diff --git a/CHANGELOG b/CHANGELOG
index f758efea904e4c5b39e7d6ebad7e281f97a8ebb0..a70f238e18f6cb41f09fdcfaf90c85926d4303a3 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,7 @@
+minerva (14.0.0~alpha.0) unstable; urgency=low
+ * Feature: log4j is replaced with log4j2 logging mechanism (#291)
+ * Feature removal: BioCompendium annotator removed (#32)
+
minerva (13.1.0~alpha.0) unstable; urgency=low
* Feature: annotators are more flexible - you can define set of input and
outputs used by annotator (#617)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
deleted file mode 100644
index 1d84a47976756c32213aec9a0092e8f87e3b82e5..0000000000000000000000000000000000000000
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
+++ /dev/null
@@ -1,389 +0,0 @@
-package lcsb.mapviewer.annotation.services.annotators;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Scanner;
-
-import lcsb.mapviewer.common.XmlParser;
-import org.apache.http.HttpEntity;
-import org.apache.http.client.methods.CloseableHttpResponse;
-import org.apache.http.client.methods.HttpPost;
-import org.apache.http.entity.ContentType;
-import org.apache.http.entity.mime.MultipartEntityBuilder;
-import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.impl.client.HttpClients;
-import org.apache.logging.log4j.*;
-import org.springframework.stereotype.Service;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.annotation.services.IExternalService;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.NoteField;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.user.annotator.AnnotatorData;
-import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
-import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
-import lcsb.mapviewer.model.user.annotator.BioEntityField;
-
-/**
- * This class is responsible for connection to Vencata annotation service. The
- * service is available on
- * http://biocompendium.embl.de/map_annotator/REST/GetAnnotation/. This service
- * is RESTful service. To query for an annotation one need to send a POST
- * message with two parameters:<br>
- * Method - this parameter should be set to GetAnnotation <br>
- * File - this parameter should bo connected to a file with a request<br>
- *
- * Request file should looks like the one in testFiles/sampleRequest.xml.<br>
- * As a result the xml file is received. An example of a xml response is in
- * testFiles/sampleResponse.xml
- *
- *
- * @author Piotr Gawron
- *
- */
-@Service
-public class BiocompendiumAnnotator extends ElementAnnotator implements IExternalService {
-
- /**
- * Address of the restfull API for biocompendium.
- */
- private static final String SERVICE_ADDRESS = "http://biocompendium.embl.de/map_annotator/REST/GetAnnotation/";
-
- /**
- * Standard class logger.
- */
- private final Logger logger = LogManager.getLogger(BiocompendiumAnnotator.class);
-
- /**
- * Xml parser used for processing notes into structured data.
- */
- private RestAnnotationParser rap = new RestAnnotationParser();
-
- /**
- * Default constructor.
- */
- public BiocompendiumAnnotator() {
- super(BiocompendiumAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, true);
- }
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- result = getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, name));
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- /**
- * Returns String with annotations for species described by {@link MiriamData}
- * with {@link MiriamType#HGNC_SYMBOL} entry.
- *
- * @param md
- * description of the element by {@link MiriamData} with
- * {@link MiriamType#HGNC_SYMBOL} entry
- * @return annotation for species with given name and type from Venkata server
- * @throws IOException
- * thrown when there is a problem with connection to the server
- */
- protected String getAnnotation(MiriamData md) throws IOException {
- if (!MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- throw new InvalidArgumentException(
- "Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
- }
-
- MiriamData miriamData = new MiriamData(md);
- miriamData.setResource(miriamData.getResource().replaceAll("[\n\r]+", " "));
-
- String annotation = getCacheValue(miriamData.getResource());
- if (annotation != null) {
- return annotation;
- }
-
- CloseableHttpClient httpClient = HttpClients.createDefault();
-
- HttpPost httppost = new HttpPost(SERVICE_ADDRESS);
- MultipartEntityBuilder builder = MultipartEntityBuilder.create();
-
- // prepare a query
- String requestXml = dataToString(miriamData);
-
- // save query to a temporary file
- File tmp = File.createTempFile("annotation-plugin", "xml");
- BufferedWriter out = new BufferedWriter(new FileWriter(tmp));
- out.write(requestXml);
- out.close();
-
- builder.addBinaryBody("File", tmp, ContentType.APPLICATION_OCTET_STREAM, tmp.getName());
- HttpEntity multipart = builder.build();
- httppost.setEntity(multipart);
- CloseableHttpResponse response = httpClient.execute(httppost);
-
- HttpEntity entity2 = response.getEntity();
- if (entity2 != null) {
- InputStream instream = entity2.getContent();
- Scanner scanner = new Scanner(instream);
- try {
- Scanner s = scanner.useDelimiter("\\A");
- // get results
- String responseXml = "";
- if (s.hasNext()) {
- responseXml = s.next();
- }
- try {
- annotation = getAnnotationsFromXml(responseXml).get(miriamData.getResource());
- } catch (InvalidXmlSchemaException e) {
- throw new IOException(e);
- }
-
- } finally {
- scanner.close();
- instream.close();
- }
- }
- if (annotation != null) {
- setCacheValue(miriamData.getResource(), annotation);
- }
- return annotation;
- }
-
- /**
- * This method convert a hgnc symbol in miriam data into xml request.
