diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
index f01300330495637f235777329ddac6edc8b15930..92d56f5401d9deed0a13ded1cd7aad46187b8b24 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
@@ -44,7 +44,7 @@ public class PermanentDatabaseLevelCache extends XmlParser
implements PermanentDatabaseLevelCacheInterface, ApplicationContextAware {
/**
- * This class represents new thread task for quering database.
+ * This class represents new thread task for querying database.
*
* @author Piotr Gawron
*
@@ -433,8 +433,8 @@ public class PermanentDatabaseLevelCache extends XmlParser
}
});
- // put in the queue empty task to make sure that everything was initializedd
- // (additional managing thread was createed)
+ // put in the queue empty task to make sure that everything was initialized
+ // (additional managing thread was created)
service.submit(new Callable<Object>() {
@Override
public Object call() throws Exception {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index 414f01a803a455b0c81fd04c244e77936e16df44..e1b8afd2d4efedbb1b486fe3327b8ecfbc70ffeb 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -419,7 +419,7 @@ public class ModelAnnotator {
* @param m
* model
* @param updater
- * updater call back function that updat information about progress of
+ * updater call back function that update information about progress of
* the function
* @param validAnnotations
* map that contains information which {@link MiriamType miriam types}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
index 0fbcd7a00e507a8d95cb43a2491c02a565fc1610..465bc8b992ab6f71e1143af666efb28cb88e2d20 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java
@@ -28,7 +28,7 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
/**
- * This class is a backend to publically available pubmed API in
+ * This class is a backend to publicly available pubmed API in
* <a href="https://europepmc.org/RestfulWebService">Europe PubMed Central </a>.
*
* @author Piotr Gawron
@@ -36,340 +36,348 @@ import lcsb.mapviewer.model.map.MiriamType;
*/
public class PubmedParser extends CachableInterface implements IExternalService {
- /**
- * Pubmed identifier used to check the status of service (functionality from
- * {@link IExternalService}).
- */
- static final int SERVICE_STATUS_PUBMED_ID = 12345;
-
- /**
- * Prefix used for caching elements with pubmed identifier as a key.
- */
- static final String PUBMED_PREFIX = "pubmed: ";
-
- /**
- * Length of {@link #PUBMED_PREFIX} string.
- */
- private static final int PUBMED_PREFIX_LENGTH = PUBMED_PREFIX.length();
-
- /**
- * Version of the remote API thnat is supported by this connecting class.
- */
- static final String SUPPORTED_VERSION = "5.2.2";
-
- static final String API_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/";
-
- /**
- * Connector used for accessing data from miriam registry.
- */
- @Autowired
- private MiriamConnector miriamConnector;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(PubmedParser.class);
-
- /**
- * Object that allows to serialize {@link Article} elements into xml string
- * and deserialize xml into {@link Article} objects.
- */
- private XmlSerializer<Article> articleSerializer;
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(PUBMED_PREFIX)) {
- Integer id = Integer.valueOf(name.substring(PUBMED_PREFIX_LENGTH));
- result = articleSerializer.objectToString(getPubmedArticleById(id));
- } else {
- throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (PubmedSearchException e) {
- throw new SourceNotAvailable(e);
- }
-
- return result;
- }
-
- /**
- * Default constructor. Initializes structures used for transforming
- * {@link Article} from/to xml.
- */
- public PubmedParser() {
- super(PubmedParser.class);
- articleSerializer = new XmlSerializer<>(Article.class);
- }
-
- /**
- * Returns article data for given pubmed identifier.
