Re: [O] ebib configuration for org-bibtex
Eric Schulte writes: > t...@tsdye.com (Thomas S. Dye) writes: > >> Eric Schulte writes: >> >>> t...@tsdye.com (Thomas S. Dye) writes: >>> Aloha all, I'm trying, partially successfully, to configure org-bibtex so it mimics some useful features of ebib. In particular, I'm wanting to add several optional fields that ebib uses. I have this in .emacs: #+begin_src emacs-lisp :tangle yes (dolist (type org-bibtex-types) (push :url (cdr (assoc :optional (cdr type (push :annote (cdr (assoc :optional (cdr type (push :abstract (cdr (assoc :optional (cdr type (push :keywords (cdr (assoc :optional (cdr type (push :file (cdr (assoc :optional (cdr type ) (push (cons :url "A URL for the reference") org-bibtex-fields) (push (cons :annote "Annotation is typically not exported") org-bibtex-fields) (push (cons :abstract "Abstract for annotated bibliography") org-bibtex-fields) (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields) (push (cons :file "A local file path used by ebib to open the reference in an appropriate application") org-bibtex-fields) #+end_src Most of it works fine, but the optional :file field doesn't respect its argument. So, the following entry in the Org-mode file: >>> >>> Hi Tom, >>> >>> The :file property is treated in a special manner when Org-mode resolves >>> properties (notice it is an element of the `org-special-properties' >>> variable). I've just pushed up a change which temporarily removes :file >>> from this list while resolving bibtex entries. This change should fix >>> your reported problem -- please let me know if it doesn't. If any other >>> elements of `org-special-properties' seem likely to cause problems we >>> can temporarily remove them as well. >>> >>> Best -- Eric >> >> Hi Eric, >> >> I think this fix is causing some mischief. In the Org-mode file where >> a :FILE: property is set to preza-thesis.pdf R source code blocks >> misbehave, as follows: >> >> #+source: land-sale-plot >> #+begin_src R :var y=sales >> str(y) >> #+end_src >> >> #+results: land-sale-plot >> [[file:preza-thesis.pdf]] >> > > Hi Tom, > > Are you still experiencing the problem mentioned above? I'm unable to > reproduce it locally. If so, would you mind trying to recreate the > problem with an emacs session launched using "emacs -Q" to see if the > cause lies somewhere in your personal configuration? > > I *do* have a file header argument for code blocks inside of subtrees > which explicitly specify a file property (which can be easily checked > using C-c C-v I), e.g., > > > ** inheriting the file property >:PROPERTIES: >:FILE: something.png >:END: > > #+begin_src ditaa >+-+ >| | >|+-+ | >|| | +-+| >|| | | || >|+-+ | || >| | || >| file | || >| inheritance +-+| >| | >+-+ > #+end_src > > #+results: > [[file:something.png]] > > > However when I do not specify such a FILE property, then no :file entry > is present in the code blocks parameters. > > Thanks -- Eric Hi Eric, I think the confusion leading to my messages has been the cause of some mischief. Apologies for that. The change you implemented to let the :FILE: property work correctly with ebib does what it is supposed to do. It does not cause the "mischief" that I was experiencing. AFAICT, your re-reversion of the code back into Org-mode was the correct action. I ran into the problem when I tried to include in my reading notes an R graphic for some newly reported data. The R source block was immediately below the bibliographic subheading with the :FILE: property. Babel saw the :FILE: property for the bibliographic subheading and applied that to the R code block, as I now believe it is supposed to do. My confusion came from the fact that I didn't recognize at the time that Babel sees the :FILE: property for the bibliographic subheading the same way it sees the :FILE: property for any other heading. When I move the R code away from the bibliographic subheading it all works as expected, as you note. Again, sorry for my noise, and thanks for your fix for the ebib integration. All the best, Tom -- T.S. Dye & Colleagues, Archaeologists 735 Bishop St, Suite 315, Honolulu, HI 96813 Tel: 808-529-0866, Fax: 808-529-0884 http://www.tsdye.com
