---
# System prepended metadata

title: 'Simon: handover doc'

---

# Simon: handover doc

https://docs.google.com/document/d/1kT-uO0jE-3oLqiEgUe0wecND5B4kmTn_rAWIFXwtmDc/edit

See also:
 - [index of currently useful docs](https://docs.google.com/document/d/1Z9Y1S5R40SPZjKreCRGeU7DH0alwmMPDkuhYoiB5Oqg/edit)
 - That along with the below, to be moved to wiki as the starting point for all docs
 - Starting points for "monitoring" et al. from the *user point of view*
 - All open PRs: https://github.com/pulls?q=is%3Aopen+is%3Apr+author%3Amanics+org%3Aome+org%3Aopenmicroscopy+org%3AIDR


## List of docs
- OME Systems Resources IP list
  - https://docs.google.com/spreadsheets/d/1nnwd-JLnb37PWT9sDwkV0a-vb_IabS3c7bbtbmTI79Y/edit?usp=sharing
    - `VLAN 33` I think this is probably the old production external facing network, IPs assigned by UoD-IT. Needs cleaning up.
    - `VLAN 15` Current production external facing network, IPs assigned by UoD-IT, use this for external facing VMs (`10ge Servers` subnet), requires Help4u ticket to open ports on the external firewall
    - `10.2.1.0/24` Old
    - `10.2.1.128/29` Old
    - `10.0.48.0/21` We have ownership of this subnet so use this for new internal VMs (`ome-idr-docker` subnet)
- List of all JRS VMware guests (UoD and OME VMware clusters)
  - https://docs.google.com/spreadsheets/d/1NQl7fhcgpbDqMAbxVZ1VE_cqbg9c8ZDxSx2yWb0aOVM/edit?usp=sharing
- Creating a new VM: on the OME VMWare cluster
  - https://docs.openmicroscopy.org/internal/sysadmin/provisioning/index.html
- GPFS management
  - https://github.com/openmicroscopy/management_tools/wiki/GPFS-%28IBM-Spectrum-Scale%29-Storage
- Expanding disk volumes on VMs
  - https://github.com/openmicroscopy/management_tools/wiki/Resizing-LVM-partitions
- IDR usage stats
  - https://github.com/openmicroscopy/management_tools/wiki/IDR-usage-stats



## Random sysadmin notes
- Recent VMs have an emergency local `omeroot` user with ssh access and sudo privileges which is automatically created by the Kickstart file when the system is provisioned.
  Try one of the passwords in `pass search omeroot`


## LSC contacts
- Jonathan Downward (day to day LSC issues, can contact on Teams)


## Monitoring and stats

### UoD Prometheus and Grafana:
- https://github.com/openmicroscopy/management_tools/wiki/Monitoring#ome-uod-prometheus-and-grafana
  - e.g. Registry hits by IP https://ome-dockr-prod1.openmicroscopy.org/grafana/d/0yuEtlPZk/registry-ips-by-component?orgId=1

### IDR/EBI
- https://github.com/IDR/deployment/blob/master/docs/monitoring.md
- https://github.com/openmicroscopy/management_tools/wiki/IDR-usage-stats


## External resources:

- OMERO.server Prometheus exporter port: https://github.com/prometheus/prometheus/wiki/Default-port-allocations
- conda-forge zeroc-ice:
  - https://github.com/conda-forge/zeroc-ice-feedstock
  - Ongoing maintenance https://github.com/conda-forge/zeroc-ice-feedstock/pull/11#issuecomment-757370161
- conda-forge omero-py:
  - https://github.com/conda-forge/staged-recipes/pull/13028


## GitHub Repositories

Transferred to https://github.com/microscopepony and OME admins added

### Python

- https://github.com/microscopepony/omero-cli-externalconfig Configure OMERO using environment variables, YAML, and JSON files
- https://github.com/microscopepony/omero-server-setup OMERO server setup and database management plugin
- https://github.com/microscopepony/omero-cli-database Manage the OMERO.server PostgreSQL database :green_apple: 
- https://github.com/microscopepony/omero-asyncio OMERO-py client and services that works with asyncio
- https://github.com/microscopepony/fs-omero-pyfs OMERO PyFileSystem2 implementation
- https://github.com/microscopepony/omero-mapr-graphql An experiment in querying OMERO.mapr IDR metadata using GraphQL
- https://github.com/microscopepony/omero-server-jupyter Run OMERO inside Jupyter
- https://github.com/microscopepony/omero-idirector https://gitlab.com/openmicroscopy/incubator/omero-idirector
- https://github.com/microscopepony/omero-shrtn https://gitlab.com/openmicroscopy/incubator/omero-shrtn
- https://github.com/microscopepony/omero-superresolution-tables Can't remember
- https://github.com/microscopepony/omero-mpcli Run OMERO python scripts using multiprocessing
- https://github.com/microscopepony/omero_copy An attempt at copying images between servers


### Conda

- https://github.com/microscopepony/conda-omero-server OMERO.server Conda package
- https://github.com/microscopepony/conda-omero-server-setup A Conda package for the OMERO server setup CLI plugin
- https://github.com/microscopepony/conda-omero-dropbox A Conda package for OMERO.dropbox
- https://github.com/microscopepony/conda-zeroc-ice36 A Conda package for Zeroc Ice 3.6 binaries compatible with OMERO
- https://github.com/microscopepony/conda-zeroc-ice-bin A Conda package for Zeroc Ice binaries and Java compatible with OMERO (alternative to the previous repo)
- https://github.com/microscopepony/conda-omero-web A Conda package for OMERO.web
- https://github.com/microscopepony/conda-whitenoise 
- https://github.com/microscopepony/conda-django-pipeline A Conda package for django-pipeline for use with OMERO.web
- https://github.com/microscopepony/conda-omero-marshal A Conda package for OMERO.marshal
- https://github.com/microscopepony/conda-libdb53 libdb53 (needed for Ice binaries)
- https://github.com/microscopepony/conda-django A Conda package for Django for use wth OMERO.web


### Docker

- https://github.com/manics/jupyter-omero-contents Jupyter OMERO ContentsManager Docker image
- https://github.com/microscopepony/docker-example-omero-certificates OMERO.server self-signed certificates (docker-compose)
- https://github.com/microscopepony/omerodev-docker Not sure
- https://github.com/microscopepony/omero-py-alpine-docker Minimal OMERO.py images based on Alpine Linux


### Jupyter

- https://github.com/microscopepony/jupyter-omero-authenticator Jupyter OMERO Authenticator
- https://github.com/microscopepony/ome-sysops-notebooks Not much
- https://github.com/microscopepony/centos-systemd-jupyter-notebook Notebook for running bash in JupyterHub with a CentOS 7 System image


### IDR notebooks

- https://github.com/microscopepony/idr-count-publications Count publications in the IDR
- https://github.com/microscopepony/idr-release-stats IDR Release Stats
- https://github.com/microscopepony/idr-montage IDR Montage
- https://github.com/microscopepony/idr0083-sars-cov2-notebook Zoomable idr0083 image
- https://github.com/microscopepony/idr0015-tara-oceans-geospatial IDR Tara oceans plot


### Old IDR

- https://github.com/microscopepony/idr-terraform Something to do with Terraform
- https://github.com/microscopepony/idr-data-munging Mentions Sysgro...
- https://github.com/microscopepony/idr-upload-js-s3-explorer Don't think this works


### Other

- https://github.com/microscopepony/omero-veewee-definitions Something to do with the old OMERO VirtualBox image
- https://github.com/microscopepony/ome-veewee Something to do with the old OMERO VirtualBox image
- https://github.com/microscopepony/alternative-storage One of the first things I worked on in OME
- https://github.com/microscopepony/ome-docker-scripts No idea


### Not transferred

- https://github.com/manics/kubernetes-omero OMERO Helm chart, linked to GitHub pages
- https://github.com/manics/ome-distribution-specific-pypi Something about attempting to create a static PyPI server with multiple wheels for Ice, linked to GitHub pages
- https://github.com/manics/github-batch-updater GitHub Batch Updater


## Gists
Copy these if you want them in case I clean them up in future

- OME2020 video access logs https://gist.github.com/manics/3140a630ab7d87fcee88397ccc0966cf
- Grafana OME registry IP query https://gist.github.com/manics/bf6e5a554d956aef6c6617d2589d60ed
- Example of creating Celery Docker tasks in OMERO https://gist.github.com/manics/a8a1a62fc3e835cfb09b45b1d584271b
- OMERO.server Virtual Machine Image https://gist.github.com/manics/036e7cfdf2d3ca2b4113511c86b78f38
- MinIO Security Token Service (STS) for temporary S3 path restricted access tokens https://gist.github.com/manics/305f4cc56d0ac6431893cde17b1ba8c4
  - also see https://github.com/ome/omero-ms-zarr/blob/7b02d060faf0df168b8a868adae9834118351fb3/src/test/java/org/openmicroscopy/s3/TestTokenCreator.java


## Outstanding OME infrastructure issues

- Some of our VMWare hypervisors may need a networking configuration fix before VMs can be successfully run on them.
- The OME managed GPFS clients (nightshade, idr0-slot3) need a [GPFS upgrade](https://github.com/openmicroscopy/management_tools/pull/975).
- VMs running CentOS 6 are EOL and should be deleted (or replaced).
- Some VMs are still hosted on UoD VMWare shared hypervisors instead of our own (mostly the CentOS 6 ones but may be others)
- ns-web.openmicroscopy.org (Nightshade OMERO.web) VM should be deleted, and OMERO.web installed on nightshade instead, this is leftover from when OMERO.web required CentOS7 but nightshade was still on CentOS 6
- Replace plaintext secrets in https://github.com/openmicroscopy/management_tools/ with credentials in `pass`, most of this is from either using K8S which didnt' integrate with pass, or due to playbooks run by Petr requiring some secrets
- [OME Systems Resources](https://docs.google.com/spreadsheets/d/1nnwd-JLnb37PWT9sDwkV0a-vb_IabS3c7bbtbmTI79Y/edit#gid=1946775410) Google doc, Ansible inventory, Google docs for each servers, etc, need a clean-up or unification.
- Replace demo server with the training-server playbook (the outreach playbook is newer and tested in molecule)
- Consider replacing the nightshade playbook with the training-server playbook to make maintainance easier
- pg-slave.openmicroscopy.org and ome-web-prod.openmicroscopy.org are running an old version of PostgreSQL (9.3)
- ome-web-prod.openmicroscopy.org is a public production web-server running CentOS 6 which is EOL and therefore unpatched
- UoD-IT are moving towards supporting use of AWS. Probably worth moving some infrastructure there if you get fed up of provisioning on VMWare.
- Consider moving all public web servers behind a single web-proxy configured with virtualhosts
- IDR is still running 5.6.0 due to the BioFormats memo change in 5.6.1+
