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Images (0, 2017-09-06)
Images\code-architecture.jpg (437070, 2017-09-06)
Images\people.png (12208, 2017-09-06)
batch-web-of-science-to-bibtex.py (9968, 2017-09-06)
out.bib (10330, 2017-09-06)
people.csv (150, 2017-09-06)
wos.shelf (45056, 2017-09-06)

# Batch download bibliographies from "Web Of Science" and save as BibTeX Table of Contents: - [Summary](https://github.com/justinpearson/Batch-Web-Of-Science-To-Bibtex/blob/master/#summary) - [Notes](https://github.com/justinpearson/Batch-Web-Of-Science-To-Bibtex/blob/master/#notes) - [How to use](https://github.com/justinpearson/Batch-Web-Of-Science-To-Bibtex/blob/master/#how-to-use) - [Code architecture](https://github.com/justinpearson/Batch-Web-Of-Science-To-Bibtex/blob/master/#code-architecture) ## Summary - Input: CSV file with columns "First name" & "Last name". - Output: `.bib` file of BibTeX entries for publications of the people listed in the CSV file. - Caches retrieved files to a [shelve](https://github.com/justinpearson/Batch-Web-Of-Science-To-Bibtex/blob/master/https://docs.python.org/2/library/shelve.html) database. - Doesn't retreive an author's publications if the cache has more than the Web of Science. ## Notes - Tested on Python 2.7. - Requires the `wos-lite` branch of the `wos` package from enricobacis ([source](https://github.com/justinpearson/Batch-Web-Of-Science-To-Bibtex/blob/master/https://github.com/enricobacis/wos)): git clone https://github.com/enricobacis/wos.git git checkout wos-lite python setup.py install - NOTE: The version installed by `pip install wos` didn't work for me; I specifically needed the `wos-lite` branch. - Requires a "Lite" or "Premium" subscription to the [Web of Science "Web Services"](https://github.com/justinpearson/Batch-Web-Of-Science-To-Bibtex/blob/master/http://ipscience-help.thomsonreuters.com/wosWebServicesLite/WebServicesLiteOverviewGroup/Introduction.html), currently owned by Clarivate Analytics. - This is not the same as signing up for a free account on webofknowledge.com. Rather, your school or work probably has to pay for API access. If you work at UC Santa Barbara, talk to Shari Laster (slaster@ucsb.edu). - I hard-coded the use of Lite. - Currently only conference papers & journal articles are exported to BibTeX. - It's a pain to map between [all the WoS doctypes](https://github.com/justinpearson/Batch-Web-Of-Science-To-Bibtex/blob/master/http://ipscience-help.thomsonreuters.com/inCites2Live/indicatorsGroup/aboutHandbook/appendix/documentTypes.html) and [all the BibTeX entry types](https://github.com/justinpearson/Batch-Web-Of-Science-To-Bibtex/blob/master/http://bib-it.sourceforge.net/help/fieldsAndEntryTypes.php). ## How to use The CSV file `people.csv` is provided:  Execute at terminal (Python 2.7): $ python batch-web-of-science-to-bibtex.py \ --user= \ --password= \ --input='people.csv' \ --output='out.bib' \ --cache='wos.shelf' Prints out: CSV line 1, Query: AU=Mayhew C* AND AD=Santa Barbara Have 0 biblios locally already in shelf file wos.shelf 22 biblios available online. Request 1 of 1: Retrieving results 1 -- 22... Attempt # 1... cli.search success! Parsing 22 records... CSV line 2, Query: AU=Danzl P* AND AD=Santa Barbara Have 0 biblios locally already in shelf file wos.shelf 8 biblios available online. Request 1 of 1: Retrieving results 1 -- 8... Attempt # 1... cli.search success! Parsing 8 records... CSV line 3, Query: AU=Obermeyer K* AND AD=Santa Barbara Have 0 biblios locally already in shelf file wos.shelf 4 biblios available online. Request 1 of 1: Retrieving results 1 -- 4... Attempt # 1... cli.search success! Parsing 4 records... All done! Produces bibtex file `out.bib`: @inproceedings{WOS:000336893605113, author={Mayhew, Christopher G. and Park, Sungbae and Ahmed, Jasim and Chaturvedi, Nalin A. and Kojic, Aleksandar and Knierim, Karl Lukas}, title={Reduced-order modeling for studying and controlling misfire in four-stroke HCCI engines}, booktitle={IEEE Conference on Decision and Control}, year={2009}, pages={5194-5199}, organization={IEEE}, } @inproceedings{WOS:000295049104123, author={Teel, Andrew R. and Mayhew, Christopher G.}, title={Hybrid Control of Spherical Orientation}, booktitle={IEEE Conference on Decision and Control}, year={2010}, pages={41***-4203}, organization={IEEE}, } ... Caches the results to [shelve](https://github.com/justinpearson/Batch-Web-Of-Science-To-Bibtex/blob/master/https://docs.python.org/2/library/shelve.html) file `wos.shelf`: ```python import shelve db = shelve.open('wos.shelf') db.keys() ['AU=Danzl P* AND AD=Santa Barbara', 'AU=Mayhew C* AND AD=Santa Barbara', 'AU=Obermeyer K* AND AD=Santa Barbara'] len(db['AU=Mayhew C* AND AD=Santa Barbara']) 22 import pprint pprint.pprint( db['AU=Mayhew C* AND AD=Santa Barbara'][0] ) {u'Authors': u'Mayhew, Christopher G. and Park, Sungbae and Ahmed, Jasim and Chaturvedi, Nalin A. and Kojic, Aleksandar and Knierim, Karl Lukas', u'BookGroupAuthors': u'IEEE', u'BookSeriesTitle': u'IEEE Conference on Decision and Control', u'Doctype': u'Proceedings Paper', u'Identifier.Eisbn': u'978-1-4244-3872-3', u'Identifier.Ids': u'BA5OA', u'Identifier.Issn': u'0743-1546', u'Identifier.Xref_Doi': u'10.1109/CDC.2009.5400597', u'Pages': u'5194-5199', u'Published.BiblioYear': u'2009', u'ResearcherID.Disclaimer': u'ResearcherID data provided by Clarivate Analytics', u'SourceTitle': u'PROCEEDINGS OF THE 48TH IEEE CONFERENCE ON DECISION AND CONTROL, 2009 HELD JOINTLY WITH THE 2009 28TH CHINESE CONTROL CONFERENCE (CDC/CCC 2009)', u'Title': u'Reduced-order modeling for studying and controlling misfire in four-stroke HCCI engines', 'uid': u'WOS:000336893605113'} ``` ## Code architecture  1. `wos_login()` logs in to WoS. 2. `get_queries()` reads the CSV file `people.csv` and returns a sequence of query strings. 3. For each query, `robust_search()` searches the Web of Science for it. - If the WoS SOAP server returns an error, `robust_search()` waits 1 second then tries again. - The flag `raw=True` requests an XML response instead of a `suds.sudsobject.searchResults` object (simpler to parse). 4. `xml_to_dicts()` takes this XML and uses [BeautifulSoup](https://github.com/justinpearson/Batch-Web-Of-Science-To-Bibtex/blob/master/https://www.crummy.com/software/BeautifulSoup/) to parse the XML into a list of dictionaries, each one storing a bibliography of some conference paper or journal article. 5. For each dictionary, `dict_to_bibtex()` converts it to a BibTeX entry and writes it to `out.bib`. 6. The dicts are also written to the shelf file `wos.shelf` for caching. - The shelf file is a dictionary: keys are queries, and values are lists of dictionaries (bibliographies) returned by WoS for that query. - A query is only sent to WoS if WoS has more results than exist in the shelf file for that query.

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