Merge pull request #2948 from IBM/issue-713

Avoid creating unnecessary tables for Resource and DomainResource resource types #713
LinuxForHealth · Nov 9, 2021 · db6813d · db6813d
2 parents 230c754 + a2521f2
commit db6813d
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Showing 21 changed files with 622 additions and 126 deletions.
diff --git a/build/audit/kafka/docker-compose.yml b/build/audit/kafka/docker-compose.yml
@@ -68,15 +68,15 @@ services:
     command: bash -c "
         java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
           --db-type derby --prop db.database=/output/derby/profile --prop db.create=Y
-          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
           --update-schema &&
         java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
           --db-type derby --prop db.database=/output/derby/reference --prop db.create=Y
-          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
           --update-schema &&
         java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
           --db-type derby --prop db.database=/output/derby/study1 --prop db.create=Y
-          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
           --update-schema &&
         /opt/ol/wlp/bin/server run"
     healthcheck:

diff --git a/build/derby-bootstrap.sh b/build/derby-bootstrap.sh
@@ -26,13 +26,13 @@ java -jar ${WORKSPACE}/fhir-persistence-schema/target/fhir-persistence-schema-*-
   --update-schema
 java -jar ${WORKSPACE}/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
   --db-type derby --prop db.database=${DB_LOC}/profile --prop db.create=Y \
-  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
   --update-schema
 java -jar ${WORKSPACE}/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
   --db-type derby --prop db.database=${DB_LOC}/reference --prop db.create=Y \
-  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
   --update-schema
 java -jar ${WORKSPACE}/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
   --db-type derby --prop db.database=${DB_LOC}/study1 --prop db.create=Y \
-  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
   --update-schema
diff --git a/build/docker/docker-compose.yml b/build/docker/docker-compose.yml
@@ -31,15 +31,15 @@ services:
     command: bash -c "
         java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
           --db-type derby --prop db.database=/output/derby/profile --prop db.create=Y
-          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
           --update-schema &&
         java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
           --db-type derby --prop db.database=/output/derby/reference --prop db.create=Y
-          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
           --update-schema &&
         java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
           --db-type derby --prop db.database=/output/derby/study1 --prop db.create=Y
-          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
           --update-schema &&
         /opt/ol/wlp/bin/server run"
     healthcheck:

diff --git a/build/migration/db2/4_current-migrate.sh b/build/migration/db2/4_current-migrate.sh
@@ -56,19 +56,19 @@ java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-sche
     --update-schema
 java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
     --db-type derby --prop db.database=${DB_LOC}/profile --prop db.create=Y \
-    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
     --update-schema
 java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
     --db-type derby --prop db.database=${DB_LOC}/reference --prop db.create=Y \
-    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
     --update-schema
 java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
     --db-type derby --prop db.database=${DB_LOC}/study1 --prop db.create=Y \
-    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
     --update-schema
 
 # Reset to Original Directory
 popd > /dev/null
 
 # EOF
-###############################################################################
+###############################################################################
diff --git a/build/migration/postgres/4_current-migrate.sh b/build/migration/postgres/4_current-migrate.sh
@@ -70,19 +70,19 @@ java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-sche
     --update-schema
 java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
     --db-type derby --prop db.database=${DB_LOC}/profile --prop db.create=Y \
-    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
     --update-schema
 java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
     --db-type derby --prop db.database=${DB_LOC}/reference --prop db.create=Y \
-    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
     --update-schema
 java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
     --db-type derby --prop db.database=${DB_LOC}/study1 --prop db.create=Y \
-    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+    --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
     --update-schema
 
 # Reset to Original Directory
 popd > /dev/null
 
 # EOF
-###############################################################################
+###############################################################################
diff --git a/build/notifications/kafka/docker-compose.yml b/build/notifications/kafka/docker-compose.yml
@@ -68,15 +68,15 @@ services:
     command: bash -c "
         java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
           --db-type derby --prop db.database=/output/derby/profile --prop db.create=Y
-          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
           --update-schema &&
         java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
           --db-type derby --prop db.database=/output/derby/reference --prop db.create=Y
-          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
           --update-schema &&
         java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
           --db-type derby --prop db.database=/output/derby/study1 --prop db.create=Y
-          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+          --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
           --update-schema &&
         /opt/ol/wlp/bin/server run"
     healthcheck:

diff --git a/build/persistence/postgres/docker-compose.yml b/build/persistence/postgres/docker-compose.yml
@@ -47,15 +47,15 @@ services:
     command: bash -c "
       java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
         --db-type derby --prop db.database=/output/derby/profile --prop db.create=Y
-        --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+        --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
         --update-schema &&
       java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
         --db-type derby --prop db.database=/output/derby/reference --prop db.create=Y
-        --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+        --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
         --update-schema &&
       java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
         --db-type derby --prop db.database=/output/derby/study1 --prop db.create=Y
-        --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
+        --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
         --update-schema &&
       /opt/ol/wlp/bin/server run"
     healthcheck:

diff --git a/build/pre-integration-test.ps1 b/build/pre-integration-test.ps1
@@ -58,15 +58,15 @@ java -jar $SCHEMATOOL `
   --update-schema
 java -jar $SCHEMATOOL `
   --db-type derby --prop db.database=${DB_LOC}\profile --prop db.create=Y `
-  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource `
+  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet `
   --update-schema
 java -jar $SCHEMATOOL `
   --db-type derby --prop db.database=${DB_LOC}\reference --prop db.create=Y `
-  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource `
+  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet `
   --update-schema
 java -jar $SCHEMATOOL `
   --db-type derby --prop db.database=${DB_LOC}\study1 --prop db.create=Y `
-  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource `
+  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet `
   --update-schema
 
 # If the Config Exists, let's wipe it outfind

diff --git a/build/pre-integration-test.sh b/build/pre-integration-test.sh
@@ -50,15 +50,15 @@ java -jar ${SIT}/fhir-server-dist/tools/fhir-persistence-schema-*-cli.jar \
   --update-schema
 java -jar ${SIT}/fhir-server-dist/tools/fhir-persistence-schema-*-cli.jar \
   --db-type derby --prop db.database=${DB_LOC}/profile --prop db.create=Y \
-  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
   --update-schema
 java -jar ${SIT}/fhir-server-dist/tools/fhir-persistence-schema-*-cli.jar \
   --db-type derby --prop db.database=${DB_LOC}/reference --prop db.create=Y \
-  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
   --update-schema
 java -jar ${SIT}/fhir-server-dist/tools/fhir-persistence-schema-*-cli.jar \
   --db-type derby --prop db.database=${DB_LOC}/study1 --prop db.create=Y \
-  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
+  --prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
   --update-schema
 
 echo "Copying configuration to install location..."

diff --git a/fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/db2/Db2CatalogAccess.java b/fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/db2/Db2CatalogAccess.java
@@ -23,14 +23,14 @@
  */
 public class Db2CatalogAccess implements ICatalogAccess {
     private static final Logger logger = Logger.getLogger(Db2CatalogAccess.class.getName());
-    
+
     private Connection connection;
     private Db2CatalogDAO dao = new Db2CatalogDAO(new Db2Translator());
 
     public Db2CatalogAccess(Connection c) {
         this.connection = c;
     }
-    
+
     @Override
     public List<PartitionInfo> getPartitionList(String schema, String table) {
         try {