Release v0.5.0

Gruntfile.js

@@ -37,7 +37,11 @@ module.exports = function(grunt) {
         "promort/src/js/clinical_annotations_manager/clinical_annotations_manager.services.js",
         "promort/src/js/clinical_annotations_manager/clinical_annotations_manager.controllers.js",
         "promort/src/js/clinical_annotations_manager/clinical_annotations_manager.directives.js",
-        "promort/src/js/ome_seadragon_tools/cell_count_guide.js"
+        "promort/src/js/ome_seadragon_tools/cell_count_guide.js",
+        "promort/src/js/questionnaires_manager/questionnaires_manager.module.js",
+        "promort/src/js/questionnaires_manager/questionnaires_manager.services.js",
+        "promort/src/js/questionnaires_manager/questionnaires_manager.controller.js",
+        "promort/src/js/questionnaires_manager/questionnaires_manager.directives.js"
     ];
 
     grunt.initConfig({

promort/VERSION

@@ -1 +1 @@
-0.4.15
+0.5.0

promort/config/config.yaml

@@ -5,6 +5,7 @@ django:
     - localhost
   static_root: ./static/
   session_cookie: promort_sessionid
+  session_expire_on_close: false
 
 database:
   engine: sqlite3

promort/promort/settings.py

@@ -62,7 +62,8 @@
     'rois_manager',
     'clinical_annotations_manager',
     'odin',
-    'utils'
+    'utils',
+    'questionnaires_manager'
 )
 
 MIDDLEWARE = (
@@ -98,6 +99,8 @@
 
 WSGI_APPLICATION = 'promort.wsgi.application'
 
+SESSION_EXPIRE_AT_BROWSER_CLOSE = cfg['django']['session_expire_on_close']
+
 # Django logger
 LOGGING = {
     'version': 1,

promort/promort/urls.py

@@ -1,18 +1,3 @@
-"""promort URL Configuration
-
-The `urlpatterns` list routes URLs to views. For more information please see:
-    https://docs.djangoproject.com/en/1.8/topics/http/urls/
-Examples:
-Function views
-    1. Add an import:  from my_app import views
-    2. Add a URL to urlpatterns:  url(r'^$', views.home, name='home')
-Class-based views
-    1. Add an import:  from other_app.views import Home
-    2. Add a URL to urlpatterns:  url(r'^$', Home.as_view(), name='home')
-Including another URLconf
-    1. Add an import:  from blog import urls as blog_urls
-    2. Add a URL to urlpatterns:  url(r'^blog/', include(blog_urls))
-"""
 #  Copyright (c) 2019, CRS4
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy of
@@ -41,7 +26,8 @@
 from authentication.views import LoginView, LogoutView, \
     GroupListView, GroupDetailsView, CheckUserView
 from slides_manager.views import LaboratoryList, LaboratoryDetail, LaboratoryCaseLink, \
-    CaseList, CaseDetail, SlideList, SlideDetail, SlideEvaluationDetail
+    CaseList, CaseDetail, SlideList, SlideDetail, SlideEvaluationDetail, SlidesSetList, SlidesSetDetail
+import questionnaires_manager.views as qmv
 import reviews_manager.views as rmv
 from worklist_manager.views import UserWorkList, UserWorklistROIsAnnotation,\
     UserWorklistClinicalAnnotation, WorkListAdmin
@@ -71,6 +57,24 @@
     url(r'^api/cases/(?P<pk>[\w\-.]+)/$', CaseDetail.as_view()),
     url(r'^api/slides/$', SlideList.as_view()),
     url(r'^api/slides/(?P<pk>[\w\-.]+)/$', SlideDetail.as_view()),
+    url(r'^api/slides_set/$', SlidesSetList.as_view()),
+    url(r'^api/slides_set/(?P<pk>[\w\-.]+)/$', SlidesSetDetail.as_view()),
+
+    # slides questionnaire
+    url(r'api/questions_sets/$', qmv.QuestionsSetList.as_view()),
+    url(r'api/questions_sets/(?P<pk>[\w\-.]+)/$', qmv.QuestionsSetDetail.as_view()),
+    url(r'api/questionnaires/$', qmv.QuestionnaireList.as_view()),
+    url(r'api/questionnaires/(?P<pk>[\w\-.]+)/$', qmv.QuestionnaireDetail.as_view()),
+    url(r'api/questionnaires/(?P<quest_pk>[\w\-.]+)/(?P<step_index>[0-9]+)/$', qmv.QuestionnaireStepDetail.as_view()),
+
+    # slides questionnaire worklist and answers
+    url(r'api/questionnaire_requests/(?P<label>[\w\-.]+)/$', qmv.QuestionnaireRequestDetail.as_view()),
+    url(r'api/questionnaire_requests/(?P<label>[\w\-.]+)/status/$', qmv.QuestionnaireRequestStatus.as_view()),
+    url(r'api/questionnaire_requests/(?P<label>[\w\-.]+)/answers/$', qmv.QuestionnaireRequestAnswers.as_view()),
+    url(r'api/questionnaire_requests/(?P<label>[\w\-.]+)/(?P<panel>panel_a|panel_b)/$',
+        qmv.QuestionnaireRequestPanelDetail.as_view()),
+    url(r'api/questionnaire_requests/(?P<label>[\w\-.]+)/(?P<panel>panel_a|panel_b)/answers/$',
+        qmv.QuestionnairePanelAnswersDetail.as_view()),
 
     # ROIs annotation steps details
     url(r'api/rois_annotation_steps/(?P<label>[A-Fa-f0-9\-.]+)/clinical_annotation_steps/$',

tools/clear_db.py → promort/questionnaires_manager/__init__.py

@@ -16,30 +16,3 @@
 #  COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
 #  IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
 #  CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-
-# =======
-# WARNING: this script is intended to be only used during the development stage of the project
-# to clean completely the database of the application
-# =======
-
-from reviews_manager.models import Review, ReviewStep
-from slides_manager.models import Case, Slide, SlideQualityControl
-from rois_manager.models import Slice
-
-# delete all slices (cores and focus regions will be deleted as well)
-Slice.objects.all().delete()
-
-# delete all review steps
-ReviewStep.objects.all().delete()
-
-# delete all reviews
-Review.objects.all().delete()
-
-# delete all quality control data
-SlideQualityControl.objects.all().delete()
-
-# delete all slides
-Slide.objects.all().delete()
-
-# ... finally delete all cases
-Case.objects.all().delete()

promort/questionnaires_manager/management/__init__.py

@@ -0,0 +1,18 @@
+#  Copyright (c) 2020, CRS4
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a copy of
+#  this software and associated documentation files (the "Software"), to deal in
+#  the Software without restriction, including without limitation the rights to
+#  use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+#  the Software, and to permit persons to whom the Software is furnished to do so,
+#  subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included in all
+#  copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+#  FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+#  COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+#  IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+#  CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

promort/questionnaires_manager/management/commands/__init__.py

@@ -0,0 +1,18 @@
+#  Copyright (c) 2020, CRS4
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a copy of
+#  this software and associated documentation files (the "Software"), to deal in
+#  the Software without restriction, including without limitation the rights to
+#  use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+#  the Software, and to permit persons to whom the Software is furnished to do so,
+#  subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included in all
+#  copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+#  FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+#  COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+#  IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+#  CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

promort/questionnaires_manager/management/commands/create_questionnaire_requests.py

@@ -0,0 +1,96 @@
+#  Copyright (c) 2020, CRS4
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a copy of
+#  this software and associated documentation files (the "Software"), to deal in
+#  the Software without restriction, including without limitation the rights to
+#  use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+#  the Software, and to permit persons to whom the Software is furnished to do so,
+#  subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included in all
+#  copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+#  FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+#  COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+#  IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+#  CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+from django.core.management.base import BaseCommand, CommandError
+from django.contrib.auth.models import User
+from django.db import IntegrityError
+from questionnaires_manager.models import QuestionnaireRequest, Questionnaire
+
+from csv import DictReader
+from uuid import uuid4
+import logging
+
+logger = logging.getLogger('promort_commands')
+
+
+class Command(BaseCommand):
+    help = """
+    
+    """
+
+    def add_arguments(self, parser):
+        parser.add_argument('--questionnaire-requests', dest='questionnaire_requests', type=str,
+                            required=True, help='The CSV containing the questionnaire requests')
+
+    def _load_requests_map(self, qreq_file):
+        try:
+            with open(qreq_file) as f:
+                reader = DictReader(f)
+                requests_map = dict()
+                for row in reader:
+                    requests_map.setdefault(row['reviewer'], []).append(row)
+            return requests_map
+        except OSError:
+            raise CommandError('File %s does not exist' % qreq_file)
+
+    def _get_request_random_label(self):
+        return str(uuid4())
+
+    def _create_requests(self, reviewer, requests):
+        logger.info('-- Creating %d questionnare requests for user %s', len(requests), reviewer)
+        try:
+            reviewer_obj = User.objects.get(username=reviewer)
+        except User.DoesNotExist:
+            logger.error('There is no reviewer with username %s', reviewer)
+            return None
+        for req in requests:
+            if req['label'] in (None, ''):
+                logger.info('Missing label, assigning a random one')
+                req['label'] = self._get_request_random_label()
+            if req['questionnaire_a'] is None:
+                logger.error('Missing mandatody questionnaire_a, skipping row')
+                continue
+            try:
+                q_panel_a_obj = Questionnaire.objects.get(label=req['questionnaire_a'])
+            except Questionnaire.DoesNotExist:
+                logger.error('There is no Questionnaire object with label %s [Quest_A]', req['questionnaire_a'])
+                continue
+            req_details = {
+                'label': req['label'],
+                'questionnaire_panel_a': q_panel_a_obj,
+                'reviewer': reviewer_obj
+            }
+            if not req['questionnaire_b'] is None:
+                try:
+                    req_details['questionnaire_panel_b'] = Questionnaire.objects.get(label=req['questionnaire_b'])
+                except Questionnaire.DoesNotExist:
+                    logger.error('There is no Questionnaire object with label %s [Quest_B]', req['questionnaire_b'])
+                    continue
+            try:
+                q_req = QuestionnaireRequest(**req_details)
+                q_req.save()
+            except IntegrityError:
+                logger.error('There is already a QuestionnaireRequest with label %s', req_details['label'])
+
+    def handle(self, *args, **opts):
+        logger.info('=== Starting import job ===')
+        requests_map = self._load_requests_map(opts['questionnaire_requests'])
+        for k, v in requests_map.iteritems():
+            self._create_requests(k, v)
+        logger.info('=== Import job completed ===')

