Dependency updates #38
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Building this PR in ome/openmicroscopy#6324 (I used my branch since this branch is not built on top of main and the version is old). |
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Have you established that removing/commenting https://github.com/ome/openmicroscopy/blob/f73008bc34d37f6034a21095c55eb2a8b6075e44/ivy.xml#L21 suffices to fix the build issues? i.e. is this component the only source of issues? |
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I have rebuilt using only ome/openmicroscopy#6323 and excluding the ZarrReader and it builds fine |
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Heres the dependency tree with this PR, other than logback the rest of these are related to jzarr: |
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Using So most of the dependencies which fail to resolve in the OMERO build system are defined at the low-level It's still not fully clear to me why this is an issue with this repository but not with As things stand, we have evidence that although our coupled CI workflow is sufficient to include the development ZarrReader into a development OMERO.server, this causes serious issue when trying to build OMERO in isolation. In addition to the impact on a developer workfow, a more critical impact is that release builds are likely to fail for similar reasons that caused ZarrReader to be excluded in the past. So solving this is a blocker to the inclusion of this reader into an OMERO.server release. Trying to come up with a list of options to explore/discuss:
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using this PR in openmicroscopy build fails with https://github.com/ome/openmicroscopy/runs/7022030936?check_suite_focus=true |
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This time If I remember correctly a bump to testng should fix that one |
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https://github.com/ome/openmicroscopy/runs/7023130718?check_suite_focus=true is now green with the last commit |
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One question about overriding vs exclusing the objenesis dependdency.
Otherwise, this seems to fix the downstream build as per #38 (comment) and potentiall unlock the release. Should we try to get this merged and released (proposing 0.3.0 as per the S3 disabling) and try to consume the released version in the openmicroscopy build?
pom.xml
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| <dependency> | ||
| <groupId>org.objenesis</groupId> | ||
| <artifactId>objenesis</artifactId> | ||
| <version>2.5.1</version> |
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This is the version shipped in ome-common (via kryo 4.0.2). From mvn dependency:tree -Dverbose it looks like it is conflicting with the version from org.mockito:mockito-inline:3.7.7.
Declaring it in the POM should suffice although I assume an alternative would be to add and exclude in the mockito dependency?
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From a quick discussion with @dgault and @jburel, a possible simpler and more effective option would simply be to declare mockito and testng as test dependencies (via scope). This might suffice to exclude these from the openmicroscopy Ivy resolution and prevent the copying of unnecessary JARs into the lib folder
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Barring the removal of the S3 functionality (which will likely need to be reviewed at a later date), the proposed change fix some dependency mismatch in the dependency declaration, classify test-only dependency and remove the usage of commons-io.
I did some minimal testing in our nightly CI server importing a multi-file single image, a WSI and a plate and everything worked as expected.
Under these assumptions, proposing to get this merged, tag the component as 0.3.0 and then bump the version in openmicroscopy in preparation of the release if no objection
Following on from conversation with @sbesson and @jburel, trying to remove some of the dependencies. Goal of this PR will be to update the below areas:
1 - formats API bumped to latest 6.10.0, this should be straight forward
2 - commons-io removed, only area impacted will be the list of used files. PR aims to keep the reproduce the same list
3 - initially remove netty-nio-client dependency, this looks safe and straight forward
As a follow up I will continue trying to strip out and remove the remaining amazon dependencies which essentially means removing the s3 functionality for the time being.