def showCompounds(request, resource):
# perform query for existing myCompounds
#(page, matches) = getMyCompounds(request)
matches = Compound.objects.filter(user=request.user)
#print("page count: "+str(page.count))
#print("page num pages: "+str(page.num_pages))
if resource:
if resource == 'deleteAll':
deleteMyCompounds(request)
matches = None
messages.error(request, 'All Compounds Deleted!')
if resource == 'downloadSMILES.smi':
smiles = makeSMILES(request.user)
return HttpResponse(smiles, content_type='text/plain')
if resource == 'downloadSDF.sdf':
sdf = makeSDF(request.user)
return HttpResponse(sdf, content_type='text/plain')
if matches:
for match in matches:
match.smiles = re.match(r"^(\S+)", match.smiles).group(1)
match.smiles = urlquote(match.smiles)
allTags = Tag.allUserTagNames(request.user)
return render(request,'showCompounds.html', dict(matches=matches,tags=allTags))
def showCompoundGrid(request):
# perform query for existing myCompounds
matches = None
givenTags = []
allTags = Tag.allUserTagNames(request.user)
if 'tags' in request.POST:
givenTags = request.POST.getlist("tags")
else:
givenTags = ["all"]
matches = Compound.byTagNames(givenTags, request.user)
return render(request, 'compoundGrid.html',
dict(matches=matches, tags=allTags, currentTags=givenTags))
def launch_job(request, category=None):
if request.is_ajax():
# for ajax requests, return HTML form for each app
currentApp = request.GET['currentApp']
try:
application = Application.objects.get(id=currentApp)
AppFormSet = getAppForm(application.id, request.user)
form = AppFormSet()
form = str(form)
response = dict(form=form, desc=application.description)
except Exception as e:
print(traceback.format_exc())
response = dict(form='ERROR')
return HttpResponse(dumps(response), 'text/json')
if request.method == 'POST':
appForm = getAppForm(request.POST['application'], request.user)
form = appForm(request.POST, request.FILES)
if form.is_valid():
try:
appid = int(form.cleaned_data['application'])
application = Application.objects.get(id=str(appid))
except Application.DoesNotExist:
messages.error(request, 'Application does not exist')
return redirect(launch_job, category=category)
else:
messages.error(request, str(form.errors))
return redirect(launch_job, category=category)
commandOptions, optionsList = parseToolForm(form)
# setup input
if application.input_type == 'chemical/x-mdl-sdfile':
input = 'chemical/x-mdl-sdfile'
elif application.input_type == 'upload':
input = request.FILES['File Upload'].read().decode("utf-8")
else:
input = ''
tagNames = []
if "tags" in request.POST:
tagNames = request.POST.getlist("tags")
#print("got tagNames: "+str(tagNames))
newJob = createJob(request.user,
application.name,
optionsList,
commandOptions,
input,
tagNames=tagNames)
messages.success(request, 'Success: job launched.')
return redirect(view_job, job_id=newJob.id, resource='')
else:
if category:
fromWorkbench = False
try:
category = ApplicationCategories.objects.get(name=category)
compoundCount = Compound.objects.filter(
user=request.user).count()
if category.name != 'Upload':
fromWorkbench = True
if category.name == 'Clustering' and compoundCount < 3:
messages.info(
request,
'Notice: you must have at least 3 compounds to perform clustering. Please use this form to add more compounds and then click "Cluster" again.'
)
return redirect(myCompounds.views.uploadCompound,
job_id=None,
resource=None)
if category.name == 'Properties' and compoundCount < 1:
messages.info(
request,
'Notice: you must have at least one compound to compute properties. Please use this form to add compounds and then click "Properties" again.'