- *
- * @param miriamData
- * - {@link MiriamData} with {@link MiriamType#HGNC_SYMBOL}
- * @return xml string that represent a request to RESTful service
- */
- String dataToString(MiriamData miriamData) {
- if (!MiriamType.HGNC_SYMBOL.equals(miriamData.getDataType())) {
- throw new InvalidArgumentException(
- "Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
- }
- String requestXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
- requestXml += "<request>\n";
- requestXml += " <species name=\"" + miriamData.getResource() + "\" type=\"PROTEIN\"/>\n";
- requestXml += "</request>\n";
- return requestXml;
- }
-
- /**
- * This method parse a response xml from annotation service into a map. A key in
- * the map is a name of species and value is a annotation received from the
- * service.
- *
- * @param xml
- * - xml string to be parsed
- * @return a map with information about annotations. A key in the map is a name
- * of species and value is a annotation received from the service.
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- Map<String, String> getAnnotationsFromXml(String xml) throws InvalidXmlSchemaException {
- Map<String, String> result = new HashMap<String, String>();
- // if xml is null or empty string then return empty map
- if (xml == null) {
- return result;
- }
- if (xml.isEmpty()) {
- return result;
- }
- // there is a bug in annotation service that create incorrect xml, therefore
- // we need to alter the xml
- xml = correctInvalidXml(xml);
-
- Document doc = XmlParser.getXmlDocumentFromString(xml);
- result = getAnnotationsFromXmlNode(doc);
- return result;
-
- }
-
- /**
- * Transforms xml retrieved from Venkata server into map of annotations. A key
- * in the map is a name of species and value is a annotation received from the
- * service.
- *
- * @param doc
- * - xml node
- * @return a map with information about annotations. A key in the map is a
- * name of species and value is a annotation received from the
- * service.
- */
- private Map<String, String> getAnnotationsFromXmlNode(Node doc) {
- Map<String, String> result = new HashMap<String, String>();
- NodeList root = doc.getChildNodes();
- Node responseNode = XmlParser.getNode("response", root);
- // root node is called "response"
- if (responseNode == null) {
- throw new InvalidArgumentException("Invalid xml returned by annotation service. No response root node");
- }
- NodeList list = responseNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- // all nodes in response are species
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("species")) {
- String name = XmlParser.getNodeAttr("name", node).replaceAll("%0A", "\n");
- String annotation = XmlParser.getNodeValue(node);
- if (annotation.contains("Symbol: " + name.split(" ")[0].toUpperCase())) {
- result.put(name, annotation);
- } else {
- logger.warn("Problem with annotation for: " + name);
- result.put(name, "");
- }
- } else {
- throw new InvalidArgumentException("Unknown node in xml response: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Corrects invalid xml retrieved from Venkata server.