Re: [O] ebib configuration for org-bibtex
t...@tsdye.com (Thomas S. Dye) writes: > Eric Schulte writes: > >> t...@tsdye.com (Thomas S. Dye) writes: >> >>> Aloha all, >>> >>> I'm trying, partially successfully, to configure org-bibtex so it mimics >>> some useful features of ebib. In particular, I'm wanting to add several >>> optional fields that ebib uses. >>> >>> >>> I have this in .emacs: >>> >>> #+begin_src emacs-lisp :tangle yes >>> (dolist (type org-bibtex-types) >>> (push :url (cdr (assoc :optional (cdr type >>> (push :annote (cdr (assoc :optional (cdr type >>> (push :abstract (cdr (assoc :optional (cdr type >>> (push :keywords (cdr (assoc :optional (cdr type >>> (push :file (cdr (assoc :optional (cdr type >>> ) >>> >>> (push (cons :url "A URL for the reference") org-bibtex-fields) >>> (push (cons :annote "Annotation is typically not exported") >>> org-bibtex-fields) >>> (push (cons :abstract "Abstract for annotated bibliography") >>> org-bibtex-fields) >>> (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields) >>> (push (cons :file "A local file path used by ebib to open the >>> reference in an appropriate application") org-bibtex-fields) >>> #+end_src >>> >>> Most of it works fine, but the optional :file field doesn't respect its >>> argument. So, the following entry in the Org-mode file: >>> >> >> Hi Tom, >> >> The :file property is treated in a special manner when Org-mode resolves >> properties (notice it is an element of the `org-special-properties' >> variable). I've just pushed up a change which temporarily removes :file >> from this list while resolving bibtex entries. This change should fix >> your reported problem -- please let me know if it doesn't. If any other >> elements of `org-special-properties' seem likely to cause problems we >> can temporarily remove them as well. >> >> Best -- Eric > > Hi Eric, > > I think this fix is causing some mischief. In the Org-mode file where > a :FILE: property is set to preza-thesis.pdf R source code blocks > misbehave, as follows: > > #+source: land-sale-plot > #+begin_src R :var y=sales > str(y) > #+end_src > > #+results: land-sale-plot > [[file:preza-thesis.pdf]] > Hi Tom, Are you still experiencing the problem mentioned above? I'm unable to reproduce it locally. If so, would you mind trying to recreate the problem with an emacs session launched using "emacs -Q" to see if the cause lies somewhere in your personal configuration? I *do* have a file header argument for code blocks inside of subtrees which explicitly specify a file property (which can be easily checked using C-c C-v I), e.g., ** inheriting the file property :PROPERTIES: :FILE: something.png :END: #+begin_src ditaa +-+ | | |+-+ | || | +-+| || | | || |+-+ | || | | || | file | || | inheritance +-+| | | +-+ #+end_src #+results: [[file:something.png]] However when I do not specify such a FILE property, then no :file entry is present in the code blocks parameters. Thanks -- Eric
Re: [O] ebib configuration for org-bibtex
Bastien writes: > Hi Eric, > > Bastien writes: > >>> I think this fix is causing some mischief. >> >> I reverted this commit -- let's wait Eric is back and can fix this with >> a better solution. > > Eric -- just making sure this is under your radar. > Thanks, I had lost track of the end of this thread. > > I reverted your fix because it was not answering Thomas' problem, > but it looks like your fix is right anyway, though not addressing > the issue at hand. Could you have another look? > I've just reverted your reversion :). I'll take a look at Toms problem (which does appear to be separate) separately. Thanks -- Eric > > Thanks in advance!
