LMS-2735 - Screening S122 Cleanup - microscopy thumbnails should be placed in...

LMS-2735 - Screening S122 Cleanup - microscopy thumbnails should be placed in a data set with MICROSCOPY_IMG_OVERVIEW type (not HCS_IMAGE_OVERVIEW)

SVN: 24095

openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DatabaseVersionHolder.java

@@ -24,7 +24,7 @@ package ch.systemsx.cisd.openbis.generic.server.dataaccess.db;
 public final class DatabaseVersionHolder
 {
     /** Current version of the database. */
-    private static final String DATABASE_VERSION = "093"; // S123
+    private static final String DATABASE_VERSION = "094"; // S123
 
     private DatabaseVersionHolder()
     {

openbis/source/sql/generic/094/data-094.sql

+----------------------------------------------------------------------------
+--  Purpose:  Insert an initial data set into the table DATABASE_INSTANCES
+----------------------------------------------------------------------------
+
+INSERT INTO database_instances(
+              id
+            , code
+	    	, uuid
+            , is_original_source)
+    VALUES (  nextval('DATABASE_INSTANCE_ID_SEQ')
+            , 'SYSTEM_DEFAULT'
+	    	, 'SYSTEM_DEFAULT'
+            , 'T');
+
+----------------------------------------------------------------------
+--  Purpose:  Insert an initial data set into the table PERSONS
+-----------------------------------------------------------------------
+
+insert into persons
+(id
+,first_name
+,last_name
+,user_id
+,email
+,dbin_id)
+values
+(nextval('PERSON_ID_SEQ')
+,''
+,'System User'
+,'system'
+,''
+,(select id from database_instances where code = 'SYSTEM_DEFAULT') );
+
+-----------------------------------------------------------------------------------
+--  Purpose:  Create Controlled Vocabulary STORAGE_FORMAT
+-----------------------------------------------------------------------------------
+insert into controlled_vocabularies 
+       ( id
+       , code
+       , is_internal_namespace      
+       , description
+       , pers_id_registerer
+       , is_managed_internally
+       , dbin_id)
+values  (nextval('CONTROLLED_VOCABULARY_ID_SEQ')
+       , 'STORAGE_FORMAT'
+       , true
+       , 'The on-disk storage format of a data set'
+       , (select id from persons where user_id ='system')
+       , true
+       , (select id from database_instances where code = 'SYSTEM_DEFAULT'));
+
+
+-----------------------------------------------------------------------------------
+--  Purpose:  Create Controlled Vocabulary Terms for STORAGE_FORMAT
+-----------------------------------------------------------------------------------
+insert into controlled_vocabulary_terms 
+       ( id
+       , code
+       , covo_id 
+       , pers_id_registerer
+       , ordinal )
+values  (nextval('CVTE_ID_SEQ')
+       , 'PROPRIETARY'
+       , (select id from controlled_vocabularies where code = 'STORAGE_FORMAT' and is_internal_namespace = true)
+       , (select id from persons where user_id ='system')
+       , 1);
+
+insert into controlled_vocabulary_terms 
+       ( id
+       , code
+       , covo_id 
+       , pers_id_registerer
+       , ordinal)
+values  (nextval('CVTE_ID_SEQ')
+       , 'BDS_DIRECTORY'
+       , (select id from controlled_vocabularies where code = 'STORAGE_FORMAT' and is_internal_namespace = true)
+       , (select id from persons where user_id ='system')
+       , 2);
+
+------------------------------------------------------------------
+--  Purpose:  Insert an initial data set into the table DATA_TYPES
+------------------------------------------------------------------
+
+insert into data_types
+(id
+,code
+,description)
+values 
+(nextval('DATA_TYPE_ID_SEQ')
+,'VARCHAR'
+,'Short text'
+);
+
+insert into data_types
+(id
+ ,code
+ ,description)
+ values 
+ (nextval('DATA_TYPE_ID_SEQ')
+ ,'MULTILINE_VARCHAR'
+ ,'Long text'
+);
+
+insert into data_types
+(id
+,code
+,description)
+values 
+(nextval('DATA_TYPE_ID_SEQ')
+,'INTEGER'
+,'Integer number'
+);
+
+insert into data_types
+(id
+,code
+,description)
+values 
+(nextval('DATA_TYPE_ID_SEQ')
+,'REAL'
+,'Real number, i.e. an inexact, variable-precision numeric type'
+);
+
+insert into data_types
+(id
+,code
+,description)
+values 
+(nextval('DATA_TYPE_ID_SEQ')
+,'BOOLEAN'
+,'True or False'
+);
+
+insert into data_types
+(id
+,code
+,description)
+values 
+(nextval('DATA_TYPE_ID_SEQ')
+,'TIMESTAMP'
+,'Both date and time. Format: yyyy-mm-dd hh:mm:ss'
+);
+
+insert into data_types
+(id
+ ,code
+ ,description)
+ values 
+ (nextval('DATA_TYPE_ID_SEQ')
+ ,'CONTROLLEDVOCABULARY'
