biosample.views.CreateUserView.create_biosample_team() - Code Metrics - Inspection of ":bug: catch errors when creating a biosample user" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#55)

by Paolo

created 2019-09-30 16:49 UTC

CreateUserView.create_biosample_team() A

↳ Parent: biosample.views

Complexity

Conditions

Size

Total Lines	48
Code Lines	20

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	20
dl	0
loc	48
rs	9.4
c	0
b	0
f	0
cc	3
nop	3


import os
import redis
import logging

from decouple import AutoConfig

from django.conf import settings
from django.urls import reverse_lazy, reverse
from django.utils.crypto import get_random_string
from django.utils.http import is_safe_url
from django.shortcuts import redirect, get_object_or_404
from django.contrib.auth import get_user_model
from django.contrib.auth.mixins import LoginRequiredMixin
from django.views.generic import TemplateView
from django.views.generic.edit import FormView, CreateView, ModelFormMixin
from django.contrib import messages
from django.http import HttpResponseRedirect

from pyUSIrest.client import User

from common.constants import WAITING
from image_app.models import Submission

from .forms import (
    GenerateTokenForm, RegisterUserForm, CreateUserForm, SubmitForm)
from .models import Account, ManagedTeam
from .helpers import get_auth, get_manager_auth
from .tasks import SplitSubmissionTask


# Get an instance of a logger
logger = logging.getLogger(__name__)


# define a decouple config object
settings_dir = os.path.join(settings.BASE_DIR, 'image')
config = AutoConfig(search_path=settings_dir)


# In programming, a mixin is a class that provides functionality to be
# inherited, but isn’t meant for instantiation on its own. In programming
# languages with multiple inheritance, mixins can be used to add enhanced
# functionality and behavior to classes.
class TokenMixin(object):
    """Get common stuff for Token visualization. Redirect to AAP registration
    if no valid AAP credentials are found for request.user"""

    def get_initial(self):
        """
        Returns the initial data to use for forms on this view.
        """

        initial = super(TokenMixin, self).get_initial()
        initial['name'] = self.request.user.biosample_account.name

        return initial

    def dispatch(self, request, *args, **kwargs):

        # get user from request and user model. This could be also Anonymous
        # user:however with metod decorator a login is required before dispatch
        # method is called
        User = get_user_model()
        user = self.request.user

        try:
            user.biosample_account

        except User.biosample_account.RelatedObjectDoesNotExist:
            logger.warning("Error for user:%s: not managed" % user)
            messages.warning(
                request=self.request,
                message='You need to register a valid AAP profile',
                extra_tags="alert alert-dismissible alert-warning")

            return redirect('accounts:registration_activation_complete')

        else:
            # call the default get method
            return super(
                TokenMixin, self).dispatch(request, *args, **kwargs)


class RegisterMixin(object):
    """If a biosample account is already registered, returns to dashboard"""

    def dispatch(self, request, *args, **kwargs):

        # get user from request and user model. This could be also Anonymous
        # user:however with metod decorator a login is required before dispatch
        # method is called
        User = get_user_model()
        user = self.request.user

        try:
            user.biosample_account

        except User.biosample_account.RelatedObjectDoesNotExist:
            # call the default get method
            return super(
                RegisterMixin, self).dispatch(request, *args, **kwargs)

        else:
            logger.warning("Error for user:%s: Already registered" % user)
            messages.warning(
                request=self.request,
                message='Your AAP profile is already registered',
                extra_tags="alert alert-dismissible alert-warning")

            return redirect('image_app:dashboard')


class MyFormMixin(object):
    """Common stuff for token generation"""

    success_url_message = "Please set this variable"
    success_url = reverse_lazy("image_app:dashboard")

    # add the request to the kwargs
    # https://chriskief.com/2012/12/18/django-modelform-formview-and-the-request-object/
    # this is needed to display messages (django.contronb) on pages
    def get_form_kwargs(self):
        kwargs = super(MyFormMixin, self).get_form_kwargs()
        kwargs['request'] = self.request
        return kwargs

    def get_success_url(self):
        """Override default function"""

        messages.success(
            request=self.request,
            message=self.success_url_message,
            extra_tags="alert alert-dismissible alert-success")

        return super(MyFormMixin, self).get_success_url()

    def form_invalid(self, form):
        messages.error(
            self.request,
            message="Please correct the errors below",
            extra_tags="alert alert-dismissible alert-danger")

        return super(MyFormMixin, self).form_invalid(form)

    def generate_token(self, form):
        """Generate token from form instance"""

        # operate on form data
        name = form.cleaned_data['name']
        password = form.cleaned_data['password']

        try:
            auth = get_auth(user=name, password=password)

        except ConnectionError as e:
            # logger exception. With repr() the exception name is rendered
            logger.error(repr(e))

            # maybe I typed a wrong password or there is an issue in biosample
            # log error in message and return form_invalid
            # HINT: deal with two conditions?

