def edit(request, did):
"Updates or creates a project"
user = request.user
data = authorize.get_data(user=user, did=did)
project = authorize.get_project(user=user, pid=data.project.id, write=False)
editable = (data.owner == user) or (project.is_manager)
# raise error on not editable data
if not editable:
raise authorize.AccessError('Data not editable by this role')
# no submission
if 'submit' not in request.POST:
form = DataForm( dict(name=data.name, info=data.info) )
return html.template( request=request, name='data-edit.html', data=data, form=form )
# form submission
form = DataForm( request.POST )
if form.is_valid():
get = form.cleaned_data.get
data.name = get('name')
data.info = get('info')
data.save()
return html.redirect("/data/details/%s/" % data.id)
else:
return html.template( request=request, name='data-edit.html', did=did, form=form )
def index(request):
"Login request"
# users are not logged in so we can't use the Django messaging system
error_message = ''
if request.user.is_authenticated and request.user.username=='public':
# someone is attempting a public access
return html.template( request, name='notice.html')
#
# a logged in superuser may 'impersonate' other users
# this behavior may be disabled in the settings
#
if request.GET and settings.SUPERUSER_PASSWORD_OVERRIDE:
uid = request.GET.get('uid', "").strip()
if request.user.is_superuser and uid:
user = User.objects.get(id=uid)
backend = auth.get_backends()[0]
user.backend = "%s.%s" % (backend.__module__, backend.__class__.__name__)
auth.login(request, user)
return html.redirect("/project/list/")
#
# normal login
#
if request.method == 'POST':
form = LoginForm(request.POST)
if form.is_valid():
email = form.cleaned_data.get('email', '').strip()
password = form.cleaned_data['password']
userlist = User.objects.filter(email=email).all()
if userlist:
first = userlist[0]
user = auth.authenticate(username=first.username, password=password)
if user and user.is_active:
auth.login(request, user)
return html.redirect("/project/list/")
else:
error_message = 'Invalid user password!'
else:
error_message = 'Invalid user email'
else:
# invalid form submission
error_message = "Please specify an email and a password!"
else:
form = LoginForm()
return html.template( request, name='login.html', form=form, error_message=error_message)
def index(request):
"Main index page"
# form submission
params = html.Params( )
return html.template( request, name='galaxy.html', params=params )
def edit(request, pid):
"Updates or creates a project"
user = request.user
form = ProjectForm(request.POST)
if form.is_valid():
# incoming data
get = form.cleaned_data.get
if pid == "new":
project = authorize.create_project(user=user, name=get("name"), info=get("info"))
user.message_set.create(message="Project created")
return html.redirect("/project/list/")
else:
authorize.update_project(user=user, pid=pid, name=get("name"), info=get("info"))
user.message_set.create(message="Project updated")
return html.redirect("/project/view/%s/" % pid)
else:
# no form data sent
if pid == "new":
title = "Create New Project"
form = ProjectForm()
else:
title = "Edit Project"
project = authorize.get_project(user=user, pid=pid)
form = ProjectForm(dict(name=project.name, info=project.info))
return html.template(request=request, name="project-edit.html", pid=pid, title=title, form=form)
def share(request, pid):
"Manages sharing to a project"
user = request.user
project = authorize.get_project(user=user, pid=pid, write=False)
members = models.Member.objects.filter(project=project).order_by("role")
text = request.GET.get("text", "").strip()
results = []
# found incoming search parameters
if text:
text = text.strip()
if text != "*":
query = models.User.objects.filter
query = query(first_name__icontains=text) | query(last_name__icontains=text)
else:
query = models.User.objects
results = query.all().order_by("last_name")
uid = request.GET.get("uid")
action = request.GET.get("action")
# update the roles according to the action parameter
if action and uid:
authorize.update_role(user=user, pid=pid, action=action, uid=uid)
return html.redirect("/project/share/%s/" % pid)
params = html.Params(results=results, text=text, members=members)
return html.template(request=request, name="project-share.html", project=project, params=params)
def delete(request, pid):
"Deletes a project (with confirmation)"
user = request.user
project = authorize.get_project(user=user, pid=pid, write=True)
if "delete" in request.POST:
project.delete()
user.message_set.create(message="Project deletion complete")
return html.redirect("/project/list/")
else:
return html.template(request=request, name="project-delete.html", project=project)
def result_upload(request, did):
"Uploads a result"
user = request.user
data = authorize.get_data(user=user, did=did)
project = authorize.get_project(user=user, pid=data.project.id, write=False)
# no submission, default page
if 'submit' not in request.POST:
form = ResultForm()
return html.template( request=request, name='result-upload.html', data=data, form=form )
# actual form submission
form = ResultForm( request.POST, request.FILES )
if form.is_valid():
get = form.cleaned_data.get
authorize.create_result(user=user, data=data, content=get('content'), image=get('image'))
return html.redirect("/data/details/%s/" % data.id)
else:
# error messages will be generated
user.message_set.create(message="Some form fields could NOT be validated.")
