git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/dataminer-pool-manager@134567 82a268e6-3cf1-43bd-a215-b396298e98cf

src/main/java/org/gcube/dataanalysys/dataminerpoolmanager/ansiblebridge/template/AlgorithmPackage.java

@@ -37,7 +37,7 @@ public class AlgorithmPackage {
   
   public Collection<Role> getRoles(TemplateManager tm) {
     Collection<Role> out = new Vector<>();
-    for(String mode:new String[]{"add", "remove", "update"}) {
+    for(String mode:new String[]{"add"}) {  // "remove", "update"
       String roleName = "gcube-algorithm-"+this.getAlgorithm().getName()+("add".equals(mode) ? "" : "-"+mode);
       try {
         // find template

src/main/java/org/gcube/dataanalysys/dataminerpoolmanager/ansiblebridge/template/CustomDependencyPackage.java

@@ -1,15 +1,10 @@
 package org.gcube.dataanalysys.dataminerpoolmanager.ansiblebridge.template;
 
-import java.io.File;
-import java.io.IOException;
 import java.util.Collection;
-import java.util.Map;
 import java.util.NoSuchElementException;
 import java.util.Vector;
 
-import org.apache.commons.io.FileUtils;
 import org.gcube.dataanalysys.dataminerpoolmanager.ansible.model.Role;
-import org.gcube.dataanalysys.dataminerpoolmanager.ansible.model.RoleFile;
 import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.Dependency;
 
 public class CustomDependencyPackage extends DependencyPackage {
@@ -47,7 +42,8 @@ public class CustomDependencyPackage extends DependencyPackage {
   
   public Collection<Role> getRoles(CustomRoleManager crm) {
     Collection<Role> out = new Vector<>();
-    for(String mode:new String[]{"add", "remove", "update"}) {
+//    for(String mode:new String[]{"add", "remove", "update"}) {
+    for(String mode:new String[]{"add"}) {  // "remove", "update"
       // role name
       String roleName = this.getDependency().getType()+"-"+this.getDependency().getName()+("add".equals(mode) ? "" : "-"+mode);
       try {

src/main/java/org/gcube/dataanalysys/dataminerpoolmanager/ansiblebridge/template/DependencyPackage.java

@@ -31,7 +31,7 @@ public class DependencyPackage {
   
   public Collection<Role> getRoles(TemplateManager tm) {
     Collection<Role> out = new Vector<>();
-    for(String mode:new String[]{"add", "remove", "update"}) {
+    for(String mode:new String[]{"add"}) {  // "remove", "update"
       String roleName = this.getDependency().getType()+"-"+this.getDependency().getName()+("add".equals(mode) ? "" : "-"+mode);
       try {
         // find template

src/main/java/org/gcube/dataanalysys/dataminerpoolmanager/datamodel/Algorithm.java

@@ -10,6 +10,8 @@ public class Algorithm {
   private String description;
 
   private String category;
+  
+  private String clazz;
 
   private Collection<Action> actions;
 
@@ -63,9 +65,18 @@ public class Algorithm {
   
   public String toString() {
     String out = "Algorithm: " + this.getName()+"\n";
+    out+="  Class Name: " + this.getClazz()+"\n";
     out+="  Description: " + this.getDescription()+"\n";
     out+="  Dependencies: " + this.getDependencies()+"\n";
     return out;
   }
 
+  public String getClazz() {
+    return clazz;
+  }
+
+  public void setClazz(String clazz) {
+    this.clazz = clazz;
+  }
+
 }

src/main/java/org/gcube/dataanalysys/dataminerpoolmanager/process/AddAlgorithmCommand.java

