#!/usr/bin/env python # -*- coding: utf-8 -*- """ validate_cli.py ^^^^^^^^^^^^^^^ Command line interface for wwPDB OneDep validation webservice API. :copyright: @wwPDB :license: Apache 2.0, see LICENSE file for more details. Updates: 22-Sep-2016 jdw adapt for onedep package 24-Sep-2016 jdw revise error handling 28-Sep-2016 jdw add exp_method argument 30-Sep-2016 jdw add additional path conditioning - 01-Dec-2016 jdw make api key functions for this cli controlled by env var ONEDEP_USE_API_KEY """ from __future__ import print_function from __future__ import unicode_literals __docformat__ = "restructuredtext en" __author__ = "John Westbrook" __email__ = "jwest@rcsb.rutgers.edu" __license__ = "Apache 2.0" import logging import datetime import sys import six import os.path try: from argparse import ArgumentParser as ArgParser from argparse import RawTextHelpFormatter except ImportError: from optparse import OptionParser as ArgParser # pylint: disable=deprecated-module from onedep import __version__ from onedep import __apiUrl__ from onedep.api.Register import Register from onedep.api.Validate import Validate log = logging.getLogger() def print_(s): sys.stdout.write(s) def version(): """Print the version and exit""" raise SystemExit(__version__) def readApiKey(filePath): apiKey = None try: fn = os.path.expanduser(filePath) with open(fn, "r") as fp: apiKey = fp.read() except: # noqa: E722 pylint: disable=bare-except pass return apiKey def writeSessionId(sessionId, filePath): try: fn = os.path.expanduser(filePath) with open(fn, "w") as fp: fp.write(sessionId) return True except: # noqa: E722 pylint: disable=bare-except,raise-missing-from raise SystemExit("Error writing file %r" % filePath) def readSessionId(filePath): sessionId = None try: fn = os.path.expanduser(filePath) log.debug("Getting session from %r", fn) with open(fn, "r") as fp: sessionId = fp.read() except: # noqa: E722 pylint: disable=bare-except log.debug("failing for file path %r", filePath) return sessionId def displayStatus(sD, exitFlag=False, 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"]) if exitFlag: raise SystemExit() def displayIndex(sD): # print_("\nOneDep Session File Index:\n") try: val = Validate() ctL = val.getContentTypes() if "index" in sD and len(sD) > 0: print_("%25s : %-25s\n" % ("Content Type", "Session File Name")) print_("%25s : %-25s\n" % ("------------", "-----------------")) for ky in sD["index"]: if ky in ctL: fn, _fmt = sD["index"][ky] print_("%25s : %-25s\n" % (ky, fn)) else: print_("No session content\n") except: # noqa: E722 pylint: disable=bare-except print_("Error processing session index") def displayActivity(sD): # dfmt = "%a %b %d %H:%M:%S %Y" print_("\nOneDep Request Activity Summary:\n") try: val = Validate() if "activity_summary" in sD and len(sD) > 0: print_("%25s : %-25s\n" % ("Category ", "Count ")) print_("%25s : %-25s\n" % ("------------", "-----------------")) for ky in sD["activity_summary"]: if ky not in ["session_list"]: val = sD["activity_summary"][ky] print_("%25s : %-25s\n" % (ky, val)) if "session_list" in sD["activity_summary"]: print_("\n%-25s : %-10s: %-25s: %-45s\n" % (" Session Creation Time", "Status ", "Time after submit (secs)", "Session Identifier")) print_("%25s : %-10s: %-25s: %-45s\n" % ("------------------------", "----------", "------------------------ ", "----------------------------------------")) for s in sD["activity_summary"]["session_list"]: tiso = s[1] dt = datetime.datetime.strptime(tiso[:19], "%Y-%m-%dT%H:%M:%S") fdt = dt.strftime(dfmt) if s[3] == "0" or s[3] == 0: print_("%25s : %-10s: %24s : %-45s\n" % (fdt, s[2], "", s[0])) else: print_("%25s : %-10s: %24.2f : %-45s\n" % (fdt, s[2], s[3], s[0])) else: print_("No session activity data\n") except: # noqa: E722 pylint: disable=bare-except print_("Error processing activity summary") def filterPath(inpPath): try: return os.path.expanduser(inpPath) except: # noqa: E722 pylint: disable=bare-except return inpPath def run(): """Command line interface for OneDep validation API""" description = """ Command line interface for OneDep validation API: Step 1: Request a new session on the validation server. onedep_validate --new_session By default, session information will be stored in your home directory in file ~/.onedep_current_session Step 2: Upload the target data files for validation X-ray: onedep_validate --input_file 1abc.cif --input_type model onedep_validate --input_file 1abc-sf.cif.gz --input_type structure-factors NMR: onedep_validate --input_file 1abc.cif --input_type model onedep_validate --input_file 1abc-shifts.cif.gz --input_type nmr-chemical-shifts or onedep_validate --input_file 1abc.nef.gz --input_type nmr-data-nef or onedep_validate --input_file 1abc.str.gz --input_type nmr-data-str 3DEM: onedep_validate --input_file 1abc.cif --input_type model onedep_validate --input_file 1abc-vol.map.gz --input_type em-volume Step 3: Submit a reqest to validate the data files in the current session onedep_validate --validate Step 4: Check the status of the validation service request onedep_validate --status Step 5: When the request is completed, recover the validation report and data files. onedep_validate --output_file report.pdf --output_type validation-report-full onedep_validate --output_file report.xml --output_type validation-data onedep_validate --output_file report.cif --output_type validation-data-cif """ # Registration is not required for the validation api registerDescription = """ To register an API Key: Request a OneDep API access Key. API keys are sent to your e-mail\n address and are valid for 30 days. onedep_validate --register --email For convenience, the API access key may be stored in a hidden file in your home directory. Copy the API access key e-mail attachment as follows. cp onedep_apikey.jwt ~/.onedep_apikey.jwt """ USEKEY = os.getenv("ONEDEP_USE_API_KEY") if os.getenv("ONEDEP_USE_API_KEY") else False if USEKEY: description += registerDescription # try: parser = ArgParser(description=description, formatter_class=RawTextHelpFormatter) except: # noqa: E722 pylint: disable=bare-except parser = ArgParser(description="Command line interface for OneDep validation API") # For optparse.OptionParser add an `add_argument` method for compatibility with argparse.ArgumentParser try: parser.add_argument = parser.add_option except AttributeError: pass ### parser.add_argument( "--session_file", dest="sessionFile", type=six.text_type, default=filterPath("~/.onedep_current_session"), help="File containing current session information (default: %(default)s)", ) ## parser.add_argument("--new_session", dest="newSessionOp", action="store_true", default=False, help="Start a new session") ## parser.add_argument("--input_file", dest="inputFile", type=six.text_type, default=None, help="Input file path") parser.add_argument( "--input_type", dest="inputType", type=six.text_type, default="model", choices=["model", "structure-factors", "nmr-chemical-shifts", "nmr-restraints", "em-volume", "nmr-data-nef", "nmr-data-str"], help="Input file type", ) ## parser.add_argument( "--exp_method", dest="expMethod", type=six.text_type, default=None, choices=["X-RAY", "NMR", "EM"], help="Use a validation protocol for this experimental method" ) parser.add_argument("--validate", dest="validateOp", action="store_true", default=False, help="Submit a request to run the validation service") ## parser.add_argument("--status", dest="statusOp", action="store_true", default=False, help="Get the status of the current session") # parser.add_argument( "--test_complete", dest="completeOp", action="store_true", default=False, help="Return competion status for the current session [1 for done or 0 otherwise]" ) # parser.add_argument("--output_file", dest="outputFile", type=six.text_type, default=None, help="Output file path") parser.add_argument( "--output_type", dest="outputType", type=six.text_type, default="validation-report-full", choices=["validation-report-full", "validation-data", "validation-data-cif", "validation-report-log", "validation-report-slider"], help="Output file type", ) ## parser.add_argument("--index", dest="indexOp", action="store_true", default=False, help="Request index of the data files in the current session") # parser.add_argument("--version", action="store_true", help="Show the version number and exit") ## parser.add_argument("--verbose", action="store_true", help="Set verbose logging") parser.add_argument("--debug", action="store_true", help="Set debug logging") parser.add_argument("--test_mode", dest="testMode", action="store_true", help="Set service in test mode") parser.add_argument("--test_duration", dest="testModeDuration", type=int, default=10, help="Mock service duration in test mode (seconds, default=10)") parser.add_argument("--log_file", dest="logFile", type=six.text_type, default=None, help="Log file path") parser.add_argument("--api_url", dest="apiUrl", type=six.text_type, default=__apiUrl__, help="API base URL") # if USEKEY: # # Api key registration is now optional for the validation web service api. parser.add_argument("--email", type=six.text_type, default=None, help="e-mail address to receive OneDep API key") parser.add_argument("--register", action="store_true", dest="register", default=False, help="Register to receive a OneDep API by e-mail") parser.add_argument( "--api_key_file", dest="apiKeyFile", type=six.text_type, default=filterPath("~/.onedep_apikey.jwt"), help="File containing a OneDep API key (default: %(default)s)" ) # # This option requires a valid apikey - parser.add_argument("--activity", dest="activityOp", action="store_true", default=False, help="Request a summary of service requests - this option requires an API key") # # options = parser.parse_args() if isinstance(options, tuple): args = options[0] else: args = options del options # Print the version and exit if args.version: version() # # Configure logging - logging.captureWarnings(True) formatter = logging.Formatter("%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s") logging.basicConfig(format="%(asctime)s [%(levelname)s]-%(module)s.%(funcName)s: %(message)s") if args.logFile: handler = logging.FileHandler(args.logFile) handler.setFormatter(formatter) log.addHandler(handler) # if args.debug: log.setLevel(logging.DEBUG) log.debug("debug logging activated") elif args.verbose: log.setLevel(logging.INFO) log.debug("info logging activated") else: log.setLevel(logging.ERROR) # apiUrl = args.apiUrl apiKey = None # if USEKEY: # Register for a new API key and exit - if args.register and args.email: reg = Register(apiUrl=apiUrl) rD = reg.register(email=args.email) displayStatus(rD, exitFlag=True) # # Read API key file - if args.apiKeyFile: apiKey = readApiKey(args.apiKeyFile) if not apiKey: parser.print_usage() raise SystemExit("\nError reading Api key file %s" % filterPath(args.apiKeyFile)) # Create a new session or recover cached session data - sessionId = None if args.newSessionOp: val = Validate(apiKey=apiKey, apiUrl=apiUrl) rD = val.createSession() displayStatus(rD) sessionId = rD["session_id"] writeSessionId(sessionId, args.sessionFile) else: sessionId = readSessionId(args.sessionFile) if not sessionId: parser.print_usage() raise SystemExit("\nError reading session file %s" % filterPath(args.sessionFile)) # Input files - if args.inputFile and args.inputType: val = Validate(apiKey=apiKey, apiUrl=apiUrl) val.setSession(sessionId) fmt = val.getContentFormatDefault(args.inputType) rD = val.inputFile(filePath=filterPath(args.inputFile), contentType=args.inputType, fileFormat=fmt) displayStatus(rD) # Output files - if args.outputFile and args.outputType: val = Validate(apiKey=apiKey, apiUrl=apiUrl) val.setSession(sessionId) rD = val.getOutputByType(filePath=filterPath(args.outputFile), contentType=args.outputType) displayStatus(rD) # Submit validation service request - if args.validateOp: pD = {} val = Validate(apiKey=apiKey, apiUrl=apiUrl) val.setSession(sessionId) # optional test mode configuration if args.testMode: pD["worker_test_mode"] = True if args.testModeDuration: pD["worker_test_duration"] = args.testModeDuration else: pD["worker_test_duration"] = 10 # if args.expMethod: pD["exp_method"] = args.expMethod # rD = val.run(**pD) displayStatus(rD) # Get index of session file content - if args.indexOp: val = Validate(apiKey=apiKey, apiUrl=apiUrl) val.setSession(sessionId) rD = val.getIndex() displayStatus(rD) displayIndex(rD) # Get session service status details - if args.statusOp: val = Validate(apiKey=apiKey, apiUrl=apiUrl) val.setSession(sessionId) rD = val.getStatus() displayStatus(rD) if args.completeOp: val = Validate(apiKey=apiKey, apiUrl=apiUrl) val.setSession(sessionId) rD = val.getStatus() if "status" in rD and rD["status"] in ["completed", "failed"]: iRet = 1 print_("%d" % iRet) else: iRet = 0 print_("%d" % iRet) # if USEKEY: if args.activityOp and apiKey and apiKey != "anonymous": val = Validate(apiKey=apiKey, apiUrl=apiUrl) val.setSession(sessionId) rD = val.getActivity() displayStatus(rD) displayActivity(rD) if __name__ == "__main__": run()