- *
- * @param id
- * pubmed identifier
- * @return article data
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing information about
- * pubmed
- */
- public Article getPubmedArticleById(Integer id) throws PubmedSearchException {
- String queryString = "pubmed: " + id;
- Article result = null;
- try {
- result = articleSerializer.xmlToObject(getCacheNode(queryString));
- } catch (SerializationException e) {
- logger.warn("Problem with deserialization of the string: " + queryString);
- }
- if (result != null && result.getTitle() != null) {
- return result;
- } else {
- logger.debug("Pubmed article (id=" + id + ") not found in cache. Accessing WebService...");
- }
-
- result = new Article();
- try {
- String url = API_URL+"search/resulttype=core&query="
- + java.net.URLEncoder.encode("src:med ext_id:" + id, "UTF-8");
-
- String content = getWebPageContent(url);
-
- Document mainDoc = super.getXmlDocumentFromString(content);
- // Document citationDoc = dBuilder.parse(citationStream);
- mainDoc.getDocumentElement().normalize();
- // citationDoc.getDocumentElement().normalize();
- XPathFactory xPathFactory = XPathFactory.newInstance();
- XPath xpath = xPathFactory.newXPath();
- NodeList nodeList = null;
- // Hit Count
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/citedByCount").evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- try {
- result.setCitationCount(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
- } catch (Exception e) {
- }
- }
- // Title
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/title").evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- result.setTitle(nodeList.item(0).getFirstChild().getNodeValue());
- }
- // Year
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/yearOfPublication").evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- try {
- result.setYear(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
- } catch (Exception e) {
- }
- }
- // Journal
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/journal/title").evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- result.setJournal(nodeList.item(0).getFirstChild().getNodeValue());
- }
- // Authors
- nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/authorString").evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
- List<String> authors = new ArrayList<String>();
- String value = nodeList.item(0).getFirstChild().getNodeValue();
- if (value != null && !value.isEmpty()) {
- authors = Arrays.asList(value.split(","));
- }
- result.setAuthors(authors);
- }
- result.setLink(miriamConnector.getUrlString(new MiriamData(MiriamType.PUBMED, id + "")));
- result.setId(id + "");
-
- if (result.getTitle() != null && !result.getTitle().trim().isEmpty()) {
- try {
- setCacheValue(queryString, articleSerializer.objectToString(result));
- } catch (SerializationException e) {
- logger.warn("Problem with serialization of the string: " + queryString);
- }
- } else {
- result = null;
- }
-
- } catch (Exception e) {
- throw new PubmedSearchException(e);
- }
- return result;
- }
-
- /**
- * This method return html \< a\ > tag with link for pubmed id (with some
- * additional information).
- *
- * @param id
- * pubmed identifier
- * @param withTextPrefix
- * should prefix be added to the tag
- * @return link to webpage with pubmed article
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing information about
- * pubmed
- */
- public String getHtmlFullLinkForId(Integer id, boolean withTextPrefix) throws PubmedSearchException {
- String result = "";
- Article article = getPubmedArticleById(id);
- result += "<div style=\"float:left;\" title=\"" + article.getTitle() + ", ";
- result += article.getStringAuthors() + ", ";
- result += article.getYear() + ", ";
- result += article.getJournal() + "\">";
- if (withTextPrefix) {
- result += "pubmed: ";
- }
- result += "<a target=\"_blank\" href = \"" + article.getLink() + "\">" + id + "</a> </div>";
- return result;
- }
-
- /**
- * This method return html \< a\ > tag with link for pubmed id (with some
- * additional information).
- *
- * @param id
- * pubmed identifier
- * @return link to webpage with pubmed article
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing information about
- * pubmed
- */
- public String getHtmlFullLinkForId(Integer id) throws PubmedSearchException {
- return getHtmlFullLinkForId(id, true);
- }
-
- /**
- * Get the summary of the article.
- *
- * @param id
- * pubmed identifier
- * @return summary of the article.
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing information about
- * pubmed
- */
- public String getSummary(Integer id) throws PubmedSearchException {
- Article article = getPubmedArticleById(id);
- if (article == null) {
- return null;
- }
- String result = article.getTitle() + ", " + article.getStringAuthors() + ", " + article.getYear() + ", " + article.getJournal();
- return result;
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("Europe PubMed Central", "https://europepmc.org/RestfulWebService");
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- Article art = getPubmedArticleById(SERVICE_STATUS_PUBMED_ID);
- if (!getApiVersion().equals(SUPPORTED_VERSION)) {
- logger.debug("New europepmc API version: " + getApiVersion());
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else if (art == null) {
- status.setStatus(ExternalServiceStatusType.DOWN);
- } else {
- status.setStatus(ExternalServiceStatusType.OK);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- /**
- * Returns current version of the pmc API.
- *
- * @return version of the api to which this class is connected
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing external databes
- */
- public String getApiVersion() throws PubmedSearchException {
- try {
- String url = API_URL+"search/resulttype=core&query=src%3Amed+ext_id%3A23644949";
-
- String content = getWebPageContent(url);
-
- Document mainDoc = super.getXmlDocumentFromString(content);
- mainDoc.getDocumentElement().normalize();
- XPathFactory xPathFactory = XPathFactory.newInstance();
- XPath xpath = xPathFactory.newXPath();
- NodeList nodeList = (NodeList) xpath.compile("/responseWrapper/version").evaluate(mainDoc, XPathConstants.NODESET);
- if (nodeList.getLength() > 0) {
- return nodeList.item(0).getTextContent();
- }
- return null;
- } catch (IOException e) {
- throw new PubmedSearchException("Problem with accessing pubmed db", e);
- } catch (InvalidXmlSchemaException | XPathExpressionException e) {
- throw new PubmedSearchException("Invalid response from pubmed db", e);
- }
- }
-
- /**
- * Get the summary of the article.
