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This page describe How to easily deploy the latest version of Cytomine (for installation procedure of V1.0 (January 2016), see this page)

Cytomine can be installed on personal computers (laptops, desktops) or on larger servers.

Cytomine uses many libraries and services but this page describe how to have a production instance of Cytomine ready to use with only four steps.

Once Cytomine's server is installed, one can access Cytomine through a modern web browser or through clients using RESTful API.


Please, before further reading, pay attention to the requirementsThis installation documentation is for an Ubuntu 14.04 LTS & 16.04 LTS.  

Please note we use Docker which is a kind of lightweight virtualization platform, so you do not need to create virtual machines to install Cytomine (it's better not do so for better performances).

If you experiment any issue, please contact us by e-mail or describe your problem precisely in our ticket system on Github.

Step 1 - Retrieve Cytomine-bootstrap

First of all, we retrieve the Cytomine-bootstrap installation procedure. Copy/paste these commands:

 

Step 2 - Install Docker

Then, we need to install the Docker engine. You will find a complete documentation on the official site (follow the Prerequisites and Install sections only, you don't need optional configurations).

 

Step 3 - Configure Cytomine installation

Now, it is required to edit the Cytomine file configuration.sh in the Cytomine-bootstrap/ directory to prepare the installation of Cytomine Docker containers, using e.g.:

In this file you might modify the variables "XXX_URL" by the desired Cytomine URLs, i.e. the URL dedicated to the Core of Cytomine must be set in the CORE_URL variable and so on. Please use URLs that are not already present in your /etc/hosts file to avoid conflicts.

This file also contains some arrays of values (e.g. : IMS_URLS to use multiple image servers). Be careful that their value are space free even between two values (example : IMS_URLS="[localhost-ims,localhost-ims2]" is correct and IMS_URLS="[localhost-ims, localhost-ims2]" is not). 

It is then mandatory to edit the variables "IMS_STORAGE_PATH", "IMS_BUFFER_PATH" by the corresponding existing paths on an available filesystem where image files will be stored. Please note you have to specify paths without a "/" at the end (e.g. "/data", not "/data/").

In the same way, backups will be stored in BACKUP_PATH, machine learning models in MODELS_PATH and some retrieval data in RETRIEVAL_PATH.

Note that you might also want to edit the other options. An explanation of these variables is below.

Explanation of some variables :

Currently, in the configuration.sh file, we have variables used in the run command of the containers.

There are mandatory variables:

  • XXX_URL : URL to connect to the corresponding part of Cytomine (CORE, IMS, UPLOAD, RETRIEVAL, ...).

  • XXX_PATH : paths for buffer, permanent storage, machine learning models, etc. These paths must pre-exists.

  • XXX_PASS : default passwords (MEMCACHED).

There are optional variables:

  • IS_LOCAL : boolean. Default true. False if services are deployed on distincts machines.
  • BACKUP_BOOL : boolean. True if you want automatic backups. In this case, the following variables are mandatory.

    • BACKUP_PATH : a directory with this name will be created in the DB container for "auto-backup".
    • SENDER_EMAIL, SENDER_EMAIL_PASS, SENDER_EMAIL_SMTP : email params of the sending account for report of the backup.
    • RECEIVER_EMAIL : email adress of the backup reports receiver.
  • BIOFORMAT_ENABLED : Enable the bioformat convertor to support more formats (VSI, OME-TIFF,...).

  • IRIS_ENABLED : Enable IRIS (see IRIS project)
  • IRIS_ID : ID. Usefull if we are admin of multiple IRIS version.
  • IRIS_ADMIN_EMAIL : The email adress where user will ask permissions for IRIS projects. 

You have two deployment options:

3.1 If you want to deploy on a local host :

First of all, the variables "XXX_URL" will not be visible outside of your local server. So, due to the Docker architecture (isolation of the Docker's containers), we need to apply some changes to authorize network communication between our IMS and CORE containers (see below for further details). To do so, add these URL values (CORE_URL, IMS_URLS, UPLOAD_URL, RETRIEVAL_URL) to your /etc/hosts file with the following format : "127.0.0.1       XXX_URL".

With the default URL your etc/hosts will contain the following lines

In the file configuration.sh, we will also need to set the variable IS_LOCAL at true.

NB : Please be careful that some problems might appear if you use localhost instead of CORE_URL for a connection to Cytomine. So, keep using CORE_URL.