@@ -0,0 +1,90 @@
+package org.gcube.dataanalysys.dataminerpoolmanager.process;
+
+import java.util.StringTokenizer;
+
+public class AddAlgorithmCommand {
+
+  private String command;
+  private String name;
+  private String category;
+  private String clazz;
+  private String vre;
+  private String p6;
+  private String p7;
+  private String url;
+  private String description;
+
+  public AddAlgorithmCommand(String cmd) {
+    StringTokenizer st = new StringTokenizer(cmd, " ");
+    if (st.hasMoreElements())
+      command = st.nextToken();
+    if (st.hasMoreElements())
+      name = st.nextToken();
+    if (st.hasMoreElements())
+      category = st.nextToken();
+    if (st.hasMoreElements())
+      clazz = st.nextToken();
+    if (st.hasMoreElements())
+      vre = st.nextToken();
+    if (st.hasMoreElements())
+      p6 = st.nextToken();
+    if (st.hasMoreElements())
+      p7 = st.nextToken();
+    if (st.hasMoreElements())
+      url = st.nextToken();
+    description = "";
+    while (st.hasMoreElements())
+      description = description + st.nextToken() + " ";
+  }
+
+  public String getCommand() {
+    return command;
+  }
+
+  public String getName() {
+    return name;
+  }
+
+  public String getCategory() {
+    return category;
+  }
+
+  public String getClazz() {
+    return clazz;
+  }
+
+  public String getVRE() {
+    return vre;
+  }
+
+  public String getP6() {
+    return p6;
+  }
+
+  public String getP7() {
+    return p7;
+  }
+
+  public String getUrl() {
+    return url;
+  }
+
+  public String getDescription() {
+    return description;
+  }
+
+  public String toString() {
+    String out = "";
+    out += String.format("%-12s: %s\n", "command", command);
+    out += String.format("%-12s: %s\n", "name", name);
+    out += String.format("%-12s: %s\n", "category", category);
+    out += String.format("%-12s: %s\n", "class", clazz);
+    out += String.format("%-12s: %s\n", "vre", vre);
+    out += String.format("%-12s: %s\n", "p6", p6);
+    out += String.format("%-12s: %s\n", "p7", p7);
+    out += String.format("%-12s: %s\n", "url", url);
+    out += String.format("%-12s: %s\n", "description", this.description);
+    return out;
+  }
+
+}

src/main/java/org/gcube/dataanalysys/dataminerpoolmanager/process/AlgorithmPackageParser.java

