http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthChecker.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthChecker.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthChecker.java deleted file mode 100644 index 7db539a..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthChecker.java +++ /dev/null @@ -1,57 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import java.io.IOException; -import java.net.HttpURLConnection; -import java.net.MalformedURLException; -import java.net.SocketTimeoutException; -import java.net.URL; -import java.net.URLConnection; -import java.util.List; - -import net.sf.taverna.t2.workflowmodel.Processor; -import net.sf.taverna.t2.workflowmodel.processor.activity.Activity; -import net.sf.taverna.t2.workflowmodel.health.HealthCheck; -import net.sf.taverna.t2.workflowmodel.health.HealthChecker; -import net.sf.taverna.t2.visit.VisitReport; -import net.sf.taverna.t2.visit.VisitReport.Status; - -import net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker; -import net.sf.taverna.t2.workflowmodel.processor.activity.DisabledActivity; - -/** - * A health checker for the Biomoby Object activity. - * - * @author David Withers - */ -public class BiomobyObjectActivityHealthChecker extends RemoteHealthChecker { - - public boolean canVisit(Object subject) { - if (subject == null) { - return false; - } - if (subject instanceof BiomobyObjectActivity) { - return true; - } - if (subject instanceof DisabledActivity) { - return (((DisabledActivity) subject).getActivity() instanceof BiomobyObjectActivity); - } - return false; - } - - public VisitReport visit(Object o, List<Object> ancestors) { - Activity activity = (Activity) o; - BiomobyObjectActivityConfigurationBean configuration = null; - if (activity instanceof BiomobyObjectActivity) { - configuration = (BiomobyObjectActivityConfigurationBean) activity.getConfiguration(); - } else if (activity instanceof DisabledActivity) { - configuration = (BiomobyObjectActivityConfigurationBean) ((DisabledActivity) activity).getActivityConfiguration(); - } - return contactEndpoint(activity, configuration.getMobyEndpoint()); - - } - -}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncCgiService.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncCgiService.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncCgiService.java deleted file mode 100644 index 552dd34..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncCgiService.java +++ /dev/null @@ -1,517 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.io.StringReader; -import java.io.UnsupportedEncodingException; -import java.util.ArrayList; -import java.util.HashMap; - -import javax.xml.parsers.DocumentBuilder; -import javax.xml.parsers.DocumentBuilderFactory; - -import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler; -import org.apache.commons.httpclient.HttpClient; -import org.apache.commons.httpclient.HttpStatus; -import org.apache.commons.httpclient.methods.PostMethod; -import org.apache.commons.httpclient.methods.RequestEntity; -import org.apache.commons.httpclient.methods.StringRequestEntity; -import org.apache.commons.httpclient.params.HttpMethodParams; -import org.apache.log4j.Logger; -import org.biomoby.shared.MobyException; -import org.biomoby.shared.MobyPrefixResolver; -import org.biomoby.shared.parser.MobyTags; -import org.biomoby.w3c.addressing.EndpointReference; -import org.jdom.Element; -import org.jdom.output.Format; -import org.jdom.output.XMLOutputter; -import org.omg.lsae.notifications.AnalysisEvent; -import org.w3c.dom.NodeList; -import org.xml.sax.InputSource; - -/** - * This class contains one method that is used to execute asynchronous HTTP POST - * services - * - * @author Edward Kawas - * - */ -public class ExecuteAsyncCgiService { - - private static final String GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION = "http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest";; - private static final String DESTROY_RESOURCE_ACTION = "http://docs.oasis-open.org/wsrf/rlw-2/ImmediateResourceTermination/DestroyRequest";; - - private static final String RESOURCE_PROPERTIES_NS = "http://docs.oasis-open.org/wsrf/rp-2";; - private static final String RESULT_PREFIX = "result_"; - private static final String STATUS_PREFIX = "status_"; - private static Logger logger = Logger - .getLogger(ExecuteAsyncCgiService.class); - - /** - * - * @param url - * @param serviceName - * @param xml - * @return - */ - public static String executeMobyCgiAsyncService(String url, - String serviceName, String xml) throws MobyException { - - // First, let's get the queryIds - org.w3c.dom.Document message = null; - - try { - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - dbf.setNamespaceAware(true); - dbf.setValidating(false); - DocumentBuilder db = dbf.newDocumentBuilder(); - - message = db.parse(new InputSource(new StringReader(xml))); - } catch (Throwable t) { - throw new MobyException("Error while parsing input query", t); - } - - NodeList l_data = message.getElementsByTagNameNS( - MobyPrefixResolver.MOBY_XML_NAMESPACE, MobyTags.MOBYDATA); - if (l_data == null || l_data.getLength() == 0) { - l_data = message.getElementsByTagNameNS( - MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID, - MobyTags.MOBYDATA); - } - - // Freeing resources - message = null; - - if (l_data == null || l_data.getLength() == 0) { - throw new MobyException("Empty asynchronous MOBY query!"); - } - - int nnode = l_data.getLength(); - String[] queryIds = new String[nnode]; - String[] tmpQueryIds = new String[nnode]; - String[] results = new String[nnode]; - for (int inode = 0; inode < nnode; inode++) { - String queryId = null; - - org.w3c.dom.Element mdata = (org.w3c.dom.Element) l_data - .item(inode); - - queryId = mdata.getAttribute(MobyTags.QUERYID); - if (queryId == null || queryId.length() == 0) - queryId = mdata - .getAttributeNS(MobyPrefixResolver.MOBY_XML_NAMESPACE, - MobyTags.QUERYID); - if (queryId == null || queryId.length() == 0) - queryId = mdata.getAttributeNS( - MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID, - MobyTags.QUERYID); - - if (queryId == null || queryId.length() == 0) { - throw new MobyException( - "Unable to extract queryId for outgoing MOBY message"); - } - - tmpQueryIds[inode] = queryIds[inode] = queryId; - results[inode] = null; - } - - // Freeing resources - l_data = null; - - // Second, let's launch - EndpointReference epr = launchCgiAsyncService(url, xml); - - // Third, waiting for the results - try { - // FIXME - add appropriate values here - long pollingInterval = 1000L; - double backoff = 1.0; - - // Max: one minute pollings - long maxPollingInterval = 60000L; - - // Min: one second - if (pollingInterval <= 0L) - pollingInterval = 1000L; - - // Backoff: must be bigger than 1.0 - if (backoff <= 1.0) - backoff = 1.5; - - do { - try { - Thread.sleep(pollingInterval); - } catch (InterruptedException ie) { - // DoNothing(R) - } - - if (pollingInterval != maxPollingInterval) { - pollingInterval = (long) ((double) pollingInterval * backoff); - if (pollingInterval > maxPollingInterval) { - pollingInterval = maxPollingInterval; - } - } - } while (pollAsyncCgiService(serviceName, url, epr, tmpQueryIds, - results)); - } finally { - - // Call destroy on this service .... - freeCgiAsyncResources(url, epr); - - } - - // Fourth, assembling back the results - - // Results array already contains mobyData - Element[] mobydatas = new Element[results.length]; - for (int x = 0; x < results.length; x++) { - // TODO remove the extra wrapping from our result - try { - Element inputElement = XMLUtilities.getDOMDocument(results[x]) - .getRootElement(); - if (inputElement.getName().indexOf( - "GetMultipleResourcePropertiesResponse") >= 0) - if (inputElement.getChildren().size() > 0) - inputElement = (Element) inputElement.getChildren() - .get(0); - if (inputElement.getName().indexOf("result_") >= 0) - if (inputElement.getChildren().size() > 0) - inputElement = (Element) inputElement.getChildren() - .get(0); - // replace results[x] - mobydatas[x] = inputElement; - } catch (MobyException e) { - // TODO what should i do? - } - } - Element e = null; - try { - e = XMLUtilities.createMultipleInvokations(mobydatas); - } catch (Exception ex) { - logger - .error("There was a problem creating our XML message ...", - ex); - } - // Fifth, returning results - return e == null ? "" : new XMLOutputter(Format.getPrettyFormat()) - .outputString(e); - } - - private static void freeCgiAsyncResources(String endpoint, - EndpointReference epr) throws MobyException { - // construct the Httpclient - HttpClient client = new HttpClient(); - client.getParams().setParameter("http.useragent", "jMoby/Taverna2"); - // create the post method - PostMethod method = new PostMethod(endpoint + "/destroy"); - - // put our data in the request - RequestEntity entity; - try { - entity = new StringRequestEntity( - "<Destroy xmlns=\"http://docs.oasis-open.org/wsrf/rl-2\"/>", - "text/xml", null); - } catch (UnsupportedEncodingException e) { - throw new MobyException("Problem posting data to webservice", e); - } - method.setRequestEntity(entity); - - // set the header - StringBuffer httpheader = new StringBuffer(); - httpheader.append("<moby-wsrf>"); - httpheader - .append("<wsa:Action xmlns:wsa=\"http://www.w3.org/2005/08/addressing\";>" - + DESTROY_RESOURCE_ACTION + "</wsa:Action>"); - httpheader - .append("<wsa:To xmlns:wsu=\"http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd\"; xmlns:wsa=\"http://www.w3.org/2005/08/addressing\"; wsu:Id=\"To\">" - + endpoint + "</wsa:To>"); - httpheader - .append("<mobyws:ServiceInvocationId xmlns:mobyws=\"http://biomoby.org/\"; xmlns:wsa=\"http://www.w3.org/2005/08/addressing\"; wsa:IsReferenceParameter=\"true\">" - + epr.getServiceInvocationId() - + "</mobyws:ServiceInvocationId>"); - httpheader.append("</moby-wsrf>"); - method.addRequestHeader("moby-wsrf", httpheader.toString().replaceAll( - "\r\n", "")); - // retry up to 10 times - client.getParams().setParameter(HttpMethodParams.RETRY_HANDLER, - new DefaultHttpMethodRetryHandler(10, true)); - - // call the method - try { - int result = client.executeMethod(method); - if (result != HttpStatus.SC_OK) - throw new MobyException( - "Async HTTP POST service returned code: " + result - + "\n" + method.getStatusLine()); - } catch (IOException e) { - throw new MobyException("Problem reading response from webservice", - e); - } finally { - // Release current connection to the connection pool once you are - // done - method.releaseConnection(); - } - } - - /** - * - * @param endpoint - * the url to the service to call - * @param xml - * the BioMOBY input message - * @return EndpointReference the EPR returned by the service - * @throws MobyException - */ - private static EndpointReference launchCgiAsyncService(String endpoint, - String xml) throws MobyException { - // construct the Httpclient - HttpClient client = new HttpClient(); - client.getParams().setParameter("http.useragent", "jMoby/Taverna2"); - // create the post method - PostMethod method = new PostMethod(endpoint); - - // put our data in the request - RequestEntity entity; - try { - entity = new StringRequestEntity(xml, "text/xml", null); - } catch (UnsupportedEncodingException e) { - throw new MobyException("Problem posting data to webservice", e); - } - method.setRequestEntity(entity); - - // retry up to 10 times - client.getParams().setParameter(HttpMethodParams.RETRY_HANDLER, - new DefaultHttpMethodRetryHandler(10, true)); - - // call the method - try { - int result = client.executeMethod(method); - if (result != HttpStatus.SC_OK) - throw new MobyException( - "Async HTTP POST service returned code: " + result - + "\n" + method.getStatusLine()); - return EndpointReference.createFromXML(method.getResponseHeader( - "moby-wsrf").getValue()); - } catch (IOException e) { - throw new MobyException("Problem reading response from webservice", - e); - } finally { - // Release current connection to the connection pool once you are - // done - method.releaseConnection(); - } - } - - private static boolean pollAsyncCgiService(String msName, String url, - EndpointReference epr, String[] queryIds, String[] result) - throws MobyException { - // Needed to remap results - HashMap<String, Integer> queryMap = new HashMap<String, Integer>(); - for (int qi = 0; qi < queryIds.length; qi++) { - String queryId = queryIds[qi]; - if (queryId != null) - queryMap.put(queryId, new Integer(qi)); - } - - if (queryMap.size() == 0) - return false; - - // construct the GetMultipleResourceProperties XML - StringBuffer xml = new StringBuffer(); - xml.append("<wsrf-rp:GetMultipleResourceProperties xmlns:wsrf-rp='" - + RESOURCE_PROPERTIES_NS - + "' xmlns:mobyws='http://biomoby.org/'>"); - for (String q : queryMap.keySet()) - xml.append("<wsrf-rp:ResourceProperty>mobyws:" + STATUS_PREFIX + q - + "</wsrf-rp:ResourceProperty>"); - xml.append("</wsrf-rp:GetMultipleResourceProperties>"); - - StringBuffer httpheader = new StringBuffer(); - httpheader.append("<moby-wsrf>"); - httpheader - .append("<wsa:Action xmlns:wsa=\"http://www.w3.org/2005/08/addressing\";>" - + GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION - + "</wsa:Action>"); - httpheader - .append("<wsa:To xmlns:wsu=\"http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd\"; xmlns:wsa=\"http://www.w3.org/2005/08/addressing\"; wsu:Id=\"To\">" - + url + "</wsa:To>"); - httpheader - .append("<mobyws:ServiceInvocationId xmlns:mobyws=\"http://biomoby.org/\"; xmlns:wsa=\"http://www.w3.org/2005/08/addressing\"; wsa:IsReferenceParameter=\"true\">" - + epr.getServiceInvocationId() - + "</mobyws:ServiceInvocationId>"); - httpheader.append("</moby-wsrf>"); - - AnalysisEvent[] l_ae = null; - // First, status from queries - String response = ""; - // construct the Httpclient - HttpClient client = new HttpClient(); - client.getParams().setParameter("http.useragent", "jMoby/Taverna2"); - // create the post method - PostMethod method = new PostMethod(url + "/status"); - // add the moby-wsrf header (with no newlines) - method.addRequestHeader("moby-wsrf", httpheader.toString().replaceAll( - "\r\n", "")); - - // put our data in the request - RequestEntity entity; - try { - entity = new StringRequestEntity(xml.toString(), "text/xml", null); - } catch (UnsupportedEncodingException e) { - throw new MobyException("Problem posting data to webservice", e); - } - method.setRequestEntity(entity); - - // retry up to 10 times - client.getParams().setParameter(HttpMethodParams.RETRY_HANDLER, - new DefaultHttpMethodRetryHandler(10, true)); - - // call the method - try { - if (client.executeMethod(method) != HttpStatus.SC_OK) - throw new MobyException( - "Async HTTP POST service returned code: " - + method.getStatusCode() + "\n" - + method.getStatusLine() - + "\nduring our polling request"); - response = stream2String(method.getResponseBodyAsStream()); - } catch (IOException e) { - throw new MobyException("Problem reading response from webservice", - e); - } finally { - // Release current connection to the connection pool once you - // are - // done - method.releaseConnection(); - } - - if (response != null) { - l_ae = AnalysisEvent.createFromXML(response); - } - - if (l_ae == null || l_ae.length == 0) { - new MobyException( - "Troubles while checking asynchronous MOBY job status from service " - + msName); - } - - ArrayList<String> finishedQueries = new ArrayList<String>(); - // Second, gather those finished queries - for (int iae = 0; iae < l_ae.length; iae++) { - AnalysisEvent ae = l_ae[iae]; - if (ae.isCompleted()) { - String queryId = ae.getQueryId(); - if (!queryMap.containsKey(queryId)) { - throw new MobyException( - "Invalid result queryId on asynchronous MOBY job status fetched from " - + msName); - } - finishedQueries.add(queryId); - } - } - - // Third, let's fetch the results from the finished queries - if (finishedQueries.size() > 0) { - String[] resQueryIds = finishedQueries.toArray(new String[0]); - for (int x = 0; x < resQueryIds.length; x++) { - // construct the GetMultipleResourceProperties XML - xml = new StringBuffer(); - xml - .append("<wsrf-rp:GetMultipleResourceProperties xmlns:wsrf-rp='" - + RESOURCE_PROPERTIES_NS - + "' xmlns:mobyws='http://biomoby.org/'>"); - for (String q : resQueryIds) - xml.append("<wsrf-rp:ResourceProperty>mobyws:" + RESULT_PREFIX + q - + "</wsrf-rp:ResourceProperty>"); - xml.append("</wsrf-rp:GetMultipleResourceProperties>"); - - httpheader = new StringBuffer(); - httpheader.append("<moby-wsrf>"); - httpheader - .append("<wsa:Action xmlns:wsa=\"http://www.w3.org/2005/08/addressing\";>" - + GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION - + "</wsa:Action>"); - httpheader - .append("<wsa:To xmlns:wsu=\"http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd\"; xmlns:wsa=\"http://www.w3.org/2005/08/addressing\"; wsu:Id=\"To\">" - + url + "</wsa:To>"); - httpheader - .append("<mobyws:ServiceInvocationId xmlns:mobyws=\"http://biomoby.org/\"; xmlns:wsa=\"http://www.w3.org/2005/08/addressing\"; wsa:IsReferenceParameter=\"true\">" - + epr.getServiceInvocationId() - + "</mobyws:ServiceInvocationId>"); - httpheader.append("</moby-wsrf>"); - client = new HttpClient(); - client.getParams().setParameter("http.useragent", - "jMoby/Taverna2"); - // create the post method - method = new PostMethod(url + "/results"); - // add the moby-wsrf header (with no newlines) - method.addRequestHeader("moby-wsrf", httpheader.toString() - .replaceAll("\r\n", "")); - - // put our data in the request - entity = null; - try { - entity = new StringRequestEntity(xml.toString(), - "text/xml", null); - } catch (UnsupportedEncodingException e) { - throw new MobyException( - "Problem posting data to webservice", e); - } - method.setRequestEntity(entity); - - // retry up to 10 times - client.getParams().setParameter(HttpMethodParams.RETRY_HANDLER, - new DefaultHttpMethodRetryHandler(10, true)); - - // call the method - try { - if (client.executeMethod(method) != HttpStatus.SC_OK) - throw new MobyException( - "Async HTTP POST service returned code: " - + method.getStatusCode() + "\n" - + method.getStatusLine() - + "\nduring our polling request"); - // place the result in the array - result[x] = stream2String(method.getResponseBodyAsStream()); - // Marking as null - queryIds[x] = null; - } catch (IOException e) { - logger.warn("Problem getting result from webservice\n" - + e.getMessage()); - } finally { - // Release current connection - method.releaseConnection(); - } - } - - } - return finishedQueries.size() != queryMap.size(); - } - - private static String stream2String(InputStream is) { - BufferedReader br = new BufferedReader(new InputStreamReader(is)); - StringBuilder sb = new StringBuilder(); - String line = null; - String newline = System.getProperty("line.separator"); - try { - while ((line = br.readLine()) != null) { - sb.append(line + newline); - } - } catch (IOException e) { - logger.warn("Exception reading input stream ...", e); - } finally { - try { - br.close(); - } catch (IOException e) { - logger.warn("Exception closing input stream ...", e); - } - } - return sb.toString(); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncMobyService.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncMobyService.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncMobyService.java deleted file mode 100644 index 10c76bc..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncMobyService.java +++ /dev/null @@ -1,695 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import java.io.StringReader; -import java.io.StringWriter; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Map; - -import javax.xml.namespace.QName; -import javax.xml.parsers.DocumentBuilder; -import javax.xml.parsers.DocumentBuilderFactory; -import javax.xml.soap.MessageFactory; -import javax.xml.soap.SOAPBody; -import javax.xml.soap.SOAPElement; -import javax.xml.soap.SOAPEnvelope; -import javax.xml.soap.SOAPException; -import javax.xml.soap.SOAPHeader; -import javax.xml.soap.SOAPMessage; -import javax.xml.soap.SOAPPart; -import javax.xml.transform.OutputKeys; -import javax.xml.transform.Transformer; -import javax.xml.transform.TransformerConfigurationException; -import javax.xml.transform.TransformerException; -import javax.xml.transform.TransformerFactory; -import javax.xml.transform.dom.DOMSource; -import javax.xml.transform.stream.StreamResult; -import javax.xml.ws.BindingProvider; -import javax.xml.ws.Dispatch; -import javax.xml.ws.Service; -import javax.xml.ws.soap.SOAPBinding; - -import org.apache.log4j.Logger; -import org.biomoby.shared.MobyException; -import org.biomoby.shared.MobyPrefixResolver; -import org.biomoby.shared.MobyService; -import org.biomoby.shared.parser.MobyTags; -import org.biomoby.w3c.addressing.EndpointReference; -import org.omg.lsae.notifications.AnalysisEvent; -import org.w3c.dom.Node; -import org.w3c.dom.NodeList; -import org.xml.sax.InputSource; - - -/** - * This class contains one method that is used to execute asynchronous moby - * services - * - * @author Edward Kawas - * - */ - -public class ExecuteAsyncMobyService { - - /* async constants */ - private static final String GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION = "http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest";; - private static final String DESTROY_RESOURCE_ACTION = "http://docs.oasis-open.org/wsrf/rlw-2/ImmediateResourceTermination/DestroyRequest";; - - private static final String RESOURCE_PROPERTIES_NS = "http://docs.oasis-open.org/wsrf/rp-2";; - private static final String RESOURCE_LIFETIME_NS = "http://docs.oasis-open.org/wsrf/rl-2";; - - @SuppressWarnings("unused") - private static final String XMLNS_NS = "http://www.w3.org/2000/xmlns/";; - private static final String XSD_NS = "http://www.w3.org/2001/XMLSchema";; - private static final String WSA_NS = "http://www.w3.org/2005/08/addressing";; - private static final String WSU_NS = "http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd";; - private static final String ANON_URI = WSA_NS + "/anonymous"; - private static final String RESULT_PREFIX = "result_"; - private static final String STATUS_PREFIX = "status_"; - - private static Logger logger = Logger.getLogger(ExecuteAsyncMobyService.class); - /** - * This method does the same as getMultipleResourceProperties, with the - * difference that it returns an String instead of a SOAPPart object. The - * result is the serialization of the SOAPPart output obtained from - * getMultipleResourceProperties. - * - * @param msName - * The MOBY service name - * @param queryIds - * The array with the queryIds to use. It may contain null - * strings - * @param epr - * The EndpointReference object which helds the MOBY asynchronous - * job information - * @param asResult - * If this parameter is true, then this call fetches the results - * associated to the input queryIds. If it is false, then this - * call only asks for the job status. - * @return When at least one of the strings from queryIds array was not - * null, an String with the serialized answer from the service. - * Otherwise, it returns null. - * @throws SOAPException - */ - private static String getMultipleResourcePropertiesAsString(String msName, - String[] queryIds, EndpointReference epr, boolean asResult) - throws TransformerConfigurationException, SOAPException, - TransformerException { - SOAPPart result = getMultipleResourceProperties(msName, queryIds, epr, - asResult); - if (result == null) - return null; - Transformer tr = TransformerFactory.newInstance().newTransformer(); - tr.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes"); - - DOMSource dombody = new DOMSource(result); - - StringWriter sw = new StringWriter(); - tr.transform(dombody, new StreamResult(sw)); - - return sw.toString(); - } - - /** - * This method does the check and fetch work related to asynchronous - * services. When all the results are fetched, it returns false. When some - * recheck must be issued, it returns true. - * - * @param msName - * The MOBY service name - * @param epr - * The EndpointReference, used for the queries - * @param queryIds - * The array which holds the queryIds to ask for. It can contain - * null strings. - * @param result - * The array which will hold the mobyData results. This one must - * have the same size as queryIds array. - * @return true, if we need more checking iterations. Otherwise, false - * @throws MobyException - */ - private static boolean checkMobyAsyncJobsStatus(String msName, - EndpointReference epr, String[] queryIds, - org.w3c.dom.Element[] result) throws MobyException { - // Needed to remap results - HashMap<String, Integer> queryMap = new HashMap<String, Integer>(); - for (int qi = 0; qi < queryIds.length; qi++) { - String queryId = queryIds[qi]; - if (queryId != null) - queryMap.put(queryId, new Integer(qi)); - } - - if (queryMap.size() == 0) - return false; - - try { - AnalysisEvent[] l_ae = null; - // First, status from queries - String response = getMultipleResourcePropertiesAsString(msName, - queryIds, epr, false); - if (response != null) { - l_ae = AnalysisEvent.createFromXML(response); - } - - if (l_ae == null || l_ae.length == 0) { - new MobyException( - "Troubles while checking asynchronous MOBY job status from service " - + msName); - } - - ArrayList<String> finishedQueries = new ArrayList<String>(); - // Second, gather those finished queries - for (int iae = 0; iae < l_ae.length; iae++) { - AnalysisEvent ae = l_ae[iae]; - if (ae.isCompleted()) { - String queryId = ae.getQueryId(); - if (!queryMap.containsKey(queryId)) { - throw new MobyException( - "Invalid result queryId on asynchronous MOBY job status fetched from " - + msName); - } - finishedQueries.add(queryId); - } - } - - // Third, let's fetch the results from the finished queries - if (finishedQueries.size() > 0) { - String[] resQueryIds = finishedQueries.toArray(new String[0]); - SOAPPart soapDOM = getMultipleResourceProperties(msName, - resQueryIds, epr, true); - NodeList l_mul = soapDOM.getElementsByTagNameNS( - RESOURCE_PROPERTIES_NS, - "GetMultipleResourcePropertiesResponse"); - if (l_mul == null || l_mul.getLength() == 0) { - throw new MobyException( - "Error while fetching asynchronous MOBY results from " - + msName); - } - - org.w3c.dom.Element mul = (org.w3c.dom.Element) l_mul.item(0); - for (org.w3c.dom.Node child = mul.getFirstChild(); child != null; child = child - .getNextSibling()) { - if (child.getNodeType() == Node.ELEMENT_NODE - && MobyService.BIOMOBY_SERVICE_URI.equals(child - .getNamespaceURI())) { - String preQueryId = child.getLocalName(); - int subpos = preQueryId.indexOf(RESULT_PREFIX); - if (subpos != 0) { - throw new MobyException( - "Invalid result prefix on asynchronous MOBY job results fetched from " - + msName); - } - String queryId = preQueryId.substring(RESULT_PREFIX - .length()); - if (!queryMap.containsKey(queryId)) { - throw new MobyException( - "Invalid result queryId on asynchronous MOBY job results fetched from " - + msName); - } - - org.w3c.dom.Element elchild = (org.w3c.dom.Element) child; - NodeList l_moby = elchild.getElementsByTagNameNS( - MobyPrefixResolver.MOBY_XML_NAMESPACE, - MobyTags.MOBYDATA); - if (l_moby == null || l_moby.getLength() == 0) - l_moby = elchild - .getElementsByTagNameNS( - MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID, - MobyTags.MOBYDATA); - - if (l_moby == null || l_moby.getLength() == 0) { - throw new MobyException( - "Recovered empty payload from asynchronous MOBY service " - + msName); - } - Integer queryPos = queryMap.get(queryId); - result[queryPos] = (org.w3c.dom.Element) l_moby.item(0); - // Marking as null - queryIds[queryPos] = null; - } - } - } - - return finishedQueries.size() != queryMap.size(); - } catch (SOAPException se) { - throw new MobyException("Error while querying MOBY job status", se); - } catch (TransformerConfigurationException tce) { - throw new MobyException( - "Error while preparing to parse MOBY job status", tce); - } catch (TransformerException te) { - throw new MobyException("Error while parsing MOBY job status", te); - } - } - - /** - * This method calls the input MOBY service