- *
- * @param xml
- * xml to correct
- * @return corrected xml
- */
- private String correctInvalidXml(String xml) {
- int size = 0;
- int size2 = 0;
- do {
- size = xml.length();
- xml = xml.replaceAll("<species name=\"[^\"]*\" type=\"[^\"]*\">(\\s)*<species", "<species");
- xml = xml.replaceAll("<species name=\"[^\"]*\" type=\"[^\"]*\">(\\s)*</response", "</response");
- size2 = xml.length();
- } while (size != size2);
- return xml;
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- String annotations = getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
-
- status.setStatus(ExternalServiceStatusType.OK);
- if (annotations == null) {
- status.setStatus(ExternalServiceStatusType.DOWN);
- } else if (!annotations.contains("ymbol")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- @Override
- public boolean annotateElement(BioEntityProxy element, MiriamData identifier, AnnotatorData parameters)
- throws AnnotatorException {
- try {
- String annotationString = getAnnotation(identifier);
- if (annotationString != null) {
- element.addMiriamData(rap.getMiriamData(annotationString));
-
- String annotations = "";
-
- String[] string = annotationString.split("\n");
- boolean remove = false;
- for (String string2 : string) {
- if (string2.startsWith("Symbol:")) {
- remove = true;
- }
- if (remove) {
- annotations += string2 + "\n";
- }
- if (string2.startsWith("Synonyms:")) {
- remove = false;
- }
- }
- element.setDescription(rap.getDescription(annotations));
- element.setSymbol(rap.getSymbol(annotations));
- element.setSynonyms(rap.getSynonyms(annotations));
- element.setAbbreviation(rap.getAbbreviation(annotations));
- element.setFormula(rap.getFormula(annotations));
- element.setFullName(rap.getFullName(annotations));
- element.setFormerSymbols(rap.getFormerSymbols(annotations));
-
- return true;
- }
- return false;
-
- } catch (IOException e) {
- throw new AnnotatorException(e);
- }
-
- }
-
- @Override
- public String getCommonName() {
- return "Biocompendium";
- }
-
- @Override
- public String getUrl() {
- return "http://biocompendium.embl.de/";
- }
-
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(BioEntityField.NAME, MiriamType.HGNC_SYMBOL));
- }
-
- @Override
- public List<AnnotatorOutputParameter> getAvailableOuputProperties() {
- List<AnnotatorOutputParameter> result = new ArrayList<>();
- for (NoteField field : NoteField.values()) {
- if (field.getMiriamType() != null) {
- result.add(new AnnotatorOutputParameter(field.getMiriamType()));
- }
- }
- result.add(new AnnotatorOutputParameter(BioEntityField.SYMBOL));
- result.add(new AnnotatorOutputParameter(BioEntityField.DESCRIPTION));
- result.add(new AnnotatorOutputParameter(BioEntityField.PREVIOUS_SYMBOLS));
- result.add(new AnnotatorOutputParameter(BioEntityField.SYNONYMS));
-
- return result;
- }
-
- @Override
- public MiriamData getExampleValidAnnotation() {
- //we don't provide example because this annotator is unstable
- return null;
- }
-}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
index e68e714fdb6155fffa807aeeed8a1507c7d71657..5c3ae3a0b5bbe7f40b0f5f5163ec78add3c21c66 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
@@ -8,7 +8,6 @@ import org.junit.runners.Suite.SuiteClasses;
@SuiteClasses({ AnnotatorExceptionTest.class,
AnnotatorExceptionTest.class,
BrendaAnnotatorTest.class,
- BiocompendiumAnnotatorTest.class,
CazyAnnotatorTest.class,
ChebiAnnotatorTest.class,
ElementAnnotatorTest.class,
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
deleted file mode 100644
index 490032e67e147414ac2d8aa94b63423c8a7409f3..0000000000000000000000000000000000000000
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
+++ /dev/null
@@ -1,363 +0,0 @@
-package lcsb.mapviewer.annotation.services.annotators;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import static org.mockito.ArgumentMatchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.util.ArrayList;
-import java.util.Map;
-
-import org.apache.logging.log4j.*;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-import org.mockito.Mockito;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
-import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-
-public class BiocompendiumAnnotatorTest extends AnnotationTestFunctions {
- Logger logger = LogManager.getLogger(BiocompendiumAnnotatorTest.class);
-
- MiriamData camk4 = new MiriamData(MiriamType.HGNC_SYMBOL, "CAMK4");
- MiriamData slc25a27 = new MiriamData(MiriamType.HGNC_SYMBOL, "SLC25A27");
- MiriamData nsmf = new MiriamData(MiriamType.HGNC_SYMBOL, "NSMF");
- MiriamData mir449a = new MiriamData(MiriamType.HGNC_SYMBOL, "MIR449A");
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Autowired
- private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
-
- @Autowired
- private BiocompendiumAnnotator restService;
-
- @Before
- public void setUp() {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- @Ignore("Bug 32")
