Merge branch '364-kpi-execution' into 'master'

Resolve "KPI Execution"

Closes #364

See merge request genesys-pgr/genesys-server!265

pom.xml

@@ -80,6 +80,7 @@
 		<querydsl.version>4.1.4</querydsl.version>
 
 		<hibernate.version>4.3.11.Final</hibernate.version>
+		<hibernate.validator.version>4.3.2.Final</hibernate.validator.version>
 		<hsqldb.version>2.3.6</hsqldb.version>
 		<ehcache.version>2.7.4</ehcache.version>
 
@@ -608,6 +609,21 @@
 			<artifactId>jna</artifactId>
 			<version>4.5.2</version>
 		</dependency>
+		<dependency>
+			<groupId>javax.validation</groupId>
+			<artifactId>validation-api</artifactId>
+			<version>1.1.0.Final</version>
+		</dependency>
+		<dependency>
+			<groupId>org.hibernate</groupId>
+			<artifactId>hibernate-validator</artifactId>
+			<version>${hibernate.validator.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.hibernate</groupId>
+			<artifactId>hibernate-validator-annotation-processor</artifactId>
+			<version>${hibernate.validator.version}</version>
+		</dependency>
 	</dependencies>
 
 	<build>

src/main/java/org/genesys2/server/api/admin/v0/KPIController.java

@@ -25,6 +25,7 @@ import javax.xml.bind.ValidationException;
 
 import org.genesys2.server.api.ApiBaseController;
 import org.genesys2.server.api.ModelValidationException;
+import org.genesys2.server.api.Pagination;
 import org.genesys2.server.api.model.ExecutionDimensionJson;
 import org.genesys2.server.api.model.ExecutionJson;
 import org.genesys2.server.exception.AuthorizationException;
@@ -32,10 +33,12 @@ import org.genesys2.server.model.kpi.BooleanDimension;
 import org.genesys2.server.model.kpi.Dimension;
 import org.genesys2.server.model.kpi.Execution;
 import org.genesys2.server.model.kpi.ExecutionDimension;
+import org.genesys2.server.model.kpi.ExecutionRun;
 import org.genesys2.server.model.kpi.KPIParameter;
 import org.genesys2.server.model.kpi.Observation;
 import org.genesys2.server.service.KPIService;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.http.MediaType;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -70,10 +73,10 @@ public class KPIController extends ApiBaseController {
 	 * @throws AuthorizationException
 	 */
 	@RequestMapping(value = "/parameter/list", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public @ResponseBody Map<String, String> listParameters() {
+	public @ResponseBody Map<String, String> listParameters(final Pagination page) {
 		LOG.info("Listing KPI parameters");
 		HashMap<String, String> m = new HashMap<>();
-		for (KPIParameter kpip : kpiService.listParameters()) {
+		for (KPIParameter kpip : kpiService.listParameters(page.toPageRequest(100))) {
 			m.put(kpip.getName(), kpip.getTitle() + "\n" + kpip.getDescription());
 		}
 		return m;
@@ -127,10 +130,10 @@ public class KPIController extends ApiBaseController {
 	 * @throws AuthorizationException
 	 */
 	@RequestMapping(value = "/dimension/list", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public @ResponseBody HashMap<Long, String> listDimensions() {
+	public @ResponseBody HashMap<Long, String> listDimensions(final Pagination page) {
 		LOG.info("Listing KPI dimensions");
 		HashMap<Long, String> m = new HashMap<>();
-		for (Dimension<?> dim : kpiService.listDimensions()) {
+		for (Dimension<?> dim : kpiService.listDimensions(page.toPageRequest(100))) {
 			m.put(dim.getId(), dim.getName() + " " + dim.getTitle());
 		}
 		return m;
@@ -187,7 +190,7 @@ public class KPIController extends ApiBaseController {
 	public @ResponseBody HashMap<String, String> listExecution() {
 		LOG.info("Listing KPI executions");
 		HashMap<String, String> m = new HashMap<>();
-		for (Execution exec : kpiService.listExecutions()) {
+		for (Execution exec : kpiService.listExecutions(new PageRequest(0, 100))) {
 			m.put(exec.getName(), exec.getTitle());
 		}
 		return m;
@@ -225,7 +228,7 @@ public class KPIController extends ApiBaseController {
 	 * @throws ValidationException
 	 */
 	@RequestMapping(value = "/observation/{executionName}/", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public @ResponseBody List<Observation> listObservations(@PathVariable("executionName") String executionName,
+	public @ResponseBody Page<Observation> listObservations(@PathVariable("executionName") String executionName,
 			@RequestParam(value = "page", required = false, defaultValue = "1") int page, @RequestBody(required = false) Map<String, String> dimensionFilters) {
 		return kpiService.listObservations(kpiService.findLastExecutionRun(kpiService.getExecution(executionName)), dimensionFilters, new PageRequest(page - 1,
 				50));
@@ -243,11 +246,9 @@ public class KPIController extends ApiBaseController {
 	public @ResponseBody List<Observation> execute(@PathVariable("executionName") String executionName) {
 		Execution execution = kpiService.getExecution(executionName);
 		LOG.info("Running execute on : {}", executionName);
-		List<Observation> res = kpiService.execute(execution);
-		LOG.info("Saving results: count={}", res.size());
-		List<Observation> x = kpiService.save(execution, res);
+		ExecutionRun run = kpiService.executeAndSave(execution);
 		LOG.info("Done saving results.");
-		return x;
+		return run.getObservations();
 	}
 
