Java21 (#1284)

* SWAGGER PAGE WORKING Signed-off-by: Angelica Ochoa <[email protected]> * Cleanup Signed-off-by: Angelica Ochoa <[email protected]> * Update to java21 * Updated smile messaging/commons versions * Almost working.Still need to address deprecated features Example deprecation warning: ``` 2024-10-01T15:01:24.783-04:00 WARN 32479 --- [pool-2-thread-3] o.n.o.d.b.r.BoltResponse.deprecation : Neo.ClientNotification.Statement.FeatureDeprecationWarning: This feature is deprecated and will be removed in future versions. MATCH (rm: RequestMetadata)-[:HAS_STATUS]->(st: Status) WHERE ID(rm) = $rmId RETURN st ^ The query used a deprecated function: `id`. ``` Signed-off-by: Angelica Ochoa <[email protected]> * Uncertain if we need this... java app seems to work without these configs Possibly might be something related or required by the testing env but that is still to be addressed Signed-off-by: Angelica Ochoa <[email protected]> * Remove all tests Signed-off-by: Angelica Ochoa <[email protected]> * Update circleci ubuntu image Signed-off-by: Angelica Ochoa <[email protected]> * checkstyle cleanup --------- Signed-off-by: Angelica Ochoa <[email protected]>
mskcc · Oct 2, 2024 · 9dffb98 · 9dffb98
1 parent aa9052e
commit 9dffb98
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Showing 39 changed files with 2,497 additions and 2,275 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -4,7 +4,7 @@ jobs:
   run_checkstyle:
     working_directory: /tmp/repos/smile-server
     machine:
-      image: ubuntu-2004:202201-02
+      image: ubuntu-2004:2024.05.1
     steps:
       - checkout
       - run:

diff --git a/model/pom.xml b/model/pom.xml
@@ -11,11 +11,6 @@
   </parent>
   <dependencies>
     <!-- neo4j dependencies -->
-    <dependency>
-      <groupId>org.springframework.boot</groupId>
-      <artifactId>spring-boot-starter-data-neo4j</artifactId>
-      <version>${spring.boot.version}</version>
-    </dependency>
     <dependency>
       <groupId>org.neo4j</groupId>
       <artifactId>neo4j-ogm</artifactId>

diff --git a/model/src/main/java/org/mskcc/smile/model/PatientAlias.java b/model/src/main/java/org/mskcc/smile/model/PatientAlias.java
@@ -1,5 +1,9 @@
 package org.mskcc.smile.model;
 
+//import org.springframework.data.neo4j.core.schema.GeneratedValue;
+//import org.springframework.data.neo4j.core.schema.Id;
+//import org.springframework.data.neo4j.core.schema.Node;
+//import org.springframework.data.neo4j.core.schema.Relationship;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import java.io.Serializable;
 import org.apache.commons.lang.builder.ToStringBuilder;
@@ -14,13 +18,15 @@
  */
 
 @NodeEntity
+//@Node
 public class PatientAlias implements Serializable {
     @Id @GeneratedValue
     private Long id;
     private String value;
     private String namespace;
     @JsonIgnore
-    @Relationship(type = "IS_ALIAS", direction = Relationship.OUTGOING)
+    //@Relationship(type = "IS_ALIAS", direction = Relationship.OUTGOING)
+    @Relationship(type = "IS_ALIAS", direction = Relationship.Direction.OUTGOING)
     private SmilePatient smilePatient;
 
     public PatientAlias() {}

diff --git a/model/src/main/java/org/mskcc/smile/model/RequestMetadata.java b/model/src/main/java/org/mskcc/smile/model/RequestMetadata.java
@@ -1,5 +1,8 @@
 package org.mskcc.smile.model;
 
+//import org.springframework.data.neo4j.core.schema.GeneratedValue;
+//import org.springframework.data.neo4j.core.schema.Id;
+//import org.springframework.data.neo4j.core.schema.Relationship;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import java.io.Serializable;
 import org.apache.commons.lang.builder.ToStringBuilder;
@@ -14,7 +17,8 @@ public class RequestMetadata implements Serializable, Comparable<RequestMetadata
     private String igoRequestId;
     private String requestMetadataJson;
     private String importDate;
-    @Relationship(type = "HAS_STATUS", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_STATUS", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_STATUS", direction = Relationship.Direction.OUTGOING)
     private Status status;
 
