Welcome to Python USI submission REST API’s documentation!¶
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.
Installation¶
Stable release¶
To install Python USI submission REST API, run this command in your terminal:
$ pip install pyUSIrest
This is the preferred method to install Python USI submission REST API, as it will always install the most recent stable release.
If you don’t have pip installed, this Python installation guide can guide you through the process.
From sources¶
The sources for Python USI submission REST API can be downloaded from the Github repo.
You can either clone the public repository:
$ git clone git://github.com/cnr-ibba/pyUSIrest
Or download the tarball:
$ curl -OJL https://github.com/cnr-ibba/pyUSIrest/tarball/master
Once you have a copy of the source, you can install it with:
$ python setup.py install
Usage¶
To use Python USI submission REST API in a project, you should import
Root and Auth
in order to interact with USI endpoint ad EBI AAP:
from pyUSIrest.auth import Auth
from pyUSIrest.usi import Root
Warning
Using the BioSamples production endpoints: pyUSIrest is written in order to explot the BioSamples testing environment. You are incuraged to understand the whole process of data submission in the test environment. In order to do a real submission, you have to override the submission endpoints after importing modules before modifying submission objects:
pyUSIrest.settings.AUTH_URL = "https://api.aai.ebi.ac.uk"
pyUSIrest.settings.ROOT_URL = "https://submission.ebi.ac.uk"
Creating an Auth object¶
With an Auth object, you’re able to generate a
AAP token from EBI and use it in browsing USI endpoint. You can instantiate a
new Auth providing your AAP username and password:
auth = Auth(user=<usi_username>, password=<usi_password>)
Alternatively you can create an Auth object
starting from a valid token:
auth = Auth(token=<token_string>)
Creating an USI User¶
In order to create a new USI user, with pyUSIrest you can use the method
create_user of the
User class:
from pyUSIrest.usi import User
user_id = User.create_user(
user=<new_usi_username>,
password=<new_password>,
confirmPwd=<new_password>,
email=<your_email>,
full_name=<your full name>,
organization=<your_organization
)
Creating a Team¶
To create a team, you will need to create a new User
from a valid Auth object, then you could create
a team using the create_team method:
from pyUSIrest.usi import User
user = User(auth)
team = user.create_team(description="Your description")
Warning
remember to ri-generate the token in order to see the new generated team using
pyUSIrest objects
Add Profile to Domain¶
Warning
You don’t need to do this with a new generated user. You should use this method only if you experience problems when creating a submission.
To create a profile for a team:
domain = user.get_domain_by_name(<team name>)
domain.create_profile(attributes={"centre name": "My Institution"})
For more informations, take a look to creating a domain profile
Adding User to Team¶
To add a user to a team, you need to provide a user_id, like the one
obtained by creating a user, or by calling get_my_id
from a User instance:
user = User(auth)
user_id = user.get_my_id()
Next, you need to find out the domain reference of a team using a team name and
get_domain_by_name method:
domain = user.get_domain_by_name(team.name)
domain_id = domain.domainReference
To add user to a team call add_user_to_team:
user.add_user_to_team(user_id=user_id, domain_id=domain_id)
Create a Submission¶
From a valid Root object, get the
Team object providing the team_name in which the
submission will be created. Then create a new Submission
using the create_submission method:
team = root.get_team_by_name(<your team name>)
submission = team.create_submission()
If you got a ConnectionError exception during last command, you need to add
a profile to your domain as described in add profile to domain.
Add Samples to a Submission¶
In order to add sample to a submission, define a dict for sample data,
then add them using create_sample.
