Re: [Bibdesk-users] HTML and dropbox

[Christiaan Hofman]

On Apr 5, 2013, at 22:33, Daniele Pontillo wrote:

> I'll try to summarize what happened during this thrilling thread.
> Jim Harrison helped me so much by writing a template which would furnish an 
> HTM export output with a link to my files on the Dropbox server
> Andreas Fishlin suggested that it was not necessary to create a custom field 
> for that pupose. He said
> ...You shouldn't use a custom field as Christiaan explained. You can simply 
> drag and drop the dropbox link to the right pane while having the publication 
> selected. Then that link should end up in the exported html if you run my 
> extraction script.

Be aware that this also should happen when you use the (corrected) default HTML 
template. I explained in my email how you can fix that template for the error 
it contained. You can now also fix that by downloading a current nightly and 
choosing Reset Default Files from the Template preferences. Or you can remove 
htmlItemExportTemplate.html and then run a current nightly.

Christiaan

> If you use a custom field, you are going to have lots of trouble, I guess, 
> since that for sure means you have to extend all the templates and tools 
> yourself for that extra feature
> I tried both options, and they worked out well.
> Thank you very much for your patience.
> Daniele Pontillo, MD




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[Bibdesk-users] HTML and dropbox

[Daniele Pontillo]

I'll try to summarize what happened during this thrilling thread.
Jim Harrison helped me so much by writing a template which would furnish an HTM 
export output with a link to my files on the Dropbox server
Andreas Fishlin suggested that it was not necessary to create a custom field 
for that pupose. He said
...You shouldn't use a custom field as Christiaan explained. You can simply 
drag and drop the dropbox link to the right pane while having the publication 
selected. Then that link should end up in the exported html if you run my 
extraction script. If you use a custom field, you are going to have lots of 
trouble, I guess, since that for sure means you have to extend all the 
templates and tools yourself for that extra feature
I tried both options, and they worked out well.
Thank you very much for your patience.
Daniele Pontillo, MD
--
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire 
the most talented Cisco Certified professionals. Visit the 
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Re: [Bibdesk-users] Publication:Send via Email

[Christiaan Hofman]

On Apr 5, 2013, at 12:33, Fischlin Andreas wrote:

> Is there a preference in which I can set the template to be used by this 
> command? I find nothing in Help nor on the wiki. That's basically a question 
> to Christiaan, since you mention a template @ 
> http://www.mail-archive.com/bibdesk-users@lists.sourceforge.net/msg05105.html 
> but I do not know which you were thinking of and how I could cause this 
> command to use a specific template instead of the default (in my case I get a 
> 'BibTeX source record', not my first choice).
> 
> Regards,
> Andreas
> 

It's a popup in the General preferences.

Christiaan

> 
> ETH Zurich
> Prof. Dr. Andreas Fischlin
> Systems Ecology - Institute of Integrative Biology
> CHN E 21.1
> Universitaetstrasse 16
> 8092 Zurich
> SWITZERLAND
> 
> andreas.fisch...@env.ethz.ch
> www.sysecol.ethz.ch
> 
> +41 44 633-6090 phone
> +41 44 633-1136 fax
> +41 79 595-4050 mobile
> 
> Make it as simple as possible, but distrust it!
> 
> 
> 
> 
> 
> 
> 
> 
> On 04/04/2013, at 18:55 , Christiaan Hofman wrote:
> 
> 
> On Apr 4, 2013, at 17:22, Christiaan Hofman wrote:
> 
> 
> On Apr 4, 2013, at 17:17, Gray, Wayne wrote:
> 
> All,
> 
> Since "discovering" this feature -- being able to go directly from BibTec to 
> my mail program with a completely formatted citation, abstract, and attached 
> PDFs, I have been using it a lot.
> 
> However, lately it seems as if it is not always working. Must be something in 
> the files I am trying to send.  But recently I have observed the following 
> behavior with no clear pattern:
> 
> A. It sends the pdfs and other files that are attached to my entry, but not 
> the BibDesk citation.
> B. It sends nothing - neither file nor citation
> C. It works as intended sending both the formatted citation and any attached 
> files.
> 
> Any ideas as to what is causing this erratic behavior?
> 
> I am using BibDesk: v1.6.0 (2779) and Mac OS 10.7.5.
> 
> Thanks for any ideas you might have on solving this mystery.
> 
> Wayne Gray
> 
> 
> Apparently somewhere in the process it runs into an exception or something 
> like that. I cannot say where from here. Try looking into Console.app to see 
> if any errors are reported.
> 
> Christiaan
> 
> 
> Another thing is the generation of the citation. What format are you using 
> for email? And for the items that give you problems, is copy/paste for that 
> format (Copy As) also failing?
> 
> Christiaan
> 
> 
> --
> Minimize network downtime and maximize team effectiveness.
> Reduce network management and security costs.Learn how to hire
> the most talented Cisco Certified professionals. Visit the
> Employer Resources Portal
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> 
> 
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> the most talented Cisco Certified professionals. Visit the 
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> https://lists.sourceforge.net/lists/listinfo/bibdesk-users


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Re: [Bibdesk-users] Publication:Send via Email

[Fischlin Andreas]

Is there a preference in which I can set the template to be used by this 
command? I find nothing in Help nor on the wiki. That's basically a question to 
Christiaan, since you mention a template @ 
http://www.mail-archive.com/bibdesk-users@lists.sourceforge.net/msg05105.html 
but I do not know which you were thinking of and how I could cause this command 
to use a specific template instead of the default (in my case I get a 'BibTeX 
source record', not my first choice).

Regards,
Andreas


ETH Zurich
Prof. Dr. Andreas Fischlin
Systems Ecology - Institute of Integrative Biology
CHN E 21.1
Universitaetstrasse 16
8092 Zurich
SWITZERLAND

andreas.fisch...@env.ethz.ch
www.sysecol.ethz.ch

+41 44 633-6090 phone
+41 44 633-1136 fax
+41 79 595-4050 mobile

 Make it as simple as possible, but distrust it!








On 04/04/2013, at 18:55 , Christiaan Hofman wrote:


On Apr 4, 2013, at 17:22, Christiaan Hofman wrote:


On Apr 4, 2013, at 17:17, Gray, Wayne wrote:

All,

Since "discovering" this feature -- being able to go directly from BibTec to my 
mail program with a completely formatted citation, abstract, and attached PDFs, 
I have been using it a lot.

However, lately it seems as if it is not always working. Must be something in 
the files I am trying to send.  But recently I have observed the following 
behavior with no clear pattern:

A. It sends the pdfs and other files that are attached to my entry, but not the 
BibDesk citation.
B. It sends nothing - neither file nor citation
C. It works as intended sending both the formatted citation and any attached 
files.

Any ideas as to what is causing this erratic behavior?

I am using BibDesk: v1.6.0 (2779) and Mac OS 10.7.5.

Thanks for any ideas you might have on solving this mystery.

Wayne Gray


Apparently somewhere in the process it runs into an exception or something like 
that. I cannot say where from here. Try looking into Console.app to see if any 
errors are reported.

Christiaan


Another thing is the generation of the citation. What format are you using for 
email? And for the items that give you problems, is copy/paste for that format 
(Copy As) also failing?

Christiaan


--
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Re: [Bibdesk-users] linking files to dropbox

[Daniele Pontillo]

Il giorno 05/apr/2013, alle ore 10:38, Fischlin Andreas 
 ha scritto:

> 
> On 04/04/2013, at 21:23 , Daniele Pontillo wrote:
> 
> Thank you very much
> Obviously this is totally useless for me.
> It's a matter of communication
> 
> No, of the way one thinks. The help given by Christiaan is indeed I believe 
> very, very helpful and probably right on the spot, so I have a hard time to 
> understand why you say it is useless. I guess it is the solution for your 
> problem from all what I have understood so far. Even a rather easy one.

Maybe you're right. Thanks again
> 
> BTW, I have written AppleScripts and offer them from my home page that do 
> extract bibliographies in html form that can be used by colleagues. I do NOT 
> offer there Dropbox links of the kind you seem to have in mind, but that may 
> not be what you really want. You could easily extract with my script 'Extract 
> Bibliography' the currently in BibDesk selected publications and then save 
> the html index together with the pdf's to a Dropbox folder that you share 
> with your colleagues. That way each of you could share fully all information, 
> e.g. by double clicking in the index file the pdf links or doi links or other 
> URL links from any browser that has the html file opened. This works also 
> very well from iOS devices, e.g. using App GoodReader in an iPad that has 
> access to the wanted Dropbox folder.
Maybe you're right. Thanks again.It doesn't create the HTML file, for me