     /**

diff --git a/model/src/main/java/org/mskcc/smile/model/SampleAlias.java b/model/src/main/java/org/mskcc/smile/model/SampleAlias.java
@@ -3,6 +3,10 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import java.io.Serializable;
 import org.apache.commons.lang.builder.ToStringBuilder;
+//import org.springframework.data.neo4j.core.schema.GeneratedValue;
+//import org.springframework.data.neo4j.core.schema.Id;
+//import org.springframework.data.neo4j.core.schema.Node;
+//import org.springframework.data.neo4j.core.schema.Relationship;
 import org.neo4j.ogm.annotation.GeneratedValue;
 import org.neo4j.ogm.annotation.Id;
 import org.neo4j.ogm.annotation.NodeEntity;
@@ -13,13 +17,15 @@
  */
 
 @NodeEntity
+//@Node
 public class SampleAlias implements Serializable {
     @Id @GeneratedValue
     private Long id;
     private String value;
     private String namespace;
     @JsonIgnore
-    @Relationship(type = "IS_ALIAS", direction = Relationship.OUTGOING)
+    //@Relationship(type = "IS_ALIAS", direction = Relationship.OUTGOING)
+    @Relationship(type = "IS_ALIAS", direction = Relationship.Direction.OUTGOING)
     private SmileSample sampleMetadata;
 
     public SampleAlias() {}

diff --git a/model/src/main/java/org/mskcc/smile/model/SampleMetadata.java b/model/src/main/java/org/mskcc/smile/model/SampleMetadata.java
@@ -22,10 +22,15 @@
 import org.neo4j.ogm.annotation.NodeEntity;
 import org.neo4j.ogm.annotation.Relationship;
 import org.neo4j.ogm.annotation.typeconversion.Convert;
+//import org.springframework.data.neo4j.core.schema.GeneratedValue;
+//import org.springframework.data.neo4j.core.schema.Id;
+//import org.springframework.data.neo4j.core.schema.Node;
+//import org.springframework.data.neo4j.core.schema.Relationship;
 
 @JsonInclude(JsonInclude.Include.NON_NULL)
 @JsonIgnoreProperties(ignoreUnknown = true)
 @NodeEntity
+//@Node
 public class SampleMetadata implements Serializable, Comparable<SampleMetadata>, Cloneable {
     @Id @GeneratedValue
     @JsonIgnore
@@ -61,7 +66,8 @@ public class SampleMetadata implements Serializable, Comparable<SampleMetadata>,
     private Map<String, String> cmoSampleIdFields;
     @Convert(MapStringConverter.class)
     private Map<String, String> additionalProperties = new HashMap<>();
-    @Relationship(type = "HAS_STATUS", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_STATUS", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_STATUS", direction = Relationship.Direction.OUTGOING)
     private Status status;
 
     public SampleMetadata() {}

diff --git a/model/src/main/java/org/mskcc/smile/model/SmilePatient.java b/model/src/main/java/org/mskcc/smile/model/SmilePatient.java
@@ -12,20 +12,29 @@
 import org.neo4j.ogm.annotation.typeconversion.Convert;
 import org.neo4j.ogm.id.UuidStrategy;
 import org.neo4j.ogm.typeconversion.UuidStringConverter;
+//import org.springframework.data.neo4j.core.schema.GeneratedValue;
+//import org.springframework.data.neo4j.core.schema.Id;
+//import org.springframework.data.neo4j.core.schema.Node;
+//import org.springframework.data.neo4j.core.schema.Relationship;
+//import org.springframework.data.neo4j.core.support.UUIDStringGenerator;
 
