nl.uu.cs.ape.configuration.APECoreConfig Maven / Gradle / Ivy
Show all versions of APE Show documentation
package nl.uu.cs.ape.configuration;
import org.apache.commons.io.FileExistsException;
import org.apache.commons.io.FileUtils;
import org.json.JSONException;
import org.json.JSONObject;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import nl.uu.cs.ape.configuration.tags.APEConfigTag;
import nl.uu.cs.ape.configuration.tags.APEConfigTagFactory;
import nl.uu.cs.ape.configuration.tags.APEConfigTags;
import nl.uu.cs.ape.configuration.tags.APEConfigTagFactory.TAGS.*;
import nl.uu.cs.ape.configuration.tags.validation.ValidationResults;
import nl.uu.cs.ape.domain.APEDimensionsException;
import nl.uu.cs.ape.utils.APEFiles;
import nl.uu.cs.ape.utils.APEUtils;
import nl.uu.cs.ape.domain.OWLReader;
import java.io.File;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
/**
* The {@link APECoreConfig} class is used to define the core configuration
* variables required for the proper execution of the library.
*
* @author Vedran Kasalica
*/
public class APECoreConfig {
/**
* The taxonomy (ontology) file
*/
public final APEConfigTag ONTOLOGY = new APEConfigTagFactory.TAGS.ONTOLOGY();
/**
* Prefix used to define OWL class IDs
*/
public final APEConfigTag ONTOLOGY_PREFIX = new APEConfigTagFactory.TAGS.ONTOLOGY_PREFIX();
/**
* Node in the ontology that corresponds to the root of the module taxonomy.
*/
public final APEConfigTag TOOL_ONTOLOGY_ROOT = new APEConfigTagFactory.TAGS.TOOL_ONTOLOGY_ROOT(
ONTOLOGY_PREFIX::getValue);
/**
* List of nodes in the ontology that correspond to the roots of disjoint
* sub-taxonomies, where each represents a data dimension (e.g. data type, data
* format, etc.).
*/
public final APEConfigTag> DIMENSIONS_ONTOLOGY = new APEConfigTagFactory.TAGS.DIMENSIONS_ONTOLOGY(
ONTOLOGY_PREFIX::getValue);
/**
* The JSON file with all tool annotations.
*/
public final APEConfigTag TOOL_ANNOTATIONS = new APEConfigTagFactory.TAGS.TOOL_ANNOTATIONS();
/**
* {@code true} if the domain expects strict tool annotations, where,
* {@code false} in case of a
* restrictive message passing structure.
*/
public final APEConfigTag STRICT_TOOL_ANNOTATIONS = new APEConfigTagFactory.TAGS.STRICT_TOOL_ANNOTATIONS();
/**
* The CWL file with all CWL annotations.
*/
public final APEConfigTag CWL_ANNOTATIONS = new APEConfigTagFactory.TAGS.CWL_ANNOTATIONS();
/**
* All the Tags specified in this class. Should be in correct order of
* dependencies.
*/
private final APEConfigTag[] all_tags = new APEConfigTag[] {
this.ONTOLOGY_PREFIX,
this.ONTOLOGY,
this.TOOL_ONTOLOGY_ROOT,
this.DIMENSIONS_ONTOLOGY,
this.TOOL_ANNOTATIONS,
this.STRICT_TOOL_ANNOTATIONS,
this.CWL_ANNOTATIONS
};
/**
* Static versions of the Tags specified in this class.
* Should be in correct order for the Web API.
*/
public static final APEConfigTags TAGS = new APEConfigTags(
new ONTOLOGY_PREFIX(),
new ONTOLOGY(),
new TOOL_ONTOLOGY_ROOT(null),
new DIMENSIONS_ONTOLOGY(null),
new TOOL_ANNOTATIONS(),
new STRICT_TOOL_ANNOTATIONS(),
new CWL_ANNOTATIONS());
/**
* Initialize the configuration of the project.
*
* @param ontology A file containing the APE configuration.
* @param ontologyPrefixIRI Prefix used to define OWL class IDs
* @param toolTaxonomyRoot Node in the ontology that corresponds to the
* root of the module taxonomy.
* @param dataDimensionRoots List of nodes in the ontology that correspond to
* the roots of disjoint sub-taxonomies, where each
* represents a data dimension (e.g. data type,
* data format, etc.).
* @param toolAnnotations The JSON file with all tool annotations.
* @param strictToolAnnotations {@code true} if the domain expects strict tool
* annotations
*/
public APECoreConfig(File ontology, String ontologyPrefixIRI, String toolTaxonomyRoot,
List dataDimensionRoots, File toolAnnotations, boolean strictToolAnnotations) {
/* Path to the OWL file. */
this.ONTOLOGY.setValue(ontology);
/* IRI of the ontology classes. */
this.ONTOLOGY_PREFIX.setValue(ontologyPrefixIRI);
/* The root class of the tool taxonomy. */
this.TOOL_ONTOLOGY_ROOT.setValue(APEUtils.createClassIRI(toolTaxonomyRoot, getOntologyPrefixIRI()));
/* Dimension classes of the data taxonomy. */
this.DIMENSIONS_ONTOLOGY.setValue(
dataDimensionRoots.stream()
.map(subTaxonomy -> APEUtils.createClassIRI(subTaxonomy, getOntologyPrefixIRI()))
.collect(Collectors.toList()));
/* Path to the tool annotations JSON file. */
this.TOOL_ANNOTATIONS.setValue(toolAnnotations);
/* Set the tool annotation model for the domain. */
this.STRICT_TOOL_ANNOTATIONS.setValue(strictToolAnnotations);
}
/**
* Initialize the configuration of the project.
*
* @param configPath Path to the APE configuration file.
* @throws IOException Error in reading the configuration file.
* @throws JSONException Error in parsing the configuration file.
* @throws APEConfigException Error in setting up the the configuration.
*/
public APECoreConfig(String configPath) throws IOException, JSONException, APEConfigException {
if (configPath == null) {
throw new NullPointerException("The provided core configuration file path is null.");
}
coreConfigSetup(APEFiles.readPathToJSONObject(configPath));
}
/**
* Initialize the configuration of the project.
*
* @param config APE configuration file.
* @throws IOException Error in reading the configuration file.
* @throws JSONException Error in parsing the configuration file.
* @throws APEConfigException Error in setting up the the configuration.
*/
public APECoreConfig(File config) throws IOException, JSONException, APEConfigException {
coreConfigSetup(new JSONObject(FileUtils.readFileToString(config, StandardCharsets.UTF_8)));
}
/**
* Initialize the configuration of the project.
*
* @param configObject The APE configuration JSONObject{@link JSONObject}.
* @throws JSONException Error in parsing the configuration file.
* @throws APEConfigException Error in setting up the the configuration.
*/
public APECoreConfig(JSONObject configObject) throws JSONException, APEConfigException {
coreConfigSetup(configObject);
}
/**
* Setting up the core configuration of the library.
*
* //@throws IOException Error in reading the configuration file.
*
* @throws JSONException Error in parsing the configuration file.
* @throws APEConfigException Error in setting up the the configuration.
* //@throws OWLException Error in setting up the
* ontology for the configuration.
*/
private void coreConfigSetup(JSONObject coreConfiguration) throws JSONException, APEConfigException {
/* JSONObject must have been parsed correctly. */
if (coreConfiguration == null) {
throw new APEConfigException(
"Cannot set up the core configuration, because the JSONObject is initialized to NULL. The configuration file might not have been parsed correctly.");
}
// set the value for each tag
for (APEConfigTag tag : all_tags) {
tag.setValueFromConfig(coreConfiguration);
}
}
/**
* Private constructor used by {@link APECoreConfig#validate(JSONObject config)}
* to create an empty instance.
