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Fixed utf8 input for xml and added basic .gitignore #4

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285040f
Fixed utf8 input for xml and added basic .gitignore
santifa Oct 17, 2017
09dbffb
Keep colons within fragments and force UTF-8 in XPath
santifa Oct 23, 2017
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26 changes: 26 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
# Compiled class file
*.class

# Log file
*.log

# BlueJ files
*.ctxt

# Mobile Tools for Java (J2ME)
.mtj.tmp/

# Package Files #
*.jar
*.war
*.ear
*.zip
*.tar.gz
*.rar

# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid*

# Idea
*.iml
.idea
31 changes: 13 additions & 18 deletions src/main/java/be/ugent/mmlab/rml/logicalsourcehandler/termmap/AbstractTermMapProcessor.java
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Original file line number Diff line number Diff line change
@@ -1,23 +1,10 @@
package be.ugent.mmlab.rml.logicalsourcehandler.termmap;

import be.ugent.mmlab.rml.model.RDFTerm.TermMap;
import static be.ugent.mmlab.rml.model.RDFTerm.TermMap.TermMapType.CONSTANT_VALUED;
import static be.ugent.mmlab.rml.model.RDFTerm.TermMap.TermMapType.REFERENCE_VALUED;
import static be.ugent.mmlab.rml.model.RDFTerm.TermMap.TermMapType.TEMPLATE_VALUED;
import be.ugent.mmlab.rml.model.RDFTerm.TermType;
import static be.ugent.mmlab.rml.model.RDFTerm.TermType.BLANK_NODE;
import static be.ugent.mmlab.rml.model.RDFTerm.TermType.IRI;
import static be.ugent.mmlab.rml.model.RDFTerm.TermType.LITERAL;
import be.ugent.mmlab.rml.model.std.StdTemplateMap;
import be.ugent.mmlab.rml.model.termMap.ReferenceMap;
import be.ugent.mmlab.rml.vocabularies.QLVocabulary.QLTerm;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.openrdf.model.URI;
import org.openrdf.model.Value;
import org.openrdf.model.impl.BNodeImpl;
Expand All @@ -26,6 +13,14 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
* RML Processor
*
Expand All @@ -49,7 +44,7 @@ public List<String> processTermMap(TermMap map, Object node) {
//Get the expression and extract the value
ReferenceMap identifier = map.getReferenceMap();
values = extractValueFromNode(
node, identifier.getReference().toString().trim());
node, identifier.getReference().trim());

for (String value : values) {
valueList.add(value.trim().replace("\n", " "));
Expand Down Expand Up @@ -107,7 +102,8 @@ public List<String> processTermMap(TermMap map, Object node) {
.replaceAll("\\%27", "'")
.replaceAll("\\%28", "(")
.replaceAll("\\%29", ")")
.replaceAll("\\%7E", "~"));
.replaceAll("\\%7E", "~"))
.replaceAll("\\%3A", ":");
} else {
temp = temp.replaceAll("\\{" + expression + "\\}",
Matcher.quoteReplacement(replacement));
Expand All @@ -116,16 +112,15 @@ public List<String> processTermMap(TermMap map, Object node) {
} catch (UnsupportedEncodingException ex) {
log.error("UnsupportedEncodingException " + ex);
}
values.set(i, temp.toString());
values.set(i, temp);

}
}

//Check if there are any placeholders left in the templates and remove uris that are not
List<String> validValues = new ArrayList<>();
for (String uri : values){
StdTemplateMap templateMap = new StdTemplateMap(uri);
if (templateMap.extractVariablesFromStringTemplate(uri).isEmpty()){
if (StdTemplateMap.extractVariablesFromStringTemplate(uri).isEmpty()){
validValues.add(uri);
}
}
Expand Down
15 changes: 11 additions & 4 deletions ...va/be/ugent/mmlab/rml/logicalsourcehandler/termmap/concrete/JSONPathTermMapProcessor.java
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Expand Up @@ -2,13 +2,14 @@

import be.ugent.mmlab.rml.logicalsourcehandler.termmap.AbstractTermMapProcessor;
import com.jayway.jsonpath.JsonPath;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import net.minidev.json.JSONArray;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

/**
* RML Processor
*
Expand All @@ -34,7 +35,13 @@ public List<String> extractValueFromNode(Object node, String expression) {
JSONArray arr = (JSONArray) val;
return Arrays.asList(arr.toArray(new String[0]));
}
list.add((String) val.toString());

// handle null values
if (val == null) {
val = "";
}

list.add(val.toString());
return list;
} catch (com.jayway.jsonpath.InvalidPathException ex) {
log.debug("InvalidPathException " + ex + "for " + expression);
Expand Down
18 changes: 10 additions & 8 deletions .../java/be/ugent/mmlab/rml/logicalsourcehandler/termmap/concrete/XPathTermMapProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,6 @@

import be.ugent.mmlab.rml.logicalsourcehandler.termmap.AbstractTermMapProcessor;
import be.ugent.mmlab.rml.xml.XOMBuilder;
import java.io.StringBufferInputStream;
import java.util.ArrayList;
import java.util.List;
import javax.xml.xpath.XPathException;
import jlibs.xml.DefaultNamespaceContext;
import jlibs.xml.sax.dog.NodeItem;
import jlibs.xml.sax.dog.XMLDog;
Expand All @@ -19,6 +15,12 @@
import org.slf4j.LoggerFactory;
import org.xml.sax.InputSource;

import javax.xml.xpath.XPathException;
import java.io.ByteArrayInputStream;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.List;

/**
* RML Processor
*
Expand Down Expand Up @@ -56,9 +58,9 @@ private List<String> extractValueFromNode(Node node, String expression) {
} catch (SAXPathException ex) {
log.error("SAXPathException " + ex);
}
StringBufferInputStream input =
new StringBufferInputStream(node.toXML().toString());
ByteArrayInputStream input =
new ByteArrayInputStream(node.toXML().getBytes(Charset.forName("UTF-8")));

InputSource source = new InputSource(input);
Event event = dog.createEvent();
event.setXMLBuilder(new XOMBuilder());
Expand All @@ -69,7 +71,7 @@ public void onNodeHit(
Expression expression, NodeItem nodeItem) {
Node node = (Node) nodeItem.xml;
//if(nodeItem instanceOf Attribute)
list.add(node.getValue().toString());
list.add(node.getValue());
}

@Override
Expand Down