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Stuck on Send to JabRef with MacOS #177

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FilipeMaia opened this issue Jun 4, 2020 · 39 comments
Closed

Stuck on Send to JabRef with MacOS #177

FilipeMaia opened this issue Jun 4, 2020 · 39 comments
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status:jabref A bug or issue that depends on a change to JabRef itself status:waiting-for-feedback type:bug

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@FilipeMaia
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I'm on MacOS 10.13.5 with JabRef 5.0 and Chrome 81.0.4044.138.
I've installed the extension from https://chrome.google.com/webstore/detail/jabref-browser-extension/bifehkofibaamoeaopjglfkddgkijdlh/
When using it, e.g. on https://www.nature.com/articles/s41598-020-65225-4 it gets stuck on Send to JabRef...
Looking into the developer console I see:
TypeError: Cannot read property 'items' of null at chrome-extension://bifehkofibaamoeaopjglfkddgkijdlh/Zotero/translate_item.js:134
@tobiasdiez
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I think currently there is a problem with the setup on MacOS.

As a workaround, you can follow the guidelines for the manual install: https://docs.jabref.org/collect/jabref-browser-extension#mac-os using this file:
https://github.com/JabRef/jabref/pull/6442/files#diff-d99aa77716bf8252215c6e3a02faf611
and replace the Firefox-specific parts by the paths outlined here: https://developer.chrome.com/apps/nativeMessaging

@LyzardKing is this fixed with JabRef/jabref#6442 ?

@tobiasdiez tobiasdiez added status:jabref A bug or issue that depends on a change to JabRef itself type:bug labels Jun 5, 2020
@LyzardKing
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Not having a mac to test this on does not simplify things...
@FilipeMaia Do you install from the .dmg or .pkg files?
There might be a difference in the way macos exposes the path variable.
JabRef/jabref#6442 is a different issue, but this might help with that as well

@FilipeMaia
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From .pkg.
Any more information I can give to help with debugging?

@LyzardKing
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Is there any file in /Library/Google/Chrome/NativeMessagingHosts?

@LyzardKing
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specifically org.jabref.jabref.json

@FilipeMaia
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No there isn't. Neither in ~/Library/Application Support/Google/Chrome/NativeMessagingHosts

@FilipeMaia
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The installation instructions mention ~/Library/Application Support/Mozilla/NativeMessagingHosts/. Is that correct?

@FilipeMaia
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I also noticed that org.jabref.jabref.json from the instructions page links to the Linux section of the tree and mentions a /opt/jabref/lib/jabrefHost.py which is not there nor could I find it anywhere.

@FilipeMaia
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FilipeMaia commented Jun 6, 2020 •
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@tobiasdiez I tried to follow your suggestion but nothing really changed. I imagine the fact that /opt/jabref/lib/jabrefHost.py does not exist must be a problem.

@tobiasdiez
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Can you try to create the /opt/jabref/lib/jabrefHost.py file by downloading https://github.com/JabRef/jabref/blob/master/buildres/linux/jabrefHost.py.
Moreover, put https://github.com/JabRef/jabref/blob/1a546922787160ed447d3a6f63f068916e17e225/buildres/mac/native-messaging-host/chromium/org.jabref.jabref.json into ~/Library/Application Support/Google/Chrome/NativeMessagingHosts.

This assumes that the JabRef executable is in /opt/jabref/bin/JabRef. If this is not the case, then every occurrence of /opt/jabref/ (in the above instructions as well as in the json file) needs to be replaced by the right path.

I'm sorry for the inconvenience. Appearently you are the first mac user that tries the extension for Chrome ;-)

@FilipeMaia
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No problem, thanks for the help :).
There is no /opt/jabref. JabRef is installed in /Applications/JabRef.app/ as most MacOS apps.
I'll try to download the file as suggested an see what I can do with the paths.

@FilipeMaia
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So I downloaded the jabrefHost.py into /Applications/JabRef.app/Contents/runtime/Contents/Home/lib and made it executable. I then edited to change the shebang to point to my python3 which is in /usr/local/bin/python3.
I finally edited org.jabref.jabref.json to point to the location in /Applications. And it now works!
But clearly this should be improved...

@LyzardKing
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... I'm looking at it in the previously mentioned PR, it wasn't it's main point, but it's probably a question of linking the correct files in the new buildres/mac folder

@LyzardKing
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With the latest push on the PR (JabRef/jabref#6442) the correct files should be included in the macos build.
The issue now is mostly with the install command, to copy the system files.. but it's a step in the right direction.
No more fiddling with the linux files in macos...hopefully we can keep the two separate (mostly)

@AriSchlesinger
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AriSchlesinger commented Sep 2, 2020 •
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Similar issue with Firefox on Mac
fixed locally following similar strategy to @FilipeMaia

updated jabrefHost.pylocated at /Applications/JabRef.app/Contents/Resources to point hashbang to /usr/local/bin/python3 (where python3 will be installed using Homebrew)
made jabrefHost.py executable.

created new folder NativeMessagingHosts at path /Users/ *yourUser* /Library/Application Support/Mozilla
downloaded org.jabref.jabref.json into this folder
finally edited org.jabref.jabref.json path to point to the executable located in Applications/JabRef.app/Contents/Resources

thx for the breadcrumbs :)

@MingLin-home
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I have the same issue. JabRef 5.1, installed by DMG. Not lucky enough to make it work...

