Merge pull request #778 from qbicsoftware/release/1.3.0

Release 1.3.0
qbicsoftware · Aug 13, 2024 · 004124e · 004124e
2 parents 22c0c75 + 39e38b2
commit 004124e
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Showing 48 changed files with 900 additions and 608 deletions.
diff --git a/identity-api/src/main/java/life/qbic/identity/api/UserInfo.java b/identity-api/src/main/java/life/qbic/identity/api/UserInfo.java
@@ -10,6 +10,6 @@
  * @since 1.0.0
  */
 public record UserInfo(String id, String fullName, String emailAddress, String platformUserName,
-                       boolean isActive) implements Serializable {
+                       boolean isActive, String oidcId, String oidcIssuer) implements Serializable {
 
 }
diff --git a/identity-api/src/main/java/life/qbic/identity/api/UserInformationService.java b/identity-api/src/main/java/life/qbic/identity/api/UserInformationService.java
@@ -55,5 +55,6 @@ public interface UserInformationService {
 
   Optional<UserInfo> findByOidc(String oidcId, String oidcIssuer);
 
-  List<UserInfo> findAllActive(String filter, int offset, int limit, List<SortOrder> sortOrders);
+  List<UserInfo> queryActiveUsersWithFilter(String filter, int offset, int limit,
+      List<SortOrder> sortOrders);
 }
diff --git a/identity-infrastructure/src/main/java/life/qbic/identity/infrastructure/QbicUserRepo.java b/identity-infrastructure/src/main/java/life/qbic/identity/infrastructure/QbicUserRepo.java
@@ -8,6 +8,7 @@
 import life.qbic.identity.domain.model.UserId;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.JpaSpecificationExecutor;
 import org.springframework.data.repository.CrudRepository;
 
 /**
@@ -21,7 +22,8 @@
  *
  * @since 1.0.0
  */
-public interface QbicUserRepo extends JpaRepository<User, UserId> {
+public interface QbicUserRepo extends JpaRepository<User, UserId>,
+    JpaSpecificationExecutor<User> {
 
   /**
    * Find users by mail address in the persistent data storage

diff --git a/...ity-infrastructure/src/main/java/life/qbic/identity/infrastructure/UserJpaRepository.java b/...ity-infrastructure/src/main/java/life/qbic/identity/infrastructure/UserJpaRepository.java
@@ -8,6 +8,7 @@
 import life.qbic.identity.domain.repository.UserDataStorage;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Pageable;
+import org.springframework.data.jpa.domain.Specification;
 import org.springframework.stereotype.Component;
 
 
@@ -60,13 +61,70 @@ public Optional<User> findUserByUserName(String userName) {
   }
 
   @Override
-  public List<User> findByUserNameContainingIgnoreCaseAndActiveTrue(String userName,
-      Pageable pageable) {
-    return userRepo.findAllByUserNameContainingIgnoreCaseAndActiveTrue(userName, pageable);
+  public List<User> queryActiveUsersWithFilter(String filter, Pageable pageable) {
+    Specification<User> userSpecification = generateUserFilterSpecification(filter);
+    return userRepo.findAll(userSpecification, pageable).getContent();
   }
 
   @Override
   public Optional<User> findByOidcIdEqualsAndOidcIssuerEquals(String oidcId, String oidcIssuer) {
     return userRepo.findByOidcIdEqualsAndOidcIssuerEquals(oidcId, oidcIssuer);
   }
+
+  private Specification<User> generateUserFilterSpecification(String filter) {
+    Specification<User> isBlankSpec = UserSpec.isBlank(filter);
+    Specification<User> isFullName = UserSpec.isFullName(filter);
+    Specification<User> isUserNameSpec = UserSpec.isUserName(filter);
+    Specification<User> isOidc = UserSpec.isOidc(filter);
+    Specification<User> isOidcIssuer = UserSpec.isOidcIssuer(filter);
+    Specification<User> isActiveSpec = UserSpec.isActive();
+    Specification<User> filterSpecification =
+        Specification.anyOf(isFullName,
+            isUserNameSpec,
+            isOidc,
+            isOidcIssuer
+        );
+    return Specification.where(isBlankSpec)
+        .and(filterSpecification)
+        .and(isActiveSpec);
+  }
+
+  private static class UserSpec {
+
+    //If no filter was provided return all Users
+    public static Specification<User> isBlank(String filter) {
+      return (root, query, builder) -> {
+        if (filter != null && filter.isBlank()) {
+          return builder.conjunction();
+        }
+        return null;
+      };
+    }
+
+    public static Specification<User> isUserName(String filter) {
+      return (root, query, builder) ->
+          builder.like(root.get("userName"), "%" + filter + "%");
+    }
+
+    public static Specification<User> isFullName(String filter) {
+      return (root, query, builder) ->
+          builder.like(root.get("fullName"), "%" + filter + "%");
+    }
+
+    // Should be extended if additional oidc providers are included, for now we only work with orcid
+    public static Specification<User> isOidc(String filter) {
+      return (root, query, builder) ->
+          builder.like(root.get("oidcId"), "%" + filter + "%");
+    }
+
+    public static Specification<User> isOidcIssuer(String filter) {
+      return (root, query, builder) ->
+          builder.like(root.get("oidcIssuer"), "%" + filter + "%");
+    }
+
+    public static Specification<User> isActive() {
+      return (root, query, builder) ->
+          builder.isTrue(root.get("active"));
+    }
+  }
 }
diff --git a/...ity/src/main/java/life/qbic/identity/application/service/BasicUserInformationService.java b/...ity/src/main/java/life/qbic/identity/application/service/BasicUserInformationService.java
@@ -82,7 +82,7 @@ public boolean isEmailAvailable(String email) {
   }
 