> 
> My webpage http://www.sysecol.ethz.ch/people/afischli link Software -> 
> BibDesk: AppleScripts
> 
> Regards,
> Andreas
> 
> 
> 
> 
> 
> Inviato da iPhone
> 
> Il giorno 04/apr/2013, alle ore 20:52, Christiaan Hofman 
> mailto:cmhof...@gmail.com>> ha scritto:
> 
> 
> On Apr 4, 2013, at 19:53, Daniele Pontillo wrote:
> 
> 
> Il giorno 04/apr/2013, alle ore 19:12, Christiaan Hofman 
> mailto:cmhof...@gmail.com>> ha scritto:
> 
> 
> On Apr 4, 2013, at 13:40, Daniele Pontillo wrote:
> 
> You almost got it right, almost
> I don't like my HTML file, but I don't know how to edit the file itself.
> Which field should I use to paste my Dropbox-generated link? And what is the 
> syntax  to edit the HTML file in order to get an appropriate output?
> 
> 
> You are still confusing different things. the problem is that what you say 
> you want to get, or what you have, is not consistent with the concrete 
> questions you ask. So what do you have, and what do you want to get? So 
> what's in your data, what linked files, linked URLs, and (URL) fields? And 
> what do you want in the HTML output? Is the information you want in there 
> available in your data? Do you know about templates, have you read the Wiki 
> and tried to look at sample templates?
> 
> Christiaan
> 
> Dear Christiaan. I appreciate so much your being straightforward, but I still 
> have to get used to it. So please try and understand, since I'd try to be 
> extremely patient and cooperative if I had to explain to you a current of 
> lesion during STEMI and PCI or the specific prognosis of the takotsubo 
> syndrome
> 
> 
> the problem is that you are implicitly making assumptions about the way 
> templates are generated and the structure of the data, which are not correct, 
> and then ask questions about the result of that assumption. Instead, you 
> should say what you have and what you want to get, not what you assume you 
> need in the intermediate to get what you want.
> 
> 
>  1.  I have a database
>  2.  I have a publication record
>  3.  This record has fields
>  4.  I am looking for a field where to paste 
> https://www.dropbox.com/s/21v1rxpvbgb65x0/2008.pdf, but actually I don't know 
> if such one exists
> 
> Here you make the assumption that you can add a field, and put something in 
> there, and somehow the content of that field turns up in the generated HTML. 
> That assumption is wrong. So you are *not* looking for such a field.
> 
> 
>  1.  I created a new field in a single publication record and called it 
> Dropbox-Url and pasted the link
> 
> That does not work because your assumption that arbitrary fields turn up in 
> the generated HTML is wrong.
> 
>  1.  I looked at templates
>  2.  I don't know how to sufficiently edit templates
>  3.  I tried to build a template with the template editor as a .txt file and 
> used for export
>  4.  Formatting was terrible, but I actually got my link to appear
>  5.  I'd like to get something like this which comes with the default html 
> template
> 
> Mokhles:2012aa
> The risk of new onset heart failure associated with dopamine agonist use in 
> Parkinson's disease
> M. M. Mokhles and G. Trifirò and J. P. Dieleman and M. D. Haag and E. M. van 
> Soest and K. M. C. Verhamme and G. Mazzaglia and R. Herings and C. d. Luise 
> and D. Ross and G. Brusselle and A. Colao and W. Haverkamp and R. Schade and 
> G. v. Camp and R. Zanettini and M. C. J. M. Sturkenboom
> Pharmacol Res  65  358-64  (2012)
> /Users/lalla/Dropbox/Papers/Mokhles/2012.nbib
> 

Re: [Bibdesk-users] linking files to dropbox

[Daniele Pontillo]

Il giorno 05/apr/2013, alle ore 10:38, Fischlin Andreas 
 ha scritto:

> 
> On 04/04/2013, at 21:23 , Daniele Pontillo wrote:
> 
> Thank you very much
> Obviously this is totally useless for me.
> It's a matter of communication
> 
> No, of the way one thinks. The help given by Christiaan is indeed I believe 
> very, very helpful and probably right on the spot, so I have a hard time to 
> understand why you say it is useless. I guess it is the solution for your 
> problem from all what I have understood so far. Even a rather easy one.

