def tagCompounds(request, action):
if request.is_ajax() and request.method == 'POST':
rawJson = request.body
data = json.loads(rawJson.decode("utf-8"))
compoundIds = []
tags = []
try:
tags = data["tags"]
compoundIds = [int(id) for id in data["ids"]]
except:
print("failed to parse json for tags and compound ids: " +
str(rawJson))
return HttpResponse("failed to parse JSON", status=404)
#print("adding tags "+str(tags)+" to compounds "+str(compoundIds))
Tag.ensureAllExist(tags, request.user)
tagObjects = Tag.objects.filter(user=request.user, name__in=tags)
compounds = Compound.objects.filter(user=request.user,
id__in=compoundIds)
for compound in compounds:
if action == 'add':
compound.tags.add(*tagObjects)
elif action == 'remove':
compound.tags.remove(*tagObjects)
else:
return HttpResponse("Unknown action given", status=404)
compound.save()
return HttpResponse('')
def tagDuplicateCompounds(request):
from django.db.models import Count
import itertools
from operator import itemgetter
#print("tagging duplicates")
if request.is_ajax() and request.method == 'GET':
# group all compounds by inchi and return groups with size > 1
groupInfo =Compound.objects.values_list('inchi') \
.annotate(duplicate_count=Count('inchi')) \
.filter(user=request.user,duplicate_count__gt=1) \
.order_by('inchi')
dupedInchis = [row[0] for row in groupInfo]
numGroups = len(groupInfo)
#print("duped inchi's: "+str(dupedInchis))
# get the id and inchi of duplicated compounds
dupedCompounds = Compound.objects \
.values_list("id","inchi") \
.filter(user=request.user,inchi__in=dupedInchis)
#print("duped compounds: "+str(dupedCompounds))
allIds = [row[0] for row in dupedCompounds]
groups = itertools.groupby(sorted(dupedCompounds, key=itemgetter(1)),
key=itemgetter(1))
#print("groups: "+str(groups))
# tag all group memebers with 'duplicated'
Tag.ensureAllExist(["duplicate-extra"], request.user)
extraTag = Tag.objects.filter(user=request.user,
name__exact="duplicate-extra").get()
#print("duplicatedTag: "+str(extraTag))
# create all tags we'll need at once
tagNames = ["duplicate-set-" + str(i) for i in range(numGroups)]
Tag.ensureAllExist(tagNames, request.user)
tags = Tag.objects.filter(user=request.user,
name__in=tagNames).order_by("id")
newTags = {}
# tag all but the first member of each group with duplicted-X
for setNum, group in enumerate(
groups
): # groups is a list of tuples, each tuple is (inchi,[ids])
ids = [row[0] for row in list(group[1])]
#print("group: "+str(ids))
for i, compound in enumerate(
Compound.objects.filter(user=request.user, id__in=ids)):
t = newTags.setdefault(compound.id, [])
if i != 0: #don't tag first compound in each group, that will be the one to keep
compound.tags.add(extraTag)
t.append(extraTag.name)
compound.tags.add(tags[setNum])
t.append(tags[setNum].name)
compound.save()
return JsonResponse(newTags)
return JsonResponse({})
def addCompoundsAjax(user, source_id, ids, tags):
if len(tags) != 0:
Tag.ensureAllExist(tags, user)
if len(ids) == 0:
raise Exception('Empty list of "ids".')
if source_id == 'chembl':
sdfs = get_chembl_sdfs(ids)
sdf = '\n$$$$\n'.join(sdfs) + '\n$$$$\n'
newJob = createJob(
user, 'Upload Compounds', '',
['--user='******'--tags=' + (','.join(tags))], sdf)
time.sleep(2)
newJob = updateJob(user, newJob.id)
if newJob.status == Job.RUNNING:
ajaxResponse = {
'success':
True,
'message':
'Compound upload in progress. Check "Past Jobs" for status.'
}
elif newJob.status == Job.FINISHED:
ajaxResponse = {
'success': True,
'message': 'Compounds uploaded successfully.'
}
else:
ajaxResponse = {
'success': False,
'message': 'An error occurred while uploading your compounds.'