- public void testGetAnnotationsForSpecies() throws Exception {
- try {
- String response = restService.getAnnotation(camk4);
- assertNotNull(response);
- assertTrue(response.contains("Symbol: CAMK4"));
-
- response = restService.getAnnotation(slc25a27);
- assertNotNull(response);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() throws Exception {
- try {
- assertNotNull(restService.getCommonName());
- assertNotNull(restService.getUrl());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsForInvalidMiriam() throws Exception {
- try {
- restService.getAnnotation(new MiriamData());
- fail("Exception expected");
-
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXml() throws Exception {
- BufferedReader reader;
- try {
- reader = new BufferedReader(new FileReader("testFiles/annotation/sampleResponse.xml"));
- String line = null;
- StringBuilder stringBuilder = new StringBuilder();
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- reader.close();
-
- Map<String, String> res = restService.getAnnotationsFromXml(stringBuilder.toString());
-
- assertEquals(2, res.keySet().size());
- String response = res.get("CAMK4");
- assertNotNull(response);
- assertTrue(response.contains("Symbol: CAMK4"));
-
- assertNotNull(res.get("SLC25A27"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 10000)
- @Ignore("Bug 32")
- public void testGetAnnotationsForMiceSpecies() throws Exception {
- ArrayList<String> names = new ArrayList<String>();
-
- names.add("Fmo3");
- names.add("Nqo1");
- names.add("Abcc12");
- names.add("Mgst3");
- names.add("Txnrd1");
- names.add("Cbr3");
- names.add("Hspa1b");
- names.add("Prdx1");
- names.add("Ppard");
- names.add("Tgfb2");
- names.add("Fth1");
- names.add("Prdx6");
- names.add("Nr4a1");
- names.add("Tgfb1");
- names.add("Abcc4");
- names.add("Ager");
- names.add("Gsr");
- names.add("Sod3");
- names.add("Maff");
- names.add("Eif2ak3");
- names.add("Tgfa");
- names.add("Hbegf");
- names.add("Mafg");
- names.add("Adh7");
- names.add("Slc7a11");
- names.add("Epha3");
- names.add("Blvrb");
- // problematic one
- // names.add("Me1");
- names.add("Csnk2a2");
- names.add("Gpx3");
- names.add("Mapk8");
- names.add("Gclm");
- names.add("Epha2");
- names.add("Bdnf");
- // problematic one
- // names.add("ACC2");
- names.add("Ptgr1");
- names.add("Pdgfb");
- names.add("Mapk7");
- names.add("Cbr1");
- names.add("Hsp90aa1");
- names.add("Pgd");
- names.add("Sqstm1");
- names.add("Aldh9a1");
- names.add("Txn");
- names.add("Txnrd3");
- names.add("Srxn1");
- names.add("Gpx2");
- names.add("Npas4");
- names.add("Mapk1");
- names.add("Nrg1");
- names.add("Cbr");
- names.add("Hspa1a");
- names.add("Mgst2");
- names.add("Tgfbr2");
- names.add("Ephx1");
- names.add("Dnajb1");
- names.add("Abcc2");
- names.add("Gclc");
- names.add("Abcc5");
- names.add("Ggt1");
- names.add("Ftl");
- names.add("Egr1");
- names.add("Fgf13");
- // problematic one
- // names.add("Hgf");
- // problematic one
- // names.add("UbcH7");
- names.add("Abcc3");
- names.add("Nfe2l2");
- // problematic one
- // names.add("Hsp70");
- names.add("Hsp90ab1");
-
- try {
- for (int i = 0; i < names.size(); i++) {
- String geneName = names.get(i);
- String annotation = restService.getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, geneName));
- assertNotNull("Problem with annotation of mouse gene: " + geneName, annotation);
- assertTrue("Problem with annotation of mouse gene: " + geneName, !annotation.trim().equals(""));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- @Ignore("Bug 451")
- public void testGetAnnotationsForNSMF() throws Exception {
- try {
- String response = restService.getAnnotation(nsmf);
- assertNotNull(response);
- assertFalse(response.trim().equals(""));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- @Ignore("Bug 451")
- public void testGetAnnotationsForMIR449A() throws Exception {
- try {
- String response = restService.getAnnotation(mir449a);
- assertNotNull(response);
- assertFalse(response.trim().equals(""));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testCachableInterfaceInvalidate() throws Exception {
- String query = "GLUD1";
- try {
- String newRes = "hello";
-
- cache.setCachedQuery(query, restService.getCacheType(), newRes);
- String res = cache.getStringByQuery(query, restService.getCacheType());
- assertEquals(newRes, res);
- cache.invalidateByQuery(query, restService.getCacheType());
-
- permanentDatabaseLevelCache.waitToFinishTasks();
-
- res = cache.getStringByQuery(query, restService.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNameWithNewLine() throws Exception {
- try {
- String response = restService.getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, "some\nname"));
- assertNotNull(response);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidValue() throws Exception {
- try {
