Merge pull request #3 from ncats/archUpdate

added actuator health and print statements
ncats · Mar 19, 2024 · 03e1a56 · 03e1a56
2 parents 515b68b + 1b9c26e
commit 03e1a56
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Showing 6 changed files with 124 additions and 6 deletions.
diff --git a/...main/java/gov/hhs/gsrs/invitropharmacology/controllers/InvitroPharmacologyController.java b/...main/java/gov/hhs/gsrs/invitropharmacology/controllers/InvitroPharmacologyController.java
@@ -37,6 +37,9 @@
 import org.springframework.web.bind.annotation.RequestParam;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import org.springframework.web.bind.annotation.GetMapping;
+
+import lombok.extern.slf4j.Slf4j;
 
 import javax.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
@@ -50,6 +53,9 @@
 import java.util.Optional;
 import java.util.stream.Stream;
 
+import net.minidev.json.JSONObject;
+
+@Slf4j
 @ExposesResourceFor(InvitroAssayInformation.class)
 @GsrsRestApiController(context = InvitroPharmacologyEntityService.CONTEXT, idHelper = IdHelpers.NUMBER)
 public class InvitroPharmacologyController extends EtagLegacySearchEntityController<InvitroPharmacologyController, InvitroAssayInformation, Long> {
@@ -102,6 +108,13 @@ protected Stream<InvitroAssayInformation> filterStream(Stream<InvitroAssayInform
         return stream;
     }
 
+    @GetGsrsRestApiMapping("/actuator/health")
+    public ResponseEntity<Object> checkHealth() throws Exception {
+        JSONObject status = new JSONObject();
+        status.put("status", "UP");
+        return new ResponseEntity(status, HttpStatus.OK);
+    }
+
     @GetGsrsRestApiMapping("/assay/{id}/screenings")
     public ResponseEntity<String> findAllScreeningsByAssayId(@PathVariable("id") Long assayId) throws Exception {
         List<InvitroAssayInformation> list = invitroPharmacologyEntityService.findAllScreeningsByAssayId(assayId);
@@ -111,14 +124,23 @@ public ResponseEntity<String> findAllScreeningsByAssayId(@PathVariable("id") Lon
 
     @GetGsrsRestApiMapping("/allAssays")
     public ResponseEntity<String> findAllAssays() throws Exception {
+        System.out.println("********** Controller: Inside findAllAssays() ********************");
+        log.error("********** ********** Controller: Inside findAllAssays() ******************** ");
         List<InvitroAssayInformation> list = invitroPharmacologyEntityService.findAllAssays();
 
         return new ResponseEntity(list, HttpStatus.OK);
     }
 
-    @GetGsrsRestApiMapping("/allTestAgents")
-    public ResponseEntity<String> findAllTestAgents() throws Exception {
-        List<InvitroTestAgent> list = invitroPharmacologyEntityService.findAllTestAgents();
+    @GetGsrsRestApiMapping("/assaysByAssaySets/{assaySet}")
+    public ResponseEntity<String> findAllAssysByAssaySet(@PathVariable("assaySet") String assaySet) throws Exception {
+        List<InvitroAssayInformation> list = invitroPharmacologyEntityService.findAllAssysByAssaySet(assaySet);
+
+        return new ResponseEntity(list, HttpStatus.OK);
+    }
+
+    @GetGsrsRestApiMapping("/allAssaySets")
+    public ResponseEntity<String> findAllAssaySets() throws Exception {
+        List<InvitroAssaySet> list = invitroPharmacologyEntityService.findAllAssaySets();
 
         return new ResponseEntity(list, HttpStatus.OK);
     }
@@ -130,6 +152,13 @@ public ResponseEntity<String> findAllReferences() throws Exception {
         return new ResponseEntity(list, HttpStatus.OK);
     }
 
+    @GetGsrsRestApiMapping("/allTestAgents")
+    public ResponseEntity<String> findAllTestAgents() throws Exception {
+        List<InvitroTestAgent> list = invitroPharmacologyEntityService.findAllTestAgents();
+
+        return new ResponseEntity(list, HttpStatus.OK);
+    }
+
     @GetGsrsRestApiMapping("/assaytargetunii/{assayTargetUnii}")
     public ResponseEntity<String> findAssayByTargetNameApprovalId(@PathVariable("assayTargetUnii") String assayTargetUnii) throws Exception {
         List<InvitroAssayInformation> list = invitroPharmacologyEntityService.findAssayByTargetNameApprovalId(assayTargetUnii);

diff --git a/...figure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssayInformation.java b/...figure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssayInformation.java
@@ -37,6 +37,10 @@ public class InvitroAssayInformation extends InvitroPharmacologyCommanData {
     @Column(name="ASSAY_ID")
     public String assayId;
 
