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#73 Problem "Finding" CDT Files Unless in Specific Directory

v0.9.6
open
Alok Saldanha
None
5
2024-09-30
2021-11-04
Jeffrey Lewis
No

Hello Alok,

I noticed an odd bug on a Mac (OS = 11.6) with TreeView 1.2.0. Unless my files are in my main user folder (i.e., Macintosh HD/Users/myname), TreeView cannot see them. In that folder, TreeView will show all files and folders, but if I click on another folder (e.g., Desktop), it appears empty (which it is not). Not a debilitating problem because I can simply place files where they can be read, but it is a nuisance for organizing analyses.

Best,

Jeff

Related

Bugs: #73

Discussion

  • Carson Stacy

    Carson Stacy - 2022-11-17

    Here is a work around I found to this issue. Posting here in case it helps anyone. It appears /bin/bash no longer has full disk access on newer versions of MacOS, which I believe the code requires. Following the following steps solved this issue for me:

    1. System Settings > Privacy & Security > Full Disk Access
    2. If present, click on lock in lower left corner to allow changes
    3. Separately, open a new finder window
    4. Select Go -> Go to Folder... from the menu bar
    5. Type /bin and click Go
    6. Drag the /bin/bash icon from this /bin folder in finder to the Full Disk Access window (right hand side)

    Warm regards,
    Carson Stacy

     

  • RICHARD FRIEDMAN

    RICHARD FRIEDMAN - 2024-09-20

    I have experienced the same problem with Somoma, Mac OSX 14.6.1 . I have tried the workaround above but it did not work. Is there a comparable work around for this OS?

    Thanks and best wishes,
    Richard Friedman

     

  • Alok Saldanha

    Alok Saldanha - 2024-09-22

    Hi Richard,

    Could you describe the issue a little more fully?

    1. Which distribution of Java TreeView are you using, and how are you launching it?
    2. What is an example location where you cannot open files?

    I seem to be able to open files in my Desktop folder on Somoma, Mac OSX 14.6.1 after fixing the bundle launcher. I am prompted to grant Java access when I navigate to that folder, but otherwise it works. There is an additional issue related to finding plugins after AppTranslocation, but after I address that I could release a new version with the updated bundle launcher that could perhaps be a useful workaround.

     
    Thumbnail
    promptToGrantJavaAccess.png

    • RICHARD FRIEDMAN

      RICHARD FRIEDMAN - 2024-09-24

      Alok,

      I am not sure if my previous reply got to you.

      Dear Alok,

      First of all, thank you for developing Java Treeview and supporting it over the years. I teach a course in bioinformatics for biologists which only uses GUIs and Java Treeview has been a great asset to my students and in my own work.

      I am using Version 1.2.0 . It resides in my /Applications directory I launch it by clicking it.
      I was unable to register, I got a "registration failed" error message.

      I got it working by allowing treeview and Jave full disk access. Then I remembered how to load the plugins.
      I went to help and then naivgated to the plugins menu, I then got the image,

      This used not to be necessary, The image used to load without navigating to plugins.
      Any suggestions?

      Thanks and best wishes,
      Rich

      From: bugs@jtreeview.p.re.sourceforge.net bugs@jtreeview.p.re.sourceforge.net on behalf of Alok Saldanha alokito@users.sourceforge.net
      Sent: Sunday, September 22, 2024 1:09 PM
      To: [jtreeview:bugs] 73@bugs.jtreeview.p.re.sourceforge.net
      Subject: [EXTERNAL] [jtreeview:bugs] #73 Problem "Finding" CDT Files Unless in Specific Directory

      You don't often get email from alokito@users.sourceforge.net. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

      Hi Richard,

      Could you describe the issue a little more fully?

      1. Which distribution of Java TreeView are you using, and how are you launching it?
      2. What is an example location where you cannot open files?

      I seem to be able to open files in my Desktop folder on Somoma, Mac OSX 14.6.1 after fixing the bundle launcher. I am prompted to grant Java access when I navigate to that folder, but otherwise it works. There is an additional issue related to finding plugins after AppTranslocation, but after I address that I could release a new version with the updated bundle launcher that could perhaps be a useful workaround.

      Attachments:

      [bugs:#73]https://sourceforge.net/p/jtreeview/bugs/73/ Problem "Finding" CDT Files Unless in Specific Directory

      Status: open
      Group: v0.9.6
      Created: Thu Nov 04, 2021 05:17 PM UTC by Jeffrey Lewis
      Last Updated: Fri Sep 20, 2024 01:29 PM UTC
      Owner: Alok Saldanha

      Hello Alok,

      I noticed an odd bug on a Mac (OS = 11.6) with TreeView 1.2.0. Unless my files are in my main user folder (i.e., Macintosh HD/Users/myname), TreeView cannot see them. In that folder, TreeView will show all files and folders, but if I click on another folder (e.g., Desktop), it appears empty (which it is not). Not a debilitating problem because I can simply place files where they can be read, but it is a nuisance for organizing analyses.

