jabref-how to get rid of abstract

[Wolfgang Engelmann]

Sorry, this is slightly off topic, but if sombody is using jabref as a data 
base program for the bib-files of Lyx,

could he/she tell me how to avoid the export of abstract, school, 
institutions? Those contain apparently sometimes wrong encodings, which 
bibtex/biblatex/biber doesn't like. 

I tired finding out from the handbook, but must have overlooked the part 
describing it. 

Wolfgang

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 10:17 AM, Wolfgang Engelmann wrote:

Sorry, this is slightly off topic, but if sombody is using jabref as a data
base program for the bib-files of Lyx,

could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.

I tired finding out from the handbook, but must have overlooked the part
describing it.



I don't use custom filters myself, but JabRef allows you to define a 
custom export filter (Help  Custom Export Filters).  They're usually 
intended for a format change (output to RTF, HTML etc.), but there is 
nothing stopping you from writing a filter that outputs a .bib file with 
some fields stripped out.


If you'd rather not write your own filter, you might look on the project 
resources page (http://jabref.sourceforge.net/resources.php) and 
particularly at the Chicago style export filters 
(http://jabref.sourceforge.net/plugins/Chicago_export_filters.pdf). 
Again, I've never used them, but one of them might accomplish what you 
want.  I think they export to RTF, but you could easily import that into 
a new JabRef file.


/Paul

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 11:17 AM, Paul A. Rubin wrote:



could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.



I think I just found an arguably easier (or at least less technical) 
method.  Load your database, go to Tools  Set/clear/rename fields, put 
'Abstract' in the field name and click the 'All entries' and 'Clear 
fields' buttons and click Ok.  Repeat for other fields. Save with a new 
name.


If you are going to do it regularly, I think the export filter is worth 
investigating, but if you are only going to do it occasionally, this 
might be the path of least resistance.


/Paul

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

I've had this problem myself because of a lot of german and french
references in my work. My solution is as follows:


   1. Use a RegExp tool like RegexBuddy (http://www.regexbuddy.com) that has
   a full-featured regular-expression engine and search and replace features
   (grep + sed + find can do this under *NIX).
   2. Search in all .bib files for characters in the range \x80-\xFF (all
   extended ASCII characters)
   3. Now you have a list of matches and you can visually identify the
   offending characters.
   4. For each offending character, simply craft a single search-and-replace
   that replaces an extended caracter to its LaTeX accented equivalent. For
   instance, I would search for all 'ü' and replace with '\u', 'é' is replaced
   with '\'e', 'À' is replaced with '\`a', etc.

I found that to replace these in about 500 references took about 20 minutes.
Then, for every new reference you add manually or download from a database,
just make sure to replace extended characters with LaTeX versions with
escaped diacritics and you should be fine.

Hope this helps.

Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)


On 21 August 2010 10:17, Wolfgang Engelmann engelm...@uni-tuebingen.dewrote:

 Sorry, this is slightly off topic, but if sombody is using jabref as a data
 base program for the bib-files of Lyx,

 could he/she tell me how to avoid the export of abstract, school,
 institutions? Those contain apparently sometimes wrong encodings, which
 bibtex/biblatex/biber doesn't like.

 I tired finding out from the handbook, but must have overlooked the part
 describing it.

 Wolfgang

Re: jabref-how to get rid of abstract

[Wolfgang Engelmann]

Am Saturday 21 August 2010 18:36:25 schrieb Paul A. Rubin:
 On 8/21/2010 11:17 AM, Paul A. Rubin wrote:
  could he/she tell me how to avoid the export of abstract, school,
  institutions? Those contain apparently sometimes wrong encodings, which
  bibtex/biblatex/biber doesn't like.

 I think I just found an arguably easier (or at least less technical)
 method.  Load your database, go to Tools  Set/clear/rename fields, put
 'Abstract' in the field name and click the 'All entries' and 'Clear
 fields' buttons and click Ok.  Repeat for other fields. Save with a new
 name.

 If you are going to do it regularly, I think the export filter is worth
 investigating, but if you are only going to do it occasionally, this
 might be the path of least resistance.

 /Paul

Thanks, Paul and Tennessee,

using Pauls proposal I got rid of the Abstract field, but not the school  and 
institution, which is shown in the preview, e.g.

Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
I would like to have
Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, 2006, 16, 547-549
only.

It does not seem to be a field. 
In preferencesentry preview it is shown as 
begin{school}...end{school}
begin{institution}...end{institution}

The log file of my pdf output refers to errors occurring in these items. Thats 
the reason I would like to get them out.

