Merge pull request #408 from matthiaskoenig/develop

PKDB-v0.6.1 changes

backend/pkdb_app/_version.py

@@ -1,4 +1,4 @@
 """
 Definition of version string.
 """
-__version__ = "0.6.0"
+__version__ = "0.6.1"

backend/pkdb_app/analysis/pharmacokinetic.py

@@ -26,6 +26,7 @@ def f_pk(
     dose_unit="mg",
     vd_unit="L",
     bodyweight_unit="kg",
+    intervention_time = 0,
 ):
     """ Calculates all the pk parameters from given time course.
 
@@ -58,6 +59,9 @@ def f_pk(
     assert isinstance(c, np.ndarray)
     assert t.size == c.size
 
+    # caculate all results relative to the intervention time
+    t = t + intervention_time
+
     # calculate pk
     auc = _auc(t, c)
     tmax, cmax = _max(t, c)

backend/pkdb_app/categorials/behaviours.py

@@ -166,22 +166,21 @@ def normalize(self):
         factor, unit = self.remove_substance_dimension()
 
         # remove substance unit
+
         if unit and self.unit:
             if ureg(unit) != ureg(self.unit):
                 for key, value in self.norm_fields.items():
                     if value is not None:
                         setattr(self, key, value*factor)
                 self.unit = unit
 
-            else:
-                self.unit = str(ureg(self.unit).u)
+            #else:
+            #    self.unit = str(ureg(self.unit).u)
 
         # normalization
         if not self.is_norm:
             for key, value in self.norm_fields.items():
                 if not value is None:
                     setattr(self, key, self.measurement_type.normalize(value, self.unit).magnitude)
-            self.unit = str(self.measurement_type.norm_unit(self.unit))
-
-
 
+            self.unit = str(self.measurement_type.norm_unit(self.unit))

backend/pkdb_app/categorials/models.py

@@ -5,13 +5,14 @@
 """
 import pint
 from pint import UndefinedUnitError
+import numpy as np
+
 from numbers import Number
 
 from django.db import models
 from pkdb_app.categorials.managers import ChoiceManager
 from pkdb_app.users.models import User
 from pkdb_app.utils import CHAR_MAX_LENGTH, create_choices, _validate_requried_key
-
 ureg = pint.UnitRegistry()
 
 # Units
@@ -241,8 +242,10 @@ def validate_numeric(self, data):
                         rule = False
 
                     if rule:
-                            raise ValueError({field: f"Numeric values need to be postive for all measurement types but"
-                                      f" <{CAN_NEGATIVE_MEASUREMENT_TYPE}>.", "detail":data})
+                            raise ValueError(
+                                {field: f"Numeric values need to be positive (>=0) "
+                                        f"for all measurement types except "
+                                        f"<{CAN_NEGATIVE_MEASUREMENT_TYPE}>.", "detail":data})
 
     def validate_complete(self, data):
         # check unit
@@ -258,8 +261,8 @@ def validate_complete(self, data):
         if time_unit:
             self.validate_time_unit(time_unit)
 
-        cumulative_measurement_types = ["cumulative amount","cumulative metabolic ratio"]
-        if self.name in cumulative_measurement_types:
+        time_requried_measurement_types = ["cumulative amount","cumulative metabolic ratio","recovery"]
+        if self.name in time_requried_measurement_types:
             details = f"for measurement type `{self.name}`"
             _validate_requried_key(data,"time", details=details)
             _validate_requried_key(data,"time_unit", details=details)

backend/pkdb_app/interventions/views.py

@@ -49,7 +49,7 @@ class ElasticInterventionViewSet(AccessView):
     pagination_class = CustomPagination
     lookup_field = "id"
     filter_backends = [FilteringFilterBackend,IdsFilterBackend,OrderingFilterBackend,MultiMatchSearchFilterBackend]
-    search_fields = ('name','measurement_type','substance.name',"form","application",'route','time_unit','normed')
+    search_fields = ('name','study','access','measurement_type','substance',"form","application",'route','time_unit')
     multi_match_search_fields = {field: {"boost": 1} for field in search_fields}
     multi_match_options = {
         'operator': 'and'
@@ -60,5 +60,5 @@ class ElasticInterventionViewSet(AccessView):
                        'choice':'choice.raw',
                        'normed':'normed',
                        'application':'application.raw',
-                       'substance':'substance.name',
+                       'substance':'substance.raw',
                        'value':'value'}

backend/pkdb_app/outputs/managers.py

@@ -5,7 +5,6 @@
 from django.db import models
 from django.apps import apps
 import time
-import pandas as pd
 import numpy as np
 