            # parse error message
            messages.error(
                self.request,
                "Unable to generate token: %s" % str(e),
                extra_tags="alert alert-dismissible alert-danger")

            # cant't return form_invalid here, since i need to process auth
            return None

        else:
            logger.debug("Token generated for user:%s" % name)

            self.request.session['token'] = auth.token

            # return an auth object
            return auth


class GenerateTokenView(LoginRequiredMixin, TokenMixin, MyFormMixin, FormView):
    """Generate AAP token. If user is not registered, redirect to accounts
    registration_activation_complete through TokenMixin. If yes generate
    token through MyFormMixin"""

    template_name = 'biosample/generate_token.html'
    form_class = GenerateTokenForm
    success_url_message = 'Token generated!'

    def dispatch(self, request, *args, **kwargs):
        # try to read next link
        next_url = request.GET.get('next', None)

        # redirect to next url. is_safe_url: is a safe redirection
        # (i.e. it doesn't point to a different host and uses a safe scheme).
        if next_url and is_safe_url(next_url):
            logger.debug("Got %s as next_url" % next_url)
            self.success_url = next_url

        return super(
            GenerateTokenView, self).dispatch(request, *args, **kwargs)

    def form_valid(self, form):
        # This method is called when valid form data has been POSTed.
        # It should return an HttpResponse.

        # call MyFormMixin method and generate token. Check user/password
        if not self.generate_token(form):
            return self.form_invalid(form)

        return redirect(self.get_success_url())


class TokenView(LoginRequiredMixin, TokenMixin, TemplateView):
    """Visualize token details"""

    template_name = 'biosample/token.html'

    def get_context_data(self, **kwargs):
        # Call the base implementation first to get a context
        context = super(TokenView, self).get_context_data(**kwargs)

        # get user and team object
        context['name'] = self.request.user.biosample_account.name
        context['team'] = self.request.user.biosample_account.team

        try:
            # add content to context
            auth = get_auth(token=self.request.session['token'])

            if auth.is_expired():
                messages.error(
                    self.request,
                    "Your token is expired",
                    extra_tags="alert alert-dismissible alert-danger")

            context["auth"] = auth

        except KeyError as e:
            logger.error(
                "No valid token found for %s: %s" % (
                    self.request.user,
                    e))

            messages.error(
                self.request,
                "You haven't generated any token yet",
                extra_tags="alert alert-dismissible alert-danger")

        return context


class RegisterUserView(LoginRequiredMixin, RegisterMixin, MyFormMixin,
                       CreateView):
    """Register an already existent AAP account"""

    template_name = 'biosample/register_user.html'
    form_class = RegisterUserForm
    success_url_message = 'Account registered'

    def form_valid(self, form):
        # This method is called when valid form data has been POSTed.
        # It should return an HttpResponse.
        team = form.cleaned_data['team']

        # call AuthMixin method and generate token. Check user/password
        auth = self.generate_token(form)

        if not auth:
            return self.form_invalid(form)

        if team.name not in auth.claims['domains']:
            messages.error(
                self.request,
                "You don't belong to team: %s" % team,
                extra_tags="alert alert-dismissible alert-danger")

            # return invalid form
            return self.form_invalid(form)

        # add a user to object (comes from section not from form)
        self.object = form.save(commit=False)
        self.object.user = self.request.user
        self.object.save()

        # call to a specific function (which does an HttpResponseRedirect
        # to success_url)
        return super(ModelFormMixin, self).form_valid(form)


class CreateUserView(LoginRequiredMixin, RegisterMixin, MyFormMixin, FormView):
    """Create a new AAP account"""

    template_name = 'biosample/create_user.html'
    form_class = CreateUserForm
    success_url_message = "Account created"

    def deal_with_errors(self, error_message, exception):
        """Add messages to view for encountered errors

        Args:
            error_message (str): An informative text
            exception (Exception): an exception instance
        """

        exception_message = "Message was: %s" % (exception)

        logger.error(error_message)
        logger.error(exception_message)

        messages.error(
            self.request,
            message=error_message,
            extra_tags="alert alert-dismissible alert-danger")
        messages.error(
            self.request,
            message=exception_message,
            extra_tags="alert alert-dismissible alert-danger")

    def get_form_kwargs(self):
        """Override get_form_kwargs"""

        kwargs = super(CreateUserView, self).get_form_kwargs()