In the following example, a test animal and a sample from that animal are created:
# define data as dictionaries. Ensure that mandatory keys
# are provided or biosample will throw an error
animal_data = {
'alias': 'animal_1',
'title': 'A Sample Organism',
'releaseDate': '2018-06-19',
'taxonId': 9940,
'taxon': 'Ovis aries',
'attributes': {'material': [{'value': 'organism',
'terms': [{'url': 'http://purl.obolibrary.org/obo/OBI_0100026'}]}],
'project': [{'value': 'A Sample Project'}]},
'sampleRelationships': []}
# add this animal to submission
sample = submission.create_sample(animal_data)
# Now generate a sample derived from the previous one.
# This link is provided by sampleRelationships key
sample_data = {'alias': 'sample_1',
'title': 'A Sample Speciemen',
'releaseDate': '2018-06-19',
'taxonId': 9940,
'taxon': 'Ovis aries',
'description': 'A Useful Description',
'attributes': {'material': [{'value': 'specimen from organism',
'terms': [{'url': 'http://purl.obolibrary.org/obo/OBI_0001479'}]}],
'project': [{'value': 'A Sample Project'}]},
'sampleRelationships': [{'alias': 'animal_1',
'relationshipNature': 'derived from'}]}
# add this sample to the submission
sample = submission.create_sample(sample_data)
Check and finalize a Submission¶
Querying for biosample validation status¶
After submitting all data, before finalize a submission, you need to ensure that
all the validation steps performed by USI are done with success. You can query
status with get_status:
status = submission.get_status()
print(status) # Counter({'Complete': 2})
status will be a collections.Counter object. In order to finalize a
submission to biosample, get_status
need to return only Complete as status (not Pending), with a number equal
to the number of samples attached to submission
Checking errors¶
Another method to check submission status before finalizing it is to check for errors
with has_errors method:
errors = submission.has_errors()
print(errors) # Counter({False: 1, True: 1})
If there is any True in this collections.Counter object,
submission has errors and can’t be finalized. You will need to search
for sample with errors in order to remove or update it. Only when this function
return False with a number equal to the number of attached samples, a
submission can be finalized.
Finalize a Submission¶
After managing sample and validation statuses, if everything is ok you can finalize
your submission with finalize:
submission.finalize()
After finalization, you can’t add more data to this submission. You may want to reload your data in order to retrieve the biosample ids, as described by get samples from a submission.
Fetch a submission by name¶
In order to get a submission by name, call get_submission_by_name
from a valid Root object:
root = Root(auth=auth)
submission = root.get_submission_by_name(
'c3a7e663-3a37-48d3-a041-8c18088e3185')
Get Sample from a submission¶
In order to get all samples for a submission, you can call the method
get_samples
on a Submission object:
samples = submission.get_samples()
You can also filter out samples by validationResult or if the have errors or not.
For a list of validationResult, check the output of get_status:
# fetching pending samples
samples_pending = submission.get_samples(validationResult='Pending')
# get samples with errors
samples_error = submission.get_samples(has_errors=True)
Advanced Usage¶
The Python USI submission REST API could be used to manage multiple submissions and samples in the same time. Most of its functions returns iterator objects, in such way some time consiming tasks can be executed lazily and can be filtered and sorted using the appropriate methods. Here there are described some useful tips useful to manage user submission data
Retrieving Submission Objects¶
You could retrieve all submission objects from Root
using get_user_submissions: such
method returns an iterator object:
from pyUSIrest.auth import Auth
from pyUSIrest.usi import Root
auth = Auth(user=<usi_username>, password=<usi_password>)
root = Root(auth)
for submission in root.get_user_submissions():
print(submission)
Submission objects could be also filtered
by status or by team name:
for submission in root.get_user_submissions(status="Draft", team='subs.test-team-19'):
print(submission)
Submission could be sorted using attributes, as described in Sorting HOW TO:
from operator import attrgetter
for submission in sorted(root.get_user_submissions(), key=attrgetter('lastModifiedDate'), reverse=True):
print(submission)