*/
private APECoreConfig() {
}
/**
* Validate tje JSONObject for each CORE tag.
* If {@link ValidationResults#success()} ()} returns true,
* the configuration object can be safely used to create
* an APECoreConfig object.
*
* @param json the json
* @return the validation results
*/
public static ValidationResults validate(JSONObject json) {
APECoreConfig dummy = new APECoreConfig();
ValidationResults results = new ValidationResults();
for (APEConfigTag tag : dummy.all_tags) {
results.add(tag.validateConfig(json));
if (results.hasFails()) {
return results;
} else {
tag.setValueFromConfig(json); // for dependencies
}
}
return results;
}
/**
* Run the initial validation of the ontology file and the corresponding tool
* and data terms. Validation will simply check the format of the ontology and
* the existence of the mentioned classes.
*
* @param ontologyFile - ontology file
* @param ontologyPrefixIRI Prefix used to define OWL class IDs
* @param toolTaxonomyRoot Node in the ontology that corresponds to the root
* of the module taxonomy.
* @param dataDimensionRoots List of nodes in the ontology that correspond to
* the roots of disjoint sub-taxonomies, where each
* represents a data dimension (e.g. data type, data
* format, etc.).
* @return return {@code true} if validation was successful, {@code false}
* otherwise.
* @throws APEDimensionsException Error when one of the terms does not
* exist in the ontology
* @throws OWLOntologyCreationException Error in file format.
* @throws FileExistsException File error.
*/
public static boolean validateOntology(File ontologyFile, String ontologyPrefixIRI, String toolTaxonomyRoot,
List dataDimensionRoots)
throws APEDimensionsException, OWLOntologyCreationException, FileExistsException {
return OWLReader.verifyOntology(ontologyFile, ontologyPrefixIRI, toolTaxonomyRoot, dataDimensionRoots);
}
/**
* Gets ontology.
*
* @return the value of tag {@link #ONTOLOGY}
*/
public File getOntologyFile() {
return ONTOLOGY.getValue();
}
/**
* Set ontology annotation.
*
* @param ontology - ontology file
*/
public void setOntologyFile(File ontology) {
ONTOLOGY.setValue(ontology);
}
/**
* Gets ontology prefix uri.
*
* @return the value of tag {@link #ONTOLOGY_PREFIX}
*/
public String getOntologyPrefixIRI() {
return ONTOLOGY_PREFIX.getValue();
}
/**
* Gets tool taxonomy root.
*
* @return the value of tag {@link #TOOL_ONTOLOGY_ROOT}
*/
public String getToolTaxonomyRoot() {
return TOOL_ONTOLOGY_ROOT.getValue();
}
/**
* Gets data dimension roots.
*
* @return the value of tag {@link #DIMENSIONS_ONTOLOGY}
*/
public List getDataDimensionRoots() {
return DIMENSIONS_ONTOLOGY.getValue();
}
/**
* Gets tool annotations path.
*
* @return the value of tag {@link #TOOL_ANNOTATIONS}
*/
public File getToolAnnotationsFile() {
return TOOL_ANNOTATIONS.getValue();
}
/**
* Set tool annotations.
*
* @param toolAnnotations - tool annotations file
*
*/
public void setToolAnnotationsFile(File toolAnnotations) {
TOOL_ANNOTATIONS.setValue(toolAnnotations);
}
/**
* Gets CWL annotations path.
*
* @return the value of tag {@link #TOOL_ANNOTATIONS}
*/
public Optional getCwlAnnotationsFile() {
if (CWL_ANNOTATIONS.getValue() == null) {
return Optional.empty();
} else {
return Optional.of(CWL_ANNOTATIONS.getValue());
}
}
/**
* Get information whether the domain was annotated under the strict rules of
* the output dependency.
*
* @return {@code true} if the strict rules apply, {@code false} otherwise.
*/
public boolean getUseStrictToolAnnotations() {
return STRICT_TOOL_ANNOTATIONS.getValue();
}
}