Working trapi 1.4 verision with legacy trapi_model.

Dockerfile

@@ -13,7 +13,7 @@ WORKDIR /usr/src/chp_api
 #	&& apt-get install -y git python3-pip python3-dev
 #dos2unix
 
-RUN git clone --single-branch --branch master https://github.com/di2ag/trapi_model.git
+RUN git clone --single-branch --branch pydantic-integration-yakaboskic https://github.com/di2ag/trapi_model.git
 RUN git clone --single-branch --branch master https://github.com/di2ag/chp_utils.git
 RUN git clone --single-branch --branch master https://github.com/di2ag/chp_look_up.git
 RUN git clone --single-branch --branch master https://github.com/di2ag/gene-specificity.git

chp_api/chp_api/settings.py

@@ -45,8 +45,6 @@
 ]
 
 INSTALLED_CHP_APPS = [
-    'chp_look_up',
-#    'chp_learn',
     'gene_specificity',
     ]
 
@@ -55,7 +53,7 @@
         ]
 
 # CHP Versions
-#VERSIONS = {app_name: app.__version__ for app_name, app in [(app_name, import_module(app_name)) for app_name in INSTALLED_CHP_APPS + OTHER_APPS]}
+VERSIONS = {app_name: app.__version__ for app_name, app in [(app_name, import_module(app_name)) for app_name in INSTALLED_CHP_APPS + OTHER_APPS]}
 
 # Sets up installed apps relevent to django 
 INSTALLED_APPS = INSTALLED_BASE_APPS + INSTALLED_CHP_APPS

chp_api/dispatcher/admin.py

@@ -1,6 +1,7 @@
 from django.contrib import admin
 
-from .models import App, ZenodoFile
+from .models import App, ZenodoFile, DispatcherSettings
 
 admin.site.register(App)
 admin.site.register(ZenodoFile)
+admin.site.register(DispatcherSettings)

chp_api/dispatcher/base.py

@@ -9,7 +9,7 @@
 from collections import defaultdict
 
 from .curie_database import merge_curies_databases, CurieDatabase
-from .models import Transaction, App
+from .models import Transaction, App, DispatcherSettings
 
 from chp_utils.trapi_query_processor import BaseQueryProcessor
 from trapi_model.meta_knowledge_graph import MetaKnowledgeGraph, merge_meta_knowledge_graphs
@@ -65,13 +65,15 @@ def get_curies(self):
         return merge_curies_databases(curies_dbs)
 
     def get_meta_knowledge_graph(self):
+        # Get current trapi and biolink versions
+        dispatcher_settings = DispatcherSettings.load()
         meta_kgs = []
         for app, app_name in zip(APPS, settings.INSTALLED_CHP_APPS):
             app_db_obj = App.objects.get(name=app_name)
             # Load location from uploaded Zenodo files
             if app_db_obj.meta_knowledge_graph_zenodo_file:
                 meta_kg = app_db_obj.meta_knowledge_graph_zenodo_file.load_file(base_url="https://sandbox.zenodo.org/api/records")
-                meta_kg = MetaKnowledgeGraph.load('1.3', None, meta_knowledge_graph=meta_kg)
+                meta_kg = MetaKnowledgeGraph.load(dispatcher_settings.trapi_version, None, meta_knowledge_graph=meta_kg)
             # Load default location    
             else:
                 get_app_meta_kg_fn = getattr(app, 'get_meta_knowledge_graph')
@@ -275,14 +277,15 @@ def add_logs_from_query_list(self, target_query, query_list):
             target_query.logger.add_logs(query.logger.to_dict())
         return target_query
 
-    def add_transaction(self, response, chp_app='dispatcher'):
+    def add_transaction(self, response, app_name='dispatcher'):
+        app_db_obj = App.objects.get(name=app_name)
         # Save the transaction
         transaction = Transaction(
             id = response.id,
             status = response.status,
             query = response.to_dict(),
             versions = settings.VERSIONS,
-            chp_app = chp_app,
+            chp_app = app_db_obj,
         )
         transaction.save()
 

chp_api/dispatcher/migrations/0006_dispatchersettings.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.2 on 2023-05-01 16:47
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('dispatcher', '0005_zenodofile_remove_app_curies_file_and_more'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='DispatcherSettings',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('trapi_version', models.CharField(default='1.4', max_length=28)),
+            ],
+            options={
+                'abstract': False,
+            },
+        ),
+    ]

chp_api/dispatcher/models.py

@@ -40,3 +40,26 @@ class Transaction(models.Model):
     versions = models.JSONField(default=dict)
     chp_app = models.ForeignKey(App, on_delete=models.CASCADE, null=True, blank=True)
 
+
+class Singleton(models.Model):
+
+    class Meta:
+        abstract = True
+
+    def save(self, *args, **kwargs):
+        self.pk = 1
+        super(Singleton, self).save(*args, **kwargs)
+
+    def delete(self, *args, **kwargs):
+        pass
+
+    @classmethod
+    def load(cls):
+        obj, _ = cls.objects.get_or_create(pk=1)
+        return obj
+
+class DispatcherSettings(Singleton):
+    trapi_version = models.CharField(max_length=28, default='1.4')
+
+    def __str__(self):
+        return 'settings'

chp_api/dispatcher/scripts/load_db_apps.py

@@ -8,3 +8,8 @@ def run():
         app_db_obj, created = App.objects.get_or_create(name=app_name)
         if created:
             app_db_obj.save()
+
+    # Create a dummy app for the dispatcher
+    app_db_obj, created = App.objects.get_or_create(name='dispatcher')
+    if created:
+        app_db_obj.save()

chp_api/dispatcher/urls.py

@@ -25,14 +25,6 @@
     path('meta_knowledge_graph/', views.meta_knowledge_graph.as_view()),
     path('curies/', views.curies.as_view()),
     path('versions/', views.versions.as_view()),
-    path('v1.1/query/', views.query.as_view(trapi_version='1.1')),
-    path('v1.1/meta_knowledge_graph/', views.meta_knowledge_graph.as_view()),
-    path('v1.1/curies/', views.curies.as_view(trapi_version='1.1')),
-    path('v1.1/versions/', views.versions.as_view(trapi_version='1.1')),
-    path('v1.2/query/', views.query.as_view(trapi_version='1.2')),
-    path('v1.2/meta_knowledge_graph/', views.meta_knowledge_graph.as_view(trapi_version='1.2')),
-    path('v1.2/curies/', views.curies.as_view(trapi_version='1.2')),
-    path('v1.2/versions/', views.versions.as_view(trapi_version='1.2')),
     path('transactions/', views.TransactionList.as_view(), name='transaction-list'),
     path('recent/', views.RecentTransactionList.as_view(), name='recent-transaction-list'),
     path('transactions/<str:pk>/', views.TransactionDetail.as_view(), name='transactions-detail')

chp_api/dispatcher/views.py

@@ -5,7 +5,7 @@
 from datetime import datetime, timedelta
 
 from .base import Dispatcher
-from .models import Transaction
+from .models import Transaction, DispatcherSettings
 from .serializers import TransactionListSerializer, TransactionDetailSerializer
 