- restService.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 testRefreshValueWhenProblemWithSource() throws Exception {
- try {
- BiocompendiumAnnotator annotatorUnderTest = Mockito.mock(BiocompendiumAnnotator.class,
- Mockito.CALLS_REAL_METHODS);
- when(annotatorUnderTest.getAnnotationsFromXml(anyString())).thenThrow(InvalidXmlSchemaException.class);
- annotatorUnderTest.refreshCacheQuery(camk4.getResource());
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetInvalidAnnotations() throws Exception {
- try {
- restService.getAnnotation(new MiriamData(MiriamType.WIKIPEDIA, "world"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testInvalidDataToStrubg() throws Exception {
- try {
- restService.dataToString(new MiriamData(MiriamType.WIKIPEDIA, "world"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsFromInvaldXml() throws Exception {
- try {
- Map<String, String> map = restService.getAnnotationsFromXml("");
- assertEquals(0, map.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAnnotationsFromInvaldXml2() throws Exception {
- try {
- Map<String, String> map = restService.getAnnotationsFromXml(null);
- assertEquals(0, map.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/MultipleAnnotatorsTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/MultipleAnnotatorsTest.java
index b5be651fd106a6efc1ccf907f77f5e2917bf5d54..56fbb37765ae5c052c3cf1c6903a1eabf6c3bb3e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/MultipleAnnotatorsTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/MultipleAnnotatorsTest.java
@@ -24,9 +24,6 @@ public class MultipleAnnotatorsTest extends AnnotationTestFunctions {
@Autowired
HgncAnnotator hgncAnnotator;
- @Autowired
- BiocompendiumAnnotator biocompendiumAnnotator;
-
@Before
public void setUp() throws Exception {
}
diff --git a/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190516__remove_biocompendium.sql b/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190516__remove_biocompendium.sql
new file mode 100644
index 0000000000000000000000000000000000000000..e5862917259cabf98b9344fbe21ab7b6e4670ea0
--- /dev/null
+++ b/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190516__remove_biocompendium.sql
@@ -0,0 +1,2 @@
+delete from cache_query_table where type in (select id from cache_type_table where class_name ='lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator');
+delete from cache_type_table where class_name ='lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator';
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDaoTest.java
index 87761eb39105d42f3a3e37f26b18cd679fa2019a..889686fc69e068dd0a57ce0ad98309e87f6028d3 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/cache/CacheTypeDaoTest.java
@@ -43,18 +43,6 @@ public class CacheTypeDaoTest extends PersistTestFunctions {
}
}
- @Test
- public void testBiocompendiumCacheData() throws Exception {
- try {
- CacheType cacheType = cacheTypeDao.getByClassName("lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator");
- assertNotNull(cacheType);
- assertEquals(1,cacheType.getId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testChemblCacheData() throws Exception {
try {
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ExternalServicesService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ExternalServicesService.java
deleted file mode 100644
index 06cc9a768d1af2f4b37df8cc75d489211dd0c54a..0000000000000000000000000000000000000000
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ExternalServicesService.java
+++ /dev/null
@@ -1,187 +0,0 @@
-package lcsb.mapviewer.services.impl;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import lcsb.mapviewer.annotation.services.ChEMBLParser;
-import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.IExternalService;
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.ChemicalParser;
-import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.EnsemblAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.EntrezAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.GoAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
-import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.services.interfaces.IExternalServicesService;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Service;
-
-/**
- * Implementation of the service that retrieves information about services that
- * access external resources (like chebi, chembl, etc.).
- *
- * @author Piotr Gawron
- *
- */
-@Service
-public class ExternalServicesService implements IExternalServicesService {
-
- /**
- * List of services that should be checked for status.
- */
- private List<IExternalService> services = new ArrayList<IExternalService>();
-
- /**
- * Service accessing <a href="http://www.drugbank.ca/">drugbank</a>.
- */
- private DrugbankHTMLParser drugbankHTMLParser;
-
-
- /**
- * Service accessing <a href="http://ctdbase.org/">ctd</a>.
- */
- private ChemicalParser ctdParser;
-
- /**
- * Service accessing <a
- * href="https://www.ebi.ac.uk/chembl/compound/inspect/">chembl</a>.
- */
- private ChEMBLParser chEMBLParser;
-
- /**
- * Service accessing <a
- * href="http://www.ebi.ac.uk/chebi/webServices.do">chebi</a>.
- */
- private ChebiAnnotator chebiBackend;
-
- /**
- * Service accessing <a
- * href="http://europepmc.org/RestfulWebService">pubmed</a>.
- */
- private PubmedParser pubmedParser;
-
- /**
- * Service accessing <a href= "http://www.ebi.ac.uk/miriam/main/" >miriam
- * registry</a>.
- */
- private MiriamConnector miriamConnector;
-
- /**
- * Service accessing <a href= "http://biocompendium.embl.de/" >internal
- * annotating service</a>.
- */
- private BiocompendiumAnnotator annotationRestService;
-
- /**
- * Service accessing <a href= "http://www.uniprot.org/" >uniprot</a>.
- */
- private UniprotAnnotator uniprotAnnotator;
-
- /**
- * Service accessing Ensembl database.
- */
- private EnsemblAnnotator ensemblAnnotator;
-
- /**
- * Service accessing Entrez database.
- */
- private EntrezAnnotator entrezAnnotator;
-
- /**
- * Service accessing <a href= "http://www.ebi.ac.uk/QuickGO/" >Gene
- * Ontology</a>.
- */
- private GoAnnotator goBackend;
-
- /**
- * Service accessing HGNC restfull API .
- */
- private HgncAnnotator hgncBackend;
-
- /**
- * Utils that help to manage the sessions in custom multithreaded
- * implementation.
- */
- private DbUtils dbUtils;
-
- @Autowired
- public ExternalServicesService(DrugbankHTMLParser drugbankHTMLParser,
- ChemicalParser ctdParser,
- ChEMBLParser chEMBLParser,
- ChebiAnnotator chebiBackend,
- PubmedParser pubmedParser,
- MiriamConnector miriamConnector,
- BiocompendiumAnnotator annotationRestService,
- UniprotAnnotator uniprotAnnotator,
- EnsemblAnnotator ensemblAnnotator,
- EntrezAnnotator entrezAnnotator,
- GoAnnotator goBackend,
- HgncAnnotator hgncBackend,
- DbUtils dbUtils) {
- this.drugbankHTMLParser = drugbankHTMLParser;
- this.ctdParser = ctdParser;
- this.chEMBLParser = chEMBLParser;
- this.chebiBackend = chebiBackend;
- this.pubmedParser = pubmedParser;
- this.miriamConnector = miriamConnector;
- this.annotationRestService = annotationRestService;
- this.uniprotAnnotator = uniprotAnnotator;
- this.ensemblAnnotator = ensemblAnnotator;
- this.entrezAnnotator = entrezAnnotator;
- this.goBackend = goBackend;
- this.hgncBackend = hgncBackend;
- this.dbUtils = dbUtils;
- }
-
- @Override
- public List<ExternalServiceStatus> getExternalServiceStatuses() {
- List<ExternalServiceStatus> result = new ArrayList<ExternalServiceStatus>();
- for (IExternalService service : services) {
- boolean sessionOpened = false;
- if (!dbUtils.isCustomSessionForCurrentThread()) {
- sessionOpened = true;
- dbUtils.createSessionForCurrentThread();
- }
- result.add(service.getServiceStatus());
- if (sessionOpened) {
- dbUtils.closeSessionForCurrentThread();
- }
- }
- return result;
- }
-
- @Override
- public void registerService(IExternalService service) {
- services.add(service);
-
- }
-
- @Override
- public void registerDefaultServices() {
- registerService(drugbankHTMLParser);
- registerService(chEMBLParser);
- registerService(chebiBackend);
- registerService(pubmedParser);
- registerService(miriamConnector);
- registerService(annotationRestService);
- registerService(ensemblAnnotator);
- registerService(entrezAnnotator);
- registerService(goBackend);
- registerService(ctdParser);
- registerService(hgncBackend);
- registerService(uniprotAnnotator);
- }
-
- @Override
- public void clearServices() {
- services.clear();
-
- }
-}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IExternalServicesService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IExternalServicesService.java
deleted file mode 100644
index 241fdc2422aadcf35674235c59bb7584ace569c8..0000000000000000000000000000000000000000
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IExternalServicesService.java
+++ /dev/null
@@ -1,42 +0,0 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.util.List;
-
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.IExternalService;
-
-/**
- * Service that retrieves information about services that access external
- * resources (like chebi, chembl, etc.).
- *
- * @author Piotr Gawron
- *
- */
-public interface IExternalServicesService {
-
- /**
- * Returns status information about all services.
- *
- * @return status information about all services
- */
- List<ExternalServiceStatus> getExternalServiceStatuses();
-
- /**
- * Registers service that access external resource.
- *
- * @param service
- * service that access external resource
- */
- void registerService(IExternalService service);
-
- /**
- * Registers default list of services.
- */
- void registerDefaultServices();
-
- /**
- * Clears list of known services.
- */
- void clearServices();
-
-}
diff --git a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
index ebc58a093a5a415e6c5082c8002581354261bc07..60fddfd73959e50564066e2707383f0e26f535c7 100644
--- a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
+++ b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
@@ -1,36 +1,14 @@
package lcsb.mapviewer.services;
-import java.io.BufferedReader;
import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileReader;
import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.io.UnsupportedEncodingException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.core.LogEvent;
-
import org.junit.After;
import org.junit.Before;
import org.junit.runner.RunWith;
@@ -40,38 +18,22 @@ import org.springframework.test.annotation.Rollback;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import org.springframework.transaction.annotation.Transactional;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-import lcsb.mapviewer.annotation.services.ChEMBLParser;
import lcsb.mapviewer.annotation.services.DrugbankHTMLParser;
import lcsb.mapviewer.annotation.services.ModelAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
-
import lcsb.mapviewer.common.MinervaLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.DbUtils;
-import lcsb.mapviewer.persist.dao.ConfigurationDao;
import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
-import lcsb.mapviewer.persist.dao.graphics.PolylineDao;
import lcsb.mapviewer.persist.dao.map.CommentDao;
import lcsb.mapviewer.persist.dao.map.ModelDao;
-import lcsb.mapviewer.persist.dao.map.ReactionDao;
-import lcsb.mapviewer.persist.dao.map.species.ElementDao;
import lcsb.mapviewer.persist.dao.map.statistics.SearchHistoryDao;
-import lcsb.mapviewer.persist.dao.user.PrivilegeDao;
import lcsb.mapviewer.persist.dao.user.UserDao;
import lcsb.mapviewer.services.interfaces.ICommentService;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
-import lcsb.mapviewer.services.interfaces.IExternalServicesService;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IProjectService;
@@ -87,18 +49,12 @@ import lcsb.mapviewer.services.search.drug.IDrugService;
public abstract class ServiceTestFunctions {
private Logger logger = LogManager.getLogger(ServiceTestFunctions.class);
- @Autowired
- protected ChEMBLParser chemblParser;
-
@Autowired
protected DrugbankHTMLParser drugBankHTMLParser;
@Autowired
protected ModelAnnotator modelAnnotator;
- @Autowired
- protected BiocompendiumAnnotator restService;
-
public double EPSILON = 1e-6;
@Autowired
@@ -107,9 +63,6 @@ public abstract class ServiceTestFunctions {
@Autowired
protected IModelService modelService;
- @Autowired
- protected IExternalServicesService externalServicesService;
-
@Autowired
protected ILayoutService layoutService;
@@ -122,9 +75,6 @@ public abstract class ServiceTestFunctions {
@Autowired
protected IUserService userService;
- @Autowired
- protected ConfigurationDao configurationDao;
-
@Autowired
protected ISearchService searchService;
@@ -140,12 +90,6 @@ public abstract class ServiceTestFunctions {
@Autowired
protected ProjectDao projectDao;
- @Autowired
- protected CacheQueryDao cacheQueryDao;
-
- @Autowired
- protected PolylineDao polylineDao;
-
@Autowired
protected ModelDao modelDao;
@@ -155,24 +99,12 @@ public abstract class ServiceTestFunctions {
@Autowired
protected UserDao userDao;
- @Autowired
- protected PrivilegeDao privilegeDao;
-
@Autowired
protected CommentDao commentDao;
@Autowired
protected DbUtils dbUtils;
- @Autowired
- protected ReactionDao reactionDao;
-
- @Autowired
- protected ElementDao aliasDao;
-
- private User user;
- protected User user2 = null;
-
private MinervaLoggerAppender appender;
@Before
@@ -199,78 +131,12 @@ public abstract class ServiceTestFunctions {
return appender.getInfos();
}
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- /**
- * This method remove model with all connections from db (used only when the db
- * must be handled manually)
- *
- * @param id
- */
- protected void removeModelById(int id) {
- modelDao.delete(modelDao.getById(id));
+ protected User createUser() {
+ return createUser("john.doe");
}
- protected User createUser() {
- user = userDao.getUserByLogin("john.doe");
+ protected User createUser(String login) {
+ User user = userDao.getUserByLogin(login);
if (user != null) {
logger.debug("remove user");
userDao.delete(user);
@@ -280,26 +146,12 @@ public abstract class ServiceTestFunctions {
user.setName("John");
user.setSurname("Doe");
user.setEmail("john.doe@uni.lu");
- user.setLogin("john.doe");
+ user.setLogin(login);
user.setCryptedPassword(passwordEncoder.encode("passwd"));
userDao.add(user);
return user;
}
- protected void createUser2() {
- user2 = userDao.getUserByLogin("john.doe.bis");
- if (user2 != null) {
- userDao.delete(user2);
- }
- user2 = new User();
- user2.setName("John");
- user2.setSurname("Doe BIS");
- user2.setEmail("john.doe@uni.lux");
- user2.setLogin("john.doe.bis");
- user2.setCryptedPassword(passwordEncoder.encode("passwd"));
- userDao.add(user2);
- }
-
private static Map<String, Model> models = new HashMap<String, Model>();
protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
@@ -318,80 +170,6 @@ public abstract class ServiceTestFunctions {
return result;
}
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public PrivilegeDao getPrivilegeDao() {
- return privilegeDao;
- }
-
- public void setPrivilegeDao(PrivilegeDao privilegeDao) {
- this.privilegeDao = privilegeDao;
- }
-
public File createTempDirectory() throws IOException {
final File temp;
@@ -407,18 +185,4 @@ public abstract class ServiceTestFunctions {
return (temp);
}
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java b/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
index cc2d3256ee8978e95d67e8393838719d1f42c26e..8f0f6c8e27e20a9e51e87b40406efc898142a125 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/AllImplServiceTests.java
@@ -7,7 +7,6 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ CommentServiceTest.class,
ConfigurationServiceTest.class,
- ExternalServicesServiceTest.class,
LayoutServiceTest.class,
LdapServiceTest.class,
Md5PasswordEncoderTest.class,
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ExternalServicesServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ExternalServicesServiceTest.java
deleted file mode 100644
index 8b1db0dd70a9f843ffce67bf3e115f37b694ddb8..0000000000000000000000000000000000000000
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ExternalServicesServiceTest.java
+++ /dev/null
@@ -1,67 +0,0 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
-import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-
-public class ExternalServicesServiceTest extends ServiceTestFunctions {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test(timeout = 60000)
- @Ignore("Bug 451")
- public void testDefaultServices() throws Exception {
- try {
- externalServicesService.clearServices();
- externalServicesService.registerDefaultServices();
- List<ExternalServiceStatus> statuses = externalServicesService.getExternalServiceStatuses();
- assertNotNull(statuses);
- assertTrue(statuses.size() > 0);
-
- for (ExternalServiceStatus externalServiceStatus : statuses) {
- assertEquals(externalServiceStatus.getName() + " is down", ExternalServiceStatusType.OK, externalServiceStatus.getStatus());
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRegister() throws Exception {
- try {
- externalServicesService.clearServices();
- externalServicesService.registerService(new OkServiceMock());
- externalServicesService.registerService(new FailServiceMock());
-
- List<ExternalServiceStatus> statuses = externalServicesService.getExternalServiceStatuses();
- assertNotNull(statuses);
- assertEquals(2, statuses.size());
-
- assertEquals(ExternalServiceStatusType.OK, statuses.get(0).getStatus());
- assertEquals(ExternalServiceStatusType.DOWN, statuses.get(1).getStatus());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
index 2f9b320135d077d196f1419e57dac0f92f2a411c..728ba963c24b18d274a2f4f97f965988d1a8d772 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
@@ -71,7 +71,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
String adminToken;
String token;
- User user;
+ private User user, user2;
ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
@@ -107,7 +107,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
projectService.addProject(project);
user = createUser();
- createUser2();
+ user2 = createUser("john.doe.bis");
originalSender = layoutService.getEmailSender();
layoutService.setEmailSender(Mockito.mock(EmailSender.class));