omero-hosts.yml

######################################################################
# Variables common to OMERO read-write and read-only servers
######################################################################


######################################################################
# Shared variables

# Force a downgrade from 5.6.1
# https://github.com/ome/omero-server/issues/93
idr_omero_server_release: 5.6.0
omero_server_checkupgrade_comparator: '!='

idr_omero_web_release: 5.14.0
# omero-web depends on omero-py but may not pin the latest release
# omero_web_python_addons:
#   - omero-py==5.9.0
# ome.omero_server role installs omero-py but this may not be the latest release
# TODO: This is an internal role variable, replace when we have a proper way
# https://github.com/ome/ansible-role-omero-server/blob/3.1.0/defaults/main.yml#L89
# _omero_py_version: ==5.9.0

artifactory_baseurl: "https://artifacts.openmicroscopy.org/artifactory/maven"

# Override the lib/client JARs on the omeroreadwrite server
# Works around the OMERO.server 5.6.3 upgrade issue - to be reverted when
# the server is upgraded
# See https://github.com/IDR/deployment/issues/327
omero_client_jars:
  - name: omero-romio
    group: org/openmicroscopy
    version: "5.6.2"
  - name: omero-blitz
    group: org/openmicroscopy
    version: "5.5.8"

# The IDR OMERO server uses a custom IDR build
idr_bf_jars:
  - name: formats-api
    group: idr
    version: "0.6.8"
  - name: formats-bsd
    group: idr
    version: "0.6.8"
  - name: formats-gpl
    group: idr
    version: "0.6.8"

ice_install_devel: false
ice_install_python: false
# If you're using a CI build you might need to disable omego SSL verification
#idr_ANSIBLE_ENVIRONMENT_VARIABLES: { OMEGO_SSL_NO_VERIFY: 1 }

# This is needed to ensure the client version matches the server
postgresql_version: "11"


######################################################################
# openmicroscopy.fluentd vars
fluentd_source_configs:
- files/fluentd/omero.conf


######################################################################
# openmicroscopy.omero-server role vars

omero_server_release: "{{ idr_omero_server_release }}"

omero_server_python3: true

# Must be defined outside
omero_server_dbhost: "{{ omero_db_host_ansible }}"
omero_server_dbname: idr
# These are separate for omeroreadwrite and omeroreadonly
#omero_server_dbuser:
#omero_server_dbpassword:

omero_server_system_uid: 546
omero_server_system_managedrepo_group: idr-data
omero_server_datadir: /data/OMERO
omero_server_datadir_bioformatscache: /data/BioFormatsCache

omero_server_systemd_limit_nofile: 16384

omero_server_python_addons:
- omero-cli-render==0.7.0
- omero-metadata==0.9.0
- omero-upload==0.4.0
- omero-rois==0.3.0
- pandas==1.1.0

omero_server_config_set:
  omero.db.poolsize: 25
  omero.jvmcfg.heap_size.blitz: "24G"
  omero.fs.repo.path: "%user%_%userId%/%thread%//%year%-%month%/%day%/%time%"
  # public user doesn;t share omero session between visitors
  #omero.sessions.timeout: 3600000
  omero.policy.binary_access: "+read,+write,-image,-plate"
  # Prevent retrieval of uncached BF data
  omero.pixeldata.fail_if_missing: True
  # Group/User drop down menu
  omero.client.ui.menu.dropdown.colleagues.enabled: False
  omero.client.ui.menu.dropdown.everyone.label: "Public data"
  omero.client.ui.menu.dropdown.leaders.enabled: False
  # Tree display
  omero.client.ui.tree.type_order: False
  omero.client.ui.tree.orphans.enabled: False
  # Websockets (no wss for now to avoid dealing with certificates)
  omero.client.icetransports: ssl,tcp,ws
  # Disable all components except Blitz and Tables
  omero.server.nodedescriptors: "master:Blitz-0,Tables-0"


######################################################################
# Other dependent role vars

java_versions:
  - "11"
# Install JDK to provide jstack
java_jdk_install: True

omero_logmonitor_basedir: /opt/omero/logmonitor
# TODO: separate server and web configurations
omero_logmonitor_logs_dir: /opt/omero/server/OMERO.server/var/log

omero_user_system: omero-server


# TODO: The rest of this file should go into a new omero-web-hosts group

######################################################################
# openmicroscopy.omero-web role vars

omero_web_python3: true

idr_omero_web_public_url_filters_webclient_exclude:
- action
- annotate_(file|tags|comment|rating|map)
- script_ui
- ome_tiff
- figure_script
- render_image_download

idr_omero_web_public_url_filters:
- api/
- webadmin/myphoto/
- mapr/
- figure/
- iviewer/
# Needed in OMERO.web 5.6.1 to allow the root app patch (/→/idr_gallery)
- '$'
- search/
- search/cell/
- search/tissue/
- gallery-api/
- gallery_settings/
- cell/
- tissue/
- webclient/(?!({{ idr_omero_web_public_url_filters_webclient_exclude | join('|') }}))
- webgateway/(?!(archived_files|download_as))


omero_web_release: "{{ idr_omero_web_release }}"

omero_web_config_set:
  # web
  omero.web.api.max_limit: 1000
  omero.web.api.absolute_url: https://idr.openmicroscopy.org/
  omero.web.application_server: wsgi-tcp
  omero.web.application_server.max_requests: 30000
  omero.web.wsgi_workers: 25
  #omero.web.wsgi_timeout 30
  #omero.web.wsgi_args -- '--forwarded-allow-ips=YOUR_IP'
  omero.web.use_x_forwarded_host: True
  # The config generated by omero web wsgi contains X-Forwarded-Proto
  # Override it in the front-end proxy by checking a different header
  omero.web.secure_proxy_ssl_header:
    - HTTP_X_FORWARDED_PROTO_OMERO_WEB
    - https
  omero.web.server_list:
    # This is overridden in the molecule test, see molecule/publicidr/molecule.yml
    - - "{{ idr_omeroreadonly_web_omero | default('localhost') }}"
      - 4064
      - omero
  # public user
  omero.web.public.enabled: True
  omero.web.public.server_id: 1
  omero.web.public.user: "{{ idr_secret_public_user | default('public') }}"
  omero.web.public.password: "{{ idr_secret_public_password | default('public') }}"
  omero.web.public.url_filter: "^/({{ idr_omero_web_public_url_filters | join('|') }})"
  omero.web.login_redirect:
    redirect:
      - webindex
    viewname: load_template
    args:
      - userdata
    query_string: experimenter=-1
  # session
  omero.web.session_cookie_name: sessionid_{{ idr_environment | default('idr') }}
  # TODO: Do we need separate cookies for each web backend?
  #omero.web.session_cookie_name: sessionid_{{ ansible_hostname }}
  omero.web.session_cookie_age: 3600
  # redis
  omero.web.session_engine: django.contrib.sessions.backends.cache
  omero.web.caches:
    default:
      BACKEND: django_redis.cache.RedisCache
      LOCATION: redis://{{ omero_redis_host_ansible | default('127.0.0.1') }}:6379/0
  # / goes to idr_gallery
  omero.web.root_application: idr_gallery
  # social media
  omero.web.sharing.twitter:
    omero: "@openmicroscopy"
  omero.web.sharing.opengraph:
    omero: "Open Microscopy"
  # top-left logo
  omero.web.top_logo: /about/img/logos/logo-idr-webclient.png
  omero.web.top_logo_link: https://idr.openmicroscopy.org/
  # Clear the top links and metadata (They will be set later)
  omero.web.ui.top_links: []
  omero.web.ui.metadata_panes: []
  omero.web.wsgi_timeout: "{{ idr_omero_web_timeout | default(60) }}"
# TODO: This needs careful review of the code
# https://github.com/openmicroscopy/openmicroscopy/blob/v5.4.0-m2/components/tools/OmeroWeb/omeroweb/decorators.py#L305
  omero.web.public.cache.enabled: True
  omero.web.public.cache.timeout: 60
  omero.web.page_size: 500
  omero.web.user_dropdown: "{{ idr_omero_web_user_dropdown | default(true) }}"
  # Feedback
  omero.web.feedback.comment.enabled: False
  # Nginx extra omero-web config
  omero.web.nginx_server_extra_config: "{{ idr_omero_web_nginx_server_extra_config | default([]) }}"


######################################################################
# Plugins and additional web configuration

omero_web_apps_packages:
- omero-mapr==0.5.0
- omero-iviewer==0.11.3
- idr-gallery==3.6.1
- omero-figure==4.4.3
omero_web_apps_names:
- omero_mapr
- omero_iviewer
- idr_gallery
- omero_figure

omero_web_apps_top_links:
- label: Studies
  link:
    viewname: webindex
    query_string: { experimenter: -1 }
  attrs:
    title: Image Data Repository
- label: Genes
  link:
    viewname: maprindex_gene
    query_string: { experimenter: -1 }
  attrs:
    title: Genes browser
- label: Phenotypes
  link:
    viewname: maprindex_phenotype
    query_string: { experimenter: -1 }
  attrs:
    title: Phenotypes browser
- label: Cell Lines
  link:
    viewname: maprindex_cellline
    query_string: {"experimenter": -1}
  attrs:
    title: Cell Lines browser
- label: siRNAs
  link:
    viewname: maprindex_sirna
    query_string: { experimenter: -1 }
  attrs:
    title: siRNAs browser
- label: Antibodies
  link:
    viewname: maprindex_antibody
    query_string: {"experimenter": -1}
  attrs:
    title: Antibodies browser
- label: Compounds
  link:
    viewname: maprindex_compound
    query_string: {"experimenter": -1}
  attrs:
    title: Compounds browser
- label: Organisms
  link:
    viewname: maprindex_organism
    query_string: {"experimenter": -1}
  attrs:
    title: Organisms browser
- label: About
  link: https://idr.openmicroscopy.org/about/
  attrs:
    title: About the Image Data Resource

