Entity sequence

src/main/java/org/ohdsi/webapi/cohortcomparison/ComparativeCohortAnalysis.java

@@ -19,7 +19,9 @@
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 /**
@@ -30,7 +32,8 @@
 public class ComparativeCohortAnalysis implements Serializable {
 
     @Id
-    @GeneratedValue
+    @SequenceGenerator(name = "cca_seq", sequenceName = "cca_sequence", allocationSize = 1)
+    @GeneratedValue(generator = "cca_seq", strategy = GenerationType.SEQUENCE)
     @Column(name = "cca_id")
     private Integer analysisId;
 

src/main/java/org/ohdsi/webapi/cohortdefinition/CohortDefinition.java

@@ -15,30 +15,26 @@
 package org.ohdsi.webapi.cohortdefinition;
 
 import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Date;
-import java.util.List;
 import java.util.Set;
 import javax.persistence.Access;
 import javax.persistence.AccessType;
 import javax.persistence.CascadeType;
-import javax.persistence.CollectionTable;
 import javax.persistence.Column;
-import javax.persistence.ElementCollection;
 import javax.persistence.Entity;
 import javax.persistence.EnumType;
 import javax.persistence.Enumerated;
 import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.NamedAttributeNode;
 import javax.persistence.NamedEntityGraph;
 import javax.persistence.NamedSubgraph;
 import javax.persistence.OneToMany;
 import javax.persistence.OneToOne;
-import javax.persistence.OrderColumn;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 /**
@@ -57,7 +53,8 @@ public class CohortDefinition implements Serializable{
   private static final long serialVersionUID = 1L;
 
   @Id
-  @GeneratedValue
+  @SequenceGenerator(name = "cohort_definition_seq",sequenceName = "cohort_definition_sequence", allocationSize = 1)
+  @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "cohort_definition_seq")
   @Access(AccessType.PROPERTY) 
   private Integer id;
 

src/main/java/org/ohdsi/webapi/conceptset/ConceptSet.java

@@ -16,14 +16,12 @@
 package org.ohdsi.webapi.conceptset;
 
 import java.io.Serializable;
-import java.util.Collection;
-import javax.persistence.CascadeType;
 import javax.persistence.Column;
 import javax.persistence.Entity;
-import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
-import javax.persistence.OneToMany;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 /**
@@ -35,7 +33,8 @@
 public class ConceptSet implements Serializable {
 
   @Id
-  @GeneratedValue  
+  @SequenceGenerator(name = "concept_set_seq", sequenceName = "concept_set_sequence", allocationSize = 1)
+  @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "concept_set_seq")
   @Column(name="concept_set_id")    
   private int id;
 

src/main/java/org/ohdsi/webapi/conceptset/ConceptSetItem.java

@@ -15,12 +15,13 @@
  */
 package org.ohdsi.webapi.conceptset;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
 import java.io.Serializable;
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 /**
@@ -33,8 +34,9 @@
 public class ConceptSetItem implements Serializable{
 
   @Id
-  @GeneratedValue  
-  @Column(name="concept_set_item_id")    
+  @SequenceGenerator(name = "concept_set_item_seq", sequenceName = "concept_set_item_sequence", allocationSize = 1)
+  @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "concept_set_item_seq")
+  @Column(name="concept_set_item_id")
   private int id;
 
   @Column(name="concept_set_id")

src/main/java/org/ohdsi/webapi/evidence/NegativeControlRecord.java

@@ -11,7 +11,9 @@
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 /**
@@ -23,7 +25,8 @@
 public class NegativeControlRecord implements Serializable {
 
     @Id
-    @GeneratedValue  
+    @SequenceGenerator(name = "concept_set_negative_controls_seq", sequenceName = "negative_controls_sequence", allocationSize = 1)
+    @GeneratedValue(generator = "concept_set_negative_controls_seq", strategy = GenerationType.SEQUENCE)
     @Access(AccessType.PROPERTY) 
     @Column(name = "id")
     private int id;

src/main/java/org/ohdsi/webapi/feasibility/FeasibilityStudy.java

@@ -29,6 +29,7 @@
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.NamedAttributeNode;
@@ -37,6 +38,7 @@
 import javax.persistence.OneToMany;
 import javax.persistence.OneToOne;
 import javax.persistence.OrderColumn;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 import org.ohdsi.webapi.cohortdefinition.CohortDefinition;
 