return html.template( request=request, name='result-upload.html', data=data, form=form )
def details(request, did):
"Renders the data view page"
user = request.user
data = authorize.get_data(user=user, did=did)
param = html.Params(file_list=data.file_list(), image_list= data.image_list())
return html.template( request=request, name='data-details.html', data=data, param=param)
def upload_simple(request, pid):
"Renders the upload page"
user = request.user
project = authorize.get_project(user=user, pid=pid, write=False)
return html.template( request=request, name='data-upload-simple.html', project=project)
def browser(request, index, url, galaxy_url, dataid=0):
""
global FORM_DEFAULTS
# incoming parameters cast into a dictionary
incoming = dict( request.POST.items() )
# alters the incoming parameters based on user interaction
incoming = browserutils.modify_incoming(incoming, FORM_DEFAULTS)
# create the necessary forms
forms = html.Params()
forms.search = formspec.make_form(index.labels)(incoming)
forms.navbar = formspec.NavbarForm()
forms.fitting = formspec.FitForm( incoming )
forms.peaks = formspec.PeakForm( incoming )
# extract the search parameters
params = browserutils.parse_parameters(forms=forms, defaults=formspec.ALL_DEFAULTS)
# run the tool or return an image
if 'runtool' in incoming:
# need to run the tool
# form the url with dictionary substitution
# TODO make parameters names consistent across Galaxy, GeneTrack and script!
strand = 'all' if params.strand=='ALL' else 'two'
mode = 'nolap' if params.smoothing_func =='GK' else 'all'
urlparams = dict(
strand = strand,
exclusion=params.feature_width,
level=int(params.minimum_peak),
mode=mode,
sigma=int(params.sigma),
input=dataid,
method='gauss',
runtool_btn="Execute"
)
url = "%s&%s" % (galaxy_url, urllib.urlencode( urlparams ))
return html.redirect(url)
# creates the multiplot
multi = dataview_multiplot(index=index, params=params, debug=False)
params.image_height = multi.h
# close the data
index.close()
# trigger the occasional cache cleaning
webutil.cache_clean(age=1, chance=10)
# creates a file representation and a name
image_name, image_path = webutil.cache_file(ext='png')
# saves the multiplot
multi.save(image_path)
params.image_name = image_name
return html.template( request=request, name='data-browse.html', forms=forms, params=params, url=url)
def listall(request):
"Lists all projects"
params = html.Params()
projects = authorize.project_list(request.user)
params.project_count = authorize.project_count(request.user)
return html.template(request=request, name="project-list.html", projects=projects, params=params)
def view(request, pid):
"Lists all projects"
project = authorize.get_project(user=request.user, pid=pid, write=False)
return html.template(request=request, name="project-view.html", project=project)
def error500(request):
"Server error page when debug flag is False"
context = RequestContext(request)
exc_type, exc_value, tb = sys.exc_info()
logger.error(exc_value)
return html.template( request, name='500.html', debug=exc_value )
def todo(request):
"Todo page"
params = html.Params(info='**test**')
return html.template( request, name='todo.html', params=params )
def index(request):
"Main index page"
params = html.Params()
params.project_count = authorize.project_count(request.user)
return html.template( request, name='index.html', params=params )