Esempio n. 1
0
def handleNonOpal(weboptions, storage_host):
    """
        Handle non opal run.
    """

    pdblist, errlist = readPDB(weboptions.pdbfile)

    dummydef = Definition()
    dummyprot = Protein(pdblist, dummydef)
    """
    if len(pdblist) == 0 and len(errlist) == 0:
        text = "Unable to find PDB file - Please make sure this is "
        text += "a valid PDB file ID!"
        #print "Content-type: text/html\n"
        print text
        sys.exit(2)
    elif dummyprot.numAtoms() > MAXATOMS and weboptions["opt"] == True:
        text = "<HTML><HEAD>"
        text += "<TITLE>PDB2PQR Error</title>"
        text += "<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">" % STYLESHEET
        text += "</HEAD><BODY><H2>PDB2PQR Error</H2><P>"
        text += "Due to server limits, we are currently unable to optimize "
        text += "proteins of greater than %i atoms on the server (PDB2PQR " % MAXATOMS
        text += "found %s atoms in the selected PDB file).  If you " % dummyprot.numAtoms()
        text += "want to forgo optimization please try the server again.<P>"
        text += "Otherwise you may use the standalone version of PDB2PQR that "
        text += "is available from the <a href=\"http://pdb2pqr.sourceforge.net\">"
        text += "PDB2PQR SourceForge project page</a>."
        text += "<script type=\"text/javascript\">"
        text += "var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");"
        text += "document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));"
        text += "</script>"
        text += "<script type=\"text/javascript\">"
        text += "try {"
        text += "var pageTracker = _gat._getTracker(\"UA-11026338-3\");"
        for key in weboptions:
            text += "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, weboptions[key])
        text += "pageTracker._trackPageview();"
        text += "} catch(err) {}</script>"
        text += "</BODY></HTML>"
        #print "Content-type: text/html\n"
        print text
        sys.exit(2)
    """

    try:
        starttime = time.time()
        name = setID(starttime)

        #Some job parameters logging.
        os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
        apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),
                             'w')
        apbsInputFile.write(str(weboptions["apbs"]))
        apbsInputFile.close()

        typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),
                                'w')
        typemapInputFile.write(str(weboptions["typemap"]))
        typemapInputFile.close()

        statusfile = open('%s%s%s/pdb2pqr_status' % (INSTALLDIR, TMPDIR, name),
                          'w')
        statusfile.write('running')
        statusfile.close()

        # Recording CGI run information for PDB2PQR Opal
        pdb2pqrLogFile = open(
            '%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, name), 'w')
        pdb2pqrLogFile.write(
            str(weboptions.getOptions()) + '\n' + str(weboptions.ff))
        #  str(weboptions.ff)+'\n'+
        #  str(os.environ["REMOTE_ADDR"]))
        pdb2pqrLogFile.close()

        pid = os.fork()
        if pid:
            from PDB2PQR_web import jobutils
            redirect = redirector(name, weboptions)
            file_list = [
                'typemap',
                'pdb2pqr_status',
                'pdb2pqr_start_time',
            ]

            print('===========')
            print(weboptions.getCommandLine())
            # for i in weboptions.getRunArguments():
            #     print(i)
            print('===========')

            if isinstance(file_list, list):
                try:
                    jobutils.send_to_storage_service(
                        storage_host, name, file_list,
                        os.path.join(INSTALLDIR, TMPDIR))
                except Exception as err:
                    with open('storage_err', 'a+') as fin:
                        fin.write(err)
            # print redirector(name, weboptions)
            return redirect
            sys.exit()
        else:
            currentdir = os.getcwd()
            os.chdir("/")
            os.setsid()
            os.umask(0)
            os.chdir(currentdir)
            os.close(1)  # not sure if these
            os.close(2)  # two lines are necessary

            pqrpath = '%s%s%s/%s.pqr' % (INSTALLDIR, TMPDIR, name, name)

            orig_stdout = sys.stdout
            orig_stderr = sys.stderr
            sys.stdout = open(
                '%s%s%s/pdb2pqr_stdout.txt' % (INSTALLDIR, TMPDIR, name), 'w')
            sys.stderr = open(
                '%s%s%s/pdb2pqr_stderr.txt' % (INSTALLDIR, TMPDIR, name), 'w')

            run_arguements = weboptions.getRunArguments()
            if weboptions.runoptions.get('ph_calc_method', '') == 'pdb2pka':
                run_arguements['ph_calc_options'][
                    'output_dir'] = '%s%s%s/pdb2pka_output' % (INSTALLDIR,
                                                               TMPDIR, name)

            header, lines, missedligands = runPDB2PQR(
                pdblist,
                weboptions.ff,
                outname=pqrpath,
                commandLine=weboptions.getCommandLine(),
                **weboptions.getRunArguments())

            sys.stdout.close()
            sys.stderr.close()
            sys.stdout = orig_stdout
            sys.stderr = orig_stderr

            endtimefile = open(
                '%s%s%s/pdb2pqr_end_time' % (INSTALLDIR, TMPDIR, name), 'w')
            endtimefile.write(str(time.time()))
            endtimefile.close()

            pqrfile = open(pqrpath, "w")
            pqrfile.write(header)

            whitespace = weboptions.otheroptions['whitespace']
            for line in lines:
                # Adding whitespaces if --whitespace is in the weboptions
                if whitespace:
                    if line[0:4] == 'ATOM':
                        newline = line[0:6] + ' ' + line[6:16] + ' ' + line[
                            16:38] + ' ' + line[38:46] + ' ' + line[46:]
                        pqrfile.write("%s\n" % string.strip(newline))
                    elif line[0:6] == 'HETATM':
                        newline = line[0:6] + ' ' + line[6:16] + ' ' + line[
                            16:38] + ' ' + line[38:46] + ' ' + line[46:]
                        pqrfile.write("%s\n" % string.strip(newline))
                else:
                    pqrfile.write("%s\n" % string.strip(line))
            pqrfile.close()

            if weboptions.otheroptions['apbs']:
                from src import inputgen
                from src import psize
                method = "mg-auto"
                size = psize.Psize()
                size.parseInput(pqrpath)
                size.runPsize(pqrpath)
                async = 0  # No async files here!
                myinput = inputgen.Input(pqrpath,
                                         size,
                                         method,
                                         async,
                                         potdx=True)
                myinput.printInputFiles()
                myinput.dumpPickle()

            endtime = time.time() - starttime
            #createResults(header, input, name, endtime, missedligands)
            #logRun(weboptions, endtime, len(lines), weboptions.ff, os.environ["REMOTE_ADDR"])
            #printHeader("PDB2PQR Job Submission",have_opal,jobid=name)
            if 'ligand' in weboptions:
                outputligandfile = open(
                    '%s%s%s/%s.mol2' % (INSTALLDIR, TMPDIR, name, name), 'w')
                outputligandfile.write(weboptions.ligandfilestring)
                outputligandfile.close()
            outputpdbfile = open(
                '%s%s%s/%s.pdb' % (INSTALLDIR, TMPDIR, name, name), 'w')
            outputpdbfile.write(weboptions.pdbfilestring)
            outputpdbfile.close()

            statusfile = open(
                '%s%s%s/pdb2pqr_status' % (INSTALLDIR, TMPDIR, name), 'w')
            statusfile.write('complete\n')
            filelist = glob.glob('%s%s%s/%s*' %
                                 (INSTALLDIR, TMPDIR, name, name))
            for filename in filelist:
                statusfile.write(filename + '\n')
            statusfile.close()
            '''Upload associated APBS run files to the storage service'''
            from PDB2PQR_web import jobutils
            jobDir = os.path.join(INSTALLDIR, TMPDIR, name)
            sys.stdout = open('%s/debug_forked_stdout.out' % (jobDir), 'a+')
            sys.stderr = open('%s/debug_forked_stderr.out' % (jobDir), 'a+')
            file_list = os.listdir(jobDir)
            if isinstance(file_list, list):
                try:
                    jobutils.send_to_storage_service(
                        storage_host, name, file_list,
                        os.path.join(INSTALLDIR, TMPDIR))
                except Exception as err:
                    with open('storage_err', 'a+') as fin:
                        fin.write(err)
            sys.stdout.close()
            sys.stderr.close()

    #TODO: Better error reporting.
    #Also, get forked job to properly write error status on failure.
    except StandardError, details:
        #except StandardError as details:
        print traceback.format_exc()
        print sys.exc_info()[0]
        #print details
        createError(name, details)
Esempio n. 2
0
        print "</script>"
        print "<script type=\"text/javascript\">"
        print "try {"
        print "var pageTracker = _gat._getTracker(\"UA-11026338-3\");"
        for key in weboptions:
            print "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (
                key, weboptions[key])
        print "pageTracker._trackPageview();"
        print "} catch(err) {}</script>"
        print "</BODY>"
        print "</HTML>"
        sys.exit(2)

    try:
        starttime = time.time()
        name = setID(starttime)

        #Some job parameters logging.
        os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
        apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),
                             'w')
        apbsInputFile.write(str(weboptions["apbs"]))
        apbsInputFile.close()

        typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),
                                'w')
        typemapInputFile.write(str(weboptions["typemap"]))
        typemapInputFile.close()

        pdb2pqrOpalJobIDFile = open(
            '%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
Esempio n. 3
0
def handleNonOpal(weboptions):
    """
        Handle non opal run.
    """
 
    pdblist, errlist = readPDB(weboptions.pdbfile)
    
    dummydef = Definition()
    dummyprot = Protein(pdblist, dummydef)
    if len(pdblist) == 0 and len(errlist) == 0:
        text = "Unable to find PDB file - Please make sure this is "
        text += "a valid PDB file ID!"
        #print "Content-type: text/html\n"
        print(text)
        sys.exit(2)
    elif dummyprot.numAtoms() > MAXATOMS and weboptions["opt"] == True:
        text = "<HTML><HEAD>"
        text += "<TITLE>PDB2PQR Error</title>"
        text += "<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">" % STYLESHEET
        text += "</HEAD><BODY><H2>PDB2PQR Error</H2><P>"
        text += "Due to server limits, we are currently unable to optimize "
        text += "proteins of greater than %i atoms on the server (PDB2PQR " % MAXATOMS
        text += "found %s atoms in the selected PDB file).  If you " % dummyprot.numAtoms()
        text += "want to forgo optimization please try the server again.<P>"
        text += "Otherwise you may use the standalone version of PDB2PQR that "
        text += "is available from the <a href=\"http://pdb2pqr.sourceforge.net\">"
        text += "PDB2PQR SourceForge project page</a>."
        text += "<script type=\"text/javascript\">"
        text += "var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");"
        text += "document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));"
        text += "</script>"
        text += "<script type=\"text/javascript\">"
        text += "try {"
        text += "var pageTracker = _gat._getTracker(\"UA-11026338-3\");"
        for key in weboptions:
            text += "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, weboptions[key])
        text += "pageTracker._trackPageview();"
        text += "} catch(err) {}</script>"
        text += "</BODY></HTML>"
        #print "Content-type: text/html\n"
        print(text)
        sys.exit(2)

    try:
        starttime = time.time()
        name = setID(starttime)

        #Some job parameters logging.
        os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
        apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),'w')
        apbsInputFile.write(str(weboptions["apbs"]))
        apbsInputFile.close()
        
        typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),'w')
        typemapInputFile.write(str(weboptions["typemap"]))
        typemapInputFile.close()

        statusfile = open('%s%s%s/pdb2pqr_status' % (INSTALLDIR, TMPDIR, name), 'w')
        statusfile.write('running')
        statusfile.close()
        
        # Recording CGI run information for PDB2PQR Opal
        pdb2pqrLogFile = open('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, name), 'w')
        pdb2pqrLogFile.write(str(weboptions.getOptions())+'\n'+
                                 str(weboptions.ff)+'\n'+
                                 str(os.environ["REMOTE_ADDR"]))
        pdb2pqrLogFile.close()


        pid = os.fork()
        if pid:
            print(redirector(name, weboptions))
            sys.exit()
        else:
            currentdir = os.getcwd()
            os.chdir("/")
            os.setsid()
            os.umask(0)
            os.chdir(currentdir)
            os.close(1) # not sure if these
            os.close(2) # two lines are necessary
            
            pqrpath = '%s%s%s/%s.pqr' % (INSTALLDIR, TMPDIR, name, name)
            
            orig_stdout = sys.stdout
            orig_stderr = sys.stderr
            sys.stdout = open('%s%s%s/pdb2pqr_stdout.txt' % (INSTALLDIR, TMPDIR, name), 'w')
            sys.stderr = open('%s%s%s/pdb2pqr_stderr.txt' % (INSTALLDIR, TMPDIR, name), 'w')
            
            run_arguements = weboptions.getRunArguments()
            if weboptions.runoptions.get('ph_calc_method', '') == 'pdb2pka':
                run_arguements['ph_calc_options']['output_dir']='%s%s%s/pdb2pka_output' % (INSTALLDIR, TMPDIR, name)
            
            
            header, lines, missedligands, _ = runPDB2PQR(pdblist,
                                                      weboptions.ff,
                                                      outname = pqrpath,
                                                      commandLine = weboptions.getCommandLine(),
                                                      **weboptions.getRunArguments())
            
            sys.stdout.close()
            sys.stderr.close()
            sys.stdout = orig_stdout
            sys.stderr = orig_stderr

            endtimefile = open('%s%s%s/pdb2pqr_end_time' % (INSTALLDIR, TMPDIR, name), 'w')
            endtimefile.write(str(time.time()))
            endtimefile.close()

            pqrfile = open(pqrpath, "w")
            pqrfile.write(header)
            
            whitespace = weboptions.otheroptions['whitespace']
            for line in lines:
                # Adding whitespaces if --whitespace is in the weboptions
                if whitespace: 
                    if line[0:4] == 'ATOM':
                        newline = line[0:6] + ' ' + line[6:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
                        pqrfile.write("%s\n" % newline.strip())
                    elif line[0:6] == 'HETATM':
                        newline = line[0:6] + ' ' + line[6:16] + ' ' + line[16:38] + ' ' + line[38:46] + ' ' + line[46:]
                        pqrfile.write("%s\n" % newline.strip())
                else: 
                    pqrfile.write("%s\n" % line.strip())
            pqrfile.close()
                    
            if weboptions.otheroptions['apbs']:
                from src import inputgen
                from src import psize
                method = "mg-auto"
                size = psize.Psize()
                size.parseInput(pqrpath)
                size.runPsize(pqrpath)
                async = 0 # No async files here!
                myinput = inputgen.Input(pqrpath, size, method, async, potdx=True)
                myinput.printInputFiles()
                myinput.dumpPickle()
                        
            endtime = time.time() - starttime
            #createResults(header, input, name, endtime, missedligands)
            #logRun(weboptions, endtime, len(lines), weboptions.ff, os.environ["REMOTE_ADDR"])
            #printHeader("PDB2PQR Job Submission",have_opal,jobid=name)
            if 'ligand' in weboptions:
                outputligandfile = open('%s%s%s/%s.mol2' % (INSTALLDIR,TMPDIR, name, name),'w')
                outputligandfile.write(weboptions.ligandfilestring)
                outputligandfile.close()
            outputpdbfile = open('%s%s%s/%s.pdb' % (INSTALLDIR,TMPDIR,name,name),'w')
            outputpdbfile.write(weboptions.pdbfilestring)
            outputpdbfile.close()

            statusfile = open('%s%s%s/pdb2pqr_status' % (INSTALLDIR, TMPDIR, name), 'w')
            statusfile.write('complete\n')
            filelist = glob.glob('%s%s%s/%s*' % (INSTALLDIR, TMPDIR, name, name))
            for filename in filelist:
                statusfile.write(filename+'\n')
            statusfile.close()

    #TODO: Better error reporting.
    #Also, get forked job to properly write error status on failure.
    except Exception as details:
    #except StandardError as details:
        print(traceback.format_exc())
        print(sys.exc_info()[0])
        #print details
        createError(name, details)
Esempio n. 4
0
def handleOpal(weboptions):
    '''
        Handle opal based run.
    '''
    # Opal-specific import statements
    from AppService_client import AppServiceLocator, launchJobRequest
    from AppService_types import ns0

    inputFiles = []
    
    if 'userff' in weboptions:
        ffFile = ns0.InputFileType_Def('inputFile')
        ffFile._name = weboptions.userfffilename
        ffFile._contents = weboptions.userffstring
        inputFiles.append(ffFile)
        
    if 'usernames' in weboptions:
        namesFile = ns0.InputFileType_Def('inputFile')
        namesFile._name = weboptions.usernamesfilename
        namesFile._contents = weboptions.usernamesstring
        inputFiles.append(namesFile)
        
    if 'ligand' in weboptions:
        ligandFile = ns0.InputFileType_Def('inputFile')
        ligandFile._name = weboptions.ligandfilename
        ligandFile._contents = weboptions.ligandfilestring
        inputFiles.append(ligandFile)
        
    pdbOpalFile = ns0.InputFileType_Def('inputFile')
    pdbOpalFile._name = weboptions.pdbfilename
    pdbOpalFile._contents = weboptions.pdbfilestring
    inputFiles.append(pdbOpalFile)
     
    # launch job   
    appLocator = AppServiceLocator()
    appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)
    
    req = launchJobRequest()
    req._argList = weboptions.getCommandLine()
    req._inputFile=inputFiles

    try:
        resp=appServicePort.launchJob(req)
    except Exception as e:
        printHeader("PDB2PQR Job Submission - Error")
        print("<BODY>\n<P>")
        print("There was an error with your job submission<br>")
        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\");")
        for key in weboptions:
            print("pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, weboptions[key]))
        print("pageTracker._trackPageview();")
        print("} catch(err) {}</script>")
        print("</BODY>")
        print("</HTML>")
        sys.exit(2)
    
    try:
        starttime = time.time()
        name = setID(starttime)
        
