def getStructures(request, job_id, format):
# takes a search job ID and returns an SDF of the compounds from this result
try:
job = updateJob(request.user, job_id)
f = open(job.output, 'r')
csvinput = csv.reader(f, delimiter=' ')
#read each line, extrace the second column, and combine all values
#into a new-line separated string
targetIds = "\n".join([line[0] for line in csvinput])
print("targetIds: " + str(targetIds))
f.close()
#result = '\n'.join(re.findall(r'^\S+', result, re.MULTILINE))
except Job.DoesNotExist:
print(traceback.format_exc())
raise Http404
newJob = createJob(request.user,
'pubchemID2SDF',
'', [],
targetIds,
format,
wait=True)
if format == 'smiles':
filename = 'search_result.smi'
else:
filename = 'search_result.sdf'
return redirect(tools.views.view_job,
job_id=newJob.id,
resource='other',
filename=filename)
def getStructures(request, job_id, format):
# takes a search job ID and returns an SDF of the compounds from this result
try:
job = updateJob(request.user, job_id)
f = open(job.output, 'r')
result = f.read()
f.close()
result = join(re.findall(r'^\S+', result, re.MULTILINE), sep='\n')
except Job.DoesNotExist:
raise Http404
newJob = createJob(request.user,
'pubchemID2SDF',
'', [],
result,
format,
async=False)
if format == 'smiles':
filename = 'search_result.smi'
else:
filename = 'search_result.sdf'
return redirect('tools.views.view_job',
job_id=newJob.id,
resource='other',
filename=filename)
def getStructures(request, job_id, format):
# takes a search job ID and returns an SDF of the compounds from this result
try:
job = updateJob(request.user, job_id)
f = open(job.output, "r")
result = f.read()
f.close()
result = join(re.findall(r"^\S+", result, re.MULTILINE), sep="\n")
except Job.DoesNotExist:
raise Http404
newJob = createJob(request.user, "pubchemID2SDF", "", [], result, format, async=False)
if format == "smiles":
filename = "search_result.smi"
else:
filename = "search_result.sdf"
return redirect("tools.views.view_job", job_id=newJob.id, resource="other", filename=filename)
def getStructures(request, job_id, format):
# takes a search job ID and returns an SDF of the compounds from this result
try:
job = updateJob(request.user, job_id)
f = open(job.output, 'r')
result = f.read()
f.close()
result = join(re.findall(r'^\S+', result, re.MULTILINE), sep='\n')
except Job.DoesNotExist:
raise Http404
newJob = createJob(request.user, 'pubchemID2SDF', '', '', result,
format, async=False)
if format == 'smiles':
filename = 'search_result.smi'
else:
filename = 'search_result.sdf'
return redirect('tools.views.view_job', job_id=newJob.id,resource='other',filename=filename)
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$$$$\n'.join(sdfs) + '\n$$$$\n'
newJob = createJob(
user, 'Upload Compounds', '',
['--user='******'--tags=' + (','.join(tags))], sdf)
time.sleep(2)
newJob = updateJob(user, newJob.id)
if newJob.status == Job.RUNNING:
ajaxResponse = {
'success':
True,
'message':
'Compound upload in progress. Check "Past Jobs" for status.'
}
elif newJob.status == Job.FINISHED:
ajaxResponse = {
'success': True,
'message': 'Compounds uploaded successfully.'
}
else:
ajaxResponse = {
'success': False,
'message': 'An error occurred while uploading your compounds.'
}
return ajaxResponse
else:
raise Exception('Unknown source_id: {}'.format(source_id))
def uploadCompound(request, resource = None, job_id = None):
if (request.method == 'GET') and (resource != u'job'):
return render_to_response('addCompounds.html',
dict(input_mode='smiles-input'),
context_instance=RequestContext(request))
else:
sdf = None
name = None
compid = None
smiles = None
if 'smiles' in request.POST:
input_mode = 'smiles-input'
sdf = u''
try:
smiles = request.POST['smiles'].split('\n')
for line in smiles:
if re.match(r"^\S+", line):
sdf = sdf + smiles_to_sdf(str(line))
except:
messages.error(request, 'Error: Invalid SMILES string!')
sdf = None
elif resource == 'job':
input_mode = 'sdf-upload'
job = updateJob(request.user, job_id)
f = open(job.output, 'r')
sdf = f.read()
f.close()
elif 'sdf' in request.FILES:
input_mode = 'sdf-upload'
try:
sdf = request.FILES['sdf']
sdf = sdf.read()
except (InputError, InvalidInputError):
messages.error(request, 'Invalid SDF!')
sdf = None
elif 'sdf' in request.POST:
if 'draw' in request.POST:
input_mode = 'draw'
sdf = request.POST['sdf'] + '$$$$'
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:
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(filteredCIDs)
except:
messages.error(request,
'Invalid CIDs or no response from PubChem!'
)
sdf = None
else:
messages.error(request, 'Error: No valid CIDs entered!')
sdf = None
if not sdf:
return render_to_response('addCompounds.html',
dict(input_mode=input_mode,
post_data=request.POST),
context_instance=RequestContext(request))
newJob = createJob(request.user, 'Upload Compounds', '',
['--user='******'tools.views.view_job', job_id=newJob.id,
resource='')
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='')