Merge branch 'master' of github.com:phyloviz/phyloDB

phyloviz · Dec 31, 2023 · 66c1fbf · 66c1fbf
2 parents 2523912 + 1f4f7ea
commit 66c1fbf
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Showing 2 changed files with 13 additions and 33 deletions.
diff --git a/docker/start-docker.sh b/docker/start-docker.sh
@@ -82,6 +82,10 @@ fi
 # Passing file contents to Neo4j container cypher via 'cat':
 # https://neo4j.com/docs/operations-manual/current/docker/operations/
 
+echo "[$SCRIPT_NAME][INFO] - waiting for containers..."
+sleep 30
+echo "[$SCRIPT_NAME][INFO] - initializing data..."
+
 # Initialize Neo4j PhyloDB schema (creates indices and properties).
 SCHEMA_QUERY_FILE="$PROJ_ROOT/scripts/init/init_schema.cypher"
 cat $SCHEMA_QUERY_FILE | docker exec --interactive phylodb-neo4j sh -c "cypher-shell -u neo4j -p password" >/dev/null 2>&1
@@ -90,4 +94,6 @@ cat $SCHEMA_QUERY_FILE | docker exec --interactive phylodb-neo4j sh -c "cypher-s
 DATA_QUERY_FILE="$PROJ_ROOT/scripts/init/init_data.cypher"
 cat $DATA_QUERY_FILE | docker exec --interactive phylodb-neo4j sh -c "cypher-shell -u neo4j -p password" >/dev/null 2>&1
 
+echo "[$SCRIPT_NAME][INFO] - done."
+
 popd
diff --git a/scripts/example/example.sh b/scripts/example/example.sh
@@ -156,23 +156,9 @@ curl -v --location --request POST 'http://localhost:8080/projects?provider=googl
     "users": [{"id": "aplf@tecnico.pt", "provider": "google"}]
   }'
 
-
-if [ -z "$PROJECT" ]; then cat << EOF
-Error: PROJECT is not defined. Please follow these steps:
-
-# TODO
-#
-# Then, execute
-#
-# > export PROJECT="YOUR_PROJECT_ID"
-#
-# and run this script again.
-EOF
-  exit 1
-else
-  echo "ok PROJECT is defined."
-fi
-
+# Set the project id.
+PROJECT=$(curl -s --location --request GET 'http://localhost:8080/projects?provider=google' --header "Authorization: Bearer $TOKEN" | python3 -c "import sys, json; print(json.load(sys.stdin)[0]['id'])")
+echo "Project: $PROJECT"
 
 log_checkpoint "List all datasets:"
 echo -n "Datasets: "
@@ -190,21 +176,9 @@ curl -v --location --request POST "http://localhost:8080/projects/$PROJECT/datas
 	  "description": "Example dataset"
   }'
 
-if [ -z "$DATASET" ]; then cat << EOF
-Error: DATASET is not defined. Please follow these steps:
-
-# TODO
-#
-# Then, execute
-#
-# > export DATASET="YOUR_DATASET_ID"
-#
-# and run this script again.
-EOF
-  exit 1
-else
-  echo "ok DATASET is defined."
-fi
+# Set dataset id:
+DATASET=$(curl -s --location --request GET "http://localhost:8080/projects/$PROJECT/datasets?provider=google" --header "Authorization: Bearer $TOKEN" | python3 -c "import sys, json; print(json.load(sys.stdin)[0]['id'])")
+echo "Dataset: $DATASET"
 
 log_checkpoint "Load profiles:"
 curl -v --location --request POST "http://localhost:8080/projects/$PROJECT/datasets/$DATASET/profiles/files?provider=google" \
@@ -239,7 +213,7 @@ echo -n "Inferences: "
 curl --location --request GET "http://localhost:8080/projects/$PROJECT/datasets/$DATASET/inferences?provider=google" \
   --header "Authorization: Bearer $TOKEN"
 echo
-INFERENCE="CHANGE_ME"
+INFERENCE=$(curl -s --location --request GET "http://localhost:8080/projects/$PROJECT/datasets/$DATASET/inferences?provider=google" --header "Authorization: Bearer $TOKEN" | python3 -c "import sys, json; print(json.load(sys.stdin)[0]['id'])")
 echo -n "Inference: "
 curl --location --request GET "http://localhost:8080/projects/$PROJECT/datasets/$DATASET/inferences/$INFERENCE?provider=google" \
   --header "Authorization: Bearer $TOKEN"