LBR Portal POC

.gitignore

@@ -2,4 +2,7 @@
 .DS_Store
 node_modules
 __MACOSX
-dist
+dist
+idmapping.csv 
+sample.csv    
+summary.csv

Makefile

@@ -8,6 +8,9 @@ help:
 	@echo "  phase3         - Start Phase 3 deployment"
 	@echo "  stage-dev      - Start Stage development environment"
 	@echo ""
+	@echo "Data Management:"
+	@echo "  data-setup     - Upload dictionaries, register entities, and load data"
+	@echo ""
 	@echo "Conductor System Management:"
 	@echo "  down           - Gracefully shutdown all containers"
 	@echo "  reset          - DANGER: Remove all containers and volumes (DATA LOSS)"
@@ -45,6 +48,12 @@ stage-dev:
 	@echo "Starting Stage development environment..."
 	PROFILE=stageDev docker compose -f ./docker-compose.yml --profile stageDev up --attach conductor
 
+# Run data setup: upload dictionaries, register entities, and load data
+data-setup:
+	@echo "Starting data setup deployment..."
+	@echo "This will upload dictionaries to Lectern, register entities with Lyric, and load tabular data."
+	PROFILE=dataSetup docker compose -f ./docker-compose.yml --profile dataSetup up --attach data-setup
+
 # Gracefully shutdown all containers while preserving volumes
 down:
 	@echo "Shutting down all running containers..."
@@ -53,7 +62,7 @@ down:
 # Restart containers and run deployment scripts for a specific profile
 restart:
 	@echo "Restarting containers with fresh deployment..."
-	@read -p "Enter profile to restart (phase1, phase2, phase3, stageDev): " profile; \
+	@read -p "Enter profile to restart (phase1, phase2, phase3, stageDev, dataSetup): " profile; \
 	echo "Shutting down containers..."; \
 	PROFILE=$$profile docker compose -f ./docker-compose.yml --profile $$profile down; \
 	echo "Starting containers with profile $$profile..."; \
@@ -67,5 +76,4 @@ reset:
 		PROFILE=default docker compose -f ./docker-compose.yml --profile default down -v ; \
 	else \
 		echo "Operation cancelled"; \
-	fi
-
+	fi

README.md

@@ -29,6 +29,54 @@ make phase0
 
 The CLI will provide you with instructions on next steps.
 
+### Phase 2 Command Setup
+
+Install the CLI utilities:
+
+For Conductor:
+
+```bash
+cd apps/conductor
+npm ci
+npm install -g . 
+```
+
+If using configuration automation services install Composer
+
+```bash
+cd apps/composer
+npm ci
+npm install -g . 
+```
+
+Run:
+
+```bash
+make phase2
+```
+
+Then run the following commands to populate the portal with data:
+
+```bash
+# Upload consolidated dictionary
+conductor lecternUpload -s ./configs/lecternDictionaries/lbr-dictionary.json
+
+# Register entities with schema
+conductor lyricRegister -c idmapping --dict-name lbr-dictionary -v 1.0 -e idmapping
+conductor lyricRegister -c sample --dict-name lbr-dictionary -v 1.0 -e sample
+conductor lyricRegister -c summary --dict-name lbr-dictionary -v 1.0 -e summary
+
+# Upload tabular data
+conductor lyricUpload -d ./data/idmapping -c 1 --max-retries 100 --lyric-url http://pantrack.genomeinformatics.org/lyric
+conductor lyricUpload -d ./data/sample -c 2 --max-retries 100
+conductor lyricUpload -d ./data/summary -c 3 --max-retries 100
+
+# Index data
+conductor maestroIndex --repository-code idmapping
+conductor maestroIndex --repository-code sample
+conductor maestroIndex --repository-code summary
+```
+
 ## Development Phases
 
 Prelude is structured into four incremental phases: