Merge pull request #3 from bioinformatics-ua/dev

0.1.1

.gitignore

@@ -5,7 +5,7 @@ env/*
 *.pyc
 
 #Put this files in somewhere private
-docker-compose.yml
+!docker-compose.yml
 
 #Ignore migrations
 Backend/accounts/migrations/*
@@ -23,4 +23,4 @@ Backend/utils/migrations/*
 !Backend/protocol_element/migrations/__init__.py
 !Backend/utils/migrations/__init__.py
 
-UI/package-lock.json
+UI/package-lock.json

Backend/genericcdss/settings.py

@@ -202,10 +202,12 @@
     'FOOTER_EXTRA': """<a href='http://www.ua.pt/'>
                     <img style='margin-left:20px' src='https://emif-catalogue.eu/taska/static/images/logo-ua2.png'>
                     </a>""",
-    'APP_SYMBOL':"""
-                    <img style='margin-left:20px' src='static/NOTFOUND'>
+    'APP_SYMBOL_SMALL':"""<img style='margin-left:20px; max-width: 70px;' src='images/logo_small.png'>
                  """,
-    'LANGUAGE':"pt - to do"
+    'APP_SYMBOL':"""<center><img style='max-width: 150px; max-height: 150px;' src='images/logo.png'></center>
+                 """,
+    'LANGUAGE':"pt - to do",
+    'SHOW_DEFAULT_HOME': True
 }
 
 CONSTANCE_BACKEND = 'constance.backends.database.DatabaseBackend'
@@ -214,13 +216,16 @@
     'copyright': (GLOBALS['COPYRIGHT'], 'Text to show as copyright'),
     'copyrightsplash': ('<a target="_blank" href="http://bioinformatics.ua.pt/">Bioinformatics, UA.</a>', 'Text to show as copyright on splash screen'),
     'footer_extra': (GLOBALS['FOOTER_EXTRA'], 'Extra HTML to be shown besides the footer'),
+    'app_symbol_small': (GLOBALS['APP_SYMBOL_SMALL'], 'Image used to represent the system (Logo) - small'),
     'app_symbol': (GLOBALS['APP_SYMBOL'], 'Image used to represent the system (Logo)'),
     'site_name': (GLOBALS['SITE_NAME'], 'Website title'),
-    'language':(GLOBALS['LANGUAGE'], 'The languge used in the GUI')
+    'language':(GLOBALS['LANGUAGE'], 'The languge used in the GUI'),
+    'show_default_home':(GLOBALS['SHOW_DEFAULT_HOME'], 'If true, it show the default home. If false, it show the home flat page')
 }
 
 CONSTANCE_CONFIG_FIELDSETS = {
-    'General Options': ('site_name', 'footer_extra', 'app_symbol', 'copyrightsplash', 'copyright','language'),
+    'General Options': ('site_name', 'footer_extra',  'copyrightsplash', 'copyright', 'language'),
+    'Home Options': ('show_default_home', 'app_symbol_small', 'app_symbol')
 }
 
 JET_DEFAULT_THEME = 'light-blue'

Backend/patients/api/serializers/AdmissionSerializer.py

@@ -11,18 +11,24 @@
 from patients.api.serializers import PatientSerializer
 
 class AdmissionSerializer(serializers.ModelSerializer):
-    physician       = serializers.SerializerMethodField(required=False)
-    next_measure    = serializers.SerializerMethodField(required=False)
-    last_measure    = serializers.SerializerMethodField(required=False)
+    admission_physician         = serializers.SerializerMethodField(required=False)
+    last_measure_physician      = serializers.SerializerMethodField(required=False)
+    next_measure                = serializers.SerializerMethodField(required=False)
+    last_measure                = serializers.SerializerMethodField(required=False)
     #protocol_id     = serializers.SerializerMethodField(required=False)
-    patient         = PatientSerializer()
+    patient                     = PatientSerializer()
 
     class Meta:
         permission_classes = [permissions.IsAuthenticated]
         model = Admission
         fields = '__all__'
 
-    def get_physician(self, obj):
+    def get_admission_physician(self, obj):
+        return obj.physician.getFullName()
+
+    def get_last_measure_physician(self, obj):
+        if(obj.getLastProtocolAssignedMeasurePhysician() != ""):
+            return obj.getLastProtocolAssignedMeasurePhysician().getFullName()
         return obj.physician.getFullName()
 
     def get_next_measure(self, obj):

