pyUSIrest 0.3.1

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

Python USI submission REST API

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

• Free software: GNU General Public License v3

• Documentation: https://pyusirest.readthedocs.io.

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:

  • Getting USI API root

  • Selecting a Team

  • Creating a Submission

  • Adding items to Submission

  • Checking Biosample Validation

  • Finalising a Submission

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