Merge pull request #2 from ncats/archUpdate

fixed export andd added new fields

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/controllers/InvitroPharmacologyController.java

@@ -118,7 +118,7 @@ public ResponseEntity<String> findAllAssays() throws Exception {
 
     @GetGsrsRestApiMapping("/allTestAgents")
     public ResponseEntity<String> findAllTestAgents() throws Exception {
-        List<InvitroAssayInformation> list = invitroPharmacologyEntityService.findAllTestAgents();
+        List<InvitroTestAgent> list = invitroPharmacologyEntityService.findAllTestAgents();
 
         return new ResponseEntity(list, HttpStatus.OK);
     }

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/exporters/InvitroPharmacologyExporter.java

@@ -84,11 +84,11 @@ public void export(InvitroAssayInformation a) throws IOException {
 
             // If there is no screening data, only export the Assay details
             if (a.invitroAssayScreenings.size() == 0) {
-                publicCreateRows(a, 0);
+                createRows(a, 0);
             // Else if there are screening data, export screening data along with Assay details
             } else if (a.invitroAssayScreenings.size() > 0) {
                 for (int i = 0; i < a.invitroAssayScreenings.size(); i++) {
-                    publicCreateRows(a, i);
+                    createRows(a, i);
                 } // for InvitroAssayScreenings
             } // invitroAssayScreenings size > 0
 
@@ -98,7 +98,7 @@ public void export(InvitroAssayInformation a) throws IOException {
         }
     }
 
-    public void publicCreateRows(InvitroAssayInformation a, int i) {
+    public void createRows(InvitroAssayInformation a, int i) {
         Spreadsheet.SpreadsheetRow row = spreadsheet.getRow(this.row++);
         int col = 0;
         this.screeningNumber = i;
@@ -120,7 +120,11 @@ public void close() throws IOException {
         DEFAULT_RECIPE_MAP = new LinkedHashMap<>();
 
         DEFAULT_RECIPE_MAP.put(InvitroPharmDefaultColumns.SCREENING_NUMBER, SingleColumnValueRecipe.create(InvitroPharmDefaultColumns.SCREENING_NUMBER, (a, cell) -> {
-            int screeningNum = screeningNumber + 1;
+            int screeningNum = screeningNumber;
+            // If there is any screening data, increment the number by 1
+            if (a.invitroAssayScreenings.size() > 0) {
+                screeningNum = screeningNumber + 1;
+            }
             cell.writeInteger((screeningNum));
         }));
 

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssayInformation.java

@@ -93,6 +93,9 @@ public class InvitroAssayInformation extends InvitroPharmacologyCommanData {
     @Column(name="TARGET_NAME_APPROVAL_ID")
     public String targetNameApprovalId;
 
+    @Column(name="TARGET_NAME_SUBSTANCE_UUID")
+    public String targetNameSubstanceUuid;
+
     @Indexable(suggest = true, facet=true, name= "Target Species", sortable = true)
     @Column(name="TARGET_SPECIES")
     public String targetSpecies;

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroAssayResult.java

@@ -55,6 +55,21 @@ public class InvitroAssayResult extends InvitroPharmacologyCommanData {
     @Column(name = "ASSAY_MEASUREMENT", length=4000)
     public String assayMeasurement;
 
+    @Column(name = "LIGAND_SUBSTRATE_CONCENT")
+    public Double ligandSubstrateConcentration;
+
+    @Column(name = "LIGAND_SUBSTRATE_CONCENT_UNITS")
+    public String ligandSubstrateConcentrationUnits;
+
+    @Column(name = "NUMBER_OF_TESTS")
+    public String numberOfTests;
+
+    @Column(name = "DATA_TYPE")
+    public String dataType;
+
+    @Column(name = "PLASMA_PROTEIN_ADDED")
+    public String plasmaProteinAdded;
+
     public InvitroAssayResult() {
     }
 

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/models/InvitroReference.java

@@ -35,7 +35,7 @@ public class InvitroReference extends InvitroPharmacologyCommanData {
     @Column(name="REFERENCE_SOURCE_TYPE")
     public String referenceSourceType;
 
-    @Indexable(suggest = true, facet=true, name= "Reference Source Number", sortable = true)
+    @Indexable(suggest = true, facet=true, name= "Reference Source", sortable = true)
     @Column(name="REFERENCE_SOURCE_NUMBER")
     public String referenceSourceNumber;
 

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/repositories/InvitroPharmacologyRepository.java

@@ -37,6 +37,9 @@ public interface InvitroPharmacologyRepository extends GsrsVersionedRepository<I
     @Query("select a from InvitroReference a")
     List<InvitroReference> findAllReferences();
 
+    @Query("select a from InvitroTestAgent a")
+    List<InvitroTestAgent> findAllTestAgents();
+
     @Query("select a from InvitroAssayInformation a JOIN a.invitroAssayScreenings s JOIN s.invitroTestAgent ta where ta.testAgent IS NOT NULL")
     List<InvitroAssayInformation> findAllScreeningTestAgents();
 }

gsrs-module-invitro-pharmacology-spring-boot-autoconfigure/src/main/java/gov/hhs/gsrs/invitropharmacology/services/InvitroPharmacologyEntityService.java

@@ -158,8 +158,8 @@ public List<InvitroAssayInformation> findAllAssays() {
         return list;
     }
 
-    public List<InvitroAssayInformation> findAllTestAgents() {
-        List<InvitroAssayInformation> list = repository.findAllScreeningTestAgents();
+    public List<InvitroTestAgent> findAllTestAgents() {
+        List<InvitroTestAgent> list = repository.findAllTestAgents();
         return list;
     }