diff --git a/.github/workflows/sonarcloud.yml b/.github/workflows/sonarcloud.yml index cf251f7fe7..60f02e50c7 100644 --- a/.github/workflows/sonarcloud.yml +++ b/.github/workflows/sonarcloud.yml @@ -5,6 +5,7 @@ on: push: branches: - development + - main pull_request: branches: - development diff --git a/THIRD-PARTY.txt b/THIRD-PARTY.txt new file mode 100644 index 0000000000..b18375a7c0 --- /dev/null +++ b/THIRD-PARTY.txt @@ -0,0 +1,449 @@ + +Lists of 447 third-party dependencies. + (BSD License) AntLR Parser Generator (antlr:antlr:2.7.7 - http://www.antlr.org/) + (Eclipse Public License - v 1.0) (GNU Lesser General Public License) Logback Classic Module (ch.qos.logback:logback-classic:1.5.12 - http://logback.qos.ch/logback-classic) + (Eclipse Public License - v 1.0) (GNU Lesser General Public License) Logback Core Module (ch.qos.logback:logback-core:1.5.12 - http://logback.qos.ch/logback-core) + (Eclipse Public License - v 1.0) (GNU Lesser General Public License) Logback Core Module (ch.qos.logback:logback-core:1.5.16 - http://logback.qos.ch/logback-core) + (Apache License, Version 2.0) Titanium JSON-LD 1.1 (JRE11) (com.apicatalog:titanium-json-ld:1.3.3 - https://github.com/filip26/titanium-json-ld) + (Apache License, Version 2.0) Internet Time Utility (com.ethlo.time:itu:1.7.0 - https://github.com/ethlo/itu) + (Apache License, Version 2.0) ClassMate (com.fasterxml:classmate:1.7.0 - https://github.com/FasterXML/java-classmate) + (The Apache Software License, Version 2.0) Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.18.1 - https://github.com/FasterXML/jackson) + (The Apache Software License, Version 2.0) Jackson-core (com.fasterxml.jackson.core:jackson-core:2.18.1 - https://github.com/FasterXML/jackson-core) + (The Apache Software License, Version 2.0) jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.18.1 - https://github.com/FasterXML/jackson) + (The Apache Software License, Version 2.0) Jackson-dataformat-YAML (com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.17.3 - https://github.com/FasterXML/jackson-dataformats-text) + (The Apache Software License, Version 2.0) Jackson datatype: jdk8 (com.fasterxml.jackson.datatype:jackson-datatype-jdk8:2.17.3 - https://github.com/FasterXML/jackson-modules-java8/jackson-datatype-jdk8) + (The Apache Software License, Version 2.0) Jackson datatype: JSR310 (com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.18.1 - https://github.com/FasterXML/jackson-modules-java8/jackson-datatype-jsr310) + (The Apache Software License, Version 2.0) Jackson-module-parameter-names (com.fasterxml.jackson.module:jackson-module-parameter-names:2.17.3 - https://github.com/FasterXML/jackson-modules-java8/jackson-module-parameter-names) + (Apache License, Version 2.0) Caffeine cache (com.github.ben-manes.caffeine:caffeine:3.1.8 - https://github.com/ben-manes/caffeine) + (Apache License, Version 2.0) JSON Compare (com.github.fslev:json-compare:6.12 - http://github.com/fslev/json-compare) + (Apache License, Version 2.0) (GNU Lesser General Public License) javaparser-core (com.github.javaparser:javaparser-core:3.25.3 - https://github.com/javaparser/javaparser-core) + (Apache License, Version 2.0) (GNU Lesser General Public License) javaparser-symbol-solver-core (com.github.javaparser:javaparser-symbol-solver-core:3.25.10 - https://github.com/javaparser/javaparser-symbol-solver-core) + (SPDX-License-Identifier: MIT) oshi-core (com.github.oshi:oshi-core:6.4.10 - https://github.com/oshi/oshi/oshi-core) + (Apache License, Version 2.0) JCIP Annotations under Apache License (com.github.stephenc.jcip:jcip-annotations:1.0-1 - http://stephenc.github.com/jcip-annotations) + (BSD License) curvesapi (com.github.virtuald:curvesapi:1.08 - https://github.com/virtuald/curvesapi) + (MIT) waffle-jna (com.github.waffle:waffle-jna:3.3.0 - https://waffle.github.io/waffle/) + (Apache 2.0) AutoService (com.google.auto.service:auto-service-annotations:1.1.1 - https://github.com/google/auto/tree/main/service) + (The Apache Software License, Version 2.0) FindBugs-jsr305 (com.google.code.findbugs:jsr305:3.0.2 - http://findbugs.sourceforge.net/) + (Apache 2.0) error-prone annotations (com.google.errorprone:error_prone_annotations:2.3.3 - http://nexus.sonatype.org/oss-repository-hosting.html/error_prone_parent/error_prone_annotations) + (The Apache Software License, Version 2.0) Guava InternalFutureFailureAccess and InternalFutures (com.google.guava:failureaccess:1.0.2 - https://github.com/google/guava/failureaccess) + (Apache License, Version 2.0) Guava: Google Core Libraries for Java (com.google.guava:guava:33.3.0-jre - https://github.com/google/guava) + (The Apache Software License, Version 2.0) Guava ListenableFuture only (com.google.guava:listenablefuture:9999.0-empty-to-avoid-conflict-with-guava - https://github.com/google/guava/listenablefuture) + (Apache License, Version 2.0) J2ObjC Annotations (com.google.j2objc:j2objc-annotations:3.0.0 - https://github.com/google/j2objc/) + (EPL 1.0) (MPL 2.0) H2 Database Engine (com.h2database:h2:2.3.232 - https://h2database.com) + (Apache 2) ph-css (com.helger:ph-css:7.0.2 - https://github.com/phax/ph-css/ph-css) + (Apache 2) ph-commons (com.helger.commons:ph-commons:11.1.5 - 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https://bitbucket.org/connect2id/oauth-2.0-sdk-with-openid-connect-extensions) + (EDL 1.0) Jakarta Activation (com.sun.activation:jakarta.activation:2.0.1 - https://github.com/eclipse-ee4j/jaf/jakarta.activation) + (Eclipse Distribution License - v 1.0) istack common utility code runtime (com.sun.istack:istack-commons-runtime:4.1.2 - https://projects.eclipse.org/projects/ee4j/istack-commons/istack-commons-runtime) + (EDL 1.0) (EPL 2.0) (GPL2 w/ CPE) Jakarta Mail API (com.sun.mail:jakarta.mail:2.0.1 - http://eclipse-ee4j.github.io/mail/jakarta.mail) + (The Apache Software License, Version 2.0) QDox (com.thoughtworks.qdox:qdox:1.12 - http://qdox.codehaus.org) + (Vaadin Commercial License and Service Terms) Collaboration Engine (com.vaadin:collaboration-engine:6.2.4 - https://vaadin.com/collaboration/collaboration-engine) + (Apache 2) copilot (com.vaadin:copilot:24.4.14 - http://vaadin.com/copilot-project/copilot) + (Apache License Version 2.0) Flow Client (com.vaadin:flow-client:24.4.9 - 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https://www.xmlunit.org/) + (Apache License, Version 2.0) SnakeYAML (org.yaml:snakeyaml:2.2 - https://bitbucket.org/snakeyaml/snakeyaml) diff --git a/application-commons/pom.xml b/application-commons/pom.xml index c7afa7effb..52063be242 100644 --- a/application-commons/pom.xml +++ b/application-commons/pom.xml @@ -5,7 +5,7 @@ datamanager life.qbic - 1.6.6 + 1.7.2 4.0.0 application-commons diff --git a/broadcasting/pom.xml b/broadcasting/pom.xml index cbe7752740..fe68d686b1 100644 --- a/broadcasting/pom.xml +++ b/broadcasting/pom.xml @@ -5,7 +5,7 @@ datamanager life.qbic - 1.6.6 + 1.7.2 4.0.0 broadcasting diff --git a/domain-concept/pom.xml b/domain-concept/pom.xml index b8f51b6f48..a6b8fc6161 100644 --- a/domain-concept/pom.xml +++ b/domain-concept/pom.xml @@ -6,7 +6,7 @@ life.qbic datamanager - 1.6.6 + 1.7.2 domain-concept diff --git a/email-service-provider/pom.xml b/email-service-provider/pom.xml index c9190c5716..645712d3f5 100644 --- a/email-service-provider/pom.xml +++ b/email-service-provider/pom.xml @@ -6,7 +6,7 @@ life.qbic datamanager - 1.6.6 + 1.7.2 life.qbic.infrastructure @@ -21,13 +21,13 @@ life.qbic identity - 1.6.6 + 1.7.2 compile life.qbic project-management - 1.6.6 + 1.7.2 compile diff --git a/finances-api/pom.xml b/finances-api/pom.xml index 1e3de5835e..690499be51 100644 --- a/finances-api/pom.xml +++ b/finances-api/pom.xml @@ -6,7 +6,7 @@ life.qbic datamanager - 1.6.6 + 1.7.2 life.qbic.finances diff --git a/finances-infrastructure/pom.xml b/finances-infrastructure/pom.xml index 8e8abe45b6..6497a06405 100644 --- a/finances-infrastructure/pom.xml +++ b/finances-infrastructure/pom.xml @@ -6,7 +6,7 @@ life.qbic datamanager - 1.6.6 + 1.7.2 finances-infrastructure @@ -20,7 +20,7 @@ life.qbic finances - 1.6.6 + 1.7.2 compile diff --git a/finances/pom.xml b/finances/pom.xml index 933debedac..837a7df681 100644 --- a/finances/pom.xml +++ b/finances/pom.xml @@ -5,7 +5,7 @@ datamanager life.qbic - 1.6.6 + 1.7.2 4.0.0 finances @@ -38,7 +38,7 @@ life.qbic.finances finances-api - 1.6.6 + 1.7.2 compile diff --git a/identity-api/pom.xml b/identity-api/pom.xml index 68463aa71d..dfac62dcdc 100644 --- a/identity-api/pom.xml +++ b/identity-api/pom.xml @@ -6,7 +6,7 @@ life.qbic datamanager - 1.6.6 + 1.7.2 life.qbic.datamanager @@ -21,7 +21,7 @@ life.qbic application-commons - 1.6.6 + 1.7.2 compile diff --git a/identity-infrastructure/pom.xml b/identity-infrastructure/pom.xml index 320d26da6b..388020d014 100644 --- a/identity-infrastructure/pom.xml +++ b/identity-infrastructure/pom.xml @@ -6,14 +6,14 @@ life.qbic datamanager - 1.6.6 + 1.7.2 identity-infrastructure life.qbic identity - 1.6.6 + 1.7.2 compile diff --git a/identity/pom.xml b/identity/pom.xml index fa80f26894..88c7ef3b89 100644 --- a/identity/pom.xml +++ b/identity/pom.xml @@ -5,7 +5,7 @@ datamanager life.qbic - 1.6.6 + 1.7.2 4.0.0 @@ -45,25 +45,25 @@ life.qbic broadcasting - 1.6.6 + 1.7.2 compile life.qbic application-commons - 1.6.6 + 1.7.2 compile life.qbic logging - 1.6.6 + 1.7.2 compile life.qbic domain-concept - 1.6.6 + 1.7.2 compile @@ -86,7 +86,7 @@ life.qbic.datamanager identity-api - 1.6.6 + 1.7.2 compile diff --git a/logging/pom.xml b/logging/pom.xml index 1c1cda5ae1..ddf72cd302 100644 --- a/logging/pom.xml +++ b/logging/pom.xml @@ -5,7 +5,7 @@ datamanager life.qbic - 1.6.6 + 1.7.2 4.0.0 logging @@ -31,7 +31,7 @@ ch.qos.logback logback-core - 1.5.11 + 1.5.16 @@ -53,7 +53,7 @@ life.qbic.logging subscription-api - 1.6.6 + 1.7.2 compile diff --git a/pom.xml b/pom.xml index d5752b5a73..4a184cdf0e 100644 --- a/pom.xml +++ b/pom.xml @@ -7,7 +7,7 @@ life.qbic datamanager Data Manager - 1.6.6 + 1.7.2 user-interface identity @@ -146,14 +146,14 @@ org.apache.groovy groovy-all - 4.0.23 + 4.0.24 pom test org.jobrunr jobrunr-spring-boot-3-starter - 7.3.1 + 7.3.2 com.fasterxml.jackson.core @@ -182,6 +182,25 @@ + + org.codehaus.mojo + license-maven-plugin + 2.0.0 + + + + aggregate-add-third-party + + + + + + ${project.build.directory}/generated-sources/license + THIRD-PARTY.txt + false + true + + org.codehaus.gmavenplus gmavenplus-plugin @@ -220,7 +239,7 @@ maven-surefire-plugin - 3.5.1 + 3.5.2 false diff --git a/project-management-infrastructure/pom.xml b/project-management-infrastructure/pom.xml index 1a08e93cd1..75ab28aaa4 100644 --- a/project-management-infrastructure/pom.xml +++ b/project-management-infrastructure/pom.xml @@ -6,7 +6,7 @@ life.qbic datamanager - 1.6.6 + 1.7.2 life.qbic.identity @@ -29,7 +29,7 @@ life.qbic project-management - 1.6.6 + 1.7.2 compile diff --git a/project-management/pom.xml b/project-management/pom.xml index 0d0c3631e6..69533dce65 100644 --- a/project-management/pom.xml +++ b/project-management/pom.xml @@ -4,7 +4,7 @@ datamanager life.qbic - 1.6.6 + 1.7.2 4.0.0 project-management @@ -37,13 +37,13 @@ life.qbic application-commons - 1.6.6 + 1.7.2 compile life.qbic logging - 1.6.6 + 1.7.2 compile @@ -54,7 +54,7 @@ life.qbic domain-concept - 1.6.6 + 1.7.2 compile @@ -77,13 +77,13 @@ life.qbic.datamanager identity-api - 1.6.6 + 1.7.2 compile life.qbic.finances finances-api - 1.6.6 + 1.7.2 compile diff --git a/project-management/src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java b/project-management/src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java index b26fa230a1..cd4ebc5781 100644 --- a/project-management/src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java +++ b/project-management/src/main/java/life/qbic/projectmanagement/application/measurement/MeasurementService.java @@ -23,6 +23,7 @@ import life.qbic.projectmanagement.application.OrganisationLookupService; import life.qbic.projectmanagement.application.ProjectInformationService; import life.qbic.projectmanagement.application.ontology.SpeciesLookupService; +import life.qbic.projectmanagement.application.ontology.TerminologyService; import life.qbic.projectmanagement.application.sample.SampleIdCodeEntry; import life.qbic.projectmanagement.application.sample.SampleInformationService; import life.qbic.projectmanagement.domain.model.OntologyTerm; @@ -65,28 +66,29 @@ public class MeasurementService { private final MeasurementDomainService measurementDomainService; private final MeasurementLookupService measurementLookupService; private final SampleInformationService sampleInformationService; - private final SpeciesLookupService speciesLookupService; private final OrganisationLookupService organisationLookupService; private final ProjectInformationService projectInformationService; private final MeasurementRepository measurementRepository; + private final TerminologyService terminologyService; @Autowired public MeasurementService(MeasurementDomainService measurementDomainService, SampleInformationService sampleInformationService, - SpeciesLookupService speciesLookupService, OrganisationLookupService organisationLookupService, MeasurementLookupService measurementLookupService, ProjectInformationService projectInformationService, MeasurementRepository measurementRepository, + TerminologyService terminologyService, ApplicationContext context) { this.measurementDomainService = Objects.requireNonNull(measurementDomainService); this.sampleInformationService = Objects.requireNonNull(sampleInformationService); - this.speciesLookupService = Objects.requireNonNull(speciesLookupService); this.organisationLookupService = Objects.requireNonNull(organisationLookupService); this.measurementLookupService = Objects.requireNonNull(measurementLookupService); this.projectInformationService = Objects.requireNonNull(projectInformationService); this.measurementRepository = Objects.requireNonNull(measurementRepository); this.context = Objects.requireNonNull(context); + this.terminologyService = Objects.requireNonNull(terminologyService); + } /** @@ -778,7 +780,7 @@ private boolean allMeasurementCodesExist(List measurementCode) { } private Optional resolveOntologyCURI(String ontologyCURI) { - return speciesLookupService.findByCURI(ontologyCURI).map(OntologyTerm::from); + return terminologyService.findByCurie(ontologyCURI); } private Optional queryIdCodePair(SampleCode sampleCode) { diff --git a/subscription-api/pom.xml b/subscription-api/pom.xml index 412f7be124..90205b1df4 100644 --- a/subscription-api/pom.xml +++ b/subscription-api/pom.xml @@ -5,7 +5,7 @@ datamanager life.qbic - 1.6.6 + 1.7.2 4.0.0 life.qbic.logging diff --git a/subscription-provider/pom.xml b/subscription-provider/pom.xml