Add many-to-many relationship InvestigationSample to the schema

.github/workflows/ci-build.yml

@@ -37,6 +37,7 @@ jobs:
         uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v4.0.0
         with:
           repository: icatproject-contrib/icat-ansible
+          ref: no-icat-install
           path: icat-ansible
       - name: Install Ansible
         run: pip install -r icat-ansible/requirements.txt

README.md

@@ -4,6 +4,6 @@
 
 General installation instructions are at https://icatproject.org/installation/component
 
-Specific installation instructions are at https://repo.icatproject.org/site/icat/server/6.0.1/installation.html
+Specific installation instructions are at https://repo.icatproject.org/site/icat/server/7.0.0/installation.html
 
-All documentation on the icat.server may be found at https://repo.icatproject.org/site/icat/server/6.0.1
+All documentation on the icat.server may be found at https://repo.icatproject.org/site/icat/server/7.0.0

pom.xml

@@ -3,7 +3,7 @@
 
 	<groupId>org.icatproject</groupId>
 	<artifactId>icat.server</artifactId>
-	<version>6.2.1-SNAPSHOT</version>
+	<version>7.0.0-SNAPSHOT</version>
 	<packaging>war</packaging>
 	<name>ICAT Server</name>
 	<description>A metadata catalogue to support Large Facility experimental data, 

src/main/java/org/icatproject/core/entity/Investigation.java

@@ -84,7 +84,7 @@ public class Investigation extends EntityBaseBean implements Serializable {
 	private Date releaseDate;
 
 	@OneToMany(cascade = CascadeType.ALL, mappedBy = "investigation")
-	private List<Sample> samples = new ArrayList<>();
+	private List<InvestigationSample> samples = new ArrayList<>();
 
 	@OneToMany(cascade = CascadeType.ALL, mappedBy = "investigation")
 	private List<Shift> shifts = new ArrayList<>();
@@ -184,7 +184,7 @@ public Date getReleaseDate() {
 		return this.releaseDate;
 	}
 
-	public List<Sample> getSamples() {
+	public List<InvestigationSample> getSamples() {
 		return samples;
 	}
 
@@ -284,7 +284,7 @@ public void setReleaseDate(Date releaseDate) {
 		this.releaseDate = releaseDate;
 	}
 
-	public void setSamples(List<Sample> samples) {
+	public void setSamples(List<InvestigationSample> samples) {
 		this.samples = samples;
 	}
 
@@ -383,11 +383,6 @@ public static Map<String, Relationship[]> getDocumentFields() throws IcatExcepti
 			Relationship[] parameterTypeRelationships = {
 					EntityInfoHandler.getRelationshipsByName(Investigation.class).get("parameters"),
 					EntityInfoHandler.getRelationshipsByName(InvestigationParameter.class).get("type") };
-			Relationship[] sampleRelationships = {
-					EntityInfoHandler.getRelationshipsByName(Investigation.class).get("samples") };
-			Relationship[] sampleTypeRelationships = {
-					EntityInfoHandler.getRelationshipsByName(Investigation.class).get("samples"),
-					EntityInfoHandler.getRelationshipsByName(Sample.class).get("type") };
 			documentFields.put("name", null);
 			documentFields.put("visitId", null);
 			documentFields.put("title", null);
@@ -411,9 +406,6 @@ public static Map<String, Relationship[]> getDocumentFields() throws IcatExcepti
 			documentFields.put("InvestigationParameter stringValue", parameterRelationships);
 			documentFields.put("InvestigationParameter numericValue", parameterRelationships);
 			documentFields.put("InvestigationParameter dateTimeValue", parameterRelationships);
-			documentFields.put("Sample sample.id", sampleRelationships);
-			documentFields.put("Sample sample.name", sampleRelationships);
-			documentFields.put("Sample type.name", sampleTypeRelationships);
 		}
 		return documentFields;
 	}

