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Update to a newer Omero version that's proxied in LabKey's Artifactory (#65)
* Update to a newer Omero version that's proxied in LabKey's Artifactory * Remove dependency on omero-blitz in favor of omero-gateway * Update dependencies.txt and jars.txt
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‎omerointegration/build.gradle‎

Lines changed: 71 additions & 64 deletions
Original file line numberDiff line numberDiff line change
@@ -6,75 +6,82 @@ repositories {
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maven {
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url 'https://artifacts.openmicroscopy.org/artifactory/maven/'
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}
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maven {
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url 'https://artifacts.glencoesoftware.com/artifactory/repo/'
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}
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}
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//excludes based on: https://github.com/glencoesoftware/omero-ms-core/blob/master/build.gradle
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dependencies {
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external (group: 'omero', name: 'blitz', version: '5.5.0-m2-ice36-b103') {
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exclude group: 'OME'
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exclude group: 'antlr'
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exclude group: 'asm'
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exclude group: 'backport-util-concurrent'
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exclude group: 'batik'
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exclude group: 'cglib'
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exclude group: 'ch.qos.logback', module: 'logback-classic' // added to prevent excessively verbose global logging
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exclude group: 'com.codahale.metrics'
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exclude group: 'com.drewnoakes'
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exclude group: 'com.esotericsoftware.kryo'
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exclude group: 'com.google.guava'
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exclude group: 'com.jamonapi'
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exclude group: 'com.mortennobel'
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exclude group: 'com.zeroc', module: 'freeze'
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exclude group: 'com.zeroc', module: 'icefreeze'
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exclude group: 'com.zeroc', module: 'icegrid'
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exclude group: 'com.zeroc', module: 'icestorm'
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exclude group: 'commons-beanutils'
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exclude group: 'commons-codec'
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exclude group: 'commons-collections'
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exclude group: 'commons-io'
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exclude group: 'commons-pool'
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exclude group: 'dom4j'
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exclude group: 'edu.ucar'
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exclude group: 'freemarker'
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exclude group: 'geronimo-spec'
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exclude group: 'gnu.getopt'
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exclude group: 'javassist'
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exclude group: 'javax.jts'
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exclude group: 'joda-time'
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exclude group: 'net.sf.ehcache'
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exclude group: 'ome', module: 'formats-gpl'
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exclude group: 'ome', module: 'jai_imageio'
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exclude group: 'ome', module: 'lwf-stubs'
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exclude group: 'ome', module: 'turbojpeg'
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exclude group: 'omero', module: 'dsl'
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exclude group: 'omero', module: 'omero-shares'
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exclude group: 'org.apache.lucene'
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exclude group: 'org.apache.httpcomponents'
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exclude group: 'org.codehaus.btm'
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exclude group: 'org.hibernate'
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exclude group: 'org.hibernate.javax.persistence'
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exclude group: 'org.ini4j'
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exclude group: 'org.postgresql'
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exclude group: 'org.scijava'
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exclude group: 'org.subethamail'
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exclude group: 'pdfbox'
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exclude group: 'quartz'
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exclude group: 'xerces'
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exclude group: 'xalan'
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exclude group: 'xml-apis'
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exclude group: 'zeroc', module: 'ice-db'
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external (group: 'org.openmicroscopy', name: 'omero-gateway', version: '5.6.3')
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{
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exclude group: 'OME'
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exclude group: 'antlr'
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exclude group: 'asm'
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exclude group: 'backport-util-concurrent'
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exclude group: 'batik'
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exclude group: 'cglib'
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exclude group: 'ch.qos.logback', module: 'logback-classic'
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// added to prevent excessively verbose global logging
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exclude group: 'com.codahale.metrics'
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exclude group: 'com.drewnoakes'
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exclude group: 'com.esotericsoftware.kryo'
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exclude group: 'com.google.guava'
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exclude group: 'com.jamonapi'
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exclude group: 'com.mortennobel'
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exclude group: 'com.sun.activation', module: 'javax.activation'
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exclude group: 'com.zeroc', module: 'freeze'
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exclude group: 'com.zeroc', module: 'icefreeze'
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exclude group: 'com.zeroc', module: 'icegrid'
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exclude group: 'com.zeroc', module: 'icestorm'
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exclude group: 'commons-beanutils'
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exclude group: 'commons-codec'
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exclude group: 'commons-collections'
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exclude group: 'commons-io'
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exclude group: 'commons-pool'
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exclude group: 'dom4j'
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exclude group: 'edu.ucar'
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exclude group: 'freemarker'
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exclude group: 'geronimo-spec'
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exclude group: 'gnu.getopt'
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exclude group: 'javassist'
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exclude group: 'javax.jts'
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exclude group: 'joda-time'
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exclude group: 'net.sf.ehcache'
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exclude group: 'ome', module: 'formats-gpl'
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exclude group: 'ome', module: 'jai_imageio'
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exclude group: 'ome', module: 'lwf-stubs'
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exclude group: 'ome', module: 'turbojpeg'
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exclude group: 'omero', module: 'dsl'
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exclude group: 'omero', module: 'omero-shares'
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exclude group: 'org.apache.lucene'
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exclude group: 'org.apache.httpcomponents'
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exclude group: 'org.codehaus.btm'
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exclude group: 'org.hibernate'
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exclude group: 'org.hibernate.javax.persistence'
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exclude group: 'org.ini4j'
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exclude group: "org.json", module: "json"
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exclude group: 'org.postgresql'
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exclude group: 'org.scijava'
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exclude group: 'org.subethamail'
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exclude group: 'pdfbox'
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exclude group: 'quartz'
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exclude group: 'xerces'
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exclude group: 'xalan'
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exclude group: 'xml-apis'
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exclude group: 'zeroc', module: 'ice-db'
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exclude group: 'org.springframework', module: 'spring-aop'
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exclude group: 'org.springframework', module: 'spring-context'
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exclude group: 'org.springframework', module: 'spring-expression'
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exclude group: 'org.springframework', module: 'spring-core'
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exclude group: 'org.springframework', module: 'spring-beans'
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exclude group: 'org.springframework', module: 'spring-jdbc'
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exclude group: 'org.springframework', module: 'spring-tx'
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}
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exclude group: 'org.springframework', module: 'spring-aop'
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exclude group: 'org.springframework', module: 'spring-context'
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exclude group: 'org.springframework', module: 'spring-expression'
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exclude group: 'org.springframework', module: 'spring-core'
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exclude group: 'org.springframework', module: 'spring-beans'
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exclude group: 'org.springframework', module: 'spring-jdbc'
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exclude group: 'org.springframework', module: 'spring-tx'
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}
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
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BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")
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BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module")
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BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "published", depExtension: "module")
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}

‎omerointegration/resources/credits/dependencies.txt‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,2 @@
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# direct external dependencies for project :server:modules:DiscvrLabKeyModules:omerointegration
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blitz-5.5.0-m2-ice36-b103.jar
2+
omero-gateway-5.6.3.jar

‎omerointegration/resources/credits/jars.txt‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
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{table}
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Filename|Component|Version|Source|License|LabKey Dev|Purpose
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blitz-5.5.0-m2-ice36-b103.jar|OMERO Client|5.5.0|{link:OMERO Client|https://www.openmicroscopy.org/site/support/omero5.2/developers/Java.html}|{link:GNU GPL, version 2|https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html}|bbimber|Used to interact with OMERO Servers
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{table}
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omero-gateway-5.6.3.jar|OMERO Client|5.6.3|{link:OMERO Client|https://docs.openmicroscopy.org/omero/5.6.3/developers/Java.html}|{link:GNU GPL, version 2|https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html}|bbimber|Used to interact with OMERO Servers
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{table}

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