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VIVO-248 Move filegraph RDF files into the home directory

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j2blake 2013-08-20 15:25:57 -04:00
parent 3f061da006
commit 2c5ce8c5ce
4 changed files with 119 additions and 62 deletions
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31
webapp/build.xml
View file

@ -69,6 +69,9 @@
<property name="solr.webapp.dir" location="${solr.build.dir}/webapp" />
<property name="solr.homeimage.dir" location="${solr.build.dir}/homeimage" />
<property name="vitrohome.build.dir" location="${build.dir}/vitrohome" />
<property name="vitrohome.image.dir" location="${vitrohome.build.dir}/image" />
<property name="distribution.dir" location="${build.dir}/distribution" />
<property name="distribution.tar.gz.file" location="${build.dir}/distribution.tar.gz" />
@ -194,6 +197,21 @@
</copy>
</target>
<!-- - - - - - - - - - - - - - - - - -
target: prepareVitroHomeDir
- - - - - - - - - - - - - - - - - -->
<target name="prepareVitroHomeDir" depends="prepare">
<mkdir dir="${vitrohome.build.dir}" />
<mkdir dir="${vitrohome.image.dir}" />
<copy todir="${vitrohome.image.dir}" file="${appbase.dir}/config/example.runtime.properties" />
<copy todir="${vitrohome.image.dir}" >
<fileset dir="${appbase.dir}" >
<include name="rdffiles/**/*" />
</fileset>
</copy>
</target>
<!-- =================================
target: clean
================================= -->
@ -370,11 +388,21 @@
</copy>
</target>
<!-- - - - - - - - - - - - - - - - - -
target: deployVitroHome
- - - - - - - - - - - - - - - - - -->
<target name="deployVitroHome" depends="deployProperties, prepareVitroHomeDir">
<copy toDir="${vitro.home}" >
<fileset dir="${vitrohome.image.dir}" />
</copy>
</target>
<!-- =================================
target: deploy
================================= -->
<target name="deploy"
depends="deployWebapp, deploySolr"
depends="deployWebapp, deploySolr, deployVitroHome"
description="--> Build the app and install in Tomcat">
</target>
@ -399,6 +427,7 @@
<jar basedir="${main.webapp.dir}" destfile="${distribution.dir}/${webapp.name}.war" />
<jar basedir="${solr.webapp.dir}" destfile="${distribution.dir}/${solr.app.name}.war" />
<tar basedir="${solr.homeimage.dir}" destfile="${distribution.dir}/solrhome.tar" />
<tar basedir="${vitrohome.image.dir}" destfile="${distribution.dir}/vitrohome.tar" />
<tar basedir="${distribution.dir}" destfile="${distribution.tar.gz.file}" compression="gzip" />
</target>

0
webapp/web/WEB-INF/filegraph/tbox/vitro-0.7.owl → webapp/rdffiles/tbox/filegraph/vitro-0.7.owl
View file

0
webapp/web/WEB-INF/filegraph/tbox/vitroPublic.owl → webapp/rdffiles/tbox/filegraph/vitroPublic.owl
View file

140
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/FileGraphSetup.java
View file

@ -2,13 +2,17 @@
package edu.cornell.mannlib.vitro.webapp.servlet.setup;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.nio.file.DirectoryStream;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
import java.util.TreeSet;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@ -26,23 +30,36 @@ import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
import edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
// This ContextListener must run after the JenaDataSourceSetup ContextListener
public class FileGraphSetup implements ServletContextListener {
private static final Log log = LogFactory.getLog(FileGraphSetup.class);
private static final String RDFFILES = "rdffiles";
private static final String ABOX = "abox";
private static final String TBOX = "tbox";
private static final String PATH_ROOT = "/WEB-INF/filegraph/";
private static final String FILEGRAPH = "filegraph";
private static final String PROPERTY_VITRO_HOME = "vitro.home";
public static final String FILEGRAPH_URI_ROOT = "http://vitro.mannlib.cornell.edu/filegraph/";
private static final Log log = LogFactory.getLog(FileGraphSetup.class);
/** Ignore hidden files when looking for filegraph RDF. */
private static final DirectoryStream.Filter<Path> REJECT_HIDDEN_FILES = new DirectoryStream.Filter<Path>() {
@Override
public boolean accept(Path entry) throws IOException {
return !Files.isHidden(entry);
}
};
public void contextInitialized(ServletContextEvent sce) {
@Override
public void contextInitialized(ServletContextEvent sce) {
boolean aboxChanged = false; // indicates whether any ABox file graph model has changed
boolean tboxChanged = false; // indicates whether any TBox file graph model has changed
@ -57,24 +74,20 @@ public class FileGraphSetup implements ServletContextListener {
RDFServiceModelMaker maker = new RDFServiceModelMaker(RDFServiceUtils.getRDFServiceFactory(ctx));
// ABox files
Set<String> pathSet = ctx.getResourcePaths(PATH_ROOT + ABOX);
Set<Path> paths = getFilegraphPaths(ctx, RDFFILES, ABOX, FILEGRAPH);
cleanupDB(dataset, pathToURI(pathSet, ABOX), ABOX);
cleanupDB(dataset, pathsToURIs(paths, ABOX), ABOX);
if (pathSet != null) {
OntModel aboxBaseModel = baseOms.getABoxModel();
aboxChanged = readGraphs(sce, pathSet, maker, ABOX, aboxBaseModel);
}
OntModel aboxBaseModel = baseOms.getABoxModel();
aboxChanged = readGraphs(paths, maker, ABOX, aboxBaseModel);
// TBox files
pathSet = ctx.getResourcePaths(PATH_ROOT + TBOX);
paths = getFilegraphPaths(ctx, RDFFILES, TBOX, FILEGRAPH);
cleanupDB(dataset, pathToURI(pathSet, TBOX),TBOX);
cleanupDB(dataset, pathsToURIs(paths, TBOX),TBOX);
if (pathSet != null) {
OntModel tboxBaseModel = baseOms.getTBoxModel();
tboxChanged = readGraphs(sce, pathSet, maker, TBOX, tboxBaseModel);
}
OntModel tboxBaseModel = baseOms.getTBoxModel();
tboxChanged = readGraphs(paths, maker, TBOX, tboxBaseModel);
} catch (ClassCastException cce) {
String errMsg = "Unable to cast servlet context attribute to the appropriate type " + cce.getLocalizedMessage();
log.error(errMsg);
@ -99,7 +112,35 @@ public class FileGraphSetup implements ServletContextListener {
}
}
/*
private Set<Path> getFilegraphPaths(ServletContext ctx, String... strings) {
StartupStatus ss = StartupStatus.getBean(ctx);
ConfigurationProperties props = ConfigurationProperties.getBean(ctx);
String homeDirProperty = props.getProperty(PROPERTY_VITRO_HOME);
Path filegraphDir = Paths.get(homeDirProperty, strings);
Set<Path> paths = new TreeSet<>();
if (Files.isDirectory(filegraphDir)) {
try (DirectoryStream<Path> stream = Files.newDirectoryStream(
filegraphDir, REJECT_HIDDEN_FILES)) {
for (Path p : stream) {
paths.add(p);
}
ss.info(this, "Read " + paths.size() + " RDF files from '"
+ filegraphDir + "'");
} catch (IOException e) {
ss.fatal(this, "Failed to read filegraph RDF from '"
+ filegraphDir + "' directory.", e);
}
} else {
ss.info(this, "Filegraph directory '" + filegraphDir
+ "' doesn't exist.");
}
log.debug("Paths from '" + filegraphDir + "': " + paths);
return paths;
}
/*
* Reads the graphs stored as files in sub-directories of
* 1. updates the SDB store to reflect the current contents of the graph.
* 2. adds the graph as an in-memory submodel of the base in-memory graph
@ -107,7 +148,7 @@ public class FileGraphSetup implements ServletContextListener {
