diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
index f90874d5d3da486df6dce2f6513da87be67b5e9d..6cf4f1819003508f194c5b31dd5d6d2311df6c78 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
@@ -21,261 +21,262 @@ import uk.ac.ebi.miriam.lib.MiriamLink;
/**
* Class responsible for connection to Miriam DB. It allows to update URI of
- * database being used and retreive urls for miriam uri.
+ * database being used and retrieve urls for miriam uri.
*
* @author Piotr Gawron
*
*/
public final class MiriamConnector extends CachableInterface implements IExternalService {
- /**
- * String used to distinguish cached data for links.
- */
- static final String LINK_DB_PREFIX = "Link: ";
+ /**
+ * String used to distinguish cached data for links.
+ */
+ static final String LINK_DB_PREFIX = "Link: ";
- /**
- * String used to distinguish cached data for checking if uri is valid.
- */
- protected static final String VALID_URI_PREFIX = "Validity: ";
+ /**
+ * String used to distinguish cached data for checking if uri is valid.
+ */
+ protected static final String VALID_URI_PREFIX = "Validity: ";
- /**
- * String describing invalid miriam entries that will be put into db (instead
- * of null).
- */
- private static final String INVALID_LINK = "INVALID";
+ /**
+ * String describing invalid miriam entries that will be put into db (instead of
+ * null).
+ */
+ private static final String INVALID_LINK = "INVALID";
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(MiriamConnector.class.getName());
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(MiriamConnector.class.getName());
- /**
- * Miriam Registry API.
- */
- private MiriamLink link;
+ /**
+ * Miriam Registry API.
+ */
+ private MiriamLink link;
- /**
- * Default class constructor. Prevent initialization.
- */
- public MiriamConnector() {
- super(MiriamConnector.class);
- link = new MiriamLink();
- }
+ /**
+ * Default class constructor. Prevent initialization.
+ */
+ public MiriamConnector() {
+ super(MiriamConnector.class);
+ link = new MiriamLink();
+ link.setAddress("https://www.ebi.ac.uk/miriamws/main/MiriamWebServices");
+ }
- /**
- * Returns url to the webpage represented by {@link MiriamData} param.
- *
- * @param miriamData
- * miriam data
- * @return url to resource pointed by miriam data
- */
- public String getUrlString(MiriamData miriamData) {
- if (miriamData.getDataType() == null) {
- throw new InvalidArgumentException("Data type cannot be empty.");
- } else if (miriamData.getDataType().getUris().size() == 0) {
- throw new InvalidArgumentException("Url for " + miriamData.getDataType() + " cannot be retreived.");
- }
- String query = LINK_DB_PREFIX + miriamData.getDataType().getUris().get(0) + "\n" + miriamData.getResource();
- String result = getCacheValue(query);
- if (result != null) {
- if (INVALID_LINK.equals(result)) {
- return null;
- }
- return result;
- }
- // hardcoded specific treatment for mesh
- if (MiriamType.MESH_2012.equals(miriamData.getDataType())) {
- result = "http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=" + miriamData.getResource();
- } else {
- String uri = miriamData.getDataType().getUris().get(0) + ":" + miriamData.getResource();
- String[] urls = getLink().getLocations(uri);
- if (urls == null) {
- result = null;
- } else if (urls.length > 0) {
- result = urls[0];
- }
- }
- if (result != null) {
- setCacheValue(query, result);
- return result;
- } else {
- logger.warn("Cannot find url for miriam: " + miriamData);
- setCacheValue(query, INVALID_LINK);
- return null;
- }
- }
+ /**
+ * Returns url to the web page represented by {@link MiriamData} parameter.
