Dockerfile

FROM girder/girder

RUN mkdir /assetstore

RUN git clone https://github.com/memex-explorer/image_space.git
RUN girder-install plugin -s image_space/imagespace
RUN girder-install plugin -s image_space/imagespace_smqtk

RUN npm install --only=prod --unsafe-perm

ENV IMAGE_SPACE_SOLR=http://imagespace-solr:8983/solr/imagespace
ENV IMAGE_SPACE_SOLR_PREFIX=/images
ENV IMAGE_SPACE_PREFIX=http://localhost:8080/images
ENV IMAGE_SPACE_IMAGE_DIR=/images

ENTRYPOINT ["python", "-m", "girder"]

gistfile1.txt

#!/bin/bash

PREFIX="imagespace"
CORE_NAME="imagespace"

SOLR_IMAGE="solr:6.0"
MONGO_IMAGE="mongo:3.0"
IMAGESPACE_IMAGE="imagespace/quickstart"

SMQTK_ENABLED=0

IMAGESPACE_DOCKER_ARGS=""

if [[ $# -eq 0 ]]; then
    echo "Usage: imagespace-quickstart DIR"
fi

while [[ $# -gt 0 ]]
do
key="$1"
shift  # past key
case ${key} in
    -i|--images)
        IMAGE_DIR="$1"
        shift
        ;;
    -n|--docker-network)
        DOCKER_NETWORK="$1"
        shift
        ;;
    --mongo-data-dir)
        MONGO_DATA_DIR="$1"
        shift
        ;;
    --smqtk-iqr-url)
        SMQTK_IQR_URL="$1"
        SMQTK_ENABLED=1
        IMAGESPACE_DOCKER_ARGS="$IMAGESPACE_DOCKER_ARGS -e IMAGE_SPACE_SMQTK_IQR_URL=$SMQTK_IQR_URL"
        shift  # past value
        ;;
    --smqtk-nn-url)
        SMQTK_NN_URL="$1"
        SMQTK_ENABLED=1
        IMAGESPACE_DOCKER_ARGS="$IMAGESPACE_DOCKER_ARGS -e IMAGE_SPACE_SMQTK_SIMILARITY_SEARCH=$SMQTK_NN_URL"
        shift
        ;;
    *)  # unknown option
        ;;
esac
done

if [ -z "${IMAGE_DIR}" ]
then
    echo "ERROR: No image directory provided. Please provide -i|--images option."
    exit 1
elif [ -z "$(ls "${IMAGE_DIR}")" ]
then
    echo "ERROR: Nothing in provided image directory: ${IMAGE_DIR}"
    exit 2
fi

if [ -z "${DOCKER_NETWORK}" ]
then
    DOCKER_NETWORK="imagespace-network"
fi

#
# Make sure docker network exists / is created
#
if [ -z "$(docker network ls 2>/dev/null | tail -n +2 | grep "${DOCKER_NETWORK}")" ]
then
    # network doesn't exist yet, create it
    echo "Creating new docker network \"${DOCKER_NETWORK}\" using bridge driver"
    docker network create --driver bridge "${DOCKER_NETWORK}"
else
    echo "Found docker network \"${DOCKER_NETWORK}\" already exists"
fi

docker run --name $PREFIX-solr -d  -P --net=$DOCKER_NETWORK $IMAGESPACE_DOCKER_ARGS $SOLR_IMAGE solr-create -c $CORE_NAME
SOLR_CONTAINER_PORT=$(docker port $PREFIX-solr 8983 | cut -d: -f2)

echo "Waiting for Solr to become available.."
SOLR_EXIT_STATUS=-1
while [ $SOLR_EXIT_STATUS -ne 0 ]; do
    # Sleep until the curl call returns an http code 200
    curl --location --write-out "%{http_code}" --silent "http://localhost:$SOLR_CONTAINER_PORT/solr" | grep -q '^200'
    SOLR_EXIT_STATUS=$?
    sleep 1
done

# Add sha1sum_s_md field as a single valued string
curl "http://localhost:$SOLR_CONTAINER_PORT/solr/$CORE_NAME/schema" -H 'Accept: application/json, text/plain, */*' -H 'Content-Type: application/json;charset=utf-8' --data '{"add-field":{"stored":"true","indexed":"true","name":"sha1sum_s_md","type":"string"}}'

echo "Importing images into Solr"
# Load images into Solr
for filename in $(find "$IMAGE_DIR" -type f); do
    sha=$(sha1sum "$filename" | cut -d' ' -f1)
    filename=/images/$(basename "$filename")
    curl --silent "http://localhost:$SOLR_CONTAINER_PORT/solr/$CORE_NAME/update?commitWithin=30000" -H 'Content-Type: application/json' --data "[{'id' : '$filename', 'sha1sum_s_md': '$sha' }]" > /dev/null
done

docker run --name $PREFIX-mongo -v "$MONGO_DATA_DIR":/data/db -d --net=$DOCKER_NETWORK $IMAGESPACE_DOCKER_ARGS $MONGO_IMAGE

# Wait for Mongo to start up
MONGO_OUTPUT=$(docker logs $PREFIX-mongo)
while [[ $MONGO_OUTPUT != *"waiting for connections on port 27017"* ]]; do
    sleep 1
    MONGO_OUTPUT=$(docker logs $PREFIX-mongo)
done


docker run --name $PREFIX-girder \
       --volume "$IMAGE_DIR":/images -d -p 8080:8080 --publish-all=true --net=$DOCKER_NETWORK $IMAGESPACE_DOCKER_ARGS $IMAGESPACE_IMAGE --database mongodb://imagespace-mongo/girder

# Wait for Girder to start up
echo $(docker logs $PREFIX-girder 2>&1) | grep -qi "engine bus started"
GIRDER_STARTED=$?
while [[ $GIRDER_STARTED -ne 0 ]]; do
    sleep 1
    echo $(docker logs $PREFIX-girder 2>&1) | grep -qi "engine bus started"
    GIRDER_STARTED=$?
done


# Create Girder admin user, enable plugins
docker exec -it $PREFIX-girder python -c "
import requests
user = requests.post('http://localhost:8080/api/v1/user', data={'login': 'girder', 'email': 'girder@girder.girder', 'firstName': 'girder', 'lastName': 'girder', 'password': 'girder'})
token = user.json()['authToken']['token']
requests.post('http://localhost:8080/api/v1/assetstore', data={'name': 'assetstore', 'type': 0, 'root': '/assetstore'}, headers={'Girder-Token': token})
requests.put('http://localhost:8080/api/v1/system/setting', data={'key': 'core.plugins_enabled', 'value': '[\"imagespace\"]'}, headers={'Girder-Token': token})
requests.put('http://localhost:8080/api/v1/system/restart', headers={'Girder-Token': token})"

if [ $SMQTK_ENABLED -eq 1 ]; then
    docker exec -it $PREFIX-girder python -c "
import requests
user = requests.get('http://localhost:8080/api/v1/user/authentication', auth=('girder', 'girder'))
token = user.json()['authToken']['token']
r = requests.put('http://localhost:8080/api/v1/system/setting', data={'key': 'core.plugins_enabled', 'value': '[\"imagespace\", \"imagespace_smqtk\"]'}, headers={'Girder-Token': token})
requests.put('http://localhost:8080/api/v1/system/restart', headers={'Girder-Token': token})
assert r.ok"
fi

echo "ImageSpace is being served at http://localhost:8080"
echo "Image similarity might not be available for all images until descriptors are computed."