def whole_pdb_submit(request):
errorDict = {}
skipNonXray = request.POST['skipNonXray']
skipAlphaCarbon = request.POST['skipAlphaCarbon']
cullMethod = request.POST['cullMethod']
intraEntryCull = request.POST['intraEntryCull']
email = request.POST['email']
incorrect = []
try:
percentIdentity = float(request.POST['pc'])
if percentIdentity < 5 or percentIdentity >= 100:
errorDict['errorPercent'] = True
incorrect.append(u"The value entered for the percentage: " + str(percentIdentity) + " is not within the permissible range of values. The percentage must be greater than or equal to 5, and less than 100.")
except:
errorDict['errorPercent'] = True
incorrect.append(u'The value for the sequence identity threshold must be greater than or equal to 5, and less than 100')
try:
minResolution = float(request.POST['minRes'])
if minResolution < 0:
errorDict['errorMinRes'] = True
incorrect.append(u"The value entered for the minimum resolution: " + str(minResolution) + " is less than 0.")
if minResolution > 100:
errorDict['errorMinRes'] = True
incorrect.append(u"The value entered for the minimum resolution: " + str(minResolution) + " is greater than 100.")
try:
maxResolution = float(request.POST['maxRes'])
if maxResolution < 0:
errorDict['errorMaxRes'] = True
incorrect.append(u"The value entered for the maximum resolution: " + str(maxResolution) + " is less than 0.")
if maxResolution > 100:
errorDict['errorMaxRes'] = True
incorrect.append(u"The value entered for the maximum resolution: " + str(maxResolution) + " is greater than 100.")
if minResolution > maxResolution:
errorDict['errorMinRes'] = True
incorrect.append(u"The value entered for the minimum resolution: " + str(minResolution) + " is greater than the value for the maximum resolution: " + str(maxResolution) + ".")
except:
errorDict['errorMaxRes'] = True
incorrect.append(u'The value for the maximum resolution must be a number.')
except:
errorDict['errorMinRes'] = True
incorrect.append(u'The value for the minimum resolution must be a number.')
try:
maxResolution = float(request.POST['maxRes'])
if maxResolution < 0:
errorDict['errorMaxRes'] = True
incorrect.append(u"The value entered for the maximum resolution: " + str(maxResolution) + " is less than 0.")
if maxResolution > 100:
errorDict['errorMaxRes'] = True
incorrect.append(u"The value entered for the maximum resolution: " + str(maxResolution) + " is greater than 100.")
except:
errorDict['errorMaxRes'] = True
incorrect.append(u'The value for the maximum resolution must be a number.')
try:
maxRVal = float(request.POST['maxRVal'])
if maxRVal < 0 or maxRVal > 1:
errorDict['errorRVal'] = True
incorrect.append(u"The value entered for the maximum R value: " + str(maxRVal) + " is not within the permissible range of values. The range allowed is: 0 to 1.")
except:
errorDict['errorRVal'] = True
incorrect.append(u'The value for the R value must be a number in the range 0 - 1.')
if request.POST['enforceMinLength'] == 'yes':
try:
minLength = int(request.POST['minLength'])
if minLength < 0:
errorDict['errorMinLength'] = True
incorrect.append(u'The value for the minimum length must be greater than or equal to 0')
if request.POST['enforceMaxLength'] == 'yes':
try:
maxLength = int(request.POST['maxLength'])
if maxLength < 0:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum length must be greater than or equal to 0')
if minLength > maxLength:
errorDict['errorMinLength'] = True
incorrect.append(u"The value entered for the minimum length: " + str(minLength) + " is greater than the value for the maximum length: " + str(maxLength) + ".")
except:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum sequence length must be an integer.')
else:
maxLength = -1
except:
errorDict['errorMinLength'] = True
incorrect.append(u'The value for the minimum sequence length must be an integer.')
if request.POST['enforceMaxLength'] == 'yes':
try:
maxLength = int(request.POST['maxLength'])
if maxLength < 0:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum length must be greater than or equal to 0')
minLength = -1
except:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum sequence length must be an integer.')
elif request.POST['enforceMaxLength'] == 'yes':
try:
maxLength = int(request.POST['maxLength'])
if maxLength < 0:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum length must be greater than or equal to 0')
minLength = -1
except:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum sequence length must be an integer.')
else:
minLength = -1
maxLength = -1
if not re.match("[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\.[a-zA-Z]+$", email):
errorDict['errorEmail'] = True
incorrect.append(u"The email address entered does not appear to be a valid email address.")
if cullMethod == 'entry' and intraEntryCull == 'yes':
try:
intraEntryPC = float(request.POST['intraEntryPC'])
if intraEntryPC < 5 or intraEntryPC >= 100:
errorDict['errorIntraEntry'] = True
incorrect.append(u"The value entered for the within entry sequence identity threshold: " + str(intraEntryPC) + " is not within the permissible range of values. The value must be a number greater than or equal to 5, and less than 100.")