- *
- * @param id
- * pubmed identifier
- * @return summary of the article.
- * @throws PubmedSearchException
- * thrown when there is a problem with accessing information about
- * pubmed
- */
- public String getSummary(String id) throws PubmedSearchException {
- return getSummary(Integer.valueOf(id));
- }
-
- /**
- * @return the miriamConnector
- * @see #miriamConnector
- */
- public MiriamConnector getMiriamConnector() {
- return miriamConnector;
- }
-
- /**
- * @param miriamConnector
- * the miriamConnector to set
- * @see #miriamConnector
- */
- public void setMiriamConnector(MiriamConnector miriamConnector) {
- this.miriamConnector = miriamConnector;
- }
-
- /**
- * @return the articleSerializer
- * @see #articleSerializer
- */
- protected XmlSerializer<Article> getArticleSerializer() {
- return articleSerializer;
- }
-
- /**
- * @param articleSerializer
- * the articleSerializer to set
- * @see #articleSerializer
- */
- protected void setArticleSerializer(XmlSerializer<Article> articleSerializer) {
- this.articleSerializer = articleSerializer;
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
+ /**
+ * Pubmed identifier used to check the status of service (functionality from
+ * {@link IExternalService}).
+ */
+ static final int SERVICE_STATUS_PUBMED_ID = 12345;
+
+ /**
+ * Prefix used for caching elements with pubmed identifier as a key.
+ */
+ static final String PUBMED_PREFIX = "pubmed: ";
+
+ /**
+ * Length of {@link #PUBMED_PREFIX} string.
+ */
+ private static final int PUBMED_PREFIX_LENGTH = PUBMED_PREFIX.length();
+
+ /**
+ * Version of the remote API that is supported by this connecting class.
+ */
+ static final String SUPPORTED_VERSION = "5.2.2";
+
+ static final String API_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/";
+
+ /**
+ * Connector used for accessing data from miriam registry.
+ */
+ @Autowired
+ private MiriamConnector miriamConnector;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(PubmedParser.class);
+
+ /**
+ * Object that allows to serialize {@link Article} elements into xml string and
+ * deserialize xml into {@link Article} objects.
+ */
+ private XmlSerializer<Article> articleSerializer;
+
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ Object result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(PUBMED_PREFIX)) {
+ Integer id = Integer.valueOf(name.substring(PUBMED_PREFIX_LENGTH));
+ result = articleSerializer.objectToString(getPubmedArticleById(id));
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ } else {
+ result = super.refreshCacheQuery(query);
+ }
+ } catch (PubmedSearchException e) {
+ throw new SourceNotAvailable(e);
+ }
+
+ return result;
+ }
+
+ /**
+ * Default constructor. Initializes structures used for transforming
+ * {@link Article} from/to xml.
+ */
+ public PubmedParser() {
+ super(PubmedParser.class);
+ articleSerializer = new XmlSerializer<>(Article.class);
+ }
+
+ /**
+ * Returns article data for given pubmed identifier.
