TEMPO/HERA sample tracker support (#1092)

* Bam complete (#1084)

* HERA Sample Tracker Support: BAM Complete

This PR includes changes for supporting a new data type: BAM Complete

BAM Complete is part of the effort to support HERA Sample Tracker data in the SMILE dashboard.

General updates:
- New Neo4j models added
- New mocked data and unit tests added
- New service and persistence layer classes added
- New message handler service for TEMPO workflow with
  message handler for BAM complete topic

Signed-off-by: Angelica Ochoa <[email protected]>

---------

Signed-off-by: Angelica Ochoa <[email protected]>
Co-authored-by: Quan Nguyen <[email protected]>

Rename BamComplete's property 'timestamp' to 'date' (#1093)

* Rename BamComplete's property 'timestamp' to 'date'

* Specify Neo4j image version in tests for compatibility with arm64 machines

* Clean up debugging logs

* Update TestContainer to avoid manually specifying Neo4j image version

* Qc complete (#1094)

* Init commit QC complete

Signed-off-by: Angelica Ochoa <[email protected]>

* Updated Tempo model with QC complete events

Signed-off-by: Angelica Ochoa <[email protected]>

* Javadocs, Tempo model changes

Signed-off-by: Angelica Ochoa <[email protected]>

* Added mocked QC complete data

Signed-off-by: Angelica Ochoa <[email protected]>

* temp

* QC Complete service layer

Signed-off-by: Angelica Ochoa <[email protected]>

* QC complete handler

Signed-off-by: Angelica Ochoa <[email protected]>

---------

Signed-off-by: Angelica Ochoa <[email protected]>

* MAF Complete Support

- Add MafComplete class
- Add to Tempo class functions to handle MafComplete events
- Define Neo4j query constructors for MafComplete events
- Modify Tempo services to handle MafComplete events
- Remove seconds from BamComplete date in mock test JSONs

* MAF Complete support pt 2

- Update application.properties.EXAMPLE to include MafComplete topic
- Add MafComplete mock JSONs for testing
- Resolve checkstyle issues
- Add missing normalPrimaryId in the mergeMafComplete query
- Handle renaming of normal_primaryId to normalPrimaryId

* Cohort & CohortComplete workflow  (#1102)

* Cohort and CohortComplete support

General updates:
- Added Cohort, CohortComplete models
- Added service layer components for Cohort, CohortComplete
- Added message handler for Cohort, CohortComplete
- Added queries to support saving and updating Cohort, CohortComplete

Signed-off-by: Angelica Ochoa <[email protected]>

* Unit tests for MAF, QC, and Cohort Complete events

Added unit tests for MAF, QC, and Cohort Complete events.

Signed-off-by: Angelica Ochoa <[email protected]>

---------

Signed-off-by: Angelica Ochoa <[email protected]>

---------

Signed-off-by: Angelica Ochoa <[email protected]>
Co-authored-by: Quan Nguyen <[email protected]>

model/src/main/java/org/mskcc/smile/model/SmileSample.java

@@ -8,6 +8,7 @@
 import java.util.List;
 import java.util.UUID;
 import org.apache.commons.lang.builder.ToStringBuilder;
+import org.mskcc.smile.model.tempo.Tempo;
 import org.neo4j.ogm.annotation.GeneratedValue;
 import org.neo4j.ogm.annotation.Id;
 import org.neo4j.ogm.annotation.NodeEntity;
@@ -28,6 +29,8 @@ public class SmileSample implements Serializable {
     private SmilePatient patient;
     @Relationship(type = "HAS_METADATA", direction = Relationship.OUTGOING)
     private List<SampleMetadata> sampleMetadataList;
+    @Relationship(type = "HAS_TEMPO", direction = Relationship.OUTGOING)
+    private Tempo tempo;
     private String sampleClass;
     private String sampleCategory;
     private String datasource;
@@ -215,6 +218,14 @@ public void setRevisable(Boolean revisable) {
         this.revisable = revisable;
     }
 