src/main/java/org/icatproject/core/entity/InvestigationSample.java

@@ -0,0 +1,41 @@
+package org.icatproject.core.entity;
+
+import java.io.Serializable;
+
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.JoinColumn;
+import jakarta.persistence.ManyToOne;
+import jakarta.persistence.Table;
+import jakarta.persistence.UniqueConstraint;
+
+@Comment("Represents a many-to-many relationship between an investigation and a sample that has been used in that investigation")
+@SuppressWarnings("serial")
+@Entity
+@Table(uniqueConstraints = { @UniqueConstraint(columnNames = { "INVESTIGATION_ID", "SAMPLE_ID" }) })
+public class InvestigationSample extends EntityBaseBean implements Serializable {
+
+	@JoinColumn(nullable = false, name = "INVESTIGATION_ID")
+	@ManyToOne(fetch = FetchType.LAZY)
+	private Investigation investigation;
+
+	@JoinColumn(nullable = false, name = "SAMPLE_ID")
+	@ManyToOne(fetch = FetchType.LAZY)
+	private Sample sample;
+
+	public Investigation getInvestigation() {
+		return this.investigation;
+	}
+
+	public Sample getSample() {
+		return this.sample;
+	}
+
+	public void setInvestigation(Investigation investigation) {
+		this.investigation = investigation;
+	}
+
+	public void setSample(Sample sample) {
+		this.sample = sample;
+	}
+}

src/main/java/org/icatproject/core/entity/Sample.java

@@ -22,23 +22,23 @@
 import org.icatproject.core.IcatException;
 import org.icatproject.core.manager.search.SearchApi;
 
-@Comment("A sample to be used in an investigation")
+@Comment("A sample to be used in one or more investigations")
 @SuppressWarnings("serial")
 @Entity
-@Table(uniqueConstraints = { @UniqueConstraint(columnNames = { "INVESTIGATION_ID", "NAME" }) })
+@Table(uniqueConstraints = { @UniqueConstraint(columnNames = { "PID" }) })
 public class Sample extends EntityBaseBean implements Serializable {
 
 	@Comment("A persistent identifier attributed to this sample")
+	@Column(nullable = false, name = "PID")
 	private String pid;
 
 	@OneToMany(cascade = CascadeType.ALL, mappedBy = "sample")
 	private List<Dataset> datasets = new ArrayList<>();
 
-	@JoinColumn(nullable = false, name = "INVESTIGATION_ID")
-	@ManyToOne(fetch = FetchType.LAZY)
-	private Investigation investigation;
+	@OneToMany(cascade = CascadeType.ALL, mappedBy = "sample")
+	private List<InvestigationSample> investigationSamples = new ArrayList<>();
 
-	@Column(nullable = false, name = "NAME")
+	@Column(nullable = false)
 	private String name;
 
 	@OneToMany(cascade = CascadeType.ALL, mappedBy = "sample")
@@ -67,8 +67,8 @@ public List<Dataset> getDatasets() {
 		return this.datasets;
 	}
 
-	public Investigation getInvestigation() {
-		return this.investigation;
+	public List<InvestigationSample> getInvestigationSamples() {
+		return this.investigationSamples;
 	}
 
 	public String getName() {
@@ -83,8 +83,8 @@ public void setDatasets(List<Dataset> datasets) {
 		this.datasets = datasets;
 	}
 
-	public void setInvestigation(Investigation investigation) {
-		this.investigation = investigation;
+	public void setInvestigationSamples(List<InvestigationSample> investigationSamples) {
+		this.investigationSamples = investigationSamples;
 	}
 
 	public void setName(String name) {
@@ -107,12 +107,6 @@ public void setType(SampleType type) {
 	public void getDoc(EntityManager entityManager, JsonGenerator gen) throws IcatException {
 		SearchApi.encodeString(gen, "sample.name", name);
 		SearchApi.encodeLong(gen, "sample.id", id);
-		if (investigation != null) {
-			// Investigation is not nullable, but it is possible to pass Samples without their Investigation
-			// relationship populated when creating Datasets, where this field is not needed anyway - so guard against
-			// null pointers
-			SearchApi.encodeLong(gen, "sample.investigation.id", investigation.id);
-		}
 		if (type != null) {
 			if (type.getName() == null) {
 				type = entityManager.find(type.getClass(), type.id);

src/main/java/org/icatproject/core/manager/EntityInfoHandler.java

@@ -68,6 +68,7 @@
 import org.icatproject.core.entity.InvestigationGroup;
 import org.icatproject.core.entity.InvestigationInstrument;
 import org.icatproject.core.entity.InvestigationParameter;
+import org.icatproject.core.entity.InvestigationSample;
 import org.icatproject.core.entity.InvestigationType;
 import org.icatproject.core.entity.InvestigationUser;
 import org.icatproject.core.entity.Job;
@@ -223,8 +224,8 @@ public String toString() {
 			Publication.class, RelatedDatafile.class, SampleParameter.class, Shift.class, Study.class,
 			DataPublicationType.class, DataPublication.class, Subject.class, DataPublicationDate.class, DataPublicationUser.class,
 			Affiliation.class, RelatedItem.class, FundingReference.class, DataPublicationFunding.class,
-			InvestigationFunding.class, InvestigationUser.class, InvestigationGroup.class, StudyInvestigation.class,
-			InvestigationInstrument.class, InstrumentScientist.class, DatasetInstrument.class,
+			InvestigationFunding.class, InvestigationUser.class, InvestigationGroup.class, InvestigationSample.class,
+			StudyInvestigation.class, InvestigationInstrument.class, InstrumentScientist.class, DatasetInstrument.class,
 			InvestigationFacilityCycle.class);
 
 	// All entities, plus the abstract classes Parameter and EntityBaseBean

src/main/resources/META-INF/persistence.xml

@@ -11,58 +11,59 @@
 
 		<class>org.icatproject.core.entity.Affiliation</class>
 		<class>org.icatproject.core.entity.Application</class>
+		<class>org.icatproject.core.entity.DataCollection</class>
 		<class>org.icatproject.core.entity.DataCollectionDatafile</class>
 		<class>org.icatproject.core.entity.DataCollectionDataset</class>
 		<class>org.icatproject.core.entity.DataCollectionInvestigation</class>
-		<class>org.icatproject.core.entity.DataCollection</class>
 		<class>org.icatproject.core.entity.DataCollectionParameter</class>
-		<class>org.icatproject.core.entity.DatafileFormat</class>
-		<class>org.icatproject.core.entity.Datafile</class>
-		<class>org.icatproject.core.entity.DatafileParameter</class>
+		<class>org.icatproject.core.entity.DataPublication</class>
 		<class>org.icatproject.core.entity.DataPublicationDate</class>
 		<class>org.icatproject.core.entity.DataPublicationFunding</class>
-		<class>org.icatproject.core.entity.DataPublication</class>
 		<class>org.icatproject.core.entity.DataPublicationType</class>
 		<class>org.icatproject.core.entity.DataPublicationUser</class>
-		<class>org.icatproject.core.entity.DatasetInstrument</class>
+		<class>org.icatproject.core.entity.Datafile</class>
+		<class>org.icatproject.core.entity.DatafileFormat</class>
+		<class>org.icatproject.core.entity.DatafileParameter</class>
 		<class>org.icatproject.core.entity.Dataset</class>
+		<class>org.icatproject.core.entity.DatasetInstrument</class>
 		<class>org.icatproject.core.entity.DatasetParameter</class>
 		<class>org.icatproject.core.entity.DatasetTechnique</class>
 		<class>org.icatproject.core.entity.DatasetType</class>
-		<class>org.icatproject.core.entity.FacilityCycle</class>
 		<class>org.icatproject.core.entity.Facility</class>
+		<class>org.icatproject.core.entity.FacilityCycle</class>
 		<class>org.icatproject.core.entity.FundingReference</class>
 		<class>org.icatproject.core.entity.Grouping</class>
 		<class>org.icatproject.core.entity.Instrument</class>
 		<class>org.icatproject.core.entity.InstrumentScientist</class>
+		<class>org.icatproject.core.entity.Investigation</class>
 		<class>org.icatproject.core.entity.InvestigationFacilityCycle</class>
 		<class>org.icatproject.core.entity.InvestigationFunding</class>
 		<class>org.icatproject.core.entity.InvestigationGroup</class>
 		<class>org.icatproject.core.entity.InvestigationInstrument</class>
-		<class>org.icatproject.core.entity.Investigation</class>
 		<class>org.icatproject.core.entity.InvestigationParameter</class>
+		<class>org.icatproject.core.entity.InvestigationSample</class>
 		<class>org.icatproject.core.entity.InvestigationType</class>
 		<class>org.icatproject.core.entity.InvestigationUser</class>
 		<class>org.icatproject.core.entity.Job</class>
 		<class>org.icatproject.core.entity.Keyword</class>
 		<class>org.icatproject.core.entity.Parameter</class>
 		<class>org.icatproject.core.entity.ParameterType</class>
 		<class>org.icatproject.core.entity.PermissibleStringValue</class>
-		<class>org.icatproject.core.entity.Publication</class>
 		<class>org.icatproject.core.entity.PublicStep</class>
+		<class>org.icatproject.core.entity.Publication</class>
 		<class>org.icatproject.core.entity.RelatedDatafile</class>
 		<class>org.icatproject.core.entity.RelatedItem</class>
 		<class>org.icatproject.core.entity.Rule</class>
 		<class>org.icatproject.core.entity.Sample</class>
 		<class>org.icatproject.core.entity.SampleParameter</class>
 		<class>org.icatproject.core.entity.SampleType</class>
 		<class>org.icatproject.core.entity.Shift</class>
-		<class>org.icatproject.core.entity.StudyInvestigation</class>
 		<class>org.icatproject.core.entity.Study</class>
+		<class>org.icatproject.core.entity.StudyInvestigation</class>
 		<class>org.icatproject.core.entity.Subject</class>
 		<class>org.icatproject.core.entity.Technique</class>
-		<class>org.icatproject.core.entity.UserGroup</class>
 		<class>org.icatproject.core.entity.User</class>
+		<class>org.icatproject.core.entity.UserGroup</class>
 		<exclude-unlisted-classes />
 