)
return redirect(myCompounds.views.uploadCompound,
job_id=None,
resource=None)
title = 'Launch ' + category.name + ' Job'
apps = Application.objects.filter(category=category)
except:
print(traceback.format_exc())
raise Http404
else:
title = 'Launch Job'
apps = Application.objects.filter()
fields = {}
fields['application'] = ModelChoiceField(queryset=apps, empty_label='')
form = type('%sForm' % 'choose application', (Form, ), fields)
allTags = Tag.allUserTagNames(request.user)
return render(
request, 'submitForm.html',
dict(title=title,
form=form,
tags=allTags,
fromWorkbench=fromWorkbench,
totalCompounds=Compound.objects.filter(
user=request.user).count()))
def view_job(
request,
job_id,
resource=None,
filename=None,
):
job = updateJob(request.user, job_id)
if job == False:
raise Http404
if resource:
if resource == 'delete':
deleteJob(request.user, job.id)
return HttpResponse('deleted', content_type='text/plain')
if resource == 'download':
f = open(job.output, 'r')
result = f.read()
f.close()
if job.application.output_type == 'application/json.canvasxpress':
result = re.search(r'smps":"(.*)"}},', result).group(1)
return HttpResponse(result,
content_type=job.application.output_type)
if request.is_ajax():
if job.status == Job.RUNNING:
response = dict(status='RUNNING', job_id=job_id)
else:
response = dict(status='DONE', job_id=job_id)
return HttpResponse(dumps(response), 'text/json')
if job.status == Job.FINISHED:
finalResult = job.output
finalResult = re.sub('.*/', '', finalResult, count=0)
finalResult = '/working/' + finalResult
job.start_time = str(job.start_time)
# select correct viewer here based on output type
if job.application.output_type == 'chemical/sdfUpload':
f = open(job.output, 'r')
sdf = f.read()
f.close()
result, error = batch_sdf_to_smiles(sdf)
quotedSmiles = []
for smiles in result.splitlines():
match = re.search(r'(\S+)\s+(\S+)', smiles)
smiOnly = match.group(1)
cid = match.group(2)
quotedSmiles.append({'smiles': urlquote(smiOnly), 'cid': cid})
return render(
request, 'sdfUpload.html',
dict(title=str(job.application) + ' Results',
job=job,
compounds=quotedSmiles))
if job.application.output_type == 'text/ei.search.result':
f = open(job.output, 'r')
csvinput = csv.reader(f, delimiter=' ')
csvOutput = []
queryColumnEmpty = True
for line in csvinput:
if line[0] != "":
queryColumnEmpty = False
#print("csv line: "+str(line))
csvOutput.append(line)
#print("query column empty? "+str(queryColumnEmpty))
f.close()
allTags = Tag.allUserTagNames(request.user)
#print("job input: "+str(job.input))
if queryColumnEmpty:
singleQuery = job.input
else:
singleQuery = None
return render(
request, 'structure_search_result.html',
dict(title=str(job.application) + ' Results',
job=job,
tags=allTags,
compounds=csvOutput,
singleQuery=singleQuery,
resultType="ei"))
if job.application.output_type == 'text/fp.search.result':
f = open(job.output, 'r')
csvinput = csv.reader(f, delimiter=' ')
csvOutput = []
queryColumnEmpty = True
for line in csvinput:
if line[0] != "":
queryColumnEmpty = False
#print("csv line: "+str(line))
csvOutput.append(line)
#print("query column empty? "+str(queryColumnEmpty))
f.close()
allTags = Tag.allUserTagNames(request.user)
if queryColumnEmpty:
singleQuery = job.input
else:
singleQuery = None
return render(
request, 'structure_search_result.html',
dict(title=str(job.application) + ' Results',
job=job,
compounds=csvOutput,
singleQuery=singleQuery,
tags=allTags,
resultType="fp"))
elif job.application.output_type == 'text/sdf.upload':
f = open(job.output, 'r')
message = f.read()
f.close()
deleteJob(request.user, job.id)
if re.search(r"^ERROR:", message):
messages.error(request, message)
return redirect(myCompounds.views.uploadCompound,
job_id=None,
resource=None)
else:
messages.success(request, message)
return redirect(myCompounds.views.showCompounds, resource='')
elif job.application.output_type \
== 'application/json.cytoscape':
f = open(job.output, 'r')
plotJSON = f.read()
f.close()
return render(
request, 'view_network.html',
dict(title=str(job.application) + ' Results',
result=finalResult,
job=job,
plotJSON=plotJSON))
elif job.application.output_type \
== 'application/json.canvasxpress':
f = open(job.output, 'r')
plotJSON = f.read()
f.close()
if (job.application.name == 'Hierarchical Clustering')\
or (job.application.name == 'Numeric Data Clustering'):
tree = True
return render(
request, 'view_job.html',
dict(title=str(job.application) + ' Results',
result=finalResult,
tree=tree,
job=job,
plotJSON=plotJSON))
else:
tree = False
return render(
request, 'view_job.html',
dict(title=str(job.application) + ' Results',
result=finalResult,
tree=tree,
job=job,
plotJSON=plotJSON))
elif job.application.output_type == 'text/properties.table':
f = open(job.output, 'r')
csvinput = csv.reader(f)
csvOutput = []
for line in csvinput:
csvOutput.append(line)
f.close()
return render(
request, 'view_csv.html',
dict(title=str(job.application) + ' Results',
result=finalResult,
job=job,
csv=csvOutput))
elif job.application.output_type == 'text/bins.table':
f = open(job.output, 'r')
csvinput = csv.reader(f)
bins = defaultdict(list)
iterCsvInput = iter(csvinput)
next(iterCsvInput) # skip first line
for line in iterCsvInput:
cid = line[0]
binSize = line[1]
bin = line[2]
bins[bin].append(cid)
f.close()
bins = OrderedDict(sorted(list(bins.items()), key=lambda t: \
int(t[0])))
return render(
request, 'bins.html',
dict(title=str(job.application) + ' Results',
result=finalResult,
job=job,
bins=bins))
elif job.application.output_type == 'chemical/x-mdl-sdfile':
f = open(job.output, 'r')
sdf = f.read()
f.close()
nextStep = job.input
deleteJob(request.user, job.id)
if nextStep == 'workbench':
newJob = createJob(request.user, 'Upload Compounds', '',
['--user='******'')
elif nextStep == 'smiles':
result, error = batch_sdf_to_smiles(sdf)
return HttpResponse(result,
content_type=job.application.output_type)
else:
return HttpResponse(sdf,
content_type=job.application.output_type)
else:
# if mimetype is unknown, just send the file to the user
return redirect(view_job,
job_id=job.id,
resource='download',
filename='output')
elif job.status == Job.RUNNING:
return render(
request, 'wait.html',
dict(title=job.application.name +
' Job Running <img src="/static/images/spinner.gif"/>'))
elif job.status == Job.FAILED:
messages.error(
request,
'Job Failed due to invalid input data and/or invalid selected options. Please double check that your uploaded data (compounds and/or numeric data), and input options are valid and try running the tool again.'
)
return render(
request, 'view_job.html',
dict(title='Error: ' + str(job.application) + ' Job Failed',
job=job))
def search(request):
if request.is_ajax():
if 'application_id' in request.GET:
form = getAppForm(request.GET['application_id'], request.user)()
return HttpResponse(str(form))
else:
return HttpResponse("", status_code=404)
elif request.method != 'POST':
smi = ''
if 'smi' in request.GET:
smi = str(request.GET['smi'])
smi = urlunquote(smi)
allTags = Tag.allUserTagNames(request.user)
fields = {}
category = ApplicationCategories.objects.get(name="Search")
apps = Application.objects.filter(category=category).exclude(
name__exact="pubchemID2SDF")
fields['application'] = ModelChoiceField(queryset=apps, empty_label='')
form = type('%sForm' % 'choose application', (Form, ), fields)
return render(request, 'search.html',
dict(mode='form', smi=smi, appsForm=form, tags=allTags))
else:
sdf = None
smiles = None
compid = u'query'
form = None
application = None
application_id = None
if 'application' in request.POST:
application_id = request.POST['application']
application = Application.objects.get(id=application_id)
if 'tags' in request.POST:
givenTags = request.POST.getlist("tags")
compoundList = Compound.byTagNames(givenTags, request.user)
if len(compoundList) == 0:
messages.error(request,
"Error: No compounds found with selected tags")
else:
sdf = u''
for compound in compoundList:
sdf = sdf + compound.sdffile_set.all()[0].sdffile.rstrip(
) + '\n'
smiles = sdf_to_smiles(sdf)
elif 'smiles' in request.POST:
input_mode = 'smiles-input'
sdf = u''
try:
smiles = request.POST['smiles']
sdf = smiles_to_sdf(smiles)
except:
messages.error(request, 'Error: Invalid SMILES string!')
sdf = None
elif 'sdf' in request.FILES:
input_mode = 'sdf-upload'
try:
sdf = request.FILES['sdf']
sdf = first_mol(sdf.read())
smiles = sdf_to_smiles(sdf)
except:
print(traceback.format_exc())
messages.error(request, 'Invalid SDF!')
sdf = None
elif 'sdf' in request.POST:
if 'draw' in request.POST:
input_mode = 'draw'
sdf = request.POST['sdf'] + '$$$$'
try:
smiles = sdf_to_smiles(sdf)
smiles = re.match(r"^(\S+)", smiles).group(1)
smiles = smiles + ' ' + compid
sdf = smiles_to_sdf(smiles)
except:
print(traceback.format_exc())
messages.error(request, 'Invalid drawing!')
sdf = None
else:
try:
input_mode = 'sdf-input'
sdf = first_mol(request.POST['sdf'])
smiles = sdf_to_smiles(sdf)
except:
print(traceback.format_exc())
messages.error(request, 'Invalid input SDF!')
sdf = None
if application_id != None:
AppFormSet = getAppForm(request.POST['application'], request.user)
form = AppFormSet(request.POST)
if form != None and form.is_valid():
commandOptions, optionsList = parseToolForm(form)
else:
sdf = None
messages.error(request, "Invalid form options!")
if not sdf:
print("no sdf found")
return redirect(structure_search.views.search)
smiles = re.search(r'(\S+)', smiles).group(1)
smiles = urlquote(smiles)
#print("command options: "+str(commandOptions))
if application.name == "PubChem Fingerprint Search":
newJob = createJob(request.user, application.name, optionsList,
commandOptions, sdf, smiles)
elif application.name == "ChEMBL Fingerprint Search":
newJob = createJob(request.user, application.name, optionsList,
commandOptions, sdf, smiles)
elif application.name == "ChEMBL EI Search":
newJob = createJob(request.user, application.name, optionsList,
commandOptions, sdf, smiles)
time.sleep(1)
return redirect(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='')
def newTS(request):
# Default local variables
query_submit = False
message = None
annotation_info = None
annotation_matches = None
drugind_json = None
activity_info = None
activity_matches = None
allTags = Tag.allUserTagNames(request.user)
compoundDbs = readSources("unichem")
proteinDbs = readSources("uniprot")
defaultCompoundDb = "1"
defaultProteinDb = "ACC+ID"
groupingCol = 0
similarityJobs = [(job.id, str(job)) for job in Job.objects.filter(
user=request.user, application__category_id=5)]
# Default GET request variables
id_type = 'compound'
ids = list()
include_activity = False
source_id = 1
similarity_job_id = -1
# Retrieve GET request variables
if 'id_type' in request.GET:
id_type = request.GET['id_type']
if 'ids' in request.GET:
if id_type == 'homolog-target':
ids = request.GET.getlist('ids')
else:
ids = list(request.GET['ids'].split())
if 'include_activity' in request.GET:
include_activity = True
if 'tags' in request.GET:
for c in [
compound.cid for compound in Compound.byTagNames(
request.GET.getlist("tags"), request.user)
]:
ids.append(c)
if 'source_id' in request.GET:
source_id = request.GET['source_id']
if 'similarity_job_id' in request.GET:
similarity_job_id = int(request.GET['similarity_job_id'])
# Generate content
try:
idMapping = {}
if id_type == 'compound' and source_id != '1':
idMapping = mapToChembl(ids, source_id)
ids = list(idMapping.keys())
elif id_type == 'target' and source_id != 'ACC':
idMapping = mapToUniprot(ids, source_id)
ids = list(idMapping.keys())
elif id_type == 'homolog-target':
#full_ids = ids # Full context for homolog handling
#ids = [ i.split(',')[2] for i in full_ids ] # Bare Accession IDs for old target-search
# Context dictionary for homolog handling
# ex:
# homolog_context = {
# 'P29274': {'paralog': 'P30542'},
# 'P29275': {'paralog': 'P30542'},
# 'P0DMS8': {'paralog': 'P30542'},
# }
homolog_context = dict()
