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Merge pull request #294 from richardrodgers/DS-1647-MDWebService
[DS-1647] Adds MetadataWebService curation task
This commit is contained in:
Mark H. Wood
@@ -499,6 +499,17 @@
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<artifactId>coverity-escapers</artifactId>
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<artifactId>coverity-escapers</artifactId>
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<version>1.1.1</version>
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<version>1.1.1</version>
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</dependency>
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</dependency>
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<dependency>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpcore</artifactId>
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<version>4.1.3</version>
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</dependency>
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<dependency>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpclient</artifactId>
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<version>4.1.2</version>
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</dependency>
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<!-- Gson: Java to Json conversion -->
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<!-- Gson: Java to Json conversion -->
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<dependency>
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<dependency>
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@@ -0,0 +1,543 @@
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/**
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* The contents of this file are subject to the license and copyright
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* detailed in the LICENSE and NOTICE files at the root of the source
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* tree and available online at
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*
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* http://www.dspace.org/license/
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*/
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package org.dspace.ctask.general;
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import java.io.InputStream;
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import java.io.IOException;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import javax.xml.parsers.DocumentBuilder;
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import javax.xml.parsers.DocumentBuilderFactory;
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.namespace.NamespaceContext;
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import javax.xml.xpath.XPath;
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import javax.xml.xpath.XPathConstants;
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import javax.xml.xpath.XPathExpression;
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import javax.xml.xpath.XPathExpressionException;
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import javax.xml.xpath.XPathFactory;
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import javax.xml.XMLConstants;
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import org.apache.http.HttpEntity;
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import org.apache.http.HttpResponse;
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import org.apache.http.HttpStatus;
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import org.apache.http.client.HttpClient;
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import org.apache.http.client.methods.HttpGet;
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import org.apache.http.impl.client.DefaultHttpClient;
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import org.apache.log4j.Logger;
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import org.w3c.dom.Document;
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import org.w3c.dom.NamedNodeMap;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import org.xml.sax.SAXException;
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import org.dspace.authorize.AuthorizeException;
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import org.dspace.content.DCValue;
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import org.dspace.content.DSpaceObject;
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import org.dspace.content.Item;
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import org.dspace.core.ConfigurationManager;
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import org.dspace.core.Constants;
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import org.dspace.curate.AbstractCurationTask;
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import org.dspace.curate.Curator;
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import org.dspace.curate.Mutative;
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import org.dspace.curate.Suspendable;
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/**
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* MetadataWebService task calls a web service using metadata from
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* passed item to obtain data. Depending on configuration, this
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* data may be assigned to item metadata fields, or just recorded in the
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* task result string. Task succeeds if web service call succeeds and
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* configured updates occur, fails if task user not authorized or item
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* lacks metadata to call service, and returns error in all other cases
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* (except skip status for non-item objects).
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* Intended use: cataloging tool in workflow and general curation.
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* The task uses a URL 'template' to compose the service call, e.g.
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*
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* http://www.sherpa.ac.uk/romeo/api29.php?issn={dc.identifier.issn}
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*
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* Task will substitute the value of the passed item's metadata field
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* in the {parameter} position. If multiple values are present in the
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* item field, the first value is used.
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*
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* The task uses another property (the datamap) to determine what data
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* to extract from the service response and how to use it, e.g.
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*
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* //publisher/name=>dc.publisher,//romeocolour
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*
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* Task will evaluate the left-hand side (or entire token) of each
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* comma-separated token in the property as an XPath 1.0 expression into
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* the response document, and if there is a mapping symbol (e.g.'=>') and
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* value, it will assign the response document value(s) to the named
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* metadata field in the passed item. If the response document contains
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* multiple values, they will all be assigned to the item field. The
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* mapping symbol governs the nature of metadata field assignment:
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*
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* '->' mapping will add to any existing values in the item field
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* '=>' mapping will replace any existing values in the item field
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* '~>' mapping will add *only* if item field has no existing values
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*
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* Unmapped data (without a mapping symbol) will simply be added to the task
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* result string, prepended by the XPath expression (a little prettified).
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* Each label/value pair in the result string is separated by a space,
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* unless the optional 'separator' property is defined.
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*
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* A very rudimentary facility for transformation of data is supported, e.g.
