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Update to latest OME artifacts
Many previous dependency exclusions are no longer needed; however, several new exclusions are now necessary to avoid classpath clashes.
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‎pom.xml‎

Lines changed: 73 additions & 128 deletions
Original file line numberDiff line numberDiff line change
@@ -107,7 +107,7 @@
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<!--
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HACK: The following list of allowed-to-be-duplicated classes
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facilitates intended combinations of artifacts:
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* omero:blitz + org.hibernate:hibernate-core
110+
* org.openmicroscopy:omero-blitz + org.hibernate:hibernate-core
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* org.apache.hadoop:hadoop-yarn-*
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* org.apache.spark:spark-*_2.11
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* org.jmockit:jmockit + junit:junit
@@ -572,7 +572,7 @@
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above.
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-->
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575-
<!-- Open Microscopy Environment - https://github.com/openmicroscopy -->
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<!-- Open Microscopy Environment - https://github.com/ome -->
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<!-- OME Common Java - https://github.com/ome/ome-common-java -->
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<ome-common.version>6.0.3</ome-common.version>
@@ -593,15 +593,15 @@
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<formats-bsd.version>${bio-formats.version}</formats-bsd.version>
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<formats-gpl.version>${bio-formats.version}</formats-gpl.version>
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596-
<!-- OMERO - https://github.com/openmicroscopy/openmicroscopy -->
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<omero.version>5.4.10-ice36-b105</omero.version>
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<blitz.version>${omero.version}</blitz.version>
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<common.version>${omero.version}</common.version>
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<dsl.version>${omero.version}</dsl.version>
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<model-psql.version>${omero.version}</model-psql.version>
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<rendering.version>${omero.version}</rendering.version>
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<romio.version>${omero.version}</romio.version>
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<server.version>${omero.version}</server.version>
596+
<!-- OMERO - https://github.com/ome/openmicroscopy -->
597+
<omero-blitz.version>5.5.3</omero-blitz.version>
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<omero-common.version>5.5.2</omero-common.version>
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<omero-dsl-plugin.version>5.5.0</omero-dsl-plugin.version>
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<omero-gateway.version>5.5.3</omero-gateway.version>
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<omero-model.version>5.5.2</omero-model.version>
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<omero-renderer.version>5.5.2</omero-renderer.version>
603+
<omero-romio.version>5.5.2</omero-romio.version>
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<omero-server.version>5.5.4</omero-server.version>
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<!-- Other SciJava components -->
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@@ -2077,7 +2077,7 @@
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<version>${trakem2-transform.version}</version>
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</dependency>
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<!-- Open Microscopy Environment - https://github.com/openmicroscopy -->
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<!-- Open Microscopy Environment - https://github.com/ome -->
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<!-- Metakit - https://github.com/ome/ome-metakit -->
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<dependency>
@@ -2124,10 +2124,6 @@
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<groupId>ch.qos.logback</groupId>
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<artifactId>logback-classic</artifactId>
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</exclusion>
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<exclusion>
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<groupId>com.google.code.findbugs</groupId>
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<artifactId>annotations</artifactId>
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</exclusion>
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<exclusion>
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<groupId>xalan</groupId>
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<artifactId>serializer</artifactId>
@@ -2153,7 +2149,7 @@
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<version>${ome-xml.version}</version>
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</dependency>
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2156-
<!-- Bio-Formats - https://github.com/openmicroscopy/bioformats -->
2152+
<!-- Bio-Formats - https://github.com/ome/bioformats -->
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<dependency>
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<groupId>ome</groupId>
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<artifactId>bio-formats_plugins</artifactId>
@@ -2199,38 +2195,28 @@
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<version>${formats-gpl.version}</version>
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</dependency>
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2202-
<!-- OMERO - https://github.com/openmicroscopy/openmicroscopy -->
2198+
<!-- OMERO - https://github.com/ome/openmicroscopy -->
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<dependency>
2204-
<groupId>omero</groupId>
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<artifactId>blitz</artifactId>
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<version>${blitz.version}</version>
2207-
</dependency>
2208-
<dependency>
2209-
<groupId>omero</groupId>
2210-
<artifactId>common</artifactId>
2211-
<version>${common.version}</version>
2200+
<groupId>org.openmicroscopy</groupId>
2201+
<artifactId>omero-blitz</artifactId>
2202+
<version>${omero-blitz.version}</version>
22122203
<exclusions>
22132204
<exclusion>
2214-
<!--
2215-
The banDuplicateClasses rule of the maven-enforcer-plugin reports a
2216-
conflict between logback-classic & slf4j-simple in some scenarios.
2217-
Both include an SLF4J binding (org.slf4j.impl.StaticLoggerBinder).
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Perhaps the classpath of the tooling also includes slf4j-simple?
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Regardless, it is generally problematic to inflict a specific SLF4J
2220-
binding on downstream consumers. "Embedded components such as
2221-
libraries or frameworks should not declare a dependency on any
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SLF4J binding but only depend on slf4j-api."
2223-
See: https://www.slf4j.org/manual.html#libraries
2224-
-->
2225-
<groupId>ch.qos.logback</groupId>
2226-
<artifactId>logback-classic</artifactId>
2205+
<!-- Conflicts with javax.activation:activation -->
2206+
<groupId>com.sun.activation</groupId>
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<artifactId>javax.activation</artifactId>
2208+
</exclusion>
2209+
<exclusion>
2210+
<!-- Uber-JAR of all batik components -->
2211+
<groupId>org.apache.xmlgraphics</groupId>
2212+
<artifactId>batik-all</artifactId>
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</exclusion>
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</exclusions>
22292215
</dependency>
22302216
<dependency>
2231-
<groupId>omero</groupId>
2232-
<artifactId>dsl</artifactId>
2233-
<version>${dsl.version}</version>
2217+
<groupId>org.openmicroscopy</groupId>
2218+
<artifactId>omero-common</artifactId>
2219+
<version>${omero-common.version}</version>
22342220
<exclusions>
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<exclusion>
22362222
<!--
@@ -2247,112 +2233,64 @@
22472233
<groupId>ch.qos.logback</groupId>
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<artifactId>logback-classic</artifactId>
22492235
</exclusion>
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<exclusion>
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<!-- Conflicts with commons-beanutils:commons-beanutils -->
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<groupId>commons-beanutils</groupId>
2253-
<artifactId>commons-beanutils-core</artifactId>
2254-
</exclusion>
2255-
<exclusion>
2256-
<!-- Conflicts with net.sourceforge.findbugs:findbugs -->
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<groupId>net.sourceforge.findbugs</groupId>
2258-
<artifactId>findbugs-ant</artifactId>
2259-
</exclusion>
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<exclusion>
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<!-- Conflicts with commons-logging:commons-logging -->
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<groupId>org.slf4j</groupId>
2263-
<artifactId>jcl-over-slf4j</artifactId>
2264-
</exclusion>
2265-
<exclusion>
2266-
<!--
2267-
HACK: The omero:dsl artifact depends on org.testng:testng and
2268-
org.uncommons:reportng. Unfortunately, org.uncommons:reportng
2269-
depends on org.testng:testng:jdk15. So omero:dsl ends up depending
2270-
on two different testng artifacts simultaneously, resulting in
2271-
illegal class duplication. Maven dependency management does not
2272-
support classifier-specific exclusion, so we exclude
2273-
org.testng:testng as a whole to avoid the issue.
2274-
-->
2275-
<groupId>org.testng</groupId>
2276-
<artifactId>testng</artifactId>
2277-
</exclusion>
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<exclusion>
2279-
<!-- Conflicts with velocity:velocity -->
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<groupId>velocity</groupId>
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<artifactId>velocity-dep</artifactId>
2282-
</exclusion>
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</exclusions>
22842237
</dependency>
22852238
<dependency>
2286-
<groupId>omero</groupId>
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<artifactId>model-psql</artifactId>
2288-
<version>${model-psql.version}</version>
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<exclusions>
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<exclusion>
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<!-- Conflicts with org.hibernate:hibernate-core -->
2292-
<groupId>org.hibernate</groupId>
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<artifactId>hibernate-commons-annotations</artifactId>
2294-
</exclusion>
2295-
<exclusion>
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<!-- Conflicts with org.hibernate.javax.persistence:hibernate-jpa-2.0-api -->
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<groupId>org.hibernate</groupId>
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<artifactId>ejb3-persistence</artifactId>
2299-
</exclusion>
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<exclusion>
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<!-- Conflicts with org.javassist:javassist -->
2302-
<groupId>javassist</groupId>
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<artifactId>javassist</artifactId>
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</exclusion>
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<exclusion>
2306-
<groupId>xml-apis</groupId>
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<artifactId>xml-apis</artifactId>
2308-
</exclusion>
2309-
</exclusions>
2239+
<groupId>org.openmicroscopy</groupId>
2240+
<artifactId>omero-dsl-plugin</artifactId>
2241+
<version>${omero-dsl-plugin.version}</version>
2242+
</dependency>
2243+
<dependency>
2244+
<groupId>org.openmicroscopy</groupId>
2245+
<artifactId>omero-gateway</artifactId>
2246+
<version>${omero-gateway.version}</version>
23102247
</dependency>
23112248
<dependency>
2312-
<groupId>omero</groupId>
2313-
<artifactId>rendering</artifactId>
2314-
<version>${rendering.version}</version>
2249+
<groupId>org.openmicroscopy</groupId>
2250+
<artifactId>omero-model</artifactId>
2251+
<version>${omero-model.version}</version>
23152252
</dependency>
23162253
<dependency>
2317-
<groupId>omero</groupId>
2318-
<artifactId>romio</artifactId>
2319-
<version>${romio.version}</version>
2254+
<groupId>org.openmicroscopy</groupId>
2255+
<artifactId>omero-renderer</artifactId>
2256+
<version>${omero-renderer.version}</version>
23202257
<exclusions>
23212258
<exclusion>
2322-
<!-- Conflicts with commons-io:commons-io and commons-lang:commons-lang -->
2323-
<groupId>ch.systems.cisd</groupId>
2324-
<artifactId>jhdf5</artifactId>
2259+
<!-- Conflicts with com.mchange:c3p0 and com.mchange:mchange-commons-java -->
2260+
<groupId>c3p0</groupId>
2261+
<artifactId>c3p0</artifactId>
23252262
</exclusion>
23262263
</exclusions>
23272264
</dependency>
23282265
<dependency>
2329-
<groupId>omero</groupId>
2330-
<artifactId>server</artifactId>
2331-
<version>${server.version}</version>
2266+
<groupId>org.openmicroscopy</groupId>
2267+
<artifactId>omero-romio</artifactId>
2268+
<version>${omero-romio.version}</version>
2269+
</dependency>
2270+
<dependency>
2271+
<groupId>org.openmicroscopy</groupId>
2272+
<artifactId>omero-server</artifactId>
2273+
<version>${omero-server.version}</version>
23322274
<exclusions>
23332275
<exclusion>
2334-
<!-- Uber-JAR of all batik components -->
2335-
<groupId>batik</groupId>
2336-
<artifactId>batik-all</artifactId>
2337-
</exclusion>
2338-
<exclusion>
2339-
<!-- Conflicts with edu.ucar:netcdf -->
2340-
<groupId>edu.ucar</groupId>
2341-
<artifactId>grib</artifactId>
2276+
<!-- Conflicts with org.springframework:spring-aop -->
2277+
<groupId>aopalliance</groupId>
2278+
<artifactId>aopalliance</artifactId>
23422279
</exclusion>
23432280
<exclusion>
2344-
<!-- Conflicts with javax.transaction:jta -->
2345-
<groupId>geronimo-spec</groupId>
2346-
<artifactId>geronimo-spec-jta</artifactId>
2281+
<!-- Conflicts with com.mchange:c3p0 and com.mchange:mchange-commons-java -->
2282+
<groupId>c3p0</groupId>
2283+
<artifactId>c3p0</artifactId>
23472284
</exclusion>
23482285
<exclusion>
2349-
<!-- Conflicts with org.aspectj:aspectjweaver -->
2350-
<groupId>org.aspectj</groupId>
2351-
<artifactId>aspectjrt</artifactId>
2286+
<!-- Conflicts with javax.mail:mail -->
2287+
<groupId>com.sun.mail</groupId>
2288+
<artifactId>javax.mail</artifactId>
23522289
</exclusion>
23532290
<exclusion>
2354-
<groupId>xml-apis</groupId>
2355-
<artifactId>xml-apis</artifactId>
2291+
<!-- Uber-JAR of all batik components -->
2292+
<groupId>org.apache.xmlgraphics</groupId>
2293+
<artifactId>batik-all</artifactId>
23562294
</exclusion>
23572295
</exclusions>
23582296
</dependency>
@@ -3420,7 +3358,14 @@
34203358
<ome-poi.version>LATEST</ome-poi.version>
34213359
<ome-xml.version>LATEST</ome-xml.version>
34223360
<bio-formats.version>LATEST</bio-formats.version>
3423-
<omero.version>LATEST</omero.version>
3361+
<omero-blitz.version>LATEST</omero-blitz.version>
3362+
<omero-common.version>LATEST</omero-common.version>
3363+
<omero-dsl-plugin.version>LATEST</omero-dsl-plugin.version>
3364+
<omero-gateway.version>LATEST</omero-gateway.version>
3365+
<omero-model.version>LATEST</omero-model.version>
3366+
<omero-renderer.version>LATEST</omero-renderer.version>
3367+
<omero-romio.version>LATEST</omero-romio.version>
3368+
<omero-server.version>LATEST</omero-server.version>
34243369
</properties>
34253370
<repositories>
34263371
<repository>

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