#1 adding datagrid user resolution

.gitignore

@@ -29,3 +29,4 @@ JargonVersion.java
 **/*.*~
 *.*~
 .dbeaver*
+test.metalnx.properties

irodsext-data-profiler/pom.xml

@@ -97,6 +97,95 @@
 							<goal>run</goal>
 						</goals>
 					</execution>
+					<execution>
+						<!-- generate metalnx test properties as standard -->
+						<id>2</id>
+						<phase>validate</phase>
+						<configuration>
+							<tasks>
+								<delete file="${basedir}/src/test/resources/test.metalnx.properties" />
+								<touch file="${basedir}/src/test/resources/test.metalnx.properties"
+									mkdirs="true" />
+								<echo file="${basedir}/src/test/resources/test.metalnx.properties"
+									append="true">
+									irods.host=${jargon.test.irods.host}
+									irods.port=${jargon.test.irods.port}
+									irods.zoneName=${jargon.test.irods.zone}
+									irods.admin.user=${jargon.test.irods.admin}
+									irods.admin.password=${jargon.test.irods.admin.password}
+
+
+									irods.auth.scheme=${metalnx.auth.scheme}
+									default.storage.resource=${jargon.test.irods.resource}
+									ssl.negotiation.policy=${metalnx.ssl.policy}
+
+									##########################################################
+
+									utilize.packing.streams=${metalnx.packing.streams}
+
+
+									compute.checksum=${metalnx.compute.checksum}
+
+									##########################################################
+
+									db.driverClassName=${metalnx.jdbc.driver}
+									db.url=${metalnx.jdbc.url}
+									db.username=${metalnx.jdbc.user}
+									db.password=${metalnx.jdbc.password}
+									hibernate.dialect=${metalnx.jdbc.dialect}
+
+
+									hibernate.show_sql=true
+									hibernate.format_sql=false
+
+
+									hibernate.hbm2ddl.auto=update
+
+
+									connection.pool_size=5
+
+									######################################
+
+									jobs.irods.username=${jargon.test.irods.admin}
+									jobs.irods.password=${jargon.test.irods.admin.password}
+									jobs.irods.auth.scheme=${metalnx.auth.scheme}
+									runSyncJobs=true
+
+
+									rmd.connection.timeout=500
+									rmd.connection.port=8000
+
+									reverse.dns.lookup=false
+
+									######################################
+
+									populate.msi.enabled=false
+									illumina.msi.enabled=true
+
+									msi.api.version=1.X.X
+
+									msi.metalnx.list=libmsiget_illumina_meta.so,libmsiobjget_microservices.so,libmsiobjget_version.so,libmsiobjjpeg_extract.so,libmsiobjput_mdbam.so,libmsiobjput_mdbam.so,libmsiobjput_mdmanifest.so,libmsiobjput_mdvcf.so,libmsiobjput_populate.so
+
+									msi.irods.list=libmsisync_to_archive.so,libmsi_update_unixfilesystem_resource_free_space.so,libmsiobjput_http.so,libmsiobjput_irods.so,libmsiobjget_irods.so,libmsiobjget_http.so,libmsiobjput_slink.so,libmsiobjget_slink.so
+
+									msi.irods.42.list=libmsisync_to_archive.so,libmsi_update_unixfilesystem_resource_free_space.so
+
+									msi.other.list=
+
+									resource.location.images=/images/,classpath:static/images/
+									resource.location.fonts=/fonts/,classpath:static/fonts/
+									resource.location.css=/css/,classpath:static/css/
+									resource.location.js=/js/,classpath:static/js/
+									resource.location.i18=classpath:i18n/messages
+									resource.location.i18-users=classpath:i18n-users/messages
+
+								</echo>
+							</tasks>
+						</configuration>
+						<goals>
+							<goal>run</goal>
+						</goals>
+					</execution>
 				</executions>
 			</plugin>
 			<plugin>

irodsext-data-profiler/src/main/java/org/irodsext/dataprofiler/IrodsextDataProfilerFactoryImpl.java