        #Some job parameters logging.
        os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
        apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),'w')
        apbsInputFile.write(str(weboptions["apbs"]))
        apbsInputFile.close()
        
        typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),'w')
        typemapInputFile.write(str(weboptions["typemap"]))
        typemapInputFile.close()
        
        pdb2pqrOpalJobIDFile = open('%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
        pdb2pqrOpalJobIDFile.write(resp._jobID)
        pdb2pqrOpalJobIDFile.close()
        
        print(redirector(name, weboptions))
        
        # Recording CGI run information for PDB2PQR Opal
        pdb2pqrOpalLogFile = open('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, name), 'w')
        pdb2pqrOpalLogFile.write(str(weboptions.getOptions())+'\n'+
                                 str(os.environ["REMOTE_ADDR"]))
        pdb2pqrOpalLogFile.close()

    except Exception as details:
        print(details)
        createError(name, details)
Esempio n. 5
0
def handleOpal(weboptions):
    '''
        Handle opal based run.
    '''
    # Opal-specific import statements
    from AppService_client import AppServiceLocator, launchJobRequest
    from AppService_types import ns0

    inputFiles = []

    if 'userff' in weboptions:
        ffFile = ns0.InputFileType_Def('inputFile')
        ffFile._name = weboptions.userfffilename
        ffFile._contents = weboptions.userffstring
        inputFiles.append(ffFile)

    if 'usernames' in weboptions:
        namesFile = ns0.InputFileType_Def('inputFile')
        namesFile._name = weboptions.usernamesfilename
        namesFile._contents = weboptions.usernamesstring
        inputFiles.append(namesFile)

    if 'ligand' in weboptions:
        ligandFile = ns0.InputFileType_Def('inputFile')
        ligandFile._name = weboptions.ligandfilename
        ligandFile._contents = weboptions.ligandfilestring
        inputFiles.append(ligandFile)

    pdbOpalFile = ns0.InputFileType_Def('inputFile')
    pdbOpalFile._name = weboptions.pdbfilename
    pdbOpalFile._contents = weboptions.pdbfilestring
    inputFiles.append(pdbOpalFile)

    # launch job
    appLocator = AppServiceLocator()
    appServicePort = appLocator.getAppServicePort(PDB2PQR_OPAL_URL)

    req = launchJobRequest()
    req._argList = weboptions.getCommandLine()
    req._inputFile = inputFiles

    try:
        resp = appServicePort.launchJob(req)
    except Exception as e:
        printHeader("PDB2PQR Job Submission - Error")
        print("<BODY>\n<P>")
        print("There was an error with your job submission<br>")
        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\");")
        for key in weboptions:
            print("pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" %
                  (key, weboptions[key]))
        print("pageTracker._trackPageview();")
        print("} catch(err) {}</script>")
        print("</BODY>")
        print("</HTML>")
        sys.exit(2)

    try:
        starttime = time.time()
        name = setID(starttime)

        #Some job parameters logging.
        os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
        apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),
                             'w')
        apbsInputFile.write(str(weboptions["apbs"]))
        apbsInputFile.close()

        typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),
                                'w')
        typemapInputFile.write(str(weboptions["typemap"]))
        typemapInputFile.close()

        pdb2pqrOpalJobIDFile = open(
            '%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
        pdb2pqrOpalJobIDFile.write(resp._jobID)
        pdb2pqrOpalJobIDFile.close()

        print(redirector(name, weboptions))

        # Recording CGI run information for PDB2PQR Opal
        pdb2pqrOpalLogFile = open(
            '%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, name), 'w')
        pdb2pqrOpalLogFile.write(
            str(weboptions.getOptions()) + '\n' +
            str(os.environ["REMOTE_ADDR"]))
        pdb2pqrOpalLogFile.close()

    except Exception as details:
        print(details)
        createError(name, details)
Esempio n. 6
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     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\");"
     for key in weboptions:
         print "pageTracker._trackPageview(\"/main_cgi/has_%s_%s.html\");" % (key, weboptions[key])
     print "pageTracker._trackPageview();"
     print "} catch(err) {}</script>"
     print "</BODY>"
     print "</HTML>"
     sys.exit(2)
 
 try:
     starttime = time.time()
     name = setID(starttime)
     
     #Some job parameters logging.
     os.makedirs('%s%s%s' % (INSTALLDIR, TMPDIR, name))
     apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, name),'w')
     apbsInputFile.write(str(weboptions["apbs"]))
     apbsInputFile.close()
     
     typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, name),'w')
     typemapInputFile.write(str(weboptions["typemap"]))
     typemapInputFile.close()
     
     pdb2pqrOpalJobIDFile = open('%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, name), 'w')
     pdb2pqrOpalJobIDFile.write(resp._jobID)
     pdb2pqrOpalJobIDFile.close()