3289 harvest via oai pmh of rein d space fails

fairchive-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/GlobalId.java

@@ -1,9 +1,9 @@
 package edu.harvard.iq.dataverse.persistence;
 
-import static java.util.logging.Level.INFO;
 import static java.util.logging.Level.SEVERE;
 import static java.util.logging.Logger.getLogger;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import static org.apache.commons.lang3.StringUtils.startsWithIgnoreCase;
 
 import java.io.Serializable;
 import java.net.MalformedURLException;
@@ -19,15 +19,68 @@ public class GlobalId implements Serializable {
 
     public static final String DOI_PROTOCOL = "doi";
     public static final String HDL_PROTOCOL = "hdl";
+    public static final String HTTP_PROTOCOL = "http";
+    public static final String HTTPS_PROTOCOL = "https";
     public static final String HDL_RESOLVER_URL = "https://hdl.handle.net/";
+    public static final String HDL_RESOLVER_URL2 = "http://hdl.handle.net/";
     public static final String DOI_RESOLVER_URL = "https://doi.org/";
+    public static final String DOI_RESOLVER_URL2 = "http://doi.org/";
+    public static final String HTTPS_RESOLVER_URL = "https://";
+    public static final String HTTP_RESOLVER_URL = "http://";
     private static final String PID_ALLOWED_CHARACTERS_PATTERN = "^[A-Za-z0-9._/:\\\\-]*";
 
     private static final Logger logger = getLogger(GlobalId.class.getName());
 
-    private String protocol;
-    private String authority;
-    private String identifier;
+    private final String protocol;
+    private final String authority;
+    private final String identifier;
+
+    public static GlobalId fromHDLUrl(final String url) {
+		final int lastSlashIndex = url.lastIndexOf('/');
+		final int authorityOffset = url.startsWith(HDL_RESOLVER_URL)
+			? HDL_RESOLVER_URL.length() : HDL_RESOLVER_URL2.length();
+		return new GlobalId(HDL_PROTOCOL, 
+				url.substring(authorityOffset, lastSlashIndex),
+				url.substring(lastSlashIndex + 1));
+    }
+
+    public static GlobalId fromDOIUrl(final String url) {
+ 		final int lastSlashIndex = url.lastIndexOf('/');
+ 		final int authorityOffset = url.startsWith(DOI_RESOLVER_URL)
+ 			? DOI_RESOLVER_URL.length() : DOI_RESOLVER_URL2.length();
+
+ 		final String authority = url.substring(authorityOffset, lastSlashIndex);
+ 		final String identifier = url.substring(lastSlashIndex + 1);
+
+ 		// sometimes DOIs come in form of
+ 		// https://doi.org/DOI: 10.19195/2353-8546.8.13 or
+ 		// https://doi.org/DOI : 10.19195/2353-8546.8.13
+ 		// https://doi.org/1https://doi.org/0.14746/eip.2023.2.8
+ 		// even after fixing, these links lead to nowhere so it is 
+ 		// better to let the caller know that it needs to find another identifier
+ 		if(startsWithIgnoreCase(authority, "DOI") || authority.startsWith("1https")) {
+ 			throw new IllegalArgumentException("Bloken DOI url: ".concat(url));
+ 		}
+ 		return new GlobalId(DOI_PROTOCOL, authority, identifier);
+   }
+
+	public static GlobalId fromHttpUrl(final String url) throws RuntimeException {
+		try {
+			final URL u = new URL(url);
+			return new GlobalId(HTTP_PROTOCOL, u.getHost(), u.getPath());
+		} catch (final MalformedURLException e) {
+			throw new IllegalArgumentException(e);
+		}
+	}
+
+	public static GlobalId fromHttpsUrl(final String url) throws RuntimeException {
+		try {
+			final URL u = new URL(url);
+			return new GlobalId(HTTPS_PROTOCOL, u.getHost(), u.getPath());
+		} catch (final MalformedURLException e) {
+			throw new IllegalArgumentException(e);
+		}
+	}
 