}
return ajaxResponse
else:
raise Exception('Unknown source_id: {}'.format(source_id))
def uploadCompound(request, resource = None, job_id = None):
allTags = Tag.allUserTagNames(request.user)
if (request.method == 'GET') and (resource != u'job'):
return render(request,'addCompounds.html',
dict(input_mode='smiles-input',
tags=allTags))
else:
sdf = None
name = None
compid = None
smiles = None
compoundTags = []
input_mode='smiles-input'
if 'tags' in request.POST:
compoundTags = set(request.POST.getlist('tags'))
Tag.ensureAllExist(compoundTags,request.user)
#existingTags = set(allTags)
#print("compound tags: "+str(compoundTags))
#for newTag in compoundTags.difference(existingTags):
# print("creating new tag: "+newTag+" for user "+request.user.username)
# Tag.objects.create(name = newTag, user=request.user)
if 'smiles' in request.POST:
input_mode = 'smiles-input'
sdf = u''
try:
smiles = request.POST['smiles'].split('\n')
for line in smiles:
if re.match(r"^\S+", line):
sdf = sdf + smiles_to_sdf(str(line))
except:
print("Unexpected error:", sys.exc_info())
traceback.print_tb(sys.exc_info()[2])
messages.error(request, 'Error: Invalid SMILES string!')
sdf = None
elif resource == 'job':
input_mode = 'sdf-upload'
job = updateJob(request.user, job_id)
f = open(job.output, 'r')
sdf = f.read()
f.close()
elif 'sdf' in request.FILES:
input_mode = 'sdf-upload'
try:
sdf = request.FILES['sdf']
sdf = sdf.read().decode("utf-8")
except (InputError, InvalidInputError):
messages.error(request, 'Invalid SDF!')
sdf = None
elif 'sdf' in request.POST:
if 'draw' in request.POST:
input_mode = 'draw'
sdf = request.POST['sdf'] + '$$$$'
compid = str(request.POST['id'])
compid = re.match(r"^(\S{0,20})", compid).group(1)
try:
smiles = sdf_to_smiles(sdf)
smiles = re.match(r"^(\S+)", smiles).group(1)
smiles = smiles + ' ' + compid
sdf = smiles_to_sdf(smiles)
except:
print("Unexpected error:", sys.exc_info())
traceback.print_tb(sys.exc_info()[2])
messages.error(request, 'Invalid drawing!')
sdf = None
else:
input_mode = 'sdf-input'
sdf = request.POST['sdf']
if not sdf:
messages.error(request, 'No input found!')
elif 'pubchem' in request.POST:
cids = request.POST['pubchem']
cids = cids.split()
input_mode = 'pubchem'
filteredCIDs = []
for cid in cids[:]:
match = re.search("(\d{1,200})", cid)
if match:
filteredCIDs.append(int(match.group(1)))
if len(filteredCIDs) > 0:
try:
sdf = DownloadCIDs(cids)
except:
print("Unexpected error:", sys.exc_info())
traceback.print_tb(sys.exc_info()[2])
messages.error(request,
'Invalid CIDs or no response from PubChem!'
)
sdf = None
else:
messages.error(request, 'Error: No valid CIDs entered!')
sdf = None
elif 'chembl' in request.POST:
cids = tuple(request.POST['chembl'].split())
if len(cids) > 0:
try:
sdfs = get_chembl_sdfs(cids)
sdf = "\n$$$$\n".join(sdfs)+"\n$$$$\n"
except:
print("Unexpected error:", sys.exc_info())
traceback.print_tb(sys.exc_info()[2])
messages.error(request,
'Invalid CIDs or no response from ChEMBL!'
)
sdf = None
else:
print("no chembl cids given")
messages.error(request, 'Error: No valid ChEMBL CIDs entered!')
sdf = None
if not sdf:
return render('addCompounds.html',
dict(input_mode=input_mode,
post_data=request.POST,
tags=compoundTags))
jobArgs = ['--user='******'dedup' in request.POST:
jobArgs += ["--deduplicate"]
newJob = createJob(request.user, 'Upload Compounds', '',jobArgs , sdf)
time.sleep(2)
return redirect(tools.views.view_job, job_id=newJob.id,
resource='')