biosample.views.CreateUserView.add_biosample_user_to_team() - Code Metrics - Inspection of ":twisted_rightwards_arrows: Merge pull request #55..." - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( ba462b...d97c8b )

by Paolo

created 2019-10-01 13:51 UTC

CreateUserView.add_biosample_user_to_team() A

↳ Parent: biosample.views

Complexity

Conditions

Size

Total Lines	49
Code Lines	29

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	29
dl	0
loc	49
rs	9.184
c	0
b	0
f	0
cc	2
nop	5


import os
import redis
import logging
import traceback

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.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 common.helpers import send_mail_to_admins
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 AccountMixin(object):
    """A generic mixin associated with biosample.models. You need to costomize
    account_found and account_not_found in to do a custom redirect in case
    a manager account is found or not"""

    def account_not_found(self, request, *args, **kwargs):
        return super().dispatch(request, *args, **kwargs)

    def account_found(self, request, *args, **kwargs):
        return super().dispatch(request, *args, **kwargs)

    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 = self.request.user

        if hasattr(user, "biosample_account"):
            return self.account_found(request, *args, **kwargs)

        else:
            return self.account_not_found(request, *args, **kwargs)


class TokenMixin(AccountMixin):
    """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

    # override AccountMixin method
    def account_not_found(self, request, *args, **kwargs):
        """If a user has not an account, redirect to activation complete"""

        logger.warning("Error for user:%s: not managed" % self.request.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')


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

    # override AccountMixin method
    def account_found(self, request, *args, **kwargs):
        """If a user has been registered, redirect to dashboard"""

        logger.warning(
            "Error for user:%s: Already registered" % self.request.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")