        # create a new biosample user
        username = "image-%s" % (get_random_string(length=8))

        # add username to instance
        kwargs['username'] = username

        return kwargs

    # create an user or throw an exception
    def create_biosample_user(self, form, full_name, affiliation):
        """Create a biosample user

        Args:
            form (:py:class:`CreateUserForm`) an instantiated form object
            full_name (str): the user full name (Name + Surname)
            affiliation (str): the organization the user belongs to

        Returns:
            str: a biosamples user id
        """

        password = form.cleaned_data['password1']
        confirmPwd = form.cleaned_data['password2']

        # get user model associated with this session
        user = self.request.user

        # get email
        email = user.email

        biosample_user_id = None

        # creating a user
        logger.debug("Creating user %s" % (form.username))

        try:
            biosample_user_id = User.create_user(
                user=form.username,
                password=password,
                confirmPwd=confirmPwd,
                email=email,
                full_name=full_name,
                organisation=affiliation
            )

            logger.info("user_id %s generated" % (biosample_user_id))

        except ConnectionError as e:
            message = "Problem in creating user %s" % (form.username)
            self.deal_with_errors(message, e)

        return biosample_user_id

    def create_biosample_team(self, full_name, affiliation):
        """Create a biosample team

        Args:
            full_name (str): the user full name (Name + Surname)
            affiliation (str): the organization the user belongs to

        Returns:
            :py:class:`pyUSIrest.client.Team`: a pyUSIrest Team instance
            :py:class:`biosample.models.ManagedTeam`: a model object
        """

        # creating a new team. First create an user object
        # create a new auth object
        logger.debug("Generate a token for 'USI_MANAGER'")

        # get an Auth instance from a helpers.method
        auth = get_manager_auth()
        admin = User(auth)

        description = "Team for %s" % (full_name)

        # the values I want to return
        team, managed_team = None, None

        # now create a team
        logger.debug("Creating team for %s" % (full_name))

        try:

            team = admin.create_team(
                description=description,
                centreName=affiliation)

            logger.info("Team %s generated" % (team.name))

            # register team in ManagedTeam table
            managed_team, created = ManagedTeam.objects.get_or_create(
                name=team.name)

            if created is True:
                logger.info("Created: %s" % (managed_team))

        except ConnectionError as e:
            message = "Problem in creating team for %s" % (full_name)
            self.deal_with_errors(message, e)

        return team, managed_team

    def add_biosample_user_to_team(self, form, user_id, team, managed_team):

        # I need to generate a new token to see the new team
        logger.debug("Generate a new token for 'USI_MANAGER'")

        auth = get_manager_auth()
        admin = User(auth)

        # list all domain for manager
        logger.debug("Listing all domains for %s" % (config('USI_MANAGER')))
        logger.debug(", ".join(auth.claims['domains']))

        # get the domain for the new team, and then the domain_id
        logger.debug("Getting domain info for team %s" % (team.name))
        domain = admin.get_domain_by_name(team.name)
        domain_id = domain.domainReference

        # the value I want to return
        account = None

        logger.debug(
            "Adding user %s to team %s" % (form.username, team.name))

        try:
            # user to team
            admin.add_user_to_team(user_id=user_id, domain_id=domain_id)

            # save objects in accounts table
            account = Account.objects.create(
                user=self.request.user,
                name=form.username,
                team=managed_team
            )

            logger.info("%s created" % (account))

            # add message
            messages.debug(
                request=self.request,
                message="User %s added to team %s" % (
                    form.username, team.name),
                extra_tags="alert alert-dismissible alert-light")

        except ConnectionError as e:
            message = "Problem in adding user %s to team %s" % (
                form.username, team.name)
            self.deal_with_errors(message, e)

        return account

    # HINT: move to a celery task?
    def form_valid(self, form):
        """Create a new team in with biosample manager user, then create a new
        user and register it"""

        # get user model associated with this session
        user = self.request.user

        # get user info
        first_name = user.first_name
        last_name = user.last_name

        # set full name as
        full_name = " ".join([first_name, last_name])

        # Affiliation is the institution the user belong
        affiliation = user.person.affiliation.name

        # model generic errors from EBI API endpoints
        try:
            user_id = self.create_biosample_user(form, full_name, affiliation)

            if user_id is None:
                # return invalid form
                return self.form_invalid(form)

            # create a biosample team
            team, managed_team = self.create_biosample_team(
                full_name, affiliation)

            if team is None:
                # return invalid form
                return self.form_invalid(form)

            account = self.add_biosample_user_to_team(
                form, user_id, team, managed_team)

            if account is None:
                # return invalid form
                return self.form_invalid(form)

        except ConnectionError as e:
            message = (
                "Problem with EBI-AAP endoints. Please contact IMAGE team")
            self.deal_with_errors(message, e)

            # return invalid form
            return self.form_invalid(form)

        # call to a inherited function (which does an HttpResponseRedirect
        # to success_url)
        return super(CreateUserView, self).form_valid(form)


class SubmitView(LoginRequiredMixin, TokenMixin, MyFormMixin, FormView):
    """Call a submission task. Check that a token exists and that it's valid"""

    form_class = SubmitForm
    template_name = 'biosample/submit.html'
    submission_id = None

    def get_success_url(self):
        return reverse('submissions:detail', kwargs={
            'pk': self.submission_id})

    def form_valid(self, form):
        submission_id = form.cleaned_data['submission_id']
        name = form.cleaned_data['name']
        password = form.cleaned_data['password']

        # get a submission object
        submission = get_object_or_404(
            Submission,
            pk=submission_id,
            owner=self.request.user)

        # track submission id in order to render page
        self.submission_id = submission_id

        # check if I can submit object (statuses)
        if not submission.can_submit():
            # return super method (which calls get_success_url)
            logger.error(
                "Can't submit submission %s: current status is %s" % (
                    submission, submission.get_status_display()))

            return HttpResponseRedirect(self.get_success_url())

        # create an auth object if credentials are provided
        if name and password:
            # call AuthMixin method and generate token. Check user/password
            auth = self.generate_token(form)

            if not auth:
                return self.form_invalid(form)

        # check token: if expired or near to expiring, return form
        elif 'token' in self.request.session:
            auth = get_auth(token=self.request.session['token'])

        else:
            logger.warning(
                "No valid token found. Redirect to tocken generation")

            messages.error(
                self.request,
                ("You haven't generated any token yet. Generate a new one"),
                extra_tags="alert alert-dismissible alert-danger")

            # redirect to this form
            return self.form_invalid(form)

        # check tocken expiration
        if auth.is_expired() or auth.get_duration().seconds < 1800:
            logger.warning(
                "Token is expired or near to expire")

            messages.error(
                self.request,
                ("Your token is expired or near to expire. Generate a new "
                 "one"),
                extra_tags="alert alert-dismissible alert-danger")

            # redirect to this form
            return self.form_invalid(form)

        # start the submission with a valid token
        self.start_submission(auth, submission)

        return redirect(self.get_success_url())

    def start_submission(self, auth, submission):
        """Change submission status and submit data with a valid token"""

        logger.debug("Connecting to redis database")

        # here token is valid, so store it in redis database
        client = redis.StrictRedis(
            host=settings.REDIS_HOST,
            port=settings.REDIS_PORT,
            db=settings.REDIS_DB)

        key = "token:submission:{submission_id}:{user}".format(
            submission_id=self.submission_id,
            user=self.request.user)

        logger.debug("Writing token in redis")

        client.set(key, auth.token, ex=auth.get_duration().seconds)

        # Update submission status
        submission.status = WAITING
        submission.message = "Waiting for biosample submission"
        submission.save()

        # a valid submission start a task
        submit_task = SplitSubmissionTask()
        res = submit_task.delay(submission.id)
        logger.info(
            "Start submission process for %s with task %s" % (
                submission,
                res.task_id))