+ *
+ * @param miriamData
+ * miriam data
+ * @return url to resource pointed by miriam data
+ */
+ public String getUrlString(MiriamData miriamData) {
+ if (miriamData.getDataType() == null) {
+ throw new InvalidArgumentException("Data type cannot be empty.");
+ } else if (miriamData.getDataType().getUris().size() == 0) {
+ throw new InvalidArgumentException("Url for " + miriamData.getDataType() + " cannot be retreived.");
+ }
+ String query = LINK_DB_PREFIX + miriamData.getDataType().getUris().get(0) + "\n" + miriamData.getResource();
+ String result = getCacheValue(query);
+ if (result != null) {
+ if (INVALID_LINK.equals(result)) {
+ return null;
+ }
+ return result;
+ }
+ // hard-coded specific treatment for mesh
+ if (MiriamType.MESH_2012.equals(miriamData.getDataType())) {
+ result = "http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=" + miriamData.getResource();
+ } else {
+ String uri = miriamData.getDataType().getUris().get(0) + ":" + miriamData.getResource();
+ String[] urls = getLink().getLocations(uri);
+ if (urls == null) {
+ result = null;
+ } else if (urls.length > 0) {
+ result = urls[0];
+ }
+ }
+ if (result != null) {
+ setCacheValue(query, result);
+ return result;
+ } else {
+ logger.warn("Cannot find url for miriam: " + miriamData);
+ setCacheValue(query, INVALID_LINK);
+ return null;
+ }
+ }
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus("MIRIAM Registry", "http://www.ebi.ac.uk/miriam/main/");
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus("MIRIAM Registry", "https://www.ebi.ac.uk/miriam/main/");
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
- try {
- String url = getUrlString(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "3453"));
- status.setStatus(ExternalServiceStatusType.OK);
- if (url == null) {
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
+ try {
+ String url = getUrlString(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, "3453"));
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (url == null) {
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
- /**
- * Check if identifier can be transformed into {@link MiriamData}.
- *
- * @param string
- * identifier in the format NAME:IDENTIFIER. Where NAME is the name
- * from {@link MiriamType#commonName} and IDENTIFIER is resource
- * identifier.
- * @return <code>true</code> if identifier can be transformed into
- * {@link MiriamData}
- */
- public boolean isValidIdentifier(String string) {
- try {
- MiriamType.getMiriamDataFromIdentifier(string);
- return true;
- } catch (InvalidArgumentException e) {
- return false;
- }
- }
+ /**
+ * Check if identifier can be transformed into {@link MiriamData}.
+ *
+ * @param string
+ * identifier in the format NAME:IDENTIFIER. Where NAME is the name
+ * from {@link MiriamType#commonName} and IDENTIFIER is resource
+ * identifier.
+ * @return <code>true</code> if identifier can be transformed into
+ * {@link MiriamData}
+ */
+ public boolean isValidIdentifier(String string) {
+ try {
+ MiriamType.getMiriamDataFromIdentifier(string);
+ return true;
+ } catch (InvalidArgumentException e) {
+ return false;
+ }
+ }
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(LINK_DB_PREFIX)) {
- String tmp = name.substring(LINK_DB_PREFIX.length());
- String[] rows = tmp.split("\n");
- if (rows.length != 2) {
- throw new InvalidArgumentException("Miriam link query is invalid: " + query);
- }
- MiriamType dataType = MiriamType.getTypeByUri(rows[0]);
- String resource = rows[1];
- result = getUrlString(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, dataType, resource));
- } else if (name.startsWith(VALID_URI_PREFIX)) {
- String tmp = name.substring(VALID_URI_PREFIX.length());
- result = "" + isValid(tmp);
- } else if (name.startsWith("http")) {
- try {
- result = getWebPageContent(name);
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- } 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());
- }
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(LINK_DB_PREFIX)) {
+ String tmp = name.substring(LINK_DB_PREFIX.length());
+ String[] rows = tmp.split("\n");
+ if (rows.length != 2) {
+ throw new InvalidArgumentException("Miriam link query is invalid: " + query);
+ }
+ MiriamType dataType = MiriamType.getTypeByUri(rows[0]);
+ String resource = rows[1];
+ result = getUrlString(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, dataType, resource));
+ } else if (name.startsWith(VALID_URI_PREFIX)) {
+ String tmp = name.substring(VALID_URI_PREFIX.length());
+ result = "" + isValid(tmp);
+ } else if (name.startsWith("http")) {
+ try {
+ result = getWebPageContent(name);
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ } 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());
+ }
- return result;
- }
+ return result;
+ }
- /**
- * Checks if uri (like the one defined in {@link MiriamType#uris}) is valid.
- *
- * @param uri
- * uri to check
- * @return <code>true</code> if uri in parameter is valid, <code>false</code>
- * otherwise
- */
- public boolean isValid(String uri) {
- String query = VALID_URI_PREFIX + uri;
- String val = getCacheValue(query);
- if (val != null) {
- return "true".equalsIgnoreCase(val);
- }
+ /**
+ * Checks if uri (like the one defined in {@link MiriamType#uris}) is valid.