 		<properties>

src/main/scripts/upgrade_mysql_7_0.sql

@@ -0,0 +1,69 @@
+-- Add table and constraints for InvestigationSamples
+
+CREATE TABLE INVESTIGATIONSAMPLE (
+    ID BIGINT NOT NULL AUTO_INCREMENT,
+    CREATE_ID VARCHAR(255) NOT NULL,
+    CREATE_TIME DATETIME NOT NULL,
+    MOD_ID VARCHAR(255) NOT NULL,
+    MOD_TIME DATETIME NOT NULL,
+    INVESTIGATION_ID BIGINT NOT NULL,
+    SAMPLE_ID BIGINT NOT NULL,
+    PRIMARY KEY (ID)
+);
+
+ALTER TABLE INVESTIGATIONSAMPLE ADD CONSTRAINT FK_INVESTIGATIONSAMPLE_INVESTIGATION_ID FOREIGN KEY (INVESTIGATION_ID) REFERENCES INVESTIGATION (ID);
+ALTER TABLE INVESTIGATIONSAMPLE ADD CONSTRAINT FK_INVESTIGATIONSAMPLE_SAMPLE_ID FOREIGN KEY (SAMPLE_ID) REFERENCES SAMPLE (ID);
+ALTER TABLE INVESTIGATIONSAMPLE ADD CONSTRAINT UNQ_INVESTIGATIONSAMPLE_0 UNIQUE (INVESTIGATION_ID, SAMPLE_ID);
+
+-- Set the PID field of existing Samples
+
+DELIMITER //
+
+CREATE PROCEDURE SET_SAMPLES_PID()
+BEGIN
+    UPDATE SAMPLE SET PID = CONCAT('_local:', LPAD(ID, 8, '0')), MOD_ID = 'schema_upgrade', MOD_TIME = NOW() WHERE PID IS NULL;
+END; //
+
+DELIMITER ;
+
+CALL SET_SAMPLES_PID();
+
+DROP PROCEDURE SET_SAMPLES_PID;
+
+-- Move existing Sample/Investigation relations over to the new table
+
+DELIMITER //
+
+CREATE PROCEDURE MOVE_SAMPLE_INVESTIGATION_RELATIONS()
+BEGIN
+    DECLARE done BOOLEAN DEFAULT FALSE;
+    DECLARE _invid BIGINT;
+    DECLARE _id BIGINT;
+    DECLARE cur CURSOR FOR SELECT INVESTIGATION_ID, ID FROM SAMPLE;
+    DECLARE CONTINUE HANDLER FOR NOT FOUND SET done := TRUE;
+
+    OPEN cur;
+    sampleLoop: LOOP
+        FETCH cur INTO _invid, _id;
+        IF done THEN
+        LEAVE sampleLoop;
+        END IF;
+
+        INSERT INTO INVESTIGATIONSAMPLE (CREATE_ID, CREATE_TIME, MOD_ID, MOD_TIME, INVESTIGATION_ID, SAMPLE_ID) VALUES ('schema_upgrade', NOW(), 'schema_upgrade', NOW(), _invid, _id);
+    END LOOP sampleLoop;
+    CLOSE cur;
+END; //
+
+DELIMITER ;
+
+CALL MOVE_SAMPLE_INVESTIGATION_RELATIONS();
+
+DROP PROCEDURE MOVE_SAMPLE_INVESTIGATION_RELATIONS;
+
+-- Alter the Sample table
+
+ALTER TABLE SAMPLE MODIFY PID VARCHAR(255) NOT NULL;
+ALTER TABLE SAMPLE DROP CONSTRAINT FK_SAMPLE_INVESTIGATION_ID;
+ALTER TABLE SAMPLE DROP CONSTRAINT UNQ_SAMPLE_0;
+ALTER TABLE SAMPLE ADD CONSTRAINT UNQ_SAMPLE_0 UNIQUE (PID);
+ALTER TABLE SAMPLE DROP COLUMN INVESTIGATION_ID;