 from django.http import HttpResponse, JsonResponse
@@ -18,19 +18,24 @@
 
 
 class query(APIView):
-    trapi_version = '1.3'
-    def __init__(self, trapi_version='1.3', **kwargs):
-        self.trapi_version = trapi_version
-        super(query, self).__init__(**kwargs)
-
+
     def post(self, request):
+        # Get current trapi and biolink versions
+        dispatcher_settings = DispatcherSettings.load()
+
         if request.method == 'POST':
             # Initialize Dispatcher
-            dispatcher = Dispatcher(request, self.trapi_version)
+            dispatcher = Dispatcher(
+                    request,
+                    dispatcher_settings.trapi_version,
+                    )
             # Process Query
             query = None
             try:
-                query = dispatcher.process_request(request, trapi_version=self.trapi_version)
+                query = dispatcher.process_request(
+                        request,
+                        trapi_version=dispatcher_settings.trapi_version,
+                        )
             except Exception as e:
                 if 'Workflow Error' in str(e):
                     return dispatcher.process_invalid_workflow(request, str(e))
@@ -40,45 +45,51 @@ def post(self, request):
             return dispatcher.get_response(query)
 
 class curies(APIView):
-    trapi_version = '1.3'
-    def __init__(self, trapi_version='1.3', **kwargs):
-        self.trapi_version = trapi_version
-        super(curies, self).__init__(**kwargs)
 
     def get(self, request):
+        # Get current trapi and biolink versions
+        dispatcher_settings = DispatcherSettings.load()
+
         if request.method == 'GET':
             # Initialize dispatcher
-            dispatcher = Dispatcher(request, self.trapi_version)
+            dispatcher = Dispatcher(
+                    request,
+                    dispatcher_settings.trapi_version,
+                    )
 
             # Get all chp app curies
             curies_db = dispatcher.get_curies()
             return JsonResponse(curies_db)
 
 class meta_knowledge_graph(APIView):
-    trapi_version = '1.3'
-    def __init__(self, trapi_version='1.3', **kwargs):
-        self.trapi_version = trapi_version
-        super(meta_knowledge_graph, self).__init__(**kwargs)
-
+
     def get(self, request):
+        # Get current trapi and biolink versions
+        dispatcher_settings = DispatcherSettings.load()
+
         if request.method == 'GET':
             # Initialize Dispatcher
-            dispatcher = Dispatcher(request, self.trapi_version)
+            dispatcher = Dispatcher(
+                    request,
+                    dispatcher_settings.trapi_version,
+                    )
 
             # Get merged meta KG
             meta_knowledge_graph = dispatcher.get_meta_knowledge_graph()
             return JsonResponse(meta_knowledge_graph.to_dict())
 
 class versions(APIView):
-    trapi_version = '1.3'
-    def __init__(self, trapi_version='1.3', **kwargs):
-        self.trapi_version = trapi_version
-        super(version, self).__init__(**kwargs)
 
     def get(self, request):
+        # Get current trapi and biolink versions
+        dispatcher_settings = DispatcherSettings.load()
+
         if request.method == 'GET':
             # Initialize Dispatcher
-            dispatcher = Dispatcher(request, self.trapi_version)
+            dispatcher = Dispatcher(
+                    request,
+                    dispatcher_settings.trapi_version,
+                    )
         return JsonResponse(dispatcher.get_versions())
 
 class TransactionList(mixins.ListModelMixin, generics.GenericAPIView):

dev-deployment-script

@@ -6,6 +6,9 @@ docker compose up -d
 
 docker compose run chp-api python3 manage.py migrate
 
+# Load apps
+docker compose run chp-api python3 manage.py runscript load_db_apps
+
 docker compose run --user root chp-api python3 manage.py collectstatic --noinput
 
 

gs-sample.json

@@ -0,0 +1,31 @@
+{
+  "message": {
+    "query_graph": {
+      "edges": {
+        "e0": {
+          "object": "n1",
+          "predicates": [
+            "biolink:expressed_in"
+          ],
+          "subject": "n0"
+        }
+      },
+      "nodes": {
+        "n0": {
+          "categories": [
+            "biolink:Gene",
+            "biolink:Protein"
+          ]
+        },
+        "n1": {
+          "categories": [
+            "biolink:GrossAnatomicalStructure"
+          ],
+          "ids": [
+            "UBERON:0000458"
+          ]
+        }
+      }
+    }
+  }
+}