1
2		import os
3		import redis
4		import logging
5
6		from decouple import AutoConfig
7
8		from django.conf import settings
9		from django.urls import reverse_lazy, reverse
10		from django.utils.crypto import get_random_string
11		from django.utils.http import is_safe_url
12		from django.shortcuts import redirect, get_object_or_404
13		from django.contrib.auth import get_user_model
14		from django.contrib.auth.mixins import LoginRequiredMixin
15		from django.views.generic import TemplateView
16		from django.views.generic.edit import FormView, CreateView, ModelFormMixin
17		from django.contrib import messages
18		from django.http import HttpResponseRedirect
19
20		from pyUSIrest.client import User
21
22		from common.constants import WAITING
23		from image_app.models import Submission
24
25		from .forms import (
26		GenerateTokenForm, RegisterUserForm, CreateUserForm, SubmitForm)
27		from .models import Account, ManagedTeam
28		from .helpers import get_auth, get_manager_auth
29		from .tasks import SplitSubmissionTask
30
31
32		# Get an instance of a logger
33		logger = logging.getLogger(__name__)
34
35
36		# define a decouple config object
37		settings_dir = os.path.join(settings.BASE_DIR, 'image')
38		config = AutoConfig(search_path=settings_dir)
39
40
41		# In programming, a mixin is a class that provides functionality to be
42		# inherited, but isn’t meant for instantiation on its own. In programming
43		# languages with multiple inheritance, mixins can be used to add enhanced
44		# functionality and behavior to classes.
45		class TokenMixin(object):
46		"""Get common stuff for Token visualization. Redirect to AAP registration
47		if no valid AAP credentials are found for request.user"""
48
49		def get_initial(self):
50		"""
51		Returns the initial data to use for forms on this view.
52		"""
53
54		initial = super(TokenMixin, self).get_initial()
55		initial['name'] = self.request.user.biosample_account.name
56
57		return initial
58
59	View Code Duplication	def dispatch(self, request, args, *kwargs):
		0 ignored issues – show Duplication introduced 2019-06-07 17:57 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
60		# get user from request and user model. This could be also Anonymous
61		# user:however with metod decorator a login is required before dispatch
62		# method is called
63		User = get_user_model()
64		user = self.request.user
65
66		try:
67		user.biosample_account
68
69		except User.biosample_account.RelatedObjectDoesNotExist:
70		logger.warning("Error for user:%s: not managed" % user)
71		messages.warning(
72		request=self.request,
73		message='You need to register a valid AAP profile',
74		extra_tags="alert alert-dismissible alert-warning")
75
76		return redirect('accounts:registration_activation_complete')
77
78		else:
79		# call the default get method
80		return super(
81		TokenMixin, self).dispatch(request, args, *kwargs)
82
83
84		class RegisterMixin(object):
85		"""If a biosample account is already registered, returns to dashboard"""
86
87	View Code Duplication	def dispatch(self, request, args, *kwargs):
		0 ignored issues – show Duplication introduced 2019-06-07 17:57 UTC by Report Bug Copy Issue Report This code seems to be duplicated in your project. Loading history...
88		# get user from request and user model. This could be also Anonymous
89		# user:however with metod decorator a login is required before dispatch
90		# method is called
91		User = get_user_model()
92		user = self.request.user
93
94		try:
95		user.biosample_account
96
97		except User.biosample_account.RelatedObjectDoesNotExist:
98		# call the default get method
99		return super(
100		RegisterMixin, self).dispatch(request, args, *kwargs)
101
102		else:
103		logger.warning("Error for user:%s: Already registered" % user)
104		messages.warning(
105		request=self.request,
106		message='Your AAP profile is already registered',
107		extra_tags="alert alert-dismissible alert-warning")
108
109		return redirect('image_app:dashboard')
110
111
112		class MyFormMixin(object):
113		"""Common stuff for token generation"""
114
115		success_url_message = "Please set this variable"
116		success_url = reverse_lazy("image_app:dashboard")
117
118		# add the request to the kwargs
119		# https://chriskief.com/2012/12/18/django-modelform-formview-and-the-request-object/
120		# this is needed to display messages (django.contronb) on pages
121		def get_form_kwargs(self):
122		kwargs = super(MyFormMixin, self).get_form_kwargs()
123		kwargs['request'] = self.request
124		return kwargs
125
126		def get_success_url(self):
127		"""Override default function"""
128
129		messages.success(
130		request=self.request,
131		message=self.success_url_message,
132		extra_tags="alert alert-dismissible alert-success")
133
134		return super(MyFormMixin, self).get_success_url()
135
136		def form_invalid(self, form):
137		messages.error(
138		self.request,
139		message="Please correct the errors below",
140		extra_tags="alert alert-dismissible alert-danger")
141
