Enhance example.sh to reduce hardcoding and improve troubleshootability

scripts/example/example.sh

@@ -1,26 +1,73 @@
+#!/bin/bash
 # API REQUEST EXAMPLES
 
+set -e
+
+cd "$(dirname "$0")"
+
+log_checkpoint() {
+  local message="$1"
+  echo
+  printf '%*s\n' "${COLUMNS:-$(tput cols)}" '' | tr ' ' -
+  echo "$message"
+  printf '%*s\n' "${COLUMNS:-$(tput cols)}" '' | tr ' ' -
+}
+
+log_checkpoint "Check server status:"
+URL="http://localhost:8080/"
+response="$(curl --write-out "%{http_code}" --silent --output /dev/null "$URL" || true)"
+if [ "$response" -eq 200 ] || [ "$response" -eq 301 ] || [ "$response" -eq 302 ]; then
+    echo "ok"
+else
+  cat << EOF
+Error: response ${response} at ${URL}. Please follow these steps:
+
+# From the root directory, run
+# > ./configure.sh
+#
+# and then
+# > ./docker/build-docker.sh
+# > ./docker/start-docker.sh
+EOF
+  exit 1
+fi
+
+
+if [ -z "$TOKEN" ]; then cat << EOF
+Error: TOKEN is not defined. Please follow these steps:
+
 # Access https://developers.google.com/oauthplayground/ with the account that
 # you added as admin in 'scripts/init/init_data.cypher', and click in 'Authorize
 # APIs' with the scope 'https://www.googleapis.com/auth/userinfo.email'. Or
 # select it in list.
 #
 # In step 2, click in 'Exchange authorization code for tokens' and copy your
 # own access token to the variable TOKEN below.
+#
+# Then, execute
+#
+# > export TOKEN="YOUR_ACCESS_TOKEN"
+#
+# and run this script again.
+EOF
+  exit 1
+else
+  echo "ok TOKEN is defined."
+fi
 
-TOKEN="CHANGE_ME"
+../init/make_init_data.cypher.sh
 
 # Let us try several requests:
 
-# List all users:
+log_checkpoint "List all users:"
 curl -v --location --request GET 'http://localhost:8080/users?provider=google' --header "Authorization: Bearer $TOKEN"
 
-# List all taxa
+log_checkpoint "List all taxa"
 echo -n "Taxa: "
 curl --location --request GET 'http://localhost:8080/taxa?provider=google' --header "Authorization: Bearer $TOKEN"
 echo
 
-# Create taxon:
+log_checkpoint "Create taxon:"
 curl -v --location --request PUT 'http://localhost:8080/taxa/bbacilliformis?provider=google' \
   --header 'Content-Type: application/json' \
   --header "Authorization: Bearer $TOKEN" \
@@ -29,17 +76,17 @@ curl -v --location --request PUT 'http://localhost:8080/taxa/bbacilliformis?prov
     "description": "Example taxon"
   }'
 
-# List all loci:
+log_checkpoint "List all loci:"
 echo -n "Loci: "
 curl --location --request GET 'http://localhost:8080/taxa/bbacilliformis/loci?provider=google' \
   --header "Authorization: Bearer $TOKEN"
 echo
 
-# Delete locus (mark deprecated):
+log_checkpoint "Delete locus (mark deprecated):"
 curl -v --location --request DELETE 'http://localhost:8080/taxa/bbacilliformis/loci/ftsZ?provider=google' \
   --header "Authorization: Bearer $TOKEN"
 
-# Create locus:
+log_checkpoint "Create locus:"
 for x in locus1 locus2 locus3 locus4 locus5 locus6 locus7; do
   curl -v --location --request PUT "http://localhost:8080/taxa/bbacilliformis/loci/$x?provider=google" \
     --header 'Content-Type: application/json' \
@@ -50,15 +97,15 @@ for x in locus1 locus2 locus3 locus4 locus5 locus6 locus7; do
     }";
 done
 
-# Load alleles:
+log_checkpoint "Load alleles:"
 for x in 1 2 3 4 5 6 7; do
   curl -v --location --request POST "http://localhost:8080/taxa/bbacilliformis/loci/locus${x}/alleles/files?provider=google" \
     --header 'Content-Type: multipart/form-data' \
     --header "Authorization: Bearer $TOKEN" \
     --form "file=@profiles_${x}.txt" ;
 done
 
-# List alleles:
+log_checkpoint "List alleles:"
 for x in 1 2 3 4 5 6 7; do
   echo -n "Alleles[locus${x}]: "
   curl --location --request GET "http://localhost:8080/taxa/bbacilliformis/loci/locus${x}/alleles?provider=google" \
@@ -71,7 +118,7 @@ curl --location --request GET "http://localhost:8080/taxa/bbacilliformis/loci/lo
   --header "Authorization: Bearer $TOKEN"
 echo
 
-# List all schemas:
+log_checkpoint "List all schemas:"
 echo -n "Schemas: "
 curl --location --request GET 'http://localhost:8080/taxa/bbacilliformis/schemas?provider=google' \
   --header "Authorization: Bearer $TOKEN"
@@ -81,7 +128,7 @@ curl --location --request GET 'http://localhost:8080/taxa/bbacilliformis/schemas
   --header "Authorization: Bearer $TOKEN"
 echo
 