except:
errorDict['errorIntraEntry'] = True
incorrect.append(u'The value for the within entry sequence identity threshold must be a number greater than or equal to 5, and less than 100.')
elif intraEntryCull == 'yes':
incorrect.append(u'Intra entry culling is selected, but cull by entry is not.')
if incorrect != []:
valueDict = {'errorMessage': incorrect, 'pc' : request.POST['pc'], 'minRes' : request.POST['minRes'],
'maxRes' : request.POST['maxRes'], 'maxRVal' : request.POST['maxRVal'],
'intraEntryPC' : request.POST['intraEntryPC'], 'email' : request.POST['email']}
if skipNonXray == 'no':
valueDict['skipNonXray'] = request.POST['skipNonXray']
if skipAlphaCarbon == 'no':
valueDict['skipAlphaCarbon'] = request.POST['skipAlphaCarbon']
if cullMethod == 'entry':
valueDict['cullMethod'] = request.POST['cullMethod']
if intraEntryCull == 'yes':
valueDict['intraEntryCull'] = request.POST['intraEntryCull']
if request.POST['enforceMinLength'] == 'yes':
valueDict['enforceMinLength'] = 'yes'
valueDict['minLength'] = request.POST['minLength']
if request.POST['enforceMaxLength'] == 'yes':
valueDict['enforceMaxLength'] = 'yes'
valueDict['maxLength'] = request.POST['maxLength']
for i in errorDict.keys():
valueDict[i] = True
return render_to_response('whole_pdb_culling.html',
valueDict,
context_instance=RequestContext(request))
# Setup the database entry
if skipNonXray == 'yes':
skipNonXray = True
else:
skipNonXray = False
if skipAlphaCarbon == 'yes':
skipAlphaCarbon = True
else:
skipAlphaCarbon = False
if cullMethod == 'chain':
cullMethod = True
else:
cullMethod = False
if intraEntryCull == 'yes':
intraEntryCull = True
else:
intraEntryCull = False
r = PDBCullRequest(
wholePDB=True,
sequenceIdentity=percentIdentity,
minResolution=minResolution,
maxResolution=maxResolution,
maxRValue=maxRVal,
minLength = minLength,
maxLength = maxLength,
skipNonXray=skipNonXray,
skipAlphaCarbon=skipAlphaCarbon,
cullByChain=cullMethod,
performIntraEntryCulling=intraEntryCull,
intraEntrySequenceIdentity=float(request.POST['intraEntryPC']),
email=str(email),
completed=False,
requestDate=datetime.datetime.now()
)
r.save()
cullinput.controlthread.RunCull(r, 'pdb')
# return HttpResponseRedirect(reverse('Leaf.views.sent'))
return HttpResponseRedirect(reverse('Leaf.views.sent', kwargs={'result_id': r.id, 'cullType' : 'pdb'}))
def handle(self, *args, **options):
os.umask(00000)
logger = open('/srv/www/vhosts.d/www.bioinf/html/doig/cgi-bin/django_projects/LeafWebApp/ErrorLogs/GENERATION.log', 'a')
logger.write('=======================================================\n=======================================================\nStarting generation on ' + time.strftime('%Y/%m/%d/ at %H:%M:%S', time.gmtime()) + '.\n')
logger.close()
# Turn all the protein chain information into a dictionary.
pdbChainsData = ProteinInformation.objects.all()
pdbChainsDict = dict([(i.chain, i) for i in pdbChainsData])
del(pdbChainsData)
# Turn all the within entry representative information into a dictionary.
entryRepData = EntryRepresentative.objects.all()
entryRepIgnore = []
entryRepDict = {}
for i in entryRepData:
entryRepIgnore.append(i.nonreprChain)
reprChain = i.reprChain
if entryRepDict.has_key(reprChain):
entryRepDict[reprChain].append(i.nonreprChain)
else:
entryRepDict[reprChain] = [i.nonreprChain]
del(entryRepData)
# Turn all the whole PDB representative information into a dictionary.
wholeRepData = Representative.objects.all()
wholeRepIgnore = []
wholeRepDict = {}
for i in wholeRepData:
wholeRepIgnore.append(i.nonreprChain)
reprChain = i.reprChain
if wholeRepDict.has_key(reprChain):
wholeRepDict[reprChain].append(i.nonreprChain)
else:
wholeRepDict[reprChain] = [i.nonreprChain]
del(wholeRepData)
# Generate the whole PDB fasta files.
pdbaa = StringIO()
gzf = GzipFile(fileobj=pdbaa, mode='wb')
for i in sorted(pdbChainsDict.keys()):
experimentType = str(pdbChainsDict[i].experimentType)
resolution = str(pdbChainsDict[i].resolution)
rValueObs = str(pdbChainsDict[i].rValueObs)
rValueFree = str(pdbChainsDict[i].rValueFree)
alphaCarbonOnly = ['no', 'yes'][pdbChainsDict[i].alphaCarbonOnly]
# alphaCarbonOnly = 'yes' if pdbChainsDict[i].alphaCarbonOnly else 'no'
description = str(pdbChainsDict[i].description)
dbName = str(pdbChainsDict[i].dbName)
dbCode = str(pdbChainsDict[i].dbCode)
organism = str(pdbChainsDict[i].organism)
sequence = str(pdbChainsDict[i].sequence)
gzf.write('>' + str(i) + '\t' + str(len(sequence)) + '\t' + experimentType + '\t' + resolution + '\t' +
rValueObs + '\t' + rValueFree + '\t' + alphaCarbonOnly + '\t' + description + '\t<' + dbName +
' ' + dbCode + '>\t[' + organism + ']\n')
gzf.write(sequence + '\n')
gzf.close()
pdbaa.seek(0, 2)
pdbaaFile = InMemoryUploadedFile(pdbaa, 'image', 'pdbaa.gz', None, pdbaa.tell(), None)
pdbaaEntry = DownloadableFiles(fileName='pdbaa')
pdbaaEntry.save()
pdbaaEntry.downloadFile.save(pdbaaFile.name, pdbaaFile)
pdbaa.close()
pdbaaent = StringIO()
gzf = GzipFile(fileobj=pdbaaent, mode='wb')
for i in sorted([j for j in pdbChainsDict.keys() if not j in entryRepIgnore]):
experimentType = str(pdbChainsDict[i].experimentType)
resolution = str(pdbChainsDict[i].resolution)
rValueObs = str(pdbChainsDict[i].rValueObs)
rValueFree = str(pdbChainsDict[i].rValueFree)
alphaCarbonOnly = ['no', 'yes'][pdbChainsDict[i].alphaCarbonOnly]
# alphaCarbonOnly = 'yes' if pdbChainsDict[i].alphaCarbonOnly else 'no'
description = str(pdbChainsDict[i].description)
dbName = str(pdbChainsDict[i].dbName)
dbCode = str(pdbChainsDict[i].dbCode)
organism = str(pdbChainsDict[i].organism)
sequence = str(pdbChainsDict[i].sequence)
if entryRepDict.has_key(i):
gzf.write('>' + str(i) + '\t' + str(len(sequence)) + '\t' + experimentType + '\t' + resolution + '\t' +
rValueObs + '\t' + rValueFree + '\t' + alphaCarbonOnly + '\t' + description + '\t<' + dbName +
' ' + dbCode + '>\t[' + organism + ']\t||\t' + '\t'.join(entryRepDict[i]) + '\n')
else:
gzf.write('>' + str(i) + '\t' + str(len(sequence)) + '\t' + experimentType + '\t' + resolution + '\t' +
rValueObs + '\t' + rValueFree + '\t' + alphaCarbonOnly + '\t' + description + '\t<' + dbName +
' ' + dbCode + '>\t[' + organism + ']\n')
gzf.write(sequence + '\n')
gzf.close()
pdbaaent.seek(0, 2)
pdbaaentFile = InMemoryUploadedFile(pdbaaent, 'image', 'pdbaaent.gz', None, pdbaaent.tell(), None)
pdbaaentEntry = DownloadableFiles(fileName='pdbaaent')
pdbaaentEntry.save()
pdbaaentEntry.downloadFile.save(pdbaaentFile.name, pdbaaentFile)
pdbaaent.close()
pdbaanr = StringIO()
gzf = GzipFile(fileobj=pdbaanr, mode='wb')
for i in sorted([j for j in pdbChainsDict.keys() if not j in wholeRepIgnore]):
sequence = str(pdbChainsDict[i].sequence)
experimentType = str(pdbChainsDict[i].experimentType)
resolution = str(pdbChainsDict[i].resolution)
rValueObs = str(pdbChainsDict[i].rValueObs)
rValueFree = str(pdbChainsDict[i].rValueFree)
alphaCarbonOnly = ['no', 'yes'][pdbChainsDict[i].alphaCarbonOnly]
# alphaCarbonOnly = 'yes' if pdbChainsDict[i].alphaCarbonOnly else 'no'
description = str(pdbChainsDict[i].description)
dbName = str(pdbChainsDict[i].dbName)
dbCode = str(pdbChainsDict[i].dbCode)
organism = str(pdbChainsDict[i].organism)
if wholeRepDict.has_key(i):
gzf.write('>' + str(i) + '\t' + str(len(sequence)) + '\t' + experimentType + '\t' + resolution + '\t' +
rValueObs + '\t' + rValueFree + '\t' + alphaCarbonOnly + '\t' + description + '\t<' + dbName +
' ' + dbCode + '>\t[' + organism + ']\t||\t' + '\t'.join(wholeRepDict[i]) + '\n')
else:
gzf.write('>' + str(i) + '\t' + str(len(sequence)) + '\t' + experimentType + '\t' + resolution + '\t' +
rValueObs + '\t' + rValueFree + '\t' + alphaCarbonOnly + '\t' + description + '\t<' + dbName +
' ' + dbCode + '>\t[' + organism + ']\n')
gzf.write(sequence + '\n')
gzf.close()
pdbaanr.seek(0, 2)
pdbaanrFile = InMemoryUploadedFile(pdbaanr, 'image', 'pdbaanr.gz', None, pdbaanr.tell(), None)
pdbaanrEntry = DownloadableFiles(fileName='pdbaanr')
pdbaanrEntry.save()
pdbaanrEntry.downloadFile.save(pdbaanrFile.name, pdbaanrFile)
pdbaanr.close()
# Generate the files needed to run the culling locally (i.e. make files of the different database tables).
proteinData = ProteinInformation.objects.all().values_list()
proteinFile = NamedTemporaryFile()
# sio = StringIO()
# gzf = GzipFile(fileobj=sio, mode='wb')
for i in proteinData:
# gzf.write('\t'.join([str(j) for j in i]) + '\n')
proteinFile.write('\t'.join([str(j) for j in i]) + '\n')
# gzf.close()
# sio.seek(0, 2)
# proteinFile = InMemoryUploadedFile(sio, 'image', 'ProteinInformation.gz', None, sio.tell(), None)
proteinFileEntry = DownloadableFiles(fileName='ProteinInformation', downloadFile=File(proteinFile))
# proteinFileEntry = DownloadableFiles(fileName='ProteinInformation')
proteinFileEntry.save()
# proteinFileEntry.downloadFile.save(proteinFile.name, proteinFile)
# sio.close()
proteinFile.close()
chainData = ChainType.objects.all().values_list()
chainFile = NamedTemporaryFile()
# sio = StringIO()
# gzf = GzipFile(fileobj=sio, mode='wb')
for i in chainData:
# gzf.write('\t'.join([str(j) for j in i]) + '\n')
chainFile.write('\t'.join([str(j) for j in i]) + '\n')
# gzf.close()
# sio.seek(0, 2)
# chainFile = InMemoryUploadedFile(sio, 'image', 'ChainType.gz', None, sio.tell(), None)
chainFileEntry = DownloadableFiles(fileName='ChainType', downloadFile=File(chainFile))
# chainFileEntry = DownloadableFiles(fileName='ChainType')
chainFileEntry.save()
# chainFileEntry.downloadFile.save(chainFile.name, chainFile)
# sio.close()
chainFile.close()
PDBEntriesData = AllPDBEntries.objects.all().values_list()
entriesFile = NamedTemporaryFile()
# sio = StringIO()
# gzf = GzipFile(fileobj=sio, mode='wb')
for i in PDBEntriesData:
# gzf.write('\t'.join([str(j) for j in i]) + '\n')
entriesFile.write('\t'.join([str(j) for j in i]) + '\n')
# gzf.close()
# sio.seek(0, 2)
# entriesFile = InMemoryUploadedFile(sio, 'image', 'AllPDBEntries.gz', None, sio.tell(), None)
entriesFileEntry = DownloadableFiles(fileName='AllPDBEntries', downloadFile=File(entriesFile))
# entriesFileEntry = DownloadableFiles(fileName='AllPDBEntries')
entriesFileEntry.save()
# entriesFileEntry.downloadFile.save(entriesFile.name, entriesFile)
# sio.close()
entriesFile.close()
similarityData = Similarity.objects.all().values_list()
similarityFile = NamedTemporaryFile()
# sio = StringIO()
# gzf = GzipFile(fileobj=sio, mode='wb')
for i in similarityData:
# gzf.write('\t'.join([str(j) for j in i]) + '\n')
similarityFile.write('\t'.join([str(j) for j in i]) + '\n')
# gzf.close()
# sio.seek(0, 2)
# similarityFile = InMemoryUploadedFile(sio, 'image', 'Similarity.gz', None, sio.tell(), None)
similarityFileEntry = DownloadableFiles(fileName='Similarity', downloadFile=File(similarityFile))
# similarityFileEntry = DownloadableFiles(fileName='Similarity')
similarityFileEntry.save()
# similarityFileEntry.downloadFile.save(similarityFile.name, similarityFile)
# sio.close()
similarityFile.close()
representativeData = Representative.objects.all().values_list()
representativeFile = NamedTemporaryFile()
# sio = StringIO()
# gzf = GzipFile(fileobj=sio, mode='wb')
for i in representativeData:
# gzf.write('\t'.join([str(j) for j in i]) + '\n')
representativeFile.write('\t'.join([str(j) for j in i]) + '\n')
# gzf.close()
# sio.seek(0, 2)
# representativeFile = InMemoryUploadedFile(sio, 'image', 'Representative.gz', None, sio.tell(), None)
representativeFileEntry = DownloadableFiles(fileName='Representative', downloadFile=File(representativeFile))
# representativeFileEntry = DownloadableFiles(fileName='Representative')
representativeFileEntry.save()
# representativeFileEntry.downloadFile.save(representativeFile.name, representativeFile)
# sio.close()
representativeFile.close()
destinationDir = settings.MEDIA_ROOT + 'TarData/PDBData'
# tar = tarfile.open(settings.MEDIA_ROOT + 'TarData/PDBData.tar.gz', mode='w:gz')
entriesInfo = DownloadableFiles.objects.filter(fileName__exact='AllPDBEntries')
subprocess.call(['cp', str(entriesInfo[0].downloadFile.path), destinationDir + '/AllPDBEntries.txt'])
# tar.add(entriesInfo[0].downloadFile.path, arcname='AllPDBEntries.txt')
chainInfo = DownloadableFiles.objects.filter(fileName__exact='ChainType')
subprocess.call(['cp', str(chainInfo[0].downloadFile.path), destinationDir + '/ChainType.txt'])
# tar.add(chainInfo[0].downloadFile.path, arcname='ChainType.txt')
proteinInfo = DownloadableFiles.objects.filter(fileName__exact='ProteinInformation')
subprocess.call(['cp', str(proteinInfo[0].downloadFile.path), destinationDir + '/ProteinInformation.txt'])
# tar.add(proteinInfo[0].downloadFile.path, arcname='ProteinInformation.txt')
representativeInfo = DownloadableFiles.objects.filter(fileName__exact='Representative')
subprocess.call(['cp', str(representativeInfo[0].downloadFile.path), destinationDir + '/Representative.txt'])
# tar.add(representativeInfo[0].downloadFile.path, arcname='Representative.txt')
similarityInfo = DownloadableFiles.objects.filter(fileName__exact='Similarity')
subprocess.call(['cp', str(similarityInfo[0].downloadFile.path), destinationDir + '/Similarity.txt'])
# tar.add(similarityInfo[0].downloadFile.path, arcname='Similarity.txt')
# tar.close()
subprocess.Popen(['tar', '-zcvf', 'PDBData.tar.gz', 'PDBData'], cwd=settings.MEDIA_ROOT + 'TarData', stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
proteinChains = []
readChainTypeData = open(destinationDir + '/ChainType.txt', 'r')
for i in readChainTypeData:
chunks = (i.strip()).split('\t')
if chunks[1] == 'Protein':
proteinChains.append(chunks[0])
readChainTypeData.close()
proteinChains = '\n'.join(proteinChains)
# Generate the culled PDB lists.
resolutionsOfInterest = [1.6, 1.8, 2.0, 2.2, 2.5, 3.0]
rValuesOfInterest = [0.25, 1.0]
sequenceIdentities = [20, 25, 30, 40, 50, 60, 70, 80, 90]
tuplesToDo = [(i, j, k) for i in resolutionsOfInterest for j in rValuesOfInterest for k in sequenceIdentities]
tuplesToDo.extend([(100.0, 1.0, i) for i in sequenceIdentities])
updatesPerformed = []
while tuplesToDo != [] or updatesPerformed != []:
# Continue looping until both lists are empty. If both are empty then all updates have been performed.
updatesDone = []
for i in updatesPerformed:
# Determine if any of the culling operations that are currently running have finished.
if i.completed:
if not i.skipNonXray:
if not i.skipAlphaCarbon:
xrayCAInfo = '_INCLNONXRAY_INCLCAONLY'
else:
xrayCAInfo = '_INCLNONXRAY'
else:
xrayCAInfo = ''
sio = StringIO()
gzf = GzipFile(fileobj=sio, mode='wb')
outputInfo = open(i.nonredSeq.path, 'r')
for line in outputInfo:
gzf.write(line)
outputInfo.close()
gzf.close()
sio.seek(0, 2)
culledFile = InMemoryUploadedFile(sio, 'image',
('SeqIden_' + str(i.sequenceIdentity) + '_Res_' + str(i.maxResolution) +
'_RVal_' + str(i.maxRValue) + xrayCAInfo + '.gz'),
None, sio.tell(), None)
newDownload = DownloadableFiles(fileName='SeqIden_' + str(i.sequenceIdentity) + '_Res_' + str(i.maxResolution) +
'_RVal_' + str(i.maxRValue) + xrayCAInfo)
newDownload.save()
newDownload.downloadFile.save(culledFile.name, culledFile)
sio.close()
updatesDone.append(i)
i.delete()
for i in updatesDone:
updatesPerformed.remove(i)
if tuplesToDo == [] or len(updatesPerformed) >= 1:
