Python API¶

Opal Python can be easily extended by using the exposed classes. The classes *Command return an Opal task object, to be followed with the TaskService. The classes *Service perform immediate operations.

Packages¶

Use the pydoc tool to get the Python documentation.

pydoc obiba_opal.<package name>

Package	Description
`obiba_opal.analysis`	Table analysis related classes, to launch an analysis command and export analysis output.
`obiba_opal.core`	Core classes for establishing a connection with an Opal server, send requests and aget responses.
`obiba_opal.data`	Table data and entities related classes, to get list of entities, values and value sets.
`obiba_opal.dictionary`	Table dictionary related classes, to list tables and variables and to manage variable annotations.
`obiba_opal.exports`	Various export commands.
`obiba_opal.file`	File management classes, to upload, download, get info and delete files.
`obiba_opal.imports`	Various import commands.
`obiba_opal.io`	Import/export base classes.
`obiba_opal.perm`	Permission management related classes, for various Opal items.
`obiba_opal.project`	Project management classes, to perform backup/restore commands and to add/delete/list projects.
`obiba_opal.security`	Encryption/decryption service.
`obiba_opal.sql`	Table SQL related classes, to perform SQL queries on tables.
`obiba_opal.subjects`	Users and Groups management classes.
`obiba_opal.system`	Various system services, to perform operations on tasks, taxonomys, plugins etc.
`obiba_opal.table`	Backup/restore views.

Usage Example¶

from obiba_opal import OpalClient, HTTPError, Formatter, ImportCSVCommand, TaskService, FileService, DictionaryService

# if 2-factor auth is enabled, user will be asked for the secret code
# Personal access token authentication is also supported (and recommended)
client = OpalClient.buildWithAuthentication(server='https://opal-demo.obiba.org', user='administrator', password='password')

try:
    # upload a local CSV data file into Opal file system
    fs = FileService(client)
    fs.upload_file('./data.csv', '/tmp')

    # import this CSV file into a project
    task = ImportCSVCommand(client).import_data('/tmp/data.csv', 'CNSIM')
    status = TaskService(client).wait_task(task['id'])

    # clean data file from Opal
    fs.delete_file('/tmp/data.csv')

    if status == 'SUCCEEDED':
        dico = DictionaryService(client)
        table = dico.get_table('CNSIM', 'data')
        # do something ...
        dico.delete_tables('CNSIM', ['data'])
    else:
        print('Import failed!')
        # do something ...
except HTTPError as e:
    Formatter.print_json(e.error, True)
finally:
    client.close()