Overview

The OpenCGA Python Client provides a user-friendly API to work with OpenCGA REST Web Services through Python.

Installation

Python client requires at least Python 3.6, though most of the code is fully compatible with Python 2.7.

Python client can be found in OpenCGA's github repository in the following path: https://github.com/opencb/opencga/tree/develop/opencga-client/src/main/python/pyOpenCGA. To install the library we will first need to clone OpenCGA repository and install the library using the setup.py file.

## Latest version
git clone -b develop https://github.com/opencb/opencga.git


## Move to the pyOpenCGA client folder
cd opencga/opencga-client/src/main/python/pyOpenCGA/


## Install the library
python setup.py install

Library

Developers only need to create an instance of the ConfigClient class passing it as an argument to the OpenCGAClient. They can optionally pass the user and password or a valid token to start doing calls as an authenticated user. The only role of the OpenCGAClient class is to work as a factory of the actual clients.

## Import OpenCGAClient and ConfigClient classes
from pyopencga.opencga_client import OpenCGAClient
from pyopencga.opencga_config import ConfigClient

## Creating ConfigClient
host = 'localhost:8080/opencga'
cc = ConfigClient()
config_dict = cc.get_basic_config_dict(host)

## Create an instance of OpenCGAClient passing the user credentials
oc = OpenCGAClient(configuration=config_dict, user="user", pwd="password")

Design

OpenCGAClient works as a factory containing all the different clients necessary to call to any REST web service.

As described in RESTful Web Services#RESTResponse, most of the web services return a QueryResponse object containing a list of QueryResults. This structure has been maintained in the Python library and everytime a call to any WS is done, the response is automatically encapsulated into a custom QueryResponse class that automatically stores all the different values returned and defines a few public methods to help users navigating through the data.

The QueryResponse methods developed are:

## Return the first QueryResult from the QueryResponse. 
first()


## Return the first result from the 'index' QueryResult. 
## If 'index' is not provided, it will automatically show the first result of the first QueryResult
result(index)


## Return an iterator to help iterating over all the results.
results()


## Return the total number of results obtained.
num_total_results()

API

The client implements at least one function for each available resource (user, project, study, etc.). Currently, the following functions are available:

## User
oc.users.login(user, pwd, **options)
oc.users.refresh_token(user, **options)
oc.users.logout()

oc.users.info(query_id, **options)
oc.users.create(data, **options)
oc.users.update(query_id, data, **options)
oc.users.delete(**options)

oc.users.projects(user, **options)
oc.users.update_password(user, pwd, newpwd, **options)
oc.users.configs(user, **options)
oc.users.update_configs(user, data, action, **options)
oc.users.filters(user, **options)
oc.users.update_filters(user, data, action, **options)
oc.users.update_filter(user, filter_name, data, **options)


## Projects
oc.projects.info(query_id, **options)
oc.projects.create(data, **options)
oc.projects.update(query_id, data, **options)
oc.projects.delete(**options)


oc.projects.search(**options)
oc.projects.studies(project, **options)
oc.projects.aggregation_stats(project, **options)
oc.projects.increment_release(project, **options)


## Studies
oc.studies.info(query_id, **options)
oc.studies.create(data, **options)
oc.studies.update(query_id, data, **options)
oc.studies.delete(**options)


oc.studies.acl(query_id, **options)
oc.studies.update_acl(memberId, data, **options)


oc.studies.groups(study, **options)
oc.studies.search(**options)
oc.studies.scan_files(study, **options)
oc.studies.resync_files(study, **options)
oc.studies.create_groups(study, data, **options)
oc.studies.update_groups(study, data, action, *options)
oc.studies.update_users_from_group(study, group, data, action, **options)
oc.studies.permission_rules(study, entity, **options)
oc.studies.update_permission_rules(study, entity, data, action, **options)
oc.studies.variablesets(study, **options)
oc.studies.update_variablesets(study, data, action, **options)
oc.studies.aggregation_stats(study, **options)
oc.studies.update_variable_from_variableset(study, variable_set, action, **options)


## Individuals
oc.individuals.info(query_id, **options)
oc.individuals.create(data, **options)
oc.individuals.update(query_id, data, **options)
oc.individuals.delete(**options)


oc.individuals.search(**options)
oc.individuals.aggregation_stats(**options)
oc.individuals.update_annotations(query_id, annotationset_id, data, **options)

oc.individuals.acl(query_id, **options)
oc.individuals.update_acl(memberId, data, **options)


## Samples
oc.samples.info(query_id, **options)
oc.samples.create(data, **options)
oc.samples.update(query_id, data, **options)
oc.samples.delete(**options)

oc.samples.search(**options)
oc.samples.load(file, **options)
oc.samples.aggregation_stats(**options)
oc.samples.update_annotations(query_id, annotationset_id, data, **options)

oc.samples.acl(query_id, **options)
oc.samples.update_acl(memberId, data, **options)


## Files
oc.files.info(query_id, **options)
oc.files.create(data, **options)
oc.files.update(query_id, data, **options)
oc.files.delete(**options)

oc.files.search(**options)
oc.files.aggregation_stats(**options)
oc.files.bioformats(**options)
oc.files.formats(**options)
oc.files.scan_folder(folder, **options)
oc.files.list_folder(folder, **options)
oc.files.content(file, **options)
oc.files.grep(file, **options)
oc.files.refresh(file, **options)
oc.files.tree_folder(folder, **options)
oc.files.upload(data, **options)
oc.files.download(file, **options)
oc.files.update_annotations(query_id, annotationset_id, data, **options)

oc.files.acl(query_id, **options)
oc.files.update_acl(memberId, data, **options)


## Jobs
oc.jobs.info(query_id, **options)
oc.jobs.create(data, **options)
oc.jobs.update(query_id, data, **options)
oc.jobs.delete(**options)

oc.jobs.search(**options)
oc.jobs.visit(job, **options)

oc.jobs.acl(query_id, **options)
oc.jobs.update_acl(memberId, data, **options)

## Families
oc.families.info(query_id, **options)
oc.families.create(data, **options)
oc.families.update(query_id, data, **options)
oc.families.delete(**options)

oc.families.search(**options)
oc.families.aggregation_stats(**options)
oc.families.update_annotations(query_id, annotationset_id, data, **options)

oc.families.acl(query_id, **options)
oc.families.update_acl(memberId, data, **options)


## Cohorts
oc.cohorts.info(query_id, **options)
oc.cohorts.create(data, **options)
oc.cohorts.update(query_id, data, **options)
oc.cohorts.delete(**options)

oc.cohorts.search(**options)
oc.cohorts.aggregation_stats(**options)
oc.cohorts.samples(self, cohort, **options)
oc.cohorts.update_annotations(query_id, annotationset_id, data, **options)

oc.cohorts.acl(query_id, **options)
oc.cohorts.update_acl(memberId, data, **options)


## Disease Panels
oc.panels.info(query_id, **options)
oc.panels.create(data, **options)
oc.panels.update(query_id, data, **options)
oc.panels.delete(**options)

oc.panels.search(**options)

oc.panels.acl(query_id, **options)
oc.panels.update_acl(memberId, data, **options)

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Python

Overview

Installation

Library

Design

API