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Revision b20c081f

Added by Andreas Kohlbecker over 8 years ago

adapting to changes in the project name and structure in drf-workflow which is now utis-core

View differences:

pom.xml
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  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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  <modelVersion>4.0.0</modelVersion>
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  <groupId>eu.etaxonomy.utis</groupId>
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  <artifactId>eubon-utis</artifactId>
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  <artifactId>utis-webapp</artifactId>
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  <packaging>war</packaging>
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  <version>1.0-SNAPSHOT</version>


  		




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  <name>eubon-utis Maven Webapp</name>


  		




  
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  <name>UTIS web application</name>


  		




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  <url>http://maven.apache.org</url>


  		




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  <properties>


  		




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    <spring.version>3.2.7.RELEASE</spring.version>


  		




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    <jackson.version>2.2.3</jackson.version>


  		




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    <java.codelevel>1.6</java.codelevel>


  		




  
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    <utis-core.version>1.1.0-SNAPSHOT</utis-core.version>


  		




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  </properties>


  		




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  <repositories>


  		




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      <scope>test</scope>


  		




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    </dependency>


  		




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    <dependency>


  		




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      <groupId>biovel.drf</groupId>


  		




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      <artifactId>drf-workflow</artifactId>


  		




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      <version>1.0.6-SNAPSHOT</version>


  		




  
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      <groupId>org.cybertaxonomy</groupId>


  		




  
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      <artifactId>utis-core</artifactId>


  		




  
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      <version>${utis-core.version}</version>


  		




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    </dependency>


  		




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    <dependency>


  		




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      <groupId>com.mangofactory</groupId>


  		












  

    
      src/main/java/org/bgbm/utis/configuration/SpringMVCConfig.java
    
  





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import org.apache.logging.log4j.LogManager;


  		




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import org.apache.logging.log4j.Logger;


  		




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import org.bgbm.biovel.drf.tnr.msg.Classification;


  		




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import org.bgbm.biovel.drf.tnr.msg.TnrMsg;


  		




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import org.bgbm.utis.jackson.ClassificationMixIn;


  		




  
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import org.cybertaxonomy.utis.tnr.msg.Classification;


  		




  
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import org.cybertaxonomy.utis.tnr.msg.TnrMsg;


  		




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import org.springframework.beans.factory.annotation.Autowired;


  		




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import org.springframework.context.annotation.Bean;


  		




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import org.springframework.context.annotation.ComponentScan;


  		












  

    
      src/main/java/org/bgbm/utis/controller/ChecklistClientRunner.java
    
  





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package org.bgbm.utis.controller;


  		




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import org.bgbm.biovel.drf.checklist.BaseChecklistClient;


  		




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import org.bgbm.biovel.drf.checklist.DRFChecklistException;


  		




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import org.bgbm.biovel.drf.checklist.SearchMode;


  		




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import org.bgbm.biovel.drf.checklist.UnsupportedIdentifierException;


  		




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import org.bgbm.biovel.drf.tnr.msg.TnrMsg;


  		




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import org.bgbm.biovel.drf.tnr.msg.Response;


  		




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import org.bgbm.biovel.drf.utils.TnrMsgUtils;


  		




  
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import org.cybertaxonomy.utis.checklist.BaseChecklistClient;


  		




  
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import org.cybertaxonomy.utis.checklist.DRFChecklistException;


  		




  
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import org.cybertaxonomy.utis.checklist.UnsupportedIdentifierException;


  		




  
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import org.cybertaxonomy.utis.tnr.msg.TnrMsg;


  		




  
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import org.cybertaxonomy.utis.utils.TnrMsgUtils;


  		




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import org.slf4j.Logger;


  		




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import org.slf4j.LoggerFactory;


  		




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    protected Logger logger = LoggerFactory.getLogger(ChecklistClientRunner.class);


  		




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    private BaseChecklistClient client;


  		




  
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    private final BaseChecklistClient client;


  		




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    private TnrMsg tnrMsg;


  		




  
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    private final TnrMsg tnrMsg;


  		




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    private long duration;


  		




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      src/main/java/org/bgbm/utis/controller/UtisController.java
    
  





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import javax.servlet.http.HttpServletRequest;


  		




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import javax.servlet.http.HttpServletResponse;


  		




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import org.bgbm.biovel.drf.checklist.BaseChecklistClient;


  		




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import org.bgbm.biovel.drf.checklist.BgbmEditClient;


  		




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import org.bgbm.biovel.drf.checklist.DRFChecklistException;


  		




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import org.bgbm.biovel.drf.checklist.PESIClient;


  		




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import org.bgbm.biovel.drf.checklist.SearchMode;


  		




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import org.bgbm.biovel.drf.checklist.WoRMSClient;


  		




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import org.bgbm.biovel.drf.rest.ServiceProviderInfo;


  		




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import org.bgbm.biovel.drf.rest.TaxoRESTClient;


  		




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import org.bgbm.biovel.drf.tnr.msg.Query;


  		




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import org.bgbm.biovel.drf.tnr.msg.Query.ClientStatus;


  		




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import org.bgbm.biovel.drf.tnr.msg.TnrMsg;


  		




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import org.bgbm.biovel.drf.tnr.msg.Response;


  		




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import org.bgbm.biovel.drf.utils.TnrMsgUtils;


  		




  
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import org.cybertaxonomy.utis.checklist.BaseChecklistClient;


  		




  
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import org.cybertaxonomy.utis.checklist.BgbmEditClient;


  		




  
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import org.cybertaxonomy.utis.checklist.DRFChecklistException;


  		




  
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import org.cybertaxonomy.utis.checklist.PESIClient;


  		




  
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import org.cybertaxonomy.utis.checklist.SearchMode;


  		




  
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import org.cybertaxonomy.utis.checklist.WoRMSClient;


  		




  
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import org.cybertaxonomy.utis.client.AbstractClient;


  		




  
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import org.cybertaxonomy.utis.client.ServiceProviderInfo;


  		




  
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import org.cybertaxonomy.utis.tnr.msg.Query;


  		




  
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import org.cybertaxonomy.utis.tnr.msg.Query.ClientStatus;


  		




  
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import org.cybertaxonomy.utis.tnr.msg.Response;


  		




  
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import org.cybertaxonomy.utis.tnr.msg.TnrMsg;


  		




  
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import org.cybertaxonomy.utis.utils.TnrMsgUtils;


  		




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import org.slf4j.Logger;


  		




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import org.slf4j.LoggerFactory;


  		




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import org.springframework.beans.factory.config.BeanDefinition;


  		




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    }


  		




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    public static <T extends TaxoRESTClient> Set<Class<T>> subclassesFor(Class<T> clazz) throws ClassNotFoundException{


  		




  
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    public static <T extends AbstractClient> Set<Class<T>> subclassesFor(Class<T> clazz) throws ClassNotFoundException{


  		




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        Set<Class<T>> subClasses = new HashSet<Class<T>>();


  		




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        ClassPathScanningCandidateComponentProvider provider = new ClassPathScanningCandidateComponentProvider(true);


  		




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        provider.addIncludeFilter(new AssignableTypeFilter(clazz));


  		




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        // scan only in org.bgbm.biovel.drf


  		




  
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        // scan only in org.cybertaxonomy.utis


  		




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        Set<BeanDefinition> components = provider.findCandidateComponents("org/bgbm/biovel/drf");


  		




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        for (BeanDefinition component : components)


  		




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        {


  		












  

    
      src/main/java/org/bgbm/utis/jackson/ClassificationMixIn.java
    
  





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 */


  		




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package org.bgbm.utis.jackson;


  		




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import org.bgbm.biovel.drf.tnr.msg.Classification;


  		




  
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import org.cybertaxonomy.utis.tnr.msg.Classification;


  		




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import com.fasterxml.jackson.annotation.JsonProperty;


  		




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      src/main/webapp/index.html
    
  





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of the various checklists.


  		




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</p>


  		




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<p>


  		




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The current implementation of the UTIS is still a prototype, which means that the API and data model may be


  		




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changed until final release. It connects the web services of the


  		




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<a href="http://www.eu-nomen.eu">Pan-European Species directories Infrastructure, PESI</a>  CoL,


  		




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the <a href="http://www.catalogueoflife.org/">Catalogue of Life</a> and of the


  		




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<a href="http://www.marinespecies.org/">World Register of Marine Species (WoRMS)</a>.


