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client for Crossref search API

Home Page: https://habanero.readthedocs.io

License: MIT License

Python 99.42% Makefile 0.58%

crossref-api api doi metadata

habanero's Introduction

habanero

This is a low level client for working with Crossref's search API. It's been named to be more generic, as other organizations are/will adopt Crossref's search API, making it possible to interact with all from one client.

Crossref API docs

Other Crossref API clients:

Ruby: serrano, https://github.com/sckott/serrano

Crossref's API issue tracker: https://gitlab.com/crossref/issues

habanero includes three modules you can import as needed (or import all):

Crossref - Crossref search API. The Crossref module includes methods matching Crossref API routes, and a few convenience methods for getting DOI agency and random DOIs:

works - /works route
members - /members route
prefixes - /prefixes route
funders - /funders route
journals - /journals route
types - /types route
licenses - /licenses route
registration_agency - get DOI minting agency
random_dois - get random set of DOIs

counts - citation counts. Includes the single citation_count method

cn - content negotiation. Includes the methods:

content_negotiation - get citations in a variety of formats
csl_styles - get CSL styles, used in content_negotation method

WorksContainer - A class for handling Crossref works. Pass output of works from methods on the Crossref class to more easily extract specific fields of works.

Note about searching:

You are using the Crossref search API described at https://api.crossref.org/swagger-ui/index.html. When you search with query terms, on Crossref servers they are not searching full text, or even abstracts of articles, but only what is available in the data that is returned to you. That is, they search article titles, authors, etc. For some discussion on this, see https://gitlab.com/crossref/issues/-/issues/101

Rate limits

See the headers X-Rate-Limit-Limit and X-Rate-Limit-Interval for current rate limits.

The Polite Pool

To get in the polite pool it's a good idea now to include a mailto email address. See docs for more information.

Installation

Stable version

pip (or pip3) install habanero

If you need to fix bibtex format citations using content negotiation use

pip (or pip3) install habanero[bibtex]

Dev version

pip install git+https://github.com/sckott/habanero.git#egg=habanero

Or build it yourself locally

git clone https://github.com/sckott/habanero.git
cd habanero
make install

Usage

Initialize a client

from habanero import Crossref
cr = Crossref()

Works route

# query
x = cr.works(query = "ecology")
x['message']
x['message']['total-results']
x['message']['items']

# fetch data by DOI
cr.works(ids = '10.1371/journal.pone.0033693')

Members route

# ids here is the Crossref Member ID; 98 = Hindawi
cr.members(ids = 98, works = True)

Citation counts

from habanero import counts
counts.citation_count(doi = "10.1016/j.fbr.2012.01.001")

Content negotiation - get citations in many formats

from habanero import cn
cn.content_negotiation(ids = '10.1126/science.169.3946.635')
cn.content_negotiation(ids = '10.1126/science.169.3946.635', format = "citeproc-json")
cn.content_negotiation(ids = "10.1126/science.169.3946.635", format = "rdf-xml")
cn.content_negotiation(ids = "10.1126/science.169.3946.635", format = "text")
cn.content_negotiation(ids = "10.1126/science.169.3946.635", format = "text", style = "apa")
cn.content_negotiation(ids = "10.1126/science.169.3946.635", format = "bibentry")

habanero's People

Contributors

Stargazers

Watchers

habanero's Issues

new 10K limit for /works

CrossRef/rest-api-doc@d8030c7?w=1

old code in some examples, clean out

filter, may not be working for duplicate filter names

make sure this works

Fix request method to work on length ids > 1

Add user agent string for habanero and ver. in requests

Allow users to set base url for content negotation

via #36

Parse http errors, to give back meaningful error messages

e.g., cr.journals(ids = "2167-8359", works = False, filter = {'from_pub_date': '2014-03-03'}) gives

HTTPError: 400 Client Error: Bad Request for url: http://api.crossref.org/journals/2167-8359?filter=from-pub-date%3A2014-03-03

But actual error is

{
  status: "failed",
  message-type: "validation-failure",
  message: [
    {
            type: "parameter-not-allowed",
            value: "filter",
            message: "This route does not support filter"
        }
    ]
}

style not functioning/not getting passed to request

I can't seem to get different citation styles to work. I think I've tracked the problem down to:
https://github.com/sckott/habanero/blob/master/habanero/cnrequest.py#L46

if I copy/duplicate the lines:
https://github.com/sckott/habanero/blob/master/habanero/cnrequest.py#L39-L40
after that line it starts working for me.

Environment: Windows 64, Python 3.4, habanero installed from: https://anaconda.org/conda-forge/habanero

I can submit a pull request if you think it worthwhile

bug in registration agency method

Add method to get CSL styles for help with whats available

Setup codecov

Maybe give user option of how to respond to errors in crossref API

document new throttling rate limit

10 requests per second per IP

gives 429 response

Fill out test suite

Add disclaimer to docs that full text/abstracts aren't searched

Point to CrossRef/rest-api-doc#101

Add remainder of paths

only works and members done now

date conversion helper

convert_crossref_date = Using the date probably important, but we need to make users convert separately, and not doing by default internally

Method to extract full text links

Possibly use module package architecture instead of classes

might be simpler, like did for pygbif

Add egs of how to process output

Filter info method

like sckott/serrano#10

DOIs for works

I want to get meta data from a known DOI. The URL is:
http://api.crossref.org/works/10.1109/MWC.2007.358967

My code is:

from habanero import Crossref

cr = Crossref()
cr.works(ids="10.1109/MWC.2007.358967")

But habanero is requesting the very unspecific url:
http://api.crossref.org/works/
I looked it up in the file request_class.py in the class function Request._url().
I'm just starting with habanero, so perhaps it's just me ...

~$ pip3 install habanero 

Collecting habanero
  Downloading habanero-0.1.1.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 20, in <module>
      File "/private/var/folders/gs/4khph0xs0436gmd2gdnwsg080000gn/T/pip-build-cjtn36i_/habanero/setup.py", line 8, in <module>
        with codecs.open('Changelog.rst', 'r', 'utf-8') as f:
      File "/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/codecs.py", line 891, in open
        file = builtins.open(filename, mode, buffering)
    FileNotFoundError: [Errno 2] No such file or directory: 'Changelog.rst'

weird that it errors on a changelog file not found, but I must have done something wrong there.

note: pip install habanero works fine for python2

import habanero
cr = habanero.Crossref()
print 'Title 1:'
title = 'On the use of fittin'
x = cr.works(query_title = title)
print len(x['message']['items'])
print 'Title 2:'
title = 'On the use of fitting'
x = cr.works(query_title = title)
print len(x['message']['items'])

The search for Title 1 works but the search for Title 2 fails with KeyError: 'content-type'

Try pytest for tests?

http://pytest.org/latest/