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Bibdesk getting clobbered #9

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supergra opened this Issue Apr 4, 2014 · 14 comments

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supergra commented Apr 4, 2014

Latexing has trashed my global bibliography file:

I use a global_bib_file_path which points to my full bibliography generated in BibDesk.

When I compiled my document, I got a pop-up saying:

47 Citation(s) in my_bibdesk.bib have been updated in your remote bibliography, update the item(s) prior the typeset?"

I assumed this would update the local copy of only the necessary entries for this manuscript. However, after clicking update, my global file got overwritten in a broken format! Bibdesk can no longer read it, and it doesn't generate a bibliography.

The culprit is that it is renaming fields:

Bdsk-File-1 becomes 1, which BibDesk cannot read.

I don't think you should be editing the global file at all. If there is a compelling reason, please warn the user explicitly that it is the global file that will be modified!

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csch0 Apr 4, 2014

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Hi thanks for that, that is not how it should be. LaTeXing do not make any changes to your global bib file (that would be useless since it should be your global file exported from somewhere else) the access is read only!!

Ok we need to figure it out what happened there. So your bib file in your project is my_bibdesk.bib and what's the name of your project bib?

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csch0 commented Apr 4, 2014

Hi thanks for that, that is not how it should be. LaTeXing do not make any changes to your global bib file (that would be useless since it should be your global file exported from somewhere else) the access is read only!!

Ok we need to figure it out what happened there. So your bib file in your project is my_bibdesk.bib and what's the name of your project bib?

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supergra Apr 4, 2014

Yes, my_bibdesk.bib is located in an entirely different folder.

My project's local bib files are called tm_adaptive.bbl and tm_adaptive.blg.

supergra commented Apr 4, 2014

Yes, my_bibdesk.bib is located in an entirely different folder.

My project's local bib files are called tm_adaptive.bbl and tm_adaptive.blg.

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Mmm, because the message says the following:

47 Citation(s) in my_bibdesk.bib have been updated in your remote bibliography, update the item(s) prior the typeset?"

So then it is clear that my_bibdesk will be updated somehow but that shouldn't be the case, it should update it in tm_adaptive.bib or however you call that file.

This only thing what I can imagine is that you also included the my_bibdesk.bib in your LaTeX project (and this files are writable by LaTeXing).

If you say you haven't done that, could you send me your LaTeX project via email do I can have a closer look what could have happen?

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csch0 commented Apr 4, 2014

Mmm, because the message says the following:

47 Citation(s) in my_bibdesk.bib have been updated in your remote bibliography, update the item(s) prior the typeset?"

So then it is clear that my_bibdesk will be updated somehow but that shouldn't be the case, it should update it in tm_adaptive.bib or however you call that file.

This only thing what I can imagine is that you also included the my_bibdesk.bib in your LaTeX project (and this files are writable by LaTeXing).

If you say you haven't done that, could you send me your LaTeX project via email do I can have a closer look what could have happen?

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supergra Apr 4, 2014

Yes, now I see that I did that. I had this line:

\bibliography{<local_path>/my_bibdesk}

So...I guess I still don't understand why that file was overwritten with modified fields.

supergra commented Apr 4, 2014

Yes, now I see that I did that. I had this line:

\bibliography{<local_path>/my_bibdesk}

So...I guess I still don't understand why that file was overwritten with modified fields.

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supergra Apr 4, 2014

Is that Latexing modifying it, or a bibtex tool, or what?

supergra commented Apr 4, 2014

Is that Latexing modifying it, or a bibtex tool, or what?

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supergra Apr 4, 2014

The problem is that a have many working latex files that include a line like that. My old typesetting code (TexShop) doesn't modify that file. So now it's dangerous for me to open an existing Latex file and compile it with Latexing.

supergra commented Apr 4, 2014

The problem is that a have many working latex files that include a line like that. My old typesetting code (TexShop) doesn't modify that file. So now it's dangerous for me to open an existing Latex file and compile it with Latexing.

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Ok let me explain it, the system is always the same for all remote bibliography systems like Mendeley, Zotero, etc and also the Global Bibliography file.

Normally you are having a Remote.bib where all the remote bib items are saved and then before every compile LaTeXing check's the remote sources for updates and saves this update on your system.

In case you just wanna continue to use it like it was (with TeXShop in your case) just don't use the global bibliography option and you are good.

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csch0 commented Apr 4, 2014

Ok let me explain it, the system is always the same for all remote bibliography systems like Mendeley, Zotero, etc and also the Global Bibliography file.

Normally you are having a Remote.bib where all the remote bib items are saved and then before every compile LaTeXing check's the remote sources for updates and saves this update on your system.

In case you just wanna continue to use it like it was (with TeXShop in your case) just don't use the global bibliography option and you are good.

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supergra Apr 4, 2014

Ok, I am not using a remote service. I just have a single, local master bibliography that all my manuscripts reference.

I would like that file to never be edited (by Latexing), but every single manuscript uses it! Is there a way to automate this in Latexing, or should I just use the method I had before (the explicit bibliography{path} command)?

I expected the global_bib_file settings to do that.

supergra commented Apr 4, 2014

Ok, I am not using a remote service. I just have a single, local master bibliography that all my manuscripts reference.

I would like that file to never be edited (by Latexing), but every single manuscript uses it! Is there a way to automate this in Latexing, or should I just use the method I had before (the explicit bibliography{path} command)?

I expected the global_bib_file settings to do that.

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supergra Apr 4, 2014

I guess you are saying that it does work that way, but that I need to remove the offending bibliography lines, because that confuses Latexing?

supergra commented Apr 4, 2014

I guess you are saying that it does work that way, but that I need to remove the offending bibliography lines, because that confuses Latexing?

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Yes a remote service and a 'local master bibliography' is the same. Yes I just figure that I should not check all bib files for update rather just the remote.bib (by default)

Yes normally exactly for that is the global_bib_file setting.

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csch0 commented Apr 4, 2014

Yes a remote service and a 'local master bibliography' is the same. Yes I just figure that I should not check all bib files for update rather just the remote.bib (by default)

Yes normally exactly for that is the global_bib_file setting.

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csch0 Apr 4, 2014

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Thanks for pointing this out, that is a very small change but could be a huge impact of data loose, will check the code an publish a fix over the weekend.

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csch0 commented Apr 4, 2014

Thanks for pointing this out, that is a very small change but could be a huge impact of data loose, will check the code an publish a fix over the weekend.

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supergra Apr 4, 2014

Great. I have it working now. Fortunately, I was able to fix all the errors using a simple find-and-replace, so I'm back to a working master copy. Thanks for taking a look at this.

supergra commented Apr 4, 2014

Great. I have it working now. Fortunately, I was able to fix all the errors using a simple find-and-replace, so I'm back to a working master copy. Thanks for taking a look at this.

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csch0 Apr 4, 2014

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I will close this issue once I published the fix, so let you know here.

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csch0 commented Apr 4, 2014

I will close this issue once I published the fix, so let you know here.

@csch0 csch0 added the on roadmap label May 20, 2014

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csch0 May 20, 2014

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Now fixed in 1.2.0

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csch0 commented May 20, 2014

Now fixed in 1.2.0

@csch0 csch0 closed this May 20, 2014

@csch0 csch0 removed the on roadmap label May 20, 2014

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