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*
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* http://www.crossref.org/openurl/?id={doi:dc.relation.isversionof}&format=unixref
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*
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* The 'doi:' prefix will cause the task to look for a 'transform' with that
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* name, which is applied to the metadata value before parameter substitution
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* occurs. Transforms are defined in a task property such as the following:
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*
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* transform.doi = match 10. trunc 60
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*
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* This means exclude the value string up to the occurrence of '10.', then
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* truncate after 60 characters. The only transform functions currently defined:
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*
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* 'cut' <number> = remove number leading characters
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* 'trunc' <number> = remove trailing characters after number length
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* 'match' <pattern> = start match at pattern
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* 'text' <characters> = append literal characters (enclose in ' ' when whitespace needed)
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*
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* If the transform results in an invalid state (e.g. cutting more characters
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* than are in the value), the condition will be logged and the
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* un-transformed value used.
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*
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* Transforms may also be used in datamaps, e.g.
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*
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* //publisher/name=>shorten:dc.publisher,//romeocolour
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*
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* which would apply the 'shorten' transform to the service response value(s)
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* prior to metadata field assignment.
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*
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* An optional property 'headers' may be defined to stipulate any HTTP headers
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* required in the service call. The property syntax is double-pipe separated headers:
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*
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* Accept: text/xml||Cache-Control: no-cache
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*
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* @author richardrodgers
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*/
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@Mutative
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@Suspendable
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public class MetadataWebService extends AbstractCurationTask implements NamespaceContext
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{
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/** log4j category */
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private static final Logger log = Logger.getLogger(MetadataWebService.class);
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// transform token parsing pattern
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private static Pattern ttPattern = Pattern.compile("\'([^\']*)\'|(\\S+)");
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// URL of web service with template parameters
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private String urlTemplate = null;
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// template parameter
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private String templateParam = null;
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// Item metadata field to use in service call
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private String lookupField = null;
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// Optional transformation of lookupField
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private String lookupTransform = null;
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// response data to map/record
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private List<DataInfo> dataList = null;
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// response document parsing tools
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private DocumentBuilder docBuilder = null;
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// language for metadata fields assigned
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private String lang = null;
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// field separator in result string
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private String fieldSeparator = null;
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// optional XML namespace map
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private Map<String, String> nsMap = new HashMap<String, String>();
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// optional HTTP headers
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private Map<String, String> headers = new HashMap<String, String>();
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/**
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* Initializes task
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* @param curator Curator object performing this task
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* @param taskId the configured local name of the task
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*/
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@Override
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public void init(Curator curator, String taskId) throws IOException {
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super.init(curator, taskId);
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lang = ConfigurationManager.getProperty("default.language");
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String fldSep = taskProperty("separator");
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fieldSeparator = (fldSep != null) ? fldSep : " ";
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urlTemplate = taskProperty("template");
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templateParam = urlTemplate.substring(urlTemplate.indexOf("{") + 1,
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urlTemplate.indexOf("}"));
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String[] parsed = parseTransform(templateParam);
