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OMERO.cloudarchive

OMERO.cloudarchive can be used to provision the infrastructure for OMERO in a local or cloud environment. This mechanism can "hydrate" a previously created archive or be empty. Once running, data can be loaded/annotated/etc and then finally "dehydrated" into object storage.

Instructions for deploying on AWS are available at: https://sorgerlab.github.io/omero.cloudarchive-cloudformation/

Instructions for deploying locally follow.

AWS

Deploy a local setup using docker

# Quickstart
docker-compose up

To customize the configuration either edit docker-compose.yml or run the docker container's manually like this:

docker run \
  -d \
  --name postgres \
  -e POSTGRES_PASSWORD=postgres \
  postgres:9.4

docker run \
  -d \
  --name omero-master \
  --link postgres:db \
  -e CONFIG_omero_db_name=postgres \
  -e CONFIG_omero_db_pass=postgres \
  -e CONFIG_omero_db_user=postgres \
  -e CONFIG_omero_web_public_enabled=true \
  -e ROOTPASS=omero \
  -p 4063:4063 \
  -p 4064:4064 \
  dpwrussell/omero.cloudarchive

docker run \
  -d \
  --name omero-web \
  --link omero-master:master \
  -e PUBLIC_GROUP=public-group \
  -p 8080:8080 \
  dpwrussell/omero-grid-web

Now the OMERO infrastructure is up and running normal importing using Insight can be commenced on localhost, standard OMERO ports (unless changed in the above examples). The web client will also be operational on port 8080 (again, unless changed in the above examples).

In-place

It is also possible to do in-place importing. This is a good way of creating an archive without losing the original file-structure of the data. This is useful if the data archive is multipurpose, being accessed through OMERO, but also directly, thus preserving the original filesystem structure can be desirable.

When running the docker container for omero-master, include an additional setting -v <data_dir>:/mnt/<data_dir> , adding a local directory to the container.

docker run \
  -d \
  --name omero-master \
  --link postgres:db \
  -e CONFIG_omero_db_name=postgres \
  -e CONFIG_omero_db_pass=postgres \
  -e CONFIG_omero_db_user=postgres \
  -e CONFIG_omero_web_public_enabled=true \
  -p 4063:4063 \
  -p 4064:4064 \
  -v /TestData:/mnt/TestData \
  dpwrussell/omero.cloudarchive

Then log into the omero container through docker:

docker exec -it --user omero omero-master /bin/bash

Once logged in, create a symlink from the mounted data directory to a directory in /OMERO, like this:

ln -s /mnt/TestData/project1 /OMERO/inplace

Warning: When dehydrating this OMERO instance, everything in the symlinked directory will be uploaded to S3. In the above example this would be everything in the /mnt/TestData/project1 via the /OMERO/inplace symlink. This is an intentional effort to retain the files from the original structure which may or may not be relevant to OMERO.

We can now do an in-place imports of anything in /OMERO/inplace, in this example we will import everything:

~/OMERO.server/bin/omero import -- --transfer=ln_s /OMERO/inplace/

Dehydrate

Once an archive is built, it can be "dehydrated" into S3. A utility script is provider for this which should be run from outside the container, on the host. The reason for this is that currently a docker container can not introspect details about itself so it is necessary to gather these details from outside.

This script requires container name and S3 bucket identifier as arguments. It also uses the aws CLI to generate temporary credentials which are then used to interact with S3.

Before running the utility script, create a bucket in S3 to dehydrate the archive into. This can be done on the AWS console or through the CLI like this (In this case I make it publicly readable to anyone, and in the us-east-1 region):

export BUCKETNAME="<bucket_name>"
aws s3api create-bucket --bucket ${BUCKETNAME} --acl public-read --region us-east-1
echo "{ \"Version\" : \"2012-10-17\", \"Statement\" : [ { \"Effect\" : \"Allow\", \"Principal\" : \"*\", \"Resource\" : [ \"arn:aws:s3:::ionewfioewn9023/*\" ], \"Sid\" : \"PublicReadGetObject\", \"Action\" : [ \"s3:GetObject\" ] } ] }" > s3_public.json
aws s3api put-bucket-policy --bucket ${BUCKETNAME} --policy file://s3_public.json --region us-east-1

Now use the utility script to start the dehydration process.

./dehydrate-docker.sh <container_id> <s3_bucket>

This may take some time depending on the size of the repository to upload.