refactoring; webapp context set to bioschemas

apps/bioschemas-api/deploy.info

@@ -1,7 +1,7 @@
 {
 		"type_source": "SVN",
 		"goal": "package -U source:jar",
-		"url": "http://svn-public.driver.research-infrastructures.eu/driver/dnet50/modules/dnet-bmuse-webapp/trunk/",
+		"url": "http://svn-public.driver.research-infrastructures.eu/driver/dnet50/modules/dnet-bioschemas-api/trunk/",
 		"deploy_repository": "dnet5-snapshots",
 		"version": "5",
 		"mail": "sandro.labruzzo@isti.cnr.it,michele.artini@isti.cnr.it, claudio.atzori@isti.cnr.it, alessia.bardi@isti.cnr.it, enrico.ottonello@isti.cnr.it",

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/AppConfigGarr.java

@@ -1,4 +1,4 @@
-package eu.dnetlib.bmuse_webapp;
+package eu.dnetlib.bioschemas.api;
 
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Profile;

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/MainApplication.java

@@ -1,4 +1,4 @@
-package eu.dnetlib.bmuse_webapp;
+package eu.dnetlib.bioschemas.api;
 
 import eu.dnetlib.common.app.AbstractDnetApp;
 import org.springframework.boot.SpringApplication;

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/ServiceScrapeDriver.java

@@ -1,10 +1,10 @@
-package eu.dnetlib.bmuse_webapp;
+package eu.dnetlib.bioschemas.api;
 
-import eu.dnetlib.bmuse_webapp.crawl.CrawlRecord;
+import eu.dnetlib.bioschemas.api.crawl.CrawlRecord;
-import eu.dnetlib.bmuse_webapp.scraper.BMUSEScraper;
+import eu.dnetlib.bioschemas.api.scraper.BMUSEScraper;
-import eu.dnetlib.bmuse_webapp.scraper.ScrapeState;
+import eu.dnetlib.bioschemas.api.scraper.ScrapeState;
-import eu.dnetlib.bmuse_webapp.scraper.ScrapeThread;
+import eu.dnetlib.bioschemas.api.scraper.ScrapeThread;
-import eu.dnetlib.bmuse_webapp.utils.UrlParser;
+import eu.dnetlib.bioschemas.api.utils.UrlParser;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.jsoup.nodes.Element;

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/crawl/CrawlRecord.java

@@ -1,4 +1,4 @@
-package eu.dnetlib.bmuse_webapp.crawl;
+package eu.dnetlib.bioschemas.api.crawl;
 
 import java.util.Date;
 

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/crawl/StatusOfScrape.java

@@ -1,8 +1,8 @@
-package eu.dnetlib.bmuse_webapp.crawl;
+package eu.dnetlib.bioschemas.api.crawl;
 
 /**
  * 
- * {@link eu.dnetlib.bmuse_webapp.crawl.StatusOfScrape} describes the possible status levels the scrape for each URL/CrawlRecord.
+ * {@link StatusOfScrape} describes the possible status levels the scrape for each URL/CrawlRecord.
  * 
  * Each URL/CrawlRecord can have one of the following:
  * DOES_NOT_EXIST = 404.

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/publisher/BioschemasAPIController.java

@@ -1,6 +1,6 @@
-package eu.dnetlib.bmuse_webapp.publisher;
+package eu.dnetlib.bioschemas.api.publisher;
 
-import eu.dnetlib.bmuse_webapp.ServiceScrapeDriver;
+import eu.dnetlib.bioschemas.api.ServiceScrapeDriver;
 import eu.dnetlib.common.controller.AbstractDnetController;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.LineIterator;
@@ -24,17 +24,17 @@ import java.nio.charset.StandardCharsets;
 
 @RestController
 @RequestMapping("/api")
-public class BMUSEWebappController extends AbstractDnetController {
+public class BioschemasAPIController extends AbstractDnetController {
 
 	@Value("${outputFolder}")
 	private String outputFolder;
 	@Value("${outputDataPattern}")
 	private String outputDataPattern;
 
-	private static Logger logger = LoggerFactory.getLogger(BMUSEWebappController.class);
+	private static Logger logger = LoggerFactory.getLogger(BioschemasAPIController.class);
 
 	@RequestMapping(value = "/startScraping", method = RequestMethod.GET)
-	public String startScraping(@RequestParam final String datasourceKey, @RequestParam final String sitemapUrl) throws BMUSEWebappException, IOException {
+	public String startScraping(@RequestParam final String datasourceKey, @RequestParam final String sitemapUrl) throws BioschemasException, IOException {
 
 		logger.info("<STARTSCRAPING> datasourceKey: "+datasourceKey+" sitemapUrl:"+sitemapUrl);
 
@@ -46,7 +46,7 @@ public class BMUSEWebappController extends AbstractDnetController {
 	}
 
 	@RequestMapping(value = "/getNQuads", method = RequestMethod.GET)
-	public String getNQuads(@RequestParam final String datasourceKey, HttpServletResponse response) throws BMUSEWebappException, IOException {
+	public String getNQuads(@RequestParam final String datasourceKey, HttpServletResponse response) throws BioschemasException, IOException {
 
 		logger.info("<GETNQUADS> datasourceKey: "+datasourceKey);
 

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/publisher/BioschemasException.java