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lookupField = parsed[0];
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lookupTransform = parsed[1];
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dataList = new ArrayList<DataInfo>();
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for (String entry : taskProperty("datamap").split(",")) {
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entry = entry.trim();
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String src = entry;
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String mapping = null;
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String field = null;
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int mapIdx = getMapIndex(entry);
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if (mapIdx > 0) {
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src = entry.substring(0, mapIdx);
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mapping = entry.substring(mapIdx, mapIdx + 2);
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field = entry.substring(mapIdx + 2);
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}
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int slIdx = src.lastIndexOf("/");
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String label = (slIdx > 0) ? src.substring(slIdx + 1) : src;
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dataList.add(new DataInfo(src, label, mapping, field));
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}
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String hdrs = taskProperty("headers");
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if (hdrs != null) {
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for (String header : hdrs.split("\\|\\|")) {
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int split = header.indexOf(":");
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headers.put(header.substring(0, split).trim(), header.substring(split + 1).trim());
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}
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}
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// initialize response document parser
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DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
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factory.setNamespaceAware(true);
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try {
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docBuilder = factory.newDocumentBuilder();
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} catch (ParserConfigurationException pcE) {
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log.error("caught exception: " + pcE);
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// no point in continuing
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throw new IOException(pcE.getMessage(), pcE);
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}
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}
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/**
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* Perform the curation task upon passed DSO
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*
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* @param dso the DSpace object
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* @throws IOException
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*/
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@Override
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public int perform(DSpaceObject dso) throws IOException {
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int status = Curator.CURATE_SKIP;
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StringBuilder resultSb = new StringBuilder();
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if (dso.getType() == Constants.ITEM) {
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Item item = (Item)dso;
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String itemId = item.getHandle();
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if (itemId == null) {
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// we are still in workflow - no handle assigned - try title
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DCValue[] titleDc = item.getMetadata("dc", "title", null, Item.ANY);
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String title = (titleDc.length > 0) ? titleDc[0].value : "untitled - dbId: " + item.getID();
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itemId = "Workflow item: " + title;
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} else {
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itemId = "handle: " + itemId;
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}
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resultSb.append(itemId);
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// Only proceed if item has a value for service template parameter
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DCValue[] dcVals = item.getMetadata(lookupField);
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if (dcVals.length > 0 && dcVals[0].value.length() > 0) {
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String value = transform(dcVals[0].value, lookupTransform);
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status = callService(value, item, resultSb);
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} else {
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resultSb.append(" lacks metadata value required for service: ").append(lookupField);
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status = Curator.CURATE_FAIL;
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}
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} else {
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resultSb.append("Object skipped");
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}
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report(resultSb.toString());
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setResult(resultSb.toString());
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return status;
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}
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private int callService(String value, Item item, StringBuilder resultSb) throws IOException {
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String callUrl = urlTemplate.replaceAll("\\{" + templateParam + "\\}", value);
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HttpClient client = new DefaultHttpClient();
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HttpGet req = new HttpGet(callUrl);
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for (Map.Entry<String, String> entry : headers.entrySet()) {
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req.addHeader(entry.getKey(), entry.getValue());
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}
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HttpResponse resp = client.execute(req);
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int status = Curator.CURATE_ERROR;
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int statusCode = resp.getStatusLine().getStatusCode();
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if (statusCode == HttpStatus.SC_OK) {
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HttpEntity entity = resp.getEntity();
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if (entity != null) {
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// boiler-plate handling taken from Apache 4.1 javadoc
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InputStream instream = entity.getContent();
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try {
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Document doc = docBuilder.parse(instream);
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status = processResponse(doc, item, resultSb);
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} catch (SAXException saxE) {
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log.error("caught exception: " + saxE);
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resultSb.append(" unable to read response document");
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} catch (RuntimeException ex) {
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// In case of an unexpected exception you may want to abort
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// the HTTP request in order to shut down the underlying
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// connection and release it back to the connection manager.
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req.abort();
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log.error("caught exception: " + ex);
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throw ex;
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} finally {
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// Closing the input stream will trigger connection release
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instream.close();
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}
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// When HttpClient instance is no longer needed,
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// shut down the connection manager to ensure
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// immediate deallocation of all system resources
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client.getConnectionManager().shutdown();
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} else {
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log.error(" obtained no valid service response");
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resultSb.append("no service response");
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}
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} else {
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log.error("service returned non-OK status: " + statusCode);
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resultSb.append("no service response");
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}
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return status;
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}
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private int processResponse(Document doc, Item item, StringBuilder resultSb) throws IOException {
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boolean update = false;
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int status = Curator.CURATE_ERROR;
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List<String> values = new ArrayList<String>();
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checkNamespaces(doc);
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try {
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for (DataInfo info : dataList) {
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NodeList nodes = (NodeList)info.expr.evaluate(doc, XPathConstants.NODESET);
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values.clear();
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// if data found and we are mapping, check assignment policy
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if (nodes.getLength() > 0 && info.mapping != null) {
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if ("=>".equals(info.mapping)) {
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item.clearMetadata(info.schema, info.element, info.qualifier, Item.ANY);
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} else if ("~>".equals(info.mapping)) {
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if (item.getMetadata(info.schema, info.element, info.qualifier, Item.ANY).length > 0) {
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||||||
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// there are values, so don't overwrite
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continue;
|
||||||
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}
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} else {
|
||||||
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for (DCValue dcVal : item.getMetadata(info.schema, info.element, info.qualifier, Item.ANY)) {
|
||||||
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values.add(dcVal.value);
|
||||||
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}
|
||||||
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}
|
||||||
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}
|
||||||
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for (int i = 0; i < nodes.getLength(); i++) {
|
||||||
|
Node node = nodes.item(i);
|
||||||
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String tvalue = transform(node.getFirstChild().getNodeValue(), info.transform);
|
||||||
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// assign to metadata field if mapped && not present
|
||||||
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if (info.mapping != null && ! values.contains(tvalue)) {
|
||||||
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item.addMetadata(info.schema, info.element, info.qualifier, lang, tvalue);
|
||||||
|
update = true;
|
||||||
|
}
|
||||||
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// add to result string in any case
|
||||||
|
resultSb.append(fieldSeparator).append(info.label).append(": ").append(tvalue);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
// update Item if it has changed
|
||||||
|
if (update) {
|
||||||
|
item.update();
|
||||||
|
}
|
||||||
|
status = Curator.CURATE_SUCCESS;
|
||||||
|
} catch (AuthorizeException authE) {
|
||||||
|
log.error("caught exception: " + authE);
|
||||||
|
resultSb.append(" not authorized to update");
|
||||||
|
status = Curator.CURATE_FAIL;
|
||||||
|
} catch (SQLException sqlE) {
|
||||||
|
log.error("caught exception: " + sqlE);
|
||||||
|
resultSb.append(" error updating metadata");
|
||||||
|
} catch (XPathExpressionException xpeE) {
|
||||||
|
log.error("caught exception: " + xpeE);
|
||||||
|
resultSb.append(" error reading response document");
|
||||||
|
}
|
||||||
|
return status;
|
||||||
|
}
|