# Metadata Panes order
omero_web_apps_ui_metadata_panes:
- name: "map"
  label: "Attributes"
  index: 0
- name: "table"
  label: "Tables"
  index: 1
- name: "file"
  label: "Attachments"
  index: 2
- name: "comment"
  label: "Comments"
  index: 3
- name: "tag"
  label: "Tags"
  index: 4
- name: "rating"
  label: "Ratings"
  index: 5
- name: "other"
  label: "Others"
  index: 6

# Additional plugin config
# append...
omero_web_apps_config_append:
  omero.web.open_with:
  - - omero_iviewer
    - omero_iviewer_index
    - script_url: omero_iviewer/openwith.js
      supported_objects:
      - image
      - dataset
      - well
      label: OMERO.iviewer

# set...
omero_web_apps_config_set:
  omero.web.mapr.config:
  - menu: "gene"
    config:
      default:
        - "Gene Symbol"
      all:
        - "Gene Symbol"
        - "Gene Identifier"
      ns:
        - "openmicroscopy.org/mapr/gene"
      label: "Gene"
      case_sensitive: True
  - menu: "genesupplementary"
    config:
      default: []
      all: []
      ns:
        - "openmicroscopy.org/mapr/gene/supplementary"
      label: "Gene supplementary"
  - menu: "sirna"
    config:
      default:
        - "siRNA Identifier"
      all:
        - "siRNA Identifier"
        - "siRNA Pool Identifier"
      ns:
        - "openmicroscopy.org/mapr/sirna"
      label: "siRNA"
  - menu: "sirnasupplementary"
    config:
      label: "siRNA supplementary"
      default: []
      all: []
      ns:
        - "openmicroscopy.org/mapr/sirna/supplementary"
  - menu: "phenotype"
    config:
      default:
        - "Phenotype"
      all:
        - "Phenotype"
        - "Phenotype Term Accession"
      ns:
        - "openmicroscopy.org/mapr/phenotype"
      label: "Phenotype"
      case_sensitive: True
      wildcard:
        enabled: True
  - menu: "compound"
    config:
      default:
        - "Compound Name"
      all:
        - "Compound Name"
      ns:
        - "openmicroscopy.org/mapr/compound"
      label: "Compound"
      case_sensitive: True
  - menu: "compoundsupplementary"
    config:
      default: []
      all: []
      ns:
        - "openmicroscopy.org/mapr/compound/supplementary"
      label: "Compound supplementary"
  - menu: "organism"
    config:
      default:
        - "Organism"
      all:
        - "Organism"
      ns:
        - "openmicroscopy.org/mapr/organism"
      label: "Organism"
      wildcard:
        enabled: True
  - menu: "antibody"
    config:
      default:
        - "Antibody Identifier"
      all:
        - "Antibody Identifier"
      ns:
        - "openmicroscopy.org/mapr/antibody"
      label: "Antibody"
      case_sensitive: True
  - menu: "antibodysupplementary"
    config:
      default: []
      all: []
      ns:
        - "openmicroscopy.org/mapr/antibody/supplementary"
      label: "Antibody supplementary"
  - menu: "orf"
    config:
      default:
        - "ORF Identifier"
      all:
        - "ORF Identifier"
      ns:
        - "openmicroscopy.org/mapr/orf"
      label: "ORF"
  - menu: "orfsupplementary"
    config:
      default: []
      all: []
      ns:
        - "openmicroscopy.org/mapr/orf/supplementary"
      label: "ORF supplementary"
  - menu: "cellline"
    config:
      default:
        - "Cell Line"
      all:
        - "Cell Line"
      ns:
        - "openmicroscopy.org/mapr/cell_line"
      label: "Cell Lines"
      wildcard:
        enabled: True
  - menu: "celllinesupplementary"
    config:
      default: []
      all: []
      ns:
        - "openmicroscopy.org/mapr/cell_line/supplementary"
      label: "Cell Lines supplementary"
  - menu: "protein"
    config:
      default:
        - "Protein"
      all:
        - "Protein"
      ns:
        - "openmicroscopy.org/mapr/protein"
      label: "Protein"
  - menu: "proteinsupplementary"
    config:
      default: []
      all: []
      ns:
        - "openmicroscopy.org/mapr/protein/supplementary"
      label: "Protein supplementary"
  - menu: "others"
    config:
      default:
        - "Others"
      all:
        - "Others"
      ns:
        - "openmicroscopy.org/omero/bulk_annotations"
      label: "Others"
  - menu: "notebook"
    config:
      default:
        - "Study Notebook"
      all:
        - "Study Notebook"
      ns:
        - "openmicroscopy.org/idr/analysis/notebook"
      label: "Analysis Notebook"
  omero.web.viewer.view: omero_iviewer.views.index
  omero.web.gallery.favicon: "https://idr.openmicroscopy.org/about/img/logos/favicon-idr.ico"
  omero.web.gallery.top_left_logo:
    src: "https://idr.openmicroscopy.org/about/img/logos/logo-idr.svg"
  omero.web.gallery.top_right_links:
    - text: "About"
      href: "https://idr.openmicroscopy.org/about/index.html"
      submenu:
        - text: "Overview"
          href: "https://idr.openmicroscopy.org/about/index.html"
        - text: "Published studies"
          href: "https://idr.openmicroscopy.org/about/studies.html"
        - text: "Linked resources"
          href: "https://idr.openmicroscopy.org/about/linked-resources.html"
        - text: "API Access"
          href: "https://idr.openmicroscopy.org/about/api.html"
        - text: "Data download"
          href: "https://idr.openmicroscopy.org/about/download.html"
        - text: "Image Tools Resource (ITR)"
          href: "https://idr.openmicroscopy.org/about/itr.html"
        - text: "Analysis Environments"
          href: "https://idr.openmicroscopy.org/about/analysis-environments.html"
        - text: "Deployment"
          href: "https://idr.openmicroscopy.org/about/deployment.html"
        - text: "FAQ"
          href: "https://idr.openmicroscopy.org/about/faq/"
    - text: "Submissions"
      href: "https://idr.openmicroscopy.org/about/submission.html"
      submenu:
        - text: "Overview"
          href: "https://idr.openmicroscopy.org/about/submission.html"
        - text: "Screens"
          href: "https://idr.openmicroscopy.org/about/screens.html"
        - text: "Experiments"
          href: "https://idr.openmicroscopy.org/about/experiments.html"
  omero.web.gallery.subheading_html: "The Image Data Resource (IDR) is a public repository of image datasets from published scientific studies,<br/>where the community can submit, search and access high-quality bio-image data."
  omero.web.gallery.footer_html: "IDR"
  omero.web.gallery.category_queries:
    latest:
      label: "Light sheet fluorescence microscopy"
      index: 0
      query: "Imaging Method: light sheet fluorescence microscopy OR Imaging Method: light sheet fluorescence microscopy, SPIM"
    infection:
      label: "Infection studies"
      index: 1
      query: "Study Type:infection"
    timelapse:
      label: "Time-lapse imaging"
      index: 2
      query: "Study Type:time OR Study Type:5D OR Study Type:3D-tracking"
    lightsheet:
      label: "Light sheet fluorescence microscopy"
      index: 3
      query: "Study Type:light sheet"
    proteinlocalization:
      label: "Protein localization studies"
      index: 4
      query: "Study Type:protein localization"
    histology:
      label: "Digital pathology imaging"
      index: 5
      query: "Study Type:histology"
    yeast:
      label: "Yeast studies"
      index: 6
      query: "Organism: Saccharomyces cerevisiae OR Organism:Schizosaccharomyces pombe"
    humancellscreen:
      label: "High-content screening (human)"
      index: 7
      query: "Organism:Homo sapiens AND Study Type:high content screen"
    others:
      label: "Others"
      index: 8
      query: "LAST1000:date"
  omero.web.gallery.filter_keys:
  - label: "Name (IDR number)"
    value: "Name"
  - "Imaging Method"
  - "License"
  - "Organism"
  - "Publication Authors"
  - "Publication Title"
  - "Screen Technology Type"
  - "Screen Type"
  - "Study Type"
  omero.web.gallery.filter_mapr_keys:
  - "antibody"
  - "cellline"
  - "compound"
  - "gene"
  - "phenotype"
  - "sirna"
  omero.web.gallery.super_categories:
    cell:
      label: "Cell - IDR"
      title: "Welcome to Cell-IDR"
      query: "Sample Type:cell"
      image: "https://idr.openmicroscopy.org/webgateway/render_image/122770/0/0/"
    tissue:
      label: "Tissue - IDR"
      title: "Welcome to Tissue-IDR"
      query: "Sample Type:tissue"
      image: "https://idr.openmicroscopy.org/webgateway/render_image_region/5470164/0/0/?region=1024,1024,696,520"
  omero.web.gallery.title: "IDR: Image Data Resource"
  omero.web.gallery.heading: "Welcome to IDR"
  omero.web.gallery.study_short_name:
  - key: "Name"
    regex: "^(.*?)-.*?(.)$"
    template: "$1$2"