No persistence of data

[hcvdwerf]

I have an issue when I restart the FDP I got Unable data. I see no volume mapping for mongodb. Is this on purpose? After adding this the issue still persist

[dennisvang]

Hi @hcvdwerf , could you tell me which compose file you're using?

There are two flavours:

• ephemeral
• persistent with the volumes defined in compose.override.yml

[hcvdwerf]

services:
  fdp:
    image: "fairdata/fairdatapoint:${FDP_VERSION:-1.18}"
    restart: no
    environment:
      SERVER_PORT: 8080
      INSTANCE_CLIENTURL: http://localhost
      INSTANCE_PERSISTENTURL: http://localhost
    depends_on:
      mongo:
        condition: service_healthy
      graphdb:
        condition: service_healthy
    healthcheck:
      test: wget --quiet --spider http://localhost:8080 || exit 1
      start_interval: 3s
      start_period: 30s

  fdp-client:
      image: "fairdata/fairdatapoint-client:${FDP_CLIENT_VERSION:-1.18}"
      restart: no
      ports:
        - "80:80"
      environment:
        FDP_HOST: fdp:8080
      depends_on:
        fdp:
          condition: service_healthy
      healthcheck:
        test: wget --quiet --spider http://localhost || exit 1
        start_interval: 3s
        start_period: 30s

  mongo:
    image: "mongo:${MONGO_VERSION:-8.0}"
    restart: no
    volumes:
      - ./mongo/data:/data/db
    healthcheck:
      test: |
        [ $(mongosh --quiet --host localhost:27017 --eval "db.runCommand('ping').ok") = 1 ] || exit 1
      start_interval: 3s
      start_period: 30s

  graphdb:
    image: ontotext/graphdb:10.7.6
    ports:
        - 7200:7200
    volumes:
        - ./graphdb:/opt/graphdb/home
        - ./repo.json:/tmp/repo.json:ro
    entrypoint:
        - bash
        - -c
        - |
          # enable bash job control
          set -m

          # start graphdb and move it to the background
          /opt/graphdb/dist/bin/graphdb &

          # wait for 10 sec
          sleep 10

          # create the repository
          curl -X POST http://localhost:7200/rest/repositories -H "Content-Type: application/json" -d "@repo.json"

          # move graphdb job to foreground
          fg
    healthcheck:
        # https://graphdb.ontotext.com/documentation/10.7/database-health-checks.html
        test: curl --fail-with-body http://localhost:7200/repositories/fdp/health || exit 1

This is my compose now

[dennisvang]

@hcvdwerf you're not using a compose file from this repository?

[hcvdwerf]

this is your compose, but combined in one overview. Added only some persistence

[dennisvang]

this is your compose, but combined in one overview. Added only some persistence

@hcvdwerf Looks like most parts of your compose file above are based on the "latest" docs, which are still outdated, unfortunately (we're working on that).

I would suggest basing your compose file on the persistent configuration from this repository (also see the compose.override.yml). This is also described in the docs develop branch.

To see the full configuration:

1. clone the compose repo
2. cd compose/fdp/persistent/v1
3. docker compose config

as described in the readme.

[hcvdwerf]

ok check I updated as following your instructions ( one file is easier for sharing)

name: fdppv1

services:
  graphdb:
    image: "ontotext/graphdb:${GRAPHDB_VERSION:-10.8.8}"
    restart: no
    ports:
      - "127.0.0.1:7200:7200"
    volumes:
      - graphdbdata:/opt/graphdb/home
    healthcheck:
      test: curl http://localhost:7200/rest/monitor/infrastructure --silent --fail || exit 1
      start_interval: 3s
      start_period: 30s

  graphdb-init:
    image: "curlimages/curl:${CURL_VERSION:-latest}"
    restart: no
    environment:
      REPO_FILE: /repo.json
    volumes:
      - ./repo.json:/repo.json:ro
    command:
      - sh
      - -c
      - |
        set -e
        if [ ! -f "$$REPO_FILE" ]; then
          echo "Repository definition not found at $$REPO_FILE" >&2
          exit 1
        fi
        echo "Initializing GraphDB repository from $$REPO_FILE"
        curl http://graphdb:7200/rest/repositories \
          --silent --show-error --fail \
          --header "Content-Type: application/json" \
          --data @"$$REPO_FILE"
    depends_on:
      graphdb:
        condition: service_healthy

  mongo:
    image: "mongo:${MONGO_VERSION:-8.0}"
    restart: no
    volumes:
      - mongodbdata:/data/db
    healthcheck:
      test: |
        [ $(mongosh --quiet --host localhost:27017 --eval "db.runCommand('ping').ok") = 1 ] || exit 1
      start_interval: 3s
      start_period: 30s

  fdp:
    image: "fairdata/fairdatapoint:${FDP_VERSION:-1.18}"
    restart: no
    environment:
      SERVER_PORT: 8080
      INSTANCE_CLIENTURL: http://localhost
      INSTANCE_PERSISTENTURL: http://localhost
      REPOSITORY_TYPE: 4
      REPOSITORY_GRAPHDB_URL: http://graphdb:7200
      REPOSITORY_GRAPHDB_REPOSITORY: fdp
    depends_on:
      mongo:
        condition: service_healthy
      graphdb-init:
        condition: service_completed_successfully
    healthcheck:
      test: wget --quiet --spider http://127.0.0.1:8080 || exit 1
      start_interval: 3s
      start_period: 30s

  fdp-client:
    image: "fairdata/fairdatapoint-client:${FDP_CLIENT_VERSION:-1.18}"
    restart: no
    ports:
      - "127.0.0.1:80:80"
    environment:
      FDP_HOST: fdp:8080
    depends_on:
      fdp:
        condition: service_healthy
    healthcheck:
      test: wget --quiet --spider http://127.0.0.1 || exit 1
      start_interval: 3s
      start_period: 30s

volumes:
  graphdbdata:
  mongodbdata:

