import java.io.InputStreamReader;\r
import java.net.HttpURLConnection;\r
import java.net.MalformedURLException;\r
+import java.net.URI;\r
+import java.net.URISyntaxException;\r
import java.net.URL;\r
import java.text.ParseException;\r
import java.util.ArrayList;\r
import java.util.Map;\r
\r
import org.apache.commons.lang.StringUtils;\r
+import org.apache.http.HttpResponse;\r
import org.apache.log4j.Logger;\r
import org.springframework.stereotype.Component;\r
\r
import eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration;\r
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;\r
-import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType;\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
+import eu.etaxonomy.cdm.common.UriUtils;\r
import eu.etaxonomy.cdm.model.agent.Person;\r
import eu.etaxonomy.cdm.model.agent.Team;\r
import eu.etaxonomy.cdm.model.common.Annotation;\r
import eu.etaxonomy.cdm.model.common.ExtensionType;\r
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;\r
import eu.etaxonomy.cdm.model.common.Language;\r
+import eu.etaxonomy.cdm.model.common.OriginalSourceType;\r
import eu.etaxonomy.cdm.model.common.TimePeriod;\r
import eu.etaxonomy.cdm.model.name.BotanicalName;\r
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;\r
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;\r
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
-import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;\r
+import eu.etaxonomy.cdm.model.reference.Reference;\r
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;\r
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;\r
-\r
+import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;\r
\r
/**\r
* @author a.mueller\r
* @created Aug 16, 2010\r
* @version 1.0\r
+ *\r
+ * TODO the whole ipni service should be refactored to use UriUtils. I did this for the queryService method only because we ran into timeout\r
+ * problems in tests. UriUtils handles these problems already.\r
*\r
*/\r
@Component\r
-public class IpniService implements IIpniService{\r
+public class IpniService implements IIpniService{\r
private static final String EAST_OR_WEST = "East or west";\r
\r
private static final String NORTH_OR_SOUTH = "North or south";\r
AUTHOR,\r
NAME,\r
PUBLICATION,\r
+ ID\r
}\r
\r
public enum IpniRank{\r
\r
\r
/**\r
+ * FIXME rewrote this method to rely on {@link UriUtils}. The whole class should be adjusted to reflect this change.\r
+ * Also see comments in the class' documentation block.\r
*\r
* @param restRequest\r
* @return\r
throw new NullPointerException("Ipni service configurator should not be null");\r
}\r
try {\r
+ \r
// create the request url\r
URL newUrl = new URL(serviceUrl.getProtocol(),\r
serviceUrl.getHost(),\r
serviceUrl.getPort(),\r
serviceUrl.getPath() \r
+ "?" + request);\r
- // open a connection\r
- HttpURLConnection connection = (HttpURLConnection) newUrl.openConnection();\r
- // set the accept property to XML so we can use jdom to handle the content\r
- //connection.setRequestProperty("Accept", "text/xml");\r
- \r
- \r
- logger.info("Firing request for URL: " + newUrl);\r
- \r
- int responseCode = connection.getResponseCode();\r
- \r
+ \r
+ \r
+ URI newUri = newUrl.toURI();\r
+ \r
+ logger.info("Firing request for URI: " + newUri);\r
+ \r
+ HttpResponse response = UriUtils.getResponse(newUri, null);\r
+ \r
+ int responseCode = response.getStatusLine().getStatusCode();\r
+ \r
// get the content at the resource\r
- InputStream content = (InputStream) connection.getContent();\r
- \r
+ InputStream content = response.getEntity().getContent();\r
// build the result\r
List<? extends IdentifiableEntity> result;\r
if (serviceType.equals(ServiceType.AUTHOR)){\r
result = buildAuthorList(content, services, config);\r
}else if (serviceType.equals(ServiceType.NAME)){\r
result = buildNameList(content, services, config);\r
- }else{\r
+ }else {\r
result = buildPublicationList(content, services, config);\r
}\r
if(responseCode == HttpURLConnection.HTTP_OK){\r
}\r
\r
} catch (IOException e) {\r
- logger.error("No content for request: " + request);\r
- }\r
+ logger.error("No content for request: " + request);\r
+ } catch (URISyntaxException e) {\r
+ logger.error("Given URL could not be transformed into URI", e);\r
+ }\r
\r
// error\r
return null;\r
}\r
+ \r
+ public InputStream queryServiceForID (String request, URL serviceUrl){\r
+ \r
+ try {\r
+ \r
+ // create the request url\r
+ URL newUrl = new URL(serviceUrl.getProtocol(),\r
+ serviceUrl.getHost(),\r
+ serviceUrl.getPort(),\r
+ serviceUrl.getPath() \r
+ + "?" + request);\r
+ \r
+ \r
+ URI newUri = newUrl.toURI();\r
+ \r
+ logger.info("Firing request for URI: " + newUri);\r
+ \r
+ HttpResponse response = UriUtils.getResponse(newUri, null);\r
+ \r
+ int responseCode = response.getStatusLine().getStatusCode();\r
+ \r
+ // get the content at the resource\r
+ InputStream content = response.getEntity().getContent();\r
+ return content;\r
+ \r
+ } catch (IOException e) {\r
+ logger.error("No content for request: " + request);\r
+ } catch (URISyntaxException e) {\r
+ logger.error("Given URL could not be transformed into URI", e);\r
+ }\r
+ \r
+ return null;\r
+ \r
+ }\r
+\r
+ \r
+\r
\r
- private List<ReferenceBase> buildPublicationList( InputStream content, ICdmApplicationConfiguration services, IIpniServiceConfigurator iConfig) throws IOException {\r
+ private List<Reference> buildPublicationList( InputStream content, ICdmApplicationConfiguration services, IIpniServiceConfigurator iConfig) throws IOException {\r
IpniServicePublicationConfigurator config = (IpniServicePublicationConfigurator)iConfig;\r
\r
- List<ReferenceBase> result = new ArrayList<ReferenceBase>(); \r
+ List<Reference> result = new ArrayList<Reference>(); \r
BufferedReader reader = new BufferedReader (new InputStreamReader(content));\r
\r
String headerLine = reader.readLine();\r
\r
String line = reader.readLine();\r
while (StringUtils.isNotBlank(line)){\r
- ReferenceBase reference = getPublicationFromLine(line, parameterMap, services, config);\r
+ Reference reference = getPublicationFromLine(line, parameterMap, services, config);\r
result.add(reference);\r
line = reader.readLine();\r
}\r
}\r
\r
\r
- private ReferenceBase getPublicationFromLine(String line, Map<Integer, String> parameterMap, ICdmApplicationConfiguration appConfig, IpniServicePublicationConfigurator config) {\r
+ /**\r
+ * @param line\r
+ * @param parameterMap\r
+ * @param appConfig\r
+ * @param config\r
+ * @return\r
+ */\r
+ private Reference getPublicationFromLine(String line, Map<Integer, String> parameterMap, ICdmApplicationConfiguration appConfig, IpniServicePublicationConfigurator config) {\r
//fill value map\r
String[] splits = line.split("%");\r
\r
}\r
\r
//create reference object\r
- ReferenceBase ref = ReferenceFactory.newGeneric();\r
+ Reference ref = ReferenceFactory.newGeneric();\r
\r
//reference\r
if (config.isUseAbbreviationAsTitle() == true){\r
ref.setPlacePublished(valueMap.get(PLACE));\r
\r
String author = valueMap.get(PUBLICATION_AUTHOR_TEAM);\r
- Team team = Team.NewTitledInstance(author, author);\r
- ref.setAuthorTeam(team);\r
+ if (StringUtils.isNotBlank(author)){\r
+ Team team = Team.NewTitledInstance(author, author);\r
+ ref.setAuthorship(team);\r
+ }\r
\r
//remarks\r
String remarks = valueMap.get(REMARKS);\r
Annotation annotation = Annotation.NewInstance(remarks, AnnotationType.EDITORIAL(), Language.ENGLISH());\r
ref.addAnnotation(annotation);\r
\r
+\r
+ String tl2AuthorString = valueMap.get(TL2_AUTHOR);\r
+ if (ref.getAuthorship() == null){\r
+ Team tl2Author = Team.NewTitledInstance(tl2AuthorString, null);\r
+ ref.setAuthorship(tl2Author);\r
+ }else{\r
+ //TODO parse name, \r
+ ref.getAuthorship().setTitleCache(tl2AuthorString, true);\r
