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Installation of RSpace add-on services

Updated by RSpace Support

This document is for IT staff at on-premises customers responsible for provisioning and maintaining the infrastructure to support RSpace.

We are now providing some additional services as web-service applications using Docker. Current applications include:

  1. MSOffice document converter. This provides the same functionality as the 'aspose-app' standalone Java application but is more performant and scalable.
  2. SnapGene viewer for DNA sequence files. See SnapGene integration for the functionality provided.
  3. A Chemistry service for generating images of uploaded Chemistry files.

Obtaining Docker images

At present, we will provide access to a private Dockerhub repository. This is likely to change in the future.

Please obtain credentials for the Docker repository from Research Space. We will only issue credentials to named technical contacts.
RSpace 1.69 or later is needed for these services. Before installing or updating any on-premise RSpace server, always refer to the version-specific .md documentation files included with the downloaded bundle for that version. Contact ResearchSpace for the download URL.
First of all you will need to install docker on the server that runs the service. We recommend running this on a different server than that running RSpace.

Document converter

Version 0.0.14 includes a new license required from January 28th 2024

docker pull rspaceops/rspace-services:aspose-web-0.0.14

SnapGene viewer:

docker pull rspaceops/rspace-services:snapgene-web-0.0.9

Chemistry viewer:

docker pull rspaceops/rspace-services:chemistry-web-1.2

Running a service

General steps:

  1. Decide on which port you want to expose the service.
  2. Decide on the URL of the service (or this can just be an IP address).
  3. Decide if you need to encrypt communications using TLS. This will be necessary if communication between RSpace and the service goes over public networks.
    None of these services require access from a browser, so can be run in a private network accessible only from RSpace web server.

You can set up and test the services without having to stop RSpace. An RSpace downtime is only necessary when you do the 'Connecting RSpace to the XXX service' section of the documentation.

Aspose Document Converter Service

Running Document converter service

Assuming you are want to expose the service on port 8081: (8060 is the port inside the container). Please note the version may change. The --restart unless-stopped will ensure the container starts up following a host reboot.

docker run -p8081:8060--restart unless-stopped --name aspose-doc-converter --mount source=aspose-logs,target=/logs,type=volume -d rspaceops/rspace-services:aspose-web-0.0.14

Testing Document converter service:

The service takes about 10s to start up. Modify these tests if you are using another command-line browser or the URL is not 'localhost'.

A simple test for 'server up':

curl localhost:8081/actuator/info

On some Ubuntu instances that use Apache shibd to handle SSO, curl cannot be installed. httpie is a good alternative.

Testing document conversion:

Download this file: br-dulabelling-orig.doc

wget https://files.helpdocs.io/6vvf1kbpym/other/1582895192769/br-dulabelling-orig.doc

and in the same directory, run:

curl -X POST -F"file=@br-dulabelling-orig.doc" -H "content-type: multipart/form-data" 'http://localhost:8081/aspose/files?format=pdf' > test-out.pdf

A PDF file should be successfully generated.

Troubleshooting:

Go into the running container, obtain logs and send to Research Space:

docker exec -it aspose-doc-converter bash

Log files will be in 'application.log' and a log file named after your installation.

Connecting RSpace to the Document converter service

In RSpace deployment.properties file, set the URL of the service. For example if the service is at http://123.79.78.21, add the following property:

aspose.web.url=http://123.79.78.21:8080

and restart RSpace.

Testing connection:

  • Export a single RSpace document to MSWord format.

SnapGene Service

Running SnapGene service

Assuming you are want to expose the service on port 8082: (8081 is the port inside the container). Please note the version may change.

docker run -it -p8082:8081 --restart unless-stopped--name snapgene-web --mount source=snapgene-logs,target=/snapgene-working,type=volume -d rspaceops/rspace-services:snapgene-web-0.0.9
Testing SnapGene service

The service takes about 30s to start up. Modify these tests if you are using another command-line browser or the URL is different.

A simple test for 'server up':

curl localhost:8082/snapgene/status

Testing SnapGene functionality:

Download this Genbank DNA sequence file: sequence.dna. Or download directly:

wget https://files.helpdocs.io/6vvf1kbpym/other/1582900258789/sequence.dna

and in the same directory, run:

curl -X POST -H"accept=application/json" -H"content-type: multipart/form-data" -F"cfg={};type=application/json" -F"file=@sequence.dna" -F"customerId=Customer1;type=text/plain" "localhost:8082/snapgene/reportEnzymes"

should output the JSON response, of restriction enzyme cutting sites.

Troubleshooting:

Go into the running container, obtain logs and send to Research Space:

docker exec -it snapgene-web bash

Log files will be in 'application.log' and a log file named after your installation.

Connecting RSpace to the SnapGene service

In RSpace deployment.properties file, set the URL of the service. For example if the service is at http://123.79.78.21:8081, add the following property:

snapgene.web.url=http://123.79.78.21:8081

and restart RSpace.

Now login as a user with 'SYSADMIN' role and enable the integration in System->Configuration->System Settings. Set it as 'Allowed' and save the changes.

Testing SnapGene connection:

  • Upload a DNA sequence file in .dna, .fa or .gb format ( you can use the example file above) and assert that the functionality described here is available.

Chemistry Service

This requires RSpace 1.71 or later
Running Chemistry service

Assuming you are want to expose the service on port 8099: (8060 is the port inside the container). Please note the version may change.

docker run  -p8083:8060 --name chemistry-web --restart always --mount source=chemistry-logs,target=/logs -d rspaceops/rspace-services:chemistry-web-1.2
Testing Chemistry service

The service takes about 3s to start up. Modify these tests if you are using another command-line browser or the URL is different.

A simple test for 'server up':

curl localhost:8083/actuator/info

Testing Chemistry functionality:

Download this file, which contains a small chemistry structure: exportChem.json. Or download directly:

wget https://files.helpdocs.io/6vvf1kbpym/other/1634206422450/export-chem.json

and in the same directory, run:

curl -vX POST http://localhost:8083/chemistry/export -d @export-chem.json --header "Content-Type: application/json" -o image_preview.png

should save a PNG image of a chemical 'image_preview.png'.

Troubleshooting:

Go into the running container, obtain logs and send to Research Space:

docker exec -it chemistry-web bash

Log files will be in 'application.log'

Connecting RSpace to the SnapGene service

In RSpace `deployment.properties` file, set the URL of the service. For example if the service is at http://123.79.78.21:8081, add the following property:

chemistry.web.url=http://123.79.78.21:8083

and restart RSpace.

Testing chemistry-web connection in RSpace:

  • Upload a Chemistry file into an RSpace document. Most common file formats should be supported. An image preview should be generated.

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