+ ,'Controlled Vocabulary'
+);
+
+insert into data_types
+(id
+ ,code
+ ,description)
+ values 
+ (nextval('DATA_TYPE_ID_SEQ')
+ ,'MATERIAL'
+ ,'Reference to a material'
+);
+
+insert into data_types
+(id
+ ,code
+ ,description)
+ values 
+ (nextval('DATA_TYPE_ID_SEQ')
+ ,'HYPERLINK'
+ ,'Address of a web page'
+);
+
+insert into data_types
+(id
+ ,code
+ ,description)
+ values 
+ (nextval('DATA_TYPE_ID_SEQ')
+ ,'XML'
+ ,'XML document'
+);
+
+----------------------------------------------------------------------
+--  Purpose:  Insert an initial data set into the table PROPERTY_TYPES
+-----------------------------------------------------------------------
+
+insert into property_types
+(id
+,code
+,description
+,label
+,daty_id
+,pers_id_registerer
+,dbin_id)
+values 
+(nextval('PROPERTY_TYPE_ID_SEQ')
+,'DESCRIPTION'
+,'A Description'
+,'Description'
+,(select id from data_types where code ='VARCHAR')
+,(select id from persons where user_id ='system')
+,(select id from database_instances where code = 'SYSTEM_DEFAULT')
+);
+
+--------------------------------------------------------------------------
+--  Purpose:  Insert an initial data set into the table DATA_SET_TYPES
+--------------------------------------------------------------------------
+
+insert into data_set_types
+(id
+,code
+,description
+,dbin_id)
+values 
+(nextval('DATA_SET_TYPE_ID_SEQ')
+,'UNKNOWN'
+,'Unknown'
+,(select id from database_instances where code = 'SYSTEM_DEFAULT')
+);
+
+-------------------------------------------------------------------------
+--  Purpose:  Insert an initial data set into the table FILE_FORMAT_TYPES
+-------------------------------------------------------------------------
+
+insert into file_format_types
+(id
+,code
+,description
+,dbin_id)
+values 
+(nextval('FILE_FORMAT_TYPE_ID_SEQ')
+,'HDF5'
+,'Hierarchical Data Format File, version 5'
+,(select id from database_instances where code = 'SYSTEM_DEFAULT')
+);
+
+insert into file_format_types
+(id
+,code
+,description
+,dbin_id)
+values 
+(nextval('FILE_FORMAT_TYPE_ID_SEQ')
+,'PROPRIETARY'
+,'Proprietary Format File'
+,(select id from database_instances where code = 'SYSTEM_DEFAULT')
+);
+
+insert into file_format_types
+(id
+,code
+,description
+,dbin_id)
+values 
+(nextval('FILE_FORMAT_TYPE_ID_SEQ')
+,'SRF'
+,'Sequence Read Format File'
+,(select id from database_instances where code = 'SYSTEM_DEFAULT')
+);
+
+insert into file_format_types
+(id
+,code
+,description
+,dbin_id)
+values 
+(nextval('FILE_FORMAT_TYPE_ID_SEQ')
+,'TIFF'
+,'TIFF File'
+,(select id from database_instances where code = 'SYSTEM_DEFAULT')
+);
+
+insert into file_format_types
+(id
+,code
+,description
+,dbin_id)
+values 
+(nextval('FILE_FORMAT_TYPE_ID_SEQ')
+,'TSV'
+,'Tab Separated Values File'
+,(select id from database_instances where code = 'SYSTEM_DEFAULT')
+);
+
+insert into file_format_types
+(id
+,code
+,description
+,dbin_id)
+values 
+(nextval('FILE_FORMAT_TYPE_ID_SEQ')
+,'XML'
+,'XML File'
+,(select id from database_instances where code = 'SYSTEM_DEFAULT')
+);
+
+---------------------------------------------------------------------
+--  Purpose:  Insert an initial data set into the table LOCATOR_TYPES
+---------------------------------------------------------------------
+
+insert into locator_types
+(id
+,code
+,description)
+values 
+(nextval('LOCATOR_TYPE_ID_SEQ')
+,'RELATIVE_LOCATION'
+,'Relative Location'
+);
+
+---------------------------------------------------------------------
+--  Purpose:  Insert an initial data into table RELATIONSHIP_TYPES
+---------------------------------------------------------------------
+
+insert into relationship_types
+(id, 
+code, 
+label, 
+parent_label, 
+child_label, 
+description, 
+pers_id_registerer, 
+is_managed_internally, 
+is_internal_namespace, 
+dbin_id) 
+values
+(
+nextval('RELATIONSHIP_TYPE_ID_SEQ'),
+'PARENT_CHILD',
+'Parent - Child', 
+'Parent', 
+'Child', 
+'Parent - Child relationship', 
+(select id from persons where user_id ='system'), 
+'T', 
+'T', 
+(select id from database_instances where code = 'SYSTEM_DEFAULT')
+);
+
+insert into relationship_types
+(id, 
+code, 
+label, 
+parent_label, 
+child_label, 
+description, 
+pers_id_registerer, 
+is_managed_internally, 
+is_internal_namespace, 
+dbin_id) 
+values
+(
+nextval('RELATIONSHIP_TYPE_ID_SEQ'),
+'PLATE_CONTROL_LAYOUT',
+'Plate - Control Layout', 
+'Plate', 
+'Control Layout', 
+'Plate - Control Layout relationship', 
+(select id from persons where user_id ='system'), 
+'T', 
+'T', 
+(select id from database_instances where code = 'SYSTEM_DEFAULT')
+);
+
+

openbis/source/sql/postgresql/094/domains-094.sql

+-- Creating domains
+
+CREATE DOMAIN AUTHORIZATION_ROLE AS VARCHAR(40) CHECK (VALUE IN ('ADMIN', 'POWER_USER', 'USER', 'OBSERVER', 'ETL_SERVER'));
+CREATE DOMAIN BOOLEAN_CHAR AS BOOLEAN DEFAULT FALSE;
+CREATE DOMAIN BOOLEAN_CHAR_OR_UNKNOWN AS CHAR(1) DEFAULT 'U' CHECK (VALUE IN ('F', 'T', 'U'));
+CREATE DOMAIN CODE AS VARCHAR(60);
+CREATE DOMAIN COLUMN_LABEL AS VARCHAR(128);
+CREATE DOMAIN DATA_STORE_SERVICE_KIND AS VARCHAR(40) CHECK (VALUE IN ('PROCESSING', 'QUERIES'));
+CREATE DOMAIN DATA_STORE_SERVICE_REPORTING_PLUGIN_TYPE AS VARCHAR(40) CHECK (VALUE IN ('TABLE_MODEL', 'DSS_LINK'));
+CREATE DOMAIN EVENT_TYPE AS VARCHAR(40) CHECK (VALUE IN ('DELETION', 'MOVEMENT'));
+CREATE DOMAIN FILE AS BYTEA;
+CREATE DOMAIN FILE_NAME AS VARCHAR(100);
+CREATE DOMAIN TEXT_VALUE AS TEXT;
+CREATE DOMAIN OBJECT_NAME AS VARCHAR(50);
+CREATE DOMAIN REAL_VALUE AS REAL;
+CREATE DOMAIN TECH_ID AS BIGINT;
+CREATE DOMAIN TIME_STAMP AS TIMESTAMP WITH TIME ZONE;
+CREATE DOMAIN TIME_STAMP_DFL AS TIMESTAMP WITH TIME ZONE NOT NULL DEFAULT CURRENT_TIMESTAMP;
+CREATE DOMAIN USER_ID AS VARCHAR(50);
+CREATE DOMAIN TITLE_100 AS VARCHAR(100);
+CREATE DOMAIN GRID_EXPRESSION AS VARCHAR(2000);
+CREATE DOMAIN GRID_ID AS VARCHAR(200);
+CREATE DOMAIN ORDINAL_INT AS BIGINT CHECK (VALUE > 0);
+CREATE DOMAIN DESCRIPTION_2000 AS VARCHAR(2000);
+CREATE DOMAIN ARCHIVING_STATUS AS VARCHAR(100) CHECK (VALUE IN ('LOCKED', 'AVAILABLE', 'ARCHIVED', 'ARCHIVE_PENDING', 'UNARCHIVE_PENDING', 'BACKUP_PENDING'));
+CREATE DOMAIN QUERY_TYPE AS VARCHAR(40) CHECK (VALUE IN ('GENERIC', 'EXPERIMENT', 'SAMPLE', 'DATA_SET', 'MATERIAL'));
+CREATE DOMAIN ENTITY_KIND AS VARCHAR(40) CHECK (VALUE IN ('SAMPLE', 'EXPERIMENT', 'DATA_SET', 'MATERIAL'));
+CREATE DOMAIN SCRIPT_TYPE AS VARCHAR(40) CHECK (VALUE IN ('DYNAMIC_PROPERTY', 'MANAGED_PROPERTY'));
\ No newline at end of file

