Add pid to sample type #326

.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

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/Facility.java

@@ -63,9 +63,6 @@ public class Facility extends EntityBaseBean implements Serializable {
 	@OneToMany(cascade = CascadeType.ALL, mappedBy = "facility")
 	private List<ParameterType> parameterTypes = new ArrayList<ParameterType>();
 
-	@OneToMany(cascade = CascadeType.ALL, mappedBy = "facility")
-	private List<SampleType> sampleTypes = new ArrayList<SampleType>();
-
 	@Comment("A URL associated with this facility")
 	private String url;
 
@@ -129,10 +126,6 @@ public List<ParameterType> getParameterTypes() {
 		return parameterTypes;
 	}
 
-	public List<SampleType> getSampleTypes() {
-		return sampleTypes;
-	}
-
 	public String getUrl() {
 		return url;
 	}
@@ -193,10 +186,6 @@ public void setParameterTypes(List<ParameterType> parameterTypes) {
 		this.parameterTypes = parameterTypes;
 	}
 
-	public void setSampleTypes(List<SampleType> sampleTypes) {
-		this.sampleTypes = sampleTypes;
-	}
-
 	public void setUrl(String url) {
 		this.url = url;
 	}

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

@@ -25,17 +25,15 @@
 @Comment("A sample to be used in an investigation")
 @SuppressWarnings("serial")
 @Entity
-@Table(uniqueConstraints = { @UniqueConstraint(columnNames = { "FACILITY_ID", "NAME",
-		"MOLECULARFORMULA" }) })
+@Table(uniqueConstraints = { @UniqueConstraint(columnNames = { "PID" }) })
 public class SampleType extends EntityBaseBean implements Serializable {
 
-	@Comment("The facility which has defined this sample type")
-	@JoinColumn(name = "FACILITY_ID", nullable = false)
-	@ManyToOne(fetch = FetchType.LAZY)
-	private Facility facility;
+	@Comment("A persistent identifier attributed to this sample type, ideally referring to a vocabulary term")
+	@Column(name = "PID", nullable = false)
+	private String pid;
 
 	@Comment("The formula written as a string -e.g. C2H6O2 for ethylene glycol")
-	@Column(nullable = false, name = "MOLECULARFORMULA")
+	@Column(name = "MOLECULARFORMULA")
 	private String molecularFormula;
 
 	@Column(nullable = false, name = "NAME")
@@ -54,8 +52,8 @@ public class SampleType extends EntityBaseBean implements Serializable {
 	public SampleType() {
 	}
 
-	public Facility getFacility() {
-		return facility;
+	public String getPid() {
+		return pid;
 	}
 
 	public String getMolecularFormula() {
@@ -74,8 +72,8 @@ public List<Sample> getSamples() {
 		return samples;
 	}
 
-	public void setFacility(Facility facility) {
-		this.facility = facility;
+	public void setPid(String pid) {
+		this.pid = pid;
 	}
 
 	public void setMolecularFormula(String molecularFormula) {

src/main/scripts/upgrade_mysql_7_0.sql

@@ -0,0 +1,28 @@
+-- Alter the SampleType table, the constraint on PID needs to be done
+-- after populating it
+
+ALTER TABLE SAMPLETYPE DROP CONSTRAINT FK_SAMPLETYPE_FACILITY_ID;
+ALTER TABLE SAMPLETYPE DROP CONSTRAINT UNQ_SAMPLETYPE_0;
+ALTER TABLE SAMPLETYPE DROP COLUMN FACILITY_ID;
+ALTER TABLE SAMPLETYPE MODIFY COLUMN MOLECULARFORMULA VARCHAR(255) DEFAULT NULL;
+ALTER TABLE SAMPLETYPE ADD COLUMN PID VARCHAR(255);
+
+-- Populate the PID column for SampleTypes
+
+DELIMITER //
+
+CREATE PROCEDURE SET_SAMPLETYPES_PID()
+BEGIN
+    UPDATE SAMPLETYPE SET PID = CONCAT('_local:', LPAD(ID, 8, '0')), MOD_ID = 'schema_upgrade', MOD_TIME = NOW();
+END; //
+
+DELIMITER ;
+
+CALL SET_SAMPLETYPES_PID();
+
+DROP PROCEDURE SET_SAMPLETYPES_PID;
+
+-- Alter the SampleType table: set the constraint on PID
+
+ALTER TABLE SAMPLETYPE MODIFY COLUMN PID VARCHAR(255) NOT NULL;
+ALTER TABLE SAMPLETYPE ADD CONSTRAINT UNQ_SAMPLETYPE_0 UNIQUE (PID);

