 rename vars to j2s_ this and that for clarity

          GitLab Commit - JAL-4059 Revert libjs/MiGLayout as new miglayout transpile of 4.0 includes...

          GitLab Commit - JAL-4059 revert to intervalstore 1.1 for VCFLoader

          GitLab Commit - JAL-4059 Send bespoke Info hash parameters into jalview.bin.Jalview instance. ...

          GitLab Commit - JAL-4059 Storing important thisApplet information in java. Some CSS loading indicators.

          GitLab Commit - JAL-4059 SwingJS from java2script github repo. It works\!

          GitLab Commit - JAL-4059 Tidy getting the namespace, and save the namespace in the Jalview...

          GitLab Commit - JAL-4059 tidyup

          GitLab Commit - JAL-4059 update intervalstore-1.2-site.zip transpiled with new j2s

          GitLab Commit - JAL-4059 updated intervalstore jars to match updating util/jalviewjs/libjs/intervalstore-site.zip

          GitLab Commit - JAL-4059 Updated SwingJS

          GitLab Commit - JAL-4059 Updated SwingJS and JSmol (March 2024). Fix gradle to spot new SwingJS zip.

          GitLab Commit - JAL-4059 Updated swingjs and removed spare library .zip

          GitLab Commit - JAL-4059 updated swingjs, Jmol-SwingJS.zip. Insignificantly altered build.gradle.

          GitLab Commit - JAL-4059 Updated SwingJS, JmolJS libraries

          GitLab Commit - JAL-4059 Updates to miglayout, varna, intervalstore, with re-transpiled...

          GitLab Commit - JAL-4059 Updates to SwingJS and JmolJS

          GitLab Commit - JAL-4059 Use namespaced query parameters in preference to Info.args. Report what's being used.

          GitLab Commit - Merge branch 'bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3' of...

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              Assignee:
              Unassigned Unassigned
              Reporter:
              jprocter James Procter
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              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated: