#!@WHICHPYTHON@ """ CGI Module for checking on the status of an OPAL job """ __date__ = "4 January 2010" __author__ = "Wes Goodman, Samir Unni, Yong Huang" import sys import cgi import cgitb import os,shutil,glob,string,time,urllib.request,urllib.parse,urllib.error from datetime import timedelta from src.server import * from src.aconf import * from src.utilities import getTrackingScriptString, getEventTrackingString cgitb.enable() form = cgi.FieldStorage() def printheader(pagetitle,refresh=None,jobid=None): str = "" str+= "\n" str+= "\n" str+= '' if refresh: str+= "\t\n" % refresh str+= "\t%s\n" % pagetitle str+= "\t\n" % STYLESHEET str+= getTrackingScriptString(jobid) str+= "\n" return str def createcube(dx_input, pqr_input, output): with open(dx_input, 'r') as in_f, open(output, 'w') as out_f, open(pqr_input, 'r') as in_pqr: out_f.write("CPMD CUBE FILE.\n" "OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n") #Discard comments at top of file. line = in_f.readline() newline = in_pqr.readline() while line.startswith('#'): line = in_f.readline() split_line = line.split() grid_sizes = [int(x)*-1 for x in split_line[-3:]] split_line = in_f.readline().split() origin = [float(x) for x in split_line[-3:]] parameter_fmt = "{:>4} {:>11.6f} {:>11.6f} {:>11.6f}\n" atom_num = 0 while newline.startswith('REMARK'): newline = in_pqr.readline() try: while newline.startswith('ATOM') or newline.startswith('HETATM'): newline = in_pqr.readline() new_split_line = newline.split() atom_num = new_split_line[1] except IndexError: pass in_pqr.seek(0) newline = in_pqr.readline() while newline.startswith('REMARK'): newline = in_pqr.readline() origin_line = parameter_fmt.format(atom_num, *origin) out_f.write(origin_line) for x in range(3): split_line = in_f.readline().split() grid_dims = [float(item) for item in split_line[-3:]] dim_lin = parameter_fmt.format(grid_sizes[x], *grid_dims) out_f.write(dim_lin) atoms_parameter_fmt = "{:>4} {:>11.6f} {:>11.6f} {:>11.6f} {:>11.6f}\n" a = True xreal_center = [] yreal_center = [] zreal_center = [] try: while newline.startswith('ATOM') or newline.startswith('HETATM'): new_split_line = newline.split() radius = new_split_line[-1] xyz = new_split_line[-5:-2] line_atom_num = new_split_line[1] atom_radius = new_split_line[-1] pqr_lin = atoms_parameter_fmt.format(int(line_atom_num), float(new_split_line[-2]), float(xyz[0]), float(xyz[1]), float(xyz[2])) out_f.write(pqr_lin) newline = in_pqr.readline() xreal_center.append(float(xyz[0])) yreal_center.append(float(xyz[1])) zreal_center.append(float(xyz[2])) except IndexError: pass x_avg = sum(xreal_center)/float(atom_num) y_avg = sum(yreal_center)/float(atom_num) z_avg = sum(zreal_center)/float(atom_num) #print origin #new_origin = [] #for item in origin: # newitem = item/0.529177 #new_new = item/2 + newitem/2 # new_origin.append(newitem) #print new_origin #Consume unneeded object lines. in_f.readline() in_f.readline() ##TODO: put atoms here value_format = ["{:< 13.5E}"] value_format = ' '.join(value_format * 6) + '\n' group = [] line = in_f.readline() while not line.startswith('attribute'): values = [float(item) for item in line.split()] group.extend(values) if len(group) >= 6: out_f.write(value_format.format(*group)) group = [] line = in_f.readline() if group: group_strs = ["{:< 13.5E}".format(item) for item in group] out_f.write(' '.join(group_strs)) def checkprogress(jobid=None,appServicePort=None,calctype=None): """ Finds out if the job has been completed """ if have_opal: # construct soap request try: status=appServicePort.queryStatus(queryStatusRequest(jobid)) except Exception as e: return ["error"] if status._code == 4: return ["error"] if status._code == 8: return ["complete",status] else: return ["running",status] else: progress = [] file = open('%s%s%s/%s_status' % (INSTALLDIR,TMPDIR,jobid, form["calctype"].value)) for line in