+ ref.addAnnotation(Annotation.NewInstance(tl2AuthorString, AnnotationType.EDITORIAL(), Language.ENGLISH()));\r
+ }\r
+\r
+ \r
//dates\r
- TimePeriod date = TimePeriod.parseString(valueMap.get(DATE));\r
+ TimePeriod date = TimePeriodParser.parseString(valueMap.get(DATE));\r
ref.setDatePublished(date);\r
\r
+\r
//source\r
- ReferenceBase citation = getIpniCitation(appConfig);\r
- ref.addSource(valueMap.get(ID), "Publication", citation, valueMap.get(VERSION));\r
+ Reference citation = getIpniCitation(appConfig);\r
+ ref.addSource(OriginalSourceType.Lineage, valueMap.get(ID), "Publication", citation, valueMap.get(VERSION));\r
\r
\r
+ \r
/* TODO\r
BPH number\r
Authors role\r
In publication facade\r
LC number\r
Preceded by\r
- TL2 author\r
TL2 number\r
TDWG abbreviation\r
*/\r
\r
String line = reader.readLine();\r
while (StringUtils.isNotBlank(line)){\r
+ \r
BotanicalName name = getNameFromLine(line,parameterMap, appConfig);\r
result.add(name);\r
line = reader.readLine();\r
+ \r
}\r
\r
\r
//rank\r
try {\r
String rankStr = nomalizeRank(valueMap.get(RANK));\r
- name.setRank(Rank.getRankByNameOrAbbreviation(rankStr, NomenclaturalCode.ICBN, true));\r
+ name.setRank(Rank.getRankByNameOrIdInVoc(rankStr, NomenclaturalCode.ICNAFP, true));\r
} catch (UnknownCdmTypeException e) {\r
logger.warn("Rank was unknown");\r
}\r
name.setCombinationAuthorTeam(Team.NewTitledInstance(valueMap.get(PUBLISHING_AUTHOR), valueMap.get(PUBLISHING_AUTHOR)));\r
\r
//publication\r
- ReferenceBase ref = ReferenceFactory.newGeneric();\r
- ref.setTitleCache(valueMap.get(PUBLICATION));\r
- TimePeriod datePublished = TimePeriod.parseString(valueMap.get(PUBLICATION_YEAR_FULL));\r
+ Reference<?> ref = ReferenceFactory.newGeneric();\r
+ ref.setTitleCache(valueMap.get(PUBLICATION), true);\r
+ TimePeriod datePublished = TimePeriodParser.parseString(valueMap.get(PUBLICATION_YEAR_FULL));\r
name.setNomenclaturalReference(ref);\r
\r
//name status\r
String statusString = valueMap.get(NAME_STATUS);\r
if (StringUtils.isNotBlank(statusString)){\r
try {\r
- statusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(statusString);\r
+ statusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(statusString, name);\r
NomenclaturalStatus nomStatus = NomenclaturalStatus.NewInstance(statusType);\r
name.addStatus(nomStatus);\r
} catch (UnknownCdmTypeException e) {\r
name.addReplacedSynonym(replacedSynoynm, null, null, null);\r
\r
//type information\r
- DerivedUnitFacade specimen = DerivedUnitFacade.NewInstance(DerivedUnitType.Specimen);\r
+ DerivedUnitFacade specimen = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen);\r
\r
\r
//gathering period\r
String collectionDateAsText = valueMap.get(COLLECTION_DATE_AS_TEXT);\r
- TimePeriod gatheringPeriod = TimePeriod.parseString(collectionDateAsText);\r
+ TimePeriod gatheringPeriod = TimePeriodParser.parseString(collectionDateAsText);\r
\r
try {\r
gatheringPeriod.setStartDay(getIntegerDateValueOrNull(valueMap, COLLECTION_DAY1));\r
String latMinutes = CdmUtils.Nz(valueMap.get(LATITUDE_MINUTES));\r
String latSeconds = CdmUtils.Nz(valueMap.get(LATITUDE_SECONDS));\r
String direction = CdmUtils.Nz(valueMap.get(NORTH_OR_SOUTH));\r
- String latitude = latDegrees + "°" + latMinutes + "'" + latSeconds + "\"" + direction;\r
+ String latitude = latDegrees + "°" + latMinutes + "'" + latSeconds + "\"" + direction;\r
\r
String lonDegrees = CdmUtils.Nz(valueMap.get(LATITUDE_DEGREES));\r
String lonMinutes = CdmUtils.Nz(valueMap.get(LATITUDE_MINUTES));\r
String lonSeconds = CdmUtils.Nz(valueMap.get(LATITUDE_SECONDS));\r
direction = CdmUtils.Nz(valueMap.get(EAST_OR_WEST));\r
- String longitude = lonDegrees + "°" + lonMinutes + "'" + lonSeconds + "\"" + direction;\r
+ String longitude = lonDegrees + "°" + lonMinutes + "'" + lonSeconds + "\"" + direction;\r
\r
\r
specimen.setExactLocationByParsing(longitude, latitude, null, null);\r
\r
\r
//source\r
- ReferenceBase citation = getIpniCitation(appConfig);\r
- name.addSource(valueMap.get(ID), "Name", citation, valueMap.get(VERSION));\r
+ Reference citation = getIpniCitation(appConfig);\r
+ name.addSource(OriginalSourceType.Lineage, valueMap.get(ID), "Name", citation, valueMap.get(VERSION));\r
\r
\r
// //TODO\r
\r
private Map<Integer, String> getParameterMap(String headerLine) {\r
Map<Integer, String> result = new HashMap<Integer, String>();\r
- String[] splits = headerLine.split("%");\r
- for (int i = 0; i < splits.length ; i ++){\r
- result.put(i, splits[i]);\r
+ if ( headerLine != null ){\r
+ String[] splits = headerLine.split("%");\r
+ for (int i = 0; i < splits.length ; i ++){\r
+ result.put(i, splits[i]);\r
+ }\r
}\r
return result;\r
}\r
person.setFirstname(valueMap.get(DEFAULT_AUTHOR_FORENAME));\r
person.setLastname(valueMap.get(DEFAULT_AUTHOR_SURNAME));\r
\r
- ReferenceBase citation = getIpniCitation(appConfig);\r
+ Reference<?> citation = getIpniCitation(appConfig);\r
\r
//id, version\r
- person.addSource(valueMap.get(ID), "Author", citation, valueMap.get(VERSION));\r
+ person.addSource(OriginalSourceType.Lineage, valueMap.get(ID), "Author", citation, valueMap.get(VERSION));\r
\r
//dates\r
- TimePeriod lifespan = TimePeriod.parseString(valueMap.get(DATES));\r
+ TimePeriod lifespan = TimePeriodParser.parseString(valueMap.get(DATES));\r
person.setLifespan(lifespan);\r
\r
//alternative_names\r
}\r
\r
\r
- private ReferenceBase getIpniCitation(ICdmApplicationConfiguration appConfig) {\r
- ReferenceBase ipniReference;\r
+ private Reference getIpniCitation(ICdmApplicationConfiguration appConfig) {\r
+ Reference<?> ipniReference;\r
if (appConfig != null){\r
ipniReference = appConfig.getReferenceService().find(uuidIpni);\r
if (ipniReference == null){\r
/**\r
* @return\r
*/\r
- private ReferenceBase getNewIpniReference() {\r
- ReferenceBase ipniReference;\r
+ private Reference getNewIpniReference() {\r
+ Reference<?> ipniReference;\r
ipniReference = ReferenceFactory.newDatabase();\r
ipniReference.setTitleCache("The International Plant Names Index (IPNI)");\r
return ipniReference;\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.ext.IIpniService#getPublications(java.lang.String, java.lang.String, boolean, eu.etaxonomy.cdm.api.application.ICdmApplicationConfiguration)\r
*/\r
- public List<ReferenceBase> getPublications(String title, String abbreviation, ICdmApplicationConfiguration services, IpniServicePublicationConfigurator config){\r
+ public List<Reference> getPublications(String title, String abbreviation, ICdmApplicationConfiguration services, IpniServicePublicationConfigurator config){\r
// http://www.uk.ipni.org/ipni/advPublicationSearch.do?find_title=Spe*plant*&find_abbreviation=&output_format=normal&query_type=by_query&back_page=publicationsearch\r
// http://www.uk.ipni.org/ipni/advPublicationSearch.do?find_title=*Hortus+Britannicus*&find_abbreviation=&output_format=delimited-classic&output_format=delimited\r
\r
"&find_abbreviation=" + abbreviation +\r
"&output_format=" + DelimitedFormat.CLASSIC.parameter;\r
\r
- List<ReferenceBase> result = (List)queryService(request, services, getServiceUrl(IIpniService.PUBLICATION_SERVICE_URL), config, ServiceType.PUBLICATION);\r
+ List<Reference> result = (List)queryService(request, services, getServiceUrl(IIpniService.PUBLICATION_SERVICE_URL), config, ServiceType.PUBLICATION);\r
return result;\r
}\r
\r
return serviceUrl;\r
}\r
\r
+\r
+ @Override\r
+ public InputStream getNamesById(String id) {\r
+ \r
+ \r
+ String request = "id="+id + "&output_format=lsid-metadata";\r
+ return queryServiceForID(request, getServiceUrl(IIpniService.ID_NAMESEARCH_SERVICE_URL));\r
+ \r
+ }\r
+ \r
+ @Override\r
+ public InputStream getPublicationsById(String id) {\r
+ \r
+ \r
+ String request = "id="+id ;\r
+ return queryServiceForID(request, getServiceUrl(IIpniService.ID_PUBLICATION_SERVICE_URL));\r
+ \r
+ }\r
+\r
\r
\r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff