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Bump zarr reader 0.5.1 #427

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merged 6 commits into from
Jun 27, 2024
Merged

Bump zarr reader 0.5.1 #427

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c3b470c
Revert "Revert OMERO.server upgrade for prod120"
dominikl Apr 11, 2024
2bffec7
Update omero-server to latest version
dominikl May 13, 2024
c7b9c3e
Bump OMEZarrReader to 0.5.1
will-moore Jun 19, 2024
f588960
Add aws sdk and dependencies to omero_client_jars
will-moore Jun 19, 2024
9e846b4
Load zarrreader_jars, including OMEZarrReader-0.5.1 from maven
will-moore Jun 20, 2024
8caf45e
Bump ansible-role-omero-server 6.1.0 to include blosc
will-moore Jun 24, 2024
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56 changes: 30 additions & 26 deletions ansible/group_vars/omero-hosts.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,7 @@
######################################################################
# Shared variables

# Force a downgrade from 5.6.1
# https://github.com/ome/omero-server/issues/93
idr_omero_server_release: 5.6.0
idr_omero_server_release: 5.6.11
omero_server_checkupgrade_comparator: '!='

idr_omero_web_release: 5.25.0
Expand All @@ -22,29 +20,35 @@ idr_omero_web_release: 5.25.0

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: "0.6.10"
- name: formats-bsd
group: idr
version: "0.6.10"
- name: formats-gpl
group: idr
version: "0.6.10"
# list from https://github.com/IDR/deployment/pull/420#issuecomment-2173437956
zarrreader_jars:
- name: aws-java-sdk-s3
group: com/amazonaws
version: "1.12.659"
- name: aws-java-sdk-kms
group: com/amazonaws
version: "1.12.659"
- name: jmespath-java
group: com/amazonaws
version: "1.12.659"
- name: aws-java-sdk-core
group: com/amazonaws
version: "1.12.659"
- name: commons-codec
group: commons-codec
version: "1.15"
- name: httpclient
group: org/apache/httpcomponents
version: "4.5.13"
- name: httpcore
group: org/apache/httpcomponents
version: "4.4.13"
- name: jackson-dataformat-cbor
group: com/fasterxml/jackson/dataformat
version: "2.12.6"
- name: OMEZarrReader
group: ome
version: "0.5.1"

ice_install_devel: false
ice_install_python: false
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4 changes: 2 additions & 2 deletions ansible/idr-omero-readonly.yml
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Expand Up @@ -211,7 +211,7 @@
url: "{{ artifactory_baseurl }}/{{ item.group }}/{{ item.name }}/{{ item.version }}/{{ item.name }}-{{ item.version }}.jar"
dest: "{{ omero_common_basedir }}/server/OMERO.server/lib/server/{{ item.name }}.jar"
force: yes
with_items: "{{ idr_bf_jars }}"
with_items: "{{ zarrreader_jars }}"
notify: restart omero-server

- name: Override lib/client JARs
Expand All @@ -220,7 +220,7 @@
url: "{{ artifactory_baseurl }}/{{ item.group }}/{{ item.name }}/{{ item.version }}/{{ item.name }}-{{ item.version }}.jar"
dest: "{{ omero_common_basedir }}/server/OMERO.server/lib/client/{{ item.name }}.jar"
force: yes
with_items: "{{ omero_client_jars + idr_bf_jars }}"
with_items: "{{ zarrreader_jars }}"
notify: restart omero-server

- name: Remove OMERO scripts
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4 changes: 2 additions & 2 deletions ansible/idr-omero.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@
url: "{{ artifactory_baseurl }}/{{ item.group }}/{{ item.name }}/{{ item.version }}/{{ item.name }}-{{ item.version }}.jar"
dest: "{{ omero_common_basedir }}/server/OMERO.server/lib/server/{{ item.name }}.jar"
force: yes
with_items: "{{ idr_bf_jars }}"
with_items: "{{ zarrreader_jars }}"
notify: restart omero-server

- name: Override lib/client JARs
Expand All @@ -90,7 +90,7 @@
url: "{{ artifactory_baseurl }}/{{ item.group }}/{{ item.name }}/{{ item.version }}/{{ item.name }}-{{ item.version }}.jar"
dest: "{{ omero_common_basedir }}/server/OMERO.server/lib/client/{{ item.name }}.jar"
force: yes
with_items: "{{ omero_client_jars + idr_bf_jars }}"
with_items: "{{ zarrreader_jars }}"
notify: restart omero-server

- name: Remove OMERO scripts
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2 changes: 1 addition & 1 deletion ansible/requirements.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@
version: 3.1.0

- src: ome.omero_server
version: 6.0.0
version: 6.1.0

- name: ome.omero_user
version: 0.4.0
Expand Down
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