Backend/patients/api/views/AdmissionViewSet.py

@@ -51,7 +51,7 @@ def new(self, request, *args, **kwargs):
         selectedProtocols  = request.data.get('seletedProtocols') #For now it is only one
         for selectedProtocol in selectedProtocols:
             protocol = Protocol.objects.get(id=selectedProtocol.get("id"))
-            ExecutedProtocol.new(protocol=protocol, patient=patient)
+            ExecutedProtocol.new(protocol=protocol, patient=patient, physician=physician)
 
         self.queryset = Admission.all(active=True)
         return super(AdmissionViewSet, self).list(request, *args, **kwargs)

Backend/patients/management/commands/populate_db_patients.py

@@ -1,6 +1,9 @@
 # coding=utf-8
 from django.core.management.base import BaseCommand
 from patients.models import CVGroup, ClinicalVariable, Patient, CVPatient, Admission
+from accounts.models import Profile
+from django.contrib.auth.models import User
+from protocol.models import Protocol, ExecutedProtocol
 import random
 import time
 
@@ -42,6 +45,8 @@ def handle(self, *args, **options):
             self.manageBodyMeasurements(options['force'])
             self.managePerfomedExams(options['force'])
 
+            self.assignPatients()
+
     def deleteAll(self):
         self.stdout.write("\tDeleting data in the CVPatients\n")
         CVPatient.objects.all().delete()
@@ -263,4 +268,38 @@ def managePerfomedExams(self, force):
                                   group = cvg,
                                   variable = "Physician",
                                   value = random.choice(drs),
-                                  measure_date=measure_date)
+                                  measure_date=measure_date)
+
+    def assignPatients(self):
+        try:
+            physician_user = User.objects.create_user('João Almeida', '[email protected]', '12345')
+            physician = Profile(user=physician_user, role=Profile.PHYSICIAN)
+            physician.save()
+            max = len(Patient.objects.all())/4
+            count = 0
+            for patient in Patient.objects.all():
+                # Create admission
+                Admission.new(patient=patient,
+                              physician=physician,
+                              room="c." + str(patient.id))
+
+                # Assign protocols
+                protocol = Protocol.objects.get(title="Hypoglycemia")
+                ExecutedProtocol.new(protocol=protocol, patient=patient, physician=physician)
+
+                if count%2 == 0: #Execute one mesurement in some patients
+                    inquiryData = {"Blood Glucose": "12", "Diet": "zero"}
+                    CVPatient.addCVSet(inquiryData, patient)
+                    assignment = ExecutedProtocol.getNextExecution(patient)
+                    result = assignment.run(inquiryData)
+                    # Next assigment
+                    protocol = assignment.protocol
+                    last_execution = assignment.schedule_time
+                    ExecutedProtocol.new(protocol=protocol, patient=patient, physician=physician, last_execution=last_execution)
+
+                count += 1
+                if count == max:
+                    break
+        except Exception as ex:
+            self.stdout.write("\tError: Probably no protocol or doctors in the database!\n")
+            self.stdout.write(ex)

Backend/patients/models/Admission.py

@@ -39,6 +39,16 @@ def getLastProtocolAssignedMeasure(self):
             return lastProtocolExecution.execution_time.strftime("%Y-%m-%d %H:%M")
         return ""
 
+    def getLastProtocolAssignedMeasurePhysician(self):
+        '''
+        Retrieves who made the last protocol measurement
+        :return: datetime in string format
+        '''
+        lastProtocolExecution = ExecutedProtocol.getLastExecution(patient=self.patient, admissionDate=self.start_date)
+        if(lastProtocolExecution):
+            return lastProtocolExecution.physician
+        return ""
+
     def getNextProtocolAssignedMeasure(self):
         '''
         It returns when the patient information should be measured

Backend/protocol/admin.py

@@ -17,7 +17,7 @@ class ProtocolAdmin(admin.ModelAdmin):
 
 @admin.register(ExecutedProtocol)
 class ExecutedProtocolAdmin(admin.ModelAdmin):
-    list_display = ("protocol", "patient", "execution_time")
+    list_display = ("protocol", "patient", "execution_time", "physician")
 
 @admin.register(Schedule)
 class ScheduleAdmin(admin.ModelAdmin):

Backend/protocol/api/serializers/ExecutedProtocolSerializer.py

@@ -6,11 +6,15 @@
 
 from protocol.models import ExecutedProtocol
 
+from patients.models import Admission
+
 
 class ExecutedProtocolSerializer(serializers.ModelSerializer):
-    title               = serializers.SerializerMethodField(required=False)
-    description         = serializers.SerializerMethodField(required=False)
-    execution_time      = serializers.SerializerMethodField(required=False)
+    title                       = serializers.SerializerMethodField(required=False)
+    description                 = serializers.SerializerMethodField(required=False)
+    execution_time              = serializers.SerializerMethodField(required=False)
+    admission_physician         = serializers.SerializerMethodField(required=False)
+    last_measure_physician      = serializers.SerializerMethodField(required=False)
 
     class Meta:
         permission_classes = [permissions.IsAuthenticated]
@@ -26,4 +30,12 @@ def get_description(self, obj):
     def get_execution_time(self, obj):
         if(obj.execution_time):
             return obj.execution_time.strftime("%Y-%m-%d %H:%M")
+        return ""
+
+    def get_admission_physician(self, obj):
+        return Admission.getLatestAdmission(obj.patient).physician.getFullName()
+
+    def get_last_measure_physician(self, obj):
+        if(obj.physician):
+            return obj.physician.getFullName()
         return ""

Backend/protocol/api/views/ProtocolViewSet.py

@@ -17,6 +17,8 @@
 from protocol_element.api.serializers import ProtocolElementSerializer, PEInquirySerializer
 from protocol_element.models import ProtocolElement, PEInquiry
 
+from accounts.models import Profile
+
 from history.models import History
 
 class ProtocolViewSet(viewsets.ModelViewSet):
@@ -104,15 +106,17 @@ def run(self, request):
                 'error': "Invalid parameters"
             })
 
+        physician = Profile.objects.get(user=request.user)
         patient = Patient.objects.get(id=patientId)
         CVPatient.addCVSet(inquiryData, patient)
 
         assignment = ExecutedProtocol.getNextExecution(patient)
-        result = assignment.run(inquiryData)
+        result = assignment.run(inquiryData=inquiryData, physician=physician)
 
         #Next assigment
         protocol = assignment.protocol
-        ExecutedProtocol.new(protocol=protocol, patient=patient)
+        last_execution = assignment.schedule_time
+        ExecutedProtocol.new(protocol=protocol, patient=patient, physician=physician, last_execution=last_execution)
 
         return Response({"results": result})
 

Backend/protocol/models/ExecutedProtocol.py

@@ -11,6 +11,8 @@
 
 from protocol_element.models import ProtocolElement, PEDecision, PEAction
 
+from accounts.models import Profile
+
 class ExecutedProtocol(models.Model):
     ASSIGNED            = 1
     EXECUTED            = 2
@@ -25,17 +27,19 @@ class ExecutedProtocol(models.Model):
     protocol            = models.ForeignKey(Protocol)
     patient             = models.ForeignKey(Patient)
     schedule            = models.ForeignKey(Schedule)
+    physician           = models.ForeignKey(Profile)
     schedule_time       = models.DateTimeField()
     execution_time      = models.DateTimeField(null=True)
     elementsExecuted    = models.ManyToManyField(ProtocolElement)
     state               = models.PositiveSmallIntegerField(choices=STATUS, default=ASSIGNED)
 
-    def run(self, inquiryData):
+    def run(self, inquiryData, physician):
         elementsExecutedInProtocol, actionsResult = self.protocol.run(inquiryData)
         for element in elementsExecutedInProtocol:
             self.elementsExecuted.add(element)
         self.state = ExecutedProtocol.EXECUTED
         self.execution_time = datetime.now()
+        self.physician = physician
         self.save()
         return self.getResult()
 