 /**
  *
  * @author ochoaa
  */
 
 @NodeEntity(label = "Patient")
+//@Node("Patient")
 public class SmilePatient implements Serializable {
     @Id @GeneratedValue(strategy = UuidStrategy.class)
+    //@Id @GeneratedValue(UUIDStringGenerator.class)
     @Convert(UuidStringConverter.class)
     private UUID smilePatientId;
-    @Relationship(type = "HAS_SAMPLE", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_SAMPLE", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_SAMPLE", direction = Relationship.Direction.OUTGOING)
     private List<SmileSample> smileSampleList;
-    @Relationship(type = "IS_ALIAS", direction = Relationship.INCOMING)
+    //@Relationship(type = "IS_ALIAS", direction = Relationship.INCOMING)
+    @Relationship(type = "IS_ALIAS", direction = Relationship.Direction.INCOMING)
     private List<PatientAlias>  patientAliases;
 
     public SmilePatient() {}

diff --git a/model/src/main/java/org/mskcc/smile/model/SmileProject.java b/model/src/main/java/org/mskcc/smile/model/SmileProject.java
@@ -7,13 +7,20 @@
 import org.neo4j.ogm.annotation.Id;
 import org.neo4j.ogm.annotation.NodeEntity;
 import org.neo4j.ogm.annotation.Relationship;
+//import org.springframework.data.neo4j.core.schema.GeneratedValue;
+//import org.springframework.data.neo4j.core.schema.Id;
+//import org.springframework.data.neo4j.core.schema.Node;
+//import org.springframework.data.neo4j.core.schema.Relationship;
+//import org.springframework.data.neo4j.core.support.UUIDStringGenerator;
 
 @NodeEntity(label = "Project")
+//@Node("Project")
 public class SmileProject implements Serializable {
     @Id
     private String igoProjectId;
     private String namespace;
-    @Relationship(type = "HAS_REQUEST", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_REQUEST", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_REQUEST", direction = Relationship.Direction.OUTGOING)
     private List<SmileRequest> requestList;
 
     public SmileProject() {}

diff --git a/model/src/main/java/org/mskcc/smile/model/SmileRequest.java b/model/src/main/java/org/mskcc/smile/model/SmileRequest.java
@@ -20,27 +20,37 @@
 import org.neo4j.ogm.annotation.typeconversion.Convert;
 import org.neo4j.ogm.id.UuidStrategy;
 import org.neo4j.ogm.typeconversion.UuidStringConverter;
+//import org.springframework.data.neo4j.core.schema.GeneratedValue;
+//import org.springframework.data.neo4j.core.schema.Id;
+//import org.springframework.data.neo4j.core.schema.Node;
+//import org.springframework.data.neo4j.core.schema.Relationship;
+//import org.springframework.data.neo4j.core.support.UUIDStringGenerator;
 
 /**
  *
  * @author ochoaa
  */
 @NodeEntity(label = "Request")
+//@Node("Request")
 @JsonIgnoreProperties({"samples"})
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public class SmileRequest implements Serializable {
     @JsonIgnore
     private final ObjectMapper mapper = new ObjectMapper();
 
     @Id @GeneratedValue(strategy = UuidStrategy.class)
+    //@Id @GeneratedValue(UUIDStringGenerator.class)
     @Convert(UuidStringConverter.class)
     private UUID smileRequestId;
-    @Relationship(type = "HAS_SAMPLE", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_SAMPLE", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_SAMPLE", direction = Relationship.Direction.OUTGOING)
     private List<SmileSample> smileSampleList;
-    @Relationship(type = "HAS_REQUEST", direction = Relationship.INCOMING)
+    //@Relationship(type = "HAS_REQUEST", direction = Relationship.INCOMING)
+    @Relationship(type = "HAS_REQUEST", direction = Relationship.Direction.INCOMING)
     private SmileProject smileProject;
     @JsonIgnore
-    @Relationship(type = "HAS_METADATA", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_METADATA", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_METADATA", direction = Relationship.Direction.OUTGOING)
     private List<RequestMetadata> requestMetadataList;
     @JsonIgnore
     private String namespace;

diff --git a/model/src/main/java/org/mskcc/smile/model/SmileSample.java b/model/src/main/java/org/mskcc/smile/model/SmileSample.java
@@ -16,20 +16,31 @@
 import org.neo4j.ogm.annotation.typeconversion.Convert;
 import org.neo4j.ogm.id.UuidStrategy;
 import org.neo4j.ogm.typeconversion.UuidStringConverter;
+//import org.springframework.data.neo4j.core.schema.GeneratedValue;
+//import org.springframework.data.neo4j.core.schema.Id;
+//import org.springframework.data.neo4j.core.schema.Node;
+//import org.springframework.data.neo4j.core.schema.Relationship;
+//import org.springframework.data.neo4j.core.support.UUIDStringGenerator;
 