Re: [O] ebib configuration for org-bibtex
Hi Eric, Bastien writes: >> I think this fix is causing some mischief. > > I reverted this commit -- let's wait Eric is back and can fix this with > a better solution. Eric -- just making sure this is under your radar. I reverted your fix because it was not answering Thomas' problem, but it looks like your fix is right anyway, though not addressing the issue at hand. Could you have another look? Thanks in advance! -- Bastien
Re: [O] ebib configuration for org-bibtex
Bastien writes: > Hi Thomas, > > t...@tsdye.com (Thomas S. Dye) writes: > >>> The :file property is treated in a special manner when Org-mode resolves >>> properties (notice it is an element of the `org-special-properties' >>> variable). I've just pushed up a change which temporarily removes :file >>> from this list while resolving bibtex entries. This change should fix >>> your reported problem -- please let me know if it doesn't. If any other >>> elements of `org-special-properties' seem likely to cause problems we >>> can temporarily remove them as well. >>> >>> Best -- Eric >> >> Hi Eric, >> >> I think this fix is causing some mischief. > > I reverted this commit -- let's wait Eric is back and can fix this with > a better solution. > > Thanks, Aloha Bastien, It appears I was wrong about this. I get the same behavior after the reversion. This is something I haven't seen before. I'll try to track down the problem. All the best, Tom -- Thomas S. Dye http://www.tsdye.com
Re: [O] ebib configuration for org-bibtex
Hi Thomas, t...@tsdye.com (Thomas S. Dye) writes: >> The :file property is treated in a special manner when Org-mode resolves >> properties (notice it is an element of the `org-special-properties' >> variable). I've just pushed up a change which temporarily removes :file >> from this list while resolving bibtex entries. This change should fix >> your reported problem -- please let me know if it doesn't. If any other >> elements of `org-special-properties' seem likely to cause problems we >> can temporarily remove them as well. >> >> Best -- Eric > > Hi Eric, > > I think this fix is causing some mischief. I reverted this commit -- let's wait Eric is back and can fix this with a better solution. Thanks, -- Bastien
Re: [O] ebib configuration for org-bibtex
Eric Schulte writes: > t...@tsdye.com (Thomas S. Dye) writes: > >> Aloha all, >> >> I'm trying, partially successfully, to configure org-bibtex so it mimics >> some useful features of ebib. In particular, I'm wanting to add several >> optional fields that ebib uses. >> >> >> I have this in .emacs: >> >> #+begin_src emacs-lisp :tangle yes >> (dolist (type org-bibtex-types) >> (push :url (cdr (assoc :optional (cdr type >> (push :annote (cdr (assoc :optional (cdr type >> (push :abstract (cdr (assoc :optional (cdr type >> (push :keywords (cdr (assoc :optional (cdr type >> (push :file (cdr (assoc :optional (cdr type >> ) >> >> (push (cons :url "A URL for the reference") org-bibtex-fields) >> (push (cons :annote "Annotation is typically not exported") >> org-bibtex-fields) >> (push (cons :abstract "Abstract for annotated bibliography") >> org-bibtex-fields) >> (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields) >> (push (cons :file "A local file path used by ebib to open the >> reference in an appropriate application") org-bibtex-fields) >> #+end_src >> >> Most of it works fine, but the optional :file field doesn't respect its >> argument. So, the following entry in the Org-mode file: >> > > Hi Tom, > > The :file property is treated in a special manner when Org-mode resolves > properties (notice it is an element of the `org-special-properties' > variable). I've just pushed up a change which temporarily removes :file > from this list while resolving bibtex entries. This change should fix > your reported problem -- please let me know if it doesn't. If any other > elements of `org-special-properties' seem likely to cause problems we > can temporarily remove them as well. > > Best -- Eric Hi Eric, I think this fix is causing some mischief. In the Org-mode file where a :FILE: property is set to preza-thesis.pdf R source code blocks misbehave, as