3.2 If you want to make your Cytomine instance accessible from anywhere :

Contact your institutional system/network administrator before installing Cytomine so that they create DNS entries and make their HTTP port (80) accessible for CORE_URL, IMS_URLS and UPLOAD_URL.

 

Step 4 - Deploy Cytomine

Then, you can deploy Cytomine by launching these two following commands in the Bootstrap directory (the installation of Cytomine can take up to 1 hour depending on network and server speed):


Step 5 - Install test data (optional)

At the end of the installation we recommend to install test data (which takes roughly 30 additional minutes) in order to follow our user guide.

Troubleshooting

In case of problems, see page Known problems of v1.0 (and specially the entry "Error : postgis_data not found/not started").

Please note that in some environments problems arise with network configuration (firewall) preventing docker to retrieve required packages from Internet. If docker fails to install the base container with error messages related to archive.ubuntu.com, you should first clean docker containers (using the first script above then the following command: sudo docker rmi $(sudo docker images -q) ) ; then you have to edit the DNS in the default docker configuration file and restart docker service as explained here: http://stackoverflow.com/questions/24151129/docker-network-calls-fail-during-image-build-on-corporate-network

Please note that server components might take one or two minutes to boot the first time (which will generate a "502 Bad Gateway message" or the browser to wait for a reponse). 

 


How to test your installation.

You can log into Cytomine through the http://CORE_URL (by default: http://localhost-core/) in your web browser using the admin session (the password was asked during installation). If you did not install the "test data", you will have an empty instance. You have to create a project, users, ...

Please have look at our Cytomine User Guide for default usernames/passwords and see examples on toy data (You have to answer "yes" at the end of the installation procedure to inject these toy data).

To add new users, you can log using the admin account (password is asked during installation). You can then open an admin session (top right menu) to have access to User Configuration options. 

In addition, you can make basic tests using the Cytomine Java client (see how to install the java client) or the Cytomine Python client.

 


How to debug your installation.

We provide a script (in the Cytomine-bootstrap directory) that outputs logs of the different containers and packs them in an reporting.tgz file for further analysis:

If you want to analyze more deeply an issue, depending on your problem (e.g. issue with image viewing), you can enter into the corresponding Docker container (e.g. ims) using the docker enter command and analyze log files.

First, install once the docker enter tool using (or use the docker exec command):

 Then enter into the corresponding docker (e.g. image server) and analyze the log:

Here is a list of log file paths in the different docker containers (sudo docker logs container):

Cytomine ComponentDocker containerlog file
Cytomine-Corecore
var/lib/tomcat7/logs/catalina.out
Image serverims
var/lib/tomcat7/logs/catalina.out
IIPImage serveriipOff, iipJ2, iipCyto, iipVent
tmp/iip-openslide.out
Database serverdb
var/log/postgresql/postgresql-9.3-main.log
MongoDBmongodb
var/log/mongodb/mongo.log
Cytomine-DataMiningsoftware_router/software_router/algo/logs/

 

To debug from the Java client, create a log4j.properties file in the directory where you execute your script with the following content (INFO/WARN/ERROR/DEBUG provides different levels of messages):

 


How to update your installation.

Docker is also used to easily update your Cytomine installation.

For example, if 

  • We update the current WAR's, 
  • A newer version of a component is available (e.g. the image server to support newer image formats),
  • You customize some Docker images,

all you need to do is to restart the containers to have an up-to-date version of Cytomine with your own customization.

Of course, restarting all the containers will make you lost all your data. To avoid this problem, some containers are specifically designed for your data and must always be running (if you need to stop them, do a backup first) !

The restart_keep_data.sh script (in Cytomine-boostrap directory) is made to re-deploy an up-to-date app without erasing your data.

So, as much as possible(*), only run the restart_keep_data.sh script to redeploy your app.

NB : If you add a custom container to your installation, you have to update this script.

* : The "data containers"  will have to be updated only if you made fundamental changes on the DBMS (e.g. update version, change postgres to mysql, ...)

 


How to uninstall Cytomine.

Please let us know why Cytomine does not meet your expectations.

In order to uninstall it, you have to delete all Docker container images using the following commands. 

!!! WARNING !!!: This will definitively delete all Cytomine data and all Docker containers.

!!! WARNING !!!: If you are using Docker for other projects, you have to delete only Cytomine containers (sudo docker images ; then for each Cytomine container: sudo docker rmi $id)

You should also delete remaining files in your local directories IMS_STORAGE_PATH, IMS_BUFFER_PATH, and BACKUP_PATH.

 

 

 

 

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