  		




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In future it will connect more


  		




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data providers like <a href="http://www.eea.europa.eu/themes/biodiversity/eunis/eunis-db">EUNIS</a>


  		




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and <a href="http://www.eea.europa.eu/data-and-maps/data/natura-5">Natura2000</a> in order to be compliant


  		




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with the <a href="http://inspire.ec.europa.eu/documents/Data_Specifications/INSPIRE_DataSpecification_SD_v3.0rc3.pdf">INSPIRE directive</a>.


  		




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Currently it is possible to <strong>search for taxa and synonyms by a scientific name or


  		




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vernacular name string</strong>. In case of matching synonyms the according accepted taxon is resolved.


  		




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The search results always include information on the classification and optionally on related taxa as far as


  		




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this data is delivered by the connected checklist providers.


  		




  
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UTIS connects the web services of the <a href="http://www.eu-nomen.eu">Pan-European Species directories 


  		




  
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Infrastructure (EU-Nomen)</a>, <a href="http://www.eea.europa.eu/themes/biodiversity/eunis/eunis-db">EUNIS</a> which 


  		




  
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fully covers <a href="http://www.eea.europa.eu/data-and-maps/data/natura-5">Natura 2000</a>. Therefore UTIS can be used in full compliance 


  		




  
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to Appendix 3 of the <a href="http://inspire.ec.europa.eu/documents/Data_Specifications/INSPIRE_DataSpecification_SD_v3.0rc3.pdf">the 


  		




  
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INSPIRE directive</a>. Furthermore it connects to the <a href="http://www.catalogueoflife.org/">Catalogue of Life (CoL)</a>,


  		




  
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 the <a href="http://www.marinespecies.org/">World Register of Marine Species (WoRMS)</a>. 


  		




  
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</p>


  		




  
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<p>


  		




  
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Currently it is possible to search for taxa and synonyms by scientific name or vernacular name strings. 


  		




  
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In case of the search string matches a synonym the according accepted taxon is resolved. UTIS provides furthermore a special 


  		




  
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search mode for resolving taxon identifiers. </br>


  		




  
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The responses of the search web service always include information 


  		




  
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on the classification and optionally on related taxa as far as this data is 


  		




  
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delivered by the connected checklist providers. 


  		




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</p>


  		




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<p>


  		




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  <a href="doc.html">Documentation of the RESTful UTIS service api.</a>


  		




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</p>


  		




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<p><div>The service is being developed by the <a href="http://www.bgbm.org/de/wissenschaft-biodiversitaetsinformatik">Department of Research and Biodiversity Informatics</a> of the Botanic Garden and Botanical Museum Berlin-Dahlem.</div></p>


  		




  
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<p>


  		




  
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This first official release (v1.0) of UTIS is stabilized regarding the API and data model. Further changes are not yet planned. 


  		




  
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</p>


  		




  
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<p><div>The service is being developed by the <a href="http://www.bgbm.org/de/wissenschaft-biodiversitaetsinformatik">Department


  		




  
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 of Research and Biodiversity Informatics</a> of the Botanic Garden and Botanical Museum Berlin-Dahlem.</div></p>


  		




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</div>


  		




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<div id="footer">


  		




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<a href="http://eubon.eu/" title=""><img src="images/eubon-logo.jpeg" alt="EU BON Logo"></a>


  		












  

    
      src/test/resources/log4j2.xml
    
  





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<!--     <Logger name="com.mangofactory.swagger" level="debug"/> -->


  		




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    <Logger name="org.bgbm.utis" level="debug"/>


  		




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    <Logger name="org.bgbm.biovel.drf" level="debug"/>


  		




  
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    <Logger name=org.apache.http.impl.conn" level="warn" />


  		




  
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    <Logger name=org.apache.http.impl.conn.Wire" level="warn" />


  		




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<!--     <Logger name="org.springframework.web.servlet.view" level="debug"/> -->


  		




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    <Root level="info">


  		




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      <AppenderRef ref="STDOUT"/>


  		












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