3 questions

[sebastian guttenberg]

Hi, today I discovered this great program referencer, which is exactly
what I was looking for, but I have five severe problems:

1. Importing my BibTex file does not import the eprint-entry. Therefore
there is no Web-Link available after the import. Adding this by hand for
all the BibTex-entries would be a lot of work...
Also any other 'extra field' is not imported, although referencer
clearly has the possibility to add extra fields...

2. For the adding of a local pdf-file, this behaviour is completely
different: there the extra field eprint is correctly added, but instead
I get no information on the journal, where the article is published.

3. This point is probably related to point 2. As I am working in high
energy physics, I usually use the information provided from SPIRES HEP
( http://www.slac.stanford.edu/spires/ ) to generate my BibTeX files.
This also assigns certain reference Labels to the entries which are not
consistent with the ones that are provided by crossref.org .
Is there a way to change the source from crossref.org to SPIRES? In
particular I have no idea how to find the DOI's of my documents...
(relation to point 2: I think, the information on crossref.org about the
papers is simply incomplete, while on SPIRES it includes the journal)

4. This seems to me like a bug:
Strange, however, that I didn't find it in the reports, although it
seems so obvious:
In the 'list-view', the column for the title is extremely large and
there is no way to make it smaller. Attempts to do so sometimes result
in an even bigger column.
Also, there are only four columns visible, and the one for the e.g. the
journal (if it exists?) is not visible and thus one cannot sort with
respect to the journal.

5. Last but not least. Is there a possibility to change the pdf-viewer
from evince to a different one? I would like to use some editing tools
which are not present in evince.

Sorry for so many complaints. I was simply very excited when I
discovered the program, but then I figured out that I can make only very
limited use of it, if the above problems are not fixed.
Thanks for any answers! Sebastian

P.S.: I am using Ubuntu Feisty Fawn, and there the referencer version
1.0.4 (32 bits)

[John Spray]

Post by sebastian guttenberg
1. Importing my BibTex file does not import the eprint-entry. Therefore
there is no Web-Link available after the import. Adding this by hand for
all the BibTex-entries would be a lot of work...
Also any other 'extra field' is not imported, although referencer
clearly has the possibility to add extra fields...

If you send me the bibtex file in question (or even better file it as a
bug) I can take a look.

Post by sebastian guttenberg
2. For the adding of a local pdf-file, this behaviour is completely
different: there the extra field eprint is correctly added, but instead
I get no information on the journal, where the article is published.

If you send me the pdf file in question (or even better file it as a
bug) I can take a look.

Post by sebastian guttenberg
3. This point is probably related to point 2. As I am working in high
energy physics, I usually use the information provided from SPIRES HEP
( http://www.slac.stanford.edu/spires/ ) to generate my BibTeX files.
This also assigns certain reference Labels to the entries which are not
consistent with the ones that are provided by crossref.org .
Is there a way to change the source from crossref.org to SPIRES? In
particular I have no idea how to find the DOI's of my documents...
(relation to point 2: I think, the information on crossref.org about the
papers is simply incomplete, while on SPIRES it includes the journal)

I'm not sure what interfaces SPIRES provides for applications. Do you
know? In the future, I'd like to have a general plugin system to
support various backends. At present, only crossref OpenURL and
arxiv.org bibtex are there.

Post by sebastian guttenberg
Strange, however, that I didn't find it in the reports, although it
In the 'list-view', the column for the title is extremely large and
there is no way to make it smaller. Attempts to do so sometimes result
in an even bigger column.
Also, there are only four columns visible, and the one for the e.g. the
journal (if it exists?) is not visible and thus one cannot sort with
respect to the journal.

The list view is somewhat rough around the edges. I wrote "ListView
users are people too" in the TODO so nobody can accuse me of not caring.

Post by sebastian guttenberg
5. Last but not least. Is there a possibility to change the pdf-viewer
from evince to a different one? I would like to use some editing tools
which are not present in evince.

Referencer uses whichever application is associated with pdfs in the
gnome environment. You can change that in gnome by right clicking on a
pdf file and opening properties->open with, I don't know about other
desktop environments. Actually I must admit this bugs me too, since
sometimes I want to open something with acrobat instead of evince. I am
pining for an "Open with..." option.

Post by sebastian guttenberg
Sorry for so many complaints. I was simply very excited when I
discovered the program, but then I figured out that I can make only very
limited use of it, if the above problems are not fixed.
Thanks for any answers! Sebastian

Feedback always welcome.

John

[sebastian guttenberg]

Hi John
Thanks a lot for the quick response!

Post by John Spray
If you send me the bibtex file in question (or even better file it as a
bug) I can take a look.

I intend to do so (filing it as a bug), but I am still waiting for the registration email...
That's why I also attached it to this Email

Post by John Spray
If you send me the pdf file in question (or even better file it as a
bug) I can take a look.

Same for this. I attached the pdf-file, but I will try to file it as a bug as well, as soon as I am registered.

Post by John Spray
I'm not sure what interfaces SPIRES provides for applications. Do you
know? In the future, I'd like to have a general plugin system to
support various backends. At present, only crossref OpenURL and
arxiv.org bibtex are there.

Sorry, I don't know neither.
What do you mean by arxiv.org bibtex? I didn't know that arxiv provides bibtex entries. For the article that I mentioned (the one of the pdf-file),
arxiv only links to SPIRES or CiteBase for citations and references. (see http://www.arxiv.org/abs/hep-th/0112160v1 )

Post by John Spray
The list view is somewhat rough around the edges. I wrote "ListView
users are people too" in the TODO so nobody can accuse me of not caring.

;-) Isn't the List View the main power of referencer?? (apart from the
tags and many other things of course...)

Post by John Spray
Referencer uses whichever application is associated with pdfs in the
gnome environment. You can change that in gnome by right clicking on a
pdf file and opening properties->open with, I don't know about other
desktop environments. Actually I must admit this bugs me too, since
sometimes I want to open something with acrobat instead of evince. I am
pining for an "Open with..." option.

Ah, thanks for the hint!!! I thought that I did not have evince as pdf-standard, but I did of course...
Open with would really be nice for the future!

Ok, so far and thanks a lot for taking your time!
Sebastian

Post by John Spray

Post by sebastian guttenberg
1. Importing my BibTex file does not import the eprint-entry. Therefore
there is no Web-Link available after the import. Adding this by hand for
all the BibTex-entries would be a lot of work...
Also any other 'extra field' is not imported, although referencer
clearly has the possibility to add extra fields...

If you send me the bibtex file in question (or even better file it as a
bug) I can take a look.

Post by sebastian guttenberg
2. For the adding of a local pdf-file, this behaviour is completely
different: there the extra field eprint is correctly added, but instead
I get no information on the journal, where the article is published.

If you send me the pdf file in question (or even better file it as a
bug) I can take a look.

Post by sebastian guttenberg
3. This point is probably related to point 2. As I am working in high
energy physics, I usually use the information provided from SPIRES HEP
( http://www.slac.stanford.edu/spires/ ) to generate my BibTeX files.
This also assigns certain reference Labels to the entries which are not
consistent with the ones that are provided by crossref.org .
Is there a way to change the source from crossref.org to SPIRES? In
particular I have no idea how to find the DOI's of my documents...
(relation to point 2: I think, the information on crossref.org about the
papers is simply incomplete, while on SPIRES it includes the journal)

I'm not sure what interfaces SPIRES provides for applications. Do you
know? In the future, I'd like to have a general plugin system to
support various backends. At present, only crossref OpenURL and
arxiv.org bibtex are there.

Post by sebastian guttenberg
Strange, however, that I didn't find it in the reports, although it
In the 'list-view', the column for the title is extremely large and
there is no way to make it smaller. Attempts to do so sometimes result
in an even bigger column.
Also, there are only four columns visible, and the one for the e.g. the
journal (if it exists?) is not visible and thus one cannot sort with
respect to the journal.

The list view is somewhat rough around the edges. I wrote "ListView
users are people too" in the TODO so nobody can accuse me of not caring.

Post by sebastian guttenberg
5. Last but not least. Is there a possibility to change the pdf-viewer
from evince to a different one? I would like to use some editing tools
which are not present in evince.

Referencer uses whichever application is associated with pdfs in the
gnome environment. You can change that in gnome by right clicking on a
pdf file and opening properties->open with, I don't know about other
desktop environments. Actually I must admit this bugs me too, since
sometimes I want to open something with acrobat instead of evince. I am
pining for an "Open with..." option.

Post by sebastian guttenberg
Sorry for so many complaints. I was simply very excited when I
discovered the program, but then I figured out that I can make only very
limited use of it, if the above problems are not fixed.
Thanks for any answers! Sebastian

Feedback always welcome.
John
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[sebastian guttenberg]

Hi John

Post by John Spray
I'm not sure what interfaces SPIRES provides for applications. Do you
know? In the future, I'd like to have a general plugin system to
support various backends. At present, only crossref OpenURL and
arxiv.org bibtex are there.

I still don't know about such an interface, but I have found a script
that generates a BiBTeX-file to a LaTeX file, where one only has to
provide the preprint-numbers. It is called findbib. See
ftp://cam.ctan.org/tex-archive/biblio/bibtex/utils/findbib/README

So suppose, I have a pdf-file that contains an arxive number (Like the
one I sent to you, which contains the number hep-th/0112160). With this
information one could build a very simple tex-File, let's call it
auxiliary.tex:

\documentclass{article}
\begin{document}
\cite{hep-th/0405007}
\end{document}

Then one can run the script ./findbib auxiliary.tex which produces an
auxiliary.bib which contains all the MetaData. (There will also be two
error messages because of missing bibliography-style and bibliography
file. One can extend the tex-file to avoid this, but the bib-file will
be the same anyway)
Would that be a possible solution to include SPIRES?

- My second comment is about the tags. I hoped that marking two tags at
the same time would lead to an intesection of the results for each
single tag. Instead it leads to the sum, which I find very unfortunate.
Let me explain why I think that the first would be much more useful.
Suppose I am interested in finding an article which has either the tag
"important" or "interesting", but I cannot really remember. In this
case, I can use the tool as it is at the moment and mark both tags. But
that does not really help, because I have to look through all of
"important" and all of "interesting" anyway, because both are now
displayed.
In the case, however, where I know that an article was interesting AND
important at the same time, an intersection method would help a lot to
find the article.
Related to that: at the moment, it is only possible to mark tags with
shift-cursor, which are directly next to each other in the list. There
is no possibility to mark in addition others with the common
ctrl-Mouseclick , which is also a pity (the same is true for the files
themselves).
At the moment, I am a bit hesitating. I wanted to start to manage all of
my downloaded pdf-files. Assigning tags to all of them is quite some
work, but would be worth doing. But my strategy to assign tags would be
very different if I knew that there will be the possibility for an
"intersecting" tag-selection in near future...

Sorry again for the long comments. Best, Sebastian

P.S.: I am now confused what you meant with 'filing the pdf-file as a
bug'. I did not find a possibility to attach pdf-files to a bug report.
Or did I misunderstand s.th.?

[Frederik Elwert]

Hi!

Post by sebastian guttenberg
- My second comment is about the tags. I hoped that marking two tags at
the same time would lead to an intesection of the results for each
single tag. Instead it leads to the sum, which I find very unfortunate.
Let me explain why I think that the first would be much more useful.
Suppose I am interested in finding an article which has either the tag
"important" or "interesting", but I cannot really remember. In this
case, I can use the tool as it is at the moment and mark both tags. But
that does not really help, because I have to look through all of
"important" and all of "interesting" anyway, because both are now
displayed.
In the case, however, where I know that an article was interesting AND
important at the same time, an intersection method would help a lot to
find the article.

I totally agree. I think it's very convenient to sharpen the selection
by selecting more tags: When one tag has too many articles, I want to
select another tag and only get those articles that have both.

For the far future, I'd love to have some sort of ad-hoc hierarchy in
this way: When I select one tag, I'd like to see all tags that appear in
conjunction with the current one, i.e., only those that would have a
result when used in intersection with the current one.

Cheers,
Frederik

[Jorge Páramos]

Hi!

I've posted before, with no reply... can anyone make a Mac OS X build
of referencer? Please? Pretty please?
Oh-my-god-rolling-on-the-floor-begging-I'll-have-your
baby-but-just-do-it please?

Thanks,

Jorge

[jcspray]

Post by Jorge Páramos
I've posted before, with no reply... can anyone make a Mac OS X build
of referencer? Please? Pretty please?
Oh-my-god-rolling-on-the-floor-begging-I'll-have-your
baby-but-just-do-it please?

I did reply:
http://icculus.org/cgi-bin/ezmlm/ezmlm-cgi?60:mss:178:200708:alglogdebjfnopippdeo

...and I still don't have a mac!

John

[jcspray]

Post by sebastian guttenberg
I still don't know about such an interface, but I have found a script
that generates a BiBTeX-file to a LaTeX file, where one only has to
provide the preprint-numbers. It is called findbib. See
ftp://cam.ctan.org/tex-archive/biblio/bibtex/utils/findbib/README

Okay, they seem to be munging it out of the SPIRES web search
interface so at least it's possible. Seems fairly straightforward.