142		return super(MyFormMixin, self).form_invalid(form)
143
144		def generate_token(self, form):
145		"""Generate token from form instance"""
146
147		# operate on form data
148		name = form.cleaned_data['name']
149		password = form.cleaned_data['password']
150
151		try:
152		auth = get_auth(user=name, password=password)
153
154		except ConnectionError as e:
155		# logger exception. With repr() the exception name is rendered
156		logger.error(repr(e))
157
158		# maybe I typed a wrong password or there is an issue in biosample
159		# log error in message and return form_invalid
160		# HINT: deal with two conditions?
161
162		# parse error message
163		messages.error(
164		self.request,
165		"Unable to generate token: %s" % str(e),
166		extra_tags="alert alert-dismissible alert-danger")
167
168		# cant't return form_invalid here, since i need to process auth
169		return None
170
171		else:
172		logger.debug("Token generated for user:%s" % name)
173
174		self.request.session['token'] = auth.token
175
176		# return an auth object
177		return auth
178
179
180		class GenerateTokenView(LoginRequiredMixin, TokenMixin, MyFormMixin, FormView):
181		"""Generate AAP token. If user is not registered, redirect to accounts
182		registration_activation_complete through TokenMixin. If yes generate
183		token through MyFormMixin"""
184
185		template_name = 'biosample/generate_token.html'
186		form_class = GenerateTokenForm
187		success_url_message = 'Token generated!'
188
189		def dispatch(self, request, args, *kwargs):
190		# try to read next link
191		next_url = request.GET.get('next', None)
192
193		# redirect to next url. is_safe_url: is a safe redirection
194		# (i.e. it doesn't point to a different host and uses a safe scheme).
195		if next_url and is_safe_url(next_url):
196		logger.debug("Got %s as next_url" % next_url)
197		self.success_url = next_url
198
199		return super(
200		GenerateTokenView, self).dispatch(request, args, *kwargs)
201
202		def form_valid(self, form):
203		# This method is called when valid form data has been POSTed.
204		# It should return an HttpResponse.
205
206		# call MyFormMixin method and generate token. Check user/password
207		if not self.generate_token(form):
208		return self.form_invalid(form)
209
210		return redirect(self.get_success_url())
211
212
213		class TokenView(LoginRequiredMixin, TokenMixin, TemplateView):
214		"""Visualize token details"""
215
216		template_name = 'biosample/token.html'
217
218		def get_context_data(self, **kwargs):
219		# Call the base implementation first to get a context
220		context = super(TokenView, self).get_context_data(**kwargs)
221
222		# get user and team object
223		context['name'] = self.request.user.biosample_account.name
224		context['team'] = self.request.user.biosample_account.team
225
226		try:
227		# add content to context
228		auth = get_auth(token=self.request.session['token'])
229
230		if auth.is_expired():
231		messages.error(
232		self.request,
233		"Your token is expired",
234		extra_tags="alert alert-dismissible alert-danger")
235
236		context["auth"] = auth
237
238		except KeyError as e:
239		logger.error(
240		"No valid token found for %s: %s" % (
241		self.request.user,
242		e))
243
244		messages.error(
245		self.request,
246		"You haven't generated any token yet",
247		extra_tags="alert alert-dismissible alert-danger")
248
249		return context
250
251
252		class RegisterUserView(LoginRequiredMixin, RegisterMixin, MyFormMixin,
253		CreateView):
254		"""Register an already existent AAP account"""
255
256		template_name = 'biosample/register_user.html'
257		form_class = RegisterUserForm
258		success_url_message = 'Account registered'
259
260		def form_valid(self, form):
261		# This method is called when valid form data has been POSTed.
262		# It should return an HttpResponse.
263		team = form.cleaned_data['team']
264
265		# call AuthMixin method and generate token. Check user/password
266		auth = self.generate_token(form)
267
268		if not auth:
269		return self.form_invalid(form)
270
271		if team.name not in auth.claims['domains']:
272		messages.error(
273		self.request,
274		"You don't belong to team: %s" % team,
275		extra_tags="alert alert-dismissible alert-danger")
276
277		# return invalid form
278		return self.form_invalid(form)
279
280		# add a user to object (comes from section not from form)
281		self.object = form.save(commit=False)
282		self.object.user = self.request.user
283		self.object.save()
284
285		# call to a specific function (which does an HttpResponseRedirect
286		# to success_url)
287		return super(ModelFormMixin, self).form_valid(form)
288
289
290		class CreateUserView(LoginRequiredMixin, RegisterMixin, MyFormMixin, FormView):
291		"""Create a new AAP account"""
292
293		template_name = 'biosample/create_user.html'
294		form_class = CreateUserForm
295		success_url_message = "Account created"
296
297		def deal_with_errors(self, error_message, exception):
298		"""Add messages to view for encountered errors
299
300		Args:
301		error_message (str): An informative text
