Installing SENAITE laboratory information management system on Ubuntu

Notes from my own recent installation:

  • At the time of writing, the official installation instructions here do not work.

  • There are a number of blog posts and SENAITE Community postings on the Internet with advice on installation, but none can be relied on alone for a successful installation.

  • There are Docker/Docker Compose options which seemed to work from limited experimentation but I didn’t pursue these as I wanted to understand the technology stack.

  • The steps are (I haven’t gone into detail for the steps from the official documentation that worked):

    • Install Ubuntu 18.04 (I suspect you might get away with a more recent version of Ubuntu, or Debian Buster, but I haven’t looked into this much)

      • I created a VM in my Proxmox setup with 4 vCPUs, 16GB of RAM and 100GB of storage (this was probably more than was needed for a demo version)

    • Create a user called senaite with sudo privileges and switch to being that user.

    • Install Miniconda (you can alternatively use virtualenv) to isolate the Python dependencies of SENAITE from system updates and then create and activate a Python virtual environment.

    • Install some system dependencies (these are the ones listed in the official instructions):

      sudo apt install build-essential  libcairo2 libffi-dev libgdk-pixbuf2.0-0 libpango-1.0-0 libpangocairo-1.0-0 libxml2 libxml2-dev libxslt1-dev libxslt1.1 python2.7 python2.7-dev zlib1g zlib1g-dev 
```

    • I also installed some additional dependencies in my various attempts to install SENAITE (not sure if it made any difference):

      sudo apt install bzip2 libbz2-1.0 libbz2-dev libexpat1-dev libjpeg-dev libjpeg-turbo8-dev libopenjp2-7-dev libpango1.0-0 libpcre3 libpcre3-dev libssl-dev libtiff5-dev python-pil

    • So far so good…

    • Install Plone: this is where things started going wrong, as you need a more recent version of Plone than is described in the official instructions; in my successful attempt I installed this version of Plone:

      wget --no-check-certificate https://launchpad.net/plone/5.2/5.2.13/+download/Plone-5.2.13-UnifiedInstaller-1.0.tgz
tar -xf Plone-5.2.13-UnifiedInstaller-1.0.tgz
cd Plone-5.2.13-UnifiedInstaller-1.0
./install.sh standalone --target=/home/senaite --instance=senaitelims --password=whateveryouwant --with-python=/home/senaite/miniconda2/envs/senaite/bin/python
cd /home/senaite/senaitelims

    • Next you need to edit the buildout.cfg file in a text editor; this is the configuration file that will be used to build your Plone app and resolve Python dependencies; the critical parts of mine look like this:

      eggs =
  Plone 
  senaite.lims 
  simplejson
# ...
user = admin:whateveryouwant 
# ...
[versions]
setuptools =
zc.buildout =
Plone = 5.2.11
plone.recipe.unifiedinstaller = 5.2b1
buildout.sanitycheck = 1.0.2
collective.recipe.backup = 4.1.0
      • Note how (by accident) I didn’t specify the right Plone version (and yet it worked); perhaps this just specifies minimum versions

    • I did not touch the requirements.txt file.

      • I did however install some specific Python package versions, which may have helped.

        pip install zc.buildout==2.13.4
pip install setuptools==44.1.1

      • At some point I think I also followed some advice to change permissions with sudo chown -R senaite:senaite /home/senaite/.cache

    • Now the moment of truth (or more likely of many errors): run the buildout script

      • If the script completes without error, then you can start an instance with bin/instance start (to stop it use bin/instance stop; run it in debug mode with bin/instance fg)
      • The service should now be running on port 8080 of that host.

  • Note that the instructions above may not work for you once a new version of SENAITE is out

  • What helped me work through the dependency issues was looking at the GitHub page for SENAITE Dockerfiles; click the link for the version you want and then look at the following files:

    • Dockerfile: for the Plone version; look under the “ENV” environment variables section
    • build_deps.txt and run_deps.txt: for system dependencies
    • docker-initialize.py: for stuff you may need for proxy server configuration (see below)
    • requirements.txt: follow the link in this file to find out what versions of Python packages you will need

  • So I now had SENAITE running on my server but my problems were not at an end: some of the functionality in the interface was not working, and there were lots of errors in the browser console, indicating that I had issues related to “Cross-Origin Resource Sharing” (CORS); basically, when your browser has opened a Web page from a server, it will not by default allow that page to access resources from another location unless specified; this is a security measure to prevent an attack called “Cross Site Request Forgery” (CSRF); however with a Web app you may well need to access resources at a different location, so you need to specify this in the “headers” that the server sends to the browser

    • As a quick fix I added a “Custom Location” to Nginx Proxy Manager as suggested here, containing the following:

      add_header 'Access-Control-Allow-Origin' '*';
add_header 'Content-Security-Policy' 'upgrade-insecure-requests';

    • This would not be sufficiently secure in itself (I think this is something that would be best addressed in the Plone configuration, as for example here), but this is just a demo version

  • Having got past that, I still couldn’t get the interface to work for one thing (related to dropdown boxes) and then discovered that this did work if I used (vanilla) Edge instead of Firefox (with lots of security add-ons)

  • I was feeling pretty good at this point and started on the Quick Start tutorial; unfortunately this is also out-of-date and will not work for you in a recent version of SENAITE

  • However I have worked out that if you do things in a different order to that specified, and do one or two things that aren’t documented in the Quick Start (this can be a future post), then it is all possible and it all seems to work well.

  • As (despite my usual tenacity) I never got OpenELIS fully working I am now delighted to say I can install a laboratory information management system!