def edit_experiment(id):
"""
Edit a experiment
"""
add_experiment = False
experiment = Experiment.query.filter_by(id=id).first()
form = ExperimentForm(obj=experiment)
if form.validate_on_submit():
experiment.name = form.name.data
experiment.description = form.description.data
experiment.content = form.content.data
experiment.courseNums = form.courseNums.data.courseNums
# type(form.courseNums.data) is app.models.course
experiment.containerName = form.containerName.data# .name
# type(form.containerName.data) is unicode
db.session.commit()
flash(u'实验修改成功')
# redirect to the experiments page
return redirect(url_for('admin.list_experiments'))
experiment.name = form.name.data
experiment.description = form.description.data
experiment.content = form.content.data
experiment.courseNums = form.courseNums.data# .courseNums
experiment.containerName = form.containerName.data
return render_template('admin/experiments/experiment.html', add_experiment=add_experiment,
form=form, title="Edit experiment")
def add_experiment():
"""
Add a experiment
"""
add_experiment = True
form = ExperimentForm()
if form.validate_on_submit():
experiment = Experiment(name=form.name.data,description=form.description.data,
content=form.content.data,courseNums=form.courseNums.data.courseNums,
containerName=form.containerName.data, teacherName=current_user.name) # .name)
try:
db.session.add(experiment)
db.session.commit()
flash(u'实验创建完成')
except:
flash(u'实验创建失败')
return redirect(url_for('admin.add_experiment'))
# redirect to the experiments page
return redirect(url_for('admin.list_experiments'))
return render_template('admin/experiments/experiment.html', add_experiment=add_experiment,
form=form, title="Add experiment")
def experiment():
form = ExperimentForm()
if request.method == "POST":
if form.validate() == False:
return render_template("experiment.html", form=form)
else:
title = form.title.data
description = form.description.data
etype = form.etype.data
protocol = form.protocol.data
duration = form.duration.data
username = session['username']
user = User.query.filter_by(username=username).first()
exp = Experiment(uid=user.id,
title=title,
duration=duration,
protocol=protocol,
description=description)
db.session.add(exp)
db.session.flush()
session['current_experiment'] = exp.eid
db.session.commit()
print(exp.eid)
return redirect(url_for('node'))
elif request.method == "GET":
return render_template("experiment.html", form=form)
def edit_experiment(request, pk):
experiment = Experiment.objects.get(pk=pk)
form = ExperimentForm(request.POST or None, instance=experiment)
if request.method == "POST" and form.is_valid():
if "cancel" in request.POST:
return redirect("/lifespan/experiments/")
with reversion.create_revision():
form.save()
reversion.set_user(request.user)
comment = request.POST["comment"] or "Changed experiment"
reversion.set_comment(comment)
log(request, experiment, comment)
return redirect("/lifespan/experiment/%s" % pk)
ctx = {"experiment": experiment, "form": form}
return render_to_response("lifespan/edit_experiment.html", ctx, context_instance=RequestContext(request))
def edit_experiment(request, pk):
experiment = Experiment.objects.get(pk=pk)
form = ExperimentForm(request.POST or None, instance=experiment)
if request.method == "POST" and form.is_valid():
if "cancel" in request.POST:
return redirect('/lifespan/experiments/')
with reversion.create_revision():
form.save()
reversion.set_user(request.user)
comment = request.POST['comment'] or "Changed experiment"
reversion.set_comment(comment)
log(request, experiment, comment)
return redirect('/lifespan/experiment/%s' % pk)
ctx = {'experiment': experiment, 'form': form}
return render_to_response('lifespan/edit_experiment.html',
ctx,
context_instance=RequestContext(request))
def add_experiment(request, pk):
form = ExperimentForm(request.POST or None, pk=pk) # A form bound to the POST data
if request.method == "POST" and form.is_valid(): # All validation rules pass
with reversion.create_revision():
experiment = form.save(commit=False)
# print("Experiment id: %s" % experiment.id)
# print form
form.save()
if isinstance(request.user, AnonymousUser):
request.user = User.objects.get(username="******")
reversion.set_user(request.user)
comment = "Added experiment."
reversion.set_comment(comment)
log(request, experiment, comment)
msg = "Successfully added experiment."
messages.add_message(request, messages.SUCCESS, ugettext(msg))
return redirect("/lifespan/experiment/%s" % experiment.pk)
return render_to_response("lifespan/add_experiment.html", {"form": form}, context_instance=RequestContext(request))
def add_experiment(request, pk):
form = ExperimentForm(request.POST or None,
pk=pk) # A form bound to the POST data
if request.method == "POST" and form.is_valid(
): # All validation rules pass
with reversion.create_revision():
experiment = form.save(commit=False)
#print("Experiment id: %s" % experiment.id)
#print form
form.save()
if isinstance(request.user, AnonymousUser):
request.user = User.objects.get(username="******")
reversion.set_user(request.user)
comment = "Added experiment."
reversion.set_comment(comment)
log(request, experiment, comment)
msg = "Successfully added experiment."