+ *
+ * @param uri
+ * uri to check
+ * @return <code>true</code> if uri in parameter is valid, <code>false</code>
+ * otherwise
+ */
+ public boolean isValid(String uri) {
+ String query = VALID_URI_PREFIX + uri;
+ String val = getCacheValue(query);
+ if (val != null) {
+ return "true".equalsIgnoreCase(val);
+ }
- boolean result = false;
- String name = getLink().getName(uri);
- if (name == null) {
- result = false;
- } else {
- result = !name.isEmpty();
- }
- setCacheValue(query, "" + result);
- return result;
- }
+ boolean result = false;
+ String name = getLink().getName(uri);
+ if (name == null) {
+ result = false;
+ } else {
+ result = !name.isEmpty();
+ }
+ setCacheValue(query, "" + result);
+ return result;
+ }
- /**
- * This is alternative versopm od {@link #getUrlString(MiriamData)} method
- * that is around 30% fatsre. But it refers to beta version of
- * <a href="http://www.ebi.ac.uk/miriamws/main/rest/">miriam Rest API</a>.
- *
- * @param md
- * miriam data for which access url will be returned
- * @return url to resource pointed by miriam data
- * @throws AnnotationException
- * thrown when there is a problem with accessing miriam REST API
- */
- protected String getUrlString2(MiriamData md) throws AnnotationException {
- try {
- String result = null;
- String uri = md.getDataType().getUris().get(0) + ":" + md.getResource();
- String query = "http://www.ebi.ac.uk/miriamws/main/rest/resolve/" + uri;
- String page;
- page = getWebPageContent(query);
- Document document = getXmlDocumentFromString(page);
- Node uris = document.getFirstChild();
- NodeList nodes = uris.getChildNodes();
- for (int i = 0; i < nodes.getLength(); i++) {
- Node node = nodes.item(i);
- if (Node.ELEMENT_NODE == node.getNodeType()) {
- if (getNodeAttr("deprecated", node).equals("")) {
- result = node.getTextContent();
- }
- }
- }
- return result;
- } catch (IOException e) {
- throw new AnnotationException("Problem with accessing miriam REST API", e);
- } catch (InvalidXmlSchemaException e) {
- throw new AnnotationException("Problem with parsing miriam REST API response", e);
- }
- }
+ /**
+ * This is alternative version of {@link #getUrlString(MiriamData)} method that
+ * is around 30% faster. But it refers to beta version of
+ * <a href="https://www.ebi.ac.uk/miriamws/main/rest/">miriam Rest API</a>.
+ *
+ * @param md
+ * miriam data for which access url will be returned
+ * @return url to resource pointed by miriam data
+ * @throws AnnotationException
+ * thrown when there is a problem with accessing miriam REST API
+ */
+ protected String getUrlString2(MiriamData md) throws AnnotationException {
+ try {
+ String result = null;
+ String uri = md.getDataType().getUris().get(0) + ":" + md.getResource();
+ String query = "https://www.ebi.ac.uk/miriamws/main/rest/resolve/" + uri;
+ String page;
+ page = getWebPageContent(query);
+ Document document = getXmlDocumentFromString(page);
+ Node uris = document.getFirstChild();
+ NodeList nodes = uris.getChildNodes();
+ for (int i = 0; i < nodes.getLength(); i++) {
+ Node node = nodes.item(i);
+ if (Node.ELEMENT_NODE == node.getNodeType()) {
+ if (getNodeAttr("deprecated", node).equals("")) {
+ result = node.getTextContent();
+ }
+ }
+ }
+ return result;
+ } catch (IOException e) {
+ throw new AnnotationException("Problem with accessing miriam REST API", e);
+ } catch (InvalidXmlSchemaException e) {
+ throw new AnnotationException("Problem with parsing miriam REST API response", e);
+ }
+ }
- /**
- * Returns uri to miriam resource.
- *
- * @param md
- * {@link MiriamData} object for which uri should be returned
- * @return uri to miriam resource
- */
- public String miriamDataToUri(MiriamData md) {
- return md.getDataType().getUris().get(0) + ":" + md.getResource();
- }
+ /**
+ * Returns uri to miriam resource.