      Best,

      Jeff

      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/jtreeview/bugs/73/

      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

       

      Related

      Bugs: #73

      alternate

      • Alok Saldanha

        Alok Saldanha - 2024-09-26

        Hi Richard, I believe this issue was caused by AppTranslocation, aka Gatekeeper path randomisation. I have addressed this issue by moving the plugins and coordinates inside of the app bundle. This means that in order to add plugins or coordiantes files you will need to use the Terminal app, but should make JTV easier to use for most people. I'll probably have time to work on the documentation (and general cleanup) the weekend of Oct 5. If you have time, could you try out the newest version?

        https://sourceforge.net/projects/jtreeview/files/jtreeview/1.2.1

         

        • RICHARD FRIEDMAN

          RICHARD FRIEDMAN - 2024-09-27

          Alok,

          Thank you for the new build. It worked better than expected in that on loading the cdt file I got a heatmap immediately. It is not clear what I should do to get additional plugins or of what use they are.
          If you would like me to test the pre-relase version once the documentation is ready I will be happy to do so.
          I will be out of e-mail contact for several Jewish Holidays in October, but I will have an automatic announcement on as to when I will be back and I will be happy to test anything you would like me to test,

          Best wishes,
          Rich

          From: bugs@jtreeview.p.re.sourceforge.net bugs@jtreeview.p.re.sourceforge.net on behalf of Alok Saldanha alokito@users.sourceforge.net
          Sent: Thursday, September 26, 2024 7:23 AM
          To: [jtreeview:bugs] 73@bugs.jtreeview.p.re.sourceforge.net
          Subject: [EXTERNAL] [jtreeview:bugs] Re: #73 Problem "Finding" CDT Files Unless in Specific Directory

          You don't often get email from alokito@users.sourceforge.net. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

          Hi Richard, I believe this issue was caused by AppTranslocation, aka Gatekeeper path randomisation. I have addressed this issue by moving the plugins and coordinates inside of the app bundle. This means that in order to add plugins or coordiantes files you will need to use the Terminal app, but should make JTV easier to use for most people. I'll probably have time to work on the documentation (and general cleanup) the weekend of Oct 5. If you have time, could you try out the newest version?

          https://sourceforge.net/projects/jtreeview/files/jtreeview/1.2.1

          [bugs:#73]https://sourceforge.net/p/jtreeview/bugs/73/ Problem "Finding" CDT Files Unless in Specific Directory

          Status: open
          Group: v0.9.6
          Created: Thu Nov 04, 2021 05:17 PM UTC by Jeffrey Lewis
          Last Updated: Sun Sep 22, 2024 05:09 PM UTC
          Owner: Alok Saldanha

          Hello Alok,

          I noticed an odd bug on a Mac (OS = 11.6) with TreeView 1.2.0. Unless my files are in my main user folder (i.e., Macintosh HD/Users/myname), TreeView cannot see them. In that folder, TreeView will show all files and folders, but if I click on another folder (e.g., Desktop), it appears empty (which it is not). Not a debilitating problem because I can simply place files where they can be read, but it is a nuisance for organizing analyses.

          Best,

          Jeff

          Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/jtreeview/bugs/73/

          To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

           

          Related

          Bugs: #73

          alternate

  • Alok Saldanha

    Alok Saldanha - 2024-09-30

    After testing the Windows install I set 1.2.1 as the default version of Java TreeView. I believe there are very few if any third party plugins, but will try to find some time document how to get them working with the new app bundle layout next weekend.

     

    Last edit: Alok Saldanha 2024-09-30

    • RICHARD FRIEDMAN

      RICHARD FRIEDMAN - 2024-10-01

      Alok,
      I wasn't referring to third party plugins.
      I saw several more plugins in the menu than I use. If they are automatically accessed, that's fine.
      No further work is necessary.

      Please let me know when the docs are ready and I will review them if you would like me to do so,

      Thanks and best wishes,
      Rich

      From: bugs@jtreeview.p.re.sourceforge.net bugs@jtreeview.p.re.sourceforge.net on behalf of Alok Saldanha alokito@users.sourceforge.net
      Sent: Monday, September 30, 2024 7:22 PM
      To: [jtreeview:bugs] 73@bugs.jtreeview.p.re.sourceforge.net
      Subject: [EXTERNAL] [jtreeview:bugs] #73 Problem "Finding" CDT Files Unless in Specific Directory

      You don't often get email from alokito@users.sourceforge.net. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

      I set 1.2.1 as the default version of Java TreeView. I believe there are very few if any third party plugins, but will try to find some time document how to get them working with the new app bundle layout next weekend.

      [bugs:#73]https://sourceforge.net/p/jtreeview/bugs/73/ Problem "Finding" CDT Files Unless in Specific Directory

      Status: open
      Group: v0.9.6
      Created: Thu Nov 04, 2021 05:17 PM UTC by Jeffrey Lewis
      Last Updated: Thu Sep 26, 2024 11:23 AM UTC
      Owner: Alok Saldanha

      Hello Alok,

      I noticed an odd bug on a Mac (OS = 11.6) with TreeView 1.2.0. Unless my files are in my main user folder (i.e., Macintosh HD/Users/myname), TreeView cannot see them. In that folder, TreeView will show all files and folders, but if I click on another folder (e.g., Desktop), it appears empty (which it is not). Not a debilitating problem because I can simply place files where they can be read, but it is a nuisance for organizing analyses.

      Best,

      Jeff

      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/jtreeview/bugs/73/

      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

       

      Related

      Bugs: #73

      alternate

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