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Python client

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javild edited this page Jun 10, 2016 · 16 revisions

(Under construction)

Note: Python client available from version 4.1 onwards (current develop branch)

Python client code is implemented for Python 3 and distributed together with the rest of the CellBase code. Client code can be found at:

cellbase/clients/python

Both a Python library for programmatic access and a CLI are provided:

Python library

The Python library code can be accessed at https://github.com/opencb/cellbase/tree/develop/clients/python/lib Programmatic API is provided by the CellBaseClient class. This class can be configured by means of a configuration.json file. CellBaseClient class will access the RESTful Web Services through the get method it implements. Thus, this method needs to be provided with those parameters which are required by the URL: appropriate species name (e.g. hsapiens), subcategory of data to query (e.g. gene, category is not required since can be inferred from the subcategory value), id to search for (e.g. HGNC symbol) and method to query (e.g. search). Not all of these values are required for al possible queries. Please, for more details on possible values and value-combinations for these parameters refer to http://bioinfo.hpc.cam.ac.uk/cellbase/webservices and https://github.com/opencb/cellbase/wiki/RESTful-web-services.

Please, find more details on how to install the python package and how to use the python library at: Using the Python client

Command Line Interface

The client provides a CLI which can be accessed through the executable at:

cellbase$ python3 clients/python/cellbase-client.py -h
usage: cellbase-client.py [-h] --type T [-o OUTPUT] --resource M
                          [--id I [I ...]] [--species S] [--conf I]
                          [--include F [F ...] | --exclude X [X ...]]
                          [--limit LIMIT] [--skip SKIP]

CellBase client 1.0

optional arguments:
  -h, --help            show this help message and exit
  --type T              String indicating the subcategory of the IDs to be
                        queried
  -o OUTPUT, --output OUTPUT
                        store the results to a json file
  --resource M          String indicating the method to be queried
  --id I [I ...]        String indicating the id(s) to be queried (if needed)
  --species S           String indicating the species to query
  --conf I              Path to a .json file containing CellBase client
                        configuration (if needed)
  --include F [F ...]   String indicating the field to be returned
  --exclude X [X ...]   String indicating the field to be excluded
  --limit LIMIT         Integer indicating the number of results to be
                        returned (if neede)
  --skip SKIP           Integer indicating the number of results to skip (if
                        needed)

The CLI will access CellBase data through the REST API and implements all its functionality. Please, for more details on possible values and value-combinations for these parameters refer to http://bioinfo.hpc.cam.ac.uk/cellbase/webservices and https://github.com/opencb/cellbase/wiki/RESTful-web-services.

Configuration

Client configuration parameters can be found at:

cellbase/clients/python/lib/resources/configuration.json

Main configuration parameters have to do with the CellBase version the client will query, host url and host port. Please see below an example of the configuration.json content:

{
  "version": "v4",
  "apiVersion": "v4.0",
  "wiki": "https://github.com/opencb/cellbase/wiki",
  "database": {
	"hosts": {
      "first": "bioinfodev.hpc.cam.ac.uk",
      "second": ""
    },
    "port": 80
  }
}

General

Tutorials

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