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LPSN-API - Programmatic Access to LPSN

Project description

LPSN API

Using the LPSN API requires registration. Registration is free but the usage of LPSN data is only permitted when in compliance with the LPSN copyright. See the LPSN copyright notice for details.

For questions, requests and comments regarding the LPSN API, please use the LPSN contact form.

Please register here.

The Python package can be initialized using your login credentials:

import lpsn

client = lpsn.LpsnClient('name@mail.example', 'password')

# the prepare method fetches all LPSN-IDs matching your query
# and returns the number of IDs found
count = client.search(taxon_name='Sulfolobus', correct_name='yes')
print(count, 'entries found.')

# the retrieve method lets you iterate over all results
# and returns the full entry as dict
# Entries can be further filtered using a list of keys (e.g. ['keywords'])
for entry in client.retrieve():
    print(entry)

Example queries:

You can use IDs to query LPSN as described here. Note that when using the parameter id, all other parameters are ignored.

# Search by LPSN-IDs (either semicolon separated or as list):
query = {"id": 520424}
query = {"id": "520424;4948;17724"}
query = {"id": [520424, 4948, 17724]}

# run query
client.search(**query)

Or you can use all the advanced search parameters that are described here.

Note that dashes (-) are replaced by underscores when used as python parameters.

# Example looking for validly published names of species in the genus Escherichia that have risk group 1:
client.search(taxon_name='Escherichia', category='species', riskgroup='1', validly_published='yes')

# The same example using a Python dictionary:
query = {
    'taxon-name': 'Escherichia', 
    'category': 'species',
    'riskgroup': '1',
    'validly-published': 'yes'
}
client.search(**query)

Filtering

Results from the retrieve Method of both clients can be further filtered. The result contains a list of matched keyword dicts:

result = client.retrieve(filter=["full_name", "lpsn_taxonomic_status"])
print({k:v for x in result for k,v in x.items()})

The printed result will look like this:

{782310: [{'full_name': 'Sulfolobus acidocaldarius'},
          {'lpsn_taxonomic_status': 'correct name'}],
 782311: [{'full_name': 'Sulfolobus brierleyi'},
          {'lpsn_taxonomic_status': 'synonym'}],
 782312: [{'full_name': 'Sulfolobus hakonensis'},
          {'lpsn_taxonomic_status': 'synonym'}],
 782313: [{'full_name': 'Sulfolobus metallicus'},
          {'lpsn_taxonomic_status': 'synonym'}],
...

Known issues

This package depends on python-keycloak for authorization and login handling. However, python-keycloak seems to have issues with older versions of requests and urllib3. See the related issue on github. This might lead to the following error when trying to access the API:

AttributeError: 'Retry' object has no attribute 'allowed_methods'

You might be able to resolve this issue by updating the mentioned libraries, e.g. via pip:

pip install requests>=2.25.1 urllib3>=1.26.5

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