follows: #+source: land-sale-plot #+begin_src R :var y=sales str(y) #+end_src #+results: land-sale-plot [[file:preza-thesis.pdf]] All the best, Tom > >> >> ** Active Documents with Org-mode >>:PROPERTIES: >>:TITLE:Active Documents with Org-mode >>:TYPE: article >>:AUTHOR: Eric Schulte and Dan Davison >>:JOURNAL: Computing in Science and Engineering >>:YEAR: 2011 >>:VOLUME: 13 >>:NUMBER: 3 >>:PAGES:2--9 >>:MONTH:May/June >>:URL: http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf >>:FILE: Schulte-Davison-Babel.pdf >>:CUSTOM_ID: schulte11:_activ_docum_org >>:END: >> >> is exported with org-bibtex like this: >> >> @article{schulte11:_activ_docum_org, >> author = {Eric Schulte and Dan Davison}, >> title ={Active Documents with Org-mode}, >> journal = {Computing in Science and Engineering}, >> year = 2011, >> file = {/Users/dk/Public/projects/916-rr/rr.org}, >> url = >> {http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf}, >> volume = 13, >> number = 3, >> pages ={2--9}, >> month ={May/June} >> } >> >> Pressing f in ebib now just takes me back to the Org-mode file, rather >> than launching a pdf reader on my local copy of the article. >> >> Any ideas how I can achieve my goal? >> >> All the best, >> Tom -- Thomas S. Dye http://www.tsdye.com
Re: [O] ebib configuration for org-bibtex
Eric Schulte writes: > t...@tsdye.com (Thomas S. Dye) writes: > >> Aloha all, >> >> I'm trying, partially successfully, to configure org-bibtex so it mimics >> some useful features of ebib. In particular, I'm wanting to add several >> optional fields that ebib uses. >> >> >> I have this in .emacs: >> >> #+begin_src emacs-lisp :tangle yes >> (dolist (type org-bibtex-types) >> (push :url (cdr (assoc :optional (cdr type >> (push :annote (cdr (assoc :optional (cdr type >> (push :abstract (cdr (assoc :optional (cdr type >> (push :keywords (cdr (assoc :optional (cdr type >> (push :file (cdr (assoc :optional (cdr type >> ) >> >> (push (cons :url "A URL for the reference") org-bibtex-fields) >> (push (cons :annote "Annotation is typically not exported") >> org-bibtex-fields) >> (push (cons :abstract "Abstract for annotated bibliography") >> org-bibtex-fields) >> (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields) >> (push (cons :file "A local file path used by ebib to open the >> reference in an appropriate application") org-bibtex-fields) >> #+end_src >> >> Most of it works fine, but the optional :file field doesn't respect its >> argument. So, the following entry in the Org-mode file: >> > > Hi Tom, > > The :file property is treated in a special manner when Org-mode resolves > properties (notice it is an element of the `org-special-properties' > variable). I've just pushed up a change which temporarily removes :file > from this list while resolving bibtex entries. This change should fix > your reported problem -- please let me know if it doesn't. If any other > elements of `org-special-properties' seem likely to cause problems we > can temporarily remove them as well. > > Best -- Eric > Hi Eric, I looked up org-special-properties: org-special-properties is a variable defined in `org.el'. Its value is ("TODO" "TAGS" "ALLTAGS" "DEADLINE" "SCHEDULED" "CLOCK" "CLOSED" "PRIORITY" "TIMESTAMP" "TIMESTAMP_IA" "BLOCKED" "FILE" "CLOCKSUM") It looks to me as if FILE is the only one likely to play mischief with bib files. Thanks for the fix, which works as expected here. All the best, Tom -- Thomas S. Dye http://www.tsdye.com
Re: [O] ebib configuration for org-bibtex
t...@tsdye.com (Thomas S. Dye) writes: > Aloha all, > > I'm trying, partially successfully, to configure org-bibtex so it mimics > some useful features of ebib. In particular, I'm wanting to add several > optional fields that ebib uses. > > > I have this in .emacs: > > #+begin_src emacs-lisp :tangle yes > (dolist (type org-bibtex-types) > (push :url (cdr (assoc :optional (cdr type > (push :annote (cdr (assoc :optional (cdr type > (push :abstract (cdr (assoc :optional (cdr type > (push :keywords (cdr (assoc :optional (cdr type > (push :file (cdr (assoc :optional (cdr type > ) > > (push (cons :url "A URL for the reference") org-bibtex-fields) > (push (cons :annote "Annotation is typically not exported") > org-bibtex-fields) > (push (cons :abstract "Abstract for annotated bibliography") > org-bibtex-fields) > (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields) > (push (cons :file "A local file path used by ebib to open the > reference in an appropriate application") org-bibtex-fields) > #+end_src > > Most of it works fine, but the optional :file field doesn't respect its > argument. So, the following entry in the Org-mode file: > Hi Tom, The :file property is treated in a special manner when Org-mode resolves properties (notice it is an element of the `org-special-properties' variable). I've just pushed up a change which temporarily removes :file from this list while resolving bibtex entries. This change should fix your reported problem -- please let me know if it doesn't. If any other elements of `org-special-properties' seem likely to cause problems we can temporarily remove them as well. Best -- Eric > > ** Active Documents with Org-mode >:PROPERTIES: >:TITLE:Active Documents with Org-mode >:TYPE: article >:AUTHOR: Eric Schulte and Dan Davison >:JOURNAL: Computing in Science and Engineering >:YEAR: 2011 >:VOLUME: 13 >:NUMBER: 3 >:PAGES:2--9 >:MONTH:May/June >:URL: http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf >:FILE: Schulte-Davison-Babel.pdf >:CUSTOM_ID: schulte11:_activ_docum_org >:END: > > is exported with org-bibtex like this: > > @article{schulte11:_activ_docum_org, > author = {Eric Schulte and Dan Davison}, > title ={Active Documents with Org-mode}, > journal = {Computing in Science and Engineering}, > year = 2011, > file = {/Users/dk/Public/projects/916-rr/rr.org}, > url = > {http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf}, > volume = 13, > number = 3, > pages ={2--9}, > month ={May/June} > } > > Pressing f in ebib now just takes me back to the Org-mode file, rather > than launching a pdf reader on my local copy of the article. > > Any ideas how I can achieve my goal? > > All the best, > Tom -- Eric Schulte http://cs.unm.edu/~eschulte/
[O] ebib configuration for org-bibtex
Aloha all, I'm trying, partially successfully, to configure org-bibtex so it mimics some useful features of ebib. In particular, I'm wanting to add several optional fields that ebib uses. I have this in .emacs: #+begin_src emacs-lisp :tangle yes (dolist (type org-bibtex-types) (push :url (cdr (assoc :optional (cdr type (push :annote (cdr (assoc :optional (cdr type (push :abstract (cdr (assoc :optional (cdr type (push :keywords (cdr (assoc :optional (cdr type (push :file (cdr (assoc :optional (cdr type ) (push (cons :url "A URL for the reference") org-bibtex-fields) (push (cons :annote "Annotation is typically not exported") org-bibtex-fields) (push (cons :abstract "Abstract for annotated bibliography") org-bibtex-fields) (push (cons :keywords "Keywords for sorting with ebib") org-bibtex-fields) (push (cons :file "A local file path used by ebib to open the reference in an appropriate application") org-bibtex-fields) #+end_src Most of it works fine, but the optional :file field doesn't respect its argument. So, the following entry in the Org-mode file: ** Active Documents with Org-mode :PROPERTIES: :TITLE:Active Documents with Org-mode :TYPE: article :AUTHOR: Eric Schulte and Dan Davison :JOURNAL: Computing in Science and Engineering :YEAR: 2011 :VOLUME: 13 :NUMBER: 3 :PAGES:2--9 :MONTH:May/June :URL: http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf :FILE: Schulte-Davison-Babel.pdf :CUSTOM_ID: schulte11:_activ_docum_org :END: is exported with org-bibtex like this: @article{schulte11:_activ_docum_org, author = {Eric Schulte and Dan Davison}, title ={Active Documents with Org-mode}, journal = {Computing in Science and Engineering}, year = 2011, file = {/Users/dk/Public/projects/916-rr/rr.org}, url = {http://www.cs.unm.edu/~eschulte/data/CISE-13-3-SciProg.pdf}, volume = 13, number = 3, pages ={2--9}, month ={May/June} } Pressing f in ebib now just takes me back to the Org-mode file, rather than launching a pdf reader on my local copy of the article. Any ideas how I can achieve my goal? All the best, Tom -- Thomas S. Dye http://www.tsdye.com