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Revision 4945

Added by Duane Costa over 15 years ago

Bug 3835: Design and implement OAI-PMH compliant harvest subsystem
1. When building the Metacat OAI-PMH catalog, modify the database query to search only for documents with public read access.
2. Change syntax used for identifiers in the repository to LSID format instead of using a URL to a specific repository.
Old syntax: 'http://metacat.lternet.edu/knb/metacat/knb-lter-gce.169'
New syntax: 'urn:lsid:knb.ecoinformatics.org:knb-lter-gce:169'

       private String repositoryIdentifier = null;
       private String context = null;
       private final String TEST_CONTEXT = "knb";
       private final String LSID_PREFIX = "urn:lsid:knb.ecoinformatics.org:";
       /**
-...
       /**
        * Utility method to parse the 'local identifier' from the OAI identifier
+       *
        * @param identifier
        *          OAI identifier (e.g.
        *          "http://metacat.lternet.edu/knb/metacat/knb-lter-gce.247")
        * @param oaiIdentifier  OAI identifier e.g.
        *                       "urn:lsid:knb.ecoinformatics.org:knb-lter-gce:169"
+       *
        * @return local identifier (e.g. "knb-lter-gce.247")
        * @return local identifier, e.g. "knb-lter-gce.169"
        */
       public String fromOAIIdentifier(String identifier) {
         try {
           if (identifier != null) {
             int i = identifier.indexOf("/metacat/");
             String tailString = identifier.substring(i + 9);
             StringTokenizer tokenizer = new StringTokenizer(tailString, "/");
             String localIdentifier = tokenizer.nextToken();
             return localIdentifier;
           } else {
             return null;
       public String fromOAIIdentifier(String oaiIdentifier) {
         String localIdentifier = null;
         if (oaiIdentifier != null) {
           String[] oaiIdentifierArray = splitOAIIdentifier(oaiIdentifier);
           int len = oaiIdentifierArray.length;
           if (len >= 2) {
             String scope = oaiIdentifierArray[len - 2];
             String identifier = oaiIdentifierArray[len - 1];
             localIdentifier = scope + "." + identifier;
+          }
         } catch (Exception e) {
           return null;
+        }
         return localIdentifier;
+      }
       /**
        * Construct an OAI identifier from the native item
+       *
        * @param  nativeItem         native Item object
        * @return OAI identifier,
        *         e.g. urn:lsid:knb.ecoinformatics.org:knb-lter-gce:169
        */
       public String getOAIIdentifier(Object nativeItem) {
         String localIdentifier = getLocalIdentifier(nativeItem);
         StringBuffer sb = new StringBuffer();
         if (localIdentifier != null) {
           String[] localIdentifierArray = splitLocalIdentifier(localIdentifier);
           if (localIdentifierArray.length >= 2) {
             sb.append(LSID_PREFIX);
             String scope = localIdentifierArray[0];
             sb.append(scope);
             sb.append(":");
             String identifier = localIdentifierArray[1];
             sb.append(identifier);
+          }
+        }
         return sb.toString();
+      }
       /**
        * Construct an OAI identifier from the native item
+       *
        * @param nativeItem
        *          native Item object
        * @return OAI identifier
        */
       public String getOAIIdentifier(Object nativeItem) {
       public String getOAIIdentifierOld(Object nativeItem) {
         String localIdentifier = getLocalIdentifier(nativeItem);
         StringBuffer sb = new StringBuffer();
-...
         return headerArray;
+      }
       private String[] splitLocalIdentifier(String s) {
         StringTokenizer tokenizer = new StringTokenizer(s, ".");
         String[] tokens = new String[tokenizer.countTokens()];
         for (int i=0; i<tokens.length; ++i) {
             tokens[i] = tokenizer.nextToken();
+        }
         return tokens;
+      }
       private String[] splitOAIIdentifier(String s) {
         StringTokenizer tokenizer = new StringTokenizer(s, ":");
         String[] tokens = new String[tokenizer.countTokens()];
         for (int i=0; i<tokens.length; ++i) {
             tokens[i] = tokenizer.nextToken();
+        }
         return tokens;
+      }
+    }

       private HashMap resumptionResults = new HashMap();
       private int maxListSize;
       /*
        * QUERY string to find all eml-2.x.y documents in the Metacat database
        * that are publicly accessible
        */
       private final String QUERY =
       "SELECT docid, doctype, date_updated " +
       "FROM xml_documents " +
       "WHERE doctype like 'eml://ecoinformatics.org/eml-2%' AND " +
       "  (docid IN " +
       "     (SELECT docid " +
       "      FROM xml_access " +
       "      WHERE( (lower(principal_name) = 'public') AND " +
       "             perm_type = 'allow' AND " +
       "             permission > 3" +
       "           )" +
       "     )" +
       "   AND " +
       "   docid NOT IN " +
       "     (SELECT docid " +
       "      FROM xml_access " +
       "      WHERE( (lower(principal_name) = 'public') AND " +
       "             perm_type = 'deny' AND " +
       "             perm_order ='allowFirst' AND " +
       "             permission > 3" +
       "           )" +
       "     )" +
       "  )";
       /* Constructors */
     /* Constructors */
       public MetacatCatalog(Properties properties) {
         String errorStr;
         String temp;
-...
             metacatURL = SystemUtil.getServletURL();
+          }
           else {
             metacatURL = "http://localhost:8080/knb/metacat";
             metacatURL = properties.getProperty("test.metacatUrl");
+          }
           logger.warn("metacatURL: " + metacatURL);
-...
        * values.
        */
       public void loadCatalog() {
         String query =
           "SELECT docid, doctype, date_updated " +
           "FROM xml_documents " +
           "WHERE doctype like 'eml://ecoinformatics.org/eml-2%'";
         Statement stmt;
         try {
-...
           if (conn != null) {
             stmt = conn.createStatement();
             ResultSet rs = stmt.executeQuery(query);
             ResultSet rs = stmt.executeQuery(QUERY);
             int documentCount = 0;
             while (rs.next()) {
               documentCount++;
               String docid = rs.getString("docid");
               String doctype = rs.getString("doctype");
               String dateUpdated = rs.getDate("date_updated").toString();
               docTypeMap.put(docid, doctype);
               dateMap.put(docid, dateUpdated);
+            }
             logger.info("Number of documents in catalog: " + documentCount);
             stmt.close();
             conn.close();

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Revision 4945

Added by Duane Costa over 15 years ago