In a similar way, submission could be filtered reling their attributes, for example you can retrieve the recent modified submissions in a similar way:
from datetime import datetime, timezone
from dateutil.relativedelta import relativedelta
recent_submission = lambda submission: submission.lastModifiedDate + relativedelta(months=+1) > datetime.now(timezone.utc)
for submission in filter(recent_submission, root.get_user_submissions()):
print(submission)
Submission could be derived also from get_submissions
from a Team instance. In this case, the submission will
be filtered accordingly to the team, and can be filtered or sorted in the same
way as described before:
team = root.get_team_by_name('subs.test-team-19')
for submission in team.get_submissions():
print(submission)
Working with samples¶
The get_samples method from
Submission returns an iterator of
Sample instances, and so can be filtered in
a similar way as Submission instances:
submission = root.get_submission_by_name('40549619-7797-4672-b703-93a72c3f984a')
# get all samples in 'Pending' validation status
for sample in submission.get_samples(status="Pending"):
print(sample)
# get all samples with errors in USI validation
for sample in submission.get_samples(has_errors=True):
print(sample)
# returning samples with errors in other checks than Ena
for sample in submission.get_samples(has_errors=True, ignorelist=['Ena'])
print(sample)
You can also filter a Sample by an attribute,
like you can do with Submission objects,
for example you can retrieve a sample in a submission by title:
for sample in filter(lambda sample: sample.title == 'SampleTitle', submission.get_samples()):
print(sample)
pyUSIrest¶
pyUSIrest package¶
Submodules¶
pyUSIrest.auth module¶
Created on Thu May 24 15:46:37 2018
@author: Paolo Cozzi <cozzi@ibba.cnr.it>
-
class
pyUSIrest.auth.Auth(user=None, password=None, token=None)[source]¶ Bases:
objectDeal with EBI AAP tokens. Starts from a token object or by providing user credentials. It parse token and provide methods like checking expiration times.
-
expire¶ when token expires
Type: datetime.datetime
-
issued¶ when token was requested
Type: datetime.datetime
-
header¶ token header read by python_jwt.process_jwt
Type: dict
-
claims¶ token claims read by python_jwt.process_jwt
Type: dict
-
__init__(user=None, password=None, token=None)[source]¶ Instantiate a new python EBI AAP Object. You can generate a new object providing both user and password, or by passing a valid token string
Parameters:
-
auth_url= None
-
get_domains()[source]¶ Returns a list of domain managed by this object
Returns: a list of managed domains Return type: list
-
get_duration()[source]¶ Get token remaining time before expiration
Returns: remaining time as timedeltaobjectReturn type: datetime.timedelta
-
is_expired()[source]¶ Return True if token is exipired, False otherwise
Returns: True if token is exipired Return type: bool
-
token¶ Get/Set token as a string
-
pyUSIrest.client module¶
Created on Thu Dec 19 16:28:46 2019
@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>
-
class
pyUSIrest.client.Client(auth)[source]¶ Bases:
objectA class to deal with EBI submission API. It perform request modelling user token in request headers. You need to call this class after instantiating an
Authobject:import getpass from pyUSIrest.auth import Auth from pyUSIrest.client import Client auth = Auth(user=<you_aap_user>, password=getpass.getpass()) client = Client(auth) response = client.get("https://submission-test.ebi.ac.uk/api/")
-
last_response¶ last response object read by this class
Type: requests.Response
-
session¶ a session object
Type: request.Session
-
auth Get/Set
Authobject
-
check_headers(headers=None)[source]¶ Checking headers and token
Parameters: headers (dict) – custom header for request Returns: an update headers tocken Return type: headers (dict)
-
check_status(response, expected_status=200)[source]¶ Check response status. See HTTP status codes
Parameters: - response (requests.Reponse) – the reponse returned by requests
- method –
-
delete(url, headers={}, params={})[source]¶ Generic DELETE method
Parameters: Returns: a response object
Return type:
-
get(url, headers={}, params={})[source]¶ Generic GET method
Parameters: Returns: a response object
Return type:
-
headers= {'Accept': 'application/hal+json', 'User-Agent': 'pyUSIrest 0.3.1'}
-
patch(url, payload={}, headers={}, params={})[source]¶ Generic PATCH method
Parameters: Returns: a response object
Return type:
-
-
class
pyUSIrest.client.Document(auth=None, data=None)[source]¶ Bases:
pyUSIrest.client.ClientBase class for pyUSIrest classes. It models common methods and attributes by calling
Clientand reading json response from biosample API-
data¶ data from USI read with
response.json()Type: dict
-
__init__(auth=None, data=None)[source]¶ Instantiate the class
Parameters: auth (Auth) – a valid Authobject
-
classmethod
clean_url(url)[source]¶ Remove stuff like
{?projection}from urlParameters: url (str) – a string url Returns: the cleaned url Return type: str
-
follow_self_url()[source]¶ Follow self url and update class attributes. For instance:
document.follow_self_url()
will reload document instance by requesting with
Client.get()usingdocument.data['_links']['self']['href']as url
-
follow_tag(tag, force_keys=True)[source]¶ Pick a url from data attribute relying on tag, perform a request and returns a document object. For instance:
document.follow_tag('userSubmissions')
will return a document instance by requesting with
Client.get()usingdocument._links['userSubmissions']['href']as urlParameters: Returns: a document object
Return type:
-
get(url, force_keys=True)[source]¶ Override the Client.get method and read data into object:
document = Document(auth) document.get(settings.ROOT_URL + "/api/")
Parameters: Returns: a response object
Return type:
-
paginate()[source]¶ Follow all the pages. Return an iterator of document objects
Parameters: response (requests.Response) – a response object Yields: Document – a new Document instance
-
read_data(data, force_keys=False)[source]¶ Read data from a dictionary object and set class attributes
Parameters: - data (dict) – a data dictionary object read with
response.json() - force_keys (bool) – If True, define a new class attribute from data keys
- data (dict) – a data dictionary object read with
-
pyUSIrest.exceptions module¶
Created on Fri Jan 10 16:44:49 2020
@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>
-
exception
pyUSIrest.exceptions.NotReadyError[source]¶ Bases:
RuntimeErrorRaised when doing stuff on not ready data (ex finalizing a Submission after validation)
-
exception
pyUSIrest.exceptions.TokenExpiredError[source]¶ Bases:
RuntimeErrorRaised when token expires while using pyUSIrest
-
exception
pyUSIrest.exceptions.USIConnectionError[source]¶ Bases:
ConnectionErrorDeal with connection issues with API
pyUSIrest.settings module¶
Created on Mon Nov 18 11:47:42 2019
@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>
pyUSIrest.usi module¶
Created on Thu May 24 16:41:31 2018
@author: Paolo Cozzi <cozzi@ibba.cnr.it>
-
class
pyUSIrest.usi.Domain(auth, data=None)[source]¶ Bases:
pyUSIrest.client.DocumentA class to deal with AAP domain objects
-
data¶ data (dict): data from AAP read with
response.json()Type: dict
-
create_profile(attributes={})[source]¶ Create a profile for this domain
Parameters: attributes (dict) – a dictionary of attributes
-
users¶ Get users belonging to this domain
-
-
class
pyUSIrest.usi.Root(auth)[source]¶ Bases:
pyUSIrest.client.DocumentModels the USI API Root endpoint
-
api_root= None
-
get_submission_by_name(submission_name)[source]¶ Got a specific submission object by providing its name
Parameters: submission_name (str) – input submission name Returns: The desidered submission as instance Return type: Submission
-
get_team_by_name(team_name)[source]¶ Get a
Teamobject by nameParameters: team_name (str) – the name of the team Returns: a team object Return type: Team
-
get_user_submissions(status=None, team=None)[source]¶ Follow the userSubmission url and returns all submission owned by the user
Parameters: Returns: A list of
SubmissionobjectsReturn type:
-
-
class
pyUSIrest.usi.Sample(auth, data=None)[source]¶ Bases:
pyUSIrest.usi.TeamMixin,pyUSIrest.client.DocumentA class to deal with USI Samples
-
get_validation_result()[source]¶ Return validation results for submission
Returns: the ValidationResultof this sampleReturn type: ValidationResult
-
has_errors(ignorelist=[])[source]¶ Return True if validation results throw an error
Parameters: ignorelist (list) – ignore errors in these databanks Returns: True if sample has an errors in one or more databank Return type: bool
-
patch(sample_data)[source]¶ Update sample by patching data with
Client.patch()Parameters: sample_data (dict) – sample data to update
-
read_data(data, force_keys=False)[source]¶ Read data from a dictionary object and set class attributes
Parameters: - data (dict) – a data dictionary object read with
response.json() - force_keys (bool) – If True, define a new class attribute from data keys
- data (dict) – a data dictionary object read with
-
-
class
