Add fields needed for DGS component #267

icatproject · Jun 8, 2022 · eb26a87 · eb26a87
1 parent 3aa8d3a
commit eb26a87
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Showing 10 changed files with 104 additions and 15 deletions.
diff --git a/src/main/java/org/icatproject/core/entity/Datafile.java b/src/main/java/org/icatproject/core/entity/Datafile.java
@@ -206,6 +206,9 @@ public void getDoc(JsonGenerator gen) {
 		if (description != null) {
 			SearchApi.encodeString(gen, "description", description);
 		}
+		if (location != null) {
+			SearchApi.encodeString(gen, "location", location);
+		}
 		if (doi != null) {
 			SearchApi.encodeString(gen, "doi", doi);
 		}
@@ -220,7 +223,15 @@ public void getDoc(JsonGenerator gen) {
 			SearchApi.encodeLong(gen, "date", modTime);
 		}
 		SearchApi.encodeString(gen, "id", id);
-		SearchApi.encodeString(gen, "investigation.id", dataset.getInvestigation().id);
+		if (dataset != null) {
+			SearchApi.encodeString(gen, "dataset.id", dataset.id);
+			SearchApi.encodeString(gen, "dataset.name", dataset.getName());
+			Investigation investigation = dataset.getInvestigation();
+			if (investigation != null) {
+				SearchApi.encodeString(gen, "investigation.id", investigation.id);
+				SearchApi.encodeString(gen, "investigation.name", investigation.getName());
+			}
+		}
 	}
 
 	/**
@@ -239,16 +250,27 @@ public static Map<String, Relationship[]> getDocumentFields() throws IcatExcepti
 			EntityInfoHandler eiHandler = EntityInfoHandler.getInstance();
 			Relationship[] datafileFormatRelationships = {
 					eiHandler.getRelationshipsByName(Datafile.class).get("datafileFormat") };
-			Relationship[] investigationRelationships = {
+			Relationship[] datasetRelationships = {
 					eiHandler.getRelationshipsByName(Datafile.class).get("dataset") };
+			Relationship[] investigationRelationships = {
+					eiHandler.getRelationshipsByName(Datafile.class).get("dataset"),
+					eiHandler.getRelationshipsByName(Dataset.class).get("investigation") };
+			Relationship[] instrumentRelationships = {
+					eiHandler.getRelationshipsByName(Investigation.class).get("investigationInstruments"),
+					eiHandler.getRelationshipsByName(InvestigationInstrument.class).get("instrument") };
 			documentFields.put("name", null);
 			documentFields.put("description", null);
+			documentFields.put("location", null);
 			documentFields.put("doi", null);
 			documentFields.put("date", null);
 			documentFields.put("id", null);
-			documentFields.put("investigation.id", investigationRelationships);
+			documentFields.put("dataset.id", null);
+			documentFields.put("dataset.name", datasetRelationships);
+			documentFields.put("investigation.id", datasetRelationships);
+			documentFields.put("investigation.name", investigationRelationships);
 			documentFields.put("datafileFormat.id", null);
 			documentFields.put("datafileFormat.name", datafileFormatRelationships);
+			documentFields.put("InvestigationInstrument instrument.id", instrumentRelationships);
 		}
 		return documentFields;
 	}

diff --git a/src/main/java/org/icatproject/core/entity/Dataset.java b/src/main/java/org/icatproject/core/entity/Dataset.java
@@ -209,6 +209,13 @@ public void getDoc(JsonGenerator gen) {
 		}
 		SearchApi.encodeString(gen, "id", id);
 		SearchApi.encodeString(gen, "investigation.id", investigation.id);
+		SearchApi.encodeString(gen, "investigation.name", investigation.getName());
+		if (investigation.getStartDate() != null) {
+			SearchApi.encodeLong(gen, "investigation.startDate", investigation.getStartDate());
+		} else {
+			SearchApi.encodeLong(gen, "investigation.startDate", investigation.getCreateTime());
+		}
+		SearchApi.encodeString(gen, "investigation.title", investigation.getTitle());
 
 		if (sample != null) {
 			sample.getDoc(gen, "sample.");
@@ -234,20 +241,29 @@ public static Map<String, Relationship[]> getDocumentFields() throws IcatExcepti
 			Relationship[] sampleTypeRelationships = { eiHandler.getRelationshipsByName(Dataset.class).get("sample"),
 					eiHandler.getRelationshipsByName(Sample.class).get("type") };
 			Relationship[] typeRelationships = { eiHandler.getRelationshipsByName(Dataset.class).get("type") };
+			Relationship[] investigationRelationships = {
+					eiHandler.getRelationshipsByName(Dataset.class).get("investigation") };
+			Relationship[] instrumentRelationships = {
+					eiHandler.getRelationshipsByName(Investigation.class).get("investigationInstruments"),
+					eiHandler.getRelationshipsByName(InvestigationInstrument.class).get("instrument") };
 			documentFields.put("name", null);
 			documentFields.put("description", null);
 			documentFields.put("doi", null);
 			documentFields.put("startDate", null);
 			documentFields.put("endDate", null);
 			documentFields.put("id", null);
 			documentFields.put("investigation.id", null);
+			documentFields.put("investigation.title", investigationRelationships);
+			documentFields.put("investigation.name", investigationRelationships);
+			documentFields.put("investigation.startDate", investigationRelationships);
 			documentFields.put("sample.id", null);
 			documentFields.put("sample.name", sampleRelationships);
 			documentFields.put("sample.investigation.id", sampleRelationships);
 			documentFields.put("sample.type.id", sampleRelationships);
 			documentFields.put("sample.type.name", sampleTypeRelationships);
 			documentFields.put("type.id", null);
 			documentFields.put("type.name", typeRelationships);
+			documentFields.put("InvestigationInstrument instrument.id", instrumentRelationships);
 		}
 		return documentFields;
 	}

diff --git a/src/main/java/org/icatproject/core/entity/Instrument.java b/src/main/java/org/icatproject/core/entity/Instrument.java
@@ -4,6 +4,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import javax.json.stream.JsonGenerator;
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
 import javax.persistence.Entity;
@@ -14,6 +15,8 @@
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
+import org.icatproject.core.manager.search.SearchApi;
+
 @Comment("Used by a user within an investigation")
 @SuppressWarnings("serial")
 @Entity
@@ -138,4 +141,13 @@ public void setShifts(List<Shift> shifts) {
 		this.shifts = shifts;
 	}
 
+	@Override
+	public void getDoc(JsonGenerator gen) {
+		if (fullName != null) {
+			SearchApi.encodeText(gen, "instrument.fullName", fullName);
+		}
+		SearchApi.encodeString(gen, "instrument.name", name);
+		SearchApi.encodeString(gen, "instrument.id", id);
+	}
+
 }
diff --git a/src/main/java/org/icatproject/core/entity/InstrumentScientist.java b/src/main/java/org/icatproject/core/entity/InstrumentScientist.java
@@ -2,13 +2,16 @@
 
 import java.io.Serializable;
 
+import javax.json.stream.JsonGenerator;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
+import org.icatproject.core.manager.search.SearchApi;
+
 @Comment("Relationship between an ICAT user as an instrument scientist and the instrument")
 @SuppressWarnings("serial")
 @Entity
@@ -43,4 +46,11 @@ public void setInstrument(Instrument instrument) {
 	public InstrumentScientist() {
 	}
 
+	@Override
+	public void getDoc(JsonGenerator gen) {
+		user.getDoc(gen);
+		SearchApi.encodeString(gen, "instrument.id", instrument.id);
+		SearchApi.encodeString(gen, "id", id);
+	}
+
 }
diff --git a/src/main/java/org/icatproject/core/entity/Investigation.java b/src/main/java/org/icatproject/core/entity/Investigation.java
@@ -310,6 +310,8 @@ public static Map<String, Relationship[]> getDocumentFields() throws IcatExcepti
 			Relationship[] typeRelationships = { eiHandler.getRelationshipsByName(Investigation.class).get("type") };
 			Relationship[] facilityRelationships = {
 					eiHandler.getRelationshipsByName(Investigation.class).get("facility") };
+			Relationship[] sampleRelationships = { eiHandler.getRelationshipsByName(Investigation.class).get("samples") };
+			Relationship[] instrumentRelationships = { eiHandler.getRelationshipsByName(Investigation.class).get("investigationInstruments"), eiHandler.getRelationshipsByName(InvestigationInstrument.class).get("instrument") };
 			documentFields.put("name", null);
 			documentFields.put("visitId", null);
 			documentFields.put("title", null);
@@ -322,6 +324,10 @@ public static Map<String, Relationship[]> getDocumentFields() throws IcatExcepti
 			documentFields.put("facility.id", null);
 			documentFields.put("type.name", typeRelationships);
 			documentFields.put("type.id", null);
+			documentFields.put("Sample name", sampleRelationships);
+			documentFields.put("InvestigationInstrument instrument.fullName", instrumentRelationships);
+			documentFields.put("InvestigationInstrument instrument.id", instrumentRelationships);
+			documentFields.put("InvestigationInstrument instrument.name", instrumentRelationships);
 		}
 		return documentFields;
 	}

diff --git a/src/main/java/org/icatproject/core/entity/InvestigationInstrument.java b/src/main/java/org/icatproject/core/entity/InvestigationInstrument.java
@@ -2,13 +2,16 @@
 
 import java.io.Serializable;
 
+import javax.json.stream.JsonGenerator;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
 
+import org.icatproject.core.manager.search.SearchApi;
+
 @Comment("Represents a many-to-many relationship between an investigation and the instruments assigned")
 @SuppressWarnings("serial")
 @Entity
@@ -39,4 +42,11 @@ public void setInvestigation(Investigation investigation) {
 		this.investigation = investigation;
 	}
 
+	@Override
+	public void getDoc(JsonGenerator gen) {
+		instrument.getDoc(gen);
+		SearchApi.encodeString(gen, "investigation.id", investigation.id);
+		SearchApi.encodeString(gen, "id", id);
+	}
+
 }
diff --git a/src/main/java/org/icatproject/core/manager/PropertyHandler.java b/src/main/java/org/icatproject/core/manager/PropertyHandler.java
@@ -397,8 +397,9 @@ private void init() {
 				 * currently override the EntityBaseBean.getDoc() method. This should
 				 * result in no change to behaviour if the property is not specified.
 				 */
-				entitiesToIndex.addAll(Arrays.asList("Datafile", "Dataset", "Investigation", "InvestigationUser",
-						"DatafileParameter", "DatasetParameter", "InvestigationParameter", "Sample"));
+				entitiesToIndex.addAll(Arrays.asList("Datafile", "Dataset", "Investigation", "InvestigationInstrument",
+						"InstrumentScientist", "InvestigationUser", "DatafileParameter", "DatasetParameter",
+						"InvestigationParameter", "Sample", "Parameter", "User"));
 				logger.info("search.entitiesToIndex not set. Defaulting to: {}", entitiesToIndex.toString());
 			}
 			formattedProps.add("search.entitiesToIndex " + entitiesToIndex.toString());
@@ -485,9 +486,9 @@ private void init() {
 				if (searchUrls.size() != 1) {
 					String msg = "Exactly one value for search.urls must be provided when using " + searchEngine;
 					throw new IllegalStateException(msg);
-				// } else if (searchUrls.size() == 0) {
-				// 	String msg = "At least one value for search.urls must be provided";
-				// 	throw new IllegalStateException(msg);
+					// } else if (searchUrls.size() == 0) {
+					// String msg = "At least one value for search.urls must be provided";
+					// throw new IllegalStateException(msg);
 				}
 				formattedProps.add("search.urls" + " " + searchUrls.toString());
 				logger.info("Using {} as search engine with url(s) {}", searchEngine, searchUrls);
@@ -514,7 +515,6 @@ private void init() {
 				logger.info("'search.engine' entry not present so no free text search available");
 			}
 
-
 			unitAliasOptions = props.getString("units", "");
 
 			/*

diff --git a/src/main/java/org/icatproject/core/manager/search/LuceneApi.java b/src/main/java/org/icatproject/core/manager/search/LuceneApi.java
@@ -62,7 +62,7 @@ public JsonObject buildSearchAfter(ScoredEntityBaseBean lastBean, String sort) t
 			builder.add("score", score);
 		}
 		JsonArrayBuilder arrayBuilder;
-		if (sort == null || sort.equals("")) {
+		if (sort == null || sort.equals("") || sort.equals("{}")) {
 			arrayBuilder = Json.createArrayBuilder().add(score);
 		} else {
 			arrayBuilder = searchAfterArrayBuilder(lastBean, sort);
@@ -99,7 +99,7 @@ public void addNow(String entityName, List<Long> ids, EntityManager manager,
 					gen.writeEnd();
 					return null;
 				} catch (Exception e) {
-					logger.error("About to throw internal exception because of", e);
+					logger.error("About to throw internal exception for ids {} because of", ids, e);
 					throw new IcatException(IcatExceptionType.INTERNAL, e.getMessage());
 				} finally {
 					manager.close();

diff --git a/src/main/java/org/icatproject/core/manager/search/SearchApi.java b/src/main/java/org/icatproject/core/manager/search/SearchApi.java
@@ -172,7 +172,7 @@ public static void encodeText(JsonGenerator gen, String name, String value) {
 	 */
 	public JsonValue buildSearchAfter(ScoredEntityBaseBean lastBean, String sort) throws IcatException {
 		JsonArrayBuilder arrayBuilder;
-		if (sort != null && !sort.equals("")) {
+		if (sort != null && !sort.equals("") || sort.equals("{}")) {
 			arrayBuilder = searchAfterArrayBuilder(lastBean, sort);
 		} else {
 			arrayBuilder = Json.createArrayBuilder();

diff --git a/src/main/java/org/icatproject/exposed/ICATRest.java b/src/main/java/org/icatproject/exposed/ICATRest.java
@@ -1256,6 +1256,11 @@ public String search(@Context HttpServletRequest request, @QueryParam("sessionId
 	 *                    "range" key should denote an array of objects with "lower"
 	 *                    and "upper" values.
 	 * 
+	 * @param restrict
+	 *                    Whether to perform a quicker search which restricts the
+	 *                    results based on an InvestigationUser or
+	 *                    InstrumentScientist being able to read their "own" data.
+	 * 
 	 * @return Set of entity ids, relevance scores and Document source encoded as
 	 *         json.
 	 * 
@@ -1267,21 +1272,29 @@ public String search(@Context HttpServletRequest request, @QueryParam("sessionId
 	@Produces(MediaType.APPLICATION_JSON)
 	public String search(@Context HttpServletRequest request, @QueryParam("sessionId") String sessionId,
 			@QueryParam("query") String query, @QueryParam("search_after") String searchAfter,
-			@QueryParam("limit") int limit, @QueryParam("sort") String sort, @QueryParam("facets") String facets)
+			@QueryParam("limit") int limit, @QueryParam("sort") String sort, @QueryParam("facets") String facets,
+			@QueryParam("restrict") boolean restrict)
 			throws IcatException {
 		if (query == null) {
 			throw new IcatException(IcatExceptionType.BAD_PARAMETER, "query is not set");
 		}
 		String userName = beanManager.getUserName(sessionId, manager);
 		JsonValue searchAfterValue = null;
-		if (searchAfter.length() > 0) {
+		if (searchAfter != null && searchAfter.length() > 0) {
 			try (JsonReader jr = Json.createReader(new StringReader(searchAfter))) {
 				searchAfterValue = jr.read();
 			}
 		}
 		ByteArrayOutputStream baos = new ByteArrayOutputStream();
 		try (JsonReader jr = Json.createReader(new StringReader(query))) {
 			JsonObject jo = jr.readObject();
+			if (restrict && !jo.containsKey("user")) {
+				JsonObjectBuilder builder = Json.createObjectBuilder();
+				for (Entry<String, JsonValue> entry : jo.entrySet()) {
+					builder.add(entry.getKey(), entry.getValue());
+				}
+				jo = builder.add("user", userName).build();
+			}
 			String target = jo.getString("target", null);
 			if (jo.containsKey("parameters")) {
 				for (JsonValue val : jo.getJsonArray("parameters")) {
@@ -1318,7 +1331,7 @@ public String search(@Context HttpServletRequest request, @QueryParam("sessionId
 			} else {
 				throw new IcatException(IcatExceptionType.BAD_PARAMETER, "target:" + target + " is not expected");
 			}
-			logger.debug("Free text search with query: {}", jo.toString());
+			logger.debug("Free text search with query: {}, facets: {}", jo.toString(), facets);
 			result = beanManager.freeTextSearchDocs(userName, jo, searchAfterValue, limit, sort, facets, manager,
 					request.getRemoteAddr(), klass);