for i in ids:
[relation, src_id, homolog_id] = i.split(',')
if homolog_id not in homolog_context.keys():
homolog_context[homolog_id] = dict()
if src_id == homolog_id:
continue # Don't bother with "X is a homolog of X"
if relation not in homolog_context[homolog_id].keys():
homolog_context[homolog_id][relation] = set()
homolog_context[homolog_id][relation].add(src_id)
ids = list(homolog_context.keys()
) # Bare Accession IDs for old target-search
# Prepare homolog relation descriptions
homolog_desc = dict()
for homolog_id, relations in homolog_context.items():
desc_parts = list()
for relation, src_ids in sorted(relations.items()):
desc_parts.append("{} of {}".format(
relation, ', '.join(sorted(list(src_ids)))))
homolog_desc[homolog_id] = '; '.join(desc_parts)
if len(ids) != 0:
query_submit = True
queryIdCol = {
"id": "query_id",
"sql": None,
"table": "Query ID",
"name": "Query ID",
"desc": "Original compound ID prior to ChEMBL conversion",
"visible": True,
}
headerTextCol = {
"id": "header_text",
"sql": None,
"table": "Header Text",
"name": "Header Text",
"desc":
"Description text to show in row-group headers (i.e. source query IDs, translations, etc.)",
"visible": False,
}
originalQueryCol = {
"id": "original_query_id",
"sql": None,
"table": "Original Query ID",
"name": "Original Query ID",
"desc":
"The compound that the current query compound was originally derived from, based on similarity",
"visible": True,
}
myAnnotationSearch = AnnotationWithDrugIndSearch(id_type, ids)
annotation_info = myAnnotationSearch.table_info
annotation_matches = myAnnotationSearch.get_grouped_results()
drugind_json = drugIndicationData(myAnnotationSearch.drugind_objs)
# Exclude ActivitySearch from search-by-target by default
if id_type in ['target', 'homolog-target'
] and not include_activity:
activity_info = None
activity_matches = None
else:
myActivitySearch = ActivitySearch(id_type, ids)
activity_info = myActivitySearch.table_info
activity_matches = myActivitySearch.get_grouped_results()
if len(idMapping) != 0:
groupingCol += 1
addMappedQueryColumn(idMapping, queryIdCol, annotation_info,
annotation_matches, activity_info,
activity_matches)
if similarity_job_id != -1:
similarityMapping = readSimilarityMappingData(
request.user, similarity_job_id)
if len(
idMapping
) != 0: # need to compose our mapping with previous mapping
similarityMapping = composeMaps(idMapping,
similarityMapping)
#print("similarity mapping: \n"+str(similarityMapping))
if len(similarityMapping) != 0:
groupingCol += 1
addMappedQueryColumn(similarityMapping, originalQueryCol,
annotation_info, annotation_matches,
activity_info, activity_matches)
#if similarity_job_id != -1, then read job_<similarity_job_id>
# map chembl id (2nd column) back to the original compound id (first column)
# insert new column to show original compound id.
if ts_paralog_cache():
homolog_type_value = 'paralog-cache'
else:
homolog_type_value = 'paralog'
except Exception as e:
print("exception in newTS:", sys.exc_info())
traceback.print_tb(sys.exc_info()[2])
message = str(e)
context = {
'query_submit': query_submit,
'message': message,
'id_type': id_type,
'annotation_info': annotation_info,
'annotation_matches': annotation_matches,
'drugind_json': json.dumps(drugind_json),
'activity_info': activity_info,
'activity_matches': activity_matches,
'tags': allTags,
'compoundDbs': compoundDbs,
'defaultCompoundDb': defaultCompoundDb,
'proteinDbs': proteinDbs,
'defaultProteinDb': defaultProteinDb,
'groupingCol': groupingCol,
'similarityJobs': similarityJobs,
'homolog_type_value': homolog_type_value,
}
return render(request, 'targetsearch/new_ts.html', context)