+    @Indexable(suggest = true, facet=true, name= "Assay Set", sortable = true)
+    @Column(name="ASSAY_SET", length=1000)
+    public String assaySet;
+
     @Indexable(suggest = true, facet=true, name= "External Assay ID", sortable = true)
     @Column(name="EXTERNAL_ASSAY_ID")
     public String externalAssayId;
@@ -52,13 +56,16 @@ public class InvitroAssayInformation extends InvitroPharmacologyCommanData {
     public String externalAssayReferenceUrl;
 
     @Indexable(suggest = true, facet=true, name= "Assay Title", sortable = true)
-    @Column(name="ASSAY_TITLE")
+    @Column(name="ASSAY_TITLE", length=1000)
     public String assayTitle;
 
     @Indexable(suggest = true, facet=true, name= "Assay Format", sortable = true)
     @Column(name="ASSAY_FORMAT")
     public String assayFormat;
 
+    @Column(name = "ASSAY_MODE")
+    public String assayMode;
+
     @Indexable(suggest = true, facet=true, name= "Bioassay Type", sortable = true)
     @Column(name="BIOASSAY_TYPE")
     public String bioassayType;
@@ -150,4 +157,11 @@ public void setInvitroAssayScreenings(List<InvitroAssayScreening> invitroAssaySc
         }
     }
 
+    // Many To Many, InvitroAssaySet
+    @ToString.Exclude
+    @LazyCollection(LazyCollectionOption.FALSE)
+    @ManyToMany(fetch = FetchType.LAZY, cascade= CascadeType.ALL)
+    @JoinTable(name="GSRS_INVITRO_ASSAY_SET_DET", joinColumns = @JoinColumn(name = "INVITRO_ASSAY_INFO_ID "),
+            inverseJoinColumns = @JoinColumn(name = "INVITRO_ASSAY_SET_ID"))
+    public List<InvitroAssaySet> invitroAssaySets = new ArrayList<>();
 }
diff --git a/...-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssaySet.java b/...-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssaySet.java
@@ -0,0 +1,47 @@
+package gov.hhs.gsrs.invitropharmacology.models;
+
+import ix.core.SingleParent;
+import ix.core.models.Indexable;
+import ix.core.models.IndexableRoot;
+import ix.core.models.ParentReference;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import lombok.ToString;
+
+import org.hibernate.annotations.LazyCollection;
+import org.hibernate.annotations.LazyCollectionOption;
+
+import javax.persistence.*;
+
+import java.util.Date;
+import java.util.ArrayList;
+import java.util.List;
+
+@SingleParent
+@Data
+@Entity
+@Table(name="GSRS_INVITRO_ASSAY_SET")
+public class InvitroAssaySet extends InvitroPharmacologyCommanData {
+
+    @Id
+    @SequenceGenerator(name="invitroAssaySetSeq", sequenceName="GSRS_INVITRO_ASSAY_SET_SEQ",allocationSize=1)
+    @GeneratedValue(strategy = GenerationType.AUTO, generator = "invitroAssaySetSeq")
+    @Column(name="ID")
+    public Long id;
+
+    @Indexable(suggest = true, facet=true, name= "Assay Set", sortable = true)
+    @Column(name="ASSAY_SET")
+    public String assaySet;
+
+    public InvitroAssaySet () {}
+
+    // Many To Many, InvitroAssayInformation
+    @JsonIgnore
+    @ManyToMany(fetch = FetchType.EAGER, cascade= CascadeType.ALL)
+    @JoinTable(name="GSRS_INVITRO_ASSAY_SET_DET", joinColumns = @JoinColumn(name = "INVITRO_ASSAY_SET_ID"),
+            inverseJoinColumns = @JoinColumn(name = "INVITRO_ASSAY_INFO_ID"))
+    public List<InvitroAssayInformation> invitroAssayInformations = new ArrayList<>();
+}
diff --git a/...ain/java/gov/hhs/gsrs/invitropharmacology/repositories/InvitroPharmacologyRepository.java b/...ain/java/gov/hhs/gsrs/invitropharmacology/repositories/InvitroPharmacologyRepository.java
@@ -31,9 +31,15 @@ public interface InvitroPharmacologyRepository extends GsrsVersionedRepository<I
     @Query("select a from InvitroAssayInformation a JOIN a.invitroAssayScreenings s JOIN s.invitroTestAgent ta WHERE ta.testAgent = ?1")
     List<InvitroAssayInformation> findAssayByTestAgent(String targetName);
 
