SSDM-7238: using bioformats 6.0.0 in build scripts

datastore_server/build.gradle

@@ -33,7 +33,7 @@ dependencies {
 			'apache:commons-fileupload:+',
 			'lyncode:xoai-data-provider:+'
 
-  runtime 'bioformats:bioformats:5.9.2'
+  runtime 'bioformats:bioformats:6.0.0'
 
 	testCompile (project(path: ':openbis', configuration: 'tests')) {
 		exclude group: 'google', module: 'gwt-user'

image_readers/build.gradle

@@ -7,7 +7,7 @@ dependencies {
     compile project(':common'),
         'imagej:ij:+',
         'sun:jai:+',
-        'bioformats:bioformats:5.9.2',
+        'bioformats:bioformats:6.0.0',
         'slf4j:slf4j:+',
         'slf4j:slf4j-log4j12:+'
         

openbis_standard_technologies/build.gradle

@@ -85,7 +85,7 @@ dependencies {
 					 project(':screening'),
 					 project(':rtd_phosphonetx'),
 					 project(':plasmid'),
-					 'bioformats:bioformats:5.9.2',
+					 'bioformats:bioformats:6.0.0',
 					 'imagej:ij:+',
 					 'cisd:cisd-openbis-knime-server:+',
 					 'apache:xml-apis:+',

openbis_standard_technologies/query-api.gradle

@@ -112,7 +112,7 @@ task apiV3Jar(type: Jar) {
           include "ch/systemsx/cisd/common/api/**/*.class"
           exclude "ch/systemsx/cisd/common/api/server/**/*.class"
           include "ch/systemsx/cisd/common/reflection/*.class"
-          include "ch/systemsx/cisd/common/shared/basic/string/*.class"
+          include "ch/systemsx/cisd/common/shared/basic/**/*.class"
           include "ch/systemsx/cisd/openbis/common/api/**/*.class"
           exclude "ch/systemsx/cisd/openbis/common/api/server/**/*.class"
           include "ch/ethz/sis/openbis/generic/asapi/v3/**/*.class"
@@ -222,6 +222,8 @@ task apiV3Sources(type: Jar) {
           include "ch/systemsx/cisd/common/spring/IRemoteSpringBeanProvider.java"
           include "ch/systemsx/cisd/common/api/**/*.java"
           exclude "ch/systemsx/cisd/common/api/server/**/*.java"
+          include "ch/systemsx/cisd/common/reflection/*.java"
+          include "ch/systemsx/cisd/common/shared/basic/**/*.java"
           include "ch/systemsx/cisd/openbis/common/api/**/*.java"
           exclude "ch/systemsx/cisd/openbis/common/api/server/**/*.java"
           include "ch/ethz/sis/openbis/generic/asapi/v3/**/*.java"

screening/build.gradle

@@ -15,7 +15,7 @@ dependencies {
             'openhms:jackcess:+',
             'reveregroup:gwt-image-loader:+',
             'imagej:ij:+',
-            'bioformats:bioformats:5.9.2'
+            'bioformats:bioformats:6.0.0'
 
     testCompile project(path: ':datastore_server', configuration: 'tests')
 }