openbis/source/sql/postgresql/094/grants-094.sql

+-- Granting SELECT privilege to group OPENBIS_READONLY
+
+GRANT SELECT ON SEQUENCE attachment_content_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE attachment_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE code_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE controlled_vocabulary_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE core_plugin_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE cvte_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE data_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE data_set_property_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE data_set_relationship_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE data_set_type_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE data_store_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE DATA_STORE_SERVICES_ID_SEQ TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE data_type_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE database_instance_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE dstpt_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE etpt_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE event_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE experiment_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE experiment_property_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE experiment_type_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE file_format_type_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE space_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE deletion_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE locator_type_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE material_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE material_property_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE material_type_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE mtpt_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE perm_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE person_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE project_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE property_type_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE role_assignment_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE sample_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE sample_property_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE sample_type_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE stpt_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE authorization_group_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE filter_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON SEQUENCE query_id_seq TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE attachment_contents TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE attachments TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE controlled_vocabularies TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE controlled_vocabulary_terms TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE core_plugins TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE data_all TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON data TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON data_deleted TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE data_set_properties TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE data_set_properties_history TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON data_set_relationships TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE data_set_relationships_all TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE data_set_type_property_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE data_set_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE data_stores TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE data_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE DATA_STORE_SERVICES TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE DATA_STORE_SERVICE_DATA_SET_TYPES TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE database_instances TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE database_version_logs TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE events TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE experiment_properties TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE experiment_properties_history TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE experiment_type_property_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE experiment_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE experiments_all TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON experiments TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON experiments_deleted TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE external_data TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE file_format_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE spaces TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE deletions TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE locator_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE material_properties TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE material_properties_history TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE material_type_property_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE material_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE materials TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE persons TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE projects TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE property_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE role_assignments TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE sample_properties TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE sample_properties_history TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE sample_type_property_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE sample_types TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE samples_all TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON samples TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON samples_deleted TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON sample_relationships TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE sample_relationships_all TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE authorization_groups TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE authorization_group_persons TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE filters TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE queries TO GROUP OPENBIS_READONLY;
+GRANT SELECT ON TABLE scripts TO GROUP OPENBIS_READONLY;

openbis/source/sql/postgresql/migration/migration-093-094.sql

+-- Migration from 093 to 094 (see screening)

screening/dist/core-plugins/screening/1/as/initialize-master-data.py

@@ -170,6 +170,10 @@ data_set_type_HCS_IMAGE_OVERVIEW = tr.createNewDataSetType('HCS_IMAGE_OVERVIEW')
 data_set_type_HCS_IMAGE_OVERVIEW.setDescription('Overview High Content Screening Images. Generated from raw images.')
 data_set_type_HCS_IMAGE_OVERVIEW.setContainerType(False)
 
+data_set_type_MICROSCOPY_IMG_OVERVIEW = tr.createNewDataSetType('MICROSCOPY_IMG_OVERVIEW')
+data_set_type_MICROSCOPY_IMG_OVERVIEW.setDescription('Overview Microscopy Images. Generated from raw images.')
+data_set_type_MICROSCOPY_IMG_OVERVIEW.setContainerType(False)
+
 data_set_type_HCS_IMAGE_RAW = tr.createNewDataSetType('HCS_IMAGE_RAW')
 data_set_type_HCS_IMAGE_RAW.setDescription('Raw High Content Screening Images')
 data_set_type_HCS_IMAGE_RAW.setContainerType(False)
@@ -342,6 +346,11 @@ assignment_DATA_SET_HCS_IMAGE_OVERVIEW_RESOLUTION.setMandatory(False)
 assignment_DATA_SET_HCS_IMAGE_OVERVIEW_RESOLUTION.setSection(None)
 assignment_DATA_SET_HCS_IMAGE_OVERVIEW_RESOLUTION.setPositionInForms(1)
 
+assignment_DATA_SET_MICROSCOPY_IMG_OVERVIEW_RESOLUTION = tr.assignPropertyType(data_set_type_MICROSCOPY_IMG_OVERVIEW, prop_type_RESOLUTION)
+assignment_DATA_SET_MICROSCOPY_IMG_OVERVIEW_RESOLUTION.setMandatory(False)
+assignment_DATA_SET_MICROSCOPY_IMG_OVERVIEW_RESOLUTION.setSection(None)
+assignment_DATA_SET_MICROSCOPY_IMG_OVERVIEW_RESOLUTION.setPositionInForms(1)
+
 assignment_SAMPLE_PLATE_PLATE_GEOMETRY = tr.assignPropertyType(samp_type_PLATE, prop_type_PLATE_GEOMETRY)
 assignment_SAMPLE_PLATE_PLATE_GEOMETRY.setMandatory(True)
 assignment_SAMPLE_PLATE_PLATE_GEOMETRY.setSection(None)

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java

@@ -207,7 +207,8 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
                 DataSetRegistrationService<ImageDataSetInformation> service)
         {
             DataSetRegistrationTransaction<ImageDataSetInformation> transaction =
-                    service.transaction(incomingDatasetFolder, service.getDataSetRegistrationDetailsFactory());
+                    service.transaction(incomingDatasetFolder,
+                            service.getDataSetRegistrationDetailsFactory());
             IDataSet newDataset = transaction.createNewDataSet(imageDatasetDetails);
             transaction.moveFile(incomingDatasetFolder.getPath(), newDataset);
             return transaction.commit();
@@ -439,7 +440,8 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
                 ThumbnailsInfo thumbnailsInfo = new ThumbnailsInfo();
                 for (ThumbnailsStorageFormat thumbnailsStorageFormat : thumbnailsStorageFormatList)
                 {
-                    IDataSet thumbnailDataset = createThumbnailDataset(thumbnailsStorageFormat);
+                    IDataSet thumbnailDataset =
+                            createThumbnailDataset(imageDataSetInformation, thumbnailsStorageFormat);
                     thumbnailDatasets.add(thumbnailDataset);
 
                     generateThumbnails(imageDataSetStructure, incomingDirectory, thumbnailDataset,
@@ -532,10 +534,12 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
             }
         }
 
-        private IDataSet createThumbnailDataset(ThumbnailsStorageFormat thumbnailsStorageFormat)
+        private IDataSet createThumbnailDataset(ImageDataSetInformation imageDataSetInformation,
+                ThumbnailsStorageFormat thumbnailsStorageFormat)
         {
-            IDataSet thumbnailDataset =
-                    createNewDataSet(ScreeningConstants.DEFAULT_OVERVIEW_IMAGE_DATASET_TYPE);
+            String thumbnailsDatasetTypeCode =
+                    findThumbnailsDatasetTypeCode(imageDataSetInformation);
+            IDataSet thumbnailDataset = createNewDataSet(thumbnailsDatasetTypeCode);
             thumbnailDataset.setFileFormatType(thumbnailsStorageFormat.getFileFormat()
                     .getOpenBISFileType());
             thumbnailDataset.setMeasuredData(false);
@@ -624,6 +628,30 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
             }
         }
 