file.readlines(): progress.append(line.strip()) file.close() return progress def mainCGI(): """ Main method for determining the query page output """ logopts = {} print("Content-type: text/html\n\n") calctype = form["calctype"].value # prints version error, if it exists if form["jobid"].value == 'False': print(printheader("%s Job Status Page" % calctype.upper())) progress = "version_mismatch" runtime = 0 elif form["jobid"].value == 'notenoughmem': print(printheader("%s Job Status Page" % calctype.upper())) progress = "not_enough_memory" runtime = 0 else: progress = None #Check for error html errorpath = '%s%s%s.html' % (INSTALLDIR, TMPDIR, form["jobid"].value) if os.path.isfile(errorpath): string = "" string+= "\n" string+= "\t\n" string+= "\t\t\n" % (WEBSITE, TMPDIR, form["jobid"].value) string+= "\t\n" string+= "\n" print(string) return # prepares for Opal query, if necessary if have_opal: if calctype=="pdb2pqr": opal_url = PDB2PQR_OPAL_URL elif calctype=="apbs": opal_url = APBS_OPAL_URL appLocator = AppServiceLocator() appServicePort = appLocator.getAppServicePort(opal_url) else: appServicePort = None # if PDB2PQR, determines if link to APBS calculation should be shown if calctype=="pdb2pqr": #if(form["apbsinput"].value=="True"): # change to use a file # apbs_input = True #else: # apbs_input = False apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, form["jobid"].value)) apbs_input = apbsInputFile.read() apbsInputFile.close() if apbs_input=="True": apbs_input = True else: apbs_input = False typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, form["jobid"].value)) typemap = typemapInputFile.read() typemapInputFile.close() if typemap=="True": typemap = True else: typemap = False if have_opal and progress == None: if form["calctype"].value=="pdb2pqr": pdb2pqrJobIDFile = open('%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, form["jobid"].value)) jobid = pdb2pqrJobIDFile.read() pdb2pqrJobIDFile.close() elif form["calctype"].value=="apbs": apbsJobIDFile = open('%s%s%s/apbs_opal_job_id' % (INSTALLDIR, TMPDIR, form["jobid"].value)) jobid = apbsJobIDFile.read() apbsJobIDFile.close() else: jobid = form["jobid"].value if progress == None: cp = checkprogress(jobid,appServicePort,calctype) # finds out status of job progress = cp[0] #initialize with bogus value just in case starttime = time.time() if progress == "running" or progress == "complete": timefile = open('%s%s%s/%s_start_time' % (INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value)) starttime = float(timefile.read()) timefile.close() if progress == "running" or (have_opal and progress not in ("version_mismatch", "not_enough_memory", "error", "complete")): runtime = time.time()-starttime runtime = int(runtime) elif progress == "complete": endTimeFileString = '%s%s%s/%s_end_time' % (INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value) if have_opal and not os.path.isfile(endTimeFileString): runtime = time.time()-starttime with open(endTimeFileString, 'w') as endTimeFile: endTimeFile.write(str(time.time())) else: with open(endTimeFileString, 'r') as endTimeFile: runtime = float(endTimeFile.read())-starttime else: runtime = -1 if progress == "running": #if have_opal: # resultsurl = cp[1]._baseURL #else: if calctype=="pdb2pqr": resultsurl = '%squerystatus.cgi?jobid=%s&apbsinput=%s&calctype=pdb2pqr' % (WEBSITE, form["jobid"].value, apbs_input) else: resultsurl = '%squerystatus.cgi?jobid=%s&calctype=apbs' % (WEBSITE, form["jobid"].value) if progress == "complete": print(printheader("%s Job Status Page" % calctype.upper(), jobid=form["jobid"].value)) elif progress == "error": print(printheader("%s Job Status Page - Error" % calctype.upper(),0, jobid=form["jobid"].value)) elif progress == "running": # job is not complete, refresh in 30 seconds print(printheader("%s Job Status Page" % calctype.upper(), refresh, jobid=form["jobid"].value)) print("\n

") print("

") print('
') print("

Status:") color = "FA3434" image = WEBSITE+"images/red_x.png" if progress == "complete": color = "2CDE56" image = WEBSITE+"images/green_check.png" elif progress == "running": color = "ffcc00" image = WEBSITE+"images/yellow_exclamation.png" print("%s" % (color, progress)) print("
" % image) print("

") print("Run time: " + str(timedelta(seconds=round(runtime))) + '
') print("Current time: %s
" % time.asctime()) print("

\n
\n

") if progress == "complete": if calctype=="pdb2pqr": nexturl = 'apbs_cgi.cgi?jobid=%s' % form["jobid"].value else: url_3dmol = 'visualize.cgi?jobid=%s&tool=%s' % (form["jobid"].value,'tool_3dmol') url_jmol = 'visualize.cgi?jobid=%s&tool=%s' % (form["jobid"].value,'tool_jmol') if have_opal: resp = appServicePort.getOutputs(getOutputsRequest(jobid)) filelist = resp._outputFile print("Here are the results:

") #if have_opal: # resp = appServicePort.getOutputs(getOutputsRequest(jobid)) # for opalfile in resp._outputFile: # if opalfile._name[-8:]!="-input.p": # print "
  • %s
    • " % (opalfile._url, opalfile._name) # print "
  • Standard output
    • " % (resp._stdOut) # print "
  • Standard error
    • " % (resp._stdErr) #else: # for line in cp[1:]: # line = os.path.basename(line) # if line[-8:]!="-input.p": # if line[-11:]=="_stdout.txt": # printname = "Standard output" # elif line[-11:]=="_stderr.txt": # printname = "Standard error" # else: # printname = line # print "
  • %s
    • " % (WEBSITE+TMPDIR+jobid+"/"+line,printname) if calctype=="pdb2pqr" and apbs_input and HAVE_APBS: print("

    Click here to run APBS with your results.

    " % nexturl) elif calctype=="apbs": #print "

    Click here to visualize your results in Jmol.

    " % nexturl print("

    Visualize your results online:") print("

    " % (url_3dmol, url_jmol)) elif progress == "error": print("There was an error with your query request. This page will not refresh.") print("") print("
  • Runtime and debugging information
      ") if have_opal: resp = appServicePort.getOutputs(getOutputsRequest(jobid)) stdouturl = resp._stdOut stderrurl = resp._stdErr else: stdouturl = "%s%s%s/%s_stdout.txt" % (WEBSITE, TMPDIR, jobid, calctype) stderrurl = "%s%s%s/%s_stderr.txt" % (WEBSITE, TMPDIR, jobid, calctype) print("
    • Program output (stdout)
      • " % stdouturl) print("
    • Program errors and warnings (stderr)
      • " % stderrurl) print("
    • ") if have_opal: print("
    If your job has been running for a prolonged period of time and failed with no reason listed in the standard out or standard error, then the job probably timed out and was terminated by the system.
    ") print('
    If you are having trouble running PDB2PQR on the webserver, please download the command line version of PDB2PQR and run the job from there.') elif progress == "running": print("Page will refresh in %d seconds
    " % refresh) print("
    ") if not have_opal: print("") print("
  • Runtime and debugging information
    • ") print("Your results will appear at this page. If you want, you can bookmark it and come back later (note: results are only stored for approximately 12-24 hours)." % resultsurl) elif progress == "version_mismatch": print("The versions of APBS on the local server and on the Opal server do not match, so the calculation could not be completed") print("

    ") print("") print("
    ") print("") print("") if __name__ == "__main__" and "REQUEST_METHOD" in os.environ: """ Determine if called from command line or CGI """ refresh=30 if "jobid" not in form and form["calctype"].value=="pdb2pqr": print("Content-type: text/html\n\n") print(printheader("PDB2PQR Job Status - Error")) text="\n" text+="\t

    Missing jobid field

    \n" text+="\t

    Your request url is missing the jobid field

    \n" text += "" text += "" text+="\n" print(text) sys.exit(2) if (form["calctype"].value=="pdb2pqr" and HAVE_PDB2PQR_OPAL) or (form["calctype"].value=="apbs" and APBS_OPAL_URL!=""): have_opal = True from AppService_client import AppServiceLocator, queryStatusRequest, getOutputsRequest else: have_opal = False mainCGI()