pyUSIrest.usi.Submission(auth, data=None)[source]¶ Bases:
pyUSIrest.usi.TeamMixin,pyUSIrest.client.DocumentA class to deal with USI Submissions
-
check_ready()[source]¶ Test if a submission can be submitted or not (Must have completed validation processes)
Returns: True if ready for submission Return type: bool
-
create_sample(sample_data)[source]¶ Create a sample from a dictionary
Parameters: sample_data (dict) – a dictionary of data Returns: a SampleobjectReturn type: Sample
-
finalize(ignorelist=[])[source]¶ Finalize a submission to insert data into biosample
Parameters: ignorelist (list) – ignore samples with errors in these databanks Returns: output of finalize submission as a DocumentobjectReturn type: Document
-
get_samples(status=None, has_errors=None, ignorelist=[])[source]¶ Returning all samples as a list. Can filter by errors and error types:
# returning samples with errors in other checks than Ena submission.get_samples(has_errors=True, ignorelist=['Ena']) # returning samples which validation is still in progress submission.get_samples(status='Pending')
Get all sample with errors in other fields than Ena databank
Parameters: Yields: Sample – a
Sampleobject
-
get_status()[source]¶ Count validation statues for submission
Returns: A counter object for different validation status Return type: collections.Counter
-
get_validation_results()[source]¶ Return validation results for submission
Yields: ValidationResult – a ValidationResultobject
-
has_errors(ignorelist=[])[source]¶ Count sample errors for a submission
Parameters: ignorelist (list) – ignore samples with errors in these databanks Returns: A counter object for samples with errors and with no errors Return type: collections.Counter
-
read_data(data, force_keys=False)[source]¶ Read data from a dictionary object and set class attributes
Parameters: - data (dict) – a data dictionary object read with
response.json() - force_keys (bool) – If True, define a new class attribute from data keys
- data (dict) – a data dictionary object read with
-
status¶ Return
submissionStatusattribute. FollowsubmissionStatuslink and update attribute is such attribute is NoneReturns: submission status as a string Return type: str
-
update_status()[source]¶ Update
submissionStatusattribute by followingsubmissionStatuslink
-
-
class
pyUSIrest.usi.Team(auth, data=None)[source]¶ Bases:
pyUSIrest.client.DocumentA class to deal with USI Team objects
-
data¶ data (dict): data from USI read with
response.json()Type: dict
-
create_submission()[source]¶ Create a new submission
Returns: the new submission as an instance Return type: Submission
-
get_submissions(status=None)[source]¶ Follows submission url and get submissions from this team
Parameters: status (str) – filter submission using status Returns: A list of SubmissionobjectsReturn type: list
-
-
class
pyUSIrest.usi.User(auth, data=None)[source]¶ Bases:
pyUSIrest.client.DocumentDeal with EBI AAP endpoint to get user information
-
data¶ data (dict): data from AAP read with
response.json()Type: dict
-
add_user_to_team(user_id, domain_id)[source]¶ Add a user to a team
Parameters: Returns: the updated
DomainobjectReturn type:
-
create_team(description, centreName)[source]¶ Create a new team
Parameters: Returns: the new team as a
TeaminstanceReturn type:
-
classmethod
create_user(user, password, confirmPwd, email, full_name, organisation)[source]¶ Create another user into biosample AAP and return its ID
Parameters: Returns: the new user_id as a string
Return type:
-
get_domain_by_name(domain_name)[source]¶ Get a domain by name
Parameters: domain_name (str) – the required team Returns: the desidered DomaininstanceReturn type: Domain
-
get_domains()[source]¶ Get domains belonging to this instance
Returns: a list of DomainobjectsReturn type: list
-
get_my_id()[source]¶ Get user id using own credentials, and set userReference attribute
Returns: the user AAP reference as a string Return type: str
-
get_team_by_name(team_name)[source]¶ Get a team by name
Parameters: team_name (str) – the required team Returns: the desidered TeaminstanceReturn type: Team
-
get_teams()[source]¶ Get teams belonging to this instance
Returns: a list of TeamobjectsReturn type: list
-
get_user_by_id(user_id)[source]¶ Get a
Userobject by user_idParameters: user_id (str) – the required user_id Returns: a user object Return type: User
-
user_url= None¶
-
-
class
pyUSIrest.usi.ValidationResult(auth, data=None)[source]¶ Bases:
pyUSIrest.client.Document
Module contents¶
Top-level package for Python EBI submission REST API.
Contributing¶
Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
You can contribute in many ways:
Types of Contributions¶
Report Bugs¶
Report bugs at https://github.com/cnr-ibba/pyUSIrest/issues.
If you are reporting a bug, please include:
- Your operating system name and version.
- Any details about your local setup that might be helpful in troubleshooting.
- Detailed steps to reproduce the bug.
Fix Bugs¶
Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.
Implement Features¶
Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.
Write Documentation¶
Python USI submission REST API could always use more documentation, whether as part of the official Python USI submission REST API docs, in docstrings, or even on the web in blog posts, articles, and such.
Submit Feedback¶
The best way to send feedback is to file an issue at https://github.com/cnr-ibba/pyUSIrest/issues.
If you are proposing a feature:
- Explain in detail how it would work.
- Keep the scope as narrow as possible, to make it easier to implement.
- Remember that this is a volunteer-driven project, and that contributions are welcome :)
Get Started!¶
Ready to contribute? Here’s how to set up pyUSIrest for local development.
Fork the pyUSIrest repo on GitHub.
Clone your fork locally:
$ git clone git@github.com:your_name_here/pyUSIrest.git
Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:
$ mkvirtualenv pyUSIrest $ cd pyUSIrest/ $ pip install -r requirements_dev.txt $ python setup.py developCreate a branch for local development:
$ git checkout -b name-of-your-bugfix-or-feature
Now you can make your changes locally.
When you’re done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:
$ flake8 pyUSIrest tests $ python setup.py test # or pytest $ tox
To get flake8 and tox, just pip install them into your virtualenv.
Commit your changes and push your branch to GitHub:
$ git add . $ git commit -m "Your detailed description of your changes." $ git push origin name-of-your-bugfix-or-featureSubmit a pull request through the GitHub website.
Pull Request Guidelines¶
Before you submit a pull request, check that it meets these guidelines:
- The pull request should include tests.
- If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
- The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check https://travis-ci.org/cnr-ibba/pyUSIrest/pull_requests and make sure that the tests pass for all supported Python versions.
Deploying¶
Current development version is created using:
$ bump2version patch # possible: major / minor / patch
Other development version (dev1, `dev2) are managed using:
$ bump2version build
A reminder for the maintainers on how to deploy. Make sure all your changes are committed (including an entry in HISTORY.rst). Then run:
$ bump2version patch # possible: major / minor / patch
$ git push
$ git push --tags
Travis will then deploy to PyPI if tests pass.
Credits¶
Development Lead¶
- Paolo Cozzi <paolo.cozzi@ibba.cnr.it>
Contributors¶
None yet. Why not be the first?
History¶
TODO¶
- get a
Teaminstance fromSubmissioninstance Submission.has_errorsmake 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
USIDataErroron40xstatus code - Change
Auth.__str__(): now it returnsToken for Foo Bar will expire in HH:MM:SS - add
Auth.get_domainswhich returnsself.claims['domains']
0.3.0 (2020-01-14)¶
Features¶
- modelled custom exceptions
- Set a default date if
releaseDateattribute 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
taxonin 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 objectsstr(auth)will report duration inhh: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,SampleValidationResultclasses insidepyUSIrest.usimodule
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.usersreturnsUserobjects in a list- improved
Submission.get_samplesmethod