     public static Optional<GlobalId> parse(final String identifierString) {
         try {
@@ -42,12 +95,68 @@ public static Optional<GlobalId> parse(final String identifierString) {
      * @throws IllegalArgumentException if the passed string cannot be parsed.
      * @Thorws NullPointerException i identifier is null
      */
-    public GlobalId(final String identifier) {
-        // set the protocol, authority, and identifier via parsePersistentId
-        if (!parsePersistentId(identifier)) {
-            throw new IllegalArgumentException("Failed to parse identifier: ".concat(identifier));
+    public GlobalId(final String identifierString) {
+        final int index1 = identifierString.indexOf(':');
+        if (index1 > 0) { // ':' found with one or more characters before it
+        	if(identifierString.startsWith(HTTPS_PROTOCOL)) {
+        		try {
+	        		final URL url = new URL(identifierString.substring(HTTPS_PROTOCOL.length() +1));
+	        		this.protocol = HTTPS_PROTOCOL;
+	        		this.authority = url.getHost();
+	        		this.identifier = url.getPath();
+	        		if(conainsNullTerminator(this.identifier)) {
+	        			throw createException(identifierString);
+	        		}
+        		} catch (final MalformedURLException e) {
+        			throw new IllegalArgumentException(e);
+        		}
+        	} else if(identifierString.startsWith(HTTP_PROTOCOL)) {
+        		try {
+	        		final URL url = new URL(identifierString.substring(HTTP_PROTOCOL.length() +1));
+	        		this.protocol = HTTP_PROTOCOL;
+	        		this.authority = url.getHost();
+	        		this.identifier = url.getPath();
+	        		if(conainsNullTerminator(this.identifier)) {
+	        			throw createException(identifierString);
+	        		}
+        		} catch (final MalformedURLException e) {
+        			throw new IllegalArgumentException(e);
+        		}
+        	} else {
+	            final int index2 = identifierString.indexOf('/', index1 + 1);
+	            if (index2 > 0 && (index2 + 1) < identifierString.length()) { // '/' found with one or more characters
+	                // between ':'
+	                this.protocol = identifierString.substring(0, index1); // and '/' and there are characters after '/'
+	                if (!DOI_PROTOCOL.equals(this.protocol) 
+	                		&& !HDL_PROTOCOL.equals(this.protocol)) {
+	                	throw createException(identifierString);
+	                }
+	                //Strip any whitespace, ; and ' from authority (should finding them cause a failure instead?)
+	                this.authority = formatIdentifierString(identifierString.substring(index1 + 1, index2));
+	                if (conainsNullTerminator(this.authority)) {
+	                	throw createException(identifierString);
+	                }
+	                if (this.protocol.equals(DOI_PROTOCOL) && !this.checkDOIAuthority(this.authority)) {
+	                	throw createException(identifierString);
+	                }
+	                // Passed all checks
+	                //Strip any whitespace, ; and ' from identifier (should finding them cause a failure instead?)
+	                this.identifier = formatIdentifierString(identifierString.substring(index2 + 1));
+	                if(conainsNullTerminator(this.identifier)) {
+	                	throw createException(identifierString);
+	                }
+	            } else {
+	            	throw createException(identifierString);
+	            }
+        	}
+        } else {
+        	throw createException(identifierString);
         }
     }
+
+    private static IllegalArgumentException createException(final String identifier) {
+    	return new IllegalArgumentException("Failed to parse identifier: ".concat(identifier));
+    }
 
     public GlobalId(final String protocol, final String authority, final String identifier) {
         this.protocol = protocol;
@@ -77,24 +186,12 @@ public String getProtocol() {
         return this.protocol;
     }
 
-    public void setProtocol(final String protocol) {
-        this.protocol = protocol;
-    }
-
-    public String getAuthority() {
-        return this.authority;
-    }
-
-    public void setAuthority(final String authority) {
-        this.authority = authority;
-    }
+	public String getAuthority() {
+		return this.authority;
+	}
 
     public String getIdentifier() {
-        return this.identifier;
-    }
-
-    public void setIdentifier(final String identifier) {
-        this.identifier = identifier;
+		return this.identifier;
     }
 
     public String toString() {
@@ -108,9 +205,13 @@ public String toString() {
      * @return The string representation of this global id.
      */
     public String asString() {
-        return this.protocol == null || this.authority == null || this.identifier == null
-            ? ""
-            : this.protocol + ':' + this.authority + '/' + this.identifier;
+        if(this.protocol == null || this.authority == null || this.identifier == null) {
+            return "";
+        } else if(HTTP_PROTOCOL.equals(this.protocol) || HTTPS_PROTOