habanero
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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 <https://github.com/CrossRef/rest-api-doc>
__
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
routemembers
- /members
routeprefixes
- /prefixes
routefunders
- /funders
routejournals
- /journals
routetypes
- /types
routelicenses
- /licenses
routeregistration_agency
- get DOI minting agencyrandom_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 formatscsl_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
.. code-block:: console
pip (or pip3) install habanero
If you need to fix bibtex format citations using content negotiation use
.. code-block:: console
pip (or pip3) install habanero[bibtex]
Dev version
.. code-block:: console
pip install git+https://github.com/sckott/habanero.git#egg=habanero
Or build it yourself locally
.. code-block:: console
git clone https://github.com/sckott/habanero.git
cd habanero
make install
Usage
Initialize a client
.. code-block:: python
from habanero import Crossref
cr = Crossref()
Works route
.. code-block:: python
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
.. code-block:: python
ids here is the Crossref Member ID; 98 = Hindawi
cr.members(ids = 98, works = True)
Citation counts
.. code-block:: python
from habanero import counts
counts.citation_count(doi = "10.1016/j.fbr.2012.01.001")
Content negotiation - get citations in many formats
.. code-block:: python
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")
Meta
- Please note that this project is released with a
Contributor Code of Conduct <https://github.com/sckott/habanero/blob/main/CODE_OF_CONDUCT.md>
__. By participating in this project you agree to abide by its terms. - License: MIT; see
LICENSE file <https://github.com/sckott/habanero/blob/main/LICENSE>
__
.. |pypi| image:: https://badge.fury.io/py/habanero.svg
:target: https://badge.fury.io/py/habanero
.. |docs| image:: https://readthedocs.org/projects/habanero/badge/?version=latest
:target: http://habanero.rtfd.org/
.. |ghactions| image:: https://github.com/sckott/habanero/actions/workflows/python.yml/badge.svg?branch=main
:target: https://github.com/sckott/habanero/actions/workflows/python.yml
.. |coverage| image:: https://codecov.io/gh/sckott/habanero/branch/main/graph/badge.svg?token=6RrgNAuQmR
:target: https://codecov.io/gh/sckott/habanero
.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/psf/black
Changelog
1.2.6 (2024-02-01)
- mark two more tests for vcr to create cassettes for (both content_negotation tests) - no user facing changes (#114)
- habanero now conditionally uses bibtexparser to roundtrip bibtex to attempt to fix any bibtex that's not formatted correctly (#144) (#153)
- generalize handling of field queries like
query.publisher-name
to allow all field queries, and any in the future (#150) (#152) - improved error handling (#123)
ids
now a required param in the Crossref.prefixes method; improved crossef API error parsing (#116)
1.2.3 (2023-02-02)
- now using typehints, tested on Python back to 3.6; though could work with older Python 3 versions. See the new docs for better information on types (#70)
- fixed problem with usage of
warn=True
; in a for loop, an internal variable warning_thrown
wasn't being reset after each loop iteration, with the result that all objects returned after a warning was thrown were None
regardless of the actual result. sorry about that! (#112) (#113)
1.2.2 (2022-05-19)
- Fixed class
WorksContainer
to work with cursor output of works results (e.g., cr.works(query, cursor="*")
) (#106) thanks @IvanSterligov
1.2 (2022-03-27)
- Added class
WorksContainer
to make handling works data easier (#101) - changed master branch to main in github development repository (#103)
- exclude tests from install (#105)
1.0 (2021-11-12)
- fixes to docs/contributing.rst and package level docs for habanero (#89) (#90) thanks @Daniel-Mietchen !
- fix limit and offset internal handling for
request
and Request
(#91) thanks @Bubblbu ! content_negotation
throws warning now on 4xx/5xx status code to allow for bad DOIs alongside good DOIS (#92)- add example to README for querying
works
by DOI (#93) - fail better when json is not returned; try json.loads and catch ValueError (JSONDecodeError is a subclass of ValueError) (#97)
- funders, journals, members, prefixes, types and works gain
warn
parameter to optionally throw a warning instead of error if a DOI is not found - not found DOI with warn=True
returns None
(#69)
0.7.4 (2020-05-29)
query.title
filter is deprecated, use query.bibliographic
instead (#85)
0.7.2 (2019-12-12)
Crossref()
class gains ua_string
option to add an additional string to the user-agent sent with every request (#84)
0.7.0 (2019-11-08)
filter_names()
and filter_details()
altered to get metadata for works, members and funders filters; and added egs to members and funders methods for using filters (#67)- many typos fixed (#80) thanks @Radcliffe !
- use of a progress bar is now possible when fetching works route data, only when doing deep paging, see
progress_bar
parameter (#77) (#82) content_negotiation
fixes: ids
parameter is now required (has no default), and must be a str or list of str (#83)- no longer testing under Python 2
0.6.2 (2018-10-22)
- changelog was missing from the pypi distribution, fixed now (#71)
- fixed
Crossref.registration_agency()
method, borked it up on a previous change (#72) - set encoding on response text for
content_negotiation()
method to UTF-8 to fix encoding issues (#73) - fix
Crossref.filter_names()
method; no sort on dict_keys
(#76)
0.6.0 (2017-10-20)
- Added verification and docs for additional Crossref search filters (#62)
- Big improvement to docs on readthedocs (#59)
- Added
mailto
support (#68) (#63) and related added docs about polite pool (#66) - Added support for
select
parameter (#65) - Added all new
/works
route filters, and simplified filter option handling within library (#60)
0.5.0 (2017-07-20)
- Now using
vcrpy
to mock all unit tests (#54) - Can now set your own base URL for content negotation (#37)
- Some field queries with
works()
were failing, but now seem to be working, likely due to fixes in Crossref API (#53) - style input to
content_negotiation
was fixed (#57) (#58) thanks @talbertc-usgs - Fix to
content_negotiation
when inputting a DOI as a unicode string (#56)
0.3.0 (2017-05-21)
- Added more documentation for field queries, describing available fields that support field queries, and how to do field queries (#50)
sample
parameter maximum value is 100 - has been for a while, but wasn't updated in Crossref docs (#44)- Updated docs that
facet
parameter can be a string query in addition to a boolean (#49) - Documented new 10,000 max value for
/works
requests - that is, for the offset
parameter - if you need more results than that use cursor
(see https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md#deep-paging-with-cursors) (#47) - Added to docs a bit about rate limiting, their current values, that they can change, and how to show them in verbose curl responses (#45)
- Now using
https://doi.org
for cn.content_negotation
- and function gains new parameter url
to specify different base URLs for content negotiation (#36) - Fixes to kwargs and fix docs for what can be passed to kwargs (#41)
- Duplicated names passed to
filter
were not working - fixed now (#48) - Raise proper HTTP errors when appropriate for
cn.content_negotiation
thanks @jmaupetit (#55)
0.2.6 (2016-06-24)
0.2.2 (2016-03-09)
- fixed some example code that included non-working examples (#34)
- fixed bug in
registration_agency()
method, works now! (#35) - removed redundant
filter_names
and filter_details
bits in docs
0.2.0 (2016-02-10)
- user-agent strings now passed in every http request to Crossref, including a
X-USER-AGENT
header in case the User-Agent
string is lost (#33) - added a disclaimer to docs about what is actually searched when searching the Crossref API - that is, only what is returned in the API, so no full text or abstracts are searched (#32)
- improved http error parsing - now passes on the hopefully meaningful error messages from the Crossref API (#31)
- more tests added (#30)
- habanero now supports cursor for deep paging. note that cursor only works with requests to the
/works
route (#18)
0.1.3 (2015-12-02)
- Fix wheel file to be a universal to install on python2 and python3 (#25)
- Added method
csl_styles
to get CSL styles for use in content negotiation (#27) - More documentation for content negotiation (#26)
- Made note in docs that
sample
param ignored unless /works
used (#24) - Made note in docs that funders without IDs don't show up on the
/funders
route (#23)
0.1.1 (2015-11-17)
0.1.0 (2015-11-17)
- Now compatible with Python 2x and 3x
agency()
method changed to registration_agency()
- New method
citation_count()
- get citation counts for DOIs - New method
crosscite()
- get a citation for DOIs, only supports simple text format - New method
random_dois()
- get a random set of DOIs - Now importing
xml.dom
to do small amount of XML parsing - Changed library structure, now with module system, separated into modules for the main Crossref search API (i.e.,
api.crossref.org
) including higher level methods (e.g., registration_agency
), content negotiation, and citation counts.
0.0.6 (2015-11-09)