Wolfgang 

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

On 21 August 2010 16:51, Wolfgang Engelmann engelm...@uni-tuebingen.dewrote:

 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends
 Cell
 Biol, Department of Molecular Biology, Sciences III, University of Geneva,
 30
 Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
 I would like to have
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends
 Cell
 Biol, 2006, 16, 547-549
 only.

 It does not seem to be a field.
 In preferencesentry preview it is shown as
 begin{school}...end{school}
 begin{institution}...end{institution}


I'm not sure I understand what you want, but maybe what could cause the
error is the - sign. There are several extended-size (long, short, medium)
dashes that are in extended character sets. They are often impossible to
tell from the regular dashes unless they are next one to another.


Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)

Re: jabref-how to get rid of abstract

[Paul Rubin]

Wolfgang Engelmann engelmann at uni-tuebingen.de writes:

 
 using Pauls proposal I got rid of the Abstract field, but not the school  and 
 institution, which is shown in the preview, e.g.
 
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
 Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
 Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
 I would like to have
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
 Biol, 2006, 16, 547-549
 only.
 
 It does not seem to be a field. 
 In preferencesentry preview it is shown as 
 begin{school}...end{school}
 begin{institution}...end{institution}

School and Institution are both fields and can be deleted the same way you got
rid of Abstract (at least in JabRef 2.5, which is what I have available as I
type this).

Of course, you could also edit individual records and just delete the field
(from a copy of the database, so as not to lose the information).

/Paul

jabref-how to get rid of abstract

[Wolfgang Engelmann]

Sorry, this is slightly off topic, but if sombody is using jabref as a data 
base program for the bib-files of Lyx,

could he/she tell me how to avoid the export of abstract, school, 
institutions? Those contain apparently sometimes wrong encodings, which 
bibtex/biblatex/biber doesn't like. 

I tired finding out from the handbook, but must have overlooked the part 
describing it. 

Wolfgang

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 10:17 AM, Wolfgang Engelmann wrote:

Sorry, this is slightly off topic, but if sombody is using jabref as a data
base program for the bib-files of Lyx,

could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.

I tired finding out from the handbook, but must have overlooked the part
describing it.



I don't use custom filters myself, but JabRef allows you to define a 
custom export filter (Help  Custom Export Filters).  They're usually 
intended for a format change (output to RTF, HTML etc.), but there is 
nothing stopping you from writing a filter that outputs a .bib file with 
some fields stripped out.


If you'd rather not write your own filter, you might look on the project 
resources page (http://jabref.sourceforge.net/resources.php) and 
particularly at the Chicago style export filters 
(http://jabref.sourceforge.net/plugins/Chicago_export_filters.pdf). 
Again, I've never used them, but one of them might accomplish what you 
want.  I think they export to RTF, but you could easily import that into 
a new JabRef file.


/Paul

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 11:17 AM, Paul A. Rubin wrote:



could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.



I think I just found an arguably easier (or at least less technical) 
method.  Load your database, go to Tools  Set/clear/rename fields, put 
'Abstract' in the field name and click the 'All entries' and 'Clear 
fields' buttons and click Ok.  Repeat for other fields. Save with a new 
name.


If you are going to do it regularly, I think the export filter is worth 
investigating, but if you are only going to do it occasionally, this 
might be the path of least resistance.


/Paul

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

I've had this problem myself because of a lot of german and french
references in my work. My solution is as follows:


   1. Use a RegExp tool like RegexBuddy (http://www.regexbuddy.com) that has
   a full-featured regular-expression engine and search and replace features
   (grep + sed + find can do this under *NIX).
   2. Search in all .bib files for characters in the range \x80-\xFF (all
   extended ASCII characters)
   3. Now you have a list of matches and you can visually identify the
   offending characters.
   4. For each offending character, simply craft a single search-and-replace
   that replaces an extended caracter to its LaTeX accented equivalent. For
   instance, I would search for all 'ü' and replace with '\u', 'é' is replaced
   with '\'e', 'À' is replaced with '\`a', etc.

I found that to replace these in about 500 references took about 20 minutes.
Then, for every new reference you add manually or download from a database,
just make sure to replace extended characters with LaTeX versions with
escaped diacritics and you should be fine.

Hope this helps.

Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)


On 21 August 2010 10:17, Wolfgang Engelmann engelm...@uni-tuebingen.dewrote:

 Sorry, this is slightly off topic, but if sombody is using jabref as a data
 base program for the bib-files of Lyx,

 could he/she tell me how to avoid the export of abstract, school,
 institutions? Those contain apparently sometimes wrong encodings, which
 bibtex/biblatex/biber doesn't like.

 I tired finding out from the handbook, but must have overlooked the part
 describing it.

 Wolfgang

Re: jabref-how to get rid of abstract

[Wolfgang Engelmann]

Am Saturday 21 August 2010 18:36:25 schrieb Paul A. Rubin:
 On 8/21/2010 11:17 AM, Paul A. Rubin wrote:
  could he/she tell me how to avoid the export of abstract, school,
  institutions? Those contain apparently sometimes wrong encodings, which
  bibtex/biblatex/biber doesn't like.

 I think I just found an arguably easier (or at least less technical)
 method.  Load your database, go to Tools  Set/clear/rename fields, put
 'Abstract' in the field name and click the 'All entries' and 'Clear
 fields' buttons and click Ok.  Repeat for other fields. Save with a new
 name.

 If you are going to do it regularly, I think the export filter is worth
 investigating, but if you are only going to do it occasionally, this
 might be the path of least resistance.

 /Paul

Thanks, Paul and Tennessee,

using Pauls proposal I got rid of the Abstract field, but not the school  and 
institution, which is shown in the preview, e.g.

Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
I would like to have
Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, 2006, 16, 547-549
only.

It does not seem to be a field. 
In preferencesentry preview it is shown as 
begin{school}...end{school}
begin{institution}...end{institution}

The log file of my pdf output refers to errors occurring in these items. Thats 
the reason I would like to get them out.

Wolfgang 

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

On 21 August 2010 16:51, Wolfgang Engelmann engelm...@uni-tuebingen.dewrote:

 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends
 Cell
 Biol, Department of Molecular Biology, Sciences III, University of Geneva,
 30
 Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
 I would like to have
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends
 Cell
 Biol, 2006, 16, 547-549
 only.

 It does not seem to be a field.
 In preferencesentry preview it is shown as
 begin{school}...end{school}
 begin{institution}...end{institution}


I'm not sure I understand what you want, but maybe what could cause the
error is the - sign. There are several extended-size (long, short, medium)
dashes that are in extended character sets. They are often impossible to
tell from the regular dashes unless they are next one to another.


Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)

Re: jabref-how to get rid of abstract

[Paul Rubin]

Wolfgang Engelmann engelmann at uni-tuebingen.de writes:

 
 using Pauls proposal I got rid of the Abstract field, but not the school  and 
 institution, which is shown in the preview, e.g.
 
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
 Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
 Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
 I would like to have
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
 Biol, 2006, 16, 547-549
 only.
 
 It does not seem to be a field. 
 In preferencesentry preview it is shown as 
 begin{school}...end{school}
 begin{institution}...end{institution}

School and Institution are both fields and can be deleted the same way you got
rid of Abstract (at least in JabRef 2.5, which is what I have available as I
type this).

Of course, you could also edit individual records and just delete the field
(from a copy of the database, so as not to lose the information).

/Paul

jabref-how to get rid of abstract

[Wolfgang Engelmann]

Sorry, this is slightly off topic, but if sombody is using jabref as a data 
base program for the bib-files of Lyx,

could he/she tell me how to avoid the export of abstract, school, 
institutions? Those contain apparently sometimes wrong encodings, which 
bibtex/biblatex/biber doesn't like. 

I tired finding out from the handbook, but must have overlooked the part 
describing it. 

Wolfgang

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 10:17 AM, Wolfgang Engelmann wrote:

Sorry, this is slightly off topic, but if sombody is using jabref as a data
base program for the bib-files of Lyx,

could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.

I tired finding out from the handbook, but must have overlooked the part
describing it.



I don't use custom filters myself, but JabRef allows you to define a 
custom export filter (Help > Custom Export Filters).  They're usually 
intended for a format change (output to RTF, HTML etc.), but there is 
nothing stopping you from writing a filter that outputs a .bib file with 
some fields stripped out.


If you'd rather not write your own filter, you might look on the project 
resources page (http://jabref.sourceforge.net/resources.php) and 
particularly at the Chicago style export filters 
(http://jabref.sourceforge.net/plugins/Chicago_export_filters.pdf). 
Again, I've never used them, but one of them might accomplish what you 
want.  I think they export to RTF, but you could easily import that into 
a new JabRef file.


/Paul

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 11:17 AM, Paul A. Rubin wrote:



could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.



