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Python USI submission REST API contain all methods to interact with EMBL-EBI Unified Submissions Interface

Project description

Python USI submission REST API

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Python USI submission REST API contain all methods to interact with EMBL-EBI Unified Submissions Interface

Features

  • Deal with EBI AAP (Authentication, Authorisation and Profile) service, generating tokens and dealing with User and Groups
  • Interact with EBI USI (Unified Submission Interface) in order to submit data to biosample as described by this guide. In details:

API Endpoints

pyUSIrest is written to exploit the BioSamples test environment endpoints. You are incuraged to understand how BioSamples submission works before do a real submission in BioSamples production servers. You can find more information on how to do a real submission in BioSamples production servers in readthedocs documentation: https://pyusirest.readthedocs.io

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

TODO

  • get a Team instance from Submission instance
  • Submission.has_errors make two identical queries, on to determine the status and one to search errors, simplify it by doing only a query
  • filtering sample by status or error make a lot of queries. Consider writing coroutines or reading ValidationResult as pages

0.3.1 (2020-01-27)

  • fix a bug when patching a sample: deal with team in relationship
  • raise USIDataError on 40x status code
  • Change Auth.__str__(): now it returns Token for Foo Bar will expire in HH:MM:SS
  • add Auth.get_domains which returns self.claims['domains']

0.3.0 (2020-01-14)

Features

  • modelled custom exceptions
  • Set a default date if releaseDate attribute is missing
  • improved documentation by describing how to sort and filter objects
  • fix bug when adding samples to a submission retrieved with team.get_submission()
  • Update documentation. Set taxon in sample data (mandatory attribute)
  • displaying dates when print(Submission) instances
  • Root.get_user_submissions() and other methods which returned list of objects now return iterator objects
  • str(auth) will report duration in hh:mm:ss
  • compiling PDF using PNG images (change badges)
  • raise no exceptions where no team is found (using Root.get_user_teams)
  • Using namespaces to configure API endpoints (pyUSIrest.settings)
  • move Root, User, Domain, Team, Submission, Sample ValidationResult classes inside pyUSIrest.usi module

0.2.2 (2019-03-28)

Features

  • Deal with API errors (50x, 40x)

0.2.1 (2019-01-15)

Features

  • test for an empty submission (no samples)
  • updated root.json, userSubmission.json test data
  • submissionStatus is no longer an attribute, when feching submission by name is present when getting user submissions
  • follow submissionStatus link (if necessary)
  • update submission status after create a new submission
  • update submission status after get_submission_by_name
  • update submission status after reload a just finalized submission
  • Domain.users returns User objects in a list
  • improved Submission.get_samples method

0.2.0 (2018-10-23)

Features

  • Fetch submission by name
  • changed library name to pyUSIrest
  • published to pypi
  • Finalize submission with PUT

0.1.0 (2018-10-17)

Features

  • submit into biosample with python methods

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