File Organization

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File Organization

Natalie Ceperley
Hello,

I am new to the list, so I apologize for my newbie questions.   I
didn't not find an answer in the archives, unfortunately.

I have two questions.

1) In the feature list, it says that "BibDesk will automatically move
and rename these files for you."  I cannot find and option to make
this happen.  How do I do this?

2) Is there a way to batch import pdf files and have fields populated
by metadata? When I import files one by one, most fields are blank or
random.

Thank you for your help!

Natalie

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Re: File Organization

Christiaan Hofman

On Feb 10, 2016, at 12:23, Natalie Ceperley <[hidden email]> wrote:

Hello,

I am new to the list, so I apologize for my newbie questions.   I
didn't not find an answer in the archives, unfortunately.

I have two questions.

1) In the feature list, it says that "BibDesk will automatically move
and rename these files for you."  I cannot find and option to make
this happen.  How do I do this?


In the Autofile preferences, check the “File papers automatically” option. You should probably also modify pother preferences there, such as your papers folder and the local file format.

Note that this will not move existing files, only newly added files. To auto-file existing files you can use the “Autofile linked file” actions, e.g. in the Publications menu or in contextual menus.

2) Is there a way to batch import pdf files and have fields populated
by metadata? When I import files one by one, most fields are blank or
random.

Thank you for your help!

Natalie

There are some hidden preferences (see the Wiki for details) to try and import meta data from imported PDFs. unfortunately metadata from PDFs is usually not available or of very bad quality, that’s why we don’t use this be default. So YMMV. Otherwise you may need to use AppleScript for any customized data handling.

Christiaan


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Re: File Organization

Paul K Egell-Johnsen
Check out this: https://www.youtube.com/watch?v=cTBJW85RuJs has a link to a applescript file. Check out if you can use it and adapt it:

A demo of two BibDesk AppleScripts that improve BibDesk import functionality. Scripts are here: https://github.com/mankoff/BibDeskApp... 

Thanks to pdfmeat and bibfetch, useful tools that are needed by this script. https://github.com/mankoff/pdfmeathttps://github.com/mankoff/bibfetch



On Wed, Feb 10, 2016 at 1:32 PM, Christiaan Hofman <[hidden email]> wrote:

On Feb 10, 2016, at 12:23, Natalie Ceperley <[hidden email]> wrote:

Hello,

I am new to the list, so I apologize for my newbie questions.   I
didn't not find an answer in the archives, unfortunately.

I have two questions.

1) In the feature list, it says that "BibDesk will automatically move
and rename these files for you."  I cannot find and option to make
this happen.  How do I do this?


In the Autofile preferences, check the “File papers automatically” option. You should probably also modify pother preferences there, such as your papers folder and the local file format.

Note that this will not move existing files, only newly added files. To auto-file existing files you can use the “Autofile linked file” actions, e.g. in the Publications menu or in contextual menus.

2) Is there a way to batch import pdf files and have fields populated
by metadata? When I import files one by one, most fields are blank or
random.

Thank you for your help!

Natalie

There are some hidden preferences (see the Wiki for details) to try and import meta data from imported PDFs. unfortunately metadata from PDFs is usually not available or of very bad quality, that’s why we don’t use this be default. So YMMV. Otherwise you may need to use AppleScript for any customized data handling.

Christiaan


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--
Paul K Egell-Johnsen

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Re: File Organization

Ken Mankoff
Hi Paul, others,

I just re-watched that video (I made it). Looks neat, but for some reason I haven't been using that workflow recently. I think the auto-downloading wasn't successful often enough. It either couldn't download the PDF, or downloaded the wrong PDF most of the time.

My new workflow follows.

1) Manually download and drag-and-drop the PDF(s) into BibDesk.
2) Run my "import" script (attached to this email). This isn't based on pdfmeat anymore.



That script tries to parse the doi from the BibDesk entry first. If the DOI isn't in BibDesk, it tries to get it from the PDF itself, and pops up a dialog that lets you correct the parsed version (sometimes the page number gets included by mistake), or enter it if it wasn't able to parse it from the PDF. At this point, you are almost guaranteed success since you've manually entered or verified the DOI, but new PDFs may not have their info published in the WWW databases yet.

The import script uses some python scripts to parse for the DOI and then fetch the BibTeX entry from the internet based on the DOI, also attached:



As always, get things working on the command line first before trying to get the whole workflow behaving properly in BibDesk, since it will be easier to debug. You'll probably need to add some packages to your python install. Use "pip install X" to add the necessary packages, which you should be able to find based on the errors produced by the attached scripts.

Paths will need to be changed based on your python install, and where you store the attached python scripts.

Hope this helps,

  -k.

On 2016-02-12 at 09:18, Paul K Egell-Johnsen <[hidden email]> wrote:

> Check out this: https://www.youtube.com/watch?v=cTBJW85RuJs has a link to a
> applescript file. Check out if you can use it and adapt it:
>
> A demo of two BibDesk AppleScripts that improve BibDesk import
> functionality. Scripts are here: https://github.com/mankoff/BibDeskApp...
> <https://github.com/mankoff/BibDeskAppleScripts>
>
> Thanks to pdfmeat and bibfetch, useful tools that are needed by this
> script. https://github.com/mankoff/pdfmeat
> https://github.com/mankoff/bibfetch
>
>
>    -
>
>
> On Wed, Feb 10, 2016 at 1:32 PM, Christiaan Hofman <[hidden email]>
> wrote:
>
>>
>> On Feb 10, 2016, at 12:23, Natalie Ceperley <[hidden email]> wrote:
>>
>> Hello,
>>
>> I am new to the list, so I apologize for my newbie questions.   I
>> didn't not find an answer in the archives, unfortunately.
>>
>> I have two questions.
>>
>> 1) In the feature list, it says that "BibDesk will automatically move
>> and rename these files for you."  I cannot find and option to make
>> this happen.  How do I do this?
>>
>>
>> In the Autofile preferences, check the “File papers automatically” option.
>> You should probably also modify pother preferences there, such as your
>> papers folder and the local file format.
>>
>> Note that this will not move existing files, only newly added files. To
>> auto-file existing files you can use the “Autofile linked file” actions,
>> e.g. in the Publications menu or in contextual menus.
>>
>> 2) Is there a way to batch import pdf files and have fields populated
>> by metadata? When I import files one by one, most fields are blank or
>> random.
>>
>> Thank you for your help!
>>
>> Natalie
>>
>>
>> There are some hidden preferences (see the Wiki for details) to try and
>> import meta data from imported PDFs. unfortunately metadata from PDFs is
>> usually not available or of very bad quality, that’s why we don’t use this
>> be default. So YMMV. Otherwise you may need to use AppleScript for any
>> customized data handling.
>>
>> Christiaan
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>> _______________________________________________
>> Bibdesk-users mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/bibdesk-users
>>
>>

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import.scpt (19K) Download Attachment
doi2bib.py (696 bytes) Download Attachment
doi_from_pdf.py (688 bytes) Download Attachment
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Re: File Organization

Christiaan Hofman
It may be helpful to link these scripts on the Wiki.

Christiaan

> On Feb 12, 2016, at 15:48, Ken Mankoff <[hidden email]> wrote:
>
> Hi Paul, others,
>
> I just re-watched that video (I made it). Looks neat, but for some reason I haven't been using that workflow recently. I think the auto-downloading wasn't successful often enough. It either couldn't download the PDF, or downloaded the wrong PDF most of the time.
>
> My new workflow follows.
>
> 1) Manually download and drag-and-drop the PDF(s) into BibDesk.
> 2) Run my "import" script (attached to this email). This isn't based on pdfmeat anymore.
>
> <import.scpt>
> That script tries to parse the doi from the BibDesk entry first. If the DOI isn't in BibDesk, it tries to get it from the PDF itself, and pops up a dialog that lets you correct the parsed version (sometimes the page number gets included by mistake), or enter it if it wasn't able to parse it from the PDF. At this point, you are almost guaranteed success since you've manually entered or verified the DOI, but new PDFs may not have their info published in the WWW databases yet.
>
> The import script uses some python scripts to parse for the DOI and then fetch the BibTeX entry from the internet based on the DOI, also attached:
>
> <doi2bib.py><doi_from_pdf.py>
> As always, get things working on the command line first before trying to get the whole workflow behaving properly in BibDesk, since it will be easier to debug. You'll probably need to add some packages to your python install. Use "pip install X" to add the necessary packages, which you should be able to find based on the errors produced by the attached scripts.
>
> Paths will need to be changed based on your python install, and where you store the attached python scripts.
>
> Hope this helps,
>
>  -k.
>
> On 2016-02-12 at 09:18, Paul K Egell-Johnsen <[hidden email]> wrote:
>> Check out this: https://www.youtube.com/watch?v=cTBJW85RuJs has a link to a
>> applescript file. Check out if you can use it and adapt it:
>>
>> A demo of two BibDesk AppleScripts that improve BibDesk import
>> functionality. Scripts are here: https://github.com/mankoff/BibDeskApp...
>> <https://github.com/mankoff/BibDeskAppleScripts>
>>
>> Thanks to pdfmeat and bibfetch, useful tools that are needed by this
>> script. https://github.com/mankoff/pdfmeat
>> https://github.com/mankoff/bibfetch
>>
>>
>>   -
>>
>>
>> On Wed, Feb 10, 2016 at 1:32 PM, Christiaan Hofman <[hidden email]>
>> wrote:
>>
>>>
>>> On Feb 10, 2016, at 12:23, Natalie Ceperley <[hidden email]> wrote:
>>>
>>> Hello,
>>>
>>> I am new to the list, so I apologize for my newbie questions.   I
>>> didn't not find an answer in the archives, unfortunately.
>>>
>>> I have two questions.
>>>
>>> 1) In the feature list, it says that "BibDesk will automatically move
>>> and rename these files for you."  I cannot find and option to make
>>> this happen.  How do I do this?
>>>
>>>
>>> In the Autofile preferences, check the “File papers automatically” option.
>>> You should probably also modify pother preferences there, such as your
>>> papers folder and the local file format.
>>>
>>> Note that this will not move existing files, only newly added files. To
>>> auto-file existing files you can use the “Autofile linked file” actions,
>>> e.g. in the Publications menu or in contextual menus.
>>>
>>> 2) Is there a way to batch import pdf files and have fields populated
>>> by metadata? When I import files one by one, most fields are blank or
>>> random.
>>>
>>> Thank you for your help!
>>>
>>> Natalie
>>>
>>>
>>> There are some hidden preferences (see the Wiki for details) to try and
>>> import meta data from imported PDFs. unfortunately metadata from PDFs is
>>> usually not available or of very bad quality, that’s why we don’t use this
>>> be default. So YMMV. Otherwise you may need to use AppleScript for any
>>> customized data handling.
>>>
>>> Christiaan
>>>


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