@@ -64,7 +66,8 @@
 public class FeasibilityStudy {
 
   @Id
-  @GeneratedValue
+  @SequenceGenerator(name = "feasibility_study_seq", sequenceName = "feasibility_study_sequence", allocationSize = 1)
+  @GeneratedValue(generator = "feasibility_study_seq", strategy = GenerationType.SEQUENCE)
   @Column(name="id")
   @Access(AccessType.PROPERTY) 
   private Integer id; 

src/main/java/org/ohdsi/webapi/ircalc/IncidenceRateAnalysis.java

@@ -26,10 +26,12 @@
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
 import javax.persistence.JoinColumn;
 import javax.persistence.OneToMany;
 import javax.persistence.OneToOne;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 /**
@@ -43,7 +45,8 @@ public class IncidenceRateAnalysis implements Serializable {
   private static final long serialVersionUID = 1L;
 
   @Id
-  @GeneratedValue
+  @SequenceGenerator(name = "ir_analysis_seq", sequenceName = "ir_analysis_sequence", allocationSize = 1)
+  @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "ir_analysis_seq")
   @Column(name="id")
   @Access(AccessType.PROPERTY) 
   private Integer id; 

src/main/java/org/ohdsi/webapi/prediction/PatientLevelPredictionAnalysis.java

@@ -9,7 +9,9 @@
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
 import javax.persistence.Id;
+import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 import org.ohdsi.circe.vocabulary.ConceptSetExpression;
 
@@ -22,7 +24,8 @@
 public class PatientLevelPredictionAnalysis {
 
     @Id
-    @GeneratedValue
+	@SequenceGenerator(name = "plp_seq", sequenceName = "plp_sequence", allocationSize = 1)
+    @GeneratedValue(generator = "plp_seq", strategy = GenerationType.SEQUENCE)
     @Column(name = "plp_id")
     private Integer analysisId;
 

src/main/resources/db/migration/oracle/V2.2.5.20180215105415__separate-sequences.sql

@@ -0,0 +1,91 @@
+-- cca
+DECLARE
+  val INTEGER;
+  stmt VARCHAR2(255);
+BEGIN
+  stmt := 'CREATE SEQUENCE ${ohdsiSchema}.cca_sequence START WITH ';
+  SELECT nvl2(max(cca_id), max(cca_id) + 1, 1) INTO val FROM ${ohdsiSchema}.cca;
+  EXECUTE IMMEDIATE stmt || val;
+END;
+/
+
+-- cohort_definition
+DECLARE
+  val INTEGER;
+  stmt VARCHAR2(255);
+BEGIN
+  stmt := 'CREATE SEQUENCE ${ohdsiSchema}.cohort_definition_sequence START WITH ';
+  SELECT nvl2(max(id), max(id) + 1, 1) INTO val FROM ${ohdsiSchema}.cohort_definition;
+  EXECUTE IMMEDIATE stmt || val;
+END;
+/
+
+DROP SEQUENCE ${ohdsiSchema}.CONCEPT_SET_SEQUENCE;
+
+-- concept_set
+DECLARE
+  val INTEGER;
+  stmt VARCHAR2(255);
+BEGIN
+  stmt := 'CREATE SEQUENCE ${ohdsiSchema}.concept_set_sequence START WITH ';
+  SELECT nvl2(max(concept_set_id), max(concept_set_id) + 1, 1) INTO val FROM ${ohdsiSchema}.concept_set;
+  EXECUTE IMMEDIATE stmt || val;
+END;
+/
+
+DROP SEQUENCE ${ohdsiSchema}.CONCEPT_SET_ITEM_SEQUENCE;
+
+-- concept_set_item
+DECLARE
+  val INTEGER;
+  stmt VARCHAR2(255);
+BEGIN
+  stmt := 'CREATE SEQUENCE ${ohdsiSchema}.concept_set_item_sequence START WITH ';
+  SELECT nvl2(max(concept_set_item_id), max(concept_set_item_id) + 1, 1) INTO val FROM ${ohdsiSchema}.concept_set_item;
+  EXECUTE IMMEDIATE stmt || val;
+END;
+/
+
+-- concept_set_negative_controls
+DECLARE
+  val INTEGER;
+  stmt VARCHAR2(255);
+BEGIN
+  stmt := 'CREATE SEQUENCE ${ohdsiSchema}.negative_controls_sequence START WITH ';
+  SELECT nvl2(max(id), max(id) + 1, 1) INTO val FROM ${ohdsiSchema}.concept_set_negative_controls;
+  EXECUTE IMMEDIATE stmt || val;
+END;
+/
+
+-- feasibility_study
+DECLARE
+  val INTEGER;
+  stmt VARCHAR2(255);
+BEGIN
+  stmt := 'CREATE SEQUENCE ${ohdsiSchema}.feasibility_study_sequence START WITH ';
+  SELECT nvl2(max(id), max(id) + 1, 1) INTO val FROM ${ohdsiSchema}.feasibility_study;
+  EXECUTE IMMEDIATE stmt || val;
+END;
+/
+
+-- ir_analysis
+DECLARE
+  val INTEGER;
+  stmt VARCHAR2(255);
+BEGIN
+  stmt := 'CREATE SEQUENCE ${ohdsiSchema}.ir_analysis_sequence START WITH ';
+  SELECT nvl2(max(id), max(id) + 1, 1) INTO val FROM ${ohdsiSchema}.ir_analysis;
+  EXECUTE IMMEDIATE stmt || val;
+END;
+/
+
+-- plp
+DECLARE
+  val INTEGER;
+  stmt VARCHAR2(255);
+BEGIN
+  stmt := 'CREATE SEQUENCE ${ohdsiSchema}.plp_sequence START WITH ';
+  SELECT nvl2(max(plp_id), max(plp_id) + 1, 1) INTO val FROM ${ohdsiSchema}.plp;
+  EXECUTE IMMEDIATE stmt || val;
+END;
+/

