Extract and improve Input/Output preparation from execution Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/commit/826c605f Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/tree/826c605f Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/diff/826c605f
Branch: refs/heads/taverna2 Commit: 826c605f02f8586fa32e0b1c2ee6fc699937627e Parents: 24e3b9d Author: edikaradumi <[email protected]> Authored: Sat Aug 6 06:29:04 2016 +0100 Committer: edikaradumi <[email protected]> Committed: Sat Aug 6 06:29:04 2016 +0100 ---------------------------------------------------------------------- .../org/apache/taverna/gis/GisActivity.java | 79 ++--- .../apache/taverna/gis/client/IGisClient.java | 12 +- .../gis/client/impl/GisClientNorthImpl.java | 318 +++++++++++++------ 3 files changed, 253 insertions(+), 156 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/826c605f/apache-taverna-plugin-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java ---------------------------------------------------------------------- diff --git a/apache-taverna-plugin-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java b/apache-taverna-plugin-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java index 6f58548..e7ac881 100644 --- a/apache-taverna-plugin-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java +++ b/apache-taverna-plugin-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java @@ -109,7 +109,7 @@ public class GisActivity extends AbstractAsynchronousActivity<GisActivityConfigu ComplexDataFormat complexFormat = new ComplexDataFormat(); complexFormat.setEncoding(null); - complexFormat.setMimeType("application/wkt"); + //complexFormat.setMimeType("application/wkt"); complexFormat.setSchema(null); ((ComplexPortDataDescriptor) activityInputPort).setComplexFormat(complexFormat); @@ -120,8 +120,30 @@ public class GisActivity extends AbstractAsynchronousActivity<GisActivityConfigu } + HashMap<String, IPortDataDescriptor> serviceOutputs = new HashMap<String, IPortDataDescriptor>(); + + for (IPortDataDescriptor activityOutputPort : configBean.getOutputPortDefinitions()) + { + if (activityOutputPort instanceof ComplexPortDataDescriptor) + { + //TODO: set format + ComplexDataFormat complexFormat = new ComplexDataFormat(); + + complexFormat.setEncoding(null); + //complexFormat.setMimeType("application/wkt"); + //complexFormat.setMimeType("text/plain"); + complexFormat.setSchema(null); + + ((ComplexPortDataDescriptor) activityOutputPort).setComplexFormat(complexFormat); + } + + serviceOutputs.put(activityOutputPort.getName(), activityOutputPort); + + } + // Execute process - HashMap<String, String> serviceOutput = gisClient.executeProcess(configBean.getProcessIdentifier().toString(), serviceInputs); + HashMap<String, String> serviceOutput = gisClient.executeProcess( + configBean.getProcessIdentifier().toString(), serviceInputs, serviceOutputs); outputs = new HashMap<String, T2Reference>(); T2Reference simpleRef = null; @@ -135,59 +157,6 @@ public class GisActivity extends AbstractAsynchronousActivity<GisActivityConfigu } -// -// -// Object responseObject = null; -// -// try { -// // execute service -// responseObject = wpsClient.execute(configBean.getOgcServiceUri().toString(), execute); -// } catch (WPSClientException e) { -// // if the an error return from service -// callback.fail(e.getServerException().xmlText()); -// } -// -// // Register outputs -// outputs = new HashMap<String, T2Reference>(); -// T2Reference simpleRef = null; -// -// if (responseObject instanceof ExecuteResponseDocument) { -// ExecuteResponseDocument response = (ExecuteResponseDocument) responseObject; -// -// // analyser is used to get complex data -// ExecuteResponseAnalyser analyser = new ExecuteResponseAnalyser( -// execute, response, processDescription); -// -// for(OutputDataType output : response.getExecuteResponse().getProcessOutputs().getOutputArray()) -// { -// DataType data = output.getData(); -// -// if (data.isSetLiteralData()) -// { -// simpleRef = referenceService.register(data.getLiteralData().getStringValue(), 0, true, context); -// -// outputs.put(output.getIdentifier().getStringValue(), simpleRef); -// } -// else -// { -// -// simpleRef = referenceService.register(data.getComplexData().toString(), 0, true, context); -// -// outputs.put(output.getIdentifier().getStringValue(), simpleRef); -// -// } -// -// } -// -// } -// -// -// } catch (WPSClientException e) { -// callback.fail(e.getMessage()); -// } catch (IOException e) { -// callback.fail(e.getMessage()); -// } - } catch (Exception e) { logger.error("Error executing service/process: " + configBean.getOgcServiceUri().toString() + "/" + configBean.getProcessIdentifier().toString(), e); http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/826c605f/apache-taverna-plugin-gis-client/src/main/java/org/apache/taverna/gis/client/IGisClient.java ---------------------------------------------------------------------- diff --git a/apache-taverna-plugin-gis-client/src/main/java/org/apache/taverna/gis/client/IGisClient.java b/apache-taverna-plugin-gis-client/src/main/java/org/apache/taverna/gis/client/IGisClient.java index 0fdbafc..6eed5a0 100644 --- a/apache-taverna-plugin-gis-client/src/main/java/org/apache/taverna/gis/client/IGisClient.java +++ b/apache-taverna-plugin-gis-client/src/main/java/org/apache/taverna/gis/client/IGisClient.java @@ -47,7 +47,15 @@ public interface IGisClient { public List<IPortDataDescriptor> getTaverna2OutputPorts(String processID); - public HashMap<String, String> executeProcess(String processID, HashMap<String, IPortDataDescriptor> inputs) - throws Exception; + + /** + * @param processID - Identifier of the process + * @param inputs - Map of input names and input objects + * @param outputs - Map of output names and output objects + * @return Return a map of port names and port values + * @throws Exception + */ + public HashMap<String, String> executeProcess(String processID, HashMap<String, IPortDataDescriptor> inputs, + HashMap<String, IPortDataDescriptor> outputs) throws Exception; } http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis/blob/826c605f/apache-taverna-plugin-gis-client/src/main/java/org/apache/taverna/gis/client/impl/GisClientNorthImpl.java ---------------------------------------------------------------------- diff --git a/apache-taverna-plugin-gis-client/src/main/java/org/apache/taverna/gis/client/impl/GisClientNorthImpl.java b/apache-taverna-plugin-gis-client/src/main/java/org/apache/taverna/gis/client/impl/GisClientNorthImpl.java index 8d168c3..170213f 100644 --- a/apache-taverna-plugin-gis-client/src/main/java/org/apache/taverna/gis/client/impl/GisClientNorthImpl.java +++ b/apache-taverna-plugin-gis-client/src/main/java/org/apache/taverna/gis/client/impl/GisClientNorthImpl.java @@ -28,6 +28,7 @@ import java.util.HashMap; import java.util.List; import org.apache.log4j.Logger; +import org.apache.taverna.gis.client.BBoxPortDataDescriptor; import org.apache.taverna.gis.client.ComplexDataFormat; import org.apache.taverna.gis.client.ComplexPortDataDescriptor; import org.apache.taverna.gis.client.IGisClient; @@ -47,6 +48,7 @@ import net.opengis.wps.x100.OutputDescriptionType; import net.opengis.wps.x100.ProcessBriefType; import net.opengis.wps.x100.ProcessDescriptionType; import net.opengis.wps.x100.ProcessDescriptionType.DataInputs; +import net.opengis.wps.x100.ProcessDescriptionType.ProcessOutputs; import net.opengis.wps.x100.WPSCapabilitiesType; import net.opengis.wps.x100.ExecuteDocument; import net.opengis.wps.x100.ExecuteResponseDocument; @@ -194,6 +196,7 @@ public class GisClientNorthImpl implements IGisClient { if (processDescription == null) return outputPorts; + // TODO: Check if there is no output port (It should have at least one port?) OutputDescriptionType[] outputList = processDescription.getProcessOutputs().getOutputArray(); for (OutputDescriptionType output : outputList) { @@ -220,12 +223,16 @@ public class GisClientNorthImpl implements IGisClient { } + /* (non-Javadoc) + * @see org.apache.taverna.gis.client.IGisClient#executeProcess(java.lang.String, java.util.HashMap, java.util.HashMap) + */ @Override - public HashMap<String, String> executeProcess(String processID, HashMap<String, IPortDataDescriptor> inputs) + public HashMap<String, String> executeProcess(String processID, + HashMap<String, IPortDataDescriptor> inputs, HashMap<String, IPortDataDescriptor> outputs) throws Exception { - HashMap<String, String> executeOutput = new HashMap<String, String>(); - + // The execution will return a map of port names and port values + HashMap<String, String> executeOutput = null; ProcessDescriptionType processDescription = null; // Get process description @@ -238,87 +245,12 @@ public class GisClientNorthImpl implements IGisClient { // Initialise execute builder ExecuteRequestBuilder executeBuilder = new ExecuteRequestBuilder(processDescription); - boolean hasInput = true; - - DataInputs dataInputs = processDescription.getDataInputs(); - - if (dataInputs == null) - hasInput = false; - - if (hasInput) { - - InputDescriptionType[] inputList = dataInputs.getInputArray(); - - // TODO: Handle input when depth > 0 - // Provide user values for each service input - for (InputDescriptionType input : inputList) { - String inputName = input.getIdentifier().getStringValue(); - Object inputValue = inputs.containsKey(inputName)?inputs.get(inputName).getValue():null; - - // Check if input is required but not provided - if (inputValue == null && input.getMinOccurs().intValue() > 0) { - throw new IOException("Required Input not set: " + inputName); - } - - // Skip not user supplied optional inputs - if (inputValue!