   @Override
-  public List<UserInfo> findAllActive(String filter, int offset, int limit,
+  public List<UserInfo> queryActiveUsersWithFilter(String filter, int offset, int limit,
       List<SortOrder> sortOrders) {
     List<Order> orders = sortOrders.stream().map(it -> {
       Order order;
@@ -93,18 +93,19 @@ public List<UserInfo> findAllActive(String filter, int offset, int limit,
       }
       return order;
     }).toList();
-    return userRepository.findByUserNameContainingIgnoreCaseAndActiveTrue(
+    return userRepository.queryActiveUsersWithFilter(
             filter, new OffsetBasedRequest(offset, limit, Sort.by(orders)))
         .stream()
         .map(user -> new UserInfo(user.id().get(), user.fullName().get(), user.emailAddress().get(),
-            user.userName(), user.isActive()))
+            user.userName(), user.isActive(), user.getOidcId().orElse(null),
+            user.getOidcIssuer().orElse(null)))
         .toList();
   }
 
   private UserInfo convert(User user) {
     return new UserInfo(user.id().get(), user.fullName().get(), user.emailAddress().get(),
         user.userName(),
-        user.isActive());
+        user.isActive(), user.getOidcId().orElse(null), user.getOidcIssuer().orElse(null));
   }
 
   @Override

diff --git a/identity/src/main/java/life/qbic/identity/domain/repository/UserDataStorage.java b/identity/src/main/java/life/qbic/identity/domain/repository/UserDataStorage.java
@@ -58,7 +58,7 @@ public interface UserDataStorage {
 
   Optional<User> findUserByUserName(String userName);
 
-  List<User> findByUserNameContainingIgnoreCaseAndActiveTrue(String username, Pageable pageable);
+  List<User> queryActiveUsersWithFilter(String filter, Pageable pageable);
 
   Optional<User> findByOidcIdEqualsAndOidcIssuerEquals(String oidcId, String oidcIssuer);
 }
diff --git a/identity/src/main/java/life/qbic/identity/domain/repository/UserRepository.java b/identity/src/main/java/life/qbic/identity/domain/repository/UserRepository.java
@@ -110,9 +110,9 @@ public void addUser(User user) throws UserStorageException {
     saveUser(user);
   }
 
-  public List<User> findByUserNameContainingIgnoreCaseAndActiveTrue(String userName,
+  public List<User> queryActiveUsersWithFilter(String filter,
       Pageable pageable) {
-    return dataStorage.findByUserNameContainingIgnoreCaseAndActiveTrue(userName, pageable);
+    return dataStorage.queryActiveUsersWithFilter(filter, pageable);
   }
 