+    public Tempo getTempo() {
+        return tempo;
+    }
+
+    public void setTempo(Tempo tempo) {
+        this.tempo = tempo;
+    }
+
     @Override
     public String toString() {
         return ToStringBuilder.reflectionToString(this);

model/src/main/java/org/mskcc/smile/model/tempo/BamComplete.java

@@ -0,0 +1,55 @@
+package org.mskcc.smile.model.tempo;
+
+import java.io.Serializable;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.neo4j.ogm.annotation.GeneratedValue;
+import org.neo4j.ogm.annotation.Id;
+import org.neo4j.ogm.annotation.NodeEntity;
+
+/**
+ *
+ * @author ochoaa
+ */
+@NodeEntity
+public class BamComplete implements Serializable {
+    @Id @GeneratedValue
+    private Long id;
+    private String date;
+    private String status;
+
+    public BamComplete() {}
+
+    public BamComplete(String date, String status) {
+        this.date = date;
+        this.status = status;
+    }
+
+    public Long getId() {
+        return id;
+    }
+
+    public void setId(Long id) {
+        this.id = id;
+    }
+
+    public String getDate() {
+        return date;
+    }
+
+    public void setDate(String date) {
+        this.date = date;
+    }
+
+    public String getStatus() {
+        return status;
+    }
+
+    public void setStatus(String status) {
+        this.status = status;
+    }
+
+    @Override
+    public String toString() {
+        return ToStringBuilder.reflectionToString(this);
+    }
+}

model/src/main/java/org/mskcc/smile/model/tempo/Cohort.java

@@ -0,0 +1,123 @@
+package org.mskcc.smile.model.tempo;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.mskcc.smile.model.SmileSample;
+import org.mskcc.smile.model.tempo.json.CohortCompleteJson;
+import org.neo4j.ogm.annotation.GeneratedValue;
+import org.neo4j.ogm.annotation.Id;
+import org.neo4j.ogm.annotation.NodeEntity;
+import org.neo4j.ogm.annotation.Relationship;
+
+/**
+ *
+ * @author ochoaa
+ */
+@NodeEntity
+public class Cohort implements Serializable {
+    @Id @GeneratedValue
+    private Long id;
+    private String cohortId;
+    @Relationship(type = "HAS_COHORT_COMPLETE", direction = Relationship.OUTGOING)
+    private List<CohortComplete> cohortCompleteList;
+    @Relationship(type = "HAS_COHORT_SAMPLE", direction = Relationship.OUTGOING)
+    private List<SmileSample> cohortSamples;
+
+    public Cohort() {}
+
+    public Cohort(CohortCompleteJson ccJson) {
+        this.cohortId = ccJson.getCohortId();
+        addCohortComplete(new CohortComplete(ccJson));
+    }
+
+    public Long getId() {
+        return id;
+    }
+
+    public void setId(Long id) {
+        this.id = id;
+    }
+
+    public String getCohortId() {
+        return cohortId;
+    }
+
+    public void setCohortId(String cohortId) {
+        this.cohortId = cohortId;
+    }
+
+    /**
+     * Returns list of CohortComplete object instances.
+     * @return
+     */
+    public List<CohortComplete> getCohortCompleteList() {
+        if (cohortCompleteList == null) {
+            this.cohortCompleteList = new ArrayList<>();
+        }
+        return cohortCompleteList;
+    }
+
+    /**
+     * Adds instance of CohortComplete to cohortCompleteList.
+     * @param cohortComplete
+     */
+    public final void addCohortComplete(CohortComplete cohortComplete) {
+        if (cohortCompleteList == null) {
+            this.cohortCompleteList = new ArrayList<>();
+        }
+        cohortCompleteList.add(cohortComplete);
+    }
+
+    public void setCohortCompleteList(List<CohortComplete> cohortCompleteList) {
+        this.cohortCompleteList = cohortCompleteList;
+    }
+
+    /**
+     * Returns list of SmileSample instances.
+     * @return
+     */
+    public List<SmileSample> getCohortSamples() {
+        if (cohortSamples == null) {
+            this.cohortSamples = new ArrayList<>();
+        }
+        return cohortSamples;
+    }
+
+    /**
+     * Adds instance of SmileSample to cohortSamples list.
+     * @param sample
+     */
+    public final void addCohortSample(SmileSample sample) {
+        if (cohortSamples == null) {
+            this.cohortSamples = new ArrayList<>();
+        }
+        cohortSamples.add(sample);
+    }
+
+    public void setCohortSamples(List<SmileSample> cohortSamples) {
+        this.cohortSamples = cohortSamples;
+    }
+
+    /**
+     * Returns latest cohort complete data.
+     * @return
+     */
+    public CohortComplete getLatestCohortComplete() {
+        if (cohortCompleteList != null && !cohortCompleteList.isEmpty()) {
+            if (cohortCompleteList.size() == 1) {
+                return cohortCompleteList.get(0);
+            }
+            Collections.sort(cohortCompleteList);
+            return cohortCompleteList.get(cohortCompleteList.size() - 1);
+        }
+        return null;
+    }
+
+    @Override
+    public String toString() {
+        return ToStringBuilder.reflectionToString(this);
+    }
+}