@@ -0,0 +1,190 @@
+package org.gcube.dataanalysys.dataminerpoolmanager.process;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.Algorithm;
+import org.gcube.dataanalysys.dataminerpoolmanager.datamodel.Dependency;
+
+public class AlgorithmPackageParser {
+
+  /**
+   * The name of the file containing algorithm metadata. Expected in the root
+   * directory of the package.
+   */
+  private static final String METADATA_FILE_NAME = "Info.txt";
+
+  private static final String METADATA_ALGORITHM_NAME = "Algorithm Name";
+
+  private static final String METADATA_ALGORITHM_DESCRIPTION = "Algorithm Description";
+
+  private static final String METADATA_CLASS_NAME = "Class Name";
+
+  private static final String METADATA_PACKAGES = "Packages";
+
+  private static final String METADATA_KEY_VALUE_SEPARATOR = ":";
+
+  private static final int BUFFER_SIZE = 4096;
+
+  /**
+   * Given an URL to an algorithm package, create an Algorithm object with its
+   * metadata. Metadata are extracted from the 'info.txt' file, if any, in the
+   * package.
+   * 
+   * @param url
+   * @return An Algorithm object or null if no 'info.txt' is found in the
+   *         package.
+   * @throws IOException
+   */
+  public Algorithm parsePackage(String url) throws IOException {
+    String packageMetadata = this.getPackageMetadata(url);
+    if (packageMetadata == null) {
+      System.out.println("WARNING: No metadata found for " + url);
+      return null;
+    } else {
+      Map<String, List<String>> parsedMetadata = this.parseMetadata(packageMetadata);
+      return this.createAlgorithm(parsedMetadata);
+    }
+  }
+
+  /**
+   * Extract the content of the metadata file from the package.
+   * 
+   * @param url
+   * @return
+   * @throws IOException
+   */
+  private String getPackageMetadata(String url) throws IOException {
+    InputStream is = new URL(url).openStream();
+    ZipInputStream zipIs = new ZipInputStream(is);
+    ZipEntry entry = zipIs.getNextEntry();
+    String out = null;
+    while (entry != null) {
+      if (METADATA_FILE_NAME.equalsIgnoreCase(entry.getName())) {
+        out = this.getEntryContent(zipIs);
+        break;
+      }
+      entry = zipIs.getNextEntry();
+    }
+    is.close();
+    zipIs.close();
+    return out;
+  }
+
+  /**
+   * Read the content of a zip entry and place it in a string.
+   * @param zipIn
+   * @return
+   * @throws IOException
+   */
+  private String getEntryContent(ZipInputStream zipIn) throws IOException {
+    StringBuilder s = new StringBuilder();
+    byte[] buffer = new byte[BUFFER_SIZE];
+    int read = 0;
+    while ((read = zipIn.read(buffer)) != -1) {
+      s.append(new String(buffer, 0, read));
+    }
+    return s.toString();
+  }
+
+  /**
+   * Parse the content of the metadata file and create a key+multivalue map.
+   * @param metadata
+   * @return
+   */
+  private Map<String, List<String>> parseMetadata(String metadata) {
+    Map<String, List<String>> out = new HashMap<String, List<String>>();
+    String[] lines = metadata.split("\n");
+
+    String key = null;
+    String value = null;
+
+    for (String line : lines) {
+      // skip empty lines
+      if (line.trim().isEmpty()) {
+        continue;
+      }
+      // scan lines one by one, looking for key and values
+      String[] parts = line.split(METADATA_KEY_VALUE_SEPARATOR);
+      if (parts.length > 1) {
+        // key and value on the same line
+        key = parts[0].trim();
+        value = line.substring(parts[0].length() + 1).trim();
+      } else if (parts.length == 1) {
+        // either a key or a value
+        if (line.trim().endsWith(METADATA_KEY_VALUE_SEPARATOR)) {
+          // key
+          key = parts[0].trim();
+          value = null;
+        } else {
+          // value
+          value = line.trim();
+        }
+      }
+      // add key+value to the map
+      if (key != null && value != null) {
+        List<String> values = out.get(key);
+        if (values == null) {
+          values = new Vector<>();
+          out.put(key, values);
+        }
+        values.add(value);
+        System.out.println(key + METADATA_KEY_VALUE_SEPARATOR + " " + values);
+      }
+    }
+    return out;
+  }
+
+  /**
+   * Create an Algorithm starting from its metadata
+   * @param metadata
+   * @return
+   */
+  private Algorithm createAlgorithm(Map<String, List<String>> metadata) {
+    Algorithm out = new Algorithm();
+    out.setName(extractSingleValue(metadata, METADATA_ALGORITHM_NAME));
+    out.setDescription(extractSingleValue(metadata,
+        METADATA_ALGORITHM_DESCRIPTION));
+    out.setClazz(extractSingleValue(metadata, METADATA_CLASS_NAME));
+    List<String> dependencies = extractMultipleValues(metadata,
+        METADATA_PACKAGES);
+    if (dependencies != null) {
+      for (String pkg : dependencies) {
+        Dependency dep = new Dependency();
+        dep.setName(pkg);
+        dep.setType("OS");
+        out.addDependency(dep);
+      }
+    }
+    return out;
+  }
+
+  
+  private static String extractSingleValue(Map<String, List<String>> metadata,
+      String key) {
+    List<String> l = metadata.get(key);
+    if (l != null && l.size() == 1) {
+      return l.get(0);
+    } else {
+      return null;
+    }
+  }
+
+  private static List<String> extractMultipleValues(
+      Map<String, List<String>> metadata, String key) {
+    List<String> l = metadata.get(key);
+    if (l != null) {
+      return new Vector<>(l);
+    } else {
+      return null;
+    }
+  }
+
+}