I think I just found an arguably easier (or at least less technical) 
method.  Load your database, go to Tools > Set/clear/rename fields, put 
'Abstract' in the field name and click the 'All entries' and 'Clear 
fields' buttons and click Ok.  Repeat for other fields. Save with a new 
name.


If you are going to do it regularly, I think the export filter is worth 
investigating, but if you are only going to do it occasionally, this 
might be the path of least resistance.


/Paul

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

I've had this problem myself because of a lot of german and french
references in my work. My solution is as follows:


   1. Use a RegExp tool like RegexBuddy (http://www.regexbuddy.com) that has
   a full-featured regular-expression engine and search and replace features
   (grep + sed + find can do this under *NIX).
   2. Search in all .bib files for characters in the range \x80-\xFF (all
   extended ASCII characters)
   3. Now you have a list of matches and you can visually identify the
   offending characters.
   4. For each offending character, simply craft a single search-and-replace
   that replaces an extended caracter to its LaTeX accented equivalent. For
   instance, I would search for all 'ü' and replace with '\"u', 'é' is replaced
   with '\'e', 'À' is replaced with '\`a', etc.

I found that to replace these in about 500 references took about 20 minutes.
Then, for every new reference you add manually or download from a database,
just make sure to replace extended characters with LaTeX versions with
escaped diacritics and you should be fine.

Hope this helps.

Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)


On 21 August 2010 10:17, Wolfgang Engelmann wrote:

> Sorry, this is slightly off topic, but if sombody is using jabref as a data
> base program for the bib-files of Lyx,
>
> could he/she tell me how to avoid the export of abstract, school,
> institutions? Those contain apparently sometimes wrong encodings, which
> bibtex/biblatex/biber doesn't like.
>
> I tired finding out from the handbook, but must have overlooked the part
> describing it.
>
> Wolfgang
>

Re: jabref-how to get rid of abstract

[Wolfgang Engelmann]

Am Saturday 21 August 2010 18:36:25 schrieb Paul A. Rubin:
> On 8/21/2010 11:17 AM, Paul A. Rubin wrote:
> >> could he/she tell me how to avoid the export of abstract, school,
> >> institutions? Those contain apparently sometimes wrong encodings, which
> >> bibtex/biblatex/biber doesn't like.
>
> I think I just found an arguably easier (or at least less technical)
> method.  Load your database, go to Tools > Set/clear/rename fields, put
> 'Abstract' in the field name and click the 'All entries' and 'Clear
> fields' buttons and click Ok.  Repeat for other fields. Save with a new
> name.
>
> If you are going to do it regularly, I think the export filter is worth
> investigating, but if you are only going to do it occasionally, this
> might be the path of least resistance.
>
> /Paul

Thanks, Paul and Tennessee,

using Pauls proposal I got rid of the Abstract field, but not the school  and 
institution, which is shown in the preview, e.g.

Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
I would like to have
Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, 2006, 16, 547-549
only.

It does not seem to be a field. 
In preferences>entry preview it is shown as 
begin{school}...end{school}
begin{institution}...end{institution}

The log file of my pdf output refers to errors occurring in these items. Thats 
the reason I would like to get them out.

Wolfgang 

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

On 21 August 2010 16:51, Wolfgang Engelmann wrote:

> Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends
> Cell
> Biol, Department of Molecular Biology, Sciences III, University of Geneva,
> 30
> Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
> I would like to have
> Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends
> Cell
> Biol, 2006, 16, 547-549
> only.
>
> It does not seem to be a field.
> In preferences>entry preview it is shown as
> begin{school}...end{school}
> begin{institution}...end{institution}
>
>
I'm not sure I understand what you want, but maybe what could cause the
error is the "-" sign. There are several extended-size (long, short, medium)
dashes that are in extended character sets. They are often impossible to
tell from the regular dashes unless they are next one to another.


Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)

Re: jabref-how to get rid of abstract

[Paul Rubin]

Wolfgang Engelmann  uni-tuebingen.de> writes:

> 
> using Pauls proposal I got rid of the Abstract field, but not the school  and 
> institution, which is shown in the preview, e.g.
> 
> Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends Cell 
> Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
> Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
> I would like to have
> Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends Cell 
> Biol, 2006, 16, 547-549
> only.
> 
> It does not seem to be a field. 
> In preferences>entry preview it is shown as 
> begin{school}...end{school}
> begin{institution}...end{institution}

School and Institution are both fields and can be deleted the same way you got
rid of Abstract (at least in JabRef 2.5, which is what I have available as I
type this).

Of course, you could also edit individual records and just delete the field
(from a copy of the database, so as not to lose the information).

/Paul