using the asynchronous protocol. - * - * @param endpoint - * The endpoint of the service. - * @param msName - * The MOBY service name. - * @param mobyXML - * The MOBY payload to be sent to the service. - * @return The MOBY payload with the results from the service. - * @throws MobyException - */ - public static String executeMobyAsyncService(String endpoint, String msName, - String mobyXML) throws MobyException { - // First, let's get the queryIds - org.w3c.dom.Document message = null; - - try { - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - dbf.setNamespaceAware(true); - dbf.setValidating(false); - DocumentBuilder db = dbf.newDocumentBuilder(); - - message = db.parse(new InputSource(new StringReader(mobyXML))); - } catch (Throwable t) { - throw new MobyException("Error while parsing input query", t); - } - - NodeList l_data = message.getElementsByTagNameNS( - MobyPrefixResolver.MOBY_XML_NAMESPACE, MobyTags.MOBYDATA); - if (l_data == null || l_data.getLength() == 0) { - l_data = message.getElementsByTagNameNS( - MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID, - MobyTags.MOBYDATA); - } - - // Freeing resources - message = null; - - if (l_data == null || l_data.getLength() == 0) { - throw new MobyException("Empty asynchronous MOBY query!"); - } - - int nnode = l_data.getLength(); - String[] queryIds = new String[nnode]; - String[] tmpQueryIds = new String[nnode]; - org.w3c.dom.Element[] results = new org.w3c.dom.Element[nnode]; - for (int inode = 0; inode < nnode; inode++) { - String queryId = null; - - org.w3c.dom.Element mdata = (org.w3c.dom.Element) l_data - .item(inode); - - queryId = mdata.getAttribute(MobyTags.QUERYID); - if (queryId == null || queryId.length() == 0) - queryId = mdata - .getAttributeNS(MobyPrefixResolver.MOBY_XML_NAMESPACE, - MobyTags.QUERYID); - if (queryId == null || queryId.length() == 0) - queryId = mdata.getAttributeNS( - MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID, - MobyTags.QUERYID); - - if (queryId == null || queryId.length() == 0) { - throw new MobyException( - "Unable to extract queryId for outgoing MOBY message"); - } - - tmpQueryIds[inode] = queryIds[inode] = queryId; - results[inode] = null; - } - - // Freeing resources - l_data = null; - - // Second, let's launch - EndpointReference epr = launchMobyAsyncService(endpoint, msName, - mobyXML); - - // Third, waiting for the results - try { - // FIXME - add appropriate values here - long pollingInterval = 1000L; // proc.getRetryDelay(); - double backoff = 1.0;// proc.getBackoff(); - - // Max: one minute pollings - long maxPollingInterval = 60000L; - - // Min: one second - if (pollingInterval <= 0L) - pollingInterval = 1000L; - - // Backoff: must be bigger than 1.0 - if (backoff <= 1.0) - backoff = 1.5; - - do { - try { - Thread.sleep(pollingInterval); - } catch (InterruptedException ie) { - // DoNothing(R) - } - - if (pollingInterval != maxPollingInterval) { - pollingInterval = (long) ((double) pollingInterval * backoff/* - * proc. - * getBackoff - * ( - * ) - */); - if (pollingInterval > maxPollingInterval) { - pollingInterval = maxPollingInterval; - } - } - } while (checkMobyAsyncJobsStatus(msName, epr, tmpQueryIds, results)); - } finally { - try { - freeAsyncResources(msName, epr); - } catch (SOAPException se) { - logger.info( - "An error was fired while freeing MOBY asynchronous resources from " - + msName, se); - } - } - - // Fourth, assembling back the results - org.w3c.dom.Document resdoc = null; - try { - DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); - dbf.setNamespaceAware(true); - dbf.setValidating(false); - DocumentBuilder db = dbf.newDocumentBuilder(); - resdoc = db.newDocument(); - - org.w3c.dom.Element mobyroot = resdoc.createElementNS( - MobyPrefixResolver.MOBY_XML_NAMESPACE, MobyTags.MOBY); - resdoc.appendChild(mobyroot); - org.w3c.dom.Element mobycontent = resdoc - .createElementNS(MobyPrefixResolver.MOBY_XML_NAMESPACE, - MobyTags.MOBYCONTENT); - mobyroot.appendChild(mobycontent); - - // Results array already contains mobyData - - for (org.w3c.dom.Element result : results) { - mobycontent.appendChild(resdoc.importNode(result, true)); - } - } catch (Throwable t) { - throw new MobyException("Error while assembling output", t); - } - - // Fifth, returning results - try { - Transformer tr = TransformerFactory.newInstance().newTransformer(); - tr.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes"); - - DOMSource dombody = new DOMSource(resdoc); - - StringWriter sw = new StringWriter(); - tr.transform(dombody, new StreamResult(sw)); - - return sw.toString(); - } catch (Throwable t) { - throw new MobyException("Error while assembling output", t); - } - } - - /** - * This method free the asynchronous MOBY resources associated to the job - * identifier tied to the EndpointReference object passed as input. - * - * @param msName - * The MOBY service name - * @param epr - * The EndpointReference object which holds the MOBY asynchronous - * job information - * @throws SOAPException - */ - private static void freeAsyncResources(String msName, EndpointReference epr) - throws SOAPException { - Service service = Service.create(new QName( - MobyService.BIOMOBY_SERVICE_URI, msName + "Service")); - QName mQName = new QName(MobyService.BIOMOBY_SERVICE_URI, - "WSRF_Operations_Port"); - service.addPort(mQName, SOAPBinding.SOAP11HTTP_BINDING, epr - .getAddress()); - - Dispatch<SOAPMessage> dispatch = service.createDispatch(mQName, - SOAPMessage.class, Service.Mode.MESSAGE); - Map<String, Object> rc = dispatch.getRequestContext(); - rc.put(BindingProvider.SOAPACTION_USE_PROPERTY, new Boolean(true)); - rc.put(BindingProvider.SOAPACTION_URI_PROPERTY, - GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION); - - MessageFactory mf = MessageFactory.newInstance(); - SOAPMessage request = mf.createMessage(); - SOAPPart part = request.getSOAPPart(); - - String mobyPrefix = "mobyws"; - String wsaPrefix = "wsa"; - String wsuPrefix = "wsu"; - // Obtain the SOAPEnvelope and header and body elements. - SOAPEnvelope env = part.getEnvelope(); - SOAPHeader header = env.getHeader(); - SOAPBody body = env.getBody(); - - header.addNamespaceDeclaration(mobyPrefix, - MobyService.BIOMOBY_SERVICE_URI); - header.addNamespaceDeclaration(wsaPrefix, WSA_NS); - header.addNamespaceDeclaration(wsuPrefix, WSU_NS); - // This is for the action - SOAPElement actionRoot = header.addChildElement("Action", wsaPrefix, - WSA_NS); - actionRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS), - "Action"); - actionRoot.addTextNode(DESTROY_RESOURCE_ACTION); - - // This is for the To - SOAPElement toRoot = header.addChildElement("To", wsaPrefix, WSA_NS); - toRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS), "To"); - toRoot.addTextNode(epr.getAddress()); - - // And this is for the mobyws - SOAPElement mobywsRoot = header.addChildElement("ServiceInvocationId", - mobyPrefix, MobyService.BIOMOBY_SERVICE_URI); - mobywsRoot.addNamespaceDeclaration(wsaPrefix, WSA_NS); - mobywsRoot.addAttribute(env.createName("isReferenceParameter", - wsaPrefix, WSA_NS), "true"); - mobywsRoot.addTextNode(epr.getServiceInvocationId()); - - // At last, the replyto - SOAPElement replyRoot = header.addChildElement("ReplyTo", wsaPrefix, - WSA_NS); - replyRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS), - "ReplyTo"); - SOAPElement addr = replyRoot.addChildElement("Address", wsaPrefix, - WSA_NS); - addr.addTextNode(ANON_URI); - - // Let's disable the headers - // ((WSBindingProvider)dispatch).setOutboundHeaders(headers); - - // Now the SOAP body - body.addChildElement("Destroy", "rl", RESOURCE_LIFETIME_NS); - - request.saveChanges(); - // We don't mind what it is returned - dispatch.invoke(request); - } - - /** - * This method is used to launch an asynchronous MOBY job. - * - * @param endpoint - * The endpoint of the service. - * @param msName - * The MOBY service name. - * @param mobyXML - * The MOBY payload to be sent to the service. - * @return The EndpointReference object which helds the details of the MOBY - * asynchronous job. - * @throws MobyException - */ - private static EndpointReference launchMobyAsyncService(String endpoint, - String msName, String mobyXML) throws MobyException { - try { - Service service = Service.create(new QName( - MobyService.BIOMOBY_SERVICE_URI, msName + "Service")); - QName mQName = new QName(MobyService.BIOMOBY_SERVICE_URI, msName - + "Port"); - - service.addPort(mQName, SOAPBinding.SOAP11HTTP_BINDING, endpoint); - Dispatch<SOAPMessage> dispatch = service.createDispatch(mQName, - SOAPMessage.class, Service.Mode.MESSAGE); - Map<String, Object> rc = dispatch.getRequestContext(); - rc.put(BindingProvider.SOAPACTION_USE_PROPERTY, new Boolean(true)); - rc.put(BindingProvider.SOAPACTION_URI_PROPERTY, - MobyService.BIOMOBY_SERVICE_URI + "#" + msName + "_submit"); - - MessageFactory mf = MessageFactory.newInstance(); - SOAPMessage request = mf.createMessage(); - SOAPPart part = request.getSOAPPart(); - - String mobyPrefix = "mobyws"; - String xsiPrefix = "xsi"; - - // Obtain the SOAPEnvelope and header and body elements. - SOAPEnvelope env = part.getEnvelope(); - SOAPBody body = env.getBody(); - - // Now the SOAP body - body.addNamespaceDeclaration(mobyPrefix, - MobyService.BIOMOBY_SERVICE_URI); - SOAPElement rootMessage = body.addChildElement(msName + "_submit", - mobyPrefix, MobyService.BIOMOBY_SERVICE_URI); - SOAPElement data = rootMessage.addChildElement("data", mobyPrefix, - MobyService.BIOMOBY_SERVICE_URI); - data.addNamespaceDeclaration(xsiPrefix, - MobyPrefixResolver.XSI_NAMESPACE2001); - data.addNamespaceDeclaration("xsd", XSD_NS); - data.addAttribute(env.createName("type", xsiPrefix, - MobyPrefixResolver.XSI_NAMESPACE2001), "xsd:string"); - data.addTextNode(mobyXML); - - request.saveChanges(); - SOAPMessage outputMessage = dispatch.invoke(request); - DOMSource output = new DOMSource(outputMessage.getSOAPPart() - .getEnvelope()); - - StringWriter sw = new StringWriter(); - Transformer tr = TransformerFactory.newInstance().newTransformer(); - tr.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes"); - tr.transform(output, new StreamResult(sw)); - - String response = sw.toString(); - return EndpointReference.createFromXML(response); - } catch (SOAPException pce) { - throw new MobyException( - "Unable to create SOAP document builder for MOBY asynchronous call submission", - pce); - } catch (TransformerConfigurationException tce) { - throw new MobyException( - "Unable to create transformer factory for MOBY asynchronous call response", - tce); - } catch (TransformerException te) { - throw new MobyException( - "Unable to create transformer for MOBY asynchronous call response", - te); - } - } - - - - /** - * This method issues WSRF getMultipleResourceProperties calls. As this call - * is used in BioMOBY for polling and for result fetching, it has an - * additional parameter which handles the call mode. - * - * @param msName - * The MOBY service name - * @param queryIds - * The array with the queryIds to use. It may contain null - * strings - * @param epr - * The EndpointReference object which helds the MOBY asynchronous - * job information - * @param asResult - * If this parameter is true, then this call fetches the results - * associated to the input queryIds. If it is false, then this - * call only asks for the job status. - * @return When at least one of the strings from queryIds array was not - * null, a SOAPPart object is returned with the answer for the - * request issued to the MOBY service. Otherwise, it returns null. - * @throws SOAPException - */ - private static SOAPPart getMultipleResourceProperties(String msName, - String[] queryIds, EndpointReference epr, boolean asResult) - throws SOAPException { - String op = asResult ? RESULT_PREFIX : STATUS_PREFIX; - - Service service = Service.create(new QName( - MobyService.BIOMOBY_SERVICE_URI, msName + "Service")); - QName mQName = new QName(MobyService.BIOMOBY_SERVICE_URI, - "WSRF_Operations_Port"); - service.addPort(mQName, SOAPBinding.SOAP11HTTP_BINDING, epr - .getAddress()); - - Dispatch<SOAPMessage> dispatch = service.createDispatch(mQName, - SOAPMessage.class, Service.Mode.MESSAGE); - Map<String, Object> rc = dispatch.getRequestContext(); - rc.put(BindingProvider.SOAPACTION_USE_PROPERTY, new Boolean(true)); - rc.put(BindingProvider.SOAPACTION_URI_PROPERTY, - GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION); - - MessageFactory mf = MessageFactory.newInstance(); - SOAPMessage request = mf.createMessage(); - SOAPPart part = request.getSOAPPart(); - - String mobyPrefix = "mobyws"; - String wsaPrefix = "wsa"; - String wsuPrefix = "wsu"; - // Obtain the SOAPEnvelope and header and body elements. - SOAPEnvelope env = part.getEnvelope(); - SOAPHeader header = env.getHeader(); - SOAPBody body = env.getBody(); - - header.addNamespaceDeclaration(mobyPrefix, - MobyService.BIOMOBY_SERVICE_URI); - header.addNamespaceDeclaration(wsaPrefix, WSA_NS); - header.addNamespaceDeclaration(wsuPrefix, WSU_NS); - // This is for the action - SOAPElement actionRoot = header.addChildElement("Action", wsaPrefix, - WSA_NS); - actionRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS), - "Action"); - actionRoot.addTextNode(GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION); - - // This is for the To - SOAPElement toRoot = header.addChildElement("To", wsaPrefix, WSA_NS); - toRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS), "To"); - toRoot.addTextNode(epr.getAddress()); - - // And this is for the mobyws - SOAPElement mobywsRoot = header.addChildElement("ServiceInvocationId", - mobyPrefix, MobyService.BIOMOBY_SERVICE_URI); - mobywsRoot.addNamespaceDeclaration(wsaPrefix, WSA_NS); - mobywsRoot.addAttribute(env.createName("isReferenceParameter", - wsaPrefix, WSA_NS), "true"); - mobywsRoot.addTextNode(epr.getServiceInvocationId()); - - // At last, the replyto - SOAPElement replyRoot = header.addChildElement("ReplyTo", wsaPrefix, - WSA_NS); - replyRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS), - "ReplyTo"); - SOAPElement addr = replyRoot.addChildElement("Address", wsaPrefix, - WSA_NS); - addr.addTextNode(ANON_URI); - - // Let's disable the headers - // ((WSBindingProvider)dispatch).setOutboundHeaders(headers); - - // Now the SOAP body - SOAPElement smrp = body.addChildElement( - "GetMultipleResourceProperties", "rp", RESOURCE_PROPERTIES_NS); - boolean doSubmit = false; - for (String queryId : queryIds) { - if (queryId != null) { - doSubmit = true; - SOAPElement sii = smrp.addChildElement("ResourceProperty", - "rp", RESOURCE_PROPERTIES_NS); - sii.addNamespaceDeclaration(mobyPrefix, - MobyService.BIOMOBY_SERVICE_URI); - sii.addTextNode(mobyPrefix + ":" + op + queryId); - } - } - - if (doSubmit) { - request.saveChanges(); - SOAPMessage output = dispatch.invoke(request); - - return output.getSOAPPart(); - } else { - return null; - } - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java deleted file mode 100644 index a221a8a..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java +++ /dev/null @@ -1,70 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import java.io.BufferedReader; -import java.io.InputStreamReader; -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -import java.io.OutputStreamWriter; -import java.net.URL; -import java.net.URLConnection; -import java.net.URLEncoder; - -import org.biomoby.shared.MobyException; - -/** - * This class contains one method that is used to execute synchronous HTTP POST - * services - * - * @author Edward Kawas - * - */ - -public class ExecuteCgiService { - - /** - * - * @param serviceEndpoint - * the URL to the HTTP POST service - * @param xml - * the XML to send the service - * @return a string representing the output from the service - * @throws MobyException - * if anything goes wrong (problems reading/writing to the - * service) - */ - public static String executeCgiService(String serviceEndpoint, String xml) - throws MobyException { - try { - // Construct data - String data = "data=" + URLEncoder.encode(xml, "UTF-8"); - - // Send data - URL url = new URL(serviceEndpoint); - URLConnection conn = url.openConnection(); - conn.setDoOutput(true); - OutputStreamWriter wr = new OutputStreamWriter(conn - .getOutputStream()); - wr.write(data); - wr.flush(); - // Get the response - BufferedReader rd = new BufferedReader(new InputStreamReader(conn - .getInputStream())); - String line; - StringBuffer sb = new StringBuffer(); - while ((line = rd.readLine()) != null) { - sb.append(line); - } - wr.close(); - rd.close(); - return sb.toString(); - } catch (Exception e) { - throw new MobyException(e.getMessage()); - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteMobyService.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteMobyService.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteMobyService.java deleted file mode 100644 index f494d47..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteMobyService.java +++ /dev/null @@ -1,38 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import org.biomoby.client.CentralImpl; -import org.biomoby.shared.MobyException; - -/** - * This class contains one method that is used to execute synchronous moby - * services - * - * @author Edward Kawas - * - */ - -public class ExecuteMobyService { - - /** - * - * @param endpoint - * the SOAP endpoint of the service to call - * @param service - * the name of the service - * @param xml - * the XML to send the service - * @return a string of XML representing the output from the service given - * our input - * @throws MobyException - * if anything goes wrong (SOAP error) - */ - public static String executeMobyService(String endpoint, String service, - String xml) throws MobyException { - return new CentralImpl(endpoint, "http://biomoby.org/";).call(service, - xml); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/GetOntologyThread.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/GetOntologyThread.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/GetOntologyThread.java deleted file mode 100644 index e2402e8..