messages.add_message(request, messages.SUCCESS, ugettext(msg))
return redirect('/lifespan/experiment/%s' % experiment.pk)
return render_to_response('lifespan/add_experiment.html', {'form': form},
context_instance=RequestContext(request))
def new_exp(request, experiment_id=None):
def generate_sample_name(sample):
"""
naming standard:
CellLine.Library.TreatmentIfAny.shON/shOFF.time.A/B/C
Example: A549.K1_2.EZH2_150nM.shON.T21.A
"""
sample_name = ".".join([sample.cell_model.CCLE_name, sample.shRNA_library.LibName])
# if sample.pool_number is not None:
# pool_str = '_P'
# tmp = ''
# for p in sample.pool_number():
# tmp += '_'+p.description
# pool_str += tmp[1:]
# else:
# pool_str = '_PNone'
# sample_name = sample_name + pool_str
if sample.treatment and sample.treatment_dose:
treatment = "_".join([sample.treatment.compoundName, str(sample.treatment_dose)])
sample_name = ".".join([sample_name, treatment])
shrna = "shON"
if not sample.shRNA_on:
shrna = "shOFF"
sample_name = ".".join([sample_name, shrna, "".join(["T", str(sample.time_in_days)]), sample.replicate])
if sample.other_tag:
sample_name = sample_name + "." + sample.other_tag
return sample_name
if experiment_id:
experiment = get_object_or_404(Experiment, experiment_id=experiment_id)
expform = ExperimentForm(instance=experiment)
samforms = SampleFormSet(instance=experiment)
# if experiment.user != request.user:
# return HttpResponseForbidden()
else:
experiment = Experiment() # (user=request.user)
if request.POST:
if "create_exp" in request.POST or "add_sample" in request.POST:
expform = ExperimentForm(request.POST, instance=experiment)
samforms = SampleFormSet(request.POST, instance=experiment)
if expform.is_valid() and samforms.is_valid():
new_exp = expform.save(commit=False)
# automatic generate or modify fields
# save modified form
new_exp.save()
expform.save_m2m()
# sample forms
samforms.instance = new_exp
if samforms.has_changed():
for samform in samforms:
if samform.is_valid() and samform.has_changed() and (samform is not None):
new_sam = samform.save(commit=False)
# new_sam.pool_number = samform.cleaned_data['pool_number']
# new_sam.sample_id = experiment.sample_set.count() + 1
new_sam.sample_name = generate_sample_name(new_sam)
# new_sam.save()
# samform.save_m2m()
new_sam = samforms.save()
return HttpResponseRedirect("/virtual/new/confirm/%s/" % new_exp.experiment_id)
elif "delete_exp" in request.POST:
exp2delete = get_object_or_404(Experiment, experiment_id=experiment.experiment_id).delete()
# return HttpResponseRedirect('/virtual/delete/%s/' % experiment.experiment_id)
return HttpResponseRedirect("/virtual/new/confirm/%s/" % experiment.experiment_id)
else:
expform = ExperimentForm(instance=experiment)
samforms = SampleFormSet(instance=experiment)
args = {}
args.update(csrf(request))
args["expform"] = expform
args["samforms"] = samforms
return render_to_response("newExpView/new.html", args)
def provision_detail(request, experimentid):
if request.method == 'GET':
#print request.data
#print experimentid
experiment = get_object_or_404(Experiment, experimentid = experimentid)
experiment_serializer = ExperimentSerializer(experiment, many=False)
#print experiment
#ansbilenodes = get_list_or_404(AnsibleNode, experiment = experiment)
ansiblenodes = list(AnsibleNode.objects.filter(experiment = experiment))
if not ansiblenodes:
ansiblenodes = list()
ansiblenodes_serializer = AnsibleNodeSerializer(ansiblenodes, many=True, show_experiment=False)
#print experiment_serializer.update_node_details(ansbilenodes_serializer.data)
#print experiment_serializer.data
return Response(experiment_serializer.include_node_details(ansiblenodes_serializer.data))
elif request.method == 'POST':
#print request.data
#print request.FILES
#print request.FILES['file']
#form = ExperimentForm(request.POST, request.FILES)
#print form.errors
#print "form"
#print form
#print "experimentid"
#delete existing entry
try:
entry = Experiment.objects.get(pk=experimentid)
entry.delete()
entry = None
except (KeyError, Experiment.DoesNotExist):
entry = None
#create new entry
form = ExperimentForm(request.POST, request.FILES)
if form.is_valid():
form.save()
new_experiment = form.save()
new_experiment.status = Experiment.unprovision
new_experiment.save()
else:
return Response(request.POST, status=status.HTTP_400_BAD_REQUEST)
entry = Experiment.objects.get(pk=experimentid)
#start provision
host_list = [x.strip() for x in entry.host_list.split(',')]
#print host_list
PlaybookHandler.run(experimentid, entry.playbook.path, host_list)
return Response(request.POST, status=status.HTTP_201_CREATED)
elif request.method == 'DELETE':
#delete existing entry
try:
entry = Experiment.objects.get(pk=experimentid)
#delete the corresponding log first
try:
print entry.display_log_path()
os.remove(entry.display_log_path())
except OSError:
pass
entry.delete()
entry = None
except (KeyError, Experiment.DoesNotExist):
entry = None
return Response()
def ckupload():
form = ExperimentForm()
response = form.upload(endpoint=admin)
return response
def experiments_create():
form = ExperimentForm()
if form.validate_on_submit():
return 'Yay!'
else:
return render_template('experiments/new.html', form=form)
def experiments_new():
form = ExperimentForm()
return render_template('experiments/new.html', form=form)