Maybe you're right. Thanks again
> 
> BTW, I have written AppleScripts and offer them from my home page that do 
> extract bibliographies in html form that can be used by colleagues. I do NOT 
> offer there Dropbox links of the kind you seem to have in mind, but that may 
> not be what you really want. You could easily extract with my script 'Extract 
> Bibliography' the currently in BibDesk selected publications and then save 
> the html index together with the pdf's to a Dropbox folder that you share 
> with your colleagues. That way each of you could share fully all information, 
> e.g. by double clicking in the index file the pdf links or doi links or other 
> URL links from any browser that has the html file opened. This works also 
> very well from iOS devices, e.g. using App GoodReader in an iPad that has 
> access to the wanted Dropbox folder.
Maybe you're right. Thanks again.It doesn't create the HTML file, for me

> 
> My webpage http://www.sysecol.ethz.ch/people/afischli link Software -> 
> BibDesk: AppleScripts
> 
> Regards,
> Andreas
> 
> 
> 
> 
> 
> Inviato da iPhone
> 
> Il giorno 04/apr/2013, alle ore 20:52, Christiaan Hofman 
> mailto:cmhof...@gmail.com>> ha scritto:
> 
> 
> On Apr 4, 2013, at 19:53, Daniele Pontillo wrote:
> 
> 
> Il giorno 04/apr/2013, alle ore 19:12, Christiaan Hofman 
> mailto:cmhof...@gmail.com>> ha scritto:
> 
> 
> On Apr 4, 2013, at 13:40, Daniele Pontillo wrote:
> 
> You almost got it right, almost
> I don't like my HTML file, but I don't know how to edit the file itself.
> Which field should I use to paste my Dropbox-generated link? And what is the 
> syntax  to edit the HTML file in order to get an appropriate output?
> 
> 
> You are still confusing different things. the problem is that what you say 
> you want to get, or what you have, is not consistent with the concrete 
> questions you ask. So what do you have, and what do you want to get? So 
> what's in your data, what linked files, linked URLs, and (URL) fields? And 
> what do you want in the HTML output? Is the information you want in there 
> available in your data? Do you know about templates, have you read the Wiki 
> and tried to look at sample templates?
> 
> Christiaan
> 
> Dear Christiaan. I appreciate so much your being straightforward, but I still 
> have to get used to it. So please try and understand, since I'd try to be 
> extremely patient and cooperative if I had to explain to you a current of 
> lesion during STEMI and PCI or the specific prognosis of the takotsubo 
> syndrome
> 
> 
> the problem is that you are implicitly making assumptions about the way 
> templates are generated and the structure of the data, which are not correct, 
> and then ask questions about the result of that assumption. Instead, you 
> should say what you have and what you want to get, not what you assume you 
> need in the intermediate to get what you want.
> 
> 
>  1.  I have a database
>  2.  I have a publication record
>  3.  This record has fields
>  4.  I am looking for a field where to paste 
> https://www.dropbox.com/s/21v1rxpvbgb65x0/2008.pdf, but actually I don't know 
> if such one exists
> 
> Here you make the assumption that you can add a field, and put something in 
> there, and somehow the content of that field turns up in the generated HTML. 
> That assumption is wrong. So you are *not* looking for such a field.
> 
> 
>  1.  I created a new field in a single publication record and called it 
> Dropbox-Url and pasted the link
> 
> That does not work because your assumption that arbitrary fields turn up in 
> the generated HTML is wrong.
> 
>  1.  I looked at templates
>  2.  I don't know how to sufficiently edit templates
>  3.  I tried to build a template with the template editor as a .txt file and 
> used for export
>  4.  Formatting was terrible, but I actually got my link to appear
>  5.  I'd like to get something like this which comes with the default html 
> template
> 
> Mokhles:2012aa
> The risk of new onset heart failure associated with dopamine agonist use in 
> Parkinson's disease
> M. M. Mokhles and G. Trifirò and J. P. Dieleman and M. D. Haag and E. M. van 
> Soest and K. M. C. Verhamme and G. Mazzaglia and R. Herings and C. d. Luise 
> and D. Ross and G. Brusselle and A. Colao and W. Haverkamp and R. Schade and 
> G. v. Camp and R. Zanettini and M. C. J. M. Sturkenboom
> Pharmacol Res  65  358-64  (2012)
> /Users/lalla/Dropbox/Papers/Mokhles/2012.nbib
> 

Re: [Bibdesk-users] linking files to dropbox

[Fischlin Andreas]

On 04/04/2013, at 21:23 , Daniele Pontillo wrote:

Thank you very much
Obviously this is totally useless for me.
It's a matter of communication

No, of the way one thinks. The help given by Christiaan is indeed I believe 
very, very helpful and probably right on the spot, so I have a hard time to 
understand why you say it is useless. I guess it is the solution for your 
problem from all what I have understood so far. Even a rather easy one.

