/
omero-hosts.yml
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/
omero-hosts.yml
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######################################################################
# Variables common to OMERO read-write and read-only servers
######################################################################
######################################################################
# Shared variables
idr_omero_release: "0.5.0"
idr_omero_ice_version: "3.6"
# Upgrades are normally disabled, set to True upgrade OMERO:
idr_omero_upgrade: False
# The IDR version system doesn't match the OMERO.server version
omero_server_checkupgrade_comparator: '!='
idr_omero_omego_additional_args: "--downloadurl https://downloads.openmicroscopy.org/idr"
# If you want to speed up Ice installation use a precompiled IcePy:
ice_python_wheel: https://github.com/openmicroscopy/zeroc-ice-py-centos7/releases/download/0.0.3/zeroc_ice-3.6.4-cp27-cp27mu-linux_x86_64.whl
# 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: "9.6"
######################################################################
# openmicroscopy.fluentd vars
fluentd_source_configs:
- files/fluentd/omero.conf
######################################################################
# openmicroscopy.omero-server role vars
# This refers to a custom IDR release URL, not an official OMERO version
omero_server_release: "{{ idr_omero_release }}"
# Upgrades are normally disabled, uncomment if you want to upgrade OMERO:
omero_server_upgrade: "{{ idr_omero_upgrade }}"
omero_server_ice_version: "{{ idr_omero_ice_version }}"
# 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_omego_additional_args: "{{ idr_omero_omego_additional_args }}"
omero_server_config_set:
omero.db.poolsize: 25
omero.jvmcfg.heap_size.blitz: "24G"
# 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
######################################################################
# Other dependent role vars
# 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_bin_omero: /opt/omero/server/OMERO.server/bin/omero
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
idr_omero_web_public_url_filters_webclient_exclude:
- action
- annotate_(file|tags|comment|rating|map)
- script_ui
- ome_tiff
- figure_script
idr_omero_web_public_url_filters:
- webadmin/myphoto/
- mapr/
- webclient/(?!({{ idr_omero_web_public_url_filters_webclient_exclude | join('|') }}))
- webgateway/(?!(archived_files|download_as))
omero_web_release: "{{ idr_omero_release }}"
# Upgrades are normally disabled, uncomment if you want to upgrade OMERO:
omero_web_upgrade: "{{ idr_omero_upgrade }}"
omero_web_ice_version: "{{ idr_omero_ice_version }}"
omero_web_omego_additional_args: "{{ idr_omero_omego_additional_args }}"
omero_web_config_set:
# web
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
# public user
omero.web.public.enabled: True
omero.web.public.server_id: 1
omero.web.public.user: 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
# social media
omero.web.sharing.twitter:
omero: "@openmicroscopy"
omero.web.sharing.opengraph:
omero: "Open Microscopy"
# 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
######################################################################
# Plugins and additional web configuration
omero_web_apps_packages:
- "omero-mapr==0.2.3"
omero_web_apps_names:
- omero_mapr
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_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: "others"
config:
default:
- "Others"
all:
- "Others"
ns:
- "openmicroscopy.org/omero/bulk_annotations"
label: "Others"