Bump server to 5.6.11 and incl ZarrReader

[dominikl]

This reverts commit 3876a0fc477c4021f6281bbf19967b886b6ee854. Currently testing this by spinning up pilot-idrngff

[will-moore]

From @sbesson: https://github.com/IDR/deployment/blob/e4cf559445f037a55b4597bcab77c9058a28fcec/ansible/requirements.yml#L81-L82 probably needs to be upgraded to 6.1.0 as the role should install [blosc] as a requirement

[sbesson]

Deployed on test122

[will-moore]

See https://github.com/ome/ZarrReader/blob/main/CHANGELOG.md

• Probably best to bump ZarrReader to 0.5.1 (Bio-Formats 7.3.0).
• Not sure where to specify the bump of Bio-Formats 7.3.0 in IDR/deployment?

[sbesson]

Not sure where to specify the bump of Bio-Formats 7.3.0 in IDR/deployment?

This PR is upgrading OMERO.server to version 5.6.11 which should ship Bio-Formats 7.3.0 by default so I don't think anything else is required.

Probably best to bump ZarrReader to 0.5.1 (Bio-Formats 7.3.0).

Agreed, I would propose to declare the version of ZarrReader as a variable in ansible/group_vars/omero-hosts.yml and consuming it in idr-omero.yml and idr-omeroreadonly.yml to ensure the same JAR is deployed everywhere.

[will-moore]

@khaledk2 - As discussed above, we will be using ZarrReader 0.5.1 (Bio-Formats 7.3.0) on idr-testing. I'm going to manually update the OMEZarrReader.jar to the released 0.5.1 now, and check that it works with the memo files that were generated with the pre-release builds.

@dominikl - Do you want to look at Seb's suggestion above:?

I would propose to declare the version of ZarrReader as a variable in ansible/group_vars/omero-hosts.yml and consuming it in idr-omero.yml and idr-omeroreadonly.yml to ensure the same JAR is deployed everywhere.

[dgault]

Following on from the Slack discussion, updating ZarrReader to 0.5.1 will mean we will also need to include the AWS SDK jar from here.

We have 2 options: 1 - Update this PR to include the AWS dependency in the same way as ZarrReader is currently added 2 - I can build and deploy an uber jar for ZarrReader that includes all the dependencies and we update to use that

My preference would be to go for option 1 in this case, but in the short term I am happy to deploy an uber jar if that is easiest.

[sbesson]

Running mvn dependency:tree, the AWS SDK brings the following dependencies

[INFO] +- com.amazonaws:aws-java-sdk-s3:jar:1.12.659:compile
[INFO] |  +- com.amazonaws:aws-java-sdk-kms:jar:1.12.659:compile
[INFO] |  +- com.amazonaws:aws-java-sdk-core:jar:1.12.659:compile
[INFO] |  |  +- commons-codec:commons-codec:jar:1.15:compile
[INFO] |  |  +- org.apache.httpcomponents:httpclient:jar:4.5.13:compile
[INFO] |  |  |  \- org.apache.httpcomponents:httpcore:jar:4.4.13:compile
[INFO] |  |  \- com.fasterxml.jackson.dataformat:jackson-dataformat-cbor:jar:2.12.6:compile
[INFO] |  \- com.amazonaws:jmespath-java:jar:1.12.659:compile
[INFO] \- commons-logging:commons-logging:jar:1.2:compile

Some of these e.g. commons-codec/commons-logging will already be included through other server dependencies although the versions probably need to be checked. Otherwise, all these JARs will need to be deployed individually (assuming from the OME artifactory as well) under lib/client and lib/server

[will-moore]

I deployed all the dependency jars manually on idr-testing last time around: https://github.com/IDR/idr-metadata/issues/675#issuecomment-2077639689 but didn't include aws

[khaledk2]

I have built the Micro-service. The packages, that Seb mentioned, are added by other Micro-service dependencies.

I have checked the lib folder and the dependencies versions which Seb mentioned are the same except jackson-dataformat-cbor.

The version of jackson-dataformat-cbor.jar is 2.14.2but Seb mentioned it is 2.12.6. I am not sure if that may cause any issue

I have used this OMEZarrReader version: in the build https://artifacts.openmicroscopy.org/artifactory/ome.releases/ome/OMEZarrReader/0.5.1/OMEZarrReader-0.5.1.jar

[sbesson]

Mid-term, I assume the goal is to resolve these dependencies using a build system and ship them with OMERO.server. As an intermediate solution, either option proposed in https://github.com/IDR/deployment/pull/420#issuecomment-2173157147 should work although using the individual JARs should be closer to the

The version of jackson-dataformat-cbor.jar is 2.14.2 but Seb mentioned it is 2.12.6. I am not sure if that may cause any issue

2.12.6 is the version that is pulled from the aws-java-sdk-s3 dependency but the same component might be declared with a different version by another dependency. In the micro-services, ./gradlew dependencies will tell you what the dependency tree looks like

[will-moore]

I'm trying to work out what changes are needed to this PR to include the list of jars at https://github.com/IDR/deployment/pull/420#issuecomment-2173437956 From that list I think I can guess the jar names , e.g. com.amazonaws:aws-java-sdk-s3:jar but not the URL. And do these get added as Override lib/server JARs tasks like this for each of the 8 jars (not including logging)?

diff --git a/ansible/idr-omero.yml b/ansible/idr-omero.yml
index 1e1c307..926843a 100644
--- a/ansible/idr-omero.yml
+++ b/ansible/idr-omero.yml
@@ -91,6 +91,22 @@
         force: yes
       notify: restart omero-server

+    - name: Override lib/server JARs
+      become: yes
+      get_url:
+        url: "com.amazonaws:aws-java-sdk-s3:jar"
+        dest: "{{ omero_common_basedir }}/server/OMERO.server/lib/server/aws-java-sdk-s3.jar"
+        force: yes
+      notify: restart omero-server
+
+    - name: Override lib/client JARs
+      become: yes
+      get_url:
+        url: "com.amazonaws:aws-java-sdk-s3:jar"
+        dest: "{{ omero_common_basedir }}/server/OMERO.server/lib/client/aws-java-sdk-s3.jar"
+        force: yes
+      notify: restart omero-server
+
     - name: Remove OMERO scripts
       become: yes
       file:

[sbesson]

Yes all required JARs need to be under lib/server minimally and lib/client if they are expected to be used e.g. for imports.

From that list I think I can guess the jar names , e.g. com.amazonaws:aws-java-sdk-s3:jar but not the URL.

Minimally, all these dependencies should be on Maven Central i.e. https://repo1.maven.org/maven2/. They might be mirrored under the OME artifactory as well @jburel?

If we can use the OME artifactory, it might be worth re-using the existing logic i.e. define a list of (group, name, version) coordinates in the group variables and have a single task that loops over these dependencies, retrieves "{{ artifactory_baseurl }}/{{ item.group }}/{{ item.name }}/{{ item.version }}/{{ item.name }}-{{ item.version }}.jar and puts it under the right place

[dominikl]

Replaced by #427