model/src/main/java/org/mskcc/smile/model/tempo/CohortComplete.java

@@ -0,0 +1,137 @@
+package org.mskcc.smile.model.tempo;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.mskcc.smile.model.tempo.json.CohortCompleteJson;
+import org.neo4j.ogm.annotation.GeneratedValue;
+import org.neo4j.ogm.annotation.Id;
+import org.neo4j.ogm.annotation.NodeEntity;
+
+/**
+ *
+ * @author ochoaa
+ */
+@NodeEntity
+public class CohortComplete implements Serializable, Comparable<CohortComplete> {
+    @Id @GeneratedValue
+    @JsonIgnore
+    private Long id;
+    private String date;
+    private String status;
+    private String type;
+    private List<String> endUsers;
+    private List<String> pmUsers;
+    private String projectTitle;
+    private String projectSubtitle;
+
+    public CohortComplete() {}
+
+    /**
+     * Basic constructor from CohortCompleteJson.
+     * @param ccJson
+     */
+    public CohortComplete(CohortCompleteJson ccJson) {
+        this.date = ccJson.getDate();
+        this.status = ccJson.getStatus();
+        this.type = ccJson.getType();
+        this.endUsers = ccJson.getEndUsers();
+        this.pmUsers = ccJson.getPmUsers();
+        this.projectTitle = ccJson.getProjectTitle();
+        this.projectSubtitle = ccJson.getProjectSubtitle();
+    }
+
+    public String getDate() {
+        return date;
+    }
+
+    public void setDate(String date) {
+        this.date = date;
+    }
+
+    public String getStatus() {
+        return status;
+    }
+
+    public void setStatus(String status) {
+        this.status = status;
+    }
+
+    public String getType() {
+        return type;
+    }
+
+    public void setType(String type) {
+        this.type = type;
+    }
+
+    /**
+     * Returns list of end users.
+     * @return
+     */
+    public List<String> getEndUsers() {
+        if (endUsers == null) {
+            this.endUsers = new ArrayList<>();
+        }
+        Collections.sort(endUsers);
+        return endUsers;
+    }
+
+    public void setEndUsers(List<String> endUsers) {
+        this.endUsers = endUsers;
+    }
+
+    /**
+     * Returns list of PM users.
+     * @return
+     */
+    public List<String> getPmUsers() {
+        if (pmUsers == null) {
+            this.pmUsers = new ArrayList<>();
+        }
+        Collections.sort(pmUsers);
+        return pmUsers;
+    }
+
+    public void setPmUsers(List<String> pmUsers) {
+        this.pmUsers = pmUsers;
+    }
+
+    public String getProjectTitle() {
+        return projectTitle;
+    }
+
+    public void setProjectTitle(String projectTitle) {
+        this.projectTitle = projectTitle;
+    }
+
+    public String getProjectSubtitle() {
+        return projectSubtitle;
+    }
+
+    public void setProjectSubtitle(String projectSubtitle) {
+        this.projectSubtitle = projectSubtitle;
+    }
+
+    /**
+     * Override to enable Collections.sorting
+     * @param cohortComplete
+     * @return
+     */
+    @Override
+    public int compareTo(CohortComplete cohortComplete) {
+        if (date == null || cohortComplete.getDate() == null) {
+            return 0;
+        }
+        return date.compareTo(cohortComplete.getDate());
+    }
+
+    @Override
+    public String toString() {
+        return ToStringBuilder.reflectionToString(this);
+    }
+}