 from pkdb_app.categorials.models import MeasurementType
@@ -110,6 +109,7 @@ def create(self, *args, **kwargs):
                                "vd":MeasurementType.objects.get(name="vd"),
                                }
                 outputs = []
+
                 for key in ["auc", "aucinf", "cl", "cmax", "kel", "thalf", "vd","tmax"]:
                     pk_unit = pk[f"{key}_unit"]
                     if not np.isnan(pk[key]):

backend/pkdb_app/outputs/models.py

@@ -9,7 +9,7 @@
 from django.core.exceptions import ObjectDoesNotExist, MultipleObjectsReturned
 from django.db import models
 from django.contrib.postgres.fields import ArrayField
-from pkdb_app.categorials.models import MeasurementType
+from pkdb_app.categorials.models import MeasurementType, ureg
 from pkdb_app.interventions.models import Intervention
 
 from ..utils import CHAR_MAX_LENGTH, create_choices
@@ -56,8 +56,7 @@ def outputs(self):
     @property
     def outputs_normed(self):
         outputs = self.outputs.filter(normed=True)
-        outputs_timecourses = Output.objects.filter(timecourse__in=self.timecourses.all())
-        return outputs | outputs_timecourses
+        return outputs
 
     @property
     def count_outputs(self):
@@ -334,8 +333,26 @@ def add_error_measures(self):
                 if isinstance(cv, np.ndarray):
                     self.cv = list(cv)
 
+
     def normalize(self):
-        """Normalizes timecourse."""
+        '''Normalizes timecourse.'''
+
+
+        factor, unit = self.remove_substance_dimension()
+
+        if unit:
+            if ureg(unit) != ureg(self.unit):
+                for key, value in self.norm_fields.items():
+                    if value is not None:
+
+                        list_norm_values = list(factor*np.array(value))
+                        setattr(self, key, list_norm_values)
+                self.unit = unit
+
+            else:
+                self.unit = str(ureg(self.unit).u)
+
+
 
         if not self.is_norm:
             for key, value in self.norm_fields.items():
@@ -352,6 +369,7 @@ def normalize(self):
             self.time = list(norm_times.m)
             self.time_unit = TIME_NORM_UNIT
 
+
     # for elastic search. NaNs are not allowed in elastic search
     @staticmethod
     def _any_not_json(value):
@@ -468,6 +486,10 @@ def get_pharmacokinetic_variables(self):
                 vd_unit = p_unit_dosing / p_unit_concentration
                 pk_dict["vd_unit"] = str(vd_unit)
                 pk_dict["dose"] = dosing.value
+                if dosing.time:
+                    pk_dict["intervention_time"] = (ureg(dosing.time_unit)*dosing.time).to(self.time_unit).magnitude
+
+
                 pk_dict["dose_unit"] = dosing.unit
 
         # bodyweight dependent values

backend/pkdb_app/serializers.py

@@ -288,10 +288,15 @@ def df_from_file(self, source, format, subset):
             if source.isnumeric():
                 pass
             else:
+                print("here I am")
+                print(type(source))
+
                 raise serializers.ValidationError(
                     {"source": f"<{str(source)}> is not existing", "detail": type(source)})
+
         else:
-            raise serializers.ValidationError({"source":f"<{str(source)}> is not existing","detail":type(source)})
+            raise serializers.ValidationError(
+                {"source":f"<{str(source)}> is not existing","detail":type(source)})
         src = DataFile.objects.get(pk=source)
         try:
             df = pd.read_csv(

backend/pkdb_app/studies/serializers.py

@@ -374,14 +374,16 @@ def create_relations(self, study, related):
             if related["comments"]:
                 create_multiple(study, related["comments"], "comments")
 
-        study.save()
 
         if "files" in related:
+            print(related["files"])
+
             study.files.clear()
             if related["files"]:
                 for file_pk in related["files"]:
                     study.files.add(file_pk)
-                study.save()
+
+        study.save()
 
         return study
 
@@ -440,8 +442,6 @@ class Meta:
 
     def get_pdf(self, obj):
         user = self.context["request"].user
-
-
         if get_study_file_permission(user,AttrDict(obj.study)):
             return obj.to_dict().get("pdf")
         else:

backend/pkdb_app/studies/views.py

@@ -163,9 +163,9 @@ def update_index_study(request):
         related_elastic = related_elastic_dict(study)
 
