Feature Request
chackoge opened this issue · comments
Hello- when submitting a list of DOIs to content_negotiation as below, if one of the DOIs isn't found no data is returned and an error is returned. Is there a way to return 'doi not found' and process the rest of the data? Thanks
Python 3.8.2 (default, Nov 4 2020, 21:23:28)
habanero 0.7.4
from habanero import cn
print(testlist)
['10.1126/science.169.3946.635', '10.1162/qss_a_00007', '10.1126/science.169.3946.637'] # the third DOI doesn't exist
cn.content_negotiation(ids = kws[0:2],format='bibtex')
['@Article{Frank_1970,\n\tdoi = {10.1126/science.169.3946.635},\n\turl = {https://doi.org/10.1126%2Fscience.169.3946.635},\n\tyear = 1970,\n\tmonth = {aug},\n\tpublisher = {American Association for the Advancement of Science ({AAAS})},\n\tvolume = {169},\n\tnumber = {3946},\n\tpages = {635--641},\n\tauthor = {H. S. Frank},\n\ttitle = {The Structure of Ordinary Water: New data and interpretations are yielding new insights into this fascinating substance},\n\tjournal = {Science}\n}',
'@Article{Bradley_2020,\n\tdoi = {10.1162/qss_a_00007},\n\turl = {https://doi.org/10.1162%2Fqss_a_00007},\n\tyear = 2020,\n\tmonth = {feb},\n\tpublisher = {{MIT} Press - Journals},\n\tvolume = {1},\n\tnumber = {1},\n\tpages = {264--276},\n\tauthor = {James Bradley and Sitaram Devarakonda and Avon Davey and Dmitriy Korobskiy and Siyu Liu and Djamil Lakhdar-Hamina and Tandy Warnow and George Chacko},\n\ttitle = {Co-citations in context: Disciplinary heterogeneity is relevant},\n\tjournal = {Quantitative Science Studies}\n}']
cn.content_negotiation(ids = kws[0:3],format='bibtex')
HTTPError Traceback (most recent call last)
in
----> 1 cn.content_negotiation(ids = kws[0:3],format='bibtex')
/opt/anaconda3/lib/python3.8/site-packages/habanero/cn/cn.py in content_negotiation(ids, format, style, locale, url, **kwargs)
80 if url is None:
81 url = cn_base_url
---> 82 return CNRequest(url, ids, format, style, locale, **kwargs)
/opt/anaconda3/lib/python3.8/site-packages/habanero/cnrequest.py in CNRequest(url, ids, format, style, locale, **kwargs)
29 coll = []
30 for i in range(len(ids)):
---> 31 tt = make_request(url, ids[i], format, style, locale, **kwargs)
32 coll.append(tt)
33
/opt/anaconda3/lib/python3.8/site-packages/habanero/cnrequest.py in make_request(url, ids, format, style, locale, **kwargs)
52
53 # Raise an HTTPError if the status code of the response is 4XX or 5XX
---> 54 response.raise_for_status()
55
56 # set encoding
/opt/anaconda3/lib/python3.8/site-packages/requests/models.py in raise_for_status(self)
939
940 if http_error_msg:
--> 941 raise HTTPError(http_error_msg, response=self)
942
943 def close(self):
HTTPError: 404 Client Error: for url: https://doi.org/10.1126/science.169.3946.637
thanks for the issue @chackoge
see also #69
reinstall from here and try again, let me know if it works for you - updated docs here https://habanero.readthedocs.io/en/latest/modules/cn.html#module-habanero with info on warnings
Works great thank you very much. I like throwing an error when only a single DOI is provided. It's a great client.
Being new to Python I ran
pip install --force-reinstall habanero
a couple of times to no effect before realizing that I needed to run
pip install --force-reinstall git+git://github.com/sckott/habanero.git#egg=habanero
I did see #69 but since it related to works rather then cn, I wasn't sure whether to create a new request but eventually did.
Was just pinging the other issue as a note to myself so I don't forget about them covering the same topic.
I don't understand very well install from github for python, so I can't help much there - so glad that worked for you.