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from django.http import HttpResponse, HttpResponseRedirectfrom django.template import Context, loaderimport os from align.bubu.models import RunningAlignmentfrom django.contrib.auth import authenticate, login, logoutfrom align.bubu.uuid import uuid1from datetime import datetimedef getBasePath():    return '/home/wojtek/Dwork/Dtest/align/bubu/media/data/'def makeDataFile(type, uid, basepath):    if(type == 1):        return basepath + 'in' + uid + '.fas'     elif(type == 20):        return basepath + 'out' + uid + '.fas'     elif(type == 21):        return basepath + 'in' + uid + '.aln'     elif(type == 3):        return basepath + 'prog' + uid + '.fas'     elif(type == 4):        return basepath + 'sa' + uid + '.showalign'def index(request):    if not request.user.is_authenticated():        return(startLogin(request))    t = loader.get_template('index.html')    c = Context({'test' : 'test text', 'username' : request.user.username})    return HttpResponse(t.render(c))def startProcess(algo, infile, outfile, progfile, fast):    if(algo == 'mafft'):        if(fast):            os.system('mafft ' + infile + ' > ' + outfile + ' 2> ' + progfile + ' & disown')        else:            os.system('mafft --retree 1 ' + infile + ' > ' + outfile + ' 2> ' + progfile + ' & disown')    else:        if(fast):            os.system('clustalw -infile=' + infile + ' -quicktree ' + ' > ' + progfile + ' & disown')        else:            os.system('clustalw -infile=' + infile + ' > ' + progfile + ' & disown')def step1(request):    algo = request.REQUEST['algo']        # Get uuid for the communication files    uid = uuid1().hex    basepath = getBasePath()     infile = makeDataFile(1, uid, basepath)    if(algo=='mafft'):        outfile = makeDataFile(20, uid, basepath)    else:        outfile = makeDataFile(21, uid, basepath)    progfile = makeDataFile(3, uid, basepath)        # Copy the data fr4om submitted file to the alignment input file    data = request.FILES['afile']    infileF = open(infile, 'w')    infileF.write(data['content'])    infileF.close()       sfile = data['filename']    fast = False;    try:        fast = request.REQUEST['fast'] != None    except:        pass    if(sfile.startswith("/")):        sfile = sfile.split("/")[-1]    else:        sfile = sfile.split("\\")[-1]       sfile = sfile.split(".")[0]       # Create a new running alignment in the queue (start_date = NILL && end_date = NULL)    ra = RunningAlignment(user_name = request.user.username,            added_date = datetime.now(), start_date = None, end_date = None,             tmp_file = progfile, result_file = outfile, input_file = infile, uid = uid,            submit_file = sfile, algo = algo)        # check if there are any alignments currenlty running (start_date != NULL && end_date == NULL)    # If no other alignments are running, start the alignment for the uploaded file.    running = RunningAlignment.objects.filter(start_date__isnull=False, end_date__isnull=True)    if(len(running)==0):        ra.start_date = datetime.now()        startProcess(algo, infile, outfile, progfile, fast)        ra.save()        tab = progress(request)    tpl = loader.get_template('step1.html')    cnt = Context({'submit' : True, 'table' : tab, 'username' : request.user.username})    return HttpResponse(tpl.render(cnt))def showStatus(request):    tab = progress(request)    tpl = loader.get_template('step1.html')    cnt = Context({'submit' : False, 'table' : tab, 'username' : request.user.username})    return HttpResponse(tpl.render(cnt))def showDoc(request):    tpl = loader.get_template('doc.html')    cnt = Context({'username' : request.user.username})    return HttpResponse(tpl.render(cnt))def doDelete(request, uid):    alignment = RunningAlignment.objects.filter(uid=uid)[0]    if(alignment.start_date != None):        if(alignment.algo == 'mafft'):            os.system('pkill mafft')            os.system('pkill disttbfast')        else:            os.system('pkill clustalw')    basepath = '/home/wojtek/Dwork/Dtest/align/bubu/media/data/'    delIfExists(makeDataFile(1, uid, basepath))    