         for doc, instances in related_elastic.items():
-            study_related_instances = doc().search().filter("match",study=study.name)
-            if study_related_instances.count() > 0:
-                study_related_instances.delete()
+            #study_related_instances = doc().search().filter("term",study=study.name)
+            #if study_related_instances.count() > 0:
+            #    study_related_instances.delete()
 
             try:
                 action = data.get("action", 'index')

backend/pkdb_app/users/permissions.py

@@ -107,6 +107,7 @@ def get_study_permission(user,obj):
 
 
 def get_study_file_permission(user,obj):
+    allow_user_get = False
     if isinstance(obj, AttrDict) or isinstance(obj, DictionaryProxy):
         username = user.username
         curator_usernames = [curator["username"] for curator in obj.curators]

backend/pkdb_app/utils.py

@@ -118,6 +118,7 @@ def create_multiple_bulk_normalized(notnormalized_instances, model_class):
         return model_class.objects.bulk_create([initialize_normed(notnorm_instance) for notnorm_instance in notnormalized_instances])
 
 def initialize_normed(notnorm_instance):
+
     norm = copy.copy(notnorm_instance)
     norm.pk = None
     norm.normed = True

frontend/src/components/Navigation.vue

@@ -1,14 +1,7 @@
 <template>
     <v-toolbar id="navigation" class="fixed-nav-bar" flat dense>
-        <!--
-        <v-toolbar-side-icon></v-toolbar-side-icon>
-        <v-toolbar-title class="white--text">PK-DB</v-toolbar-title>
-        -->
-        <v-btn icon to="/" title="Home">
-            <v-icon>{{ icon('home') }}</v-icon>
-        </v-btn>
-        <!--<v-spacer></v-spacer>-->
 
+        <v-btn icon to="/" title="Home"><v-icon>{{ icon('home') }}</v-icon></v-btn>
         <v-btn icon to="/studies" title="Studies"><v-icon>{{ icon('studies') }}</v-icon></v-btn>
         <v-btn icon to="/groups" title="Groups"><v-icon>{{ icon('groups') }}</v-icon></v-btn>
         <v-btn icon to="/individuals" title="Individuals"><v-icon>{{ icon('individuals') }}</v-icon></v-btn>
@@ -18,28 +11,22 @@
         <v-btn icon to="/references" title="References"><v-icon>{{ icon('references') }}</v-icon></v-btn>
 
         <v-spacer></v-spacer>
-        <!--user -->
-        <v-chip v-if="this.$store.state.username" flat>
-            <user-avatar :username="this.$store.state.username"></user-avatar>
-            {{this.$store.state.username}}
-        </v-chip>
-
 
-        <v-dialog v-model="showUserDialog">
-            <template v-slot:activator="{on}">
-                    <v-btn icon v-on="on">
-                        <v-icon>{{ icon('account') }}</v-icon>
-                    </v-btn>
-            </template>
-            <user-login :dialog.sync="showUserDialog" ></user-login>
+        <!-- account -->
+        <v-chip v-if="username" flat title="Logout" @click.stop="dialog=true">
+            <user-avatar :username="username"></user-avatar>
+            {{ username }}
+        </v-chip>
+        <v-btn v-if="username==null" icon title="Login" @click.stop="dialog=true">
+            <v-icon>{{ icon('account') }}</v-icon>
+        </v-btn>
+        <v-dialog v-model="dialog" max-width="500">
+            <user-login></user-login>
         </v-dialog>
 
-
+        <!-- links -->
         <v-btn icon to="/curation" title="Curation information"><v-icon>{{ icon('curation') }}</v-icon></v-btn>
         <v-btn icon :href="api_url" title="REST API"><v-icon>{{ icon('api') }}</v-icon></v-btn>
-        <!--
-        <v-btn icon to="/about" title="About PK-DB"><v-icon>{{ icon('about') }}</v-icon></v-btn>
-        -->
         <v-btn icon :href="admin_url" title="Django admin interface">
             <v-icon>{{ icon('admin') }}</v-icon>
         </v-btn>
@@ -55,14 +42,12 @@
 
     export default {
         name: 'Navigation',
-        data(){
-            return {
-                showUserDialog : false,
-            }
-        },
-        components: {UserLogin,
-
+        components: {
+            UserLogin,
         },
+        data: () => ({
+            dialog: false
+        }),
         computed: {
             // vuex store
             admin_url() {
@@ -72,6 +57,9 @@
 
                 return this.$store.state.endpoints.api;
             },
+            username(){
+                return this.$store.state.username
+            }
         },
         methods: {
             icon: function (key) {