promort/questionnaires_manager/management/commands/import_questionnaire_steps.py

@@ -0,0 +1,113 @@
+#  Copyright (c) 2020, CRS4
+#
+#  Permission is hereby granted, free of charge, to any person obtaining a copy of
+#  this software and associated documentation files (the "Software"), to deal in
+#  the Software without restriction, including without limitation the rights to
+#  use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+#  the Software, and to permit persons to whom the Software is furnished to do so,
+#  subject to the following conditions:
+#
+#  The above copyright notice and this permission notice shall be included in all
+#  copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+#  FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+#  COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+#  IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+#  CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+from django.core.management.base import BaseCommand, CommandError
+from django.db import IntegrityError
+from questionnaires_manager.models import Questionnaire, QuestionnaireStep, QuestionsSet
+from slides_manager.models import SlidesSet
+
+from csv import DictReader
+from uuid import uuid4
+import logging
+
+logger = logging.getLogger('promort_commands')
+
+
+class Command(BaseCommand):
+    help = """
+    
+    """
+
+    def add_arguments(self, parser):
+        parser.add_argument('--questionnaire-steps', dest='questionnaire_steps_file', type=str, required=True,
+                            help='The CSV file containing the questionnare steps definitions')
+
+    def _load_questionnaires_map(self, qsteps_file):
+        try:
+            with open(qsteps_file) as f:
+                reader = DictReader(f)
+                questionnaire_map = dict()
+                for row in reader:
+                    questionnaire_map.setdefault(row['questionnaire'], []).append(row)
+                return questionnaire_map
+        except OSError:
+            raise CommandError('File %s does not exist' % qsteps_file)
+
+    def _get_slides_set_random_label(self):
+        return str(uuid4())
+
+    def _import_questionnaire_steps(self, questionnaire_label, steps):
+        logger.info('-- Creating %d steps for Questionnaire %s', len(steps), questionnaire_label)
+        try:
+            questionnaire_obj = Questionnaire.objects.get(label=questionnaire_label)
+            # create random labels to be used for all the steps of the questionnaire if label is not specified in CSV
+            step_a_random_label = self._get_slides_set_random_label()
+            step_b_random_label = self._get_slides_set_random_label()
+            for i, step in enumerate(steps):
+                step_config = {
+                    'questionnaire': questionnaire_obj,
+                    'step_index': i
+                }
+                logger.debug('Creating step %d for questionnaire %s', i, questionnaire_label)
+                try:
+                    step_config['questions'] = QuestionsSet.objects.get(label=step['questions_set'])
+                except QuestionsSet.DoesNotExist:
+                    logger.error('There is no QuestionsSet object with label %s', step['questions_set'])
+                    break
+                if not step['slides_set_a'] is None:
+                    if step['slides_set_a_label'] in (None, ''):
+                        logger.info('Using random label %s for slides set A', step_a_random_label)
+                        step['slides_set_a_label'] = step_a_random_label
+                    try:
+                        step_config.update({
+                            'slides_set_a': SlidesSet.objects.get(id=step['slides_set_a']),
+                            'slides_set_a_label': step['slides_set_a_label']
+                        })
+                    except SlidesSet.DoesNotExist:
+                        logger.error('There is no SlidesSet object with ID %s', step['slides_set_a'])
+                        break
+                if not step['slides_set_b'] is None:
+                    if step['slides_set_b_label'] in (None, ''):
+                        logger.info('Using random label %s for slides set B', step_b_random_label)
+                        step['slides_set_b_label'] = step_b_random_label
+                    try:
+                        step_config.update({
+                            'slides_set_b': SlidesSet.objects.get(id=step['slides_set_b']),
+                            'slides_set_b_label': step['slides_set_b_label']
+                        })
+                    except SlidesSet.DoesNotExist:
+                        logger.error('There is no SlidesSet object with ID %s', step['slides_set_b'])
+                        break
+                try:
+                    qstep = QuestionnaireStep(**step_config)
+                    qstep.save()
+                    logger.info('Saved questionnaire step with index %d', i)
+                except IntegrityError:
+                    logger.error('Questionnaire %s already has a step with index %d', questionnaire_label, i)
+                    break
+        except Questionnaire.DoesNotExist:
+            logger.error('There is no Questionnaire object with label %s, skipping records',
+                         questionnaire_label)
+
+    def handle(self, *args, **opts):
+        logger.info('=== Starting import job ===')
+        questionnaires_map = self._load_questionnaires_map(opts['questionnaire_steps_file'])
+        for k, v in questionnaires_map.iteritems():
+            self._import_questionnaire_steps(k, v)
+        logger.info('=== Import job completed ===')