+    @Query("select a from InvitroAssayInformation a JOIN a.invitroAssaySets s where s.assaySet = ?1")
+    List<InvitroAssayInformation> findAllAssysByAssaySet(String assaySet);
+
     @Query("select a from InvitroAssayInformation a")
     List<InvitroAssayInformation> findAllAssays();
 
+    @Query("select a from InvitroAssaySet a")
+    List<InvitroAssaySet> findAllAssaySets();
+
     @Query("select a from InvitroReference a")
     List<InvitroReference> findAllReferences();
 

diff --git a/...main/java/gov/hhs/gsrs/invitropharmacology/services/InvitroPharmacologyEntityService.java b/...main/java/gov/hhs/gsrs/invitropharmacology/services/InvitroPharmacologyEntityService.java
@@ -17,11 +17,14 @@
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
+import lombok.extern.slf4j.Slf4j;
+
 import java.io.IOException;
 import java.util.List;
 import java.util.Optional;
 import java.util.UUID;
 
+@Slf4j
 @Service
 public class InvitroPharmacologyEntityService extends AbstractGsrsEntityService<InvitroAssayInformation, Long> {
     public static final String  CONTEXT = "invitropharmacology";
@@ -126,11 +129,14 @@ public long count() {
 
     @Override
     public Optional<InvitroAssayInformation> get(Long id) {
+        System.out.println("********** Inside get(Long id) " + id);
+        log.error("********** Inside get(Long id) " + id);
         return repository.findById(id);
     }
 
     @Override
     public Optional<InvitroAssayInformation> flexLookup(String someKindOfId) {
+        System.out.println("********** Inside flexLookup(String someKindOfId) " + someKindOfId);
         if (someKindOfId == null){
             return Optional.empty();
         }
@@ -154,12 +160,19 @@ public List<InvitroAssayInformation> findAllScreeningsByAssayId(Long id) {
     }
 
     public List<InvitroAssayInformation> findAllAssays() {
+        System.out.println("********** Inside findAllAssays() ********************");
+        log.error("********** Inside findAllAssays() ******************** ");
         List<InvitroAssayInformation> list = repository.findAllAssays();
         return list;
     }
 
-    public List<InvitroTestAgent> findAllTestAgents() {
-        List<InvitroTestAgent> list = repository.findAllTestAgents();
+    public List<InvitroAssayInformation> findAllAssysByAssaySet(String assaySet) {
+        List<InvitroAssayInformation> list = repository.findAllAssysByAssaySet(assaySet);
+        return list;
+    }
+
+    public List<InvitroAssaySet> findAllAssaySets() {
+        List<InvitroAssaySet> list = repository.findAllAssaySets();
         return list;
     }
 
@@ -168,6 +181,11 @@ public List<InvitroReference> findAllReferences() {
         return list;
     }
 
+    public List<InvitroTestAgent> findAllTestAgents() {
+        List<InvitroTestAgent> list = repository.findAllTestAgents();
+        return list;
+    }
+
     public List<InvitroAssayInformation> findAssayByTargetNameApprovalId(String assayTargetUnii) {
         List<InvitroAssayInformation> list = repository.findAssayByTargetNameApprovalId(assayTargetUnii);
         return list;

diff --git a/.../main/java/gov/hhs/gsrs/invitropharmacology/validators/RequiredFieldNonNullValidator.java b/.../main/java/gov/hhs/gsrs/invitropharmacology/validators/RequiredFieldNonNullValidator.java
@@ -17,6 +17,10 @@ public boolean supports(InvitroAssayInformation newValue, InvitroAssayInformatio
     @Override
     public void validate(InvitroAssayInformation objnew, InvitroAssayInformation objold, ValidatorCallback callback) {
 
+        if (objnew.assaySet == null || objnew.assaySet.isEmpty()) {
+            callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("Assay Set is required."));
+        }
+
         if ((objnew.externalAssayId == null) || (objnew.externalAssayId.isEmpty())) {
             callback.addMessage(GinasProcessingMessage.ERROR_MESSAGE("External Assay ID is required"));
         }