   public Optional<User> findByOidc(String oidcId, String oidcIssuer) {

diff --git a/...in/java/life/qbic/projectmanagement/infrastructure/sample/SamplePreviewJpaRepository.java b/...in/java/life/qbic/projectmanagement/infrastructure/sample/SamplePreviewJpaRepository.java
@@ -68,8 +68,9 @@ private Specification<SamplePreview> generateExperimentIdandFilterSpecification(
     Specification<SamplePreview> isBlankSpec = SamplePreviewSpecs.isBlank(filter);
     Specification<SamplePreview> experimentIdSpec = SamplePreviewSpecs.experimentIdEquals(
         experimentId);
+    Specification<SamplePreview> organismIdSpec = SamplePreviewSpecs.organismIdContains(filter);
     Specification<SamplePreview> sampleCodeSpec = SamplePreviewSpecs.sampleCodeContains(filter);
-    Specification<SamplePreview> sampleLabelSpec = SamplePreviewSpecs.sampleLabelContains(filter);
+    Specification<SamplePreview> sampleNameSpec = SamplePreviewSpecs.sampleNameContains(filter);
     Specification<SamplePreview> batchLabelSpec = SamplePreviewSpecs.batchLabelContains(filter);
     Specification<SamplePreview> conditionSpec = SamplePreviewSpecs.conditionContains(filter);
     Specification<SamplePreview> speciesSpec = SamplePreviewSpecs.speciesContains(filter);
@@ -79,7 +80,7 @@ private Specification<SamplePreview> generateExperimentIdandFilterSpecification(
         filter);
     Specification<SamplePreview> commentSpec = SamplePreviewSpecs.commentContains(filter);
     Specification<SamplePreview> containsFilterSpec = Specification.anyOf(sampleCodeSpec,
-        sampleLabelSpec, batchLabelSpec, conditionSpec, speciesSpec,
+        sampleNameSpec, organismIdSpec, batchLabelSpec, conditionSpec, speciesSpec,
         specimenSpec, analyteSpec, analysisMethodContains, commentSpec);
     Specification<SamplePreview> isDistinctSpec = SamplePreviewSpecs.isDistinct();
     return Specification.where(experimentIdSpec).and(isBlankSpec)
@@ -126,9 +127,9 @@ public static Specification<SamplePreview> batchLabelContains(String filter) {
           builder.like(root.get("batchLabel"), "%" + filter + "%");
     }
 
-    public static Specification<SamplePreview> sampleLabelContains(String filter) {
+    public static Specification<SamplePreview> sampleNameContains(String filter) {
       return (root, query, builder) ->
-          builder.like(root.get("sampleLabel"), "%" + filter + "%");
+          builder.like(root.get("sampleName"), "%" + filter + "%");
     }
 
     public static Specification<SamplePreview> conditionContains(String filter) {
@@ -157,6 +158,11 @@ private static Specification<SamplePreview> ontologyColumnContains(String col, S
       };
     }
 
+    public static Specification<SamplePreview> organismIdContains(String filter) {
+      return (root, query, builder) ->
+          builder.like(root.get("organismId"), "%" + filter + "%");
+    }
+
     public static Specification<SamplePreview> speciesContains(String filter) {
       return ontologyColumnContains("species", filter);
     }

diff --git a/...ment/src/main/java/life/qbic/projectmanagement/application/batch/SampleUpdateRequest.java b/...ment/src/main/java/life/qbic/projectmanagement/application/batch/SampleUpdateRequest.java
@@ -17,7 +17,7 @@ public record SampleUpdateRequest(SampleId sampleId, SampleInformation sampleInf
   /**
    * Sample update request.
    * <p>
-   * @param sampleLabel          a human-readable semantic descriptor of the sample
+   * @param sampleName          a human-readable semantic descriptor of the sample
    * @param organismId           optional identifier of the sample's source patient or organism
    * @param analysisMethod       analysis method to be performed
    * @param experimentalGroup    the experimental group the sample is part of
@@ -26,7 +26,7 @@ public record SampleUpdateRequest(SampleId sampleId, SampleInformation sampleInf
    * @param analyte              the analyte the sample belongs to
    * @param comment              comment relating to the sample
    */
-  public record SampleInformation(String sampleLabel, String organismId,
+  public record SampleInformation(String sampleName, String organismId,
                                   AnalysisMethod analysisMethod,
                                   ExperimentalGroup experimentalGroup, OntologyTerm species,
                                   OntologyTerm specimen, OntologyTerm analyte,

diff --git a/...agement/src/main/java/life/qbic/projectmanagement/application/dataset/RawDataService.java b/...agement/src/main/java/life/qbic/projectmanagement/application/dataset/RawDataService.java
@@ -169,7 +169,7 @@ public record RawData(MeasurementCode measurementCode,
    * Sample Information associated with the measurements to which the {@link RawData} is linked and
    * meant to be employed in the frontend
    */
-  public record RawDataSampleInformation(SampleCode sampleCode, String sampleLabel) {
+  public record RawDataSampleInformation(SampleCode sampleCode, String sampleName) {
 
   }
 

diff --git a/...fe/qbic/projectmanagement/application/measurement/validation/MeasurementNGSValidator.java b/...fe/qbic/projectmanagement/application/measurement/validation/MeasurementNGSValidator.java
@@ -118,7 +118,7 @@ public ValidationResult validateUpdate(NGSMeasurementMetadata metadata, ProjectI
 
   public enum NGS_PROPERTY {
     QBIC_SAMPLE_ID("qbic sample id"),
-    SAMPLE_LABEL("sample label"),
+    SAMPLE_LABEL("sample name"),
     ORGANISATION_ID("organisation id"),
     FACILITY("facility"),
     INSTRUMENT("instrument"),

diff --git a/.../projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java b/.../projectmanagement/application/measurement/validation/MeasurementProteomicsValidator.java
@@ -129,7 +129,7 @@ public ValidationResult validateUpdate(ProteomicsMeasurementMetadata metadata,
 
   public enum PROTEOMICS_PROPERTY {
     QBIC_SAMPLE_ID("qbic sample id"),
-    SAMPLE_LABEL("sample label"),
+    SAMPLE_LABEL("sample name"),
     ORGANISATION_ID("organisation id"),
     FACILITY("facility"),
     INSTRUMENT("instrument"),

diff --git a/...anagement/src/main/java/life/qbic/projectmanagement/application/sample/SamplePreview.java b/...anagement/src/main/java/life/qbic/projectmanagement/application/sample/SamplePreview.java
@@ -39,7 +39,7 @@ public class SamplePreview {
   private String batchLabel;
 
   @Column(name = "label")
-  private String sampleLabel;
+  private String sampleName;
 
   @Column(name = "organism_id")
   private String organismId;
@@ -58,14 +58,14 @@ protected SamplePreview() {
   }
 
   private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampleCode,
-      String batchLabel, String sampleLabel, String organismId,
+      String batchLabel, String sampleName, String organismId,
       ExperimentalGroup experimentalGroup, OntologyTerm species,
       OntologyTerm specimen, OntologyTerm analyte, String analysisMethod, String comment) {
     Objects.requireNonNull(experimentId);
     Objects.requireNonNull(sampleId);
     Objects.requireNonNull(sampleCode);
     Objects.requireNonNull(batchLabel);
-    Objects.requireNonNull(sampleLabel);
+    Objects.requireNonNull(sampleName);
     Objects.requireNonNull(experimentalGroup);
     Objects.requireNonNull(species);
     Objects.requireNonNull(specimen);
@@ -75,7 +75,7 @@ private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampl
     this.sampleId = sampleId;
     this.sampleCode = sampleCode;
     this.batchLabel = batchLabel;
-    this.sampleLabel = sampleLabel;
+    this.sampleName = sampleName;
     this.experimentalGroup = experimentalGroup;
     this.species = species;
     this.specimen = specimen;
@@ -95,7 +95,7 @@ private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampl
    * @param batchLabel        the label of the {@link Batch} which contains the {@link Sample}
    *                          associated with this preview
    *                          associated with this preview
-   * @param sampleLabel       the label of the {@link Sample} associated with this preview
+   * @param sampleName       the name of the {@link Sample} associated with this preview
    * @param organismId        optional identifier of the patient or organism a {@link Sample} was taken of
    * @param experimentalGroup the {@link ExperimentalGroup} for the {@link Sample} associated with
    *                          this preview
@@ -112,11 +112,11 @@ private SamplePreview(ExperimentId experimentId, SampleId sampleId, String sampl
   public static SamplePreview create(ExperimentId experimentId, SampleId sampleId,
       String sampleCode,
       String batchLabel,
-      String sampleLabel, String organismId, ExperimentalGroup experimentalGroup,
+      String sampleName, String organismId, ExperimentalGroup experimentalGroup,
       OntologyTerm species, OntologyTerm specimen, OntologyTerm analyte,
       String analysisMethod, String comment) {
     return new SamplePreview(experimentId, sampleId, sampleCode, batchLabel,
-        sampleLabel, organismId, experimentalGroup, species, specimen, analyte, analysisMethod,
+        sampleName, organismId, experimentalGroup, species, specimen, analyte, analysisMethod,
         comment);
   }
 
