Bulk exec an action on selected accessions

- Increased threadpool queue to 30 items

package-lock.json

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       "resolved": "https://registry.npmjs.org/setprototypeof/-/setprototypeof-1.1.0.tgz",
-      "integrity": "sha512-BvE/TwpZX4FXExxOxZyRGQQv651MSwmWKZGqvmPcRIjDqWub67kTKuIMx43cZZrS/cBBzwBcNDWoFxt2XEFIpQ==",
+      "integrity": "sha1-0L2FU2iHtv58DYGMuWLZ2RxU5lY=",
       "dev": true
     },
     "shelljs": {
@@ -2428,7 +2428,7 @@
     "spdx-correct": {
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/spdx-correct/-/spdx-correct-3.0.0.tgz",
-      "integrity": "sha512-N19o9z5cEyc8yQQPukRCZ9EUmb4HUpnrmaL/fxS2pBo2jbfcFRVuFZ/oFC+vZz0MNNk0h80iMn5/S6qGZOL5+g==",
+      "integrity": "sha1-BaW01xU6GVvJLDxCW2nzsqlSTII=",
       "requires": {
         "spdx-expression-parse": "^3.0.0",
         "spdx-license-ids": "^3.0.0"
@@ -2437,12 +2437,12 @@
     "spdx-exceptions": {
       "version": "2.1.0",
       "resolved": "https://registry.npmjs.org/spdx-exceptions/-/spdx-exceptions-2.1.0.tgz",
-      "integrity": "sha512-4K1NsmrlCU1JJgUrtgEeTVyfx8VaYea9J9LvARxhbHtVtohPs/gFGG5yy49beySjlIMhhXZ4QqujIZEfS4l6Cg=="
+      "integrity": "sha1-LHrmEFbHFKW5ubKyr30xHvXHj+k="
     },
     "spdx-expression-parse": {
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/spdx-expression-parse/-/spdx-expression-parse-3.0.0.tgz",
-      "integrity": "sha512-Yg6D3XpRD4kkOmTpdgbUiEJFKghJH03fiC1OPll5h/0sO6neh2jqRDVHOQ4o/LMea0tgCkbMgea5ip/e+MkWyg==",
+      "integrity": "sha1-meEZt6XaAOBUkcn6M4t5BII7QdA=",
       "requires": {
         "spdx-exceptions": "^2.1.0",
         "spdx-license-ids": "^3.0.0"
@@ -2596,7 +2596,7 @@
     "tiny-lr": {
       "version": "1.1.1",
       "resolved": "https://registry.npmjs.org/tiny-lr/-/tiny-lr-1.1.1.tgz",
-      "integrity": "sha512-44yhA3tsaRoMOjQQ+5v5mVdqef+kH6Qze9jTpqtVufgYjYt08zyZAwNwwVBj3i1rJMnR52IxOW0LK0vBzgAkuA==",
+      "integrity": "sha1-n6VHQS8jj+2waO4pWvi2gsmLKqs=",
       "dev": true,
       "requires": {
         "body": "^5.1.0",
@@ -2610,7 +2610,7 @@
         "debug": {
           "version": "3.1.0",
           "resolved": "https://registry.npmjs.org/debug/-/debug-3.1.0.tgz",
-          "integrity": "sha512-OX8XqP7/1a9cqkxYw2yXss15f26NKWBpDXQd0/uK/KPqdQhxbPa994hnzjcE2VqQpDslf55723cKPUOGSmMY3g==",
+          "integrity": "sha1-W7WgZyYotkFJVmuhaBnmFRjGcmE=",
           "dev": true,
           "requires": {
             "ms": "2.0.0"
@@ -2657,7 +2657,7 @@
         "source-map": {
           "version": "0.6.1",
           "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.6.1.tgz",
-          "integrity": "sha512-UjgapumWlbMhkBgzT7Ykc5YXUT46F0iKu8SGXq0bcwP5dz/h0Plj6enJqjz1Zbq2l5WaqYnrVbwWOWMyF3F47g==",
+          "integrity": "sha1-dHIq8y6WFOnCh6jQu95IteLxomM=",
           "dev": true
         }
       }
@@ -2718,13 +2718,13 @@
     "websocket-extensions": {
       "version": "0.1.3",
       "resolved": "https://registry.npmjs.org/websocket-extensions/-/websocket-extensions-0.1.3.tgz",
-      "integrity": "sha512-nqHUnMXmBzT0w570r2JpJxfiSD1IzoI+HGVdd3aZ0yNi3ngvQ4jv1dtHt5VGxfI2yj5yqImPhOK4vmIh2xMbGg==",
+      "integrity": "sha1-XS/yKXcAPsaHpLhwc9+7rBRszyk=",
       "dev": true
     },
     "which": {
       "version": "1.3.1",
       "resolved": "https://registry.npmjs.org/which/-/which-1.3.1.tgz",
-      "integrity": "sha512-HxJdYWq1MTIQbJ3nw0cqssHoTNU267KlrDuGZ1WYlxDStUtKUhOaJmh112/TZmHxxUfuJqPXSOm7tDyas0OSIQ==",
+      "integrity": "sha1-pFBD1U9YBTFtqNYvn1CRjT2nCwo=",
       "dev": true,
       "requires": {
         "isexe": "^2.0.0"

src/main/java/org/genesys2/server/component/elastic/ElasticJPAListener.java

@@ -75,7 +75,7 @@ public class ElasticJPAListener {
 	 */
 	@AfterReturning(value = "execution(* org.springframework.data.jpa.repository.JpaRepository.save(..))", returning = "result")
 	public void afterPersist(final JoinPoint joinPoint, final Object result) {
-		LOG.debug("JPA afterPersist {} {}", joinPoint.toLongString(), joinPoint.getTarget());
+		LOG.trace("JPA afterPersist {} {}", joinPoint.toLongString(), joinPoint.getTarget());
 
 		try {
 			scheduleReindexing(result);

src/main/java/org/genesys2/server/mvc/admin/AccessionProcessor.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.mvc.admin;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.EntityManager;
+
+import org.apache.commons.lang3.time.StopWatch;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.QAccession;
+import org.genesys2.server.persistence.AccessionRepository;
+import org.genesys2.server.service.AccessionService;
+import org.genesys2.server.service.AccessionService.IAccessionAction;
+import org.genesys2.server.service.filter.AccessionFilter;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.jpa.repository.support.Querydsl;
+import org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor;
+import org.springframework.stereotype.Component;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
+
+import com.querydsl.core.types.Predicate;
+import com.querydsl.core.types.dsl.PathBuilder;
+import com.querydsl.core.types.dsl.PathBuilderFactory;
+import com.querydsl.jpa.JPQLQuery;
+
+/**
+ * Executes actions on filtered accessions.
+ */
+@Component
+public class AccessionProcessor {
+
+	private static final Logger LOG = LoggerFactory.getLogger(AccessionProcessor.class);
+
+	@Autowired
+	private ThreadPoolTaskExecutor threadPoolTaskExecutor;
+
+	@Autowired
+	private AccessionService accessionService;
+
+	@Autowired
+	private AccessionRepository accessionRepository;
+
+	@Autowired
+	private EntityManager em;
+
+	/// Size of database batch scan for IDs
+	private int batchSize = 1000;
+
+	/**
+	 * Apply action on accessions matching the provided filter.
+	 *
+	 * @param filter the filter
+	 * @param action the action
+	 */
+	@Transactional(readOnly = true, propagation = Propagation.REQUIRES_NEW)
+	public void apply(AccessionFilter filter, IAccessionAction action) {
+
+		Predicate predicate = filter.buildQuery();
+		long count = accessionRepository.count(predicate);
+
+		PathBuilder<Accession> builder = new PathBuilderFactory().create(Accession.class);
+		Querydsl querydsl = new Querydsl(em, builder);
+		JPQLQuery<Long> query = querydsl.createQuery(QAccession.accession)
+			// select id only
+			.select(QAccession.accession.id)
+			// order by id
+			.orderBy(QAccession.accession.id.asc());
+
+		// apply filter
+		query.where(predicate);
+
+		int startPosition = 0;
+		query.offset(startPosition);
+		query.limit(batchSize);
+
+		StopWatch stopWatch = new StopWatch();
+		stopWatch.start();
+
+		List<Long> results;
+
+		do {
+			stopWatch.split();
+			LOG.debug("Reading Accessions. Stopwatch={}s {}+{} of {}. Processing at {} accessions/s", stopWatch.getSplitTime() / 1000, startPosition, batchSize, count, (double)(startPosition+batchSize)/(stopWatch.getSplitTime() / 1000));
+			results = query.fetch();
+			asyncUpdate(results, action);
+
+			// Next page
+			query.offset(startPosition += results.size());
+			
+			// Clear anything cached in the entity manager
+			em.clear();
+		} while (results.size() > 0);
+
+		stopWatch.stop();
+		LOG.info("Processing Accessions for filter {} took {}ms", filter, stopWatch.getTime());
+	}
+
+	private void asyncUpdate(List<Long> accessionIds, IAccessionAction action) {
+		if (accessionIds.size() == 0) {
+			return;
+		}
+
+		final ArrayList<Long> copy = new ArrayList<>(accessionIds);
+
+		threadPoolTaskExecutor.execute(() -> {
+			try {
+				LOG.trace("Executing action on {} Accessions.", copy.size());
+				accessionService.processAccessions(copy, action);
+			} catch (Throwable e) {
+				LOG.warn("Error executing action on batch: {}", e.getMessage(), e);
+			} finally {
+				LOG.trace("Done executing action on {} accessions.", copy.size());
+			}
+		});
+	}
+
+}

src/main/java/org/genesys2/server/mvc/admin/AdminController.java

@@ -29,8 +29,11 @@ import javax.xml.parsers.ParserConfigurationException;
 
 import org.apache.commons.lang.time.StopWatch;
 import org.genesys.catalog.service.DatasetService;
+import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.genesys.PDCI;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.persistence.AccessionRepository;
+import org.genesys2.server.persistence.PDCIRepository;
 import org.genesys2.server.service.ContentService;
 import org.genesys2.server.service.CountryNamesUpdater;
 import org.genesys2.server.service.CropService;
@@ -39,9 +42,11 @@ import org.genesys2.server.service.GeoRegionService;
 import org.genesys2.server.service.GeoService;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.TaxonomyService;
+import org.genesys2.server.service.filter.AccessionFilter;
 import org.genesys2.server.service.worker.ITPGRFAStatusUpdater;
 import org.genesys2.server.service.worker.InstituteUpdater;
 import org.genesys2.server.service.worker.SGSVUpdate;
+import org.genesys2.util.PDCICalculator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -53,8 +58,11 @@ import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.PostMapping;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
 import org.xml.sax.SAXException;
 
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 @Controller
@@ -111,6 +119,12 @@ public class AdminController {
 	@Autowired
 	private ContentService contentService;
 
+	@Autowired
+	private AccessionProcessor accessionProcessor;
+	
+	@Autowired
+	private PDCIRepository pdciRepository;
+	
 	@RequestMapping("/")
 	public String root(Model model) {
 		return "/admin/index";
@@ -212,7 +226,7 @@ public class AdminController {
 		return "redirect:/admin/";
 	}
 
-	@RequestMapping(value = "/pdci", method = RequestMethod.POST, params = "updatePdciStats")
+	@RequestMapping(value = "/pdci", method = RequestMethod.POST, params = "action=institute-pdci")
 	public String updatePDCI() {
 		for (FaoInstitute institute: instituteService.listActive(new PageRequest(0, Integer.MAX_VALUE))) {
 			LOG.info("Updating PDCI for {}", institute.getCode());
@@ -222,6 +236,37 @@ public class AdminController {
 		return "redirect:/admin/";
 	}
 
+	@RequestMapping(value = "/pdci", method = RequestMethod.POST, params = "action=filtered-pdci")
+	public String updateFilteredPDCI(@RequestParam(name = "filter") String filters) throws JsonParseException, JsonMappingException, IOException {
+		
+		AccessionFilter filter = mapper.readValue(filters, AccessionFilter.class);
+		LOG.warn("Recalculating PDCI for accessions matching filter: {}", filter);
+
+		accessionProcessor.apply(filter, (accession) -> {
+