Data Services

The typical functional goal of this work is the development and use of a Graph that can be accessed via a triplestore (Graph Database). To do that we need a set of additional containers to support this and expose these services on the web through a single domain with https support.

  • Object Store
    An S3 compliant object store supporting S3 APIs including S3Select. For open source this is best satisfied with the Minio Object Store. For commercial cloud AWS S3 or hosted Ceph services will work.

  • Graph Database

  • Web Router (technically optional)

Gleaner Data Services (DS)

If you wish to work with a triplestore and wish to use the default app used by OIH you can use the compose file that sets up the Gleaner Data Services environment.

This adds the Blazegraph triplestore to the configuration along with the object store.

The details of the OIH data services are found in the Data Services section.

../_images/gleaner2.png

Fig. 3 Gleaner Data Service Activity Workflow

Typically, a user would wish to run the full Gleaner DS stack which supports both the indexing process and the serving of the resulting data warehouse and graph database capacity.

Combined, these would then look like the following where the indexing and data services shared a common object store.

../_images/gleaner3.png

Fig. 4 Gleaner Indexing and Data Service Combined

Object store pattern

Within in the object store the following digital object pattern is used.
This is based on the work of the RDA Digital Fabric working group.

../_images/do.png

Fig. 5 Gleaner Digital Object Pattern

At this point the graph and data warehouse (object store) can be exposed to the net for use by clients such as jupyter notebooks or direct client calls to the S3 object APIs and SPARQL endpoint.

Gleaner Data Services (DS) Environment Variables The Docker Compose file used to launch the Gleaner DS has a set of configurable elements that can be set and passed to the orchestration system with environment variables.

These can be set manually or through the command line. A simple script to set the variables could look like:

– Environment Var settings script

The actual services can be deployed via a Docker Compose file (also works with Podman). An example of that file and details about it follow.

Let’s take a look at this.

 1#!/bin/bash
 2
 3# domains 
 4export GLEANER_ADMIN_DOMAIN=admin.local.dev
 5export GLEANER_OSS_DOMAIN=oss.local.dev
 6export GLEANER_GRAPH_DOMAIN=graph.local.dev
 7export GLEANER_WEB_DOMAIN=web.local.dev
 8export GLEANER_WEB2_DOMAIN=web2.local.dev
 9
10# Object store keys
11export MINIO_ACCESS_KEY=worldsbestaccesskey
12export MINIO_SECRET_KEY=worldsbestsecretkey
13
14# local data volumes
15export GLEANER_BASE=/tmp/gleaner/
16export GLEANER_TRAEFIK=${GLEANER_BASE}/config
17export GLEANER_OBJECTS=${GLEANER_BASE}/datavol/s3
18export GLEANER_GRAPH=${GLEANER_BASE}/datavol/graph
19

– Break down the compose file here

  1version: '3'
  2
  3# ${GLEANER_ADMIN_DOMAIN}
  4# ${GLEANER_OSS_DOMAIN}
  5# ${GLEANER_GRAPH_DOMAIN}
  6# ${GLEANER_WEB_DOMAIN}  
  7# ${GLEANER_WEB2_DOMAIN}
  8# ${MINIO_ACCESS_KEY}  
  9# ${MINIO_SECRET_KEY}
 10#
 11# ${GLEANER_TRAEFIK}
 12# ${GLEANER_OBJECTS}
 13# ${GLEANER_GRAPH}
 14
 15services:
 16  triplestore:
 17    image: nawer/blazegraph 
 18    environment:
 19      JAVA_XMS: 2g
 20      JAVA_XMX: 8g
 21      JAVA_OPTS: -Xmx6g -Xms2g --XX:+UseG1GC
 22    ports:
 23      - 9999:9999
 24    labels:
 25      - "traefik.enable=true"
 26      - "traefik.http.routers.triplestore.entrypoints=http"
 27      - "traefik.http.routers.triplestore.rule=Host(`${GLEANER_GRAPH_DOMAIN}`)"
 28      - "traefik.http.middlewares.triplestore-https-redirect.redirectscheme.scheme=https"
 29      - "traefik.http.routers.triplestore.middlewares=triplestore-https-redirect"
 30      - "traefik.http.routers.triplestore-secure.entrypoints=https"
 31      - "traefik.http.routers.triplestore-secure.rule=Host(`${GLEANER_GRAPH_DOMAIN}`)"
 32      - "traefik.http.routers.triplestore-secure.tls=true"
 33      - "traefik.http.routers.triplestore-secure.tls.certresolver=http"
 34      - "traefik.http.routers.triplestore-secure.service=triplestore"
 35      - "traefik.http.middlewares.triplestore-secure.headers.accesscontrolallowmethods=GET,OPTIONS,PUT,POST"
 36      - "traefik.http.middlewares.triplestore-secure.headers.accesscontrolalloworigin=*"
 37      - "traefik.http.middlewares.triplestore-secure.headers.accesscontrolmaxage=200"
 38      - "traefik.http.middlewares.triplestore-secure.headers.addvaryheader=true"
 39      - "traefik.http.middlewares.triplestore-secure.headers.accesscontrolallowcredentials=true"
 40      - "traefik.http.middlewares.triplestore-secure.headers.accesscontrolallowheaders=Authorization,Origin,Content-Type,Accept"
 41      - "traefik.http.middlewares.triplestore-secure.headers.customresponseheaders.Access-Control-Allow-Headers=Authorization,Origin,Content-Type,Accept"
 42      - "traefik.http.routers.triplestore-secure.middlewares=triplestore-secure@docker" 
 43      - "traefik.http.services.triplestore.loadbalancer.server.port=9999"
 44      - "traefik.docker.network=traefik_default"
 45    volumes:
 46      - ${GLEANER_GRAPH}:/var/lib/blazegraph
 47    networks:
 48      - traefik_default
 49
 50  s3system:
 51    image: minio/minio:latest
 52    ports:
 53      - 9000:9000
 54    labels:
 55      - "traefik.enable=true"
 56      - "traefik.http.routers.s3system.entrypoints=http"
 57      - "traefik.http.routers.s3system.rule=Host(`${GLEANER_OSS_DOMAIN}`)"
 58      - "traefik.http.middlewares.s3system-https-redirect.redirectscheme.scheme=https"
 59      - "traefik.http.routers.s3system.middlewares=s3system-https-redirect"
 60      - "traefik.http.routers.s3system-secure.entrypoints=https"
 61      - "traefik.http.routers.s3system-secure.rule=Host(`${GLEANER_OSS_DOMAIN}`)"
 62      - "traefik.http.routers.s3system-secure.tls=true"
 63      - "traefik.http.routers.s3system-secure.tls.certresolver=http"
 64      - "traefik.http.routers.s3system-secure.service=s3system"
 65      - "traefik.http.services.s3system.loadbalancer.server.port=9000"
 66      - "traefik.docker.network=traefik_default"
 67    volumes:
 68      - ${GLEANER_OBJECTS}:/data
 69    environment:
 70      - MINIO_ACCESS_KEY=${MINIO_ACCESS_KEY}
 71      - MINIO_SECRET_KEY=${MINIO_SECRET_KEY}
 72    networks:
 73      - traefik_default
 74    command: ["server", "/data"]
 75
 76  features:
 77    image: fils/grow-general:latest
 78    ports:
 79      - 8080:8080
 80    environment:
 81      - S3ADDRESS=s3system:9000
 82      - S3BUCKET=sites
 83      - S3PREFIX=domain
 84      - DOMAIN=https://${GLEANER_WEB_DOMAIN}/
 85      - S3KEY=${MINIO_ACCESS_KEY}
 86      - S3SECRET=${MINIO_SECRET_KEY}
 87    labels:
 88      - "traefik.enable=true"
 89      - "traefik.http.routers.features.entrypoints=http"
 90      - "traefik.http.routers.features.rule=Host(`${GLEANER_WEB_DOMAIN}`, `${GLEANER_WEB2_DOMAIN}`)"
 91      - "traefik.http.middlewares.features-https-redirect.redirectscheme.scheme=https"
 92      - "traefik.http.routers.features.middlewares=features-https-redirect"
 93      - "traefik.http.routers.features-secure.entrypoints=https"
 94      - "traefik.http.routers.features-secure.rule=Host(`${GLEANER_WEB_DOMAIN}`,`${GLEANER_WEB2_DOMAIN}`)"
 95      - "traefik.http.routers.features-secure.tls=true"
 96      - "traefik.http.routers.features-secure.tls.certresolver=http"
 97      - "traefik.http.routers.features-secure.service=features"
 98      - "traefik.http.services.features.loadbalancer.server.port=8080"
 99      - "traefik.docker.network=traefik_default"
100      - "traefik.http.middlewares.features.headers.accesscontrolallowmethods=GET,OPTIONS,PUT,POST"
101      - "traefik.http.middlewares.features.headers.accesscontrolalloworigin=*"
102      - "traefik.http.middlewares.features.headers.accesscontrolmaxage=100"
103      - "traefik.http.middlewares.features.headers.addvaryheader=true"
104      - "traefik.http.middlewares.features-secure.headers.accesscontrolallowheaders=*"
105      - "traefik.http.middlewares.features-secure.headers.customresponseheaders.Access-Control-Allow-Headers=*"
106    networks:
107      - traefik_default
108
109networks:
110  traefik_default:
111

NOTE: DS also needs the object -> graph sync (via Nabu) NOTE: Should also add in (here or to the side) the ELT local Data Lake to Data Warehouse path (ala CSDCO VaultWalker)