def getOutputFiles(self): """ it returns a list of strings containing the URLs of the output files produced by the job """ resp = self.opalService.appServicePort.getOutputs(getOutputsRequest(self.jobID)) outputFile = [] for i in resp._outputFile: outputFile.append(i._url) return outputFile
def getOutputs(self): if self.status is None: raise RuntimeError("No job has been launched yet") from AppService_client import getOutputsRequest import socket req = getOutputsRequest(self.jobID) try: resp = self.appServicePort.getOutputs(req) except socket.error, e: from chimera import NonChimeraError raise NonChimeraError(str(e))
def getOutputs(self): if self.status is None: raise RuntimeError("No job has been launched yet") from AppService_client import getOutputsRequest import socket req = getOutputsRequest(self.jobID) try: resp = self.appServicePort.getOutputs(req) except socket.error, e: from chimera import NonChimeraError raise NonChimeraError(str(e))
def displayResults(jobID): """ Displays URLs of resulting files, if they are not to be fetched automatically. """ global service_url appServicePort = AppServiceLocator().getAppServicePort(service_url) resp = appServicePort.getOutputs(getOutputsRequest(jobID)) # Retrieve a listing of all output files stdout.write("\tStandard Output: %s\n" % resp._stdOut, "\n") stdout.write("\tStandard Error: %s\n", resp._stdErr) if (resp._outputFile != None): for i in range(0, resp._outputFile.__len__()): stdout.write("\t%s: %s\n" % (resp._outputFile[i]._name, resp._outputFile[i]._url)) stdout.write("\tStandard Error: %s\n" % resp._stdErr)
def displayResults(jobID): """ Displays URLs of resulting files, if they are not to be fetched automatically. """ global service_url appServicePort = AppServiceLocator().getAppServicePort(service_url) resp = appServicePort.getOutputs(getOutputsRequest(jobID)) # Retrieve a listing of all output files stdout.write("\tStandard Output: %s\n" % resp._stdOut, "\n") stdout.write("\tStandard Error: %s\n", resp._stdErr) if (resp._outputFile != None): for i in range(0, resp._outputFile.__len__()): stdout.write("\t%s: %s\n" % (resp._outputFile[i]._name, resp._outputFile[i]._url)) stdout.write("\tStandard Error: %s\n" % resp._stdErr)
def pollStatus(jobID,outputDirectory): """ Determines current status of run and executes fetching of results if the run is completed. """ global service_url appServicePort = AppServiceLocator().getAppServicePort(service_url) status = appServicePort.queryStatus(queryStatusRequest(jobID)) if status._code == 4: stderr.write("Error! The calculation failed!\n") stderr.write("Message: %s\n" % status._message) sys.exit(13) elif status._code != 8: stderr.write("Sorry, the calculation hasn't been completed yet. Please wait a short while and attempt to fetch the files again.\n") sys.exit(13) else: resp = appServicePort.getOutputs(getOutputsRequest(jobID)) fetchResults(jobID, outputDirectory, resp._outputFile, status._code==4)
def pollStatus(jobID, outputDirectory): """ Determines current status of run and executes fetching of results if the run is completed. """ global service_url appServicePort = AppServiceLocator().getAppServicePort(service_url) status = appServicePort.queryStatus(queryStatusRequest(jobID)) if status._code == 4: stderr.write("Error! The calculation failed!\n") stderr.write("Message: %s\n" % status._message) sys.exit(13) elif status._code != 8: stderr.write( "Sorry, the calculation hasn't been completed yet. Please wait a short while and attempt to fetch the files again.\n" ) sys.exit(13) else: resp = appServicePort.getOutputs(getOutputsRequest(jobID)) fetchResults(jobID, outputDirectory, resp._outputFile, status._code == 4)
def initVars(): #global serviceURL if not form.has_key("jobid"): pass # add code to redirect to PDB2PQR input page here else: jobid = form['jobid'].value #aspFile = open('./tmp/%s/%s-asp' % (logTime, logTime)) #appServicePort = pickle.load(aspFile) #aspFile.close() #jobInfoFile = open('./tmp/%s/%s-jobinfo' % (logTime, logTime)) #jobID = jobInfoFile.read() #jobInfoFile.close() aoFile = open('%s%s%s/%s-ao' % (INSTALLDIR, TMPDIR, jobid, jobid)) apbsOptions = pickle.load(aoFile) aoFile.close() if APBS_OPAL_URL != "": from AppService_client import AppServiceLocator, getOutputsRequest apbsOpalJobIDFile = open('%s%s%s/apbs_opal_job_id' % (INSTALLDIR, TMPDIR, jobid)) apbsOpalJobID = apbsOpalJobIDFile.read() apbsOpalJobIDFile.close() appLocator = AppServiceLocator() resp = appLocator.getAppServicePort(APBS_OPAL_URL).getOutputs( getOutputsRequest(apbsOpalJobID)) if not os.access('%s%s%s' % (INSTALLDIR, TMPDIR, jobid), os.F_OK): os.mkdir('%s%s%s' % (INSTALLDIR, TMPDIR, jobid)) for file in resp._outputFile: fileName = file._name if fileName != "Standard Output" and fileName != "Standard Error": urllib.urlretrieve( file._url, '%s%s%s/%s' % (INSTALLDIR, TMPDIR, jobid, fileName)) return apbsOptions
def initVars(): #global serviceURL if not form.has_key("jobid"): pass # add code to redirect to PDB2PQR input page here else: jobid = form['jobid'].value #aspFile = open('./tmp/%s/%s-asp' % (logTime, logTime)) #appServicePort = pickle.load(aspFile) #aspFile.close() #jobInfoFile = open('./tmp/%s/%s-jobinfo' % (logTime, logTime)) #jobID = jobInfoFile.read() #jobInfoFile.close() aoFile = open('%s%s%s/%s-ao' % (INSTALLDIR, TMPDIR, jobid, jobid)) apbsOptions = pickle.load(aoFile) aoFile.close() if APBS_OPAL_URL!="": from AppService_client import AppServiceLocator, getOutputsRequest apbsOpalJobIDFile = open('%s%s%s/apbs_opal_job_id' % (INSTALLDIR, TMPDIR, jobid)) apbsOpalJobID = apbsOpalJobIDFile.read() apbsOpalJobIDFile.close() appLocator = AppServiceLocator() resp = appLocator.getAppServicePort(APBS_OPAL_URL).getOutputs(getOutputsRequest(apbsOpalJobID)) if not os.access('%s%s%s' % (INSTALLDIR, TMPDIR, jobid), os.F_OK): os.mkdir('%s%s%s' % (INSTALLDIR, TMPDIR, jobid)) for file in resp._outputFile: fileName = file._name if fileName!="Standard Output" and fileName!="Standard Error": urllib.urlretrieve(file._url, '%s%s%s/%s' % (INSTALLDIR, TMPDIR, jobid, fileName)) return apbsOptions