if(alignment.algo == 'mafft'):        delIfExists(makeDataFile(20, uid, basepath))    else:        delIfExists(makeDataFile(21, uid, basepath))    delIfExists(makeDataFile(3, uid, basepath))    alignment.delete()    return(HttpResponse(""))def delIfExists(filename):    try:        os.remove(makeDataFile(1, uid, basepath))    except:        passdef getShowAlign(infile, outfile):    os.system('showalign -sequence ' + infile + ' -outfile ' + outfile)def progress(request):    allrunning = RunningAlignment.objects.filter(end_date__isnull=True, start_date__isnull=False)    if(len(allrunning) != 0):        running = allrunning[0]        if(running.algo == 'mafft'):            tmpfile = open(running.tmp_file, 'r')            tmpstr = tmpfile.read()            tmpfile.close()            if(tmpstr.rstrip().endswith("mafft page.")):                running.end_date = datetime.now()                getShowAlign(makeDataFile(20, running.uid, getBasePath()), makeDataFile(4, running.uid, getBasePath()))                running.save()        else:            try:                tmpfile = open(running.tmp_file, 'r')                tmpstr = tmpfile.read()                tmpfile.close()                if(tmpstr.rfind("CLUSTAL-Alignment file created") != -1):                    running.end_date = datetime.now()                    getShowAlign(makeDataFile(21, running.uid, getBasePath()), makeDataFile(4, running.uid, getBasePath()))                    running.save()            except:                pass    allrunning = RunningAlignment.objects.filter(end_date__isnull=True, start_date__isnull=False)    if(len(allrunning) == 0):        queuedAndRunning = RunningAlignment.objects.filter(end_date__isnull=True, start_date__isnull=True).order_by('added_date')        if(len(queuedAndRunning) != 0):            torun = queuedAndRunning[0]            torun.start_date = datetime.now()            torun.save()            os.system('mafft ' + torun.input_file + ' > ' + torun.result_file + ' 2> ' + torun.tmp_file + ' & disown')    queuedAndRunning = RunningAlignment.objects.filter(end_date__isnull=True).order_by('-start_date', 'added_date')       finished = RunningAlignment.objects.filter(end_date__isnull=False).order_by('-start_date')       t = loader.get_template('progress.html')    c = Context({'running' : queuedAndRunning, 'finished' : finished, 'username' : request.user.username})    ret = t.render(c)    return retdef doProgress(request):    return HttpResponse(progress(request))def doFileProgress(request):    allrunning = RunningAlignment.objects.filter(end_date__isnull=True, start_date__isnull=False)    if(len(allrunning) != 0):        running = allrunning[0]        if(running.algo != 'mafft'):            return(HttpResponse("n/a"))        tmpfile = open(running.tmp_file, 'r')        tmpstr = tmpfile.read()        tmpfile.close()        if(tmpstr.rfind("STEP")==-1):            return(HttpResponse("0"))        progs = tmpstr[tmpstr.rfind("STEP"):].split(" ")        if(progs == ""):            return(HttpResponse("0"))        vals = filter(lambda x: x!='' and x!='STEP' and x!='f', progs)        try:            ret = 100*float(vals[0])/float(vals[2])        except:            return(HttpResponse("0"))        return(HttpResponse(str(round(ret))))    return(HttpResponse("0"))def startLogin(request):    t = loader.get_template('startLogin.html')    c = Context()    return HttpResponse(t.render(c))def doLogin(request):    user = authenticate(username=request.POST['username'], password=request.POST['password'])    if user is not None:        login(request, user)        return index(request)    else:        return startLogin(request)def getResultFile(request, uid):    align = RunningAlignment.objects.filter(uid=uid)[0]    if(align.algo == 'mafft'):        path = makeDataFile(20, uid, '/site_media/data/')    else:        path = makeDataFile(21, uid, '/site_media/data/')    return HttpResponseRedirect(path)def getShowAlignFile(request, uid):    return HttpResponseRedirect(makeDataFile(4, uid, '/site_media/data/'))def doLogout(request):    logout(request)    return index(request)