        # get exception info
        einfo = traceback.format_exc()

        # send a mail to admin
        send_mail_to_admins(error_message, einfo)

    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			import traceback
6
7			from decouple import AutoConfig
8
9			from django.conf import settings
10			from django.urls import reverse_lazy, reverse
11			from django.utils.crypto import get_random_string
12			from django.utils.http import is_safe_url
13			from django.shortcuts import redirect, get_object_or_404
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 common.helpers import send_mail_to_admins
24			from image_app.models import Submission
25
26			from .forms import (
27			GenerateTokenForm, RegisterUserForm, CreateUserForm, SubmitForm)
28			from .models import Account, ManagedTeam
29			from .helpers import get_auth, get_manager_auth
30			from .tasks import SplitSubmissionTask
31
32
33			# Get an instance of a logger
34			logger = logging.getLogger(__name__)
35
36
37			# define a decouple config object
38			settings_dir = os.path.join(settings.BASE_DIR, 'image')
39			config = AutoConfig(search_path=settings_dir)
40
41
42			# In programming, a mixin is a class that provides functionality to be
43			# inherited, but isn’t meant for instantiation on its own. In programming
44			# languages with multiple inheritance, mixins can be used to add enhanced
45			# functionality and behavior to classes.
46			class AccountMixin(object):
47			"""A generic mixin associated with biosample.models. You need to costomize
48			account_found and account_not_found in to do a custom redirect in case
49			a manager account is found or not"""
50
51			def account_not_found(self, request, args, *kwargs):
52			return super().dispatch(request, args, *kwargs)
53
54			def account_found(self, request, args, *kwargs):
55			return super().dispatch(request, args, *kwargs)
56
57			def dispatch(self, request, args, *kwargs):
58			# get user from request and user model. This could be also Anonymous
59			# user:however with metod decorator a login is required before dispatch
60			# method is called
61			user = self.request.user
62
63			if hasattr(user, "biosample_account"):
64			return self.account_found(request, args, *kwargs)
65
66			else:
67			return self.account_not_found(request, args, *kwargs)
68
69
70			class TokenMixin(AccountMixin):
71			"""Get common stuff for Token visualization. Redirect to AAP registration
72			if no valid AAP credentials are found for request.user"""
73
74			def get_initial(self):
75			"""
76			Returns the initial data to use for forms on this view.
77			"""
78
79			initial = super(TokenMixin, self).get_initial()
80			initial['name'] = self.request.user.biosample_account.name
81
82			return initial
83
84			# override AccountMixin method
85			def account_not_found(self, request, args, *kwargs):
86			"""If a user has not an account, redirect to activation complete"""
87
88			logger.warning("Error for user:%s: not managed" % self.request.user)
89
90			messages.warning(
91			request=self.request,
92			message='You need to register a valid AAP profile',
93			extra_tags="alert alert-dismissible alert-warning")
94
95			return redirect('accounts:registration_activation_complete')
96
97
98			class RegisterMixin(AccountMixin):
99			"""If a biosample account is already registered, returns to dashboard"""
100
101			# override AccountMixin method
102			def account_found(self, request, args, *kwargs):
103			"""If a user has been registered, redirect to dashboard"""
104
105			logger.warning(
106			"Error for user:%s: Already registered" % self.request.user)
107
108			messages.warning(
109			request=self.request,
110			message='Your AAP profile is already registered',
111			extra_tags="alert alert-dismissible alert-warning")
112
113			return redirect('image_app:dashboard')
114
115
116			class MyFormMixin(object):
117			"""Common stuff for token generation"""
118
119			success_url_message = "Please set this variable"
120			success_url = reverse_lazy("image_app:dashboard")
121
122			# add the request to the kwargs
123			# https://chriskief.com/2012/12/18/django-modelform-formview-and-the-request-object/
124			# this is needed to display messages (django.contronb) on pages
125			def get_form_kwargs(self):
126			kwargs = super(MyFormMixin, self).get_form_kwargs()
127			kwargs['request'] = self.request
128			return kwargs
129
130			def get_success_url(self):
131			"""Override default function"""
132
133			messages.success(
134			request=self.request,
135			message=self.success_url_message,
136			extra_tags="alert alert-dismissible alert-success")
137
138			return super(MyFormMixin, self).get_success_url()
139
140			def form_invalid(self, form):
141			messages.error(
142			self.request,
143			message="Please correct the errors below",
144			extra_tags="alert alert-dismissible alert-danger")
145
146			return super(MyFormMixin, self).form_invalid(form)
147
148			def generate_token(self, form):
149			"""Generate token from form instance"""
150
151			# operate on form data
152			name = form.cleaned_data['name']
153			password = form.cleaned_data['password']
