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Task #9359 (closed)

Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

Bug: OmeroImporter.jar sometimes lacks CommandLineImporter.class

Reported by: jamoore Owned by: jamoore
Priority: blocker Milestone: OMERO-4.4.4
Component: Deployment Version: n.a.
Keywords: n.a. Cc: cneves, cxallan, cmacleod-x, cblackburn, wmoore
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2012-08-14 (2)


The build system sometimes fails to add (or overwrites??) critical CLI import classes in the lib/client/OmeroImporter.jar.

See: https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=1254

This is also the cause of the OMERO-trunk-components/linux build sometimes failing.

Change History (7)

comment:1 Changed 10 years ago by wmoore

  • Cc wmoore added

This is critical for me since many OmeroPy/tests use CLI...

$ python gatewaytest/chgrp.py

.I<./../bin/omero -s localhost -k 35913d9b-a240-4ebc-97b1-86dce99edd69 -p 4064 import -d 403 -n weblitz_test_priv_image /Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/scripts/imgs/CHOBI_d3d.dv
('', 'Joined session 35913d9b-a240-4ebc-97b1-86dce99edd69 (weblitz_test_author@localhost:4064). Idle timeout: 10.0 min. Current group: weblitz_test_author_group\nException in thread "main" 
java.lang.NoClassDefFoundError: ome/formats/importer/cli/CommandLineImporter\nCaused by: java.lang.ClassNotFoundException: ome.formats.importer.cli.CommandLineImporter\n\tat 
java.net.URLClassLoader$1.run(URLClassLoader.java:202)\n\tat java.security.AccessController.doPrivileged(Native Method)\n\tat java.net.URLClassLoader.findClass(URLClassLoader.java:190)\n\tat 
java.lang.ClassLoader.loadClass(ClassLoader.java:306)\n\tat sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)\n\tat java.lang.ClassLoader.loadClass(ClassLoader.java:247)\n')
ERROR: testTwoDatasetsChgrp (__main__.ChgrpTest)
Traceback (most recent call last):
  File "gatewaytest/chgrp.py", line 27, in setUp
    super(ChgrpTest, self).setUp()
  File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/scripts/testdb_create.py", line 61, in setUp
  File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/scripts/testdb_create.py", line 145, in prepTestDB
  File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/scripts/dbhelpers.py", line 471, in bootstrap
    i = i.create()
  File "/Users/will/Desktop/OMERO/dist/lib/python/omero/gateway/scripts/dbhelpers.py", line 414, in create
    img = omero.gateway.ImageWrapper(dataset._conn, dataset._conn.getQueryService().find('Pixels', long(pid[0].split('\n')[0].strip())).image)
ValueError: invalid literal for long() with base 10: ''

Ran 5 tests in 23.327s

FAILED (errors=4)
jrs-macbookpro-25107:test will$

comment:2 Changed 10 years ago by jmoore

  • Owner set to jmoore
  • Sprint set to 2012-08-14 (2)
  • Status changed from new to accepted

Running tests locally.

comment:3 Changed 10 years ago by jmoore

The issue looks to be references to OmeroImporter.jar (or more specifically, ${ivy.module}.jar) in OmeroImporter/build.xml rather than ${ivy.module}-UNSIGNED.jar. Checking now.

comment:4 Changed 10 years ago by jmoore

Remaining OK uses of ${ivy.module}.jar:

$ git grep   -E '[$][{]ivy.module[}][.]jar' -- "**/*.xml"
components/antlib/resources/lifecycle.xml:      <jar destfile="${target.dir}/${ivy.module}.jar"> -- LIFECYCLE DEFINES PHASES
components/antlib/resources/lifecycle.xml:                        signedjar="${target.dir}/${ivy.module}.jar" -- DITTO
components/insight/build/dist.xml:          <fileset dir="${base.runtimelib.dir}" includes="${ivy.module}.jar"/> -- RUNTIME
components/tools/OmeroImporter/build.xml:                includes="${ivy.module}.jar"/> -- POST-INSTALL
components/tools/OmeroImporter/build.xml:            <jarfileset dir="${target.dir}" includes="${ivy.module}.jar"/> -- POST-INSTALL
components/tools/OmeroImporter/build.xml:                includes="${ivy.module}.jar,*.exe"/> -- POST-INSTALL
components/tools/OmeroImporter/build.xml:        <unjar src="${target.dir}/${ivy.module}.jar" dest="${tools.classes}"> -- POST-INSTALL

comment:5 Changed 10 years ago by jmoore

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

Merged into origin/develop

comment:6 Changed 10 years ago by jmoore <josh@…>

  • Remaining Time set to 0

(In [ee203242c846e0edf4315b72265efba98c3e5477/ome.git] on branch develop) Fix build by referencing UNSIGNED jar (Fix #9359)

During the "package" phase of the build, the regular
jar does not exist. Only ${ivy.module}-UNSIGNED
exists. The "install" phase turns the unsigned version
into the final version.

comment:7 Changed 10 years ago by Josh Moore <josh@…>

(In [fd1b41b17aa649dac8937506e1f6c984e3068660/ome.git] on branch develop) Merge pull request #282 from joshmoore/9359-importer-jar

Fix build by referencing UNSIGNED jar (Fix #9359)

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