gmane.comp.gnome.apps.pybliographer

Re: bib file / no refs displayed/ pybliographer: warning: unable to convert `\textit'

Patrick — 2012-01-25T13:10:31



Hi!

Here's what helped me:
directly below the menu and toolbar is a small handle (3 small vertical lines
next to each other in my case). You can drag it down to reveal the missing
entries. It's hard to spot, which is probably why I didn't notice it at first.
Hope this pretty easy solution helps you as well!

Best,
Patrick



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Re: pybliographer 1.2.14 broken?

Patrick — 2012-01-25T13:03:09

Ernesto Posse <eposse< at >...> writes:



Hi!

I'm on Ubuntu 11.10 too and had the same problem.
I just found out that the file actually is opened correctly, but the default
layout of Pybliographer "hides" all entries (maybe due to the Ubuntu theme?).

I noticed that directly below the menu you can find a small handle or bar which
can be dragged down with the mouse, revealing all the missing entries.

Hope that helps, for me at least it solved the problem!

Best,
Patrick



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bib file / no refs displayed/ pybliographer: warning: unable to convert `\textit'

Sam McClatchie — 2011-12-22T18:46:58

Hi

I've been using pybliographer for years on linux, but am having trouble 
displaying my database (bibtex *.bib file) since upgrading to ubuntu 
11.10 using the gnome 3 desktop. The file appears to load by the 
pybliographic window stays blank.

Loading from the terminal returns a GTK warning:

smc< at >nakrasana:~$ pybliographic

(pybliographer:9283): Gtk-WARNING **: Unable to locate theme engine in 
module_path: "pixmap",

(pybliographer:9283): Gtk-WARNING **: Unable to locate theme engine in 
module_path: "pixmap",

(pybliographer:9283): Gtk-WARNING **: Unable to locate theme engine in 
module_path: "pixmap",

(pybliographer:9283): Gtk-WARNING **: Unable to locate theme engine in 
module_path: "pixmap",
This is Pybliographic 1.2.14 [Python 2.7.2, Gtk 2.24.6, PyGTK 2.24.0]

It looks to me like there is some dependency that was unmet when I 
installed pybliographer from synaptic software manager. I tried a 
reinstall with no success.

So I uninstalled the package with sysnaptic, and tried a reinstall from 
the

Re: pybliographer 1.2.14 broken?

Zoltan Kota — 2011-11-22T14:03:14

Are you sure that all of the dependencies are installed? Have you
tried to remove pybliographer, and install it again via the package
manager?

Zoltan

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Re: pybliographer 1.2.14 broken?

Ernesto Posse — 2011-11-22T13:39:17

Hi,

On Tue, Nov 22, 2011 at 3:37 AM, Zoltan Kota <zoltank-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

 I installed pybliographer via the Software Center and I upgraded from
Ubuntu 11.04.

Re: pybliographer 1.2.14 broken?

Zoltan Kota — 2011-11-22T08:37:55

Hi,

I have a fresh installation of Ubuntu 11.10 in VirtualBox now. I
installed pybliographer with the Ubuntu's package manager. It works
for me. Your bib file is ok, Preferences tabs have the stuff.
How did you install pybliographer, manually or through the package
manager? Did you upgrade Ubuntu from a previous version, or it's a
fresh installation?

Zoltan


On Fri, Nov 18, 2011 at 7:04 PM, Ernesto Posse <eposse-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

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Re: pybliographer 1.2.14 broken?

Zoltan Kota — 2011-11-19T10:32:46

Hi,

Is there any other Ubuntu user here to check it? Under latest Fedora
with pyblio 1.2.15 I can open your bibfile without any problem.

Zoltan


On Fri, Nov 18, 2011 at 7:04 PM, Ernesto Posse <eposse-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

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pybliographer 1.2.14 broken?

Ernesto Posse — 2011-11-18T18:04:54

Hello, I've been using Pybliographer for a long time and recently I
upgraded to version 1.2.14 (with Ubuntu 11.10), but it no longer opens
any .bib files!

I tried a minimalistic example (attached) starting from a command line
and got a message


pybliographer: warning: unable to convert `\pi'


Then I tried removing all embedded latex commands, and it doesn't give
a message but it doesn't display the records either! I only get a
blank window.

What is the problem? Am I missing something?

By the way, the dialog "Settings->Preferences" shows tabs for
different things, but all of them are empty !?

Thanks.

pybliographer 1.2.15

Zoltan Kota — 2011-10-06T21:17:21

Hi,

pybliographer 1.2.15 is out. You can download it from Sourceforge.

Zoltan

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Re: no access to medline/pubmed

Zoltan Kota — 2011-09-13T20:27:15

Hi,

It seems we should update the query link. We should use eutils. See eg.
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=science[journal]+AND+breast+cancer+AND+2008[pdat]

I'm checking the manual, and trying to find out how the code should be updated.
Zoltan


2011/9/13 Vitaly V. Ganusov <vitaly-otZVQ2jzgsFAfugRpC6u6w< at >public.gmane.org>:

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Re: no access to medline/pubmed

Vitaly V. Ganusov — 2011-09-13T20:20:54

Yes, it is the most likely explanation. Other applications work fine, 
e.g., jabref, so they probably know what happened.