+ *
+ * @param md
+ * {@link MiriamData} object for which uri should be returned
+ * @return uri to miriam resource
+ */
+ public String miriamDataToUri(MiriamData md) {
+ return md.getDataType().getUris().get(0) + ":" + md.getResource();
+ }
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
- /**
- * @return the link
- * @see #link
- */
- MiriamLink getLink() {
- return link;
- }
+ /**
+ * @return the link
+ * @see #link
+ */
+ MiriamLink getLink() {
+ return link;
+ }
- /**
- * @param link
- * the link to set
- * @see #link
- */
- void setLink(MiriamLink link) {
- this.link = link;
- }
+ /**
+ * @param link
+ * the link to set
+ * @see #link
+ */
+ void setLink(MiriamLink link) {
+ this.link = link;
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
index 8814930e8ddd1ff50b723d84098f482f71d18d8c..e9dff58fee609e7fcc5e18ec14b658aaf3f9783e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
@@ -33,350 +33,349 @@ import lcsb.mapviewer.model.map.MiriamType;
import uk.ac.ebi.miriam.lib.MiriamLink;
public class MiriamConnectorTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(MiriamConnectorTest.class);
-
- @Autowired
- MiriamConnector miriamConnector;
-
- GeneralCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- cache = miriamConnector.getCache();
- }
-
- @After
- public void tearDown() throws Exception {
- miriamConnector.setCache(cache);
- }
-
- @Test
- public void testGoUri() throws Exception {
- try {
- assertFalse(MiriamType.GO.getUris().size() == 1);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testMeshUrl() throws Exception {
- try {
- // exclude first cached value
- miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.MESH_2012, "D004249");
-
- String pageContent = getWebpage(miriamConnector.getUrlString(md));
- assertTrue(pageContent.contains("DNA Damage"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrl() throws Exception {
- try {
- // exclude first cached value
- miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
- MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
-
- String url = miriamConnector.getUrlString(md);
- assertNotNull(url);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrlForInvalidMiriam() throws Exception {
- try {
- miriamConnector.getUrlString(new MiriamData());
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Data type cannot be empty"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrlForInvalidMiriam2() throws Exception {
- try {
- miriamConnector.getUrlString(new MiriamData(MiriamType.UNKNOWN,""));
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("cannot be retreived"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrlForInvalidMiriam3() throws Exception {
- try {
- String url = miriamConnector.getUrlString(new MiriamData(MiriamType.ENTREZ,"abc"));
- assertNull(url);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testIsValidIdentifier() throws Exception {
- try {
- assertTrue(miriamConnector.isValidIdentifier(MiriamType.ENTREZ.getCommonName()+":"+"1234"));
- assertFalse(miriamConnector.isValidIdentifier("blablabla"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testResolveUrl() throws Exception {
- try {
- // exclude first cached value
- miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
- for (MiriamType mt : MiriamType.values()) {
- if (!MiriamType.UNKNOWN.equals(mt)) {
- assertTrue("Invalid URI for MiriamType: " + mt, miriamConnector.isValid(mt.getUris().get(0)));
- }
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefresh() throws Exception {
- String query = MiriamConnector.VALID_URI_PREFIX + MiriamType.HGNC.getUris().get(0);
- try {
- String res = miriamConnector.refreshCacheQuery(query);
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefresh2() throws Exception {
- MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
- String query = MiriamConnector.LINK_DB_PREFIX + md.getDataType().getUris().get(0) + "\n" + md.getResource();
- try {
- String res = miriamConnector.refreshCacheQuery(query);
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefresh3() throws Exception {
- try {
- String res = miriamConnector.refreshCacheQuery("https://www.google.pl/");
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrl2() throws Exception {
- try {
- // exclude first cached value
- miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
- MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
-
- String url = miriamConnector.getUrlString2(md);
- assertNotNull(url);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMiriamDataToUri() throws Exception {
- try {
- assertNotNull(miriamConnector.miriamDataToUri(TaxonomyBackend.HUMAN_TAXONOMY));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetUrl2WithInvalidApiResponse() throws Exception {
- WebPageDownloader downloader = miriamConnector.getWebPageDownloader();
- GeneralCacheInterface cache = miriamConnector.getCache();
- try {
- // exclude first cached value
- miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
- miriamConnector.setWebPageDownloader(mockDownloader);
-
- miriamConnector.getUrlString2(TaxonomyBackend.HUMAN_TAXONOMY);
-
- } catch (AnnotationException e) {
- assertTrue(e.getMessage().contains("Problem with accessing miriam REST API"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miriamConnector.setWebPageDownloader(downloader);
- miriamConnector.setCache(cache);
- }
- }
-
- @Test
- public void testGetUrl2WithInvalidApiResponse2() throws Exception {
- WebPageDownloader downloader = miriamConnector.getWebPageDownloader();
- GeneralCacheInterface cache = miriamConnector.getCache();
- try {
- // exclude first cached value
- miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
- miriamConnector.setWebPageDownloader(mockDownloader);
-
- miriamConnector.getUrlString2(TaxonomyBackend.HUMAN_TAXONOMY);
-
- } catch (AnnotationException e) {
- assertTrue(e.getMessage().contains("Problem with parsing miriam REST API response"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miriamConnector.setWebPageDownloader(downloader);
- miriamConnector.setCache(cache);
- }
- }
-
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = miriamConnector.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
- miriamConnector.setWebPageDownloader(mockDownloader);
- miriamConnector.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miriamConnector.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- miriamConnector.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- miriamConnector.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery3() throws Exception {
- try {
- miriamConnector.refreshCacheQuery(MiriamConnector.LINK_DB_PREFIX);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Miriam link query is invalid"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCheckValidyOfEmptyUri() throws Exception {
- try {
- //user connector without cache
- boolean value = new MiriamConnector().isValid("");
- assertFalse(value);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, miriamConnector.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- MiriamLink link = miriamConnector.getLink();
- try {
- MiriamLink mockDownloader = Mockito.mock(MiriamLink.class);
- when(mockDownloader.getLocations(any())).thenThrow(new InvalidStateException());
- miriamConnector.setLink(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, miriamConnector.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miriamConnector.setLink(link);
- }
- }
-
- @Test
- public void testSimulateDownStatus2() throws Exception {
- MiriamLink link = miriamConnector.getLink();
- try {
- MiriamLink mockDownloader = Mockito.mock(MiriamLink.class);
- when(mockDownloader.getLocations(any())).thenReturn(null);
- miriamConnector.setLink(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, miriamConnector.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- miriamConnector.setLink(link);
- }
- }
+ Logger logger = Logger.getLogger(MiriamConnectorTest.class);
+
+ @Autowired
+ MiriamConnector miriamConnector;
+
+ GeneralCacheInterface cache;
+
+ @Before
+ public void setUp() throws Exception {
+ cache = miriamConnector.getCache();
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ miriamConnector.setCache(cache);
+ }
+
+ @Test
+ public void testGoUri() throws Exception {
+ try {
+ assertFalse(MiriamType.GO.getUris().size() == 1);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testMeshUrl() throws Exception {
+ try {
+ // exclude first cached value
+ miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.MESH_2012, "D004249");
+
+ String pageContent = getWebpage(miriamConnector.getUrlString(md));
+ assertTrue(pageContent.contains("DNA Damage"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrl() throws Exception {
+ try {
+ // exclude first cached value
+ miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
+ MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
+
+ String url = miriamConnector.getUrlString(md);
+ assertNotNull(url);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrlForInvalidMiriam() throws Exception {
+ try {
+ miriamConnector.getUrlString(new MiriamData());
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Data type cannot be empty"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrlForInvalidMiriam2() throws Exception {
+ try {
+ miriamConnector.getUrlString(new MiriamData(MiriamType.UNKNOWN, ""));
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("cannot be retreived"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrlForInvalidMiriam3() throws Exception {
+ try {
+ String url = miriamConnector.getUrlString(new MiriamData(MiriamType.ENTREZ, "abc"));
+ assertNull(url);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testIsValidIdentifier() throws Exception {
+ try {
+ assertTrue(miriamConnector.isValidIdentifier(MiriamType.ENTREZ.getCommonName() + ":" + "1234"));
+ assertFalse(miriamConnector.isValidIdentifier("blablabla"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testResolveUrl() throws Exception {
+ try {
+ // exclude first cached value
+ miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
+ for (MiriamType mt : MiriamType.values()) {