@LyzardKing
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@AriSchlesinger @FilipeMaia
Could you test something? Try replacing the hashbang with:
#!/usr/bin/env python3
This should fetch the correct python version without hardcoding it.
Thanks

@LyzardKing
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@MingLin-home
Can you verify that the file jabrefHost.py exists in /Applications/JabRef.app/Contents/Resources?
Also try changing the first line as described in the previous comment.

@clecap
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clecap commented Sep 20, 2020

Same problem here on MacOS 10.15.6

JabRef 5.1 installed via DMG.

jabrefHost.py confirmed in JabRef.app/Contents/Resources

shebang is /usr/bin/python3

/usr/bin/python3 is installed

org.jabref.jabref.json is in NativeMessagingHosts

In Firefox: Extension does not show up
In Chrome: Extension throws ERR_FILE_NOT_FOUND

@kddjenejfkffksd
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First time trying JabRef at all but No luck on Brave either.

  1. Installed dmg,
  2. placed the newer ~/Library/Application\ Support/BraveSoftware/Brave-Browser/NativeMessagingHosts/org.jabref.jabref.json,
  3. changed jabrefHost.py shebang to /usr/bin/env python3
  4. and copied it on /Applications/JabRef.app/Contents/runtime/Contents/Home/lib because I don't know what I'm doing.

But all I ever got was ERR_FILE_NOT_FOUND.

@LyzardKing
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LyzardKing commented Oct 2, 2020 •
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@clecap "org.jabref.jabref.json is in NativeMessagingHosts". In what folders?
It should be in:
~/Library/Application Support/Google/Chrome/NativeMessagingHosts/<name>.json for chrome (and brave @coughingmouse )
~/Library/Application Support/Mozilla/NativeMessagingHosts/<name>.json for firefox.

Let me know if those paths work.

@kddjenejfkffksd
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kddjenejfkffksd commented Oct 2, 2020 •
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@LyzardKing Why should it be placed in a Google folder for Brave? I don't even have Chrome installed.

I did copy the json file onto the directory to see if it works, just to be clear, to no avail.

@LyzardKing
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Brave (and many other browsers) are chrome-based, so they often use the same folder structure as chrome..
There are many issues (by looking at different support tickets on extensions) like the following:
browserpass/browserpass-native#43 (comment)
They seem to point to inconsistencies with the folder structure in brave.

Another path to try is: ~/Library/Application Support/Chromium/NativeMessagingHosts/

@clecap
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clecap commented Oct 2, 2020 via email

@AriSchlesinger
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Heads up, in Firefox, it appears in the URL bar:

Screen Shot 2020-10-02 at 11 55 45

@AriSchlesinger
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AriSchlesinger commented Oct 2, 2020 •
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Have you all made the file jabrefHost.py executable?

(see link below on creating an executable if you are unsure)
https://stackoverflow.com/questions/36564320/how-to-make-python-script-executable-on-osx

@AriSchlesinger
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@AriSchlesinger @FilipeMaia
Could you test something? Try replacing the hashbang with:
#!/usr/bin/env python3
This should fetch the correct python version without hardcoding it.
Thanks

I am fairly certain I tried this with no luck.

@LyzardKing
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@AriSchlesinger
Thanks for the testing...
Does it work with #! /usr/bin/python3?

@tobiasdiez tobiasdiez mentioned this issue Oct 6, 2020
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@clecap
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clecap commented Oct 14, 2020

Yes, jabrefHost.py, which is in the JabRef.app Contents folder, is executable.

/usr/bin/env python3 or /usr/bin/python3 makes no difference in the reaction. ERR_FILE_NOT_FOUND error.

@tobiasdiez
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Does this error still occurs? I don't have a mac, so I sadly cannot test this. @LyzardKing @Siedlerchr can you reproduce the ERR_FILE_NOT_FOUND error?

@Siedlerchr
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Firefox and jabref latest dev version on Mac I do not have any issues

@LyzardKing
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@Siedlerchr does it work with the system version of python3? Without installing from other sources like brew?

@Siedlerchr
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Good question, I may have installed python3 form another source:
Python 3.9.0 (default, Nov 21 2020, 14:55:42)

@LyzardKing
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what do you get if you run which python3 in the terminal?

@Siedlerchr
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/usr/local/bin/python3

@LyzardKing
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As far as I can tell that should be the version pulled from the python website...
brew should install in a /cellar/... dir, and the system version should be in /ust/bin/python3...
The strange thing is that the env shebang doesn't work...

@Siedlerchr
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hm, I only found this thread here https://stackoverflow.com/questions/52969383/shebang-line-for-python-does-not-work-at-all
maybe something with permissions?

@tobiasdiez
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So it seems this is fixed now, right?

@clecap
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clecap commented Jan 31, 2021

@tobiasdiez thank you for coming back on this.

I installed JabRef and the extension from a completely new download to test it.

Result: I cannot test this error as now there is a new error which does not let me test this effect any longer. I get stuck at "searching bibliographic data" and get a "cannot read property of configOptions of undefined" error in the browser console. See my new issue.

Sorry for that

@juhannc juhannc mentioned this issue Feb 15, 2021
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@FilipeMaia @Siedlerchr @tobiasdiez @clecap @LyzardKing @kddjenejfkffksd @MingLin-home @AriSchlesinger