Vitaly

On 09/13/2011 02:58 AM, Zoltan Kota wrote:

Re: no access to medline/pubmed

Zoltan Kota — 2011-09-13T06:58:05

Hi,

On Tue, Sep 6, 2011 at 10:19 PM, Vitaly V. Ganusov
<vitaly.ganusov-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

Hm. I think it is not an Ubuntu issue. The same for me under Fedora.
The URL pyblio has used gives the message 'Wrong DB name' upon medline
query. The links we have used:
query_url = 'http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi'
fetch_url = 'http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi'

So, maybe these urls don't work anymore? Does anybody have any
information regarding this ussue?

I'm afraid we have to change the url (eutils?), and update the code.

Zoltan

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no access to medline/pubmed

Vitaly V. Ganusov — 2011-09-06T20:19:25

I cannot download references from medline anymore - the query returns
status that "Query return no results" no matter what I search. It used
to work fine until recently.

I run Ubuntu 10.04 LTS, version 1.2.12

Any help on the matter is appreciated.

Vitaly

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Fwd: email registration

Zoltan Kota — 2011-08-24T11:15:06

---------- Forwarded message ----------
Date: Fri, 19 Aug 2011 13:54:35 -0400
From: Vitaly V. Ganusov <vitaly-otZVQ2jzgsFAfugRpC6u6w< at >public.gmane.org>
To: pybliographer-general-owner-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org
Subject: email registration

Colleagues,

I am using Ubuntu and 1.2.12 stable version of pybliographer and just
recently encounter the problem that I cannot fetch references from
medline anymore. I get the result "Your query returned no results" no
matter what I send as a query. Anybody knows why this could be a problem?

Thanks,

Vitaly
--
Vitaly V. Ganusov
Assistant Professor
M409 Walters Life Sciences
Department of Microbiology
University of Tennessee
Knoxville, TN 37996-0845
USA
Phone: +1 865 974-4547
FAX:   +1 865 974-4007
http://web.bio.utk.edu/ganusov/index.html

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Re: documentation? other similar projects? maintenance?

Zoltan Kota — 2011-08-16T09:35:32


It would be nice! :-)
At the moment pyblio-1.2 is in a bug-fixing maintenance mode, on 1.3
we haven't any updates recently.


If you check pyblio-1.2 source, it might be useful to check the python
scripts in the scripts directory.
You can also check the python-bibtex source code.
pyblio-core-devel-1.3 has a rewritten bibtex module (as I remember),
it might be also useful.

cheers,
Zoltan

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Re: documentation? other similar projects? maintenance?

Jochen Schröder — 2011-08-08T23:08:13

Hi Rory,

if you're just looking for reading/writing of bibtex files you might 
want to also evaluate pybtex (http://pybtex.sourceforge.net/), which is 
still maintained AFAIK (last release was in February this year). I was 
playing around with it a while ago and thought it was quite good.

Cheers
Jochen


On 09/08/11 04:24, Rory Solomon wrote:


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Re: documentation? other similar projects? maintenance?

Rory Solomon — 2011-08-08T18:24:15

Hello,

I am developing a Python application that needs to read/write from
BibTex. Pybliographer seems like an obvious choice to use. Three questions:

(1) Due to the lack of maintenance, I'm beginning to wonder if using this
would be a wise choice, or if, perhaps, there might be another similar
project out there. Does anyone on this list know of such a thing?

(2) Alternatively, if I were to start using it, I could possibly be able to
do some maintenance on the project.

(3) In the short term, I am just trying to evaluate if this does what I
need, which is reading and writing BibTex from my application, and saving
this data into the application's database schema. I am starting to look
through the code now, but wondering if there is any documentation about this
functionality specifically, or, if anyone has any tips about which source
code files to start looking at for this.

thanks very much,
Rory
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pyblio 1.2.14

Zoltan Kota — 2010-10-14T12:59:06

Hi,

pybliographer-1.2.14 is out. For changes see
http://www.pybliographer.org/News/2010-10-14

Zoltan

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pybliographer-1.2.13, python-bibtex-1.2.5

Zoltan Kota — 2010-07-16T07:37:07

Hi,

I've pushed minor update releases of python-bibtex and pybliographer. They 
can be downloaded from sourceforge.

Zoltan


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Re: using with MS word

Zoltan Kota — 2010-02-02T14:38:57


You can check the Help or the online documentation to get some info on how 
pybliographer works. You can import bibtex or other file formats, or you 
can search in external databases like Pubmed or WOS (pyblio 1.3) to get 
biliographic entries.


There is no way for a direct interaction between pybliographer and MS 
Word. Pyblio can connect to Lyx or Openoffice (pyblio 1.3) only.

Zoltan

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using with MS word

Bala subramanian — 2010-01-20T17:49:12

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