Merge branch 'development' into production

Former-commit-id: 897792337eec1edf41625c36b9209b0452a734bd [formerly f05671f8579a368f06aa57f5b94e2b3116692704]
Former-commit-id: 43793317a13b531e3c9cd68b8c0137332e372698

Dockerfile

-FROM andimajore/miniconda3_lunar
+FROM andimajore/miniconda3_mantic
 
 WORKDIR /usr/src/drugstone/
 
@@ -10,8 +10,8 @@ ENV LANG=C.UTF-8
 RUN apt update && apt upgrade -y
 RUN apt install -y supervisor nginx libgtk-3-dev
 
-RUN conda install -y conda python=3.8
-#RUN conda install -c conda-forge -y graph-tool=2.46
+RUN conda install -y conda python=3.9
+
 RUN conda install -c conda-forge -y graph-tool=2.55
 
 RUN pip install gunicorn

drugstone/models.py

@@ -317,10 +317,14 @@ class ProteinProteinInteraction(models.Model):
 class ProteinDrugInteraction(models.Model):
     id = models.BigAutoField(primary_key=True)
     pdi_dataset = models.ForeignKey(
-        PDIDataset, null=True, on_delete=models.CASCADE, related_name='pdi_dataset_relation')
-    protein = models.ForeignKey('Protein', on_delete=models.CASCADE)
-    drug = models.ForeignKey('Drug', on_delete=models.CASCADE)
-    actions = models.CharField(max_length=255, default='[]')
+        PDIDataset,
+        null=True,
+        on_delete=models.CASCADE,
+        related_name="pdi_dataset_relation",
+    )
+    protein = models.ForeignKey("Protein", on_delete=models.CASCADE)
+    drug = models.ForeignKey("Drug", on_delete=models.CASCADE)
+    actions = models.CharField(max_length=255, default="[]")
 
     class Meta:
         unique_together = ("pdi_dataset", "protein", "drug")
@@ -329,7 +333,12 @@ class ProteinDrugInteraction(models.Model):
         return f"{self.pdi_dataset}-{self.protein}-{self.drug}"
 
     def __eq__(self, other):
-        return self.pdi_dataset_id == other.pdi_dataset_id and self.protein_id == other.protein_id and self.drug_id == other.drug_id and self.actions == other.actions
+        return (
+            self.pdi_dataset_id == other.pdi_dataset_id
+            and self.protein_id == other.protein_id
+            and self.drug_id == other.drug_id
+            and self.actions == other.actions
+        )
 
     def __ne__(self, other):
         return not self.__eq__(other)

drugstone/serializers.py

@@ -2,20 +2,31 @@
 import json
 from rest_framework import serializers
 from drugstone import models
-from drugstone.models import Protein, Task, Drug, ProteinDrugInteraction, \
-    Tissue, ProteinProteinInteraction, Network, ProteinDisorderAssociation, Disorder, DrugDisorderIndication
+from drugstone.models import (
+    Protein,
+    Task,
+    Drug,
+    ProteinDrugInteraction,
+    Tissue,
+    ProteinProteinInteraction,
+    Network,
+    ProteinDisorderAssociation,
+    Disorder,
+    DrugDisorderIndication,
+)
 
 
 class PDIDatasetSerializer(serializers.ModelSerializer):
     class Meta:
         model = models.PDIDataset
-        fields = '__all__'
+        fields = "__all__"
 
 
 class PPIDatasetSerializer(serializers.ModelSerializer):
     class Meta:
         model = models.PPIDataset
-        fields = '__all__'
+        fields = "__all__"
+
 
 
 class PDisDatasetSerializer(serializers.ModelSerializer):
@@ -177,7 +188,7 @@ class ProteinDrugInteractionSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = ProteinDrugInteraction
-        fields = ['dataset', 'protein', 'drug', 'actions']
+        fields = ["dataset", "protein", "drug", "actions"]
 
 
 class ProteinDisorderAssociationSerializer(serializers.ModelSerializer):

drugstone/settings/settings.py

@@ -30,6 +30,7 @@ ALLOWED_HOSTS = [
     "localhost",
     "127.0.0.1",
     "drugstone-backend.zbh.uni-hamburg.de",
+    "drugstone-dev-api.zbh.uni-hamburg.de",
     "drugst.one",
 ]
 

requirements.txt

@@ -26,7 +26,6 @@ pyflakes==3.0.1
 python-dateutil==2.8.1
 pytz==2021.3
 redis==4.3.6
-requests==2.28.1
 rq==1.11.1
 six==1.15.0
 sqlalchemy==1.3.23