+ if (!MiriamType.UNKNOWN.equals(mt)) {
+ assertTrue("Invalid URI for MiriamType: " + mt, miriamConnector.isValid(mt.getUris().get(0)));
+ }
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefresh() throws Exception {
+ String query = MiriamConnector.VALID_URI_PREFIX + MiriamType.HGNC.getUris().get(0);
+ try {
+ String res = miriamConnector.refreshCacheQuery(query);
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefresh2() throws Exception {
+ MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
+ String query = MiriamConnector.LINK_DB_PREFIX + md.getDataType().getUris().get(0) + "\n" + md.getResource();
+ try {
+ String res = miriamConnector.refreshCacheQuery(query);
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefresh3() throws Exception {
+ try {
+ String res = miriamConnector.refreshCacheQuery("https://www.google.pl/");
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrl2() throws Exception {
+ try {
+ // exclude first cached value
+ miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
+ MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
+
+ String url = miriamConnector.getUrlString2(md);
+ assertNotNull(url);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMiriamDataToUri() throws Exception {
+ try {
+ assertNotNull(miriamConnector.miriamDataToUri(TaxonomyBackend.HUMAN_TAXONOMY));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetUrl2WithInvalidApiResponse() throws Exception {
+ WebPageDownloader downloader = miriamConnector.getWebPageDownloader();
+ GeneralCacheInterface cache = miriamConnector.getCache();
+ try {
+ // exclude first cached value
+ miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ miriamConnector.setWebPageDownloader(mockDownloader);
+
+ miriamConnector.getUrlString2(TaxonomyBackend.HUMAN_TAXONOMY);
+
+ } catch (AnnotationException e) {
+ assertTrue(e.getMessage().contains("Problem with accessing miriam REST API"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miriamConnector.setWebPageDownloader(downloader);
+ miriamConnector.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testGetUrl2WithInvalidApiResponse2() throws Exception {
+ WebPageDownloader downloader = miriamConnector.getWebPageDownloader();
+ GeneralCacheInterface cache = miriamConnector.getCache();
+ try {
+ // exclude first cached value
+ miriamConnector.setCache(new GeneralCacheWithExclusion(cache, 1));
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString())).thenReturn("");
+ miriamConnector.setWebPageDownloader(mockDownloader);
+
+ miriamConnector.getUrlString2(TaxonomyBackend.HUMAN_TAXONOMY);
+
+ } catch (AnnotationException e) {
+ assertTrue(e.getMessage().contains("Problem with parsing miriam REST API response"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miriamConnector.setWebPageDownloader(downloader);
+ miriamConnector.setCache(cache);
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = miriamConnector.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString())).thenThrow(new IOException());
+ miriamConnector.setWebPageDownloader(mockDownloader);
+ miriamConnector.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miriamConnector.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ miriamConnector.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ miriamConnector.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery3() throws Exception {
+ try {
+ miriamConnector.refreshCacheQuery(MiriamConnector.LINK_DB_PREFIX);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Miriam link query is invalid"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCheckValidyOfEmptyUri() throws Exception {
+ try {
+ // user connector without cache
+ boolean value = new MiriamConnector().isValid("");
+ assertFalse(value);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, miriamConnector.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ MiriamLink link = miriamConnector.getLink();
+ try {
+ MiriamLink mockDownloader = Mockito.mock(MiriamLink.class);
+ when(mockDownloader.getLocations(any())).thenThrow(new InvalidStateException());
+ miriamConnector.setLink(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, miriamConnector.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miriamConnector.setLink(link);
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus2() throws Exception {
+ MiriamLink link = miriamConnector.getLink();
+ try {
+ MiriamLink mockDownloader = Mockito.mock(MiriamLink.class);
+ when(mockDownloader.getLocations(any())).thenReturn(null);
+ miriamConnector.setLink(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, miriamConnector.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ miriamConnector.setLink(link);
+ }
+ }
}
diff --git a/frontend-js/.settings/org.eclipse.wst.validation.prefs b/frontend-js/.settings/org.eclipse.wst.validation.prefs
new file mode 100644
index 0000000000000000000000000000000000000000..04cad8cb752a9761c4e5167d0301d3a27674430f
--- /dev/null
+++ b/frontend-js/.settings/org.eclipse.wst.validation.prefs
@@ -0,0 +1,2 @@
+disabled=06target
+eclipse.preferences.version=1