* Note: no connection needs to be maintained between the in-memory copy of the
* graph and the DB copy.
*/
public boolean readGraphs(ServletContextEvent sce, Set<String> pathSet, RDFServiceModelMaker dataset, String type, OntModel baseModel) {
public boolean readGraphs(Set<Path> pathSet, RDFServiceModelMaker dataset, String type, OntModel baseModel) {
int count = 0;
@ -115,18 +156,17 @@ public class FileGraphSetup implements ServletContextListener {
// For each file graph in the target directory update or add that graph to
// the Jena SDB, and attach the graph as a submodel of the base model
for ( String p : pathSet ) {
for ( Path p : pathSet ) {
count++; // note this will count the empty files too
File file = new File(sce.getServletContext().getRealPath(p));
try {
FileInputStream fis = new FileInputStream( file );
FileInputStream fis = new FileInputStream( p.toFile() );
try {
OntModel model = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
if ( p.endsWith(".n3") || p.endsWith(".N3") || p.endsWith(".ttl") || p.endsWith(".TTL") ) {
String fn = p.getFileName().toString().toLowerCase();
if ( fn.endsWith(".n3") || fn.endsWith(".ttl") ) {
model.read( fis, null, "N3" );
} else if ( p.endsWith(".owl") || p.endsWith(".OWL") || p.endsWith(".rdf") || p.endsWith(".RDF") || p.endsWith(".xml") || p.endsWith(".XML") ) {
} else if ( fn.endsWith(".owl") || fn.endsWith(".rdf") || fn.endsWith(".xml") ) {
model.read( fis, null, "RDF/XML" );
} else {
log.warn("Ignoring " + type + " file graph " + p + " because the file extension is unrecognized.");
@ -134,7 +174,7 @@ public class FileGraphSetup implements ServletContextListener {
if ( !model.isEmpty() ) {
baseModel.addSubModel(model);
log.info("Attached file graph as " + type + " submodel " + p);
log.info("Attached file graph as " + type + " submodel " + pathToURI(p, type));
}
modelChanged = modelChanged | updateGraphInDB(dataset, model, type, p);
@ -156,7 +196,7 @@ public class FileGraphSetup implements ServletContextListener {
}
} // end - for
System.out.println("Read " + count + " " + type + " file graph" + ((count == 1) ? "" : "s") + " from " + PATH_ROOT + type);
log.info("Read " + count + " " + type + " file graph" + ((count == 1) ? "" : "s"));
return modelChanged;
}
@ -171,7 +211,7 @@ public class FileGraphSetup implements ServletContextListener {
* Otherwise, if a graph with the given name is in the DB and is isomorphic with
* the graph that was read from the files system, then do nothing.
*/
public boolean updateGraphInDB(RDFServiceModelMaker dataset, Model fileModel, String type, String path) {
public boolean updateGraphInDB(RDFServiceModelMaker dataset, Model fileModel, String type, Path path) {
String graphURI = pathToURI(path,type);
Model dbModel = dataset.getModel(graphURI);
boolean modelChanged = false;
@ -224,41 +264,29 @@ public class FileGraphSetup implements ServletContextListener {
return;
}
/*
* Takes a set of path names for file graphs and returns a set containing
* a graph uri for each path name in the input set. If pathSet is null
* returns an empty set.
*/
public Set<String> pathToURI (Set<String> pathSet, String type) {
HashSet<String> uriSet = new HashSet<String>();
if (pathSet != null) {
for ( String path : pathSet ) {
uriSet.add(pathToURI(path,type));
}
}
return uriSet;
}
/*
* Takes a set of paths for file graphs and returns a set containing a graph
* uri for each path.
*/
private Set<String> pathsToURIs(Set<Path> paths, String type) {
HashSet<String> uriSet = new HashSet<String>();
for (Path path : paths) {
uriSet.add(pathToURI(path, type));
}
log.debug("uriSet = " + uriSet);
return uriSet;
}
/*
* Takes a path name for a file graph and returns the corresponding SDB URI
* Takes a path for a file graph and returns the corresponding SDB URI
* for the graph. The correspondence is by defined convention.
*/
public String pathToURI(String path, String type) {
String uri = null;
if (path != null) {
File file = new File(path);
uri = FILEGRAPH_URI_ROOT + type + "/" + file.getName();
}
return uri;
private String pathToURI(Path path, String type) {
return FILEGRAPH_URI_ROOT + type + "/" + path.getFileName();
}
public void contextDestroyed( ServletContextEvent sce ) {
@Override
public void contextDestroyed( ServletContextEvent sce ) {
// nothing to do
}