 	/**

src/main/java/org/genesys2/server/api/v1/KPIController.java

+/*
+ * Copyright 2018 Global Crop Diversity Trust
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.genesys2.server.api.v1;
+
+import java.util.List;
+
+import org.apache.commons.lang3.StringUtils;
+import org.genesys.blocks.model.JsonViews;
+import org.genesys2.server.api.ApiBaseController;
+import org.genesys2.server.api.Pagination;
+import org.genesys2.server.exception.NotFoundElement;
+import org.genesys2.server.model.kpi.Dimension;
+import org.genesys2.server.model.kpi.Execution;
+import org.genesys2.server.model.kpi.ExecutionRun;
+import org.genesys2.server.model.kpi.KPIParameter;
+import org.genesys2.server.service.KPIService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.web.bind.annotation.DeleteMapping;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+import com.fasterxml.jackson.annotation.JsonView;
+
+import io.swagger.annotations.Api;
+
+@RestController("kpiApi1")
+@RequestMapping(value = { KPIController.CONTROLLER_URL })
+@Api(tags = { "kpi" })
+public class KPIController {
+	public static final String CONTROLLER_URL = ApiBaseController.APIv1_BASE + "/kpi";
+
+	@Autowired
+	private KPIService kpiService;
+
+	/**
+	 * First declare the KPI parameters: e.g. `Accession where `
+	 * 
+	 * @param parameter
+	 * @return
+	 */
+	@PostMapping(value = "/parameters/save")
+	public KPIParameter saveParameter(@RequestBody KPIParameter parameter) {
+		return kpiService.save(parameter);
+	}
+
+	@DeleteMapping(value = "/parameters/{name}")
+	public KPIParameter deleteParameter(@PathVariable String name) {
+		return kpiService.delete(kpiService.getParameter(name));
+	}
+	
+	@GetMapping(value="/parameters")
+	public Page<KPIParameter> listParameters(final Pagination page) {
+		return kpiService.listParameters(page.toPageRequest(100));
+	}
+
+	/**
+	 * Then declare the KPI dimensions: e.g. `FaoInstitute#code where accessionCount gt 0`
+	 * Dimensions provide query parameters to KPI execution
+	 * 
+	 * @param dimension
+	 * @return
+	 */
+	@PostMapping(value = "/dimensions/save")
+	public Dimension<?> saveDimension(@RequestBody Dimension<?> dimension) {
+		return kpiService.save(dimension);
+	}
+	
+	@DeleteMapping(value = "/dimensions/{name}")
+	public Dimension<?> deleteDimension(@PathVariable String name) {
+		return kpiService.delete(kpiService.getDimension(name));
+	}
+	
+	@GetMapping(value="/dimensions")
+	public Page<Dimension<?>> listDimensions(final Pagination page) {
+		return kpiService.listDimensions(page.toPageRequest(100));
+	}
+
+	/**
+	 * Declare execution with a {@link KPIParameter} and one or more {@link Dimension} 
+	 * 
+	 * @param execution
+	 * @return
+	 */
+	@PostMapping(value = "/executions/save")
+	public Execution saveExecution(@RequestBody Execution execution) {
+		return kpiService.save(execution);
+	}
+
+	@DeleteMapping(value = "/executions/{name}")
+	public Execution deleteExecution(@PathVariable String name) {
+		return kpiService.save(kpiService.getExecution(name));
+	}
+	
+	@GetMapping(value="/executions")
+	public Page<Execution> listExecution(final Pagination page) {
+		return kpiService.listExecutions(page.toPageRequest(100));
+	}
+
+	@PostMapping(value = "/executions/{name}/execute")
+	public ExecutionRun runExecution(@PathVariable String name) {
+		return kpiService.executeAndSave(kpiService.getExecution(name));
+	}
+
+	/**
+	 * Execution details
+	 */
+	@GetMapping(value = "/executions/{name}")
+	public ExecutionDetails executionDetails(@PathVariable String name) {
+		Execution execution = kpiService.getExecution(name);
+		return ExecutionDetails.from(execution, kpiService.listExecutionRuns(execution, new PageRequest(0, 10)));
+	}
+
+	@GetMapping(value = "/executions/{name}/runs")
+	public List<ExecutionRun> executionRuns(final @PathVariable String name, final Pagination page) {
+		return kpiService.listExecutionRuns(kpiService.getExecution(name), page.toPageRequest(100));
+	}
+
+	@GetMapping(value = "/executions/{name}/runs/{id}")
+	public ExecutionRun executionRun(final @PathVariable String name, final long runId) {
+		ExecutionRun run = kpiService.getExecutionRun(runId);
+		if (! StringUtils.equals(run.getExecution().getName(), name)) {
+			throw new NotFoundElement("No run " + runId + " for execution " + name);
+		}
+		return run;
+	}
+	
+	/**
+	 * Details
+	 */
+	public static class ExecutionDetails {
+		public Execution execution;
+		public List<ExecutionRun> runs;
+		
+		public static ExecutionDetails from(Execution execution, List<ExecutionRun> runs) {
+			ExecutionDetails ed=new ExecutionDetails();
+			ed.execution=execution;
+			ed.runs = runs;
+			return ed;
+		}
+	}
+}