154
155			try:
156			auth = get_auth(user=name, password=password)
157
158			except ConnectionError as e:
159			# logger exception. With repr() the exception name is rendered
160			logger.error(repr(e))
161
162			# maybe I typed a wrong password or there is an issue in biosample
163			# log error in message and return form_invalid
164			# HINT: deal with two conditions?
165
166			# parse error message
167			messages.error(
168			self.request,
169			"Unable to generate token: %s" % str(e),
170			extra_tags="alert alert-dismissible alert-danger")
171
172			# cant't return form_invalid here, since i need to process auth
173			return None
174
175			else:
176			logger.debug("Token generated for user:%s" % name)
177
178			self.request.session['token'] = auth.token
179
180			# return an auth object
181			return auth
182
183
184			class GenerateTokenView(LoginRequiredMixin, TokenMixin, MyFormMixin, FormView):
185			"""Generate AAP token. If user is not registered, redirect to accounts
186			registration_activation_complete through TokenMixin. If yes generate
187			token through MyFormMixin"""
188
189			template_name = 'biosample/generate_token.html'
190			form_class = GenerateTokenForm
191			success_url_message = 'Token generated!'
192
193			def dispatch(self, request, args, *kwargs):
194			# try to read next link
195			next_url = request.GET.get('next', None)
196
197			# redirect to next url. is_safe_url: is a safe redirection
198			# (i.e. it doesn't point to a different host and uses a safe scheme).
199			if next_url and is_safe_url(next_url):
200			logger.debug("Got %s as next_url" % next_url)
201			self.success_url = next_url
202
203			return super(
204			GenerateTokenView, self).dispatch(request, args, *kwargs)
205
206			def form_valid(self, form):
207			# This method is called when valid form data has been POSTed.
208			# It should return an HttpResponse.
209
210			# call MyFormMixin method and generate token. Check user/password
211			if not self.generate_token(form):
212			return self.form_invalid(form)
213
214			return redirect(self.get_success_url())
215
216
217			class TokenView(LoginRequiredMixin, TokenMixin, TemplateView):
218			"""Visualize token details"""
219
220			template_name = 'biosample/token.html'
221
222			def get_context_data(self, **kwargs):
223			# Call the base implementation first to get a context
224			context = super(TokenView, self).get_context_data(**kwargs)
225
226			# get user and team object
227			context['name'] = self.request.user.biosample_account.name
228			context['team'] = self.request.user.biosample_account.team
229
230			try:
231			# add content to context
232			auth = get_auth(token=self.request.session['token'])
233
234			if auth.is_expired():
235			messages.error(
236			self.request,
237			"Your token is expired",
238			extra_tags="alert alert-dismissible alert-danger")
239
240			context["auth"] = auth
241
242			except KeyError as e:
243			logger.error(
244			"No valid token found for %s: %s" % (
245			self.request.user,
246			e))
247
248			messages.error(
249			self.request,
250			"You haven't generated any token yet",
251			extra_tags="alert alert-dismissible alert-danger")
252
253			return context
254
255
256			class RegisterUserView(LoginRequiredMixin, RegisterMixin, MyFormMixin,
257			CreateView):
258			"""Register an already existent AAP account"""
259
260			template_name = 'biosample/register_user.html'
261			form_class = RegisterUserForm
262			success_url_message = 'Account registered'
263
264			def form_valid(self, form):
265			# This method is called when valid form data has been POSTed.
266			# It should return an HttpResponse.
267			team = form.cleaned_data['team']
268
269			# call AuthMixin method and generate token. Check user/password
270			auth = self.generate_token(form)
271
272			if not auth:
273			return self.form_invalid(form)
274
275			if team.name not in auth.claims['domains']:
276			messages.error(
277			self.request,
278			"You don't belong to team: %s" % team,
279			extra_tags="alert alert-dismissible alert-danger")
280
281			# return invalid form
282			return self.form_invalid(form)
283
284			# add a user to object (comes from section not from form)
285			self.object = form.save(commit=False)
286			self.object.user = self.request.user
287			self.object.save()
288
289			# call to a specific function (which does an HttpResponseRedirect
290			# to success_url)
291			return super(ModelFormMixin, self).form_valid(form)
292
293
294			class CreateUserView(LoginRequiredMixin, RegisterMixin, MyFormMixin, FormView):
295			"""Create a new AAP account"""
296
297			template_name = 'biosample/create_user.html'
298			form_class = CreateUserForm
299			success_url_message = "Account created"
300
301			def deal_with_errors(self, error_message, exception):
302			"""Add messages to view for encountered errors
303
304			Args:
305			error_message (str): An informative text
306			exception (Exception): an exception instance
307			"""
308
309			exception_message = "Message was: %s" % (exception)
310
311			logger.error(error_message)
312			logger.error(exception_message)
313
314			messages.error(