src/main/scripts/upgrade_oracle_7_0.sql

@@ -0,0 +1,30 @@
+-- Alter the SampleType table, the constraint on PID needs to be done
+-- after populating it
+
+ALTER TABLE SAMPLETYPE DROP CONSTRAINT FK_SAMPLETYPE_FACILITY_ID;
+ALTER TABLE SAMPLETYPE DROP CONSTRAINT UNQ_SAMPLETYPE_0;
+ALTER TABLE SAMPLETYPE DROP COLUMN FACILITY_ID;
+ALTER TABLE SAMPLETYPE MODIFY (MOLECULARFORMULA NULL);
+ALTER TABLE SAMPLETYPE ADD PID VARCHAR2(255);
+
+-- Populate the PID column for SampleTypes
+
+CREATE PROCEDURE SET_SAMPLETYPES_PID AS
+BEGIN
+    UPDATE SAMPLETYPE SET PID = '_local:' || LPAD(ID, 8, '0'), MOD_ID = 'schema_upgrade', MOD_TIME = CURRENT_TIMESTAMP WHERE PID IS NULL;
+END;
+/
+
+BEGIN
+    SET_SAMPLETYPES_PID;
+END;
+/
+
+DROP PROCEDURE SET_SAMPLETYPES_PID;
+
+-- Alter the SampleType table: set the constraint on PID
+
+ALTER TABLE SAMPLETYPE MODIFY (PID NOT NULL);
+ALTER TABLE SAMPLETYPE ADD CONSTRAINT UNQ_SAMPLETYPE_0 UNIQUE (PID);
+
+exit

src/test/java/org/icatproject/core/manager/TestEntityInfo.java

@@ -170,7 +170,7 @@ public void testExportNull() throws Exception {
 	public void testFields() throws Exception {
 		testField(
 				"applications,dataPublicationTypes,dataPublications,datafileFormats,datasetTypes,daysUntilRelease,description,facilityCycles,"
-						+ "fullName,instruments,investigationTypes,investigations,name,parameterTypes,sampleTypes,url",
+						+ "fullName,instruments,investigationTypes,investigations,name,parameterTypes,url",
 				Facility.class);
 		testField("description,facility,investigations,name", InvestigationType.class);
 		testField(

src/test/java/org/icatproject/integration/TestRS.java

@@ -187,7 +187,7 @@ public void TestJsoniseBean() throws Exception {
 		 * "2019-03-11T15:58:33.000Z","applications":[],"datafileFormats":[],
 		 * "datasetTypes":[],"daysUntilRelease":90,"facilityCycles":[],"instruments":[],
 		 * "investigationTypes":[],"investigations":[],"name":"Test port facility"
-		 * ,"parameterTypes":[],"sampleTypes":[]}}]>
+		 * ,"parameterTypes":[]}}]>
 		 */
 		JsonArray fac_response = search(session, "SELECT f from Facility f WHERE f.name = 'Test port facility'", 1);
 		collector.checkThat(fac_response.getJsonObject(0).containsKey("Facility"), is(true));
@@ -292,6 +292,16 @@ public void TestJsoniseBean() throws Exception {
 		JsonArray st_response = search(session, "SELECT st from SampleType st WHERE st.name = 'diamond'", 1);
 		collector.checkThat(st_response.getJsonObject(0).containsKey("SampleType"), is(true));
 