@@ -10,6 +10,8 @@
 import org.irods.jargon.extensions.dataprofiler.DataProfilerService;
 import org.irods.jargon.extensions.dataprofiler.DataProfilerSettings;
 import org.irods.jargon.extensions.datatyper.DataTypeResolutionServiceFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import com.emc.metalnx.core.domain.entity.DataGridUser;
@@ -24,6 +26,10 @@
  */
 public class IrodsextDataProfilerFactoryImpl implements DataProfilerFactory {
 
+	public static final Logger log = LoggerFactory.getLogger(IrodsextDataProfilerFactoryImpl.class);
+
+	public static final String DATA_GRID_USER_KEY = "DataGridUser";
+
 	@Autowired
 	private IRODSAccessObjectFactory irodsAccessObjectFactory;
 
@@ -62,6 +68,7 @@ public DataProfilerService instanceDataProfilerService(final IRODSAccount irodsA
 		dataProfilerService.setDataTypeResolutionService(
 				dataTypeResolutionServiceFactory.instanceDataTypeResolutionService(irodsAccount));
 		dataProfilerService.setFavoritesService(getFavoritesService());
+		dataProfilerService.setDataGridUser(resolveDataGridUser(irodsAccount));
 		return dataProfilerService;
 	}
 
@@ -126,4 +133,9 @@ public void setUserService(UserService userService) {
 		this.userService = userService;
 	}
 
+	private DataGridUser resolveDataGridUser(final IRODSAccount irodsAccount) {
+		log.info("resolveDataGridUser");
+		return userService.findByUsernameAndAdditionalInfo(irodsAccount.getUserName(), irodsAccount.getZone());
+	}
+
 }

irodsext-data-profiler/src/test/java/org/irodsext/dataprofiler/IrodsextDataProfilerServiceTest.java

@@ -30,6 +30,10 @@
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.mockito.Mockito;
+
+import com.emc.metalnx.core.domain.entity.DataGridUser;
+import com.emc.metalnx.services.interfaces.FavoritesService;
 
 /**
  * @author Mike Conway - NIEHS
@@ -76,6 +80,47 @@ public void afterEach() throws Exception {
 		irodsFileSystem.closeAndEatExceptions();
 	}
 
+	/**
+	 * Test method for
+	 * {@link org.irodsext.dataprofiler.IrodsextDataProfilerService#retrieveDataProfile(java.lang.String, org.irods.jargon.extensions.dataprofiler.DataProfilerSettings)}.
+	 */
+	@Test
+	public void testProfileWithCollectionWithStar() throws Exception {
+		IRODSAccount irodsAccount = testingPropertiesHelper.buildIRODSAccountFromTestProperties(testingProperties);
+		IRODSAccessObjectFactory accessObjectFactory = irodsFileSystem.getIRODSAccessObjectFactory();
+		String targetIrodsCollection = testingPropertiesHelper
+				.buildIRODSCollectionAbsolutePathFromTestProperties(testingProperties, IRODS_TEST_SUBDIR_PATH);
+
+		DataProfilerSettings dataProfilerSettings = new DataProfilerSettings();
+		dataProfilerSettings.setDetectMimeAndInfoType(false);
+		dataProfilerSettings.setRetrieveAcls(true);
+		dataProfilerSettings.setRetrieveMetadata(true);
+		dataProfilerSettings.setRetrieveReplicas(false);
+		dataProfilerSettings.setRetrieveShared(false);
+		dataProfilerSettings.setRetrieveStarred(true);
+		dataProfilerSettings.setRetrieveTickets(false);
+		DataTyperSettings dataTyperSettings = new DataTyperSettings();
+		dataTyperSettings.setDetailedDetermination(false);
+		dataTyperSettings.setPersistDataTypes(false);
+		DataTypeResolutionService dataTyperService = new IrodsextDataTypeResolutionService(accessObjectFactory,
+				irodsAccount, dataTyperSettings);
+		DataGridUser dataGridUser = new DataGridUser();
+		dataGridUser.setUsername(irodsAccount.getUserName());
+
+		FavoritesService favoritesService = Mockito.mock(FavoritesService.class);
+		Mockito.when(favoritesService.isPathFavoriteForUser(dataGridUser, targetIrodsCollection)).thenReturn(true);
+
+		IrodsextDataProfilerService dataProfilerService = new IrodsextDataProfilerService(dataProfilerSettings,
+				accessObjectFactory, irodsAccount);
+		dataProfilerService.setFavoritesService(favoritesService);
+		dataProfilerService.setDataTypeResolutionService(dataTyperService);
+		@SuppressWarnings("rawtypes")
+		DataProfile dataProfile = dataProfilerService.retrieveDataProfile(targetIrodsCollection);
+
+		Assert.assertTrue("should be starred", dataProfile.isStarred());
+
+	}
+
 	/**
 	 * Test method for
 	 * {@link org.irodsext.dataprofiler.IrodsextDataProfilerService#retrieveDataProfile(java.lang.String, org.irods.jargon.extensions.dataprofiler.DataProfilerSettings)}.

irodsext-data-profiler/src/test/resources/test.metalnx.properties

@@ -0,0 +1,70 @@
+irods.host=server4.local
+									irods.port=1247
+									irods.zoneName=zone1
+									irods.admin.user=rods
+									irods.admin.password=rods
+
+
+									irods.auth.scheme=STANDARD
+									default.storage.resource=test1-resc
+									ssl.negotiation.policy=CS_NEG_REFUSE
+
+									##########################################################
+
+									utilize.packing.streams=true
+
+
+									compute.checksum=true
+
+									##########################################################
+
+									db.driverClassName=org.postgresql.Driver
+									db.url=jdbc:postgresql://localhost:5432/IRODS-EXT
+									db.username=irodsext
+									db.password=password
+									hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect
+
+
+									hibernate.show_sql=true
+									hibernate.format_sql=false
+
+
+									hibernate.hbm2ddl.auto=update
+
+
+									connection.pool_size=5
+
+									######################################
+
+									jobs.irods.username=rods
+									jobs.irods.password=rods
+									jobs.irods.auth.scheme=STANDARD
+									runSyncJobs=true
+
+
+									rmd.connection.timeout=500
+									rmd.connection.port=8000
+
+									reverse.dns.lookup=false
+
+									######################################
+
+									populate.msi.enabled=false
+									illumina.msi.enabled=true
+
+									msi.api.version=1.X.X
+
+									msi.metalnx.list=libmsiget_illumina_meta.so,libmsiobjget_microservices.so,libmsiobjget_version.so,libmsiobjjpeg_extract.so,libmsiobjput_mdbam.so,libmsiobjput_mdbam.so,libmsiobjput_mdmanifest.so,libmsiobjput_mdvcf.so,libmsiobjput_populate.so
+
+									msi.irods.list=libmsisync_to_archive.so,libmsi_update_unixfilesystem_resource_free_space.so,libmsiobjput_http.so,libmsiobjput_irods.so,libmsiobjget_irods.so,libmsiobjget_http.so,libmsiobjput_slink.so,libmsiobjget_slink.so
+
+									msi.irods.42.list=libmsisync_to_archive.so,libmsi_update_unixfilesystem_resource_free_space.so
+
+									msi.other.list=
+
+									resource.location.images=/images/,classpath:static/images/
+									resource.location.fonts=/fonts/,classpath:static/fonts/
+									resource.location.css=/css/,classpath:static/css/
+									resource.location.js=/js/,classpath:static/js/
+									resource.location.i18=classpath:i18n/messages
+									resource.location.i18-users=classpath:i18n-users/messages