EDIT

cdmlib-pesi/LICENSE.TXT -text

cdmlib-pesi/README.TXT -text

cdmlib-pesi/pom.xml -text

cdmlib-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/merging/FaunaEuErmsMerging.java -text

cdmlib-pesi/src/test/java/eu/etaxonomy/cdm/io/erms/ermsErrors.txt -text

cdmlib-pesi/.classpath

cdmlib-pesi/.project

cdmlib-pesi/.settings

cdmlib-pesi/target

The contents of this file are subject to the Mozilla Public License

Version 1.1 (the "License"); you may not use this file except in

compliance with the License. You may obtain a copy of the License at

http://www.mozilla.org/MPL/

Software distributed under the License is distributed on an "AS IS"

basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the

License for the specific language governing rights and limitations

under the License.

The project uses Maven2 and AspectJ.

Please see http://dev.e-taxonomy.eu/trac/wiki/CdmLibrary for details on installation and usage

<?xml version="1.0" encoding="UTF-8"?>

<project xmlns="http://maven.apache.org/POM/4.0.0" 

  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">

  <!-- 

    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"

   -->

  <parent>

    <groupId>eu.etaxonomy</groupId>

    <artifactId>cdmlib-parent</artifactId>

    <version>2.5</version>

	<relativePath>pom.xml</relativePath>

  </parent>

  <modelVersion>4.0.0</modelVersion>

  <artifactId>cdmlib-pesi</artifactId>

  <name>CDM PESI</name>

  <description>The PESI package for EDIT's CdmLibrary</description>

  <scm>

    <connection>scm:svn:http://dev.e-taxonomy.eu/svn/trunk/cdmlib/cdmlib-pesi/</connection>

    <developerConnection>scm:svn:https://dev.e-taxonomy.eu/svn/trunk/cdmlib/cdmlib-pesi/</developerConnection>

    <url>http://dev.e-taxonomy.eu/trac/browser/trunk/cdmlib/cdmlib-pesi/</url>

  </scm>

  <build>

    <plugins>

      <plugin>

        <groupId>org.apache.maven.plugins</groupId>

        <artifactId>maven-jar-plugin</artifactId>

        <executions>

          <execution>

            <goals>

              <goal>test-jar</goal>

            </goals>

          </execution>

        </executions>

      </plugin>

    </plugins>

  </build>

  <dependencies>   

  <dependency>

  		<groupId>eu.etaxonomy</groupId>

  		<artifactId>cdmlib-persistence</artifactId>

  		<type>test-jar</type>

  		<scope>test</scope> 

  		<version>${parent.version}</version>

  	</dependency>

   	<dependency>

  		<groupId>eu.etaxonomy</groupId>

  		<artifactId>cdmlib-io</artifactId>

  	</dependency>

  	<dependency>

        <groupId>org.unitils</groupId>

        <artifactId>unitils</artifactId>

    </dependency>

    <dependency>

      <groupId>org.dbunit</groupId>

      <artifactId>dbunit</artifactId>

    </dependency>

    <dependency>

      <groupId>xmlunit</groupId>

      <artifactId>xmlunit</artifactId>

  	</dependency>

  </dependencies>

</project>

package eu.etaxonomy.cdm.io.pesi.merging;

public class FaunaEuErmsMerging {

	private String uuidFaunaEu;

	private String uuidErms;

	private String idInFaunaEu;

	private String idInErms;

	private String nameCacheInFaunaEu;

	private String nameCacheInErms;

	private boolean statInFaunaEu;

	private boolean statInErms;

	private String authorInFaunaEu;

	private String authorInErms;

	private String rankInFaunaEu;

	private String rankInErms;

	private String phylumInFaunaEu;

	private String phylumInErms;

	private String parentStringInFaunaEu;

	private String parentStringInErms;

	private String parentRankStringInFaunaEu;

	private String parentRankStringInErms;

	public String getUuidFaunaEu() {

		return uuidFaunaEu;

	}

	public void setUuidFaunaEu(String uuidFaunaEu) {

		this.uuidFaunaEu = uuidFaunaEu;

	}

	public String getUuidErms() {

		return uuidErms;

	}

	public void setUuidErms(String uuidErms) {

		this.uuidErms = uuidErms;

	}

	public String getParentRankStringInFaunaEu() {

		return parentRankStringInFaunaEu;

	}

	public void setParentRankStringInFaunaEu(String parentRankStringInFaunaEu) {

		this.parentRankStringInFaunaEu = parentRankStringInFaunaEu;

	}

	public String getParentRankStringInErms() {

		return parentRankStringInErms;

	}

	public void setParentRankStringInErms(String parentRankStringInErms) {

		this.parentRankStringInErms = parentRankStringInErms;

	}

	public String getParentStringInFaunaEu() {

		return parentStringInFaunaEu;

	}

	public void setParentStringInFaunaEu(String parentStringInFaunaEu) {

		this.parentStringInFaunaEu = parentStringInFaunaEu;

	}

	public String getParentStringInErms() {

		return parentStringInErms;

	}

	public void setParentStringInErms(String parentStringInErms) {

		this.parentStringInErms = parentStringInErms;

	}

	public String getRankInFaunaEu() {

		return rankInFaunaEu;

	}

	public void setRankInFaunaEu(String rankInFaunaEu) {

		this.rankInFaunaEu = rankInFaunaEu;

	}

	public String getPhylumInFaunaEu() {

		return phylumInFaunaEu;

	}

	public void setPhylumInFaunaEu(String phylumInFaunaEu) {

		this.phylumInFaunaEu = phylumInFaunaEu;

	}

	public String getPhylumInErms() {

		return phylumInErms;

	}

	public void setPhylumInErms(String phylumInErms) {

		this.phylumInErms = phylumInErms;

	}

	public String getRankInErms() {

		return rankInErms;

	}

	public void setRankInErms(String rankInErms) {

		this.rankInErms = rankInErms;

	}

	public static FaunaEuErmsMerging newInstance(){

		return new FaunaEuErmsMerging();

	}

	public boolean isStatInFaunaEu() {

		return statInFaunaEu;

	}

	public void setStatInFaunaEu(boolean statInFaunaEu) {

		this.statInFaunaEu = statInFaunaEu;

	}

	public boolean isStatInErms() {

		return statInErms;

	}

	public void setStatInErms(boolean statInErms) {

		this.statInErms = statInErms;

	}

	public String getAuthorInFaunaEu() {

		return authorInFaunaEu;

	}

	public void setAuthorInFaunaEu(String authorInFaunaEu) {

		this.authorInFaunaEu = authorInFaunaEu;

	}

	public String getAuthorInErms() {

		return authorInErms;

	}

	public void setAuthorInErms(String authorInErms) {

		this.authorInErms = authorInErms;

	}

	public String getIdInFaunaEu() {

		return idInFaunaEu;

	}

	public void setIdInFaunaEu(String idInFaunaEu) {

		this.idInFaunaEu = idInFaunaEu;

	}

	public String getIdInErms() {

		return idInErms;

	}

	public void setIdInErms(String idInErms) {

		this.idInErms = idInErms;

	}

	public String getNameCacheInFaunaEu() {

		return nameCacheInFaunaEu;

	}

	public void setNameCacheInFaunaEu(String nameCacheInFaunaEu) {

		this.nameCacheInFaunaEu = nameCacheInFaunaEu;

	}

	public String getNameCacheInErms() {

		return nameCacheInErms;

	}

	public void setNameCacheInErms(String nameCacheInErms) {

		this.nameCacheInErms = nameCacheInErms;

	}

}

ERRORS in ERMS

=====================

- there is one case, where a nomen nudum is the accepted taxon for an other taxon

SELECT     dbo.tu.tu_status, tu_1.tu_acctaxon, tu_1.id, dbo.tu.tu_displayname

FROM         dbo.tu INNER JOIN

                      dbo.tu AS tu_1 ON dbo.tu.id = tu_1.tu_acctaxon

WHERE     (dbo.tu.tu_status = 3) OR

                      (tu_1.id = 111846) OR

                      (tu_1.id = 111850)

- there are 448 cases where the tu_acctaxon has not a status "accepted"

SELECT     dbo.tu.tu_status AS acceptedStatus, dbo.tu.tu_displayname AS acceptedName, unaccepted.tu_status AS unacceptedStatus, 

                      unaccepted.tu_displayname AS unacceptedName

FROM         dbo.tu INNER JOIN

                      dbo.tu AS unaccepted ON dbo.tu.id = unaccepted.tu_acctaxon

WHERE     (dbo.tu.tu_status <> 1)

ORDER BY acceptedStatus, unacceptedStatus 

- 289 cases where parent taxon is not accepted (is this allowed ?)

- there are 46 taxa with a status not accepted, a parent not accepted and an parent.tu_acctaxon not accepted 

SELECT     TOP (100) PERCENT tu_1.id, tu_1.tu_status, accTaxon.tu_status AS accStatus, parent.tu_status AS parentStatus, 

                      accParent.tu_status AS accParentStatus, tu_1.tu_displayname AS displayname, parent.tu_displayname AS parentdisplayname, tu_1.tu_acctaxon, 

                      dbo.status.status_name, dbo.status.status_id AS myStatus, parent.id AS parentId, tu_1.tu_sp

FROM         dbo.status RIGHT OUTER JOIN

                      dbo.tu AS accTaxon RIGHT OUTER JOIN

                      dbo.tu AS tu_1 ON accTaxon.id = tu_1.tu_acctaxon LEFT OUTER JOIN

                      dbo.tu AS parent ON tu_1.tu_parent = parent.id ON dbo.status.status_id = tu_1.tu_status LEFT OUTER JOIN

                      dbo.tu AS accParent ON parent.tu_acctaxon = accParent.id

WHERE     (tu_1.tu_status <> 1) AND (parent.tu_status <> 1) AND (accParent.tu_status <> 1)

ORDER BY accParentStatus, parentStatus

- there are 27 taxa with a status not accepted, a parent not accepted and an parent.tu_acctaxon not accepted and an tu_acctaxon not accepted

SELECT     TOP (100) PERCENT tu_1.id, tu_1.tu_status, accTaxon.tu_status AS accStatus, parent.tu_status AS parentStatus, 

                      accParent.tu_status AS accParentStatus, tu_1.tu_displayname AS displayname, parent.tu_displayname AS parentdisplayname, tu_1.tu_acctaxon, 

                      dbo.status.status_name, dbo.status.status_id AS myStatus, parent.id AS parentId, tu_1.tu_sp

FROM         dbo.status RIGHT OUTER JOIN

                      dbo.tu AS accTaxon RIGHT OUTER JOIN

                      dbo.tu AS tu_1 ON accTaxon.id = tu_1.tu_acctaxon LEFT OUTER JOIN

                      dbo.tu AS parent ON tu_1.tu_parent = parent.id ON dbo.status.status_id = tu_1.tu_status LEFT OUTER JOIN

                      dbo.tu AS accParent ON parent.tu_acctaxon = accParent.id

WHERE     (tu_1.tu_status <> 1) AND (parent.tu_status <> 1) AND (accParent.tu_status <> 1) AND (accTaxon.tu_status <> 1)

ORDER BY accParentStatus, parentStatus