broken pipes error with zotxt

broken pipes error with zotxt

[willo]

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I had been using pandoc for about 6 months now to successfully to convert 
.md files to.docx and .html. I've been using zotxt to manage citations. 
Then I installed new versions of pandoc and of zotxt. 

Now when I run pandoc in a command like: 

pandoc ch6.md -o ch6.html --filter pandoc-zotxt -F pandoc-citeproc --csl=chicago-note-bibliography.csl

 It gives me the following error:
pandoc: Error running filter pandoc-zotxt fd:4: hPutBuf: resource vanished (
Broken pipe)


I tried a reinstall of pandoc-citeproc, to no avail. 


Any ideas? I'm using OSX 10.9.5. 

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Re: broken pipes error with zotxt

[John MacFarlane]

The best way to diagnose filter problems is to run the filters manually.

    pandoc ch6.md -s -t json --csl=chicago-note-bibliography.csl | \
      pandoc-zotxt | \
      pandoc-citeproc | \
      pandoc -f json -s -o ch6.html

This may give you more information about what is breaking.
You can also use the first line of this sequence to find out what
input is being passed to pandoc-zotxt.

+++ willo [Mar 02 15 19:52 ]:
>
>
>I had been using pandoc for about 6 months now to successfully to convert
>.md files to.docx and .html. I've been using zotxt to manage citations.
>Then I installed new versions of pandoc and of zotxt.
>
>Now when I run pandoc in a command like:
>
>pandoc ch6.md -o ch6.html --filter pandoc-zotxt -F pandoc-citeproc --csl=chicago-note-bibliography.csl
>
> It gives me the following error:
>pandoc: Error running filter pandoc-zotxt fd:4: hPutBuf: resource vanished (
>Broken pipe)
>
>
>I tried a reinstall of pandoc-citeproc, to no avail.
>
>
>Any ideas? I'm using OSX 10.9.5.
>
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Re: broken pipes error with zotxt

[Tom Okie]

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Thanks for the quick response! I've tried running the filters manually, and
I get the following, which I'm not sure how to interpret:

  File
"/Library/Frameworks/Python.framework/Versions/2.7/bin/pandoc-zotxt", line
9, in <module>
    load_entry_point('pandoc-zotxt==0.1.26', 'console_scripts',
'pandoc-zotxt')()
  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandoczotxt/__init__.py",
line 82, in run
    toJSONFilter(filters=[extractCites], metafilters=[alterMetadata])
  File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandoczotxt/__init__.py",
line 29, in toJSONFilter
    doc = json.loads(sys.stdin.read('utf8'))
TypeError: an integer is required
pandoc-citeproc: not enough input
pandoc: not enough input

I also tried running the conversion without the pandoc-zotxt filter, and I
didn't get the error. So perhaps it's an issue with zotxt alone?



On Mon, Mar 2, 2015 at 11:10 PM, John MacFarlane <jgm-TVLZxgkOlNX2fBVCVOL8/A@public.gmane.org> wrote:

> The best way to diagnose filter problems is to run the filters manually.
>
>    pandoc ch6.md -s -t json --csl=chicago-note-bibliography.csl | \
>      pandoc-zotxt | \
>      pandoc-citeproc | \
>      pandoc -f json -s -o ch6.html
>
> This may give you more information about what is breaking.
> You can also use the first line of this sequence to find out what
> input is being passed to pandoc-zotxt.
>
> +++ willo [Mar 02 15 19:52 ]:
>
>>
>>
>> I had been using pandoc for about 6 months now to successfully to convert
>> .md files to.docx and .html. I've been using zotxt to manage citations.
>> Then I installed new versions of pandoc and of zotxt.
>>
>> Now when I run pandoc in a command like:
>>
>> pandoc ch6.md -o ch6.html --filter pandoc-zotxt -F pandoc-citeproc
>> --csl=chicago-note-bibliography.csl
>>
>> It gives me the following error:
>> pandoc: Error running filter pandoc-zotxt fd:4: hPutBuf: resource
>> vanished (
>> Broken pipe)
>>
>>
>> I tried a reinstall of pandoc-citeproc, to no avail.
>>
>>
>> Any ideas? I'm using OSX 10.9.5.
>>
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>
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Re: broken pipes error with zotxt

[Richard Lawrence]

Tom Okie <wtokie-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:
> ...
> "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandoczotxt/__init__.py",
> line 29, in toJSONFilter
>     doc = json.loads(sys.stdin.read('utf8'))
> TypeError: an integer is required
> pandoc-citeproc: not enough input
> pandoc: not enough input
>
> I also tried running the conversion without the pandoc-zotxt filter, and I
> didn't get the error. So perhaps it's an issue with zotxt alone?

Yes, that looks like a zotxt bug.  The 'read' method on a Python file
object takes a number of bytes to read, not an encoding.

I'll add a comment to the BitBucket issue:
https://bitbucket.org/egh/zotxt/issue/19/pandoc-error-after-fresh-install

Best,
Richard

Re: broken pipes error with zotxt

[John MacFarlane]

+++ Tom Okie [Mar 03 15 08:40 ]:
>Thanks for the quick response! I've tried running the filters manually, and
>I get the following, which I'm not sure how to interpret:
>
>  File
>"/Library/Frameworks/Python.framework/Versions/2.7/bin/pandoc-zotxt", line
>9, in <module>
>    load_entry_point('pandoc-zotxt==0.1.26', 'console_scripts',
>'pandoc-zotxt')()
>  File
>"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandoczotxt/__init__.py",
>line 82, in run
>    toJSONFilter(filters=[extractCites], metafilters=[alterMetadata])
>  File
>"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandoczotxt/__init__.py",
>line 29, in toJSONFilter
>    doc = json.loads(sys.stdin.read('utf8'))
>TypeError: an integer is required
>pandoc-citeproc: not enough input
>pandoc: not enough input
>
>I also tried running the conversion without the pandoc-zotxt filter, and I
>didn't get the error. So perhaps it's an issue with zotxt alone?

One possibility is that the zotxt version you're using is expecting the
kind of json encoding produced by an earlier (or later) version of
pandoc.  What version of pandoc?

Re: broken pipes error with zotxt

[Tom Okie]

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I'm using 1.13.2.

On Tue, Mar 3, 2015 at 1:41 PM, John MacFarlane <jgm-TVLZxgkOlNX2fBVCVOL8/A@public.gmane.org> wrote:

> +++ Tom Okie [Mar 03 15 08:40 ]:
>
>> Thanks for the quick response! I've tried running the filters manually,
>> and
>> I get the following, which I'm not sure how to interpret:
>>
>>  File
>> "/Library/Frameworks/Python.framework/Versions/2.7/bin/pandoc-zotxt",
>> line
>> 9, in <module>
>>    load_entry_point('pandoc-zotxt==0.1.26', 'console_scripts',
>> 'pandoc-zotxt')()
>>  File
>> "/Library/Frameworks/Python.framework/Versions/2.7/lib/
>> python2.7/site-packages/pandoczotxt/__init__.py",
>> line 82, in run
>>    toJSONFilter(filters=[extractCites], metafilters=[alterMetadata])
>>  File
>> "/Library/Frameworks/Python.framework/Versions/2.7/lib/
>> python2.7/site-packages/pandoczotxt/__init__.py",
>> line 29, in toJSONFilter
>>    doc = json.loads(sys.stdin.read('utf8'))
>> TypeError: an integer is required
>> pandoc-citeproc: not enough input
>> pandoc: not enough input
>>
>> I also tried running the conversion without the pandoc-zotxt filter, and I
>> didn't get the error. So perhaps it's an issue with zotxt alone?
>>
>
> One possibility is that the zotxt version you're using is expecting the
> kind of json encoding produced by an earlier (or later) version of
> pandoc.  What version of pandoc?
>
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Re: broken pipes error with zotxt

[John MacFarlane]

+++ Tom Okie [Mar 03 15 14:09 ]:
>   I'm using 1.13.2.

You might want to confirm with the zotxt author that it
works with this version of pandoc.

Re: broken pipes error with zotxt

[Andrew Dunning]

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This was a bug introduced in a recent update, and is fixed with 
pandoc-zotxt 0.1.27.

On Tuesday, March 3, 2015 at 2:41:39 PM UTC-5, John MacFarlane wrote:
>
> +++ Tom Okie [Mar 03 15 14:09 ]: 
> >   I'm using 1.13.2. 
>
> You might want to confirm with the zotxt author that it 
> works with this version of pandoc. 
>

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Re: broken pipes error with zotxt

[Tom Okie]

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I posted this over at the zotxt page (
https://bitbucket.org/egh/zotxt/issue/19/pandoc-error-after-fresh-install#comment-16141475)
as well, but after updating zotxt 0.1.27 and running

pandoc ch0.md -o ch0.docx -F pandoc-zotxt -F pandoc-citeproc
--csl=chicago-note-bibliography.csl

I get the following:

Traceback (most recent call last):

File "/Library/Frameworks/Python.framework/Versions/2.7/bin/pandoc-zotxt",
line 9, in <module>
    load_entry_point('pandoc-zotxt==0.1.27', 'console_scripts',
'pandoc-zotxt')()

File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandoczotxt/__init__.py",
line 84, in run
    toJSONFilter(filters=[extractCites], metafilters=[alterMetadata])

File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandoczotxt/__init__.py",
line 40, in toJSONFilter
    action(altered[0]['unMeta'])

File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandoczotxt/__init__.py",
line 74, in alterMetadata
    cites.append(fetchItem('betterbibtexkey', citekey))

File
"/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pandoczotxt/__init__.py",
line 61, in fetchItem
    cite = json.load(urllib2.urlopen(url))[0]

IndexError: list index out of range

pandoc: Error running filter pandoc-zotxt

On Fri, Mar 6, 2015 at 3:17 PM, Andrew Dunning <andunning-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

> This was a bug introduced in a recent update, and is fixed with
> pandoc-zotxt 0.1.27.
>
> On Tuesday, March 3, 2015 at 2:41:39 PM UTC-5, John MacFarlane wrote:
>>
>> +++ Tom Okie [Mar 03 15 14:09 ]:
>> >   I'm using 1.13.2.
>>
>> You might want to confirm with the zotxt author that it
>> works with this version of pandoc.
>>
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