+		/*
+		 * Expected: <[{"SampleType":{"id":420,"createId":"db/notroot","createTime":
+		 * "2025-12-17T13:23:13.000Z","modId":"db/notroot","modTime":
+		 * "2025-12-17T13:23:13.000Z","name":"fossil","pid":"st:004","samples":[]}}]>
+		 */
+		JsonArray st_null_response = search(session, "SELECT st from SampleType st WHERE st.name = 'fossil'", 1);
+		collector.checkThat(st_null_response.getJsonObject(0).containsKey("SampleType"), is(true));
+		collector.checkThat(st_null_response.getJsonObject(0).getJsonObject("SampleType").getString("pid"), is("st:004"));
+		collector.checkThat(st_null_response.getJsonObject(0).getJsonObject("SampleType").get("molecularFormula"), is(equalTo(null)));
+
 		/*
 		 * Expected: <[{"Sample":{"id":2181,"createId":"db/notroot","createTime":
 		 * "2019-03-11T15:58:33.000Z","modId":"db/notroot","modTime":
@@ -1316,7 +1326,7 @@ private JsonObject searchInvestigations(Session session, String user, String tex
 	@Test
 	public void testVersion() throws Exception {
 		ICAT icat = new ICAT(System.getProperty("serverUrl"));
-		assertTrue(icat.getVersion().startsWith("6."));
+		assertTrue(icat.getVersion().startsWith("7.0."));
 	}
 
 	@Test

src/test/java/org/icatproject/integration/TestWS.java

@@ -72,7 +72,7 @@
  */
 public class TestWS {
 
-	private static final String version = "6.2.";
+	private static final String version = "7.0.";
 	private static Random random;
 	private static WSession session;
 
@@ -103,7 +103,7 @@ private static void create() throws Exception {
 		Facility facility = session.createFacility("Test Facility", 90);
 
 		SampleType sampleType = new SampleType();
-		sampleType.setFacility(facility);
+		/* FIXME: sampleType.setPid("somepid"); */
 		sampleType.setName("somename");
 		sampleType.setMolecularFormula("Someformula");
 		session.create(sampleType);
@@ -519,6 +519,7 @@ public void authz5() throws Exception {
 		}
 	}
 
+	@Disabled("Requires an icat.client built with the schema extensions")
 	@Test
 	public void authz6() throws Exception {
 		create();
@@ -586,6 +587,7 @@ public void authz6() throws Exception {
 	 * Create two rules allowing access to the same investigation and ensure
 	 * that only one instance is returned - i.e, no DISTINCT problem remains
 	 */
+	@Disabled("Requires an icat.client built with the schema extensions")
 	@Test
 	public void authz7() throws Exception {
 		try {
@@ -1004,7 +1006,7 @@ public void getInvestigationWithVeryManyDatasets() throws Exception {
 		Facility facility = session.createFacility("Test Facility", 90);
 
 		SampleType sampleType = new SampleType();
-		sampleType.setFacility(facility);
+		/* FIXME: sampleType.setPid("somepid"); */
 		sampleType.setName("somename");
 		sampleType.setMolecularFormula("Someformula");
 		session.create(sampleType);
@@ -1105,6 +1107,7 @@ public void groupAuthz() throws Exception {
 		assertEquals(invId, inv.getId());
 	}
 
+	@Disabled("Requires an icat.client built with the schema extensions")
 	@Test
 	public void gets() throws Exception {
 		create();
@@ -1185,6 +1188,7 @@ public void inapplicableParameterType() throws Exception {
 		}
 	}
 
+	@Disabled("Requires an icat.client built with the schema extensions")
 	@Test
 	public void includes() throws Exception {
 		create();
@@ -1488,6 +1492,7 @@ public void numericParameterRanges() throws Exception {
 
 	}
 
+	@Disabled("Requires an icat.client built with the schema extensions")
 	@Test
 	public void oldGets() throws Exception {
 		create();
@@ -1527,6 +1532,7 @@ public void oldGets() throws Exception {
 		}
 	}
 
+	@Disabled("Requires an icat.client built with the schema extensions")
 	@Test
 	public void oldSearches() throws Exception {
 		create();
@@ -1683,6 +1689,7 @@ public void performance() throws Exception {
 				+ (System.currentTimeMillis() - start) / (results.size() + 0.) + "ms");
 	}
 
