dwca-io

Formerly know as dwca-reader

The dwca-oi library provides:

• Reader for DarwinCore Archive file with or without extensions
• Writer for simple DarwinCore Archive file with or without extensions

To build the project

mvn clean install

Usage

Reading DarwinCore archive

Read an archive and display the scientific name of each records:

File myArchiveFile = new File("myArchive.zip");
File extractToFolder = new File("/tmp/myarchive");
Archive dwcArchive = ArchiveFactory.openArchive(myArchiveFile, extractToFolder);

// loop over core darwin core records and display scientificName
Iterator<DarwinCoreRecord> it = dwcArchive.iteratorDwc();
while (it.hasNext()) {
  DarwinCoreRecord dwc = it.next();
  System.out.println(dwc.getScientificName());
}

Reading DarwinCore archive + extensions

Read from a folder(extracted archive) and display the scientific name of each records + vernacular name(s) from the extension:

//WARNING: StarRecord requires underlying data files(including extensions) to be sorted by the coreid column
Archive dwcArchive = ArchiveFactory.openArchive(new File("/tmp/myarchive"));
System.out.println("Archive rowtype: " + dwcArchive.getCore().getRowType() + ", "
    + dwcArchive.getExtensions().size() + " extension(s)");
// loop over core darwin core star records
for (StarRecord rec : dwcArchive) {
  System.out.println(rec.core().id() + " scientificName: " + rec.core().value(DwcTerm.scientificName));
  if (rec.hasExtension(GbifTerm.VernacularName)) {
    for (Record extRec : rec.extension(GbifTerm.VernacularName)) {
      System.out.println(" -" + extRec.value(DwcTerm.vernacularName));
    }
  }
}

Other supported file types

The ArchiveFactory.openArchive method also supports the following file types:

• Single meta.xml file
• Single data file with terms as header

Maven

Ensure you have the GBIF repository in your pom.xml

<repositories>
  <repository>
    <id>gbif-repository</id>
    <url>http://repository.gbif.org/content/groups/gbif</url>
  </repository>
</repositories>

Add the dwca-io artifact

  <dependency>
    <groupId>org.gbif</groupId>
    <artifactId>dwca-io</artifactId>
    <version>1.23</version>
  </dependency>

Documentation

JavaDocs