index 85caf9768c..4b3a6c7777 100644 --- a/subscription-provider/pom.xml +++ b/subscription-provider/pom.xml @@ -5,7 +5,7 @@ datamanager life.qbic - 1.6.6 + 1.7.2 4.0.0 life.qbic.logging @@ -14,7 +14,7 @@ life.qbic.logging subscription-api - 1.6.6 + 1.7.2 compile diff --git a/user-interface/pom.xml b/user-interface/pom.xml index 89486daf67..b015d77a69 100644 --- a/user-interface/pom.xml +++ b/user-interface/pom.xml @@ -11,7 +11,7 @@ life.qbic datamanager - 1.6.6 + 1.7.2 @@ -239,31 +239,31 @@ life.qbic identity - 1.6.6 + 1.7.2 compile life.qbic identity-infrastructure - 1.6.6 + 1.7.2 compile life.qbic broadcasting - 1.6.6 + 1.7.2 compile life.qbic application-commons - 1.6.6 + 1.7.2 compile life.qbic logging - 1.6.6 + 1.7.2 compile @@ -273,24 +273,24 @@ life.qbic project-management - 1.6.6 + 1.7.2 compile life.qbic.logging subscription-provider - 1.6.6 + 1.7.2 life.qbic domain-concept - 1.6.6 + 1.7.2 compile life.qbic finances-infrastructure - 1.6.6 + 1.7.2 compile @@ -300,13 +300,13 @@ life.qbic.identity project-management-infrastructure - 1.6.6 + 1.7.2 compile life.qbic.infrastructure email-service-provider - 1.6.6 + 1.7.2 compile diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementEditTemplate.java b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementEditTemplate.java index 300fc77480..3de6d64e5f 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementEditTemplate.java +++ b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementEditTemplate.java @@ -167,7 +167,6 @@ public byte[] getContent() { } var startIndex = 1; // start in row number 2 with index 1 as the header row has number 1 index 0 - var helperStopIndex = 1; //stop in row number 2 with index 1 as the header row has number 1 index 0 int rowIndex = startIndex; for (NGSMeasurementEntry measurement : measurements) { Row row = getOrCreateRow(sheet, rowIndex); @@ -190,18 +189,6 @@ public byte[] getContent() { DEFAULT_GENERATED_ROW_COUNT - 1, sequencingReadTypeArea); - for (NGSMeasurementEditColumn column : NGSMeasurementEditColumn.values()) { - column.getFillHelp().ifPresent( - helper -> XLSXTemplateHelper.addInputHelper(sheet, - column.columnIndex(), - startIndex, - column.columnIndex(), - helperStopIndex, - helper.exampleValue(), - helper.description()) - ); - } - setAutoWidth(sheet); workbook.setActiveSheet(0); diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementRegisterTemplate.java b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementRegisterTemplate.java index f160f820e3..5c0038c456 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementRegisterTemplate.java +++ b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/NGSMeasurementRegisterTemplate.java @@ -110,7 +110,6 @@ public byte[] getContent() { } var startIndex = 1; // start in row number 2 with index 1 as the header row has number 1 index 0 - var helperStopIndex = 1; //stop in row number 2 with index 1 as the header row has number 1 index 0 // make sure to create the visible sheet first Sheet hiddenSheet = workbook.createSheet("hidden"); Name sequencingReadTypeArea = createOptionArea(hiddenSheet, @@ -123,17 +122,6 @@ public byte[] getContent() { DEFAULT_GENERATED_ROW_COUNT - 1, sequencingReadTypeArea); - for (NGSMeasurementRegisterColumn column : NGSMeasurementRegisterColumn.values()) { - column.getFillHelp().ifPresent( - helper -> XLSXTemplateHelper.addInputHelper(sheet, - column.columnIndex(), - startIndex, - column.columnIndex(), - helperStopIndex, - helper.exampleValue(), - helper.description())); - } - // add property information order of columns matters!! for (NGSMeasurementRegisterColumn column : Arrays.stream( NGSMeasurementRegisterColumn.values()) diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementEditTemplate.java b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementEditTemplate.java index e1391964b4..91b675033e 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementEditTemplate.java +++ b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementEditTemplate.java @@ -111,7 +111,7 @@ public byte[] getContent() { } try (Workbook workbook = new XSSFWorkbook(); - ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();) { + ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream()) { CellStyle readOnlyHeaderStyle = XLSXTemplateHelper.createReadOnlyHeaderCellStyle(workbook); CellStyle boldStyle = createBoldCellStyle(workbook); @@ -172,7 +172,6 @@ public byte[] getContent() { } var startIndex = 1; // start in row number 2 with index 1 skipping the header in the first row - var helperStopIndex = 1; //stop in row number 2 with index 1 as the header row has number 1 index 0 var rowIndex = startIndex; for (ProteomicsMeasurementEntry pxpEntry : measurements) { @@ -194,18 +193,6 @@ public byte[] getContent() { DEFAULT_GENERATED_ROW_COUNT - 1, digestionMethodArea); - for (ProteomicsMeasurementEditColumn column : ProteomicsMeasurementEditColumn.values()) { - column.getFillHelp().ifPresent( - helper -> XLSXTemplateHelper.addInputHelper(sheet, - column.columnIndex(), - startIndex, - column.columnIndex(), - helperStopIndex, - helper.exampleValue(), - helper.description()) - ); - } - setAutoWidth(sheet); workbook.setActiveSheet(0); diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementRegisterTemplate.java b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementRegisterTemplate.java index 6b34836450..13b3e395e8 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementRegisterTemplate.java +++ b/user-interface/src/main/java/life/qbic/datamanager/templates/measurement/ProteomicsMeasurementRegisterTemplate.java @@ -123,7 +123,7 @@ public byte[] getContent() { } var startIndex = 1; // start in row number 2 with index 1 skipping the header in the first row - var helperStopIndex = 1; //stop in row number 2 with index 1 as the header row has number 1 index 0 + // make sure to create the visible sheet first Sheet hiddenSheet = workbook.createSheet("hidden"); Name digestionMethodArea = createOptionArea(hiddenSheet, "Digestion Method", @@ -135,18 +135,6 @@ public byte[] getContent() { DEFAULT_GENERATED_ROW_COUNT - 1, digestionMethodArea); - for (ProteomicsMeasurementRegisterColumn column : ProteomicsMeasurementRegisterColumn.values()) { - column.getFillHelp().ifPresent( - helper -> XLSXTemplateHelper.addInputHelper(sheet, - column.columnIndex(), - startIndex, - column.columnIndex(), - helperStopIndex, - helper.exampleValue(), - helper.description()) - ); - } - setAutoWidth(sheet); workbook.setActiveSheet(0); diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchRegistrationTemplate.java b/user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchRegistrationTemplate.java index acf1f9ce39..6f9117aca6 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchRegistrationTemplate.java +++ b/user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchRegistrationTemplate.java @@ -129,7 +129,6 @@ public static XSSFWorkbook createRegistrationTemplate(List conditions, } var startIndex = 1; //start in the second row with index 1. - var helperStopIndex = 1; //stop in the second row with index 1 var hiddenSheet = workbook.createSheet("hidden"); Name analysisToBePerformedOptions = createOptionArea(hiddenSheet, "Analysis to be performed", @@ -170,18 +169,6 @@ public static XSSFWorkbook createRegistrationTemplate(List conditions, MAX_ROW_INDEX_TO, specimenOptions); - for (var column : RegisterColumn.values()) { - column.getFillHelp().ifPresent( - helper -> XLSXTemplateHelper.addInputHelper(sheet, - column.columnIndex(), - startIndex, - column.columnIndex(), - helperStopIndex, - helper.exampleValue(), - helper.description()) - ); - } - setColumnAutoWidth(sheet, 0, RegisterColumn.maxColumnIndex()); // Auto width ignores cell validation values (e.g. a list of valid entries). So we need // to set them explicit diff --git a/user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchUpdateTemplate.java b/user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchUpdateTemplate.java index 25801db9fe..ce03c12bc6 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchUpdateTemplate.java +++ b/user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchUpdateTemplate.java @@ -131,7 +131,6 @@ public static XSSFWorkbook createUpdateTemplate(List samples, List samples, List XLSXTemplateHelper.addInputHelper(sheet, - column.columnIndex(), - startIndex, - column.columnIndex(), - helperStopIndex, - helper.exampleValue(), - helper.description()) - ); - } - - setColumnAutoWidth(sheet, 0, EditColumn.maxColumnIndex() + confoundingVariables.size()); + setColumnAutoWidth(sheet, 0, EditColumn.maxColumnIndex()); workbook.setActiveSheet(0); lockSheet(hiddenSheet); hideSheet(workbook, hiddenSheet); diff --git a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementDetailsComponent.java b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementDetailsComponent.java index c92265119d..fb10b1eeee 100644 --- a/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementDetailsComponent.java +++ b/user-interface/src/main/java/life/qbic/datamanager/views/projects/project/measurements/MeasurementDetailsComponent.java @@ -325,12 +325,16 @@ private void createProteomicsGrid() { proteomicsMeasurement -> renderInstrument().createComponent( proteomicsMeasurement.msDevice())) .setHeader("MS Device") - .setTooltipGenerator( - proteomicsMeasurement -> proteomicsMeasurement.msDevice().formatted()) + .setTooltipGenerator(proteomicsMeasurement -> proteomicsMeasurement.msDevice().formatted()) + .setAutoWidth(true); + proteomicsMeasurementGrid.addColumn( + measurement -> measurement.technicalReplicateName().orElse("")) + .setHeader("Technical Replicate") + .setTooltipGenerator(measurement -> measurement.technicalReplicateName().orElse("")) .setAutoWidth(true); proteomicsMeasurementGrid.addColumn(ProteomicsMeasurement::digestionEnzyme) - .setHeader("Digestion Enzyme").setTooltipGenerator( - ProteomicsMeasurement::digestionEnzyme) + .setHeader("Digestion Enzyme") + .setTooltipGenerator(ProteomicsMeasurement::digestionEnzyme) .setAutoWidth(true); proteomicsMeasurementGrid.addColumn(ProteomicsMeasurement::digestionMethod) .setHeader("Digestion Method") @@ -599,7 +603,6 @@ public MeasurementPooledSamplesDialog(NGSMeasurement ngsMeasurement) { setLayout(); setMeasurementId(ngsMeasurement.measurementCode().value()); setPooledNgsMeasurementDetails(ngsMeasurement); - //Todo Replace with specific metadata setPooledNgsSampleDetails(ngsMeasurement.specificMeasurementMetadata()); } @@ -662,7 +665,6 @@ private void setPooledNgsMeasurementDetails( measurementDetailsDiv.add( pooledMeasurementEntry("Sample Pool Group", ngsMeasurement.samplePoolGroup() .orElseThrow())); - //Todo Add measurement specific pooled properties once defined for NGS } private void setPooledNgsSampleDetails( @@ -698,7 +700,6 @@ private void setPooledNgsSampleDetails( add(sampleDetailsGrid); } - //Todo This is non-performant and should be changed private Optional retrieveSampleById(SampleId sampleId) { return sampleInformationService.findSample(sampleId); }