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 += "<html>\n" string += "\t<head>\n" string += "\t\t<meta http-equiv=\"Refresh\" content=\"0; url=%s%s%s.html\">\n" % ( WEBSITE, TMPDIR, form["jobid"].value) string += "\t</head>\n" string += "</html>\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 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 "<BODY>\n<P>" print "<h3>Status" print "</h3>" print "Message: %s<br />" % progress print "Run time: %s seconds<br />" % int(runtime) print "Current time: %s<br />" % time.asctime() print "</P>\n<HR>\n<P>" if progress == "complete": if calctype == "pdb2pqr": nexturl = 'apbs_cgi.cgi?jobid=%s' % form["jobid"].value else: nexturl = 'visualize.cgi?jobid=%s' % form["jobid"].value if have_opal: resp = appServicePort.getOutputs(getOutputsRequest(jobid)) filelist = resp._outputFile print "Here are the results:<ul>" print "<li>Input files<ul>" if calctype == "pdb2pqr": # this code should be cleaned up once local PDB2PQR runs output the PDB file with the .pdb extension if have_opal: for i in range(0, len(filelist)): if len(filelist[i]._name) == 4: print "<li><a href=%s>%s</a></li>" % ( filelist[i]._url, filelist[i]._name) else: print "<li><a href=%s%s%s/%s.pdb>%s.pdb</a></li>" % ( WEBSITE, TMPDIR, jobid, jobid, jobid) elif calctype == "apbs": if have_opal: for i in range(0, len(filelist)): if filelist[i]._name == "apbsinput.in" or filelist[ i]._name[-4:] == ".pqr": print "<li><a href=%s>%s</a></li>" % ( filelist[i]._url, filelist[i]._name) else: print "<li><a href=%s%s%s/apbsinput.in>apbsinput.in</a></li>" % ( WEBSITE, TMPDIR, jobid) print "<li><a href=%s%s%s/%s.pqr>%s.pqr</a></li>" % ( WEBSITE, TMPDIR, jobid, jobid, jobid) print "</ul></li>" print "<li>Output files<ul>" queryString = [str(os.environ["REMOTE_ADDR"])] # Getting PDB2PQR run log info if os.path.isfile('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid)): pdb2pqrLogFile = open( '%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid), 'r') logstr = pdb2pqrLogFile.read().split('\n') templogopts = eval(logstr[0]) pdb2pqrLogFile.close() queryString.insert(0, templogopts.get('pdb', '')) if calctype == "pdb2pqr": if have_opal: for i in range(0, len(filelist)): if filelist[i]._name.endswith( (".propka", "-typemap.html", ".pqr", ".in")): # if filelist[i]._name[-4:]==".pqr": # # Getting pqr file length for PDB2PQR Opal run # f=urllib.urlopen(filelist[i]._url) # #pqrOpalFileLength = len(f.readlines()) # f.close() print "<li><a href=%s>%s</a></li>" % ( filelist[i]._url, filelist[i]._name) #Get the first line of the summary file. if filelist[i]._name.endswith(".summary"): f = urllib.urlopen(filelist[i]._url) summaryLine = f.readline().strip() #logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine queryString.append(summaryLine) f.close() # logRun(logopts, runtime, pqrOpalFileLength, logff, REMOTE_ADDR) else: #Get the first line of the summary file. summaryFile = '%s%s%s/%s%s' % (INSTALLDIR, TMPDIR, jobid, jobid, ".summary") if os.path.isfile(summaryFile): with open(summaryFile) as f: summaryLine = f.readline().strip() #logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine queryString.append(summaryLine) outputfilelist = glob.glob('%s%s%s/*.propka' % (INSTALLDIR, TMPDIR, jobid)) for i in range(0, len(outputfilelist)): outputfilelist[i] = os.path.basename(outputfilelist[i]) for extension in ["-typemap.html", ".pqr", ".in"]: if extension != ".in" or apbs_input != False: if extension == "-typemap.html" and typemap == False: continue outputfilelist.append('%s%s' % (jobid, extension)) for outputfile in outputfilelist: print "<li><a href=%s%s%s/%s>%s</a></li>" % ( WEBSITE, TMPDIR, jobid, outputfile, outputfile) logopts['queryPDB2PQR'] = '|'.join(queryString) #for extension in ["-typemap.html", ".pqr", ".in"]: # print "<li><a href=%s%s%s/%s%s>%s%s</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, extension, jobid, extension) elif calctype == "apbs": if have_opal: for i in range(0, len(filelist)): if filelist[i]._name[-3:] == ".dx": # compressing APBS OpenDX output files currentpath = os.getcwd() zipjobid = filelist[i]._name.split("-")[0] urllib.urlretrieve( filelist[i]._url, '%s%s%s/%s' % (INSTALLDIR, TMPDIR, zipjobid, filelist[i]._name)) os.chdir('%s%s%s' % (INSTALLDIR, TMPDIR, zipjobid)) # making both the dx file and the compressed file (.gz) available in the directory syscommand = 'cp %s dxbkupfile' % (filelist[i]._name) os.system(syscommand) syscommand = 'gzip -9 ' + filelist[i]._name os.system(syscommand) syscommand = 'mv dxbkupfile %s' % (filelist[i]._name) os.system(syscommand) os.chdir(currentpath) outputfilezip = filelist[i]._name + '.gz' print "<li><a href=%s%s%s/%s>%s</a></li>" % ( WEBSITE, TMPDIR, zipjobid, outputfilezip, outputfilezip) else: outputfilelist = glob.glob('%s%s%s/%s-*.dx' % (INSTALLDIR, TMPDIR, jobid, jobid)) for outputfile in outputfilelist: # compressing APBS OpenDX output files currentpath = os.getcwd() workingpath = os.path.dirname(outputfile) os.chdir(workingpath) # making both the dx file and the compressed file (.gz) available in the directory syscommand = 'cp %s dxbkupfile' % ( os.path.basename(outputfile)) os.system(syscommand) syscommand = 'gzip -9 ' + os.path.basename(outputfile) os.system(syscommand) syscommand = 'mv dxbkupfile %s' % ( os.path.basename(outputfile)) os.system(syscommand) os.chdir(currentpath) outputfilezip = outputfile + ".gz" print "<li><a href=%s%s%s/%s>%s</a></li>" % ( WEBSITE, TMPDIR, jobid, os.path.basename(outputfilezip), os.path.basename(outputfilezip)) logopts['queryAPBS'] = '|'.join(queryString) print "</ul></li>" print "<li>Runtime and debugging information<ul>" if have_opal: 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 "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl print "</ul></li></ul>" #if have_opal: # resp = appServicePort.getOutputs(getOutputsRequest(jobid)) # for opalfile in resp._outputFile: # if opalfile._name[-8:]!="-input.p": # print "<li><a href=%s>%s</a></li>" % (opalfile._url, opalfile._name) # print "<li><a href=%s>Standard output</a></li>" % (resp._stdOut) # print "<li><a href=%s>Standard error</a></li>" % (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 "<li><a href=%s>%s</a></li>" % (WEBSITE+TMPDIR+jobid+"/"+line,printname) if calctype == "pdb2pqr" and apbs_input and HAVE_APBS != "": print "</ul></p><hr><p><b><a href=%s>Click here</a> to run APBS with your results.</b></p>" % nexturl elif calctype == "apbs": print "</ul></p><hr><p><b><a href=%s>Click here</a> to visualize your results.</b></p>" % nexturl elif progress == "error": print "There was an error with your query request. This page will not refresh." elif progress == "running": print "Page will refresh in %d seconds<br />" % refresh print "<HR>" print "<small>Your results will appear at <a href=%s>this page</a>. If you want, you can bookmark it and come back later (note: results are only stored for approximately 12-24 hours).</small>" % 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 "</P>" print "<script type=\"text/javascript\">" for key in logopts: print getEventTrackingString('queryData', key, logopts[key]), #print "_gaq.push(['_trackPageview', '/main_cgi/has_%s_%s.html']);" % (key, logopts[key]) print "</script>" print "</BODY>" print "</HTML>"
print "Waiting 30 seconds" sleep(30) # Query job status status = appServicePort.queryStatus(queryStatusRequest(jobID)) # If execution is successful retrieve job outputs. if status._code == 8: # 8 = GramJob.STATUS_DONE # Create local directory to hold output files output_dir = 'meme_out' mkdir(output_dir); # Instantiate a collection of outputs outputs = appServicePort.getOutputs(getOutputsRequest(jobID)) # Instantiate a request object for retrieving output files fileRequest = getOutputAsBase64ByNameRequest() # Retreive each output file and save to local directory. # MEME writes stdout and stderr to files that aren't listed # in the response, so we handle those separately. print "\tStandard Output:", outputs._stdOut localOutput = open(output_dir + '/' + "stdout.txt", "w") fileRequest._jobID = jobID fileRequest._fileName = "stdout.txt" content = appServicePort.getOutputAsBase64ByName(fileRequest) print >>localOutput, content localOutput.close() print "\tStandard Error:", outputs._stdErr
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 += "<html>\n" string += "\t<head>\n" string += '\t\t<meta http-equiv="Refresh" content="0; url=%s%s%s.html">\n' % ( WEBSITE, TMPDIR, form["jobid"].value, ) string += "\t</head>\n" string += "</html>\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 != "version_mismatch" and progress != "not_enough_memory" and progress != "error" ): runtime = time.time() - starttime elif progress == "complete": endtimefile = open("%s%s%s/%s_end_time" % (INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value)) 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()) elif progress == "error": print printheader("%s Job Status Page - Error" % calctype.upper(), 0) elif progress == "running": # job is not complete, refresh in 30 seconds print printheader("%s Job Status Page" % calctype.upper(), refresh) print "<BODY>\n<P>" print "<h3>Status" print "</h3>" print "Message: %s<br />" % progress print "Run time: %s seconds<br />" % int(runtime) print "Current time: %s<br />" % time.asctime() print "</P>\n<HR>\n<P>" if progress == "complete": if calctype == "pdb2pqr": nexturl = "apbs_cgi.cgi?jobid=%s" % form["jobid"].value else: nexturl = "visualize.cgi?jobid=%s" % form["jobid"].value if have_opal: resp = appServicePort.getOutputs(getOutputsRequest(jobid)) filelist = resp._outputFile print "Here are the results:<ul>" print "<li>Input files<ul>" if calctype == "pdb2pqr": # this code should be cleaned up once local PDB2PQR runs output the PDB file with the .pdb extension if have_opal: for i in range(0, len(filelist)): if len(filelist[i]._name) == 4: print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name) else: print "<li><a href=%s%s%s/%s.pdb>%s.pdb</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, jobid) elif calctype == "apbs": if have_opal: for i in range(0, len(filelist)): if filelist[i]._name == "apbsinput.in" or filelist[i]._name[-4:] == ".pqr": print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name) else: print "<li><a href=%s%s%s/apbsinput.in>apbsinput.in</a></li>" % (WEBSITE, TMPDIR, jobid) print "<li><a href=%s%s%s/%s.pqr>%s.pqr</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, jobid) print "</ul></li>" print "<li>Output files<ul>" if calctype == "pdb2pqr": if have_opal: # Getting PDB2PQR Opal run log info if os.path.isfile("%s%s%s/pdb2pqr_opal_log" % (INSTALLDIR, TMPDIR, form["jobid"].value)): pdb2pqrOpalLogFile = open( "%s%s%s/pdb2pqr_opal_log" % (INSTALLDIR, TMPDIR, form["jobid"].value), "r" ) logstr = pdb2pqrOpalLogFile.read().split("\n") logopts = eval(logstr[0]) # logff = logstr[1] # REMOTE_ADDR = logstr[2] pdb2pqrOpalLogFile.close() for i in range(0, len(filelist)): if ( filelist[i]._name[-7:] == ".propka" or (filelist[i]._name[-13:] == "-typemap.html" and typemap == True) or filelist[i]._name[-4:] == ".pqr" or filelist[i]._name[-3:] == ".in" ): if filelist[i]._name[-4:] == ".pqr": # Getting pqr file length for PDB2PQR Opal run f = urllib.urlopen(filelist[i]._url) pqrOpalFileLength = len(f.readlines()) f.close() print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name) # logRun(logopts, runtime, pqrOpalFileLength, logff, REMOTE_ADDR) else: outputfilelist = glob.glob("%s%s%s/*.propka" % (INSTALLDIR, TMPDIR, jobid)) for i in range(0, len(outputfilelist)): outputfilelist[i] = os.path.basename(outputfilelist[i]) for extension in ["-typemap.html", ".pqr", ".in"]: if extension != ".in" or apbs_input != False: if extension == "-typemap.html" and typemap == False: continue outputfilelist.append("%s%s" % (jobid, extension)) for outputfile in outputfilelist: print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, jobid, outputfile, outputfile) # for extension in ["-typemap.html", ".pqr", ".in"]: # print "<li><a href=%s%s%s/%s%s>%s%s</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, extension, jobid, extension) elif calctype == "apbs": if have_opal: for i in range(0, len(filelist)): if filelist[i]._name[-3:] == ".dx": # compressing APBS OpenDX output files currentpath = os.getcwd() zipjobid = filelist[i]._name.split("-")[0] urllib.urlretrieve( filelist[i]._url, "%s%s%s/%s" % (INSTALLDIR, TMPDIR, zipjobid, filelist[i]._name) ) os.chdir("%s%s%s" % (INSTALLDIR, TMPDIR, zipjobid)) # making both the dx file and the compressed file (.gz) available in the directory syscommand = "cp %s dxbkupfile" % (filelist[i]._name) os.system(syscommand) syscommand = "gzip -9 " + filelist[i]._name os.system(syscommand) syscommand = "mv dxbkupfile %s" % (filelist[i]._name) os.system(syscommand) os.chdir(currentpath) outputfilezip = filelist[i]._name + ".gz" print "<li><a href=%s%s%s/%s>%s</a></li>" % ( WEBSITE, TMPDIR, zipjobid, outputfilezip, outputfilezip, ) else: outputfilelist = glob.glob("%s%s%s/%s-*.dx" % (INSTALLDIR, TMPDIR, jobid, jobid)) for outputfile in outputfilelist: # compressing APBS OpenDX output files currentpath = os.getcwd() workingpath = os.path.dirname(outputfile) os.chdir(workingpath) # making both the dx file and the compressed file (.gz) available in the directory syscommand = "cp %s dxbkupfile" % (os.path.basename(outputfile)) os.system(syscommand) syscommand = "gzip -9 " + os.path.basename(outputfile) os.system(syscommand) syscommand = "mv dxbkupfile %s" % (os.path.basename(outputfile)) os.system(syscommand) os.chdir(currentpath) outputfilezip = outputfile + ".gz" print "<li><a href=%s%s%s/%s>%s</a></li>" % ( WEBSITE, TMPDIR, jobid, os.path.basename(outputfilezip), os.path.basename(outputfilezip), ) print "</ul></li>" print "<li>Runtime and debugging information<ul>" if have_opal: 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 "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl print "</ul></li></ul>" # if have_opal: # resp = appServicePort.getOutputs(getOutputsRequest(jobid)) # for opalfile in resp._outputFile: # if opalfile._name[-8:]!="-input.p": # print "<li><a href=%s>%s</a></li>" % (opalfile._url, opalfile._name) # print "<li><a href=%s>Standard output</a></li>" % (resp._stdOut) # print "<li><a href=%s>Standard error</a></li>" % (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 "<li><a href=%s>%s</a></li>" % (WEBSITE+TMPDIR+jobid+"/"+line,printname) if calctype == "pdb2pqr" and apbs_input and HAVE_APBS != "": print "</ul></p><hr><p><a href=%s>Click here</a> to run APBS with your results.</p>" % nexturl elif calctype == "apbs": print "</ul></p><hr><p><a href=%s>Click here</a> to visualize your results.</p>" % nexturl elif progress == "error": print "There was an error with your query request. This page will not refresh." elif progress == "running": print "Page will refresh in %d seconds<br />" % refresh print "<HR>" print "<small>Your results will appear at <a href=%s>this page</a>. If you want, you can bookmark it and come back later (note: results are only stored for approximately 12-24 hours).</small>" % 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 "</P>" print '<script type="text/javascript">' print 'var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");' print "document.write(unescape(\"%3Cscript src='\" + gaJsHost + \"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E\"));" print "</script>" print '<script type="text/javascript">' print "try {" print 'var pageTracker = _gat._getTracker("UA-11026338-3");' if logopts != {}: for key in logopts: print 'pageTracker._trackPageview("/main_cgi/has_%s_%s.html");' % (key, logopts[key]) print "pageTracker._trackPageview();" print "} catch(err) {}</script>" print "</BODY>" print "</HTML>"