+ *
+ * @param id
+ * pubmed identifier
+ * @return article data
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public Article getPubmedArticleById(Integer id) throws PubmedSearchException {
+ String queryString = "pubmed: " + id;
+ Article result = null;
+ try {
+ result = articleSerializer.xmlToObject(getCacheNode(queryString));
+ } catch (SerializationException e) {
+ logger.warn("Problem with deserialization of the string: " + queryString);
+ }
+ if (result != null && result.getTitle() != null) {
+ return result;
+ } else {
+ logger.debug("Pubmed article (id=" + id + ") not found in cache. Accessing WebService...");
+ }
+
+ result = new Article();
+ try {
+ String url = API_URL + "search/resulttype=core&query="
+ + java.net.URLEncoder.encode("src:med ext_id:" + id, "UTF-8");
+
+ String content = getWebPageContent(url);
+
+ Document mainDoc = super.getXmlDocumentFromString(content);
+ // Document citationDoc = dBuilder.parse(citationStream);
+ mainDoc.getDocumentElement().normalize();
+ // citationDoc.getDocumentElement().normalize();
+ XPathFactory xPathFactory = XPathFactory.newInstance();
+ XPath xpath = xPathFactory.newXPath();
+ NodeList nodeList = null;
+ // Hit Count
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/citedByCount").evaluate(mainDoc,
+ XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ try {
+ result.setCitationCount(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
+ } catch (Exception e) {
+ }
+ }
+ // Title
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/title").evaluate(mainDoc,
+ XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ result.setTitle(nodeList.item(0).getFirstChild().getNodeValue());
+ }
+ // Year
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/yearOfPublication")
+ .evaluate(mainDoc, XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ try {
+ result.setYear(Integer.valueOf(nodeList.item(0).getFirstChild().getNodeValue()));
+ } catch (Exception e) {
+ }
+ }
+ // Journal
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/journalInfo/journal/title")
+ .evaluate(mainDoc, XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ result.setJournal(nodeList.item(0).getFirstChild().getNodeValue());
+ }
+ // Authors
+ nodeList = (NodeList) xpath.compile("/responseWrapper/resultList/result/authorString").evaluate(mainDoc,
+ XPathConstants.NODESET);
+ if (nodeList != null && nodeList.getLength() > 0 && nodeList.item(0).getFirstChild() != null) {
+ List<String> authors = new ArrayList<String>();
+ String value = nodeList.item(0).getFirstChild().getNodeValue();
+ if (value != null && !value.isEmpty()) {
+ authors = Arrays.asList(value.split(","));
+ }
+ result.setAuthors(authors);
+ }
+ result.setLink(miriamConnector.getUrlString(new MiriamData(MiriamType.PUBMED, id + "")));
+ result.setId(id + "");
+
+ if (result.getTitle() != null && !result.getTitle().trim().isEmpty()) {
+ try {
+ setCacheValue(queryString, articleSerializer.objectToString(result));
+ } catch (SerializationException e) {
+ logger.warn("Problem with serialization of the string: " + queryString);
+ }
+ } else {
+ result = null;
+ }
+
+ } catch (Exception e) {
+ throw new PubmedSearchException(e);
+ }
+ return result;
+ }
+
+ /**
+ * This method return html \< a\ > tag with link for pubmed id (with some
+ * additional information).
+ *
+ * @param id
+ * pubmed identifier
+ * @param withTextPrefix
+ * should prefix be added to the tag
+ * @return link to webpage with pubmed article
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getHtmlFullLinkForId(Integer id, boolean withTextPrefix) throws PubmedSearchException {
+ String result = "";
+ Article article = getPubmedArticleById(id);
+ result += "<div style=\"float:left;\" title=\"" + article.getTitle() + ", ";
+ result += article.getStringAuthors() + ", ";
+ result += article.getYear() + ", ";
+ result += article.getJournal() + "\">";
+ if (withTextPrefix) {
+ result += "pubmed: ";
+ }
+ result += "<a target=\"_blank\" href = \"" + article.getLink() + "\">" + id + "</a> </div>";
+ return result;
+ }
+
+ /**
+ * This method return html \< a\ > tag with link for pubmed id (with some
+ * additional information).
+ *
+ * @param id
+ * pubmed identifier
+ * @return link to webpage with pubmed article
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getHtmlFullLinkForId(Integer id) throws PubmedSearchException {
+ return getHtmlFullLinkForId(id, true);
+ }
+
+ /**
+ * Get the summary of the article.
+ *
+ * @param id
+ * pubmed identifier
+ * @return summary of the article.
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getSummary(Integer id) throws PubmedSearchException {
+ Article article = getPubmedArticleById(id);
+ if (article == null) {
+ return null;
+ }
+ String result = article.getTitle() + ", " + article.getStringAuthors() + ", " + article.getYear() + ", "
+ + article.getJournal();
+ return result;
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus("Europe PubMed Central",
+ "https://europepmc.org/RestfulWebService");
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ Article art = getPubmedArticleById(SERVICE_STATUS_PUBMED_ID);
+ if (!getApiVersion().equals(SUPPORTED_VERSION)) {
+ logger.debug("New europepmc API version: " + getApiVersion());
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else if (art == null) {
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ } else {
+ status.setStatus(ExternalServiceStatusType.OK);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ /**
+ * Returns current version of the pmc API.