315			self.request,
316			message=error_message,
317			extra_tags="alert alert-dismissible alert-danger")
318
319			messages.error(
320			self.request,
321			message=exception_message,
322			extra_tags="alert alert-dismissible alert-danger")
323
324			# get exception info
325			einfo = traceback.format_exc()
326
327			# send a mail to admin
328			send_mail_to_admins(error_message, einfo)
329
330			def get_form_kwargs(self):
331			"""Override get_form_kwargs"""
332
333			kwargs = super(CreateUserView, self).get_form_kwargs()
334
335			# create a new biosample user
336			username = "image-%s" % (get_random_string(length=8))
337
338			# add username to instance
339			kwargs['username'] = username
340
341			return kwargs
342
343			# create an user or throw an exception
344			def create_biosample_user(self, form, full_name, affiliation):
345			"""Create a biosample user
346
347			Args:
348			form (:py:class:`CreateUserForm`) an instantiated form object
349			full_name (str): the user full name (Name + Surname)
350			affiliation (str): the organization the user belongs to
351
352			Returns:
353			str: a biosamples user id
354			"""
355
356			password = form.cleaned_data['password1']
357			confirmPwd = form.cleaned_data['password2']
358
359			# get user model associated with this session
360			user = self.request.user
361
362			# get email
363			email = user.email
364
365			biosample_user_id = None
366
367			# creating a user
368			logger.debug("Creating user %s" % (form.username))
369
370			try:
371			biosample_user_id = User.create_user(
372			user=form.username,
373			password=password,
374			confirmPwd=confirmPwd,
375			email=email,
376			full_name=full_name,
377			organisation=affiliation
378			)
379
380			logger.info("user_id %s generated" % (biosample_user_id))
381
382			except ConnectionError as e:
383			message = "Problem in creating user %s" % (form.username)
384			self.deal_with_errors(message, e)
385
386			return biosample_user_id
387
388			def create_biosample_team(self, full_name, affiliation):
389			"""Create a biosample team
390
391			Args:
392			full_name (str): the user full name (Name + Surname)
393			affiliation (str): the organization the user belongs to
394
395			Returns:
396			:py:class:`pyUSIrest.client.Team`: a pyUSIrest Team instance
397			:py:class:`biosample.models.ManagedTeam`: a model object
398			"""
399
400			# creating a new team. First create an user object
401			# create a new auth object
402			logger.debug("Generate a token for 'USI_MANAGER'")
403
404			# get an Auth instance from a helpers.method
405			auth = get_manager_auth()
406			admin = User(auth)
407
408			description = "Team for %s" % (full_name)
409
410			# the values I want to return
411			team, managed_team = None, None
412
413			# now create a team
414			logger.debug("Creating team for %s" % (full_name))
415
416			try:
417
418			team = admin.create_team(
419			description=description,
420			centreName=affiliation)
421
422			logger.info("Team %s generated" % (team.name))
423
424			# register team in ManagedTeam table
425			managed_team, created = ManagedTeam.objects.get_or_create(
426			name=team.name)
427
428			if created is True:
429			logger.info("Created: %s" % (managed_team))
430
431			except ConnectionError as e:
432			message = "Problem in creating team for %s" % (full_name)
433			self.deal_with_errors(message, e)
434
435			return team, managed_team
436
437			def add_biosample_user_to_team(self, form, user_id, team, managed_team):
438
439			# I need to generate a new token to see the new team
440			logger.debug("Generate a new token for 'USI_MANAGER'")
441
442			auth = get_manager_auth()
443			admin = User(auth)
444
445			# list all domain for manager
446			logger.debug("Listing all domains for %s" % (config('USI_MANAGER')))
447			logger.debug(", ".join(auth.claims['domains']))
448
449			# get the domain for the new team, and then the domain_id
450			logger.debug("Getting domain info for team %s" % (team.name))
451			domain = admin.get_domain_by_name(team.name)
452			domain_id = domain.domainReference
453
454			# the value I want to return
455			account = None
456
457			logger.debug(
458			"Adding user %s to team %s" % (form.username, team.name))
459
460			try:
461			# user to team
462			admin.add_user_to_team(user_id=user_id, domain_id=domain_id)
463
464			# save objects in accounts table
465			account = Account.objects.create(
466			user=self.request.user,
467			name=form.username,
468			team=managed_team
469			)
470
471			logger.info("%s created" % (account))
472
473			# add message
474			messages.debug(
475			request=self.request,
476			message="User %s added to team %s" % (
477			form.username, team.name),
478			extra_tags="alert alert-dismissible alert-light")
479
480			except ConnectionError as e:
481			message = "Problem in adding user %s to team %s" % (
482			form.username, team.name)
483			self.deal_with_errors(message, e)
484
485			return account
486
487			# HINT: move to a celery task?
488			def form_valid(self, form):
489			"""Create a new team in with biosample manager user, then create a new
490			user and register it"""
491
492			# get user model associated with this session
493			user = self.request.user
494
495			# get user info
496			first_name = user.first_name
497			last_name = user.last_name
498
499			# set full name as
500			full_name = " ".join([first_name, last_name])
501
502			# Affiliation is the institution the user belong
503			affiliation = user.person.affiliation.name
504
505			# model generic errors from EBI API endpoints
506			try:
507			user_id = self.create_biosample_user(form, full_name, affiliation)
508
509			if user_id is None:
510			# return invalid form
511			return self.form_invalid(form)
512
513			# create a biosample team
514			team, managed_team = self.create_biosample_team(
515			full_name, affiliation)
516
517			if team is None:
518			# return invalid form
519			return self.form_invalid(form)
520
521			account = self.add_biosample_user_to_team(
522			form, user_id, team, managed_team)
523
524			if account is None:
525			# return invalid form
526			return self.form_invalid(form)
527
528			except ConnectionError as e:
529			message = (
530			"Problem with EBI-AAP endoints. Please contact IMAGE team")
531			self.deal_with_errors(message, e)
532
533			# return invalid form
534			return self.form_invalid(form)
535
536			# call to a inherited function (which does an HttpResponseRedirect
537			# to success_url)
538			return super(CreateUserView, self).form_valid(form)
539
540
541			class SubmitView(LoginRequiredMixin, TokenMixin, MyFormMixin, FormView):
542			"""Call a submission task. Check that a token exists and that it's valid"""
543
544			form_class = SubmitForm
545			template_name = 'biosample/submit.html'
546			submission_id = None
547
548			def get_success_url(self):
549			return reverse('submissions:detail', kwargs={
550			'pk': self.submission_id})
551
552			def form_valid(self, form):
553			submission_id = form.cleaned_data['submission_id']
554			name = form.cleaned_data['name']
555			password = form.cleaned_data['password']
556
557			# get a submission object
558			submission = get_object_or_404(
559			Submission,
560			pk=submission_id,
561			owner=self.request.user)
562
563			# track submission id in order to render page
564			self.submission_id = submission_id
565
566			# check if I can submit object (statuses)
567			if not submission.can_submit():
568			# return super method (which calls get_success_url)
569			logger.error(
570			"Can't submit submission %s: current status is %s" % (
571			submission, submission.get_status_display()))
572
573			return HttpResponseRedirect(self.get_success_url())
574
575			# create an auth object if credentials are provided
576			if name and password:
577			# call AuthMixin method and generate token. Check user/password
578			auth = self.generate_token(form)
579
580			if not auth:
581			return self.form_invalid(form)
582
583			# check token: if expired or near to expiring, return form
584			elif 'token' in self.request.session:
585			auth = get_auth(token=self.request.session['token'])
586
587			else:
588			logger.warning(
589			"No valid token found. Redirect to tocken generation")
590
591			messages.error(
592			self.request,
593			("You haven't generated any token yet. Generate a new one"),
594			extra_tags="alert alert-dismissible alert-danger")
595
596			# redirect to this form
597			return self.form_invalid(form)
598
599			# check tocken expiration
600			if auth.is_expired() or auth.get_duration().seconds < 1800:
601			logger.warning(
602			"Token is expired or near to expire")
603
604			messages.error(
605			self.request,
606			("Your token is expired or near to expire. Generate a new "
607			"one"),
608			extra_tags="alert alert-dismissible alert-danger")
609
610			# redirect to this form
611			return self.form_invalid(form)
612
613			# start the submission with a valid token
614			self.start_submission(auth, submission)
615
616			return redirect(self.get_success_url())
617
618			def start_submission(self, auth, submission):
619			"""Change submission status and submit data with a valid token"""
620
621			logger.debug("Connecting to redis database")
622
623			# here token is valid, so store it in redis database
624			client = redis.StrictRedis(
625			host=settings.REDIS_HOST,
626			port=settings.REDIS_PORT,
627			db=settings.REDIS_DB)
628
629			key = "token:submission:{submission_id}:{user}".format(
630			submission_id=self.submission_id,
631			user=self.request.user)
632
633			logger.debug("Writing token in redis")
634
635			client.set(key, auth.token, ex=auth.get_duration().seconds)
636
637			# Update submission status
638			submission.status = WAITING
639			submission.message = "Waiting for biosample submission"
640			submission.save()
641
642			# a valid submission start a task
643			submit_task = SplitSubmissionTask()
644			res = submit_task.delay(submission.id)
645			logger.info(
646			"Start submission process for %s with task %s" % (
647			submission,
648			res.task_id))
649

cnr-ibba / IMAGE-InjectTool

Push — master ( ba462b...d97c8b )

CreateUserView.add_biosample_user_to_team() A

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

Filter issues like