- Created by Nacho Medina, last modified by Pedro Furio on Nov 15, 2019
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pyOpenCGA Overview
The OpenCGA Python Client provides a user-friendly API to work with OpenCGA through the REST Web Services. Python client is called pyOpenCGA, some of the main features include:
- full RESTful web service API implemented, all endpoints are supported including new alignment or clinical functionality
- data is returned in a new QueryResponse object which contains metadata and the results, some handy methods and iterators implemented
- it uses the OpenCGA client-configuration.yml file and the stored session
- several Jupyter Notebooks iimplemented
pyOpenCGA has been implemented and contributed by Pablo Marin and David Gomez and it is based on the previous pyCGA library implemented by Antonio Rueda and Daniel Perez from Genomics England.
You can find some examples in the Tutorials section at Using the Python client.
Installation
Python client requires at least Python 3.x, although most of the code is fully compatible with Python 2.7. You can install pyOpenCGA either from PyPI repository or from the source code.
PyPI
You can find stable releases of pyOpenCGA at https://pypi.org/project/pyopencga/, installing is as simple as:
## Latest stable version pip install pyopencga
Source Code
Python client source code can be found in OpenCGA GitHub repository at https://github.com/opencb/opencga/tree/develop/opencga-client/src/main/python/pyOpenCGA. To install any stable of development version of pyOpenCGA we will first need to clone the right branch of OpenCGA repository and install the library using the setup.py file.
## Latest stable version git clone -b master 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 Implementation
Developers only need to create an instance of the ClientConfiguration class passing it as an argument to the OpenCGAClient. They can optionally pass 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 ClientConfiguration classes from pyopencga.opencga_client import OpenCGAClient from pyopencga.opencga_config import ClientConfiguration ## Creating a ClientConfiguration: # This can be done by passing the path to the main client-configuration.yml file config = ClientConfiguration('/opt/opencga/conf/client-configuration.yml') # Or by creating a dictionary using the below format passing the OpenCGA host to point to config = ClientConfiguration({ "rest": { "host": "http://bioinfo.hpc.cam.ac.uk/opencga-demo" } }) ## Create an instance of OpenCGAClient passing the configuration oc = OpenCGAClient(config) ## Authenticate the user. Password is optional and if this is not passed to the login method, it will be prompted to the user oc.login('user') # or oc.login('user', 'password')
Design
OpenCGAClient class 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 RESTResponse class that automatically stores all the different values returned and defines a few public methods to help users navigating through the data.
The RESTResponse methods developed are:
## Return an iterator to help iterating over all the results. results() ## Return the total number of matches taking of all the QueryResponses. num_matches() ## Return the total number of results taking of all the QueryResponses. num_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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