# Only allow 1 culling operation to occur at once, to prevent overloading.
# pass
time.sleep(30)
else:
# Fill the buffer of culling operations up.
while len(updatesPerformed) < 1 and tuplesToDo != []:
newCull = tuplesToDo.pop()
resolution = newCull[0]
rValue = newCull[1]
seqIdentity = newCull[2]
if resolution == 100.0:
skipNonXray = False
skipAlphaCarbon = False
else:
skipNonXray = True
skipAlphaCarbon = True
r = PDBCullRequest(
wholePDB=False,
sequenceIdentity=seqIdentity,
minResolution=0.0,
maxResolution=resolution,
maxRValue=rValue,
minLength = -1,
maxLength = -1,
skipNonXray=skipNonXray,
skipAlphaCarbon=skipAlphaCarbon,
cullByChain=True,
performIntraEntryCulling=False,
intraEntrySequenceIdentity=100.0,
email='No Email',
completed=False,
requestDate=datetime.datetime.now()
)
r.save()
r.userInput.save('', ContentFile(proteinChains))
cullinput.controlthread.RunCull(r, 'pdb')
updatesPerformed.append(r)
logger = open('/srv/www/vhosts.d/www.bioinf/html/doig/cgi-bin/django_projects/LeafWebApp/ErrorLogs/GENERATION.log', 'a')
logger.write('Finished generation on ' + time.strftime('%Y/%m/%d/ at %H:%M:%S', time.gmtime()) + '.\n')
logger.close()
def user_pdb_submit(request):
errorDict = {}
pastedChains = request.POST['pastedInfo'].rstrip()
pastedChains = pastedChains.lstrip()
pastedChains = pastedChains.split('\n')
speciesDropBox = request.POST['speciesDropBox']
speciesTextBox = request.POST['speciesTextBox']
try:
uploaded = request.FILES['upload']
except:
uploaded = ""
skipNonXray = request.POST['skipNonXray']
skipAlphaCarbon = request.POST['skipAlphaCarbon']
cullMethod = request.POST['cullMethod']
intraEntryCull = request.POST['intraEntryCull']
email = request.POST['email']
incorrect = []
try:
percentIdentity = float(request.POST['pc'])
if percentIdentity < 5 or percentIdentity >= 100:
errorDict['errorPercent'] = True
incorrect.append(u"The value entered for the percentage: " + str(percentIdentity) + " is not within the permissible range of values. The percentage must be greater than or equal to 5, and less than 100.")
except:
errorDict['errorPercent'] = True
incorrect.append(u'The value for the sequence identity threshold must be greater than or equal to 5, and less than 100.')
try:
minResolution = float(request.POST['minRes'])
if minResolution < 0:
errorDict['errorMinRes'] = True
incorrect.append(u"The value entered for the minimum resolution: " + str(minResolution) + " is less than 0.")
if minResolution > 100:
errorDict['errorMinRes'] = True
incorrect.append(u"The value entered for the minimum resolution: " + str(minResolution) + " is greater than 100.")
try:
maxResolution = float(request.POST['maxRes'])
if maxResolution < 0:
errorDict['errorMaxRes'] = True
incorrect.append(u"The value entered for the maximum resolution: " + str(maxResolution) + " is less than 0.")
if maxResolution > 100:
errorDict['errorMaxRes'] = True
incorrect.append(u"The value entered for the maximum resolution: " + str(maxResolution) + " is greater than 100.")
if minResolution > maxResolution:
errorDict['errorMinRes'] = True
incorrect.append(u"The value entered for the minimum resolution: " + str(minResolution) + " is greater than the value for the maximum resolution: " + str(maxResolution) + ".")
except:
errorDict['errorMaxRes'] = True
incorrect.append(u'The value for the maximum resolution must be a number.')
except:
errorDict['errorMinRes'] = True
incorrect.append(u'The value for the minimum resolution must be a number.')
try:
maxResolution = float(request.POST['maxRes'])
if maxResolution < 0:
errorDict['errorMaxRes'] = True
incorrect.append(u"The value entered for the maximum resolution: " + str(maxResolution) + " is less than 0.")
if maxResolution > 100:
errorDict['errorMaxRes'] = True
incorrect.append(u"The value entered for the maximum resolution: " + str(maxResolution) + " is greater than 100.")
except:
errorDict['errorMaxRes'] = True
incorrect.append(u'The value for the maximum resolution must be a number.')
try:
maxRVal = float(request.POST['maxRVal'])
if maxRVal < 0 or maxRVal > 1:
errorDict['errorRVal'] = True
incorrect.append(u"The value entered for the maximum R value: " + str(maxRVal) + " is not within the permissible range of values. The range allowed is: 0 to 1.")
except:
errorDict['errorRVal'] = True
incorrect.append(u'The maximum R value must be a number in the range 0 - 1.')
if request.POST['enforceMinLength'] == 'yes':
try:
minLength = int(request.POST['minLength'])
if minLength < 0:
errorDict['errorMinLength'] = True
incorrect.append(u'The value for the minimum length must be greater than or equal to 0')
if request.POST['enforceMaxLength'] == 'yes':
try:
maxLength = int(request.POST['maxLength'])
if maxLength < 0:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum length must be greater than or equal to 0')
if minLength > maxLength:
errorDict['errorMinLength'] = True
incorrect.append(u"The value entered for the minimum length: " + str(minLength) + " is greater than the value for the maximum length: " + str(maxLength) + ".")
except:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum sequence length must be an integer.')
else:
maxLength = -1
except:
errorDict['errorMinLength'] = True
incorrect.append(u'The value for the minimum sequence length must be an integer.')
if request.POST['enforceMaxLength'] == 'yes':
try:
maxLength = int(request.POST['maxLength'])
if maxLength < 0:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum length must be greater than or equal to 0')
minLength = -1
except:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum sequence length must be an integer.')
elif request.POST['enforceMaxLength'] == 'yes':
try:
maxLength = int(request.POST['maxLength'])
if maxLength < 0:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum length must be greater than or equal to 0')
minLength = -1
except:
errorDict['errorMaxLength'] = True
incorrect.append(u'The value for the maximum sequence length must be an integer.')
else:
minLength = -1
maxLength = -1
if not re.match("[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\.[a-zA-Z]+$", email):
errorDict['errorEmail'] = True
incorrect.append(u"The email address entered does not appear to be a valid email address.")
# Determine whether the user input is correct.
errorList = [pastedChains == [''], uploaded == "", speciesDropBox == 'Nothing', speciesTextBox == '']
if errorList.count(True) == 4:
errorDict['errorPasted'] = True
errorDict['errorUploaded'] = True
errorDict['errorSpeciesDrop'] = True
errorDict['errorSpeciesText'] = True
incorrect.append(u"You have not provided a source of chains/entries to cull.")
elif errorList.count(False) != 1:
if errorList[0] == False:
errorDict['errorPasted'] = True
if errorList[1] == False:
errorDict['errorUploaded'] = True
if errorList[2] == False:
errorDict['errorSpeciesDrop'] = True
if errorList[3] == False:
errorDict['errorSpeciesText'] = True
incorrect.append(u'You have provided more than one source of chains/entries to cull.')
else:
# Determine if the PDB chains/entries input are acceptable.
if errorList[0] == False:
fileString = str(request.POST['pastedInfo'])
inputList = fileString.split()
chainInfo = ChainType.objects.all()
if cullMethod == 'chain':
# If the user has supplied any entries in the list of input chains, then extract all chains corresponding to
# the input entry.
processedInputList = set([])
for i in inputList:
if len(i) == 4:
# Possibly an entry.
chainsFromEntry = ProteinInformation.objects.filter(entry__exact=i)
if len(chainsFromEntry) == 0:
processedInputList.add(i)
else:
for j in chainsFromEntry:
processedInputList.add(str(j.chain))
else:
processedInputList.add(i)
processedInputList = list(processedInputList)
chainDict = {}
for i in chainInfo:
chainDict[i.chain] = i.chainType
retCode, retVal = cullinput.checkPDBinput.main(processedInputList, allChains=chainDict, checkType='chain')
else:
allEntries = AllPDBEntries.objects.all().values_list('entry', flat=True)
allProtEntries = set([i.chain[:4] for i in chainInfo if i.chainType == 'Protein'])
retCode, retVal = cullinput.checkPDBinput.main(inputList, allEntries=allEntries, allProtEntries=allProtEntries, checkType='entry')
if retCode != 0:
errorDict['errorPasted'] = True
incorrect.append(retVal)
elif uploaded != '':
fileString = ''
for chunk in uploaded.chunks():
fileString += chunk
inputList = fileString.split()
inputList = [i.strip() for i in inputList]
chainInfo = ChainType.objects.all()
if cullMethod == 'chain':
# If the user has supplied any entries in the list of input chains, then extract all chains corresponding to
# the input entry.
processedInputList = set([])
for i in inputList:
if len(i) == 4:
# Possibly an entry.
chainsFromEntry = ProteinInformation.objects.filter(entry__exact=i)
if len(chainsFromEntry) == 0:
processedInputList.add(i)
else:
for j in chainsFromEntry:
processedInputList.add(str(j.chain))
else:
processedInputList.add(i)
processedInputList = list(processedInputList)
chainDict = {}
for i in chainInfo:
chainDict[i.chain] = i.chainType
retCode, retVal = cullinput.checkPDBinput.main(processedInputList, allChains=chainDict, checkType='chain')
else:
allEntries = AllPDBEntries.objects.all().values_list('entry', flat=True)
allProtEntries = set([i.chain[:4] for i in chainInfo if i.chainType == 'Protein'])
retCode, retVal = cullinput.checkPDBinput.main(inputList, allEntries=allEntries, allProtEntries=allProtEntries, checkType='entry')
if retCode != 0:
errorDict['errorUploaded'] = True
incorrect.append(retVal)
elif speciesDropBox != 'Nothing':
allChains = ProteinInformation.objects.filter(organism__iexact=speciesDropBox)
if cullMethod == 'chain':
allChains = [str(i.chain) for i in allChains]
if len(allChains) < 2:
errorDict['errorSpeciesDrop'] = True
incorrect.append(u'There are less than 2 chains in the PDB from the organism you selected.')
retVal = '\n'.join(allChains)
else:
allEntries = list(set([str(i.entry) for i in allChains]))
if len(allEntries) < 2:
errorDict['errorSpeciesDrop'] = True
incorrect.append(u'There are less than 2 entries in the PDB from the organism you selected.')
retVal = '\n'.join(allEntries)
elif speciesTextBox != '':
allChains = ProteinInformation.objects.filter(organism__iexact=speciesTextBox)
if cullMethod == 'chain':
allChains = [i.chain for i in allChains]
if len(allChains) < 2:
errorDict['errorSpeciesText'] = True
incorrect.append(u'There are less than 2 chains in the PDB from the organism you entered.' +
' This is possibly due to the species being spelled incorrectly.')
retVal = '\n'.join(allChains)
else:
allEntries = list(set([i.entry for i in allChains]))
if len(allEntries) < 2:
errorDict['errorSpeciesText'] = True
incorrect.append(u'There are less than 2 entries in the PDB from the organism you entered.' +
' This is possibly due to the species being spelled incorrectly.')
retVal = '\n'.join(allEntries)
if cullMethod == 'entry' and intraEntryCull == 'yes':
try:
intraEntryPC = float(request.POST['intraEntryPC'])
if intraEntryPC < 5 or intraEntryPC >= 100:
errorDict['errorIntraEntry'] = True
incorrect.append(u"The value entered for the within entry sequence identity threshold: " + str(intraEntryPC) + " is not within the permissible range of values. The value must be a number greater than or equal to 5, and less than 100.")
except:
errorDict['errorIntraEntry'] = True
incorrect.append(u'The value for the within entry sequence identity threshold must be a number greater than or equal to 5, and less than 100.')
elif intraEntryCull == 'yes':
incorrect.append(u'Intra entry culling is selected, but cull by entry is not.')
if incorrect != []:
valueDict = {'errorMessage': incorrect, 'pastedChains' : request.POST['pastedInfo'],
'speciesDropBox' : request.POST['speciesDropBox'], 'speciesTextBox' : request.POST['speciesTextBox'],
'pc' : request.POST['pc'], 'minRes' : request.POST['minRes'], 'maxRes' : request.POST['maxRes'],
'maxRVal' : request.POST['maxRVal'], 'intraEntryPC' : request.POST['intraEntryPC'],
'email' : request.POST['email']
}
if skipNonXray == 'no':
valueDict['skipNonXray'] = request.POST['skipNonXray']
if skipAlphaCarbon == 'no':
valueDict['skipAlphaCarbon'] = request.POST['skipAlphaCarbon']
if cullMethod == 'entry':
valueDict['cullMethod'] = request.POST['cullMethod']
if intraEntryCull == 'yes':
valueDict['intraEntryCull'] = request.POST['intraEntryCull']
if request.POST['enforceMinLength'] == 'yes':
valueDict['enforceMinLength'] = 'yes'
valueDict['minLength'] = request.POST['minLength']
if request.POST['enforceMaxLength'] == 'yes':
valueDict['enforceMaxLength'] = 'yes'
valueDict['maxLength'] = request.POST['maxLength']
for i in errorDict.keys():
valueDict[i] = True
return render_to_response('user_pdb_culling.html',
valueDict,
context_instance=RequestContext(request))
# Setup the database entry
if skipNonXray == 'yes':
skipNonXray = True
else:
skipNonXray = False
if skipAlphaCarbon == 'yes':
skipAlphaCarbon = True
else:
skipAlphaCarbon = False
if cullMethod == 'chain':
cullMethod = True
else:
cullMethod = False
if intraEntryCull == 'yes':
intraEntryCull = True
else:
intraEntryCull = False
r = PDBCullRequest(
wholePDB=False,
sequenceIdentity=percentIdentity,
minResolution=minResolution,
maxResolution=maxResolution,
maxRValue=maxRVal,
minLength = minLength,
maxLength = maxLength,
skipNonXray=skipNonXray,
skipAlphaCarbon=skipAlphaCarbon,
cullByChain=cullMethod,
performIntraEntryCulling=intraEntryCull,
intraEntrySequenceIdentity=float(request.POST['intraEntryPC']),
email=str(email),
completed=False,
requestDate=datetime.datetime.now()
)
r.save()
r.userInput.save('', ContentFile(retVal))
cullinput.controlthread.RunCull(r, 'pdb')
# return HttpResponseRedirect(reverse('Leaf.views.sent'))
return HttpResponseRedirect(reverse('Leaf.views.sent', kwargs={'result_id': r.id, 'cullType' : 'pdb'}))