@@ -136,8 +136,8 @@ public String batchLabel() {
     return batchLabel;
   }
 
-  public String sampleLabel() {
-    return sampleLabel;
+  public String sampleName() {
+    return sampleName;
   }
 
   public OntologyTerm species() {
@@ -179,8 +179,8 @@ public boolean equals(Object o) {
     SamplePreview that = (SamplePreview) o;
     return Objects.equals(experimentId, that.experimentId) && Objects.equals(
         sampleCode, that.sampleCode) && Objects.equals(sampleId, that.sampleId)
-        && Objects.equals(batchLabel, that.batchLabel) && Objects.equals(sampleLabel,
-        that.sampleLabel) && Objects.equals(organismId, that.organismId)
+        && Objects.equals(batchLabel, that.batchLabel) && Objects.equals(sampleName,
+        that.sampleName) && Objects.equals(organismId, that.organismId)
         && Objects.equals(species, that.species) && Objects.equals(specimen,
         that.specimen) && Objects.equals(analyte, that.analyte) && Objects.equals(
         experimentalGroup, that.experimentalGroup) && Objects.equals(analysisMethod,
@@ -190,7 +190,7 @@ public boolean equals(Object o) {
   @Override
   public int hashCode() {
     return Objects.hash(experimentId, sampleCode, sampleId, batchLabel,
-        sampleLabel, organismId,
+        sampleName, organismId,
         species, specimen, analyte, experimentalGroup, analysisMethod, comment);
   }
 
@@ -201,7 +201,7 @@ public String toString() {
         ", sampleCode='" + sampleCode + '\'' +
         ", sampleId='" + sampleId + '\'' +
         ", batchLabel='" + batchLabel + '\'' +
-        ", sampleLabel='" + sampleLabel + '\'' +
+        ", sampleName='" + sampleName + '\'' +
         ", organismId='" + organismId + '\'' +
         ", species='" + species + '\'' +
         ", specimen='" + specimen + '\'' +

diff --git a/project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/Sample.java b/project-management/src/main/java/life/qbic/projectmanagement/domain/model/sample/Sample.java
@@ -164,7 +164,7 @@ public void setSampleOrigin(SampleOrigin sampleOrigin) {
   }
 
   public void update(SampleUpdateRequest sampleInfo) {
-    setLabel(sampleInfo.sampleInformation().sampleLabel());
+    setLabel(sampleInfo.sampleInformation().sampleName());
     setOrganismId(sampleInfo.sampleInformation().organismId());
     setAnalysisMethod(sampleInfo.sampleInformation().analysisMethod());
     setSampleOrigin(SampleOrigin.create(sampleInfo.sampleInformation().species(),

diff --git a/...agement/src/main/java/life/qbic/projectmanagement/domain/service/SampleDomainService.java b/...agement/src/main/java/life/qbic/projectmanagement/domain/service/SampleDomainService.java
@@ -85,7 +85,7 @@ public void updateSamples(Project project, Collection<SampleUpdateRequest> updat
       var sampleInfo = updatedSamples.stream()
           .filter(sampleUpdateRequest -> sampleUpdateRequest.sampleId().equals(sample.sampleId()))
           .findFirst().orElseThrow();
-      sample.setLabel(sampleInfo.sampleInformation().sampleLabel());
+      sample.setLabel(sampleInfo.sampleInformation().sampleName());
       sample.setOrganismId(sampleInfo.sampleInformation().organismId());
       sample.setAnalysisMethod(sampleInfo.sampleInformation().analysisMethod());
       sample.setSampleOrigin(SampleOrigin.create(sampleInfo.sampleInformation().species(),

diff --git a/...ctmanagement/application/measurement/validation/MeasurementProteomicsValidatorSpec.groovy b/...ctmanagement/application/measurement/validation/MeasurementProteomicsValidatorSpec.groovy
@@ -47,7 +47,7 @@ class MeasurementMeasurementProteomicsValidatorSpec extends Specification {
 
     final ProjectInformationService projectInformationService = Mock(ProjectInformationService.class)
 
-    final static List<String> validPXPProperties = Collections.unmodifiableList(["qbic sample id", "sample label", "organisation id", "facility", "instrument",
+    final static List<String> validPXPProperties = Collections.unmodifiableList(["qbic sample id", "sample name", "organisation id", "facility", "instrument",
                                                     "sample pool group", "cycle/fraction name", "digestion method", "digestion enzyme",
                                                     "enrichment method", "injection volume (uL)", "lc column",
                                                     "lcms method", "labeling type", "label", "comment"])

diff --git a/user-interface/frontend/themes/datamanager/components/dialog.css b/user-interface/frontend/themes/datamanager/components/dialog.css
@@ -100,8 +100,8 @@ Since we want to remove the spacing between the cancel and confirm button we rep
 }
 
 .add-user-to-project-dialog::part(overlay) {
-  height: fit-content;
-  min-width: fit-content;
+  height: clamp(700px, 100%, 700px);
+  width: clamp(700px, 100%, 700px);
 }
 
 .add-user-to-project-dialog::part(content) {