diff --git a/apps/bioschemas-api/deploy.info b/apps/bioschemas-api/deploy.info index 015b818c..63c79ac8 100644 --- a/apps/bioschemas-api/deploy.info +++ b/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", diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/AppConfigGarr.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/AppConfigGarr.java similarity index 85% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/AppConfigGarr.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/AppConfigGarr.java index 529980e9..6b4865a3 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/AppConfigGarr.java +++ b/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; diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/MainApplication.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/MainApplication.java similarity index 97% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/MainApplication.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/MainApplication.java index 44bbd5ad..53713a06 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/MainApplication.java +++ b/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; diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/ServiceScrapeDriver.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/ServiceScrapeDriver.java similarity index 95% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/ServiceScrapeDriver.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/ServiceScrapeDriver.java index f87578c8..bbe7adc8 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/ServiceScrapeDriver.java +++ b/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.bmuse_webapp.scraper.BMUSEScraper; -import eu.dnetlib.bmuse_webapp.scraper.ScrapeState; -import eu.dnetlib.bmuse_webapp.scraper.ScrapeThread; -import eu.dnetlib.bmuse_webapp.utils.UrlParser; +import eu.dnetlib.bioschemas.api.crawl.CrawlRecord; +import eu.dnetlib.bioschemas.api.scraper.BMUSEScraper; +import eu.dnetlib.bioschemas.api.scraper.ScrapeState; +import eu.dnetlib.bioschemas.api.scraper.ScrapeThread; +import eu.dnetlib.bioschemas.api.utils.UrlParser; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.jsoup.nodes.Element; diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/crawl/CrawlRecord.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/crawl/CrawlRecord.java similarity index 98% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/crawl/CrawlRecord.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/crawl/CrawlRecord.java index e711d745..c4d4ff28 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/crawl/CrawlRecord.java +++ b/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; diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/crawl/StatusOfScrape.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/crawl/StatusOfScrape.java similarity index 74% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/crawl/StatusOfScrape.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/crawl/StatusOfScrape.java index 9ecd7ba1..d23bb1c7 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/crawl/StatusOfScrape.java +++ b/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. diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/publisher/BMUSEWebappController.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/publisher/BioschemasAPIController.java similarity index 82% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/publisher/BMUSEWebappController.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/publisher/BioschemasAPIController.java index 2339a8b3..36fe207d 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/publisher/BMUSEWebappController.java +++ b/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(" 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(" datasourceKey: "+datasourceKey); diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/publisher/BioschemasException.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/publisher/BioschemasException.java new file mode 100644 index 00000000..594016d2 --- /dev/null +++ b/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); + } +} diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/publisher/HomeController.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/publisher/HomeController.java similarity index 88% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/publisher/HomeController.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/publisher/HomeController.java index ab7143f2..cad79265 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/publisher/HomeController.java +++ b/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; diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/BMUSEScraper.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/BMUSEScraper.java similarity index 98% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/BMUSEScraper.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/BMUSEScraper.java index 763c9f64..ec98a69f 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/BMUSEScraper.java +++ b/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; diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/ScrapeState.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/ScrapeState.java similarity index 96% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/ScrapeState.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/ScrapeState.java index 11aababe..d544c984 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/ScrapeState.java +++ b/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.bmuse_webapp.crawl.StatusOfScrape; +import eu.dnetlib.bioschemas.api.crawl.StatusOfScrape; +import eu.dnetlib.bioschemas.api.crawl.CrawlRecord; import java.util.ArrayList; import java.util.Collections; diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/ScrapeThread.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/ScrapeThread.java similarity index 94% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/ScrapeThread.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/ScrapeThread.java index 27847ad3..7b149c46 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/ScrapeThread.java +++ b/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.bmuse_webapp.utils.CompressorUtil; +import eu.dnetlib.bioschemas.api.crawl.CrawlRecord; +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); diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/ServiceScraper.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/ServiceScraper.java similarity index 95% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/ServiceScraper.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/scraper/ServiceScraper.java index fbcc0483..9454cab2 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/scraper/ServiceScraper.java +++ b/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; diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/utils/CompressorUtil.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/utils/CompressorUtil.java similarity index 96% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/utils/CompressorUtil.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/utils/CompressorUtil.java index cab5102a..1ef1508e 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/utils/CompressorUtil.java +++ b/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; diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/utils/UrlParser.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/utils/UrlParser.java similarity index 97% rename from apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/utils/UrlParser.java rename to apps/bioschemas-api/src/main/java/eu/dnetlib/bioschemas/api/utils/UrlParser.java index 39c64791..9c37246e 100644 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/utils/UrlParser.java +++ b/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; diff --git a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/publisher/BMUSEWebappException.java b/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/publisher/BMUSEWebappException.java deleted file mode 100644 index 9687ebfa..00000000 --- a/apps/bioschemas-api/src/main/java/eu/dnetlib/bmuse_webapp/publisher/BMUSEWebappException.java +++ /dev/null @@ -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); - } -} diff --git a/apps/bioschemas-api/src/main/resources/application.properties b/apps/bioschemas-api/src/main/resources/application.properties index 7bec4ba6..43ac7dad 100644 --- a/apps/bioschemas-api/src/main/resources/application.properties +++ b/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