From 62d0566867e0f5435970f5272043b44778302eb4 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 16 May 2019 17:12:36 +0200
Subject: [PATCH] Biocompendium annotator removed
---
CHANGELOG | 4 +
.../annotators/BiocompendiumAnnotator.java | 389 ------------------
.../annotators/AllAnnotatorTests.java | 1 -
.../BiocompendiumAnnotatorTest.java | 363 ----------------
.../annotators/MultipleAnnotatorsTest.java | 3 -
...V14.0.0.20190515__remove_biocompendium.sql | 2 +
.../impl/ExternalServicesService.java | 187 ---------
.../services/ServiceTestFunctions.java | 9 +-
8 files changed, 8 insertions(+), 950 deletions(-)
delete mode 100644 annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
delete mode 100644 annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
create mode 100644 persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190515__remove_biocompendium.sql
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/impl/ExternalServicesService.java
diff --git a/CHANGELOG b/CHANGELOG
index f758efea90..a70f238e18 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 1d84a47976..0000000000
--- 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 e68e714fdb..5c3ae3a0b5 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 490032e67e..0000000000
--- 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 b5be651fd1..56fbb37765 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/V14.0.0.20190515__remove_biocompendium.sql b/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190515__remove_biocompendium.sql
new file mode 100644
index 0000000000..e586291725
--- /dev/null
+++ b/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190515__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/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 06cc9a768d..0000000000
--- 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/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
index ebc58a093a..fdc74c0f97 100644
--- a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
+++ b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
@@ -28,9 +28,9 @@ 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;
@@ -49,8 +49,6 @@ 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;
@@ -96,9 +94,6 @@ public abstract class ServiceTestFunctions {
@Autowired
protected ModelAnnotator modelAnnotator;
- @Autowired
- protected BiocompendiumAnnotator restService;
-
public double EPSILON = 1e-6;
@Autowired
--
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