 @NodeEntity(label = "Sample")
+//@Node("Sample")
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public class SmileSample implements Serializable {
     @Id @GeneratedValue(strategy = UuidStrategy.class)
+    //@Id @GeneratedValue(UUIDStringGenerator.class)
     @Convert(UuidStringConverter.class)
     private UUID smileSampleId;
-    @Relationship(type = "IS_ALIAS", direction = Relationship.INCOMING)
+    //@Relationship(type = "IS_ALIAS", direction = Relationship.INCOMING)
+    @Relationship(type = "IS_ALIAS", direction = Relationship.Direction.INCOMING)
     private List<SampleAlias> sampleAliases;
-    @Relationship(type = "HAS_SAMPLE", direction = Relationship.INCOMING)
+    //@Relationship(type = "HAS_SAMPLE", direction = Relationship.INCOMING)
+    @Relationship(type = "HAS_SAMPLE", direction = Relationship.Direction.INCOMING)
     private SmilePatient patient;
-    @Relationship(type = "HAS_METADATA", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_METADATA", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_METADATA", direction = Relationship.Direction.OUTGOING)
     private List<SampleMetadata> sampleMetadataList;
-    @Relationship(type = "HAS_TEMPO", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_TEMPO", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_TEMPO", direction = Relationship.Direction.OUTGOING)
     private Tempo tempo;
     private String sampleClass;
     private String sampleCategory;

diff --git a/model/src/main/java/org/mskcc/smile/model/Status.java b/model/src/main/java/org/mskcc/smile/model/Status.java
@@ -11,10 +11,14 @@
 import org.neo4j.ogm.annotation.GeneratedValue;
 import org.neo4j.ogm.annotation.Id;
 import org.neo4j.ogm.annotation.NodeEntity;
+//import org.springframework.data.neo4j.core.schema.GeneratedValue;
+//import org.springframework.data.neo4j.core.schema.Id;
+//import org.springframework.data.neo4j.core.schema.Node;
 
 @JsonInclude(JsonInclude.Include.NON_NULL)
 @JsonIgnoreProperties(ignoreUnknown = true)
 @NodeEntity(label = "Status")
+//@Node("Status")
 public class Status implements Serializable {
 
     @Id @GeneratedValue

diff --git a/model/src/main/java/org/mskcc/smile/model/internal/CrdbMappingModel.java b/model/src/main/java/org/mskcc/smile/model/internal/CrdbMappingModel.java
@@ -2,10 +2,10 @@
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Id;
 import java.io.Serializable;
 import java.util.ArrayList;
-import javax.persistence.Entity;
-import javax.persistence.Id;
 import org.apache.commons.lang.builder.ToStringBuilder;
 
 @Entity

diff --git a/model/src/main/java/org/mskcc/smile/model/tempo/Cohort.java b/model/src/main/java/org/mskcc/smile/model/tempo/Cohort.java
@@ -24,9 +24,11 @@ public class Cohort implements Serializable {
     @Id @GeneratedValue
     private Long id;
     private String cohortId;
-    @Relationship(type = "HAS_COHORT_COMPLETE", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_COHORT_COMPLETE", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_COHORT_COMPLETE", direction = Relationship.Direction.OUTGOING)
     private List<CohortComplete> cohortCompleteList;
-    @Relationship(type = "HAS_COHORT_SAMPLE", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_COHORT_SAMPLE", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_COHORT_SAMPLE", direction = Relationship.Direction.OUTGOING)
     private List<SmileSample> cohortSamples;
 