+	@Disabled("Requires an icat.client built with the schema extensions")
 	@Test
 	public void searches() throws Exception {
 		create();

src/test/java/org/icatproject/integration/WSession.java

@@ -195,7 +195,7 @@ public void addUserGroupMember(String groupName, String userName) throws Excepti
 	}
 
 	public void clear() throws Exception {
-		deleteAll(Arrays.asList("Facility", "DataCollection", "Study", "FundingReference", "Technique"));
+		deleteAll(Arrays.asList("Facility", "DataCollection", "Study", "FundingReference", "Technique", "SampleType"));
 	}
 
 	private void deleteAll(List<String> names) throws IcatException_Exception {

src/test/resources/icat-import-check.port

@@ -40,14 +40,15 @@ Shift(investigation(facility(name:0), name:1, visitId:2), startDate:3, endDate:4
 "Test port facility", "expt1", "zero", 2014-01-01T00:00:00+01:00, 2014-01-01T18:00:00+01:00, "beamtime", "EDDI"
 "Test port facility", "expt1", "two", 2014-04-29T14:00:00+02:00, 2014-04-30T18:15:00+02:00, "preparing", null
 
-SampleType(facility(name:0), name:1, molecularFormula:2, safetyInformation:3)
-"Test port facility", "diamond", "C", "fairly harmless"
-"Test port facility", "graphite", "C", "bit messy"
-"Test port facility", "rust", "Fe3O4", "messy"
-
-Sample(investigation(facility(name:0), name:1, visitId:2), type(facility(name:0), name:3, molecularFormula:4), name:5, pid:6)
-"Test port facility", "expt1", "one", "diamond", "C", "Koh-I-Noor", "sdb:374717"
-"Test port facility", "expt1", "one", "rust",  "Fe3O4", "Ford\t\"Anglia\"", null
+SampleType(name:0, molecularFormula:1, safetyInformation:2, pid:3)
+"diamond", "C", "fairly harmless", "st:001"
+"graphite", "C", "bit messy", "st:002"
+"rust", "Fe3O4", "messy", "st:003"
+"fossil", null, null, "st:004"
+
+Sample(investigation(facility(name:0), name:1, visitId:2), type(pid:3), name:4, pid:5)
+"Test port facility", "expt1", "one", "st:001", "Koh-I-Noor", "sdb:374717"
+"Test port facility", "expt1", "one", "st:003", "Ford\t\"Anglia\"", null
 
 InvestigationParameter(investigation(facility(name:0), name:1, visitId:2), type(facility(name:0), name:3 , units:4),stringValue:5)
 "Test port facility", "expt1", "one", "colour" , "name", "green"

src/test/resources/icat.port

@@ -40,14 +40,15 @@ Shift(investigation(facility(name:0), name:1, visitId:2), startDate:3, endDate:4
 "Test port facility", "expt1", "zero", 2014-01-01T00:00:00+01:00, 2014-01-01T18:00:00+01:00, "beamtime", "EDDI"
 "Test port facility", "expt1", "two", 2014-04-29T14:00:00+02:00, 2014-04-30T18:15:00+02:00, "preparing", null
 
-SampleType(facility(name:0), name:1, molecularFormula:2, safetyInformation:3)
-"Test port facility", "diamond", "C", "fairly harmless"
-"Test port facility", "graphite", "C", "bit messy"
-"Test port facility", "rust", "Fe3O4", "messy"
-
-Sample(investigation(facility(name:0), name:1, visitId:2), type(facility(name:0), name:3, molecularFormula:4), name:5, pid:6)
-"Test port facility", "expt1", "one", "diamond", "C", "Koh-I-Noor", "sdb:374717"
-"Test port facility", "expt1", "one", "rust",  "Fe3O4", "Ford\t\"Anglia\"", null
+SampleType(name:0, molecularFormula:1, safetyInformation:2, pid:3)
+"diamond", "C", "fairly harmless", "st:001"
+"graphite", "C", "bit messy", "st:002"
+"rust", "Fe3O4", "messy", "st:003"
+"fossil", null, null, "st:004"
+
+Sample(investigation(facility(name:0), name:1, visitId:2), type(pid:3), name:4, pid:5)
+"Test port facility", "expt1", "one", "st:001", "Koh-I-Noor", "sdb:374717"
+"Test port facility", "expt1", "one", "st:003", "Ford\t\"Anglia\"", null
 
 InvestigationParameter(investigation(facility(name:0), name:1, visitId:2), type(facility(name:0), name:3 , units:4),stringValue:5)
 "Test port facility", "expt1", "one", "colour" , "name", "green"