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Task #8797 (closed)

Opened 7 years ago

Closed 6 years ago

Fix remaining issues with Maven build system

Reported by: crueden-x Owned by: mlinkert
Priority: critical Milestone: 5.x
Component: Bio-Formats Version: 4.4.8
Keywords: n.a. Cc: mhiner-x, cxallan
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

When building Bio-Formats with the Maven-based build system, there are some remaining issues:

  1. For bio-formats, there are two failing NetCDF-related unit tests. The discrepancy is due to NetCDF 4.0 being used with Ant, while the Maven build uses 4.2.20. The tests pass on the netcdf-update branch, which upgrades NetCDF to 4.2.20 across the board (but introduces a requirement on Java 6).
  2. For common, there is a @PARALLEL@ token that is nonstandard and throws off the test engine unless it gets replaced.
  3. For metakit, there is a filename system property that is expected to be set ad hoc. As such, the tests are not true unit tests.
  4. For bio-formats and ome-io, the missing dependency tests are not included because they only pass when dependencies are missing.
  5. The loci_tools.jar and ome_tools.jar built by Maven are substantially larger than those built by Ant. The reason is that Ant has a whitelist of JARs to include in the bundle, whereas Maven's assembly plugin includes all dependencies recursively (excluding a blacklist). The latter is a better way to ensure the bundle will work standalone—but either way, best would be to unify the behavior between the two build systems.

This ticket originated from ImageJ ticket #503.

Change History (16)

comment:1 Changed 7 years ago by mlinkert

  • Milestone changed from Unscheduled to OMERO-4.4.1

comment:2 Changed 7 years ago by mhiner-x

  • Cc mhiner-x added

comment:3 Changed 7 years ago by mlinkert

  • Milestone changed from OMERO-4.4.3 to OMERO-4.5

comment:4 Changed 7 years ago by mlinkert

It also looks like the "@date", "@version", etc. tokens are not being replaced correctly.

comment:5 Changed 7 years ago by mhiner-x

As a temporary workaround to #1, the NetCDF 4.0.03 jar was uploaded to the imagej maven repository.

This does not fully resolve the issue as this entry in a public repository makes no guarantees to its dependencies and thus should not be coded against by external consumers (despite the implicit public contract).

Also, if we ever want to put SCIFIO/Bio-Formats on Maven central, this dependency to a 3rd party repository will have to be removed in favor of a version concurrently supported by Maven central. Currently that's only NetCDF 4.2.20

comment:6 Changed 7 years ago by mlinkert

  • Cc cxallan added
  • Milestone changed from OMERO-5 to OMERO-4.5
  • Priority changed from minor to critical
  • Sprint set to 2012-11-20 (2)

Also:

  • make source packages
  • move version numbers into a single properties file
  • make sure that the version number/commit hash/build date information is set correctly

comment:7 Changed 7 years ago by jburel

  • Sprint changed from 2012-11-20 (2) to 2012-12-18 (3)

Moved from sprint 2012-11-20 (2)

comment:8 Changed 7 years ago by jburel

  • Sprint changed from 2012-12-18 (3) to 2013-01-15 (4)

Moved from sprint 2012-12-18 (3)

comment:9 Changed 7 years ago by jburel

  • Sprint changed from 2013-01-15 (4) to 2013-02-12 (5)

Moved from sprint 2013-01-15 (4)

comment:10 Changed 7 years ago by jburel

  • Sprint changed from 2013-02-12 (5) to 2013-03-12 (6))

Moved from sprint 2013-02-12 (5)

comment:11 Changed 7 years ago by jburel

  • Sprint changed from 2013-03-12 (6)) to 2013-04-09 (7))

Moved from sprint 2013-03-12 (6))

comment:12 Changed 6 years ago by jburel

  • Sprint changed from 2013-04-09 (7)) to 2013-05-07 (8)

Moved from sprint 2013-04-09 (7))

comment:13 Changed 6 years ago by jburel

  • Sprint changed from 2013-05-07 (8) to Blocker 4.4.9 (1)

Moved from sprint 2013-05-07 (8)

comment:14 Changed 6 years ago by mlinkert

  • Milestone changed from OMERO-4.4.9 to Testing
  • Sprint changed from Blocker 4.4.9 (1) to Testing and Docs (1)
  • Version set to 4.4.8

comment:15 Changed 6 years ago by mlinkert

  • Milestone changed from Testing and Docs to OMERO-5
  • Sprint Testing and Docs (1) deleted

comment:16 Changed 6 years ago by mlinkert

  • Resolution set to fixed
  • Status changed from new to closed
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