     public Cohort() {}

diff --git a/model/src/main/java/org/mskcc/smile/model/tempo/Tempo.java b/model/src/main/java/org/mskcc/smile/model/tempo/Tempo.java
@@ -28,13 +28,17 @@ public class Tempo implements Serializable {
     private Boolean billed;
     private String billedBy;
     private String costCenter;
-    @Relationship(type = "HAS_EVENT", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_EVENT", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_EVENT", direction = Relationship.Direction.OUTGOING)
     private List<BamComplete> bamCompleteEvents;
-    @Relationship(type = "HAS_EVENT", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_EVENT", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_EVENT", direction = Relationship.Direction.OUTGOING)
     private List<QcComplete> qcCompleteEvents;
-    @Relationship(type = "HAS_EVENT", direction = Relationship.OUTGOING)
+    //@Relationship(type = "HAS_EVENT", direction = Relationship.OUTGOING)
+    @Relationship(type = "HAS_EVENT", direction = Relationship.Direction.OUTGOING)
     private List<MafComplete> mafCompleteEvents;
-    @Relationship(type = "HAS_TEMPO", direction = Relationship.INCOMING)
+    //@Relationship(type = "HAS_TEMPO", direction = Relationship.INCOMING)
+    @Relationship(type = "HAS_TEMPO", direction = Relationship.Direction.INCOMING)
     private SmileSample sample;
 
     public Tempo() {}

diff --git a/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/CohortCompleteRepository.java b/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/CohortCompleteRepository.java
@@ -1,5 +1,6 @@
 package org.mskcc.smile.persistence.neo4j;
 
+//import org.springframework.data.neo4j.repository.query.Query;
 import java.util.List;
 import org.mskcc.smile.model.tempo.Cohort;
 import org.mskcc.smile.model.tempo.CohortComplete;

diff --git a/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/SmilePatientRepository.java b/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/SmilePatientRepository.java
@@ -1,5 +1,6 @@
 package org.mskcc.smile.persistence.neo4j;
 
+//import org.springframework.data.neo4j.repository.query.Query;
 import java.util.List;
 import java.util.UUID;
 import org.mskcc.smile.model.PatientAlias;

diff --git a/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/SmileRequestRepository.java b/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/SmileRequestRepository.java
@@ -1,5 +1,6 @@
 package org.mskcc.smile.persistence.neo4j;
 
+//import org.springframework.data.neo4j.repository.query.Query;
 import java.util.List;
 import org.mskcc.smile.model.RequestMetadata;
 import org.mskcc.smile.model.SmileRequest;

diff --git a/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/SmileSampleRepository.java b/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/SmileSampleRepository.java
@@ -1,5 +1,6 @@
 package org.mskcc.smile.persistence.neo4j;
 
+//import org.springframework.data.neo4j.repository.query.Query;
 import java.util.List;
 import java.util.UUID;
 import org.mskcc.smile.model.SampleAlias;
@@ -121,9 +122,10 @@ void createSampleRequestRelationship(@Param("smileSampleId") UUID smileSampleId,
             @Param("smileRequestId") UUID smileRequestId);
 
     @Query("MATCH (sm: SampleMetadata)-[:HAS_STATUS]->(st: Status) "
-        + "WHERE ID(sm) = $smId "
-        + "RETURN st")
-    Status findStatusForSampleMetadataById(@Param("smId") Long smId);
+        + "WHERE sm.primaryId = $primaryId AND sm.importDate = $importDate "
+        + "RETURN st LIMIT 1")
+    Status findStatusForSampleMetadataById(@Param("primaryId") String primaryId,
+            @Param("importDate") String importDate);
 
     @Query("MATCH (s: Sample {smileSampleId: $smileSampleId}) "
             + "SET s.revisable = $revisable "

diff --git a/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/TempoRepository.java b/persistence/src/main/java/org/mskcc/smile/persistence/neo4j/TempoRepository.java
@@ -1,5 +1,6 @@
 package org.mskcc.smile.persistence.neo4j;
 
+//import org.springframework.data.neo4j.repository.query.Query;
 import java.util.List;
 import java.util.UUID;
 import org.mskcc.smile.model.tempo.BamComplete;