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Python bindings for the Ophidia Data Analytics Platform

Project description

PyOphidia is a GPLv3-licensed Python package for interacting with the Ophidia framework.

It is an alternative to Oph_Term, the Ophidia no-GUI interpreter component, and a convenient way to submit SOAP HTTPS requests to an Ophidia server or to develop your own application using Python.

It runs on Python 2.7, 3.3, 3.4 and 3.5, has no dependencies and is pure-Python.

It provides 2 main modules:

  • client.py: generic low level class to submit any type of requests (simple tasks and workflows), using SSL and SOAP with the client ophsubmit.py;

  • cube.py: high level cube-oriented class to interact directly with cubes, with several methods wrapping the operators.

Installation

To install PyOphidia package run the following command:

pip install pyophidia

Installation from sources

To install the latest developement version run the following commands:

git clone https://github.com/OphidiaBigData/PyOphidia
cd PyOphidia
python setup.py install

Examples

Import PyOphidia

Import client module from PyOphidia package:

from PyOphidia import client

Instantiate a client

Create a new Client() using the login parameters username, password, host and port. It will also try to resume the last session the user was connected to, as well as the last working directory and the last produced cube.

ophclient = client.Client("oph-user","oph-passwd","127.0.0.1","11732")

Client attributes

  • username: Ophidia username

  • password: Ophidia password

  • server: Ophidia server address

  • port: Ophidia server port (default is 11732)

  • session: ID of the current session

  • cwd: Current Working Directory

  • cube: Last produced cube PID

  • exec_mode: Execution mode, ‘sync’ for synchronous mode (default), ‘async’ for asynchronous mode

  • ncores: Number of cores for each operation (default is 1)

  • last_request: Last submitted query

  • last_response: Last response received from the server (JSON string)

  • last_jobid: Job ID associated to the last request

Client methods

  • submit(query, display) -> self: Submit a query like ‘operator=myoperator;param1=value1;’ or ‘myoperator param1=value1;’ to the Ophidia server according to all login parameters of the Client and its state.

  • deserialize_response() -> dict: Return the last_response JSON string attribute as a Python dictionary.

  • resume_session(display) -> self: Resume the last session the user was connected to.

  • resume_cwd(display) -> self: Resume the last cwd (current working directory) the user was located into.

  • resume_cube(display) -> self: Resume the last cube produced by the user.

  • wsubmit(workflow, *params) -> self: Submit an entire workflow passing a JSON string or the path of a JSON file and an optional series of parameters that will replace $1, $2 etc. in the workflow. The workflow will be validated against the Ophidia Workflow JSON Schema.

  • wisvalid(workflow) -> bool: Return True if the workflow (a JSON string or a Python dict) is valid against the Ophidia Workflow JSON Schema or False.

To display the command output set “display=True”

Submit a request

Execute the request oph_list level=2:

ophclient.submit("oph_list level=2", display=True)

Set a Client for the Cube class

Instantiate a new Client common to all Cube instances:

from PyOphidia import cube
cube.Cube.setclient('oph-user','oph-password','127.0.0.1','11732')

Cube attributes

Instance attributes:

  • pid: Cube PID

  • creation_date: Creation date of the cube

  • measure: Name of the variable imported into the cube

  • measure_type: Measure data type

  • level: Number of operations between the original imported cube and the actual cube

  • nfragments: Total number of fragments

  • source_file: Parent of the actual cube

  • hostxcube: Number of hosts on which the cube is stored

  • dbmsxhost: Number of DBMS instances on each host

  • dbxdbms: Number of databases for each DBMS

  • fragxdb: Number of fragments for each database

  • rowsxfrag: Number of rows for each fragment

  • elementsxrow: Number of elements for each row

  • compressed: If the cube is compressed or not

  • size: Size of the cube

  • nelements: Total number of elements

  • dim_info: List of dict with information on each cube dimension

Class attributes:

  • client: instance of class Client through which it is possible to submit all requests

Create a new container

Create a new container to contain our cubes called test, with 3 double dimensions (lat, lon and time):

cube.Cube.createcontainer(container='test',dim='lat|lon|time',dim_type='double|double|double',hierarchy='oph_base|oph_base|oph_time')

Import a new cube

Import the variable T2M from the NetCDF file /path/to/file.nc into a new cube inside the test container. Use lat and lon as explicit dimensions and time as implicit dimension expressed in days:

mycube = cube.Cube(container='test',exp_dim='lat|lon',imp_dim='time',measure='T2M',src_path='/path/to/file.nc',exp_concept_level='c|c',imp_concept_level='d')

Create a Cube object from an existing cube identifier

Instantiate a new Cube using the PID of an existing cube:

mycube2 = cube.Cube(pid='http://127.0.0.1/1/2')

Show a Cube structure and info

To shows metadata information about a data cube, its size and the dimensions related to it:

mycube2.info()

For the operators such as “cubeschema”, “cubesize”, “cubeelements”, “explore”, “hierarchy”, “info”, “list”, “loggingbk”, “operators”, “search”, “showgrid”, “man”, “metadata”, “primitives”, “provenance”, “search”, “showgrid”, “tasks” and other operators that provide verbose output, the display parameter by default is “True”. For the rest of operators, to display the result, “dispay=True” should be set.

Subset a Cube

To perform a subsetting operation along dimensions of a data cube (dimension values are used as input filters):

mycube3 = mycube2.subset2(subset_dims='lat|lon',subset_filter='1:10|20:30')

Explore Cube

To explore a data cube filtering the data along its dimensions:

mycube2.explore(subset_dims='lat|lon',subset_filter='1:10|20:30')

Export to NetCDF file

To export data into a single NetCDF file:

mycube3.exportnc2(output_path='/home/user')

Export to Python array

To exports data in a python-friendly format:

data = mycube3.export_array(show_time='yes')

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