Feature/local development

Makefile

@@ -6,6 +6,8 @@ DOCKER_OWNER = helxplatform
 DOCKER_APP	 = tranql
 DOCKER_TAG   = ${VERSION}
 DOCKER_IMAGE = ${DOCKER_OWNER}/${DOCKER_APP}:$(DOCKER_TAG)
+TEST_REDIS_DUMP_FILE = "https://stars.renci.org/var/kgx_data/v3.0/roger-mini.rdb"
+
 
 .DEFAULT_GOAL = help
 
@@ -58,3 +60,15 @@ build:
 publish:
 	docker tag ${DOCKER_IMAGE} ${DOCKER_REPO}/${DOCKER_IMAGE}
 	docker push ${DOCKER_REPO}/${DOCKER_IMAGE}
+
+#download: Downloads example dataset for redis
+download:
+	mkdir -p redis_data/
+	if [ ! -f "./redis_data/dump.rdb" ] ; then \
+	wget ${TEST_REDIS_DUMP_FILE} -O redis_data/dump.rdb; \
+	fi
+
+#run.local: seeds redis with data, builds web page and runs tranql docker container
+run.local: download
+	docker-compose up -d
+	cd src/tranql/web; npm start;

QUICKSTART.md

@@ -1,8 +1,18 @@
+## Setting up server
 
-## Setting up the Frontend
+Note: For building react app nodejs and npm are required.
 
-1. cd web
-1. npm install
-1. node --max-old-space-size=4000 ./node_modules/react-scripts/scripts/build.js
-1. cd ..
-1. cp -r web/build/static/ src/tranql/static
+1. Install node js dependencies.
+```shell
+make install.npm
+```
+2. Runs Tranql in a docker container, with reload enabled for the web server. UI is not reloaded on change but one can start 
+cd
+```shell
+make run.local 
+```
+
+3. Browse to 
+    1. [Tranql UI](http://localhost:8001) 
+    2. [Openapi Swagger UI](http://localhost:8001/apidocs)
+    3. [Tranql UI served from Nodejs](http://localhost:3000) 

dev-schema.yaml

@@ -0,0 +1,16 @@
+---
+doc : |
+  The Translator schema aggregates reasoner schemas. Reasoner schemas
+  describe transitions between biolink-model types. These transitions are
+  expressed as predicates, also from the biolink-model.
+schema:
+  redis:
+    doc: |
+      Roger is a knowledge graph built by aggregeting several kgx formatted knowledge graphs from several sources.
+    url: "redis:test"
+    redis: true
+    redis_connection_params:
+      host: redis_graph
+      port: 6379
+        # SET USERNAME and PASSWORD
+        # via ROGER_USERNAME , ROGER_PASSWORD Env vars (i.e capitialize service name)

docker-compose.yml

@@ -1,18 +1,18 @@
 version: "3"
 services:
-  backplane:
-    image: cschreep/tranql:0.2.dev0
-#    build:
-#      dockerfile: Dockerfile
-#      context: .
-    ports:
-      - "${BACKPLANE_PORT}:${BACKPLANE_PORT}"
-    command: gunicorn --workers=2 --bind=0.0.0.0:$BACKPLANE_PORT --name=backplane --timeout=600 tranql.backplane.server:app
   tranql:
-    image: cschreep/tranql:0.2.dev0
-#    build:
-#      dockerfile: Dockerfile
-#      context: .
+    build:
+      dockerfile: Dockerfile
+      context: .
     ports:
-      - "${APP_PORT}:${APP_PORT}"
-    command: gunicorn --workers=2 --bind=0.0.0.0:$APP_PORT --name=tranql --timeout=600 tranql.api:app
+      - "8001:8001"
+    command: gunicorn --workers=1 --bind=0.0.0.0:8001 --name=tranql --timeout=600 --reload tranql.api:app
+    environment:
+      - SCHEMA_CONFIG_PATH=/home/tranql/dev-schema.yaml
+    volumes:
+      - ./src:/home/tranql/tranql/src
+      - ./dev-schema.yaml:/home/tranql/dev-schema.yaml
+  redis_graph:
+    image: redislabs/redisgraph
+    volumes:
+      - ./redis_data:/data

src/tranql/conf/schema.yaml

@@ -63,7 +63,7 @@ schema:
     url: "redis:test"
     redis: true
     redis_connection_params:
-      host: localhost
-      port: 6380
+      host: redis_graph
+      port: 6379
         # SET USERNAME and PASSWORD
         # via ROGER_USERNAME , ROGER_PASSWORD Env vars (i.e capitialize service name)

src/tranql/tranql_schema.py

@@ -238,7 +238,9 @@ def __init__(self, backplane, use_registry, tranql_config, skip_redis=False):
 
         """ Load the schema, a map of reasoner systems to maps of their schemas. """
         self.config = None
-        config_file = os.path.join(os.path.dirname(__file__), "conf", "schema.yaml")
+        config_file = os.environ.get("SCHEMA_CONFIG_PATH",
+                                    os.path.join(os.path.dirname(__file__), "conf", "schema.yaml")
+                                    )
         with open(config_file) as stream:
             self.config = yaml.safe_load(stream)