Accessing metadata

This page explains you everything there is to know about accessing metadata from PhyloData.

What is metadata?

Every experiment has a bunch of metadata associated with it. You can explore almost everything about an experiment by looking at its page on this website. However, you can also access the metadata using the PhyloData Java library.

Every loadExperiment methods return a PaperWithExperiment object. It has the following structure:

public class PaperWithExperiment {
    Paper getPaper();
    Experiment getExperiment();
    List<File> getFiles();
    List<Sample> getSamples();
    Object getTrees();
    List<EvolutionaryModelComponent> getEvolutionaryModel();
    Metadata getMetadata();
}

As you can see, the structure closesly matches the experiment pages on the website.

Paper metadata

PaperWithExperiment experiment = new ExperimentLoader(
    "munro-2019-climate-6tvf", 1
).load();

System.out.println(experiment.getPaper().getTitle());
System.out.println(experiment.getPaper().getYear());
System.out.println(experiment.getPaper().getAbstract());
System.out.println(experiment.getPaper().getAuthors());
System.out.println(experiment.getPaper().getDoi());
System.out.println(experiment.getPaper().getBibtex());

Experiment metadata

PaperWithExperiment experiment = new ExperimentLoader(
    "munro-2019-climate-6tvf", 1
).load();

System.out.println(experiment.getExperiment().getType());
System.out.println(experiment.getExperiment().getHumanReadableId());
System.out.println(experiment.getExperiment().getUploadDate());
System.out.println(experiment.getExperiment().getVersion());

File metadata

PaperWithExperiment experiment = new ExperimentLoader(
    "munro-2019-climate-6tvf", 1
).load();

for (File file : experiment.getAllFiles()) {
    System.out.println(file.getName());
    System.out.println(file.getType());
    System.out.println(file.getLocalPath());
    System.out.println(file.getSizeBytes());
    System.out.println(file.getMd5());
    System.out.println(file.getIsPreview());
}

getAllFiles returns all files, including preview files and files that haven’t been downloaded. getFiles and alike only return the files that have been downloaded and respect the preview preferences.

Sample metadata

PaperWithExperiment experiment = new ExperimentLoader(
    "munro-2019-climate-6tvf", 1
).load();

for (Sample sample : experiment.getSamples()) {
    System.out.println(sample.getSampleId());
    System.out.println(sample.getScientificName());
    System.out.println(sample.getClassification());
    System.out.println(sample.getSampleData());
}

Trees metadata

PaperWithExperiment experiment = new ExperimentLoader(
        "munro-2019-climate-6tvf", 1
).load();

System.out.println(experiment.getTrees().getNumberOfTrees());
System.out.println(experiment.getTrees().getNumberOfTips());
System.out.println(experiment.getTrees().getRooted());
System.out.println(experiment.getTrees().getUltrametric());
System.out.println(experiment.getTrees().getAverageRootAge());

Evolutionary model metadata

PaperWithExperiment experiment = new ExperimentLoader(
    "munro-2019-climate-6tvf", 1
).load();

for (EvolutionaryModelComponent model : experiment.getEvolutionaryModel()) {
    System.out.println(model.getName());
    System.out.println(model.getType());
}