Post by sebastian guttenberg
- My second comment is about the tags. I hoped that marking two tags at
the same time would lead to an intesection of the results for each
single tag. Instead it leads to the sum, which I find very unfortunate.
Let me explain why I think that the first would be much more useful.
Suppose I am interested in finding an article which has either the tag
"important" or "interesting", but I cannot really remember. In this
case, I can use the tool as it is at the moment and mark both tags. But
that does not really help, because I have to look through all of
"important" and all of "interesting" anyway, because both are now
displayed.

I had vaguely intended to make it an option whether to do AND or OR,
but now that I'm clearly not getting around to that it's probably more
generally useful to make it AND. Will probs get around to it soon.

Post by sebastian guttenberg
Related to that: at the moment, it is only possible to mark tags with
shift-cursor, which are directly next to each other in the list. There
is no possibility to mark in addition others with the common
ctrl-Mouseclick , which is also a pity (the same is true for the files
themselves).

I'm not seeing that behaviour: control-button1 is working for me to
toggle selection of individual documents and tags. Are we talking
about something different?

Post by sebastian guttenberg
P.S.: I am now confused what you meant with 'filing the pdf-file as a
bug'. I did not find a possibility to attach pdf-files to a bug report.
Or did I misunderstand s.th.?

You generally have to file a bug report and then add a comment with
the attachment.

Cheers,
John

[sebastian guttenberg]

Thanks again for your promising response!
I did now two bug reports: the one with the pdf file, and also one for
the ctrl-button1.

Post by jcspray
I'm not seeing that behaviour: control-button1 is working for me to
toggle selection of individual documents and tags. Are we talking
about something different?

Strange that it works for you. I am sure, we are talking about the same.
I thought that perhaps s.b. else can confirm, that's why I made another
bug report.
Cheers, Sebastian

[Frederik Elwert]

Post by sebastian guttenberg

Post by jcspray
I'm not seeing that behaviour: control-button1 is working for me to
toggle selection of individual documents and tags. Are we talking
about something different?

Strange that it works for you. I am sure, we are talking about the same.
I thought that perhaps s.b. else can confirm, that's why I made another
bug report.

FYI, works for me, too.

Cheers,
Frederik

[Michael Banck]

Hi,

Post by sebastian guttenberg
Thanks again for your promising response!
I did now two bug reports: the one with the pdf file, and also one for
the ctrl-button1.

Post by jcspray
I'm not seeing that behaviour: control-button1 is working for me to
toggle selection of individual documents and tags. Are we talking
about something different?

Strange that it works for you. I am sure, we are talking about the same.
I thought that perhaps s.b. else can confirm, that's why I made another
bug report.

Last time I had issues with ctrl+button1, I had foolishly remapped that
to "move window" in gnome-keybinding-properties. Maybe check whether it
works fine in Nautilus and other applications?


Michael

[sebastian guttenberg]

Thanks for the hint, Michael, but it works fine in all other
applications. Really nobody else with the same problem??

Post by Michael Banck
Last time I had issues with ctrl+button1, I had foolishly remapped that
to "move window" in gnome-keybinding-properties. Maybe check whether it
works fine in Nautilus and other applications?
Michael
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[John Spray]

Post by jcspray

Post by sebastian guttenberg
- My second comment is about the tags. I hoped that marking two tags at
the same time would lead to an intesection of the results for each
single tag. Instead it leads to the sum, which I find very unfortunate.
Let me explain why I think that the first would be much more useful.
Suppose I am interested in finding an article which has either the tag
"important" or "interesting", but I cannot really remember. In this
case, I can use the tool as it is at the moment and mark both tags. But
that does not really help, because I have to look through all of
"important" and all of "interesting" anyway, because both are now
displayed.

I had vaguely intended to make it an option whether to do AND or OR,
but now that I'm clearly not getting around to that it's probably more
generally useful to make it AND. Will probs get around to it soon.

And have just committed a change to svn to make it so. Could use some
testing to make sure I haven't screwed anything up.

John

[sebastian guttenberg]

Post by John Spray
And have just committed a change to svn to make it so. Could use some
testing to make sure I haven't screwed anything up.

Wow, that was fast! Also the bugfix with the bibtex-import! Great! :-)

[Kevin Goldstein]

Post by jcspray

Post by sebastian guttenberg
I still don't know about such an interface, but I have found a script
that generates a BiBTeX-file to a LaTeX file, where one only has to
provide the preprint-numbers. It is called findbib. See
ftp://cam.ctan.org/tex-archive/biblio/bibtex/utils/findbib/README

Okay, they seem to be munging it out of the SPIRES web search
interface so at least it's possible. Seems fairly straightforward.