print "Waiting 30 seconds" sleep(30) # Query job status status = appServicePort.queryStatus(queryStatusRequest(jobID)) # If execution is successful retrieve job outputs. if status._code == 8: # 8 = GramJob.STATUS_DONE # Create local directory to hold output files output_dir = "meme_out" mkdir(output_dir) # Instantiate a collection of outputs outputs = appServicePort.getOutputs(getOutputsRequest(jobID)) # Instantiate a request object for retrieving output files fileRequest = getOutputAsBase64ByNameRequest() # Retreive each output file and save to local directory. # MEME writes stdout and stderr to files that aren't listed # in the response, so we handle those separately. print "\tStandard Output:", outputs._stdOut localOutput = open(output_dir + "/" + "stdout.txt", "w") fileRequest._jobID = jobID fileRequest._fileName = "stdout.txt" content = appServicePort.getOutputAsBase64ByName(fileRequest) print >> localOutput, content localOutput.close() print "\tStandard Error:", outputs._stdErr
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+= "<html>\n" string+= "\t<head>\n" string+= "\t\t<meta http-equiv=\"Refresh\" content=\"0; url=%s%s%s.html\">\n" % (WEBSITE, TMPDIR, form["jobid"].value) string+= "\t</head>\n" string+= "</html>\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 "<BODY>\n<P>" print "<p></p>" print '<div id="content">' print "<h3>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 "<strong style=\"color:#%s;\">%s</strong>" % (color, progress) print "<img src=\"%s\"><br />" % image print "</h3>" print "Run time: " + str(timedelta(seconds=round(runtime))) + '<br />' print "Current time: %s<br />" % time.asctime() print "</P>\n<HR>\n<P>" 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:<ul>" print "<li>Input files<ul>" if calctype=="pdb2pqr": # this code should be cleaned up once local PDB2PQR runs output the PDB file with the .pdb extension if have_opal: for i in range(0,len(filelist)): file_name = filelist[i]._name if ((len(file_name) == 4 and '.' not in file_name) or (file_name.lower().endswith(".pdb") and "pdb2pka_output" not in file_name)): print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name) if file_name.lower().endswith((".mol", ".mol2", ".names", ".dat")) and "pdb2pka_output" not in file_name: print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name) else: print "<li><a href=%s%s%s/%s.pdb>%s.pdb</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, jobid) elif calctype=="apbs": if have_opal: for i in range(0,len(filelist)): if filelist[i]._name == "apbsinput.in" or filelist[i]._name[-4:] == ".pqr": print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name) else: print "<li><a href=%s%s%s/apbsinput.in>apbsinput.in</a></li>" % (WEBSITE, TMPDIR, jobid) print "<li><a href=%s%s%s/%s.pqr>%s.pqr</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, jobid) print "</ul></li>" print "<li>Output files<ul>" queryString = [str(os.environ["REMOTE_ADDR"])] # Getting PDB2PQR run log info if os.path.isfile('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid)): pdb2pqrLogFile=open('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid), 'r') logstr=pdb2pqrLogFile.read().split('\n') templogopts = eval(logstr[0]) pdb2pqrLogFile.close() queryString.insert(0, templogopts.get('pdb','')) if calctype=="pdb2pqr": if have_opal: for i in range(0,len(filelist)): if filelist[i]._name.endswith((".propka", "-typemap.html")): print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name) if filelist[i]._name.endswith(".in") and "pdb2pka_output" not in filelist[i]._name: print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name) if filelist[i]._name.endswith(".pqr") and not filelist[i]._name.endswith("background_input.pqr"): print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name) #Get the first line of the summary file. if filelist[i]._name.endswith(".summary"): f=urllib.urlopen(filelist[i]._url) summaryLine = f.readline().strip() #logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine queryString.append(summaryLine) f.close() # logRun(logopts, runtime, pqrOpalFileLength, logff, REMOTE_ADDR) else: #Get the first line of the summary file. summaryFile = '%s%s%s/%s%s' % (INSTALLDIR, TMPDIR, jobid, jobid, ".summary") if os.path.isfile(summaryFile): with open(summaryFile) as f: summaryLine = f.readline().strip() #logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine queryString.append(summaryLine) outputfilelist = glob.glob('%s%s%s/*.propka' % (INSTALLDIR, TMPDIR, jobid)) for i in range(0,len(outputfilelist)): outputfilelist[i] = os.path.basename(outputfilelist[i]) for extension in ["-typemap.html", ".pqr", ".in"]: if extension != ".in" or apbs_input != False: if extension == "-typemap.html" and typemap == False: continue outputfilelist.append('%s%s' % (jobid, extension)) for outputfile in outputfilelist: print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, jobid, outputfile, outputfile) logopts['queryPDB2PQR'] = '|'.join(queryString) #for extension in ["-typemap.html", ".pqr", ".in"]: # print "<li><a href=%s%s%s/%s%s>%s%s</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, extension, jobid, extension) elif calctype=="apbs": if have_opal: for i in range(0,len(filelist)): if filelist[i]._name[-3:]==".dx": # compressing APBS OpenDX output files currentpath = os.getcwd() zipjobid = filelist[i]._name.split("-")[0] dxfilename = '%s%s%s/%s' % (INSTALLDIR, TMPDIR, zipjobid, filelist[i]._name) urllib.urlretrieve(filelist[i]._url, dxfilename) os.chdir('%s%s%s' % (INSTALLDIR, TMPDIR, zipjobid)) # making both the dx file and the compressed file (.gz) available in the directory syscommand = 'cp %s dxbkupfile' % (filelist[i]._name) os.system(syscommand) syscommand = 'gzip -9 ' + filelist[i]._name os.system(syscommand) syscommand = 'mv dxbkupfile %s' % (filelist[i]._name) os.system(syscommand) outputfilezip = filelist[i]._name + '.gz' pqrfilename = '%s%s%s/%s.pqr' % (INSTALLDIR, TMPDIR, zipjobid, zipjobid) cubefilename = '%s%s%s/%s.cube' % (INSTALLDIR, TMPDIR, zipjobid, zipjobid) # making both the cube file and the compressed file (.gz) available in the directory createcube(dxfilename, pqrfilename, cubefilename) cubefilebasename = os.path.basename(cubefilename) syscommand = 'cp %s cubebkupfile' % cubefilebasename os.system(syscommand) syscommand = 'gzip -9 ' + cubefilebasename os.system(syscommand) syscommand = 'mv cubebkupfile %s' % cubefilebasename os.system(syscommand) os.chdir(currentpath) outputcubefilezip = cubefilebasename+".gz" print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, zipjobid, outputfilezip, outputfilezip) print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, zipjobid, outputcubefilezip, outputcubefilezip) else: outputfilelist = glob.glob('%s%s%s/%s-*.dx' % (INSTALLDIR, TMPDIR, jobid, jobid)) for dxfile in outputfilelist: # compressing APBS OpenDX output files currentpath = os.getcwd() workingpath = os.path.dirname(dxfile) os.chdir(workingpath) # making both the dx file and the compressed file (.gz) available in the directory syscommand = 'cp %s dxbkupfile' % (os.path.basename(dxfile)) os.system(syscommand) syscommand = 'gzip -9 ' + os.path.basename(dxfile) os.system(syscommand) syscommand = 'mv dxbkupfile %s' % (os.path.basename(dxfile)) os.system(syscommand) os.chdir(currentpath) outputfilezip = dxfile+".gz" cubefilename = '%s%s%s/%s.cube' % (INSTALLDIR, TMPDIR, jobid, jobid) pqrfilename = '%s%s%s/%s.pqr' % (INSTALLDIR, TMPDIR, jobid, jobid) createcube(dxfile, pqrfilename, cubefilename) print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, jobid, os.path.basename(outputfilezip), os.path.basename(outputfilezip)) outputcubefilelist = glob.glob('%s%s%s/%s.cube' % (INSTALLDIR, TMPDIR, jobid, jobid)) for cubefile in outputcubefilelist: # compressing cube output file currentpath = os.getcwd() os.chdir(workingpath) # making both the cube file and the compressed file (.gz) available in the directory syscommand = 'cp %s cubebkupfile' % (os.path.basename(cubefile)) os.system(syscommand) syscommand = 'gzip -9 ' + os.path.basename(cubefile) os.system(syscommand) syscommand = 'mv cubebkupfile %s' % (os.path.basename(cubefile)) os.system(syscommand) os.chdir(currentpath) outputcubefilezip = cubefile+".gz" print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, jobid, os.path.basename(outputcubefilezip), os.path.basename(outputcubefilezip)) logopts['queryAPBS'] = '|'.join(queryString) if calctype=="pdb2pqr": if have_opal: outputfilelist = [] for i in range(0,len(filelist)): if filelist[i]._name.endswith((".DAT", ".txt")): outputfilelist.append((filelist[i]._url, os.path.basename(filelist[i]._name))) #print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name) if outputfilelist: print "</ul></li>" print "<li>PDB2PKA files<ul>" for outputfile in outputfilelist: print "<li><a href=%s>%s</a></li>" % (outputfile[0], outputfile[1]) else: outputfilelist = glob.glob('%s%s%s/pdb2pka_output/*.DAT' % (INSTALLDIR, TMPDIR, jobid)) outputfilelist.extend(glob.glob('%s%s%s/pdb2pka_output/*.txt' % (INSTALLDIR, TMPDIR, jobid))) outputfilelist = [os.path.basename(outputfile) for outputfile in outputfilelist] if outputfilelist: print "</ul></li>" print "<li>PDB2PKA files<ul>" for outputfile in outputfilelist: print "<li><a href=%s%s%s/pdb2pka_output/%s>%s</a></li>" % (WEBSITE, TMPDIR, jobid, outputfile, outputfile) print "</ul></li>" print "<li>Runtime and debugging information<ul>" if have_opal: 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 "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl print "</ul></li></ul>" #if have_opal: # resp = appServicePort.getOutputs(getOutputsRequest(jobid)) # for opalfile in resp._outputFile: # if opalfile._name[-8:]!="-input.p": # print "<li><a href=%s>%s</a></li>" % (opalfile._url, opalfile._name) # print "<li><a href=%s>Standard output</a></li>" % (resp._stdOut) # print "<li><a href=%s>Standard error</a></li>" % (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 "<li><a href=%s>%s</a></li>" % (WEBSITE+TMPDIR+jobid+"/"+line,printname) if calctype=="pdb2pqr" and apbs_input and HAVE_APBS: print "</ul></p><hr><p><b><a href=%s>Click here</a> to run APBS with your results.</b></p>" % nexturl elif calctype=="apbs": #print "</ul></p><hr><p><b><a href=%s>Click here</a> to visualize your results in Jmol.</b></p>" % nexturl print "</ul></p><hr><p><b>Visualize your results online:" print "<ul> <li><a href=%s>3Dmol</a></li><li><a href=%s>Jmol</a></li></ul>" % (url_3dmol, url_jmol) elif progress == "error": print "There was an error with your query request. This page will not refresh." print "</ul></li>" print "<li>Runtime and debugging information<ul>" 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 "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl print "</ul></li></ul>" if have_opal: print " <br />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.<br />" print '<br />If you are having trouble running PDB2PQR on the webserver, please download the <a href="http://www.poissonboltzmann.org/docs/downloads/">command line version of PDB2PQR</a> and run the job from there.' elif progress == "running": print "Page will refresh in %d seconds<br />" % refresh print "<HR>" if not have_opal: print "</ul></li>" print "<li>Runtime and debugging information<ul>" stdouturl = "%s%s%s/%s_stdout.txt" % (WEBSITE, TMPDIR, jobid, calctype) stderrurl = "%s%s%s/%s_stderr.txt" % (WEBSITE, TMPDIR, jobid, calctype) print "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl print "</ul></li></ul>" print "<small>Your results will appear at <a href=%s>this page</a>. If you want, you can bookmark it and come back later (note: results are only stored for approximately 12-24 hours).</small>" % 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 "</P>" print "<script type=\"text/javascript\">" for key in logopts: print getEventTrackingString('queryData', key, logopts[key]), #print "_gaq.push(['_trackPageview', '/main_cgi/has_%s_%s.html']);" % (key, logopts[key]) print "</script>" print "</div> <!--end content div-->" print "</BODY>" print "</HTML>"
def ws_compute(self): if self._port_list[0][3]['url'] != None: url = self._port_list[0][3]['url'] adv = self._port_list[0][3]['adv'] else: url = "" print "ERROR: There are no input arguments provided for this web service" cmdline = "" numProcs = None tagged = [] untagged = [] flags = [] files = [] for i in self._port_list: pn = i[0] meta = i[3] if ((self.hasInputFromPort(pn) and self.getInputFromPort(pn) != "") or meta['default'] != None) and adv == True: # print "META" # print meta if meta['type'] == 'FLAG': if self.hasInputFromPort(pn): if self.getInputFromPort(pn) == True: flags.append(meta['arg']) elif meta['default'] == 'True': flags.append(meta['arg']) elif meta['type'] == 'TAGGED': if self.hasInputFromPort(pn): val = self.getInputFromPort(pn) elif meta['default'] != None: val = meta['default'] if meta['file'] == True: file_an = core.modules.basic_modules.File.translate_to_string(val) file_bn = os.path.basename(file_an) tagged.append(meta['arg'] + file_bn) files.append(file_an) else: tagged.append(meta['arg'] + val) elif meta['type'] == 'UNTAGGED': if self.hasInputFromPort(pn): val = self.getInputFromPort(pn) elif meta['default'] != None: val = meta['default'] if meta['file'] == True: file_an = core.modules.basic_modules.File.translate_to_string(val) file_bn = os.path.basename(file_an) untagged.append(file_bn) files.append(file_an) else: untagged.append(val) cmdline = "" for i in flags: cmdline += i + " " for i in tagged: cmdline += i + " " for i in untagged: cmdline += i + " " inputFiles = [] for i in files: inputFile = ns0.InputFileType_Def('inputFile') inputFile._name = os.path.basename(i) inputFile._attachment = open(i, "r") inputFiles.append(inputFile) if cmdline == "": if self.hasInputFromPort('commandLine'): cmdline = self.getInputFromPort('commandLine') if self.hasInputFromPort('numProcs'): numProcs = self.getInputFromPort('numProcs') if self.hasInputFromPort("inFiles"): inFilesPath = self.getInputFromPort("inFiles") if inFilesPath != None: for i in inFilesPath: inputFile = ns0.InputFileType_Def('inputFile') inputFile._name = os.path.basename(i) inputFile._attachment = open(i, "r") inputFiles.append(inputFile) print os.path.basename(url) + " from " + os.path.dirname(url) + " is going to run with arguments:\n " + cmdline appLocator = AppServiceLocator() appServicePort = appLocator.getAppServicePort(url) req = launchJobRequest() req._argList = cmdline req._inputFile = inputFiles if numProcs != None: req._numProcs = numProcs resp = appServicePort.launchJob(req) self.jobID = resp._jobID print "Job outputs URL: " + resp._status._baseURL # urlparse.urljoin(url, '/' + self.jobID) status = resp._status._code while (status != 4 and status != 8): status = appServicePort.queryStatus(queryStatusRequest(self.jobID))._code time.sleep(5) if (status == 8): resp = appServicePort.getOutputs(getOutputsRequest(self.jobID)) outurls = [str(resp._stdOut), str(resp._stdErr)] if (resp._outputFile != None): for i in resp._outputFile: outurls.append(str(i._url)) print "Opal job completed successfully" else: print "ERROR: Opal job failed" resp = appServicePort.getOutputs(getOutputsRequest(self.jobID)) outurls = [str(resp._stdOut), str(resp._stdErr)] self.setResult("outurls", tuple(outurls))
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 else: progress = None # 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] 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 != "version_mismatch"): runtime = time.time() - starttime elif progress == "complete": endtimefile = open( '%s%s%s/%s_end_time' % (INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value)) runtime = float(endtimefile.read()) - starttime 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()) elif progress == "error": print printheader("%s Job Status Page - Error" % calctype.upper(), 0) elif progress == "running": # job is not complete, refresh in 30 seconds print printheader("%s Job Status Page" % calctype.upper(), refresh) print "<BODY>\n<P>" print "<h3>Status" print "</h3>" print "Message: %s<br />" % progress print "Run time: %s seconds<br />" % int(runtime) print "Current time: %s<br />" % time.asctime() print "</P>\n<HR>\n<P>" if progress == "complete": if calctype == "pdb2pqr": nexturl = 'apbs_cgi.cgi?jobid=%s' % form["jobid"].value else: nexturl = 'visualize.cgi?jobid=%s' % form["jobid"].value if have_opal: resp = appServicePort.getOutputs(getOutputsRequest(jobid)) filelist = resp._outputFile print "Here are the results:<ul>" print "<li>Input files<ul>" if calctype == "pdb2pqr": # this code should be cleaned up once local PDB2PQR runs output the PDB file with the .pdb extension if have_opal: for i in range(0, len(filelist)): if len(filelist[i]._name) == 4: print "<li><a href=%s>%s</a></li>" % ( filelist[i]._url, filelist[i]._name) else: print "<li><a href=%s%s%s/%s.pdb>%s.pdb</a></li>" % ( WEBSITE, TMPDIR, jobid, jobid, jobid) elif calctype == "apbs": if have_opal: for i in range(0, len(filelist)): if filelist[i]._name == "apbsinput.in" or filelist[ i]._name[-4:] == ".pqr": print "<li><a href=%s>%s</a></li>" % ( filelist[i]._url, filelist[i]._name) else: print "<li><a href=%s%s%s/apbsinput.in>apbsinput.in</a></li>" % ( WEBSITE, TMPDIR, jobid) print "<li><a href=%s%s%s/%s.pqr>%s.pqr</a></li>" % ( WEBSITE, TMPDIR, jobid, jobid, jobid) print "</ul></li>" print "<li>Output files<ul>" if calctype == "pdb2pqr": if have_opal: # Getting PDB2PQR Opal run log info if os.path.isfile('%s%s%s/pdb2pqr_opal_log' % (INSTALLDIR, TMPDIR, form["jobid"].value)): pdb2pqrOpalLogFile = open( '%s%s%s/pdb2pqr_opal_log' % (INSTALLDIR, TMPDIR, form["jobid"].value), 'r') logstr = pdb2pqrOpalLogFile.read().split('\n') logopts = eval(logstr[0]) logff = logstr[1] REMOTE_ADDR = logstr[2] pdb2pqrOpalLogFile.close() for i in range(0, len(filelist)): if filelist[i]._name[-7:] == ".propka" or ( filelist[i]._name[-13:] == "-typemap.html" and typemap == True ) or filelist[i]._name[-4:] == ".pqr" or filelist[i]._name[ -3:] == ".in": if filelist[i]._name[-4:] == ".pqr": # Getting pqr file length for PDB2PQR Opal run f = urllib.urlopen(filelist[i]._url) pqrOpalFileLength = len(f.readlines()) f.close() print "<li><a href=%s>%s</a></li>" % ( filelist[i]._url, filelist[i]._name) logRun(logopts, runtime, pqrOpalFileLength, logff, REMOTE_ADDR) else: outputfilelist = glob.glob('%s%s%s/*.propka' % (INSTALLDIR, TMPDIR, jobid)) for i in range(0, len(outputfilelist)): outputfilelist[i] = os.path.basename(outputfilelist[i]) for extension in ["-typemap.html", ".pqr", ".in"]: if extension != ".in" or apbs_input != False: if extension == "-typemap.html" and typemap == False: continue outputfilelist.append('%s%s' % (jobid, extension)) for outputfile in outputfilelist: print "<li><a href=%s%s%s/%s>%s</a></li>" % ( WEBSITE, TMPDIR, jobid, outputfile, outputfile) #for extension in ["-typemap.html", ".pqr", ".in"]: # print "<li><a href=%s%s%s/%s%s>%s%s</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, extension, jobid, extension) elif calctype == "apbs": if have_opal: for i in range(0, len(filelist)): if filelist[i]._name[-3:] == ".dx": # compressing APBS OpenDX output files currentpath = os.getcwd() zipjobid = filelist[i]._name.split("-")[0] urllib.urlretrieve( filelist[i]._url, '%s%s%s/%s' % (INSTALLDIR, TMPDIR, zipjobid, filelist[i]._name)) os.chdir('%s%s%s' % (INSTALLDIR, TMPDIR, zipjobid)) syscommand = 'zip -9 ' + filelist[ i]._name + '.zip ' + filelist[i]._name os.system(syscommand) os.chdir(currentpath) outputfilezip = filelist[i]._name + '.zip' print "<li><a href=%s%s%s/%s>%s</a></li>" % ( WEBSITE, TMPDIR, zipjobid, outputfilezip, outputfilezip) else: outputfilelist = glob.glob('%s%s%s/%s-*.dx' % (INSTALLDIR, TMPDIR, jobid, jobid)) for outputfile in outputfilelist: # compressing APBS OpenDX output files currentpath = os.getcwd() workingpath = os.path.dirname(outputfile) os.chdir(workingpath) syscommand = 'zip -9 ' + os.path.basename( outputfile) + '.zip ' + os.path.basename(outputfile) os.system(syscommand) os.chdir(currentpath) outputfilezip = outputfile + ".zip" print "<li><a href=%s%s%s/%s>%s</a></li>" % ( WEBSITE, TMPDIR, jobid, os.path.basename(outputfilezip), os.path.basename(outputfilezip)) print "</ul></li>" print "<li>Runtime and debugging information<ul>" if have_opal: 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 "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl print "</ul></li></ul>" #if have_opal: # resp = appServicePort.getOutputs(getOutputsRequest(jobid)) # for opalfile in resp._outputFile: # if opalfile._name[-8:]!="-input.p": # print "<li><a href=%s>%s</a></li>" % (opalfile._url, opalfile._name) # print "<li><a href=%s>Standard output</a></li>" % (resp._stdOut) # print "<li><a href=%s>Standard error</a></li>" % (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 "<li><a href=%s>%s</a></li>" % (WEBSITE+TMPDIR+jobid+"/"+line,printname) if calctype == "pdb2pqr" and apbs_input and HAVE_APBS != "": print "</ul></p><hr><p><a href=%s>Click here</a> to run APBS with your results.</p>" % nexturl elif calctype == "apbs": print "</ul></p><hr><p><a href=%s>Click here</a> to visualize your results.</p>" % nexturl elif progress == "error": print "There was an error with your query request. This page will not refresh." elif progress == "running": print "Page will refresh in %d seconds<br />" % refresh print "<HR>" print "<small>Your results will appear at <a href=%s>this page</a>. If you want, you can bookmark it and come back later (note: results are only stored for approximately 12-24 hours).</small>" % 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 "</P>" print "<script type=\"text/javascript\">" print "var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");" print "document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));" print "</script>" print "<script type=\"text/javascript\">" print "try {" print "var pageTracker = _gat._getTracker(\"UA-11026338-3\");" if logopts != {}: for key in logopts: print "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % ( key, logopts[key]) print "pageTracker._trackPageview();" print "} catch(err) {}</script>" print "</BODY>" print "</HTML>"