src/main/java/org/genesys2/server/model/kpi/BooleanDimension.java

@@ -60,7 +60,7 @@ public class BooleanDimension extends Dimension<Boolean> {
 		if (hasTrue()) {
 			b.add(Boolean.TRUE);
 		}
-		if ((mode ^ 2) > 0) {
+		if (hasFalse()) {
 			b.add(Boolean.FALSE);
 		}
 		return b;

src/main/java/org/genesys2/server/model/kpi/Dimension.java

@@ -25,6 +25,8 @@ import javax.persistence.Entity;
 import javax.persistence.Inheritance;
 import javax.persistence.InheritanceType;
 import javax.persistence.Table;
+import javax.validation.constraints.NotNull;
+import javax.validation.constraints.Size;
 
 import org.genesys.blocks.model.AuditedVersionedModel;
 import org.genesys2.server.model.genesys.Parameter;
@@ -54,9 +56,15 @@ public abstract class Dimension<T> extends AuditedVersionedModel {
 	 * 
 	 */
 	private static final long serialVersionUID = 1672379271657218936L;
-	@Column(length = 100, nullable = false)
+	
+	@NotNull
+	@Size(max = 100)
+	@Column(length = 100, unique = true, nullable = false)
 	private String name;
-	@Column(length = 100, nullable = false)
+
+	@NotNull
+	@Size(max = 100)
+	@Column(length = 100, unique = true, nullable = false)
 	private String title;
 
 	final public String getName() {

src/main/java/org/genesys2/server/model/kpi/Execution.java

@@ -27,11 +27,13 @@ import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.OneToMany;
 import javax.persistence.Table;
-
-import net.sf.oval.constraint.NotBlank;
+import javax.validation.constraints.NotNull;
+import javax.validation.constraints.Size;
 
 import org.genesys.blocks.model.AuditedVersionedModel;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
 /**
  * Evaluates {@link KPIParameter} by {@link Dimension}s.
  * 
@@ -47,23 +49,44 @@ public class Execution extends AuditedVersionedModel {
 	 */
 	private static final long serialVersionUID = 1102563708369373562L;
 
+	public static enum ExecutionType {
+		COUNT, SUM, AVERAGE
+	}
+
 	/**
 	 * This specifies the "key" under which observations are filed
 	 */
-	@NotBlank
+	@NotNull
+	@Size(max = 100)
 	@Column(length = 100, unique = true, nullable = false)
 	private String name;
 
+	@NotNull
+	@Column(nullable = false)
+	private ExecutionType type = ExecutionType.COUNT;
+
+	@Size(max = 100)
+	@Column(length = 100)
+	private String title;
+
+	@NotNull
 	@ManyToOne(cascade = {}, fetch = FetchType.EAGER, optional = false)
 	@JoinColumn(name = "parameterId")
 	private KPIParameter parameter;
 
+	/** This is the property of {@link #parameter} we're observing */
+	@NotNull
+	@Size(max = 30)
+	@Column(nullable = false, length = 30)
+	private String property = "id";
+
 	@OneToMany(orphanRemoval = true, fetch = FetchType.EAGER, cascade = { CascadeType.ALL })
 	@JoinColumn(name = "executionId")
 	private List<ExecutionDimension> dimensions = new ArrayList<ExecutionDimension>();
 
-	@Column(length = 100)
-	private String title;
+	@JsonIgnore
+	@OneToMany(mappedBy="execution", orphanRemoval = true, fetch = FetchType.LAZY, cascade = { CascadeType.REMOVE })
+	private List<ExecutionRun> runs;
 
 	public String getName() {
 		return name;
@@ -81,8 +104,41 @@ public class Execution extends AuditedVersionedModel {
 		return parameter;
 	}
 
+	/**
+	 * Defaults to {@link ExecutionType#COUNT}.
+	 * 
+	 * @param type
+	 */
+	public void setType(ExecutionType type) {
+		this.type = type;
+	}
+
+	public ExecutionType getType() {
+		return type;
+	}
+
+	/**
+	 * Set the property of the {{@link #parameter} that we're observing. Defaults to
+	 * `id`, but you will use `accessionCount` or similar for AVERAGE
+	 * 
+	 * @param property
+	 */
+	public void setProperty(String property) {
+		this.property = property;
+	}
+
+	public String getProperty() {
+		return property;
+	}
+
+	/**
+	 * Order of dimensions matters!
+	 * 
+	 * @param dimension
+	 * @param link
+	 * @param field
+	 */
 	public void addDimension(Dimension<?> dimension, String link, String field) {
-		// what do we do?
 		ExecutionDimension ped = new ExecutionDimension();
 		ped.setDimension(dimension);
 		ped.setLink(link);
@@ -94,9 +150,23 @@ public class Execution extends AuditedVersionedModel {
 	public String query() {
 		StringBuffer sb = new StringBuffer(), where = new StringBuffer();
 		String alias = "_base";
-		sb.append("select count(distinct ");
-		sb.append(alias);
-		sb.append(") from ");
+		sb.append("select ");
+		switch (type) {
+		case SUM:
+			sb.append("sum(").append(alias).append(".").append(property).append(")");
+			break;
+
+		case AVERAGE:
+			sb.append("avg(").append(alias).append(".").append(property).append(")");
+			sb.append(", ");
+			sb.append("stddev(").append(alias).append(".").append(property).append(")");
+			break;
+
+		case COUNT:
+		default:
+			sb.append("count(distinct ").append(alias).append(".").append(property).append(")");
+		}
+		sb.append(" from ");
 		sb.append(parameter.getEntity());
 		sb.append(" ").append(alias);
 

src/main/java/org/genesys2/server/model/kpi/ExecutionDimension.java

@@ -21,6 +21,8 @@ import javax.persistence.Entity;
 import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.Table;
+import javax.validation.constraints.NotNull;
+import javax.validation.constraints.Size;
 
 import org.genesys.blocks.model.BasicModel;
 
@@ -33,12 +35,18 @@ public class ExecutionDimension extends BasicModel {
 	 */
 	private static final long serialVersionUID = 5401855589899745004L;
 
