litvinovg/vivo
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Do not offer UMLS vocabulary in interface if umls.properties is absent. (#241)

Browse source 
* Replace hardcoded en locale with current locale in lang attributes

* Do not offer UMLS vocabulary service in interface if umls.properties is absent
This commit is contained in:
Brian Lowe 2021-06-09 17:02:46 +03:00 • committed by GitHub
parent e3027841aa
commit 603e7f6bc8
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
2 changed files with 21 additions and 7 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

22
api/src/main/java/edu/cornell/mannlib/semservices/service/impl/UMLSService.java
View file

@ -4,12 +4,18 @@ package edu.cornell.mannlib.semservices.service.impl;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.net.URL;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Properties; import java.util.Properties;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import org.apache.http.HttpVersion;
import org.apache.http.client.fluent.Form;
import org.apache.http.client.fluent.Request;
import org.apache.http.client.utils.URIBuilder;
import org.springframework.util.StringUtils;
import com.fasterxml.jackson.databind.node.ArrayNode; import com.fasterxml.jackson.databind.node.ArrayNode;
import com.fasterxml.jackson.databind.node.ObjectNode; import com.fasterxml.jackson.databind.node.ObjectNode;
@ -18,11 +24,6 @@ import edu.cornell.mannlib.semservices.bo.Concept;
import edu.cornell.mannlib.semservices.exceptions.ConceptsNotFoundException; import edu.cornell.mannlib.semservices.exceptions.ConceptsNotFoundException;
import edu.cornell.mannlib.semservices.service.ExternalConceptService; import edu.cornell.mannlib.semservices.service.ExternalConceptService;
import edu.cornell.mannlib.vitro.webapp.utils.json.JacksonUtils; import edu.cornell.mannlib.vitro.webapp.utils.json.JacksonUtils;
import org.apache.http.HttpVersion;
import org.apache.http.client.fluent.Form;
import org.apache.http.client.fluent.Request;
import org.apache.http.client.utils.URIBuilder;
import org.springframework.util.StringUtils;
/** /**
* @author jaf30 * @author jaf30
@ -54,11 +55,13 @@ public class UMLSService implements ExternalConceptService {
private static String UMLS_AUTH_USER_URL = "https://utslogin.nlm.nih.gov/cas/v1/tickets"; private static String UMLS_AUTH_USER_URL = "https://utslogin.nlm.nih.gov/cas/v1/tickets";
private static String UMLS_AUTH_KEY_URL = "https://utslogin.nlm.nih.gov/cas/v1/api-key"; private static String UMLS_AUTH_KEY_URL = "https://utslogin.nlm.nih.gov/cas/v1/api-key";
private static String UTS_SERVICE_URL = "http://umlsks.nlm.nih.gov"; private static String UTS_SERVICE_URL = "http://umlsks.nlm.nih.gov";
private static final String UMLS_PROPERTIES = "/umls.properties";
private static final Log log = LogFactory.getLog(UMLSService.class);
{ {
if (username == null || apikey == null) { if (username == null || apikey == null) {
final Properties properties = new Properties(); final Properties properties = new Properties();
try (InputStream stream = getClass().getResourceAsStream("/umls.properties")) { try (InputStream stream = getClass().getResourceAsStream(UMLS_PROPERTIES)) {
properties.load(stream); properties.load(stream);
username = properties.getProperty("username"); username = properties.getProperty("username");
password = properties.getProperty("password"); password = properties.getProperty("password");
@ -73,12 +76,19 @@ public class UMLSService implements ExternalConceptService {
} }
} }
} catch (Exception e) { } catch (Exception e) {
log.error(e, e);
} }
} catch (IOException e) { } catch (IOException e) {
log.error(e, e);
} }
} }
} }
public static boolean configurationFileExists() {
URL config = UMLSService.class.getResource(UMLS_PROPERTIES);
return (config != null);
}
public boolean isConfigured() { public boolean isConfigured() {
return !(StringUtils.isEmpty(username) && StringUtils.isEmpty(apikey)); return !(StringUtils.isEmpty(username) && StringUtils.isEmpty(apikey));
} }

4
api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/ConceptSearchService/ConceptSearchServiceUtils.java
View file

@ -12,6 +12,7 @@ import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.semservices.bo.Concept; import edu.cornell.mannlib.semservices.bo.Concept;
import edu.cornell.mannlib.semservices.service.ExternalConceptService; import edu.cornell.mannlib.semservices.service.ExternalConceptService;
import edu.cornell.mannlib.semservices.service.impl.UMLSService;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest; import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
/** /**
* Utilities for search * Utilities for search
@ -38,7 +39,9 @@ public class ConceptSearchServiceUtils {
//URL to label //URL to label
public static HashMap<String, VocabSourceDescription> getVocabSources() { public static HashMap<String, VocabSourceDescription> getVocabSources() {
HashMap<String, VocabSourceDescription> map = new HashMap<String, VocabSourceDescription>(); HashMap<String, VocabSourceDescription> map = new HashMap<String, VocabSourceDescription>();
if(UMLSService.configurationFileExists()) {
map.put(UMLSVocabSource, new VocabSourceDescription("UMLS", UMLSVocabSource, "http://www.nlm.nih.gov/research/umls/", "Unified Medical Language System")); map.put(UMLSVocabSource, new VocabSourceDescription("UMLS", UMLSVocabSource, "http://www.nlm.nih.gov/research/umls/", "Unified Medical Language System"));
}
//Commenting out agrovoc for now until implementation is updated //Commenting out agrovoc for now until implementation is updated
map.put(AgrovocVocabSource, new VocabSourceDescription("AGROVOC", AgrovocVocabSource, "http://www.fao.org/agrovoc/", "Agricultural Vocabulary")); map.put(AgrovocVocabSource, new VocabSourceDescription("AGROVOC", AgrovocVocabSource, "http://www.fao.org/agrovoc/", "Agricultural Vocabulary"));
map.put(GemetVocabSource, new VocabSourceDescription("GEMET", GemetVocabSource, "http://www.eionet.europa.eu/gemet", "GEneral Multilingual Environmental Thesaurus")); map.put(GemetVocabSource, new VocabSourceDescription("GEMET", GemetVocabSource, "http://www.eionet.europa.eu/gemet", "GEneral Multilingual Environmental Thesaurus"));
@ -53,6 +56,7 @@ public class ConceptSearchServiceUtils {
//Get the hashmap mapping service name to Service class //Get the hashmap mapping service name to Service class
private static HashMap<String, String> getMapping() { private static HashMap<String, String> getMapping() {
HashMap<String, String> map = new HashMap<String, String>(); HashMap<String, String> map = new HashMap<String, String>();
map.put(UMLSVocabSource, "edu.cornell.mannlib.semservices.service.impl.UMLSService"); map.put(UMLSVocabSource, "edu.cornell.mannlib.semservices.service.impl.UMLSService");
map.put(AgrovocVocabSource, "edu.cornell.mannlib.semservices.service.impl.AgrovocService"); map.put(AgrovocVocabSource, "edu.cornell.mannlib.semservices.service.impl.AgrovocService");
map.put(GemetVocabSource, "edu.cornell.mannlib.semservices.service.impl.GemetService"); map.put(GemetVocabSource, "edu.cornell.mannlib.semservices.service.impl.GemetService");