302		exception (Exception): an exception instance
303		"""
304
305		exception_message = "Message was: %s" % (exception)
306
307		logger.error(error_message)
308		logger.error(exception_message)
309
310		messages.error(
311		self.request,
312		message=error_message,
313		extra_tags="alert alert-dismissible alert-danger")
314		messages.error(
315		self.request,
316		message=exception_message,
317		extra_tags="alert alert-dismissible alert-danger")
318
319		def get_form_kwargs(self):
320		"""Override get_form_kwargs"""
321
322		kwargs = super(CreateUserView, self).get_form_kwargs()
323
324		# create a new biosample user
325		username = "image-%s" % (get_random_string(length=8))
326
327		# add username to instance
328		kwargs['username'] = username
329
330		return kwargs
331
332		# create an user or throw an exception
333		def create_biosample_user(self, form, full_name, affiliation):
334		"""Create a biosample user
335
336		Args:
337		form (:py:class:`CreateUserForm`) an instantiated form object
338		full_name (str): the user full name (Name + Surname)
339		affiliation (str): the organization the user belongs to
340
341		Returns:
342		str: a biosamples user id
343		"""
344
345		password = form.cleaned_data['password1']
346		confirmPwd = form.cleaned_data['password2']
347
348		# get user model associated with this session
349		user = self.request.user
350
351		# get email
352		email = user.email
353
354		biosample_user_id = None
355
356		# creating a user
357		logger.debug("Creating user %s" % (form.username))
358
359		try:
360		biosample_user_id = User.create_user(
361		user=form.username,
362		password=password,
363		confirmPwd=confirmPwd,
364		email=email,
365		full_name=full_name,
366		organisation=affiliation
367		)
368
369		logger.info("user_id %s generated" % (biosample_user_id))
370
371		except ConnectionError as e:
372		message = "Problem in creating user %s" % (form.username)
373		self.deal_with_errors(message, e)
374
375		return biosample_user_id
376
377		def create_biosample_team(self, full_name, affiliation):
378		"""Create a biosample team
379
380		Args:
381		full_name (str): the user full name (Name + Surname)
382		affiliation (str): the organization the user belongs to
383
384		Returns:
385		:py:class:`pyUSIrest.client.Team`: a pyUSIrest Team instance
386		:py:class:`biosample.models.ManagedTeam`: a model object
387		"""
388
389		# creating a new team. First create an user object
390		# create a new auth object
391		logger.debug("Generate a token for 'USI_MANAGER'")
392
393		# get an Auth instance from a helpers.method
394		auth = get_manager_auth()
395		admin = User(auth)
396
397		description = "Team for %s" % (full_name)
398
399		# the values I want to return
400		team, managed_team = None, None
401
402		# now create a team
403		logger.debug("Creating team for %s" % (full_name))
404
405		try:
406
407		team = admin.create_team(
408		description=description,
409		centreName=affiliation)
410
411		logger.info("Team %s generated" % (team.name))
412
413		# register team in ManagedTeam table
414		managed_team, created = ManagedTeam.objects.get_or_create(
415		name=team.name)
416
417		if created is True:
418		logger.info("Created: %s" % (managed_team))
419
420		except ConnectionError as e:
421		message = "Problem in creating team for %s" % (full_name)
422		self.deal_with_errors(message, e)
423
424		return team, managed_team
425
426		def add_biosample_user_to_team(self, form, user_id, team, managed_team):
427
428		# I need to generate a new token to see the new team
429		logger.debug("Generate a new token for 'USI_MANAGER'")
430
431		auth = get_manager_auth()
432		admin = User(auth)
433
434		# list all domain for manager
435		logger.debug("Listing all domains for %s" % (config('USI_MANAGER')))
436		logger.debug(", ".join(auth.claims['domains']))
437
438		# get the domain for the new team, and then the domain_id
439		logger.debug("Getting domain info for team %s" % (team.name))
440		domain = admin.get_domain_by_name(team.name)
441		domain_id = domain.domainReference
442
443		# the value I want to return
444		account = None
445
446		logger.debug(
447		"Adding user %s to team %s" % (form.username, team.name))
448
449		try:
450		# user to team
451		admin.add_user_to_team(user_id=user_id, domain_id=domain_id)
452
453		# save objects in accounts table
454		account = Account.objects.create(
455		user=self.request.user,
456		name=form.username,
457		team=managed_team
458		)
459
460		logger.info("%s created" % (account))
461
462		# add message
463		messages.debug(
464		request=self.request,
465		message="User %s added to team %s" % (
466		form.username, team.name),
467		extra_tags="alert alert-dismissible alert-light")
468
469		except ConnectionError as e:
470		message = "Problem in adding user %s to team %s" % (
471		form.username, team.name)
472		self.deal_with_errors(message, e)
473
474		return account
475
476		# HINT: move to a celery task?
477		def form_valid(self, form):
478		"""Create a new team in with biosample manager user, then create a new
479		user and register it"""
480
481		# get user model associated with this session
482		user = self.request.user
483
484		# get user info
485		first_name = user.first_name
486		last_name = user.last_name
487
488		# set full name as
489		full_name = " ".join([first_name, last_name])
490
491		# Affiliation is the institution the user belong
492		affiliation = user.person.affiliation.name
493
494		# model generic errors from EBI API endpoints
495		try:
496		user_id = self.create_biosample_user(form, full_name, affiliation)
497
498		if user_id is None:
499		# return invalid form
500		return self.form_invalid(form)
501
502		# create a biosample team
503		team, managed_team = self.create_biosample_team(
504		full_name, affiliation)
505
506		if team is None:
507		# return invalid form
508		return self.form_invalid(form)
509
510		account = self.add_biosample_user_to_team(
511		form, user_id, team, managed_team)
512
513		if account is None:
514		# return invalid form
515		return self.form_invalid(form)
516
517		except ConnectionError as e:
518		message = (
519		"Problem with EBI-AAP endoints. Please contact IMAGE team")
520		self.deal_with_errors(message, e)
521
522		# return invalid form
523		return self.form_invalid(form)
524
525		# call to a inherited function (which does an HttpResponseRedirect
526		# to success_url)
527		return super(CreateUserView, self).form_valid(form)
528
529
530		class SubmitView(LoginRequiredMixin, TokenMixin, MyFormMixin, FormView):
531		"""Call a submission task. Check that a token exists and that it's valid"""
532
533		form_class = SubmitForm
534		template_name = 'biosample/submit.html'
535		submission_id = None
536
537		def get_success_url(self):
538		return reverse('submissions:detail', kwargs={
539		'pk': self.submission_id})
540
541		def form_valid(self, form):
542		submission_id = form.cleaned_data['submission_id']
543		name = form.cleaned_data['name']
544		password = form.cleaned_data['password']
545
546		# get a submission object
547		submission = get_object_or_404(
548		Submission,
549		pk=submission_id,
550		owner=self.request.user)
551
552		# track submission id in order to render page
553		self.submission_id = submission_id
554
555		# check if I can submit object (statuses)
556		if not submission.can_submit():
557		# return super method (which calls get_success_url)
558		logger.error(
559		"Can't submit submission %s: current status is %s" % (
560		submission, submission.get_status_display()))
561
562		return HttpResponseRedirect(self.get_success_url())
563
564		# create an auth object if credentials are provided
565		if name and password:
566		# call AuthMixin method and generate token. Check user/password
567		auth = self.generate_token(form)
568
569		if not auth:
570		return self.form_invalid(form)
571
572		# check token: if expired or near to expiring, return form
573		elif 'token' in self.request.session:
574		auth = get_auth(token=self.request.session['token'])
575
576		else:
577		logger.warning(
578		"No valid token found. Redirect to tocken generation")
579
580		messages.error(
581		self.request,
582		("You haven't generated any token yet. Generate a new one"),
583		extra_tags="alert alert-dismissible alert-danger")
584
585		# redirect to this form
586		return self.form_invalid(form)
587
588		# check tocken expiration
589		if auth.is_expired() or auth.get_duration().seconds < 1800:
590		logger.warning(
591		"Token is expired or near to expire")
592
593		messages.error(
594		self.request,
595		("Your token is expired or near to expire. Generate a new "
596		"one"),
597		extra_tags="alert alert-dismissible alert-danger")
598
599		# redirect to this form
600		return self.form_invalid(form)
601
602		# start the submission with a valid token
603		self.start_submission(auth, submission)
604
605		return redirect(self.get_success_url())
606
607		def start_submission(self, auth, submission):
608		"""Change submission status and submit data with a valid token"""
609
610		logger.debug("Connecting to redis database")
611
612		# here token is valid, so store it in redis database
613		client = redis.StrictRedis(
614		host=settings.REDIS_HOST,
615		port=settings.REDIS_PORT,
616		db=settings.REDIS_DB)
617
618		key = "token:submission:{submission_id}:{user}".format(
619		submission_id=self.submission_id,
620		user=self.request.user)
621
622		logger.debug("Writing token in redis")
623
624		client.set(key, auth.token, ex=auth.get_duration().seconds)
625
626		# Update submission status
627		submission.status = WAITING
628		submission.message = "Waiting for biosample submission"
629		submission.save()
630
631		# a valid submission start a task
632		submit_task = SplitSubmissionTask()
633		res = submit_task.delay(submission.id)
634		logger.info(
635		"Start submission process for %s with task %s" % (
636		submission,
637		res.task_id))
638

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#55)

CreateUserView.create_biosample_team() A

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