-# Create schema:
+log_checkpoint "Create schema:"
 curl -v --location --request PUT "http://localhost:8080/taxa/bbacilliformis/schemas/mlst7?provider=google" \
   --header 'Content-Type: application/json' \
   --header "Authorization: Bearer $TOKEN" \
@@ -93,12 +140,12 @@ curl -v --location --request PUT "http://localhost:8080/taxa/bbacilliformis/sche
 	  "loci": ["locus1", "locus2", "locus3", "locus4", "locus5", "locus6", "locus7"]
   }';
 
-# List all projects:
+log_checkpoint "List all projects:"
 echo -n "Projects: "
 curl --location --request GET 'http://localhost:8080/projects?provider=google' --header "Authorization: Bearer $TOKEN"
 echo
 
-# Create project:
+log_checkpoint "Create project:"
 curl -v --location --request POST 'http://localhost:8080/projects?provider=google' \
   --header 'Content-Type: application/json' \
   --header "Authorization: Bearer $TOKEN" \
@@ -109,16 +156,31 @@ curl -v --location --request POST 'http://localhost:8080/projects?provider=googl
     "users": [{"id": "[email protected]", "provider": "google"}]
   }'
 
-# Set the project id.
-PROJECT="CHANGE_ME"
 
-# List all datasets:
+if [ -z "$PROJECT" ]; then cat << EOF
+Error: PROJECT is not defined. Please follow these steps:
+
+# TODO
+#
+# Then, execute
+#
+# > export PROJECT="YOUR_PROJECT_ID"
+#
+# and run this script again.
+EOF
+  exit 1
+else
+  echo "ok PROJECT is defined."
+fi
+
+
+log_checkpoint "List all datasets:"
 echo -n "Datasets: "
 curl --location --request GET "http://localhost:8080/projects/$PROJECT/datasets?provider=google" \
   --header "Authorization: Bearer $TOKEN"
 echo
 
-# Create dataset:
+log_checkpoint "Create dataset:"
 curl -v --location --request POST "http://localhost:8080/projects/$PROJECT/datasets?provider=google" \
   --header 'Content-Type: application/json' \
   --header "Authorization: Bearer $TOKEN" \
@@ -128,16 +190,29 @@ curl -v --location --request POST "http://localhost:8080/projects/$PROJECT/datas
 	  "description": "Example dataset"
   }'
 
-# Set dataset id:
-DATASET="CHANGE_ME"
+if [ -z "$DATASET" ]; then cat << EOF
+Error: DATASET is not defined. Please follow these steps:
 
-# Load profiles:
+# TODO
+#
+# Then, execute
+#
+# > export DATASET="YOUR_DATASET_ID"
+#
+# and run this script again.
+EOF
+  exit 1
+else
+  echo "ok DATASET is defined."
+fi
+
+log_checkpoint "Load profiles:"
 curl -v --location --request POST "http://localhost:8080/projects/$PROJECT/datasets/$DATASET/profiles/files?provider=google" \
   --header 'Content-Type: multipart/form-data' \
   --header "Authorization: Bearer $TOKEN" \
   --form '[email protected]'
 
-# List profiles:
+log_checkpoint "List profiles:"
 echo -n "Profiles: "
 curl --location --request GET "http://localhost:8080/projects/$PROJECT/datasets/$DATASET/profiles?provider=google" \
   --header "Authorization: Bearer $TOKEN"
@@ -149,7 +224,7 @@ for x in $(seq 10); do
   echo;
 done
 
-# Run inference:
+log_checkpoint "Run inference:"
 curl -v --location --request POST "http://localhost:8080/projects/$PROJECT/jobs?provider=google" \
   --header 'Content-Type: application/json' \
   --header "Authorization: Bearer $TOKEN" \
@@ -159,7 +234,7 @@ curl -v --location --request POST "http://localhost:8080/projects/$PROJECT/jobs?
     \"parameters\": [\"$DATASET\", 3]
   }"
 
-# List inferences:
+log_checkpoint "List inferences:"
 echo -n "Inferences: "
 curl --location --request GET "http://localhost:8080/projects/$PROJECT/datasets/$DATASET/inferences?provider=google" \
   --header "Authorization: Bearer $TOKEN"

scripts/init/.gitignore

@@ -0,0 +1 @@
+init_data.cypher

scripts/init/make_init_data.cypher.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+set -e
+
+cd "$(dirname "$0")"
+
+if [ -z "$USER_ID" ]; then cat << EOF
+Error: USER_ID is not defined. Please follow these steps:
+
+# Execute
+#
+# > export USER_ID="YOUR_USER_ID"
+#
+# where YOUR_USER_ID is the email address associated with the account used to
+# create TOKEN.
+EOF
+  exit 1
+else
+  echo "ok USER_ID defined as ${USER_ID}"
+fi
+
+cat << EOF > init_data.cypher
+CALL apoc.cypher.runMany("MATCH(n) DETACH DELETE n;
+CREATE (:User {provider: 'google', id: '${USER_ID}', deprecated: false})-[:CONTAINS_DETAILS {from: datetime(), version: 1}]->(:UserDetails {role: 'admin'})
+EOF