||||||
|
|
||||||
|
private String transform(String value, String transDef) {
|
||||||
|
if (transDef == null) {
|
||||||
|
return value;
|
||||||
|
}
|
||||||
|
String[] tokens = tokenize(transDef);
|
||||||
|
String retValue = value;
|
||||||
|
for (int i = 0; i < tokens.length; i+= 2) {
|
||||||
|
if ("cut".equals(tokens[i]) || "trunc".equals(tokens[i])) {
|
||||||
|
int index = Integer.parseInt(tokens[i+1]);
|
||||||
|
if (retValue.length() > index) {
|
||||||
|
if ("cut".equals(tokens[i])) {
|
||||||
|
retValue = retValue.substring(index);
|
||||||
|
} else {
|
||||||
|
retValue = retValue.substring(0, index);
|
||||||
|
}
|
||||||
|
} else if ("cut".equals(tokens[i])) {
|
||||||
|
log.error("requested cut: " + index + " exceeds value length");
|
||||||
|
return value;
|
||||||
|
}
|
||||||
|
} else if ("match".equals(tokens[i])) {
|
||||||
|
int index2 = retValue.indexOf(tokens[i+1]);
|
||||||
|
if (index2 > 0) {
|
||||||
|
retValue = retValue.substring(index2);
|
||||||
|
} else {
|
||||||
|
log.error("requested match: " + tokens[i+1] + " failed");
|
||||||
|
return value;
|
||||||
|
}
|
||||||
|
} else if ("text".equals(tokens[i])) {
|
||||||
|
retValue = retValue + tokens[i+1];
|
||||||
|
} else {
|
||||||
|
log.error(" unknown transform operation: " + tokens[i]);
|
||||||
|
return value;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return retValue;
|
||||||
|
}
|
||||||
|
|
||||||
|
private String[] tokenize(String text) {
|
||||||
|
List<String> list = new ArrayList<String>();
|
||||||
|
Matcher m = ttPattern.matcher(text);
|
||||||
|
while (m.find()) {
|
||||||
|
if (m.group(1) != null) {
|
||||||
|
list.add(m.group(1));
|
||||||
|
} else if (m.group(2) != null) {
|
||||||
|
list.add(m.group(2));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return list.toArray(new String[0]);
|
||||||
|
}
|
||||||
|
|
||||||
|
private int getMapIndex(String mapping) {
|
||||||
|
int index = mapping.indexOf("->");
|
||||||
|
if (index == -1) {
|
||||||
|
index = mapping.indexOf("=>");
|
||||||
|
}
|
||||||
|
if (index == -1) {
|
||||||
|
index = mapping.indexOf("~>");
|
||||||
|
}
|
||||||
|
return index;
|
||||||
|
}
|
||||||
|
|
||||||
|
private String[] parseTransform(String field) {
|
||||||
|
String[] parsed = new String[2];
|
||||||
|
parsed[0] = field;
|
||||||
|
int txIdx = field.indexOf(":");
|
||||||
|
if (txIdx > 0) {
|
||||||
|
// transform specified
|
||||||
|
String txName = field.substring(0, txIdx);
|
||||||
|
parsed[1] = taskProperty("transform." + txName);
|
||||||
|
if (parsed[1] == null) {
|
||||||
|
log.error("no transform found for: " + txName);
|
||||||
|
}
|
||||||
|
parsed[0] = field.substring(txIdx + 1);
|
||||||
|
}
|
||||||
|
return parsed;
|
||||||
|
}
|
||||||
|
|
||||||
|
private void checkNamespaces(Document document) throws IOException {
|
||||||
|
// skip if already done
|
||||||
|
if (dataList.get(0).expr != null) {
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
try {
|
||||||
|
XPath xpath = XPathFactory.newInstance().newXPath();
|
||||||
|
String prefix = null;
|
||||||
|
NamedNodeMap attrs = document.getDocumentElement().getAttributes();
|
||||||
|
for (int i = 0; i < attrs.getLength(); i++) {
|
||||||
|
Node n = attrs.item(i);
|
||||||
|
String name = n.getNodeName();
|
||||||
|
// remember if a namespace
|
||||||
|
if (name.startsWith("xmlns")) {
|
||||||
|
if (! "xmlns".equals(name)) {
|
||||||
|
// it is a declared (non-default) namespace - capture prefix
|
||||||
|
nsMap.put(name.substring(name.indexOf(":") + 1), n.getNodeValue());
|
||||||
|
} else {
|
||||||
|
// it is the default name space - mint a unique prefix
|
||||||
|
prefix = "pre";
|
||||||
|
nsMap.put(prefix, n.getNodeValue());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (nsMap.size() > 0) {
|
||||||
|
xpath.setNamespaceContext(this);
|
||||||
|
}
|
||||||
|
// now compile the XPath expressions
|
||||||
|
for (DataInfo info : dataList) {
|
||||||
|
info.expr = xpath.compile(mangleExpr(info.xpsrc, prefix));
|
||||||
|
}
|
||||||
|
} catch (XPathExpressionException xpeE) {
|
||||||
|
log.error("caught exception: " + xpeE);
|
||||||
|
// no point in continuing
|
||||||
|
throw new IOException(xpeE.getMessage(), xpeE);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
private String mangleExpr(String expr, String prefix) {
|
||||||
|
if (prefix == null) {
|
||||||
|
return expr;
|
||||||
|
}
|
||||||
|
// OK the drill is to prepend all node names with the prefix
|
||||||
|
// *unless* the node name already has a prefix.
|
||||||
|
StringBuilder sb = new StringBuilder();
|
||||||
|
int i = 0;
|
||||||
|
while (i < expr.length()) {
|
||||||
|
if (expr.charAt(i) == '/') {
|
||||||
|
sb.append("/");
|
||||||
|
i++;
|
||||||
|
} else {
|
||||||
|
int next = expr.indexOf("/", i);
|
||||||
|
String token = (next > 0) ? expr.substring(i, next) : expr.substring(i);
|
||||||
|
if (! token.startsWith("@") && token.indexOf(":") < 0) {
|
||||||
|
sb.append(prefix).append(":");
|
||||||
|
}
|
||||||
|
sb.append(token);
|
||||||
|
i += token.length();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return sb.toString();
|
||||||
|
}
|
||||||
|
|
||||||
|
// ---- NamespaceContext methods ---- //
|
||||||
|
|
||||||
|
public String getNamespaceURI(String prefix) {
|
||||||
|
if (prefix == null) {
|
||||||
|
throw new NullPointerException("Null prefix");
|
||||||
|
} else if ("xml".equals(prefix)) {
|
||||||
|
return XMLConstants.XML_NS_URI;
|
||||||
|
}
|
||||||
|
String nsURI = nsMap.get(prefix);
|
||||||
|
return (nsURI != null) ? nsURI : XMLConstants.NULL_NS_URI;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getPrefix(String uri) {
|
||||||
|
throw new UnsupportedOperationException();
|
||||||
|
}
|
||||||
|
|
||||||
|
public Iterator getPrefixes(String uri) {
|
||||||
|
throw new UnsupportedOperationException();
|
||||||
|
}
|
||||||
|
|
||||||
|
private class DataInfo {
|
||||||
|
public XPathExpression expr; // compiled XPath espression for data
|
||||||
|
public String xpsrc; // uncompiled XPath expression
|
||||||
|
public String label; // label for data in result string
|
||||||
|
public String mapping; // data mapping symbol: ->,=>,~>, or null = unmapped
|
||||||
|
public String schema; // item metadata field mapping target, null = unmapped
|
||||||
|
public String element; // item metadata field mapping target, null = unmapped
|
||||||
|
public String qualifier; // item metadata field mapping target, null = unmapped
|
||||||
|
public String transform; // optional transformation of data before field assignment
|
||||||
|
|
||||||
|
public DataInfo(String xpsrc, String label, String mapping, String field) {
|
||||||
|
this.xpsrc = xpsrc;
|
||||||
|
this.expr = expr;
|
||||||
|
this.label = label;
|
||||||
|
this.mapping = mapping;
|
||||||
|
if (field != null) {
|
||||||
|
String[] parsed = parseTransform(field);
|
||||||
|
String[] parts = parsed[0].split("\\.");
|
||||||
|
this.schema = parts[0];
|
||||||
|
this.element = parts[1];
|
||||||
|
this.qualifier = (parts.length == 3) ? parts[2] : null;
|
||||||
|
this.transform = parsed[1];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
Reference in New Issue
Block a user