@@ -0,0 +1,28 @@
+package eu.dnetlib.bioschemas.api.publisher;
+
+/**
+ * @author enrico.ottonello
+ *
+ */
+
+public class BioschemasException extends Exception{
+
+	public BioschemasException() {
+	}
+
+	public BioschemasException(final String message) {
+		super(message);
+	}
+
+	public BioschemasException(final String message, final Throwable cause) {
+		super(message, cause);
+	}
+
+	public BioschemasException(final Throwable cause) {
+		super(cause);
+	}
+
+	public BioschemasException(final String message, final Throwable cause, final boolean enableSuppression, final boolean writableStackTrace) {
+		super(message, cause, enableSuppression, writableStackTrace);
+	}
+}

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/publisher/HomeController.java

@@ -1,4 +1,4 @@
-package eu.dnetlib.bmuse_webapp.publisher;
+package eu.dnetlib.bioschemas.api.publisher;
 
 import eu.dnetlib.common.controller.AbstractDnetController;
 import org.springframework.stereotype.Controller;

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/BMUSEScraper.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.bmuse_webapp.scraper;
+package eu.dnetlib.bioschemas.api.scraper;
 
 import hwu.elixir.scrape.exceptions.MissingMarkupException;
 import hwu.elixir.scrape.scraper.ScraperFilteredCore;

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/ScrapeState.java

@@ -1,7 +1,7 @@
-package eu.dnetlib.bmuse_webapp.scraper;
+package eu.dnetlib.bioschemas.api.scraper;
 
-import eu.dnetlib.bmuse_webapp.crawl.CrawlRecord;
+import eu.dnetlib.bioschemas.api.crawl.StatusOfScrape;
-import eu.dnetlib.bmuse_webapp.crawl.StatusOfScrape;
+import eu.dnetlib.bioschemas.api.crawl.CrawlRecord;
 
 import java.util.ArrayList;
 import java.util.Collections;

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/ScrapeThread.java

@@ -1,7 +1,7 @@
-package eu.dnetlib.bmuse_webapp.scraper;
+package eu.dnetlib.bioschemas.api.scraper;
 
-import eu.dnetlib.bmuse_webapp.crawl.CrawlRecord;
+import eu.dnetlib.bioschemas.api.crawl.CrawlRecord;
-import eu.dnetlib.bmuse_webapp.utils.CompressorUtil;
+import eu.dnetlib.bioschemas.api.utils.CompressorUtil;
 import hwu.elixir.scrape.exceptions.CannotWriteException;
 import hwu.elixir.scrape.exceptions.FourZeroFourException;
 import hwu.elixir.scrape.exceptions.JsonLDInspectionException;
@@ -63,7 +63,7 @@ public class ScrapeThread extends Thread {
 			
 			try {
 				String nquads = process.getNQUADSFromUrl(record.getUrl(), true);
-				logger.info("downloaded "+record.getUrl() + " leftToScrape:" + scrapeState.pagesLeftToScrape());
+				logger.info("downloaded "+record.getUrl() + " leftToScrape:" + scrapeState.getNumberPagesLeftToScrape());
 				record.setNquads(CompressorUtil.compressValue(nquads));
 				if (!nquads.isEmpty()) {
 					scrapeState.addSuccessfulScrapedURL(record);

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/ServiceScraper.java

@@ -1,6 +1,6 @@
-package eu.dnetlib.bmuse_webapp.scraper;
+package eu.dnetlib.bioschemas.api.scraper;
 
-import eu.dnetlib.bmuse_webapp.crawl.StatusOfScrape;
+import eu.dnetlib.bioschemas.api.crawl.StatusOfScrape;
 import hwu.elixir.scrape.exceptions.*;
 import hwu.elixir.scrape.scraper.ScraperFilteredCore;
 import org.slf4j.Logger;

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/utils/CompressorUtil.java

@@ -1,4 +1,4 @@
-package eu.dnetlib.bmuse_webapp.utils;
+package eu.dnetlib.bioschemas.api.utils;
 
 import org.apache.commons.codec.binary.Base64;
 import org.apache.commons.io.IOUtils;

apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/utils/UrlParser.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.bmuse_webapp.utils;
+package eu.dnetlib.bioschemas.api.utils;
 
 import hwu.elixir.utils.Helpers;
 import org.jsoup.Jsoup;

apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/publisher/BMUSEWebappException.java

@@ -1,28 +0,0 @@
-package eu.dnetlib.bmuse_webapp.publisher;
-
-/**
- * @author enrico.ottonello
- *
- */
-
-public class BMUSEWebappException extends Exception{
-
-	public BMUSEWebappException() {
-	}
-
-	public BMUSEWebappException(final String message) {
-		super(message);
-	}
-
-	public BMUSEWebappException(final String message, final Throwable cause) {
-		super(message, cause);
-	}
-
-	public BMUSEWebappException(final Throwable cause) {
-		super(cause);
-	}
-
-	public BMUSEWebappException(final String message, final Throwable cause, final boolean enableSuppression, final boolean writableStackTrace) {
-		super(message, cause, enableSuppression, writableStackTrace);
-	}
-}

apps/bioschemas-api/src/main/resources/application.properties

@@ -1,4 +1,4 @@
-server.servlet.context-path=/dnet-bmuse-webapp
+server.servlet.context-path=/bioschemas
 server.port=8281
 
 spring.profiles.active=garr