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/GetOntologyThread.java +++ /dev/null @@ -1,59 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -/* - * This file is a component of the Taverna project, - * and is licensed under the GNU LGPL. - * Copyright Edward Kawas, The BioMoby Project - */ - -package net.sf.taverna.t2.activities.biomoby; - - -import org.biomoby.client.CentralImpl; - -/** - * This class is used to speed up the running of workflows. Basically, whenever - * a new Biomoby activity is added to taverna, a call out to RESOURCES/Objects - * is made to download the datatype ontology. - * - * Uses BiomobyCache to process the registry - * - * This should speed up the execution of workflows, since the ontologies will - * have already been downloaded. - * - * @author Eddie Kawas - * @author Stuart Owen - * - * @see BiomobyCache - * - */ -public class GetOntologyThread extends Thread { - - - // the registry endpoint - String worker = null; - - /** - * - * @param url - * the registry endpoint URL - */ - public GetOntologyThread(String url) { - super("BioMOBY GetOntologyThread"); - if (url == null || url.trim().equals("")) - url = CentralImpl.getDefaultURL(); - this.worker = url; - setDaemon(true); - } - - /* - * (non-Javadoc) - * - * @see java.lang.Thread#run() - */ - public void run() { - BiomobyCache.cacheForRegistryEndpoint(worker); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivity.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivity.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivity.java deleted file mode 100644 index c33a5bf..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivity.java +++ /dev/null @@ -1,417 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Iterator; -import java.util.List; -import java.util.Map; -import java.util.Scanner; - -import net.sf.taverna.t2.annotation.annotationbeans.MimeType; -import net.sf.taverna.t2.reference.ExternalReferenceSPI; -import net.sf.taverna.t2.reference.ReferenceService; -import net.sf.taverna.t2.reference.ReferenceServiceException; -import net.sf.taverna.t2.reference.T2Reference; -import net.sf.taverna.t2.workflowmodel.EditException; -import net.sf.taverna.t2.workflowmodel.OutputPort; -import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity; -import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException; -import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback; - -import org.apache.log4j.Logger; -import org.biomoby.client.CentralImpl; -import org.biomoby.shared.Central; -import org.biomoby.shared.MobyDataType; -import org.biomoby.shared.MobyException; -import org.biomoby.shared.MobyRelationship; -import org.biomoby.shared.NoSuccessException; - -/** - * An Activity that breaks up a Moby datatype into its component parts minus all - * the moby wrappings. - * - * Copied from org.biomoby.client.taverna.plugin.MobyParseDatatypeActivityProcessor and - * org.biomoby.client.taverna.plugin.MobyParseDatatypeActivityTask and converted to a Taverna 2 - * Activity. - * - * @author Edward Kawas - * @author David Withers - */ -public class MobyParseDatatypeActivity extends AbstractAsynchronousActivity<MobyParseDatatypeActivityConfigurationBean> { - - public static final String URI = "http://ns.taverna.org.uk/2010/activity/biomoby/parser";; - - private static Logger logger = Logger.getLogger(MobyParseDatatypeActivity.class); - - private MobyParseDatatypeActivityConfigurationBean configurationBean = new MobyParseDatatypeActivityConfigurationBean(); - - private Central central = null; - - private MobyDataType datatype = null; - - @Override - public void configure(MobyParseDatatypeActivityConfigurationBean configurationBean) throws ActivityConfigurationException { - this.configurationBean = configurationBean; - init(); - } - - @Override - public void executeAsynch(final Map<String, T2Reference> data, - final AsynchronousActivityCallback callback) { - callback.requestRun(new Runnable() { - - @SuppressWarnings("unchecked") - public void run() { - ReferenceService referenceService = callback.getContext().getReferenceService(); - - Map<String, T2Reference> output = new HashMap<String, T2Reference>(); - - try { - - //cache ontology and namespace if not done so already. Immediately returns if already cached. - BiomobyCache.cacheForRegistryEndpoint(getConfiguration().getRegistryEndpoint()); - - String inputMapKey = getInputPorts().iterator().next().getName(); - // inputMap wasnt as expected - if (!data.containsKey(inputMapKey)) { - callback.receiveResult(output, new int[0]); - return; - } - - T2Reference inputId = data.get(inputMapKey); - - Object input = referenceService.renderIdentifier(inputId, String.class, callback.getContext()); - - if (input instanceof String) { - //logger.error(inputMapKey + " is a string!\n"); - String inputXML = (String) input; - for (OutputPort outPort : getOutputPorts()) { - String outputPortName = outPort.getName(); - String[] invocations = XMLUtilities.getSingleInvokationsFromMultipleInvokations(inputXML); - ArrayList<String> names = new ArrayList<String>(); - int type = 0; - // get the type, names list, etc - if (outputPortName.equalsIgnoreCase("namespace")) { - // extract the namespace from the top element - names.add(configurationBean.getArticleNameUsedByService()); - type = ParseMobyXML.NAMESPACE; - } else if (outputPortName.equalsIgnoreCase("id")) { - // extract the id from the top element - names.add(configurationBean.getArticleNameUsedByService()); - type = ParseMobyXML.ID; - } else { - names = getNames(outputPortName); - if (outputPortName.endsWith("_ns")) { - type = ParseMobyXML.NAMESPACE; - if (names.size() > 1) // added nov15-2007 - names.remove(names.size()-1); - } else if (outputPortName.endsWith("_id")) { - type = ParseMobyXML.ID; - if (names.size() > 1)//added nov15-2007 - names.remove(names.size()-1); - } else { - type = ParseMobyXML.VALUE; - } - } - ArrayList<String> stuff = new ArrayList<String>(); - for (int i = 0; i < invocations.length; i++) { - String invocation = invocations[i]; - if (XMLUtilities.isCollection(invocation)) { - String[] simples = XMLUtilities.getAllSimplesByArticleName(configurationBean.getArticleNameUsedByService(), invocation); - for (int j = 0; j < simples.length; j++) { - ArrayList<String> content = ParseMobyXML.getContentForDataType(names, type, XMLUtilities.createMobyDataElementWrapper(simples[j],"a1", null), configurationBean.getRegistryEndpoint()); - stuff.addAll(content); - } - } else { - ArrayList<String> content = ParseMobyXML.getContentForDataType(names, type, invocations[i],configurationBean.getRegistryEndpoint()); - stuff.addAll(content); - } - } - output.put(outputPortName, referenceService.register(stuff, 1, true, callback.getContext())); - } - - } else if (input instanceof List) { - //logger.error(inputMapKey + " is a list!\n"); - List<String> list = (List) input; - // holder contains a list of strings indexed by output port name - // TODO put stuff in the map and in the end put it in the output map - HashMap<String, ArrayList<String>> holder = new HashMap<String, ArrayList<String>>(); - for (Iterator<String> it = list.iterator(); it.hasNext();) { - String inputXML = (String) it.next(); - for (OutputPort outPort : getOutputPorts()) { - String outputPortName = outPort.getName(); - String[] invocations = XMLUtilities.getSingleInvokationsFromMultipleInvokations(inputXML); - ArrayList<String> names = new ArrayList<String>(); - int type = 0; - // get the type, names list, etc - if (outputPortName.equalsIgnoreCase("namespace")) { - // extract the namespace from the top element - names.add(configurationBean.getArticleNameUsedByService()); - type = ParseMobyXML.NAMESPACE; - } else if (outputPortName.equalsIgnoreCase("id")) { - // extract the id from the top element - names.add(configurationBean.getArticleNameUsedByService()); - type = ParseMobyXML.ID; - } else { - names = getNames(outputPortName); - if (outputPortName.endsWith("_ns")) { - type = ParseMobyXML.NAMESPACE; - if (names.size() > 1)//added nov-15-07 - names.remove(names.size()-1); - } else if (outputPortName.endsWith("_id")) { - type = ParseMobyXML.ID; - if (names.size() > 1)//added nov-15-07 - names.remove(names.size()-1); - } else { - type = ParseMobyXML.VALUE; - } - } - ArrayList<String> stuff = new ArrayList<String>(); - for (int i = 0; i < invocations.length; i++) { - String invocation = invocations[i]; - if (XMLUtilities.isCollection(invocation)) { - String[] simples = XMLUtilities.getAllSimplesByArticleName(configurationBean.getArticleNameUsedByService(), invocation); - for (int j = 0; j < simples.length; j++) { - ArrayList<String> content = ParseMobyXML.getContentForDataType(names, type, XMLUtilities.createMobyDataElementWrapper(simples[j],"a1", null),configurationBean.getRegistryEndpoint()); - stuff.addAll(content); - } - } else { - ArrayList<String> content = ParseMobyXML.getContentForDataType(names, type, invocations[i],configurationBean.getRegistryEndpoint()); - stuff.addAll(content); - } - } - if (holder.containsKey(outputPortName)) { - ArrayList<String> al = holder.get(outputPortName); - al.addAll(stuff); - holder.put(outputPortName, al); - } else { - holder.put(outputPortName, stuff); - } - } - } - // fill output map - for (Iterator<String> it = holder.keySet().iterator(); it.hasNext();) { - String key = it.next(); - output.put(key, referenceService.register(holder.get(key), 1, true, callback.getContext())); - } - } - - callback.receiveResult(output, new int[0]); - } catch (ReferenceServiceException e) { - callback.fail("Error accessing input/output data", e); - } catch (Exception e) { - callback.fail("rror parsing moby data", e); - } - - } - }); - } - - @Override - public MobyParseDatatypeActivityConfigurationBean getConfiguration() { - return configurationBean; - } - - @SuppressWarnings("unchecked") - private void init() throws ActivityConfigurationException { - try { - central = new CentralImpl(configurationBean.getRegistryEndpoint()); - } catch (MobyException e) { - throw new ActivityConfigurationException("Couldn't create MobyCentral client for endpoint " - + configurationBean.getRegistryEndpoint() + System.getProperty("line.separator") - + e.getLocalizedMessage()); - } - if (this.datatype == null) { - try { - this.datatype = central.getDataType(configurationBean.getDatatypeName()); - } catch (MobyException e) { - throw new ActivityConfigurationException( - "There was a problem getting information from the MobyCentral registry at " - + configurationBean.getRegistryEndpoint() + System.getProperty("line.separator") - + e.getLocalizedMessage()); - } catch (NoSuccessException e) { - throw new ActivityConfigurationException( - "There was no success in getting information from the MobyCentral registry at " - + configurationBean.getRegistryEndpoint() + System.getProperty("line.separator") - + e.getLocalizedMessage()); - } - } - -// setDescription("Service to parse the datatype " + this.datatype.getName()); - - ArrayList list = new ArrayList(); - if (isPrimitive(this.datatype.getName())) { - list.add(configurationBean.getArticleNameUsedByService() + "_" + this.datatype.getName()); - } else if (this.datatype.getName().equals("Object")) { - // dont do anything because object has no value - } else { - processDatatype(this.datatype, central, configurationBean.getArticleNameUsedByService(), list); - } - // add the input port called mobyData('datatypeName') - addInput("mobyData('" + this.datatype.getName() + "')", 0, true, - new ArrayList<Class<? extends ExternalReferenceSPI>>(), - String.class); - // add the namespace/id ports to the processor - addOutput("namespace", 1, "text/xml"); - addOutput("id", 1, "text/xml"); - - // list contains the output ports i have to create - for (Iterator it = list.iterator(); it.hasNext();) { - String portName = (String) it.next(); - if (portName.equals(configurationBean.getArticleNameUsedByService()+"_id") || portName.equals(configurationBean.getArticleNameUsedByService()+"_ns")) - continue; - addOutput(portName, 1, "text/xml"); - } - } - - private boolean isPrimitive(String name) { - if (name.equals("Integer") || name.equals("String") || name.equals("Float") - || name.equals("DateTime") || name.equals("Boolean") - ) - return true; - return false; - } - - @SuppressWarnings("unchecked") - private void processDatatype(MobyDataType dt, Central central, String currentName, List list) throws ActivityConfigurationException { - - if (dt.getParentName() == null || dt.getParentName().trim().equals("")) { - //TODO should we throw an error or just return ... - return; - } - - if (!dt.getParentName().equals("Object")) { - flattenChildType(dt.getParentName(), central, currentName, list); - } else { - list.add(currentName + "_id"); - list.add(currentName + "_ns"); - } - - MobyRelationship[] relations = dt.getChildren(); - for (int i = 0; i < relations.length; i++) { - MobyRelationship relation = relations[i]; - switch (relation.getRelationshipType()) { - case CentralImpl.iHAS: { - // check for object or primitives - if (isPrimitive(relation.getDataTypeName()) || relation.getDataTypeName().equals("Object")) { - // object has no value ... only primitives do - if (!relation.getDataTypeName().equals("Object")) - list.add(currentName + (currentName.equals("") ? "" : "_'") - + relation.getName() + (currentName.equals("") ? "" : "'")); - list.add(currentName + (currentName.equals("") ? "" : "_'") - + relation.getName() + (currentName.equals("") ? "" : "'")+"_id"); - list.add(currentName + (currentName.equals("") ? "" : "_'") - + relation.getName() + (currentName.equals("") ? "" : "'")+"_ns"); - } - else { - flattenChildType(relation.getDataTypeName(), central, currentName - + (currentName.equals("") ? "" : "_'") + relation.getName() + (currentName.equals("") ? "" : "'"), list); - } - } - break; - case CentralImpl.iHASA: { - // check for object or primitives ... - if (isPrimitive(relation.getDataTypeName()) || relation.getDataTypeName().equals("Object")) { - // object has no value ... only primitives do - if (!relation.getDataTypeName().equals("Object")) - list.add(currentName + (currentName.equals("") ? "" : "_'") - + relation.getName()+ (currentName.equals("") ? "" : "'")); - list.add(currentName + (currentName.equals("") ? "" : "_'") - + relation.getName() + (currentName.equals("") ? "" : "'")+"_id"); - list.add(currentName + (currentName.equals("") ? "" : "_'") - + relation.getName() + (currentName.equals("") ? "" : "'")+"_ns"); - } - else { - - flattenChildType(relation.getDataTypeName(), central, currentName - + (currentName.equals("") ? "" : "_'") + relation.getName() + (currentName.equals("") ? "" : "'"), list); - } - } - break; - default: - break; - } - } - - } - - @SuppressWarnings("unchecked") - private void flattenChildType(String name, Central central, String current, List list) throws ActivityConfigurationException { - MobyDataType dt = null; - try { - dt = central.getDataType(name); - } catch (MobyException e) { - throw new ActivityConfigurationException( - "There was a problem getting information from the MobyCentral registry at " - + configurationBean.getRegistryEndpoint() + System.getProperty("line.separator") - + e.getLocalizedMessage()); - } catch (NoSuccessException e) { - throw new ActivityConfigurationException( - "There was no success in getting information from the MobyCentral registry at " - + configurationBean.getRegistryEndpoint() + System.getProperty("line.separator") - + e.getLocalizedMessage()); - } - processDatatype(dt, central, current, list); - } - - private ArrayList<String> getNames(String names) { - ArrayList<String> list = new ArrayList<String>(); - ArrayList<String> temp = new ArrayList<String>(); - if (names == null || names.trim().length() == 0) - return list; - Scanner s = new Scanner(names).useDelimiter("_'"); - while (s.hasNext()) { - temp.add(s.next()); - } - s.close(); - - for (String str : temp) { - if (str.indexOf("'_") >= 0) { - String[] strings = str.split("'_"); - for (int i = 0; i < strings.length; i++) { - list.add(strings[i].replaceAll("'", "")); - } - } else { - list.add(str.replaceAll("'", "")); - } - } - - if (list.size() == 1) { - if (endsWithPrimitive(list.get(0))) { - String name = list.remove(0); - int i = name.lastIndexOf("_"); - name = name.substring(0, i); - list.add(name); - } - } else if (isPrimitive(list.get(list.size()-1))) { - // remove the last entry if its a primitive ... legacy reasons - list.remove(list.size()-1); - } - return list; - } - - private static boolean endsWithPrimitive(String name) { - if (name.endsWith("_Integer") || name.endsWith("_String") || name.endsWith("_Float") - || name.endsWith("_DateTime") || name.endsWith("_Boolean")) - return true; - return false; - } - - protected void addOutput(String portName, int portDepth, String type) { - OutputPort port = edits.createActivityOutputPort( - portName, portDepth, portDepth); - MimeType mimeType = new MimeType(); - mimeType.setText(type); - try { - edits.getAddAnnotationChainEdit(port, mimeType).doEdit(); - } catch (EditException e) { - logger.debug("Error adding MimeType annotation to port", e); - } - outputPorts.add(port); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityConfigurationBean.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityConfigurationBean.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityConfigurationBean.java deleted file mode 100644 index 1f02e7e..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityConfigurationBean.java +++ /dev/null @@ -1,81 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean; -import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty; - -/** - * A configuration bean specific to the Moby Parse Datatype activity. - * - * @author David Withers - */ -@ConfigurationBean(uri = MobyParseDatatypeActivity.URI + "#Config") -public class MobyParseDatatypeActivityConfigurationBean { - - private String datatypeName=""; - - private String registryEndpoint=""; - - private String articleNameUsedByService=""; - - /** - * Returns the datatypeName. - * - * @return the datatypeName - */ - public String getDatatypeName() { - return datatypeName; - } - - /** - * Sets the datatypeName. - * - * @param datatypeName the new datatypeName - */ - @ConfigurationProperty(name = "datatypeName", label = "Datatype Name", description = "") - public void setDatatypeName(String datatypeName) { - this.datatypeName = datatypeName; - } - - /** - * Returns the registryEndpoint. - * - * @return the registryEndpoint - */ - public String getRegistryEndpoint() { - return registryEndpoint; - } - - /** - * Sets the registryEndpoint. - * - * @param registryEndpoint the new registryEndpoint - */ - @ConfigurationProperty(name = "registryEndpoint", label = "Registry Endpoint", description = "") - public void setRegistryEndpoint(String registryEndpoint) { - this.registryEndpoint = registryEndpoint; - } - - /** - * Returns the articleNameUsedByService. - * - * @return the articleNameUsedByService - */ - public String getArticleNameUsedByService() { - return articleNameUsedByService; - } - - /** - * Sets the articleNameUsedByService. - * - * @param articleNameUsedByService the new articleNameUsedByService - */ - @ConfigurationProperty(name = "articleNameUsedByService", label = "Article Name Used By Service", description = "") - public void setArticleNameUsedByService(String articleNameUsedByService) { - this.articleNameUsedByService = articleNameUsedByService; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityFactory.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityFactory.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityFactory.java deleted file mode 100644 index 8da531e..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityFactory.java +++ /dev/null @@ -1,49 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2011 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import java.net.URI; - -import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory; - -/** - * An {@link ActivityFactory} for creating <code>MobyParseDatatypeActivity</code>. - * - * @author David Withers - */ -public class MobyParseDatatypeActivityFactory implements ActivityFactory { - - @Override - public MobyParseDatatypeActivity createActivity() { - return new MobyParseDatatypeActivity(); - } - - @Override - public URI getActivityURI() { - return URI.create(MobyParseDatatypeActivity.URI); - } - - @Override - public Object createActivityConfiguration() { - return new MobyParseDatatypeActivityConfigurationBean(); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthChecker.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthChecker.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthChecker.java deleted file mode 100644 index 0ca0d38..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthChecker.java +++ /dev/null @@ -1,58 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import java.io.IOException; -import java.net.HttpURLConnection; -import java.net.MalformedURLException; -import java.net.SocketTimeoutException; -import java.net.URL; -import java.net.URLConnection; -import java.util.List; - -import net.sf.taverna.t2.workflowmodel.Processor; -import net.sf.taverna.t2.workflowmodel.processor.activity.Activity; -import net.sf.taverna.t2.workflowmodel.health.HealthCheck; -import net.sf.taverna.t2.workflowmodel.health.HealthChecker; -import net.sf.taverna.t2.visit.VisitReport; -import net.sf.taverna.t2.visit.VisitReport.Status; - -import net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker; -import net.sf.taverna.t2.workflowmodel.processor.activity.DisabledActivity; - - -/** - * A health checker for the Moby Parse Datatype activity. - * - * @author David Withers - */ -public class MobyParseDatatypeActivityHealthChecker extends RemoteHealthChecker { - - - public boolean canVisit(Object subject) { - if (subject == null) { - return false; - } - if (subject instanceof MobyParseDatatypeActivity) { - return true; - } - if (subject instanceof DisabledActivity) { - return (((DisabledActivity) subject).getActivity() instanceof MobyParseDatatypeActivity); - } - return false; - } - - public VisitReport visit(Object o, List<Object> ancestors) { - Activity activity = (Activity) o; - MobyParseDatatypeActivityConfigurationBean configuration = null; - if (activity instanceof MobyParseDatatypeActivity) { - configuration = (MobyParseDatatypeActivityConfigurationBean) activity.getConfiguration(); - } else if (activity instanceof DisabledActivity) { - configuration = (MobyParseDatatypeActivityConfigurationBean) ((DisabledActivity) activity).getActivityConfiguration(); - } - return contactEndpoint(activity, configuration.getRegistryEndpoint()); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ParseMobyXML.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ParseMobyXML.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ParseMobyXML.java deleted file mode 100644 index 042b6e8..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ParseMobyXML.java +++ /dev/null @@ -1,192 +0,0 @@ -/* - * This file is a component of the Taverna project, - * and is licensed under the GNU LGPL. - * Copyright Edward Kawas, The BioMoby Project - */ -package net.sf.taverna.t2.activities.biomoby; - -import java.io.ByteArrayInputStream; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - -import org.apache.log4j.Logger; -import org.biomoby.shared.MobyNamespace; -import org.biomoby.shared.data.MobyContentInstance; -import org.biomoby.shared.data.MobyDataBoolean; -import org.biomoby.shared.data.MobyDataComposite; -import org.biomoby.shared.data.MobyDataFloat; -import org.biomoby.shared.data.MobyDataInstance; -import org.biomoby.shared.data.MobyDataInt; -import org.biomoby.shared.data.MobyDataJob; -import org.biomoby.shared.data.MobyDataObject; -import org.biomoby.shared.data.MobyDataObjectVector; -import org.biomoby.shared.data.MobyDataString; -import org.biomoby.shared.data.MobyDataUtils; -import org.biomoby.registry.meta.Registry; - -/** - * This class is used to help parse BioMOBY messages. - * - * @author Edward Kawas - * - */ -public class ParseMobyXML { - - private static Logger logger = Logger.getLogger(ParseMobyXML.class); - - public static final int NAMESPACE = -10; - - public static final int ID = -20; - - public static final int VALUE = -30; - - private static final List<Integer> allowables; - - static { - allowables = new ArrayList<Integer>(); - allowables.add(NAMESPACE); - allowables.add(ID); - allowables.add(VALUE); - } - - /** - * PRECONDITION: XML is valid MOBY xml and contains exactly 1 invocation - * message containing our simple element - * - * @param names - * an array of article names in the order that we will - * extract our information - * @param type - * one of {NAMESPACE | ID | VALUE} denoting what exactly it - * is that you would like returned - * @param xml - * the MOBY xml containing the data to extract - * @param endpoint - * the BioMOBY registry endpoint to use - * @return a list of strings representing what it is you asked for - */ - public static ArrayList<String> getContentForDataType( - ArrayList<String> names, int type, String xml, String endpoint) { - if (!allowables.contains(type) || names == null || names.size() == 0 - || xml == null || xml.trim().length() == 0) { - // nothing to return - logger.warn("Parser invoked on an empty message ..."); - return new ArrayList<String>(); - } - MobyContentInstance contents; - try { - contents = MobyDataUtils.fromXMLDocument(new ByteArrayInputStream( - xml.getBytes("UTF8")), new Registry(endpoint, endpoint, - "http://domain.com/MOBY/Central";)); - } catch (Exception e) { - logger.error("There was a problem parsing the input XML:\n" + xml - + "\n", e); - return new ArrayList<String>(); - } - if (contents.keySet().size() != 1) { - return new ArrayList<String>(); - } - - ArrayList<String> clone = new ArrayList<String>(); - clone.addAll(names); - ArrayList<String> output = new ArrayList<String>(); - // should be exactly 1 job! - Iterator<String> jobIDs = contents.keySet().iterator(); - while (jobIDs.hasNext()) { - MobyDataJob job = (MobyDataJob) contents.get(jobIDs.next()); - // get the instance - MobyDataInstance data = job.get(clone.remove(0)); - if (data == null) - return output; - recurse(clone, data, output, type); - } - return output; - } - - @SuppressWarnings("unchecked") - private static void recurse(ArrayList<String> names, MobyDataInstance data, - ArrayList<String> output, int type) { - // base case => we have finally found the element of interest - if (names.isEmpty()) { - baseCase(data, output, type); - return; - } - if (data instanceof MobyDataObjectVector) { - // recurse on the children -- the recursion will extract by - // articlename - MobyDataObjectVector vector = (MobyDataObjectVector) data; - // recurse on the has relationship - for (Iterator i = vector.iterator(); i.hasNext();) { - recurse((ArrayList) (names.clone()), (MobyDataInstance) i - .next(), output, type); - } - - } else if (data instanceof MobyDataComposite) { - // recurse on the child given by name.get(0) - MobyDataInstance d = ((MobyDataComposite) data).remove(names - .remove(0)); - recurse((ArrayList) (names.clone()), d, output, type); - } else if (data instanceof MobyDataBoolean) { - baseCase(data, output, type); - } else if (data instanceof MobyDataFloat) { - baseCase(data, output, type); - } else if (data instanceof MobyDataInt) { - baseCase(data, output, type); - } else if (data instanceof MobyDataString) { - baseCase(data, output, type); - } - - } - - private static void baseCase(MobyDataInstance data, - ArrayList<String> output, int type) { - if (data == null) - return; - switch (type) { - case NAMESPACE: { - if (data instanceof MobyDataObjectVector) { - MobyDataObjectVector vector = (MobyDataObjectVector) data; - for (Iterator i = vector.iterator(); i.hasNext();) { - MobyNamespace[] namespaces = ((MobyDataObject) i.next()) - .getNamespaces(); - for (int j = 0; j < namespaces.length; j++) { - output.add(namespaces[j].getName()); - } - } - } else { - MobyNamespace[] namespaces = ((MobyDataObject) data) - .getNamespaces(); - for (int j = 0; j < namespaces.length; j++) { - output.add(namespaces[j].getName()); - } - } - } - break; - case ID: { - if (data instanceof MobyDataObjectVector) { - MobyDataObjectVector vector = (MobyDataObjectVector) data; - for (Iterator i = vector.iterator(); i.hasNext();) { - output.add(((MobyDataObject) i.next()).getId()); - } - } else { - output.add(((MobyDataObject) data).getId()); - } - } - break; - case VALUE: { - if (data instanceof MobyDataObjectVector) { - MobyDataObjectVector vector = (MobyDataObjectVector) data; - for (Iterator i = vector.iterator(); i.hasNext();) { - output.add(((MobyDataObject) i.next()).getValue()); - } - } else { - output.add(((MobyDataObject) data).getValue()); - } - } - break; - default: - break; - } - } -}