=null) - { - if (input.getLiteralData() != null) { - if (inputValue instanceof String) { - executeBuilder.addLiteralData(inputName, (String) inputValue); - } - - } else if (input.getComplexData() != null) { - - // Check if the selected format (mimeType, encoding, schema) - // is supported by the service - ComplexPortDataDescriptor complexData = (ComplexPortDataDescriptor) inputs.get(inputName); - ComplexDataFormat selectedFormat = complexData.getComplexFormat(); - - if (!complexData.getSupportedComplexFormats().contains(selectedFormat)) { - throw new IllegalArgumentException( - "Unsupported format: " + complexData.getComplexFormat().toString()); - } - - if (inputValue instanceof String) { - // Check if complex data is provided by reference or by - // value - boolean isReference = true; - - try { - URI.create((String) inputValue); - } catch (IllegalArgumentException ex) { - isReference = false; - } - - if (isReference) { - // complex data by reference - executeBuilder.addComplexDataReference(inputName, (String) inputValue, - selectedFormat.getSchema(), selectedFormat.getEncoding(), - selectedFormat.getMimeType()); - } else { - - // complex data by value - try { - - executeBuilder.addComplexData(inputName, (String) inputValue, - selectedFormat.getSchema(), selectedFormat.getEncoding(), - selectedFormat.getMimeType()); - - } catch (WPSClientException e) { - throw new Exception("Failed to set complex data: " + processID, e); - } - } - } - } else if (input.getBoundingBoxData() != null) { - // TODO: Handle BBox data - } - } - - - } // End input loop - - } + // Add inputs to the execute builder + prepareExecuteBuilderInput(processID, inputs, processDescription, executeBuilder); + + // Add outputs to the execute builder + prepareExecuteBuilderOutput(processID, outputs, processDescription, executeBuilder); + ExecuteDocument execute = executeBuilder.getExecute(); execute.getExecute().setService("WPS"); @@ -332,37 +264,225 @@ public class GisClientNorthImpl implements IGisClient { throw new Exception(e.getServerException().xmlText()); } - // Register outputs + // Get outputs + executeOutput = getResponseOutput(processDescription, execute, responseObject); + + return executeOutput; + } + + private HashMap<String, String> getResponseOutput(ProcessDescriptionType processDescription, + ExecuteDocument execute, Object responseObject) throws WPSClientException { + + HashMap<String, String> executeOutput = new HashMap<String, String>(); + if (responseObject instanceof ExecuteResponseDocument) { ExecuteResponseDocument response = (ExecuteResponseDocument) responseObject; // analyser is used to get complex data ExecuteResponseAnalyser analyser = new ExecuteResponseAnalyser(execute, response, processDescription); - + for (OutputDataType output : response.getExecuteResponse().getProcessOutputs().getOutputArray()) { DataType data = output.getData(); + + if (output.isSetReference()) + { + // output by reference + executeOutput.put(output.getIdentifier().getStringValue(), output.getReference().getHref()); + } + else if (output.isSetData()) + { + if (data.isSetLiteralData()) + { + executeOutput.put(output.getIdentifier().getStringValue(), data.getLiteralData().getStringValue()); + } + else if (data.isSetComplexData()) + { + executeOutput.put(output.getIdentifier().getStringValue(), data.getComplexData().toString()); + } + else if (data.isSetBoundingBoxData()) + { + //TODO: Handle bounding box data + } + } + } + } + + return executeOutput; + + } - if (data.isSetLiteralData()) { + private InputDescriptionType[] getProcessInputs(ProcessDescriptionType processDescription) + { + InputDescriptionType[] result = {}; + + DataInputs dataInputs = processDescription.getDataInputs(); - // simpleRef = - // referenceService.register(data.getLiteralData().getStringValue(), - // 0, true, context); + if (dataInputs == null) + return result; - executeOutput.put(output.getIdentifier().getStringValue(), data.getLiteralData().getStringValue()); - } else { + result = dataInputs.getInputArray(); + + return result; + + } + + private OutputDescriptionType[] getProcessOutputs(ProcessDescriptionType processDescription) + { + OutputDescriptionType[] result = {}; + + ProcessOutputs dataOutputs = processDescription.getProcessOutputs(); - // simpleRef = - // referenceService.register(data.getComplexData().toString(), - // 0, true, context); + if (dataOutputs == null) + return result; - executeOutput.put(output.getIdentifier().getStringValue(), data.getComplexData().toString()); + result = dataOutputs.getOutputArray(); + + return result; + + } - } + private ComplexDataFormat checkComplexDataSupportedFormats(ComplexPortDataDescriptor complexPort) + { + // Check if the selected format (mimeType, encoding, schema) + // is supported by the service + ComplexDataFormat selectedFormat = complexPort.getComplexFormat(); + + if (!complexPort.getSupportedComplexFormats().contains(selectedFormat)) + { + logger.warn("Provided format not supported."); + + // TODO: Should throw exception or set to default? + ComplexDataFormat defaultFormat = complexPort.getDefaultComplexFormat(); + if (defaultFormat==null) + { +// throw new IllegalArgumentException( +// "Unsupported format: MimeType=" + selectedFormat.getMimeType() + " Schema=" +// + selectedFormat.getSchema() + " Encoding=" + selectedFormat.getEncoding()); + + defaultFormat = new ComplexDataFormat(null,null,null); + + } + + selectedFormat = defaultFormat; + + } + + return selectedFormat; + + } + + private String checkBBoxDataSupportedFormats(BBoxPortDataDescriptor bboxPort) + { + // Check if the selected SRS is supported by the service + String selectedFormat = bboxPort.getBoundingBoxFormat(); + + if (!bboxPort.getSupportedBoundingBoxFormats().contains(selectedFormat)) + { + throw new IllegalArgumentException( + "Unsupported SRS: " + selectedFormat.toString()); + } + + return selectedFormat; + + } + + private void prepareExecuteBuilderInput(String processID, HashMap<String, IPortDataDescriptor> inputs, + ProcessDescriptionType processDescription, ExecuteRequestBuilder executeBuilder) + throws IOException, Exception { + + InputDescriptionType[] processInputList = getProcessInputs(processDescription); + // TODO: Handle input when depth > 0 + // Provide user values for each service input + for (InputDescriptionType input : processInputList) { + String inputName = input.getIdentifier().getStringValue(); + Object inputValue = inputs.containsKey(inputName) ? inputs.get(inputName).getValue() : null; + + // Check if input is required but not provided + if (inputValue == null && input.getMinOccurs().intValue() > 0) { + throw new IOException("Required Input not set: " + inputName); } - } + // Skip optional inputs not supplied by the user + if (inputValue != null) { + if (input.getLiteralData() != null) { + if (inputValue instanceof String) { + executeBuilder.addLiteralData(inputName, (String) inputValue); + } - return executeOutput; + } else if (input.getComplexData() != null) { + + // Check if the selected format (mimeType, encoding, schema) + // is supported by the service + ComplexDataFormat selectedFormat = checkComplexDataSupportedFormats( + (ComplexPortDataDescriptor) inputs.get(inputName)); + + if (inputValue instanceof String) { + // Check if complex data is provided by reference or value + boolean isReference = true; + + try { + // if URI is valid URI then data is By Reference + URI.create((String) inputValue); + } catch (IllegalArgumentException ex) { + isReference = false; + } + + if (isReference) { + // complex data by reference + executeBuilder.addComplexDataReference(inputName, (String) inputValue, + selectedFormat.getSchema(), selectedFormat.getEncoding(), + selectedFormat.getMimeType()); + } else { + + // complex data by value + try { + + executeBuilder.addComplexData(inputName, (String) inputValue, + selectedFormat.getSchema(), selectedFormat.getEncoding(), + selectedFormat.getMimeType()); + + } catch (WPSClientException e) { + throw new Exception("Failed to set complex data: " + processID, e); + } + } + } + } else if (input.getBoundingBoxData() != null) { + // TODO: Handle BBox data + } + } + } // End input loop + } + + private void prepareExecuteBuilderOutput(String processID, HashMap<String, IPortDataDescriptor> outputs, + ProcessDescriptionType processDescription, ExecuteRequestBuilder executeBuilder) + throws IOException, Exception { + + OutputDescriptionType[] processOutputList = getProcessOutputs(processDescription); + + for(OutputDescriptionType output : processOutputList) + { + String outputName = output.getIdentifier().getStringValue(); + + if (outputs.containsKey(outputName)) + { + if (output.isSetComplexOutput()) + { + ComplexDataFormat selectedFormat = checkComplexDataSupportedFormats( + (ComplexPortDataDescriptor) outputs.get(outputName)); + + if (selectedFormat!=null) + { + // "text/xml" if null + executeBuilder.setMimeTypeForOutput(selectedFormat.getMimeType(), outputName); + // sample schema "http://schemas.opengis.net/gml/3.1.1/base/feature.xsd"; + executeBuilder.setSchemaForOutput(selectedFormat.getSchema(), outputName); + + executeBuilder.setEncodingForOutput(selectedFormat.getEncoding(), outputName); + } + } + } + } } + }