@@ -50,12 +54,13 @@ def getResult(self):
         return actionsResult
 
     @staticmethod
-    def new(protocol, patient):
-        schedule_time, scheduleTitle = protocol.getNextScheduleTime()
+    def new(protocol, patient, physician, last_execution=None):
+        schedule_time, scheduleTitle = protocol.getNextScheduleTime(last_execution)
         scheduleObj = Schedule.objects.get(title=scheduleTitle)
         protocol = ExecutedProtocol.objects.create(protocol=protocol,
                                                    patient=patient,
                                                    schedule=scheduleObj,
+                                                   physician=physician,
                                                    schedule_time=schedule_time,
                                                    state=ExecutedProtocol.ASSIGNED)
         protocol.save()

Backend/protocol/models/Protocol.py

@@ -3,7 +3,7 @@
 
 from django.db import models
 from django.utils import timezone
-from datetime import datetime
+from datetime import datetime, timedelta
 
 from protocol.models import Schedule
 
@@ -63,13 +63,22 @@ def edit(id, title, description, schedules):#, type, public):
     @staticmethod
     def all():
         '''
-        Returns all executed protocol instances
+        Returns all protocol instances
         '''
         tmpAll = Protocol.objects.all().filter(removed=False)
 
         return tmpAll.order_by('title')
 
-    def getNextScheduleTime(self):
+    @staticmethod
+    def get(title):
+        '''
+        Returns a active protocol instance
+        '''
+        tmpAll = Protocol.all()
+
+        return tmpAll.get(title=title)
+
+    def getNextScheduleTime(self, last_execution=None):
         '''
         Returns next schedule time
         :return: tuple (datetime, schedule title)
@@ -81,22 +90,33 @@ def getNextScheduleTime(self):
         nextScheduleTime = None
         nextScheduleTitle = None
         allPossibleTimes = sorted(allPossibleTimes)
-
         for timeObj, scheduleTitle in allPossibleTimes:
-            if(datetime.now().time() < timeObj.time): #the time is after now
-                if(nextScheduleTime):
-                    if (timeObj.time < nextScheduleTime.time):
+            compareTimes = False
+            if(last_execution):
+                if (last_execution.date() == datetime.now().date()):
+                    if(timeObj.time.hour != last_execution.hour or timeObj.time.minute != last_execution.minute):
+                        if(datetime.now().time() < timeObj.time and last_execution.time() < timeObj.time): #the time is after now
+                            compareTimes = True
+                else:
+                    compareTimes = True
+            else:
+                compareTimes = True
+
+            if(compareTimes):
+                if (datetime.now().time() < timeObj.time):  # the time is after now
+                    if (nextScheduleTime):
+                        if (timeObj.time < nextScheduleTime.time):
+                            nextScheduleTime = timeObj
+                            nextScheduleTitle = scheduleTitle
+                    else:
                         nextScheduleTime = timeObj
                         nextScheduleTitle = scheduleTitle
-                else:
-                    nextScheduleTime = timeObj
-                    nextScheduleTitle = scheduleTitle
 
         if(nextScheduleTime == None):
             nextScheduleTime, nextScheduleTitle = allPossibleTimes[0]
 
         if(nextScheduleTime.time < datetime.now().time()): #Tomorrow
-            nextSchedule = datetime.now() + datetime.timedelta(days=1)
+            nextSchedule = datetime.now() + timedelta(days=1)
             return (nextSchedule.replace(hour=nextScheduleTime.time.hour, minute=nextScheduleTime.time.minute), nextScheduleTitle)
         else: #Today
             nextSchedule = datetime.now()

Backend/utils/api/views/ConstanceView.py

@@ -24,18 +24,32 @@ def __getAppSymbol(self):
         except:
             return "Error"
 
+    def __getAppSymbolSmall(self):
+        try:
+            return config.app_symbol_small
+        except:
+            return "Error"
+
     def __getTitle(self):
         try:
             return config.site_name
         except:
             return "Error"
 
+    def __getShowDefaultHome(self):
+        try:
+            return config.show_default_home
+        except:
+            return "Error"
+
     @detail_route(methods=['get'])
     def getSettings(self, request, *args, **kwargs):
         response = {}
 
         response["title"] = self.__getTitle()
         response["footer"] = self.__getFooter()
         response["appSymbol"] = self.__getAppSymbol()
+        response["appSymbolSmall"] = self.__getAppSymbolSmall()
+        response["showDefaultHome"] = self.__getShowDefaultHome()
 
         return Response(response)