[hcvdwerf]

Current script you cannot run again

If you run for second time I got this:
graphdb-init-1 | Initializing GraphDB repository from /repo.json
graphdb-init-1 | curl: (22) The requested URL returned error: 400
graphdb-init-1 exited with code 22
Gracefully stopping... (press Ctrl+C again to force)
service "graphdb-init" didn't complete successfully: exit 22

[dennisvang]

@hcvdwerf Could you specify what you mean by "run again"? What's your exact command line input?

Also your graphdb-init.command looks different from the one in this repo:

compose/fdp/components/db/graphdb.yml

Lines 26 to 37 in e6e953f

	# the following curl request returns status 201 if the repo does not exist, or status 400 otherwise
	command:
	- sh
	- -c
	- |
	for name in $$REPO_NAMES
	do
	# substitute "repo-name" by variable name in graphdb repo template
	data=$$(sed s/repo-name/$$name/g /templates/graphdb-repo-template.json)
	# post repo definition to graphdb rest api
	curl http://graphdb:7200/rest/repositories --verbose --silent --header "Content-Type: application/json" --data "$$data"
	done

[hcvdwerf]

does your code check if the repo already exist ?

[dennisvang]

No, it does not check if the repo already exists, because the graphdb API handles that:

compose/fdp/components/db/graphdb.yml

Line 26 in e6e953f

# the following curl request returns status 201 if the repo does not exist, or status 400 otherwise

[dennisvang]

I just verified again that fdp/persistent/v1 works with restart, down/up, and pause/unpause.

[hcvdwerf]

Great! Tnx for feedback. I think it is now also robust at our side

name: fdppv1

services:
  graphdb:
    image: "ontotext/graphdb:${GRAPHDB_VERSION:-10.8.8}"
    restart: no
    ports:
      - "127.0.0.1:7200:7200"
    volumes:
      - graphdbdata:/opt/graphdb/home
    healthcheck:
      test: curl http://localhost:7200/rest/monitor/infrastructure --silent --fail || exit 1
      start_interval: 3s
      start_period: 30s

  graphdb-init:
    image: "curlimages/curl:${CURL_VERSION:-latest}"
    restart: no
    environment:
      REPO_FILE: /repo.json
      REPO_NAMES: fdp
    volumes:
      - ./repo.json:/repo.json:ro
    # the following curl request returns status 201 if the repo does not exist, or status 400 otherwise
    command:
      - sh
      - -c
      - |
        for name in $$REPO_NAMES
        do
        # substitute "repo-name" by variable name in graphdb repo template
        data=$$(sed s/repo-name/$$name/g /repo.json)
        # post repo definition to graphdb rest api
        curl http://graphdb:7200/rest/repositories --verbose --silent --header "Content-Type: application/json" --data "$$data"
        done
    depends_on:
      graphdb:
        condition: service_healthy

  mongo:
    image: "mongo:${MONGO_VERSION:-8.0}"
    restart: no
    volumes:
      - mongodbdata:/data/db
    healthcheck:
      test: |
        [ $(mongosh --quiet --host localhost:27017 --eval "db.runCommand('ping').ok") = 1 ] || exit 1
      start_interval: 3s
      start_period: 30s

  fdp:
    image: "fairdata/fairdatapoint:${FDP_VERSION:-1.18}"
    restart: no
    environment:
      SERVER_PORT: 8080
      INSTANCE_CLIENTURL: http://localhost
      INSTANCE_PERSISTENTURL: http://localhost
      REPOSITORY_TYPE: 4
      REPOSITORY_GRAPHDB_URL: http://graphdb:7200
      REPOSITORY_GRAPHDB_REPOSITORY: fdp
    depends_on:
      mongo:
        condition: service_healthy
      graphdb-init:
        condition: service_completed_successfully
    healthcheck:
      test: wget --quiet --spider http://127.0.0.1:8080 || exit 1
      start_interval: 3s
      start_period: 30s

  fdp-client:
    image: "fairdata/fairdatapoint-client:${FDP_CLIENT_VERSION:-1.18}"
    restart: no
    ports:
      - "127.0.0.1:80:80"
    environment:
      FDP_HOST: fdp:8080
    depends_on:
      fdp:
        condition: service_healthy
    healthcheck:
      test: wget --quiet --spider http://127.0.0.1 || exit 1
      start_interval: 3s
      start_period: 30s

volumes:
  graphdbdata:
  mongodbdata: