262 add config to allow download of exports in the frontend

README.md

@@ -5,7 +5,7 @@ MoPat is a web-based platform designed to transform conventional paper-based que
 Currently MoPat supports the automatic export to the following data formats or systems: 
 
 - [CDISC ODM v1.3.2](https://www.cdisc.org/standards/data-exchange/odm) 
-- [HL7 FHIR R3](https://hl7.org/fhir/) (R4B coming soon) 
+- [HL7 FHIR (STU3, R4B, R5)](https://hl7.org/fhir/) 
 - [HL7 v2.3](https://www.hl7.org/implement/standards/product_brief.cfm?product_id=185) 
 - [REDCap v14+](https://www.project-redcap.org/) 
 

db/installationInit.sql

@@ -115,7 +115,8 @@ INSERT INTO `configuration` (`id`, `type`, `configuration_group_id`, `parent`, `
 (90, 'GENERAL', 11, 87, 9, 'FHIRViaHL7v2SendingFacility', 'STRING', NULL, 'de.imi.mopat.io.impl.EncounterExporterTemplateFHIR', 'configuration.label.ODMviaHL7SendingFacility', NULL, NULL, '87e35940-97e2-4c3e-ae6c-b35ea65717e3', '', NULL),
 (91, 'GENERAL', 11, 87, 10, 'FHIRViaHL7v2ReceivingApplication', 'STRING', NULL, 'de.imi.mopat.io.impl.EncounterExporterTemplateFHIR', 'configuration.label.ODMviaHL7ReceivingApplication', NULL, NULL, 'd500a3a1-c1ce-4091-ace9-4557481dba37', '', NULL),
 (92, 'GENERAL', 11, 87, 11, 'FHIRViaHL7v2ReceivingFacility', 'STRING', NULL, 'de.imi.mopat.io.impl.EncounterExporterTemplateFHIR', 'configuration.label.ODMviaHL7ReceivingFacility', NULL, NULL, '613cc529-396e-4a06-b785-158c15629d02', '', NULL),
-(93, 'GENERAL', 11, 87, 11, 'FHIRViaHL7v2OBRFillerOrderNumber', 'STRING', NULL, 'de.imi.mopat.io.impl.EncounterExporterTemplateFHIR', 'configuration.label.ODMviaHL7OBRFillerOrderNumber', NULL, NULL, 'e78a6310-b2b1-4ee7-aea0-378ab33c3f73', '', NULL);
+(93, 'GENERAL', 11, 87, 11, 'FHIRViaHL7v2OBRFillerOrderNumber', 'STRING', NULL, 'de.imi.mopat.io.impl.EncounterExporterTemplateFHIR', 'configuration.label.ODMviaHL7OBRFillerOrderNumber', NULL, NULL, 'e78a6310-b2b1-4ee7-aea0-378ab33c3f73', '', NULL),
+(96, 'GENERAL', 1, NULL, 19, 'enableEncounterTemplateDownload', 'BOOLEAN', 'configuration.label.enableEncounterTemplateDownload', 'GLOBAL', 'configuration.label.enableEncounterTemplateDownload', NULL, NULL,'d8219938-021c-49b9-838e-1880b04e7e2e', false, NULL);
 
 
 

db/installationInitTest.sql

@@ -122,7 +122,8 @@ INSERT INTO `configuration` (`id`, `type`, `configuration_group_id`, `parent`, `
 (90, 'GENERAL', 11, 87, 9, 'FHIRViaHL7v2SendingFacility', 'STRING', NULL, 'de.imi.mopat.io.impl.EncounterExporterTemplateFHIR', 'configuration.label.ODMviaHL7SendingFacility', NULL, NULL, '87e35940-97e2-4c3e-ae6c-b35ea65717e3', '', NULL),
 (91, 'GENERAL', 11, 87, 10, 'FHIRViaHL7v2ReceivingApplication', 'STRING', NULL, 'de.imi.mopat.io.impl.EncounterExporterTemplateFHIR', 'configuration.label.ODMviaHL7ReceivingApplication', NULL, NULL, 'd500a3a1-c1ce-4091-ace9-4557481dba37', '', NULL),
 (92, 'GENERAL', 11, 87, 11, 'FHIRViaHL7v2ReceivingFacility', 'STRING', NULL, 'de.imi.mopat.io.impl.EncounterExporterTemplateFHIR', 'configuration.label.ODMviaHL7ReceivingFacility', NULL, NULL, '613cc529-396e-4a06-b785-158c15629d02', '', NULL),
-(93, 'GENERAL', 11, 87, 11, 'FHIRViaHL7v2OBRFillerOrderNumber', 'STRING', NULL, 'de.imi.mopat.io.impl.EncounterExporterTemplateFHIR', 'configuration.label.ODMviaHL7OBRFillerOrderNumber', NULL, NULL, 'e78a6310-b2b1-4ee7-aea0-378ab33c3f73', '', NULL);
+(93, 'GENERAL', 11, 87, 11, 'FHIRViaHL7v2OBRFillerOrderNumber', 'STRING', NULL, 'de.imi.mopat.io.impl.EncounterExporterTemplateFHIR', 'configuration.label.ODMviaHL7OBRFillerOrderNumber', NULL, NULL, 'e78a6310-b2b1-4ee7-aea0-378ab33c3f73', '', NULL),
+(96, 'GENERAL', 1, NULL, 19, 'enableEncounterTemplateDownload', 'BOOLEAN', 'configuration.label.enableEncounterTemplateDownload', 'GLOBAL', 'configuration.label.enableEncounterTemplateDownload', NULL, NULL,'d8219938-021c-49b9-838e-1880b04e7e2e', false, NULL);
 
 
 CREATE TABLE IF NOT EXISTS `clinic_configuration` (

db/update/v3.4.0.sql

@@ -0,0 +1,54 @@
+USE
+`moPat`;
+
+ALTER TABLE moPat.configuration MODIFY COLUMN value TEXT DEFAULT NULL NULL;
+
+UPDATE export_template
+SET export_template_type = REPLACE(export_template_type, 'FHIR', 'FHIR_DSTU3')
+WHERE export_template_type LIKE 'FHIR';
+
+UPDATE moPat.export_template
+SET export_template_type = 'HL7v2'
+WHERE export_template_type = 'ORBIS';
+
+SELECT id
+INTO @ORBIS_CONFIG_GROUP
+FROM moPat.configuration_group
+WHERE label_message_code = 'configurationGroup.label.ORBIS' LIMIT 1;
+
+SELECT id
+INTO @HL7v2_CONFIG_GROUP
+FROM moPat.configuration_group
+WHERE label_message_code = 'configurationGroup.label.HLSeven' LIMIT 1;
+
+UPDATE moPat.export_template
+SET configuration_group = @HL7v2_CONFIG_GROUP
+WHERE configuration_group = @ORBIS_CONFIG_GROUP;
+
+DELETE
+FROM moPat.configuration
+WHERE label_message_code = 'configuration.label.exportOrbisPath';
+DELETE
+FROM moPat.configuration_group
+WHERE label_message_code = 'configurationGroup.label.ORBIS';
+
+ALTER TABLE question
+    ADD COLUMN is_just_info TINYINT(1) NOT NULL DEFAULT 0;
+
+SELECT MAX(id)
+INTO @largest_id
+FROM moPat.configuration;
+
+-- Configuration may change with changing groups added. Please make sure this fits to your server config.
+-- Adjust configuration_group_id to fit to your FHIR config group. Copy the values for all available FHIR configs on the server
+-- You can find the ids with this query:
+-- SELECT id FROM moPat.configuration_group WHERE configuration_group.label_message_code LIKE '%FHIR';
+-- On a server with no additional config groups, the id should be 11
+INSERT INTO moPat.configuration (`id`, `type`, `configuration_group_id`, `parent`, `position`,
+                                 `attribute`, `configuration_type`, `description_message_code`,
+                                 `class`, `label_message_code`, `test_method`, `update_method`,
+                                 `uuid`, `value`, `pattern`)
+VALUES (@largest_id + 1, 'GENERAL', 1, NULL, 19, 'enableEncounterTemplateDownload', 'BOOLEAN',
+        'configuration.label.enableEncounterTemplateDownload', 'GLOBAL',
+        'configuration.label.enableEncounterTemplateDownload', NULL, NULL,
+        'd8219938-021c-49b9-838e-1880b04e7e2e', false, NULL);

pom.xml

@@ -169,6 +169,7 @@
                 </exclusion>
             </exclusions>
         </dependency>
+
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-caching-caffeine</artifactId>
@@ -178,16 +179,9 @@
                     <groupId>com.github.ben-manes.caffeine</groupId>
                     <artifactId>caffeine</artifactId>
                 </exclusion>
-                <exclusion>
-                    <groupId>com.google.errorprone</groupId>
-                    <artifactId>error_prone_annotations</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.checkerframework</groupId>
-                    <artifactId>checker-qual</artifactId>
-                </exclusion>
             </exclusions>
         </dependency>
+
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-client</artifactId>

src/main/java/de/imi/mopat/config/AppConfig.java

@@ -3,6 +3,10 @@
 import de.imi.mopat.helper.controller.ClinicPatientDataRetrieverFactoryBean;
 import de.imi.mopat.helper.controller.MailSender;
 import de.imi.mopat.helper.controller.PatientDataRetriever;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Set;
 import nz.net.ultraq.thymeleaf.layoutdialect.LayoutDialect;
 import org.apache.commons.lang.LocaleUtils;
 import org.springframework.cache.CacheManager;
@@ -52,7 +56,8 @@
 @ComponentScan(basePackages = {"de.imi.mopat.auth", "de.imi.mopat.config",
     "de.imi.mopat.controller", "de.imi.mopat.cron", "de.imi.mopat.dao", "de.imi.mopat.helper.model",
     "de.imi.mopat.helper.controller", "de.imi.mopat.io", "de.imi.mopat.io.impl", "de.imi.mopat.io.importer",
-    "de.imi.mopat.io.importer.fhir", "de.imi.mopat.io.importer.odm", "de.imi.mopat.model", "de.imi.mopat.validator"})
+    "de.imi.mopat.io.importer.fhir", "de.imi.mopat.io.importer.odm", "de.imi.mopat.model",
+    "de.imi.mopat.validator","de.imi.mopat.service"})
 
 @PropertySources({
     @PropertySource("classpath:mopat.properties"),

src/main/java/de/imi/mopat/controller/BundleController.java

@@ -3,18 +3,13 @@
 import de.imi.mopat.dao.AnswerDao;
 import de.imi.mopat.dao.BundleDao;
 import de.imi.mopat.dao.ConditionDao;
-import de.imi.mopat.dao.ExportTemplateDao;
 import de.imi.mopat.dao.QuestionnaireDao;
 import de.imi.mopat.dao.ScoreDao;
 import de.imi.mopat.dao.user.AclClassDao;
 import de.imi.mopat.dao.user.AclObjectIdentityDao;
-import de.imi.mopat.helper.controller.AuthService;
-import de.imi.mopat.helper.controller.BundleService;
+import de.imi.mopat.service.BundleService;
 import de.imi.mopat.helper.controller.LocaleHelper;
-import de.imi.mopat.helper.controller.UserService;
-import de.imi.mopat.helper.controller.ClinicService;
-import de.imi.mopat.helper.model.BundleDTOMapper;
-import de.imi.mopat.helper.model.QuestionnaireDTOMapper;
+import de.imi.mopat.service.ClinicService;
 import de.imi.mopat.model.Answer;
 import de.imi.mopat.model.Bundle;
 import de.imi.mopat.model.BundleClinic;
@@ -26,7 +21,6 @@
 import de.imi.mopat.model.conditions.SelectAnswerCondition;
 import de.imi.mopat.model.conditions.SliderAnswerThresholdCondition;
 import de.imi.mopat.model.dto.BundleDTO;
-import de.imi.mopat.model.dto.BundleQuestionnaireDTO;
 import de.imi.mopat.model.dto.QuestionnaireDTO;
 import de.imi.mopat.validator.BundleDTOValidator;
 

src/main/java/de/imi/mopat/controller/ClinicController.java

@@ -13,14 +13,14 @@
 import de.imi.mopat.helper.model.BundleDTOMapper;
 import de.imi.mopat.helper.model.ClinicConfigurationDTOMapper;
 import de.imi.mopat.helper.model.ClinicDTOMapper;
-import de.imi.mopat.helper.controller.UserService;
+import de.imi.mopat.service.UserService;
 import de.imi.mopat.model.Bundle;
 import de.imi.mopat.model.BundleClinic;
 import de.imi.mopat.model.Clinic;
-import de.imi.mopat.helper.controller.ClinicConfigurationMappingService;
-import de.imi.mopat.helper.controller.ClinicConfigurationService;
-import de.imi.mopat.helper.controller.ClinicService;
-import de.imi.mopat.helper.controller.ConfigurationService;
+import de.imi.mopat.service.ClinicConfigurationMappingService;
+import de.imi.mopat.service.ClinicConfigurationService;
+import de.imi.mopat.service.ClinicService;
+import de.imi.mopat.service.ConfigurationService;
 import de.imi.mopat.model.*;
 import de.imi.mopat.model.dto.*;
 import de.imi.mopat.model.user.User;

src/main/java/de/imi/mopat/controller/ConditionController.java

@@ -5,7 +5,7 @@
 import de.imi.mopat.dao.ConditionDao;
 import de.imi.mopat.dao.QuestionDao;
 import de.imi.mopat.dao.QuestionnaireDao;
-import de.imi.mopat.helper.controller.ConditionService;
+import de.imi.mopat.service.ConditionService;
 import de.imi.mopat.helper.model.BundleDTOMapper;
 import de.imi.mopat.helper.model.ConditionDTOMapper;
 import de.imi.mopat.model.Answer;

src/main/java/de/imi/mopat/controller/ConfigurationController.java

@@ -3,7 +3,7 @@
 import com.mchange.v1.db.sql.UnsupportedTypeException;
 import de.imi.mopat.dao.ConfigurationDao;
 import de.imi.mopat.dao.ConfigurationGroupDao;
-import de.imi.mopat.helper.controller.ConfigurationService;
+import de.imi.mopat.service.ConfigurationService;
 import de.imi.mopat.helper.controller.MailSender;
 import de.imi.mopat.helper.controller.MultiPartFileUploadBean;
 import de.imi.mopat.helper.controller.StringUtilities;