Github user stain commented on a diff in the pull request:
https://github.com/apache/incubator-taverna-common-activities/pull/13#discussion_r72437990
--- Diff:
taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
---
@@ -16,72 +16,167 @@
*******************************************************************************/
package org.apache.taverna.cwl.ui.serviceprovider;
-import java.io.File;
import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FilenameFilter;
+import java.io.IOException;
import java.net.URI;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
import javax.swing.Icon;
+import org.apache.log4j.Logger;
+import org.apache.taverna.scufl2.api.common.Visitor;
+import org.apache.taverna.scufl2.api.configurations.Configuration;
+import
org.apache.taverna.servicedescriptions.AbstractConfigurableServiceProvider;
+import org.apache.taverna.servicedescriptions.ConfigurableServiceProvider;
+import org.apache.taverna.servicedescriptions.ServiceDescriptionProvider;
import org.yaml.snakeyaml.Yaml;
-import
net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
-import net.sf.taverna.t2.servicedescriptions.ConfigurableServiceProvider;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ObjectNode;
-public class CwlServiceProvider extends
AbstractConfigurableServiceProvider<CwlServiceProviderConfig>
- implements
ConfigurableServiceProvider<CwlServiceProviderConfig> {
+public class CwlServiceProvider extends
AbstractConfigurableServiceProvider implements ConfigurableServiceProvider {
+
+ public static final String TOOL_NAME = "toolName";
+ public static final String CWL_CONF = "cwl_conf";
+ public static final String CWL_PATH = "cwl_path";
+
+ public static final String DEFAULT_PATH_1 = "/usr/share/commonwl/";
+ public static final String DEFAULT_PATH_2 =
"/usr/local/share/commonwl/";
+ public static final String XDF_DATA_HOME = "XDF_DATA_HOME";
+ public static final String COMMONWL = "commonwl/";
+ private static Logger logger =
Logger.getLogger(CwlServiceProvider.class);
CwlServiceProvider() {
- super(new CwlServiceProviderConfig());
+ // FIXME
+ super(getDefaultConfiguration());
}
- private static final String providerName ="CWL Services";
- private static final URI providerId = URI
-
.create("http://cwl.com/2016/service-provider/cwlcommandlinetools";);
- private File cwlFilesLocation;
+
+ private static final String providerName = "CWL Services";
+ private static final URI providerId =
CwlServiceDesc.ACTIVITY_TYPE.resolve("#provider");
@Override
public void
findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) {
// get the location of the cwl tool from the workbench
- cwlFilesLocation = new File(getConfiguration().getPath());
- // This is holding the CWL configuration beans
- List<CwlServiceDesc> result = new ArrayList<CwlServiceDesc>();
-
- File[] cwlFiles = getCwlFiles();
-
- // Load the CWL file using SnakeYaml lib
- Yaml cwlReader = new Yaml();
+ ArrayList<Path> paths = getPath();
- for (File file : cwlFiles) {
- Map cwlFile = null;
+ for (Path path : paths) {
+ // figure out the dots in the path ex:
/maanadev/../cwltools
+ Path normalizedPath = path.normalize();
+ DirectoryStream<Path> stream = null;
try {
- cwlFile = (Map) cwlReader.load(new
FileInputStream(file));
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
- if (cwlFile != null) {
- // Creating CWl service Description
- CwlServiceDesc cwlServiceDesc = new
CwlServiceDesc();
- cwlServiceDesc.setCwlConfiguration(cwlFile);
-
cwlServiceDesc.setToolName(file.getName().split("\\.")[0]);
-
- // add to the result
- result.add(cwlServiceDesc);
- // return the service description
- callBack.partialResults(result);
+ stream =
Files.newDirectoryStream(normalizedPath, "*.cwl");
+ } catch (IOException e) {
+ logger.warn("Path is not correct !");
+ return;
}
+ // create stream with parallel capabilities
+ Stream<Path> paralleStream =
StreamSupport.stream(stream.spliterator(), true);
+
+ paralleStream.forEach(p -> {
+ Yaml reader = getYamlReader();
+
+ Map cwlFile;
+ try (FileInputStream file = new
FileInputStream(path.toFile())) {
+ cwlFile = (Map) reader.load(file);
+ JsonNode config = createJsonNode(p,
cwlFile);
+ // Creating CWl service Description
+ CwlServiceDesc cwlServiceDesc =
createCWLDesc(config);
+ // return the service description
+
callBack.partialResults(Arrays.asList(cwlServiceDesc));
+
+ } catch (IOException e) {
+
+ logger.warn("File not Found !");
+ }
+
+ });
+
+ callBack.finished();
}
- callBack.finished();
}
+/**
+ * This method checks whether provided path is valid or not and if it's
valid the it's added to the list
+ * @param defaultPaths arrylist to hold valid paths
+ * @param path
+ * @param path1 if there is no second path argument this should be set to
null
+ */
+ public void addPath(ArrayList<Path> defaultPaths, String path, String
path1) {
+
+ Path defaultPath;
+ if (path1 == null)
+ defaultPath = Paths.get(path);
+ else
+ defaultPath = Paths.get(path, path1);
+
+ if (defaultPath.isAbsolute())
+ defaultPaths.add(defaultPath);
+ }
-
+ private ArrayList<Path> getPath() {
--- End diff --
Return as interface `List<Path>` instead of hard-coding `ArrayList` - we
don't need ArrayList-specific features.
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