getting bibtex from researchgate, Zotero fails

Tue Jul 2 20:01:37 CEST 2024

Toobib encountered a problem with this and the zoterro
webform also failed,

https://www.researchgate.net/publication/289502317_Canine_tracheal_collapse

ResearchGate is handy sometimes although often you can find other
sites.  A remember years ago there were a few issues as you could extract
a DOI or get bibtex info by scraping the html. Now it looks like it
blocks headless chrome. I had to invoke toobib in the "head" mode
( passing bit vector 2 to chromate the headless chrome interface  ) 
and by default it temperarily disconnects the debug port
which appears to work on all sites that block headless.
Its a kluge but seems pretty effective. 

Sure, I'm trying to highlight the Toobib philosophy but also
alerting anyone who cares to the largre problem if the full Zoterro
install also fails. This is a daily problem though as I try to 
get "filler" citations to document conventional wisdom and
check a few details. Usually it takes all day and derails pretty
fast due to citability of "teasers" not even AI generated.  In this
case, I don't need solid academic journals and stable informational 
webpages from reputable professional sites or universiites
would be ok but typically they don't include ability to generate
bibtex. This seemingly simple mundane thing doesn't seem like
it should be so hard :)  

Anyway this is what toobib scraped, 

toobib -chromate 2 -clip
mjm>clip xxxx
./toobib.h588  cmd=clip p1=xxxx p2= flags=18 x.flag_to_string(flags,0)=show_trial paste_citation 
./mjm_med2bib_guesses.h997  uin=https://www.researchgate.net/publication/289502317_Canine_tracheal_collapse dest=xxxx flags=18
./mjm_chromate.h1716  enabling mjm_chromate with head 
./mjm_med2bib_guesses.h1179 % mjmhandler: toobib handledoi(crossref)
% date 2024-07-02:13:29:06 Tue 02 Jul 2024 01:29:06 PM EDT
% srcurl: https://www.researchgate.net/publication/289502317_Canine_tracheal_collapse
% citeurl: http://api.crossref.org/works/10.1111/jsap.12436
@article{Tappin_Canine_tracheal_collapse_2016,
X_TooBib = {date: 2016},
X_TooBib = {year: 2016,  infield_fix_dates },
X_TooBib = {urldate: FixBeKvp s= cmd=date "+%Y-%m-%d" d=2024-07-02 dn=urldate},
X_TooBib = {author: Tappin , S. W.},
abbrvjrnl = {J of Small Animal Practice},
abstract = {<jats:p>Tracheal collapse occurs most commonly in middleaged, small breed dogs. Clinical signs are usually proportional to the degree of collapse, ranging from mild airway irritation and paroxysmal coughing to respiratory distress and dyspnoea. Diagnosis is made by documenting dynamic airway collapse with radiographs, bronchoscopy or fluoroscopy. Most dogs respond well to medical management and treatment of any concurrent comorbidities. Surgical intervention may need to be considered in dogs that do not respond or have respiratory compromise. A variety of surgical techniques have been reported although extraluminal ring prostheses or intraluminal stenting are the most commonly used. Both techniques have numerous potential complications and require specialised training and experience but are associated with good short and longterm outcomes.</jats:p>},
abstract_as_rcvd = {<jats:p>Tracheal collapse occurs most commonly in middle�aged, small breed dogs. Clinical signs are usually proportional to the degree of collapse, ranging from mild airway irritation and paroxysmal coughing to respiratory distress and dyspnoea. Diagnosis is made by documenting dynamic airway collapse with radiographs, bronchoscopy or fluoroscopy. Most dogs respond well to medical management and treatment of any concurrent comorbidities. Surgical intervention may need to be considered in dogs that do not respond or have respiratory compromise. A variety of surgical techniques have been reported although extraluminal ring prostheses or intraluminal stenting are the most commonly used. Both techniques have numerous potential complications and require specialised training and experience but are associated with good short� and long�term outcomes.</jats:p>},
affiliation = {Dick White Referrals Cambridgeshire CB8 0UH},
alternative-id = {10.1111/jsap.12436},
archive = {Portico},
author = {Tappin , S. W.},
author_orig = {S. W. Tappin},
bib-source = {Crossref},
container-title = {Journal of Small Animal Practice},
content-domain = {false},
date = {2016},
date-created = {2016-01-05T20:08:29Z},
date-deposited = {2024-06-132024-06-13T16:41:02Z},
date-indexed = {2024-06-21T22:54:20Z},
date-issued = {2016-01},
date-journal-issue = {2016-01},
date-license = {2016-01-042016-01-04T00:00:00Z},
date-published-online = {2016-01-04},
date-published-print = {2016-01},
date_orig = { 2016-01   2016-01 2016-01     2016-01-04 },
deposited = {1718296862000},
doi = {10.1111/jsap.12436},
is-referenced-by-count = {38},
issn = {1748-5827},
issn-type = {0022-4510, print, 1748-5827, electronic},
issue = {1},
journal = {Journal of Small Animal Practice},
journal-issue = {1},
language = {en},
license = {1451865600000, vor, 3, http://onlinelibrary.wiley.com/termsAndConditions#vor},
link = {https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fjsap.12436, unspecified, vor, text-mining, https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fjsap.12436, application/pdf, vor, text-mining, https://onlinelibrary.wiley.com/doi/pdf/10.1111/jsap.12436, unspecified, vor, similarity-checking},
member = {311},
page = {9-17},
prefix = {10.1111},
publication-date = {2016-01},
publisher = {Wiley},
reference = {deleted},
reference-count = {57},
references-count = {57},
resource = {https://onlinelibrary.wiley.com/doi/10.1111/jsap.12436},
score = {1},
title = {Canine tracheal collapse},
type = {journal-article},
url = {http://dx.doi.org/10.1111/jsap.12436},
urldate = {2024-07-02},
volume = {57},
year = {2016},
final_assembly ={ TooBib handler handledoi(crossref)},
srcurl={https://www.researchgate.net/publication/289502317_Canine_tracheal_collapse},
xsrcurl={https://www.researchgate.net/publication/289502317_Canine_tracheal_collapse},
citeurl={http://api.crossref.org/works/10.1111/jsap.12436},
toobib-date={2024-07-02:13:29:06 Tue 02 Jul 2024 01:29:06 PM EDT}

}

./mjm_med2bib_guesses.h1187  saving to  df=xxxx
./mjm_med2bib_guesses.h1201  have citation   nfound=1 cite=\cite{Tappin_Canine_tracheal_collapse_2016} something=1 paste_citation=1
mjm>
marchywka at happy:/home/documents/latex/proj/copper$ toobib -add copper
mjm>add copper xxxx
./toobib.h574  cmd=add p1=copper p2=xxxx flags=1 x.flag_to_string(flags,1)=
./mjm_assemble_putative_bibtex.h937 
)

Output written on xxxx.pdf (1 page, 48260 bytes).

./mjm_med2bib_guesses.h1341 References
[1] S. W. Tappin. Canine tracheal collapse. Journal of Small Animal Practice, 57, 2016. Available from: http://dx.doi.org/10.1111/jsap.12436, doi:10.1111/jsap.12436.
1

./mjm_med2bib_guesses.h1342  see  vfn=checkbib_test_output.xxx for more details on latex 
./mjm_med2bib_guesses.h1432  writing   fullfile=./non_pmc_copper.bib exists=0 bib.name()=Tappin_Canine_tracheal_collapse_2016
mjm>

-- 

mike marchywka
44 Crosscreek Trail
Jasper GA 30143
USA, Earth marchywka at hotmail.com
 404-788-1216 ORCID: 0000-0001-9237-455X