BTW, I have written AppleScripts and offer them from my home page that do 
extract bibliographies in html form that can be used by colleagues. I do NOT 
offer there Dropbox links of the kind you seem to have in mind, but that may 
not be what you really want. You could easily extract with my script 'Extract 
Bibliography' the currently in BibDesk selected publications and then save the 
html index together with the pdf's to a Dropbox folder that you share with your 
colleagues. That way each of you could share fully all information, e.g. by 
double clicking in the index file the pdf links or doi links or other URL links 
from any browser that has the html file opened. This works also very well from 
iOS devices, e.g. using App GoodReader in an iPad that has access to the wanted 
Dropbox folder.

My webpage http://www.sysecol.ethz.ch/people/afischli link Software -> BibDesk: 
AppleScripts

Regards,
Andreas





Inviato da iPhone

Il giorno 04/apr/2013, alle ore 20:52, Christiaan Hofman 
mailto:cmhof...@gmail.com>> ha scritto:


On Apr 4, 2013, at 19:53, Daniele Pontillo wrote:


Il giorno 04/apr/2013, alle ore 19:12, Christiaan Hofman 
mailto:cmhof...@gmail.com>> ha scritto:


On Apr 4, 2013, at 13:40, Daniele Pontillo wrote:

You almost got it right, almost
I don't like my HTML file, but I don't know how to edit the file itself.
Which field should I use to paste my Dropbox-generated link? And what is the 
syntax  to edit the HTML file in order to get an appropriate output?


You are still confusing different things. the problem is that what you say you 
want to get, or what you have, is not consistent with the concrete questions 
you ask. So what do you have, and what do you want to get? So what's in your 
data, what linked files, linked URLs, and (URL) fields? And what do you want in 
the HTML output? Is the information you want in there available in your data? 
Do you know about templates, have you read the Wiki and tried to look at sample 
templates?

Christiaan

Dear Christiaan. I appreciate so much your being straightforward, but I still 
have to get used to it. So please try and understand, since I'd try to be 
extremely patient and cooperative if I had to explain to you a current of 
lesion during STEMI and PCI or the specific prognosis of the takotsubo syndrome


the problem is that you are implicitly making assumptions about the way 
templates are generated and the structure of the data, which are not correct, 
and then ask questions about the result of that assumption. Instead, you should 
say what you have and what you want to get, not what you assume you need in the 
intermediate to get what you want.


  1.  I have a database
  2.  I have a publication record
  3.  This record has fields
  4.  I am looking for a field where to paste 
https://www.dropbox.com/s/21v1rxpvbgb65x0/2008.pdf, but actually I don't know 
if such one exists

Here you make the assumption that you can add a field, and put something in 
there, and somehow the content of that field turns up in the generated HTML. 
That assumption is wrong. So you are *not* looking for such a field.


  1.  I created a new field in a single publication record and called it 
Dropbox-Url and pasted the link

That does not work because your assumption that arbitrary fields turn up in the 
generated HTML is wrong.

  1.  I looked at templates
  2.  I don't know how to sufficiently edit templates
  3.  I tried to build a template with the template editor as a .txt file and 
used for export
  4.  Formatting was terrible, but I actually got my link to appear
  5.  I'd like to get something like this which comes with the default html 
template

Mokhles:2012aa
The risk of new onset heart failure associated with dopamine agonist use in 
Parkinson's disease
M. M. Mokhles and G. Trifirò and J. P. Dieleman and M. D. Haag and E. M. van 
Soest and K. M. C. Verhamme and G. Mazzaglia and R. Herings and C. d. Luise and 
D. Ross and G. Brusselle and A. Colao and W. Haverkamp and R. Schade and G. v. 
Camp and R. Zanettini and M. C. J. M. Sturkenboom
Pharmacol Res  65  358-64  (2012)
/Users/lalla/Dropbox/Papers/Mokhles/2012.nbib


  *   But instead of /Users/lalla/Dropbox/Papers/mypaper
  *   id like
  *   https://www.dropbox.com/s/21v1rxpvbgb65x0/2008.pdf

Again, one question is: is this information available somewhere in your 
publication items? If it is not, it will never turn up in the template. So you 
should somehow add it.

  *   maybe some automation to retrieve the cloud link for any file stored in 
the local Dropb