+        private static String findThumbnailsDatasetTypeCode(
+                ImageDataSetInformation imageDataSetInformation)
+        {
+            String dataSetTypeCode =
+                    imageDataSetInformation.getDataSetType().getCode().toUpperCase();
+
+            if (isHCSImageDataSetType(dataSetTypeCode))
+            {
+                return ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PREFIX
+                        + ScreeningConstants.IMAGE_THUMBNAIL_DATASET_TYPE_MARKER;
+            } else if (isMicroscopyImageDataSetType(dataSetTypeCode))
+            {
+                return dataSetTypeCode.replace(ScreeningConstants.MICROSCOPY_IMAGE_TYPE_SUBSTRING,
+                        ScreeningConstants.MICROSCOPY_THUMBNAIL_TYPE_SUBSTRING);
+            } else
+            {
+                throw UserFailureException
+                        .fromTemplate(
+                                "The image dataset type '%s' is neither standard HCS type (starts with '%s') nor a microscopy type (contains '%s').",
+                                dataSetTypeCode, ScreeningConstants.HCS_IMAGE_DATASET_TYPE_PREFIX,
+                                ScreeningConstants.MICROSCOPY_IMAGE_SAMPLE_TYPE_PATTERN);
+            }
+        }
+
         private static void setSameDatasetOwner(IDataSet templateDataset,
                 IDataSet destinationDataset)
         {

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java

@@ -44,6 +44,12 @@ public class ScreeningConstants
      */
     public static final String IMAGE_CONTAINER_DATASET_TYPE_MARKER = "_CONTAINER";
 
+    /**
+     * All image datasets (both hcs and microscopy) which contain this marker in the dataset type
+     * code are considered to be thumbnail datasets.
+     */
+    public static final String IMAGE_THUMBNAIL_DATASET_TYPE_MARKER = "_OVERVIEW";
+
     // --- HCS dataset types
 
     /** Prefix of a dataset's type which stores hcs data. */
@@ -104,6 +110,9 @@ public class ScreeningConstants
     public static final String MICROSCOPY_CONTAINER_TYPE_SUBSTRING =
             MICROSCOPY_IMAGE_TYPE_SUBSTRING + "_CONTAINER";
 
+    public static final String MICROSCOPY_THUMBNAIL_TYPE_SUBSTRING =
+            MICROSCOPY_IMAGE_TYPE_SUBSTRING + "_OVERVIEW";
+
     /** type of the dataset which stores microscopy images. */
     public static final String ANY_MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN = "MICROSCOPY_IMAGE|"// legacy
             + MICROSCOPY_IMAGE_TYPE_PATTERN;

screening/source/sql/postgresql/migration/migration-093-094.sql

+-------------------------------------------------------
+-- Create MICROSCOPY_IMG_OVERVIEW data set type
+-------------------------------------------------------
+
+insert into data_set_types (id, code, description, dbin_id, is_container) values (
+  nextval('data_set_type_id_seq'),
+  'MICROSCOPY_IMG_OVERVIEW',
+  'Overview Microscopy Images. Generated from raw images.',
+  (select id from database_instances where is_original_source = 'T'),
+  'F'
+);
+
+-----------------------------------------------------------------------
+-- Assign RESOLUTION property to MICROSCOPY_IMG_OVERVIEW data set type
+-----------------------------------------------------------------------
+
+CREATE OR REPLACE FUNCTION assign_resolution_property() RETURNS integer AS $$
+DECLARE
+    rec RECORD;
+    next_ordinal ordinal_int;
+BEGIN
+    FOR rec IN select id from data_set_types where code = 'MICROSCOPY_IMG_OVERVIEW' LOOP
+        next_ordinal = (select max(ordinal)+1 from data_set_type_property_types where id = rec.id);
+        if next_ordinal is null then
+            next_ordinal = 1;
+        end if;
+        insert into data_set_type_property_types
+        (   id
+           ,dsty_id
+           ,prty_id
+           ,is_mandatory
+           ,is_managed_internally
+           ,pers_id_registerer
+           ,ordinal
+           )
+        values 
+           (nextval('DSTPT_ID_SEQ')
+           ,rec.id
+           ,(select id from property_types where code = 'RESOLUTION' and is_internal_namespace = true)
+           ,false
+           ,false
+           ,(select id from persons where user_id ='system')
+           ,next_ordinal
+        );
+    END LOOP;
+    RETURN 1;
+END;
+$$ LANGUAGE 'plpgsql';
+
+SELECT assign_resolution_property();
+DROP FUNCTION assign_resolution_property();
\ No newline at end of file