src/main/resources/db/migration/postgresql/V2.2.5.20180215105415__separate-sequences.sql

@@ -0,0 +1,23 @@
+CREATE SEQUENCE ${ohdsiSchema}.cca_sequence;
+SELECT setval('${ohdsiSchema}.cca_sequence', coalesce(max(cca_id), 1)) FROM ${ohdsiSchema}.cca;
+
+CREATE SEQUENCE ${ohdsiSchema}.cohort_definition_sequence;
+SELECT setval('${ohdsiSchema}.cohort_definition_sequence', coalesce(max(id), 1)) FROM ${ohdsiSchema}.cohort_definition;
+
+-- concept_set_sequence already exists - no need to create
+SELECT setval('${ohdsiSchema}.concept_set_sequence', coalesce(max(concept_set_id), 1)) FROM ${ohdsiSchema}.concept_set;
+
+-- concept_set_item_sequence already exists - no need to create
+SELECT setval('${ohdsiSchema}.concept_set_item_sequence', coalesce(max(concept_set_item_id), 1)) FROM ${ohdsiSchema}.concept_set_item;
+
+-- negative_controls_sequence already exists - no need to create
+SELECT setval('${ohdsiSchema}.negative_controls_sequence', coalesce(max(id), 1)) FROM ${ohdsiSchema}.concept_set_negative_controls;
+
+CREATE SEQUENCE ${ohdsiSchema}.feasibility_study_sequence;
+SELECT setval('${ohdsiSchema}.feasibility_study_sequence', coalesce(max(id), 1)) FROM ${ohdsiSchema}.feasibility_study;
+
+CREATE SEQUENCE ${ohdsiSchema}.ir_analysis_sequence;
+SELECT setval('${ohdsiSchema}.ir_analysis_sequence', coalesce(max(id), 1)) FROM ${ohdsiSchema}.ir_analysis;
+
+CREATE SEQUENCE ${ohdsiSchema}.plp_sequence;
+SELECT setval('${ohdsiSchema}.plp_sequence', coalesce(max(plp_id), 1)) FROM ${ohdsiSchema}.plp;

src/main/resources/db/migration/sqlserver/V2.2.0.20180215143000__remove_password.sql

@@ -1,2 +1,2 @@
-ALTER TABLE ${ohdsiSchema}.sec_user DROP COLUMN IF EXISTS password; 
-ALTER TABLE ${ohdsiSchema}.sec_user DROP COLUMN IF EXISTS salt; 
+ALTER TABLE ${ohdsiSchema}.sec_user DROP COLUMN password; 
+ALTER TABLE ${ohdsiSchema}.sec_user DROP COLUMN salt;