Bibtex not working

[rafed]

Is the extracting bibtex working? I've been trying for a few days and it doesnt seem to work. Any suggestions?

[soreana]

same issue

[MooersLab]

same issue

[EthanS94]

What worked for me was changing line 485 from:

self.article['url_citation'] = self._path2url(tag.get('href'))

to:

self.article['url_citation'] = tag.get('href')

[MooersLab]

Thank EthaS94. This change did not work for me. I got back a blank line.

…

On Tue, Feb 13, 2018 at 4:50 PM, EthanS94 ***@***.***> wrote: What worked for me was changing line 485 from: self.article['url_citation'] = self._path2url(tag.get('href')) to: self.article['url_citation'] = tag.get('href') — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#102 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AOeSCyce0U2FfEDqJcADXRnadrIdHTTlks5tUhHBgaJpZM4RS304> .

-- Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 975 NE 10th Street <https://maps.google.com/?q=975+NE+10th+Street&entry=gmail&source=g>, BRC 466 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 Faculty webpage <http://tinyurl.com/ouhscMooers> X-ray lab (LBSF) <http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStructureandFunction.aspx> COBRE in Structural Biology <http://structuralbiology.ou.edu/> SSRL UEC Facebook Page <https://www.facebook.com/ssrluec/> SSRL UEC <https://www-ssrl.slac.stanford.edu/content/about-ssrl/advisory-panels/ssrl-users-organization/members/ssrluo-2016-executive-committee-members> SSRL SAC <https://www-ssrl.slac.stanford.edu/content/about-ssrl/scientific-advisory-committee> LCLS UEC <https://www-ssrl.slac.stanford.edu/lcls-resources/lcls-users-organization-executive-committee> EasyPyMOL <https://github.com/MooersLab/EasyPyMOL> Molecular Graphics <https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/moleculargraphicslinks.html> <https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/MolecularGraphicsLinks.html> Small Angle Scattering <http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0> office: (405) 271-8300 lab: (405) 271-8313 e-mail: [email protected] (or [email protected])

[EthanS94]

Sorry, this went along with a change from @portalgun's comment on issue #101. I also changed line 985.

tag = soup.find(name='form', attrs={'id': 'gs_settings_form'})
to
tag = soup.find(name='form', attrs={'id': 'gs_bdy_frm'})

Try adding this change along with mine and see if it works.

[soreana]

That's working 👍
Thanks :)

[MooersLab]

scholar.py is now working for me too. Many thank yous for the help getting the script to run and many thank yous for developing this useful tool!

…

On Wed, Feb 14, 2018 at 1:53 PM, soreana ***@***.***> wrote: That's working 👍 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#102 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AOeSC6hDj9A_-J9xF5e2FANhzUJjyylZks5tUzmigaJpZM4RS304> .

-- Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 975 NE 10th Street <https://maps.google.com/?q=975+NE+10th+Street&entry=gmail&source=g>, BRC 466 Oklahoma City, OK 73104-5419 office: (405) 271-8300 lab: (405) 271-8313 Faculty webpage <http://tinyurl.com/ouhscMooers> X-ray lab (LBSF) <http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStructureandFunction.aspx> COBRE in Structural Biology <http://structuralbiology.ou.edu/> SSRL UEC Facebook Page <https://www.facebook.com/ssrluec/> SSRL UEC <https://www-ssrl.slac.stanford.edu/content/about-ssrl/advisory-panels/ssrl-users-organization/members/ssrluo-2016-executive-committee-members> SSRL SAC <https://www-ssrl.slac.stanford.edu/content/about-ssrl/scientific-advisory-committee> LCLS UEC <https://www-ssrl.slac.stanford.edu/lcls-resources/lcls-users-organization-executive-committee> EasyPyMOL <https://github.com/MooersLab/EasyPyMOL> Molecular Graphics <https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/moleculargraphicslinks.html> <https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/MolecularGraphicsLinks.html> Small Angle Scattering <http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0> office: (405) 271-8300 lab: (405) 271-8313 e-mail: [email protected] (or [email protected])

[mcnesium]

so I applied the suggested patches like this:

$ git diff
diff --git a/scholar.py b/scholar.py
index 13ccd43..2133d67 100755
--- a/scholar.py
+++ b/scholar.py
@@ -482,7 +482,7 @@ class ScholarArticleParser(object):
-        self.article['url_citation'] = self._path2url(tag.get('href'))
+        self.article['url_citation'] = tag.get('href')

@@ -982,7 +982,7 @@ class ScholarQuerier(object):
-        tag = soup.find(name='form', attrs={'id': 'gs_settings_form'})
+        tag = soup.find(name='form', attrs={'id': 'gs_bdy_frm'})

but trying to run the example command throws the following errors:

$ python scholar.py -c 1 --author "albert einstein" --phrase "quantum theory" --citation bt
Traceback (most recent call last):
File "scholar.py", line 1310, in <module>
    sys.exit(main())
File "scholar.py", line 1300, in main
    citation_export(querier)
File "scholar.py", line 1145, in citation_export
    print(art.as_citation() + '\n')
TypeError: can't concat str to bytes
$ 

So I removed the + '\n' from line 1145:

@@ -1142,7 +1142,7 @@ def citation_export(querier):
-        print(art.as_citation() + '\n')
+        print(art.as_citation())

then the Google API blocked me, but I saw this work once…

[SvennoNito]

I needed to apply both changes from issue #101,

tag = soup.find(name='form', attrs={'id': 'gs_settings_form'})
to
tag = soup.find(name='form', attrs={'id': 'gs_bdy_frm'})

and

print(art.as_citation() + '\n')
to
art.as_citation().decode("utf-8") + "\n"

Together with the fix from @EthanS94 it finally worked for me to use the --citation bt option :-)
Even though the output is not as nicely formatted as the example in the README.