+	@NotNull
 	@ManyToOne(cascade = {}, optional = false)
 	@JoinColumn(name = "dimensionId")
 	private Dimension<?> dimension;
 
+	/** Linked entity from the Parameter to inner join directly (e.g. accession.institute) **/
+	@Size(max=100)
 	@Column(length = 100, nullable = true)
 	private String link;
+	
+	/** Field in the Parameter (e.g. accession.instCode) or Linked entity ({@link #link} (e.g. accession.institute.code) **/
+	@Size(max=100)
 	@Column(length = 100, nullable = false)
 	private String field;
 
@@ -71,4 +79,8 @@ public class ExecutionDimension extends BasicModel {
 		return "id=" + getId() + " link=" + link + " field=" + field + " dim=" + dimension.getName();
 	}
 
+	public String toName() {
+		return (link == null ? "" : link + ".") + field;
+	}
+
 }

src/main/java/org/genesys2/server/model/kpi/ExecutionRun.java

@@ -17,18 +17,22 @@
 package org.genesys2.server.model.kpi;
 
 import java.util.Date;
+import java.util.List;
 
+import javax.persistence.CascadeType;
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
 import javax.persistence.Table;
 import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
+import javax.validation.constraints.NotNull;
 
 import org.genesys.blocks.model.BasicModel;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
 @Entity
 @Table(name = "kpiexecutionrun")
 public class ExecutionRun extends BasicModel {
@@ -38,13 +42,18 @@ public class ExecutionRun extends BasicModel {
 	 */
 	private static final long serialVersionUID = -2475286586650646568L;
 
+	@NotNull
 	@Column(nullable = false)
 	@Temporal(TemporalType.TIMESTAMP)
 	private Date timestamp = new Date();
 
+	@NotNull
 	@JsonIgnore
 	@ManyToOne(cascade = {}, optional = false)
 	private Execution execution;
+	
+	@OneToMany(mappedBy="executionRun", cascade = { CascadeType.PERSIST }, orphanRemoval = true)
+	private List<Observation> observations;
 
 	public Date getTimestamp() {
 		return timestamp;
@@ -61,4 +70,12 @@ public class ExecutionRun extends BasicModel {
 	public void setExecution(Execution execution) {
 		this.execution = execution;
 	}
+	
+	public List<Observation> getObservations() {
+		return observations;
+	}
+	
+	public void setObservations(List<Observation> observations) {
+		this.observations = observations;
+	}
 }

src/main/java/org/genesys2/server/model/kpi/JpaDimension.java

@@ -20,20 +20,25 @@ import java.util.Set;
 
 import javax.persistence.Column;
 import javax.persistence.Entity;
+import javax.validation.constraints.NotNull;
+import javax.validation.constraints.Size;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
 
 @Entity
 public class JpaDimension extends Dimension<Object> {
 
-	/**
-	 * 
-	 */
 	private static final long serialVersionUID = 4337653920991433997L;
+
+	@NotNull @Size(min=1, max=100)
 	@Column(length = 100)
 	private String entity;
+	
+	@NotNull @Size(min=1, max=100)
 	@Column(length = 50)
 	private String field;
+	
+	@Size(max=100)
 	@Column(name = "`condition`", length = 100)
 	private String condition;
 

src/main/java/org/genesys2/server/model/kpi/KPIParameter.java

@@ -21,6 +21,8 @@ import javax.persistence.Entity;
 import javax.persistence.Lob;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
+import javax.validation.constraints.NotNull;
+import javax.validation.constraints.Size;
 
 import org.genesys.blocks.model.AuditedVersionedModel;
 import org.hibernate.annotations.Type;
@@ -49,15 +51,22 @@ public class KPIParameter extends AuditedVersionedModel {
 	 */
 	private static final long serialVersionUID = 5773482399613068571L;
 
+	@NotNull
+	@Size(max = 100)
 	@Column(length = 100, nullable = false)
 	private String name;
 
+	@NotNull
+	@Size(max = 100)
 	@Column(length = 100, nullable = false)
 	private String title;
 
+	@NotNull
+	@Size(max = 100)
 	@Column(length = 100, nullable = false)
 	private String entity;
 
+	@Size(max = 300)