+ *
+ * @return version of the api to which this class is connected
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing external databes
+ */
+ public String getApiVersion() throws PubmedSearchException {
+ try {
+ String url = API_URL + "search/resulttype=core&query=src%3Amed+ext_id%3A23644949";
+
+ String content = getWebPageContent(url);
+
+ Document mainDoc = super.getXmlDocumentFromString(content);
+ mainDoc.getDocumentElement().normalize();
+ XPathFactory xPathFactory = XPathFactory.newInstance();
+ XPath xpath = xPathFactory.newXPath();
+ NodeList nodeList = (NodeList) xpath.compile("/responseWrapper/version").evaluate(mainDoc,
+ XPathConstants.NODESET);
+ if (nodeList.getLength() > 0) {
+ return nodeList.item(0).getTextContent();
+ }
+ return null;
+ } catch (IOException e) {
+ throw new PubmedSearchException("Problem with accessing pubmed db", e);
+ } catch (InvalidXmlSchemaException | XPathExpressionException e) {
+ throw new PubmedSearchException("Invalid response from pubmed db", e);
+ }
+ }
+
+ /**
+ * Get the summary of the article.
+ *
+ * @param id
+ * pubmed identifier
+ * @return summary of the article.
+ * @throws PubmedSearchException
+ * thrown when there is a problem with accessing information about
+ * pubmed
+ */
+ public String getSummary(String id) throws PubmedSearchException {
+ return getSummary(Integer.valueOf(id));
+ }
+
+ /**
+ * @return the miriamConnector
+ * @see #miriamConnector
+ */
+ public MiriamConnector getMiriamConnector() {
+ return miriamConnector;
+ }
+
+ /**
+ * @param miriamConnector
+ * the miriamConnector to set
+ * @see #miriamConnector
+ */
+ public void setMiriamConnector(MiriamConnector miriamConnector) {
+ this.miriamConnector = miriamConnector;
+ }
+
+ /**
+ * @return the articleSerializer
+ * @see #articleSerializer
+ */
+ protected XmlSerializer<Article> getArticleSerializer() {
+ return articleSerializer;
+ }
+
+ /**
+ * @param articleSerializer
+ * the articleSerializer to set
+ * @see #articleSerializer
+ */
+ protected void setArticleSerializer(XmlSerializer<Article> articleSerializer) {
+ this.articleSerializer = articleSerializer;
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
}
diff --git a/frontend-js/package-lock.json b/frontend-js/package-lock.json
index 378ebd38856bbe27a33730663ce7dda52de9c70f..29898ad842e00b3eb7c8dd24e29d521cd5cf3cef 100644
--- a/frontend-js/package-lock.json
+++ b/frontend-js/package-lock.json
@@ -45,38 +45,30 @@
"litemol": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b"
},
"dependencies": {
- "ProtVista": {
- "version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
- "dev": true,
- "requires": {
- "d3": "3.5.17",
- "file-saver": "1.3.3",
- "jquery": "2.2.4",
- "jszip": "3.1.4",
- "underscore": "1.8.3"
- },
- "dependencies": {
- "jquery": {
- "version": "2.2.4",
- "resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
- "integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
- "dev": true
- }
- }
- },
"jquery": {
"version": "3.3.1",
"resolved": "https://registry.npmjs.org/jquery/-/jquery-3.3.1.tgz",
"integrity": "sha512-Ubldcmxp5np52/ENotGxlLe6aGMvmF4R8S6tZjsP6Knsaxd/xp3Zrh50cG93lR6nPXyUFwzN3ZSOQI0wRJNdGg==",
"dev": true
- },
- "litemol": {
- "version": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b",
- "dev": true,
- "requires": {
- "@types/react": "15.6.14",
- "@types/react-dom": "15.5.7"
- }
+ }
+ }
+ },
+ "ProtVista": {
+ "version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
+ "dev": true,
+ "requires": {
+ "d3": "3.5.17",
+ "file-saver": "1.3.3",
+ "jquery": "2.2.4",
+ "jszip": "3.1.4",
+ "underscore": "1.8.3"
+ },
+ "dependencies": {
+ "jquery": {
+ "version": "2.2.4",
+ "resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
+ "integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
+ "dev": true
}
}
},
@@ -2058,6 +2050,14 @@
"immediate": "3.0.6"
}
},
+ "litemol": {
+ "version": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b",
+ "dev": true,
+ "requires": {
+ "@types/react": "15.6.14",
+ "@types/react-dom": "15.5.7"
+ }
+ },
"lodash": {
"version": "4.17.4",
"resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.4.tgz",