This eLife API code performs the following:

• Read NLM 3.0 XML (tested for eLife XML) into a Python object named article
• Write an article to Fluidinfo
• Read from Fluidinfo data into an article object, when supplied a DOI

The quickstart below demonstrates how to use it.

Project discsussion is happening on Basecamp at https://basecamp.com/1860005/projects/520904-elifesciences-api

Beautiful soup, install via

$ pip install beautifulsoup4

lxml for robust xml parsing

$ pip install lxml

fom for using Fluidinfo Objects

$ pip install fom

Lettuce for testing.

$ pip install lettuce

1. Resave the settings-example.py file as settings.py
2. Create a Fluidinfo account.
3. Enter your Fluidinfo username and password into settings.py.
4. The namespace of elifesciences.org/api_v1 can remain if only using read-only access to eLife's Fluidinfo API, version 1. If you want to write to Fluidinfo, you will need to specify a Fluidinfo namespace for which you have write access.

The basic command-line loader load_article.py contains logic for basic input and output.

To parse XML and print out a JSON representation of an article object, using a sample XML file provided:

$ python load_article.py -i sample-xml/elife00013.xml -o article

Parsing XML alone does not require valid Fluidinfo account username and password in the settings file. More eLife XML files can be downloaded from the elife-articles Github repository.

To read Fluidinfo objects and print out a JSON representation of an article object, you must specify a valid DOI stored in Fluidinfo, for example:

$ python load_article.py -i fluidinfo -d "10.7554/eLife.00013" -o article

The namespace specified in the settings.py file will be the base namespace to search for eLife API schemas. The DOI is case-sensitive. It may take some time to find all associated Fluidinfo objects and assemble the results (10 to 15 seconds).

The necessary namespaces and tags to represent eLife API article data will be created automatically in your Fluidinfo namespace upon first using this procedure.

In the example below, parse XML and write data to Fluidinfo.

$ python load_article.py -i sample-xml/elife00013.xml -o fluidinfo

This will print details about the objects found or created as part of the process. For example, loading eLife00270.xml,

$ python load_article.py -i sample-xml/elife00270.xml -o fluidinfo
http://dx.doi.org/10.7554/eLife.00270
article UID: 0c0e0ea4-1530-441a-bb97-9d26ebf65647
http://dx.doi.org/10.7554/eLife.00270
author UID: 8d246784-5085-4187-bd5c-0aa2c6341948
author UID: 72679377-8c6c-4d5a-b597-0dd4f133948b
author UID: cbe5d2dd-f70e-46a4-a11c-72e25d7310e4
author UID: a40ecf2a-02f4-4df5-8b2c-f83096bf3e84

Please keep in mind, if your namespace is readable to all users, the tags you added will be attached to the live eLife API objects. To test this function using eLife XML, you may want to set your namespace as private.

The MIT License (MIT)