I've been maintaining the findbib script - its a bit of a bash hack
but it does what I need.

You might find the following python script:

http://www.stringwiki.org/wiki/SPIRES_script

easier to mould to your needs.

[John Spray]

Post by Kevin Goldstein

Post by jcspray

Post by sebastian guttenberg
I still don't know about such an interface, but I have found a script
that generates a BiBTeX-file to a LaTeX file, where one only has to
provide the preprint-numbers. It is called findbib. See
ftp://cam.ctan.org/tex-archive/biblio/bibtex/utils/findbib/README

Okay, they seem to be munging it out of the SPIRES web search
interface so at least it's possible. Seems fairly straightforward.

I've been maintaining the findbib script - its a bit of a bash hack
but it does what I need.
http://www.stringwiki.org/wiki/SPIRES_script
easier to mould to your needs.

Interesting, thanks for the pointer. Currently papers with arxiv
eprint numbers are getting looked up on citebase[1] by referencer,
is the SPIREs server likely to provide more/different information?
Sebastian's original issue was that volume/number fields weren't
being provided but I've since fixed that with the citebase code.

John

[1] Which uses the UK arxiv mmirror as a datasource

[Kevin Goldstein]

Post by John Spray

Post by Kevin Goldstein

Post by jcspray

Post by sebastian guttenberg
I still don't know about such an interface, but I have found a script
that generates a BiBTeX-file to a LaTeX file, where one only has to
provide the preprint-numbers. It is called findbib. See
ftp://cam.ctan.org/tex-archive/biblio/bibtex/utils/findbib/README

Okay, they seem to be munging it out of the SPIRES web search
interface so at least it's possible. Seems fairly straightforward.

I've been maintaining the findbib script - its a bit of a bash hack
but it does what I need.
http://www.stringwiki.org/wiki/SPIRES_script
easier to mould to your needs.

Interesting, thanks for the pointer. Currently papers with arxiv
eprint numbers are getting looked up on citebase[1] by referencer,
is the SPIREs server likely to provide more/different information?
Sebastian's original issue was that volume/number fields weren't
being provided but I've since fixed that with the citebase code.

Hmmmm...

Maybe not for automatically getting bibliographic information for papers.

The SPIRES data base includes (mainly high energy) papers which
preceed the arxiv but I'm not sure how you could easily use it.

You can for example look up papers based on various institutional
preprint codes which predate the arxiv. There are such a huge number
of these codes though...

It might be nice to be able to automatically import a SPIRES search as
a bibliography into referencer since there are a lot of was to search
SPIRES:

http://www.slac.stanford.edu/spires/hep/help/

On of the most useful thing about SPIRES is being able to search the
papers referenced or cited by a paper.

On the other hands its only takes a few clicks (or a relatively simple
script) to save the results of a SPIRES search as a Bibtex file and
then import it into referencer.

-kevin

[sebastian guttenberg]

Post by John Spray
Currently papers with arxiv
eprint numbers are getting looked up on citebase[1] by referencer,
is the SPIREs server likely to provide more/different information?
Sebastian's original issue was that volume/number fields weren't
being provided but I've since fixed that with the citebase code.

Just a very small thing. BiBTeX-entries from SPIRES have this additional
"SLACcitation"-field. This simplifies the counting of citations for
SPIRES, so most of the people in high-energy physics have it included in
their references. In addition, the generated label for the references is
different. In principle that does not matter, but as I have already a
huge number of references from SPIRES, it would be a bit confusing to
change to a different source for my references, with different labeling.
Last but not least, SPIRES offers now a feature to automatically update
BiBTeX-files. (If the Bibtex-file was generated when the article did not
yet appear in a journal but just in the arxive, then later it is
necessary to update this information).

[John Spray]

Post by sebastian guttenberg
Just a very small thing. BiBTeX-entries from SPIRES have this additional
"SLACcitation"-field. This simplifies the counting of citations for
SPIRES, so most of the people in high-energy physics have it included in
their references. In addition, the generated label for the references is
different. In principle that does not matter, but as I have already a
huge number of references from SPIRES, it would be a bit confusing to
change to a different source for my references, with different labeling.
Last but not least, SPIRES offers now a feature to automatically update
BiBTeX-files. (If the Bibtex-file was generated when the article did not
yet appear in a journal but just in the arxive, then later it is
necessary to update this information).

Sebastian,

All useful info, thanks. I'll bear it in mind moving forward.

Regards,
John