OneDep Validation Web Service Interface

Introduction

The OneDep validation web service was developed as a wwPDB effort to augment the stand alone validation server by providing a programmatic remote access to such services.

This service is provided as a Python package. Once installed, access is provided using a command line client or pragmatically using a Python API.

Installation

Installation is via the program pip .

pip install onedep_api

Command Line Usage

A binary script is installed called onedep_validate_cli which is a front end that invokes the packages APIs.

Example scripts that utilize the client and API can be found here .

Start a new session

You must start a new session. The system keeps track of the current working session in the file ~/.onedep_current_session This can be changed with the --session_file argument.

onedep_validate_cli --new_session

Upload data

The validation API supports a limited number of file types and formats. To upload a file, you need to specify the file type with the filetype from the following table.

Data file	Format	filetype
model	PDBx/mmCIF	model
structure factor	mmCIF	structure-factors
NMR chemical shifts	mmCIF	nmr-chemical-shifts
NMR restraints	any	nmr-restraints
EM map	CCP4 map	em-volume
NMRstar combined data	NMRstar	nmr-data-str
NEF combined data	NMRstar	nmr-data-nef

PDBx/mmCIF formatted files are available from REFMAC and Phenix, or can be created by using pdb_extract . MTZ to mmCIF conversion can be performed with sf-tool or in CCP4 with mtz2various .

onedep_validate_cli --input_file <filename> --input_type <filetype>

Repeat until all files are uploaded.

Run validation

Initiate the validation with the command:

onedep_validate_cli --validate

You can periodically check if the validation is running or complete with the command:

onedep_validate_cli --status

or if you would like a value of 0 or 1:

onedep_validate_cli --test_complete

Retrieving results

When complete, you can retrieve the results of the validation

onedep_validate_cli --output_file <pdf file> --output_type validation-report-full
onedep_validate_cli --output_file <xml file> --output_type validation-data

Python API

The Python API was developed to provide simple access to the web validation services in a programmatic manner.

Validation

The Validate class provides access to all services, from session creation, file upload and download, calculation initiation and status retrieval.

from onedep import __apiUrl__
from onedep.api.Validate import Validate
import time

def displayStatus(sD, exitOnError=True):
    if 'onedep_error_flag' in sD and sD['onedep_error_flag']:
        print("OneDep error: %s\n" % sD['onedep_status_text'])
        if exitOnError:
            raise SystemExit()
    else:
        if 'status' in sD:
            print("OneDep status: %s\n" % sD['status'])

# Given:
# modelFilePath contains the path to the model file
# sfFilePath contains the path to the structure factor file
val = Validate(apiUrl=__apiUrl__)
rD = val.newSession()
displayStatus(rD)
rD = val.inputModelXyzFile(modelFilePath)
rD = val.inputStructureFactorFile(sfFilePath)
displayStatus(rD)
rD = val.run()
displayStatus(rD)
#
#   Poll for service completion -
#
it = 0
sl = 2
while (True):
   #    Pause -
   it += 1
   pause = it * it * sl
   time.sleep(pause)
   rD = val.getStatus()
   if rD['status'] in ['completed', 'failed']:
      break
   print("[%4d] Pausing for %4d (seconds)\n" % (it, pause))
   #
   #
lt = time.strftime("%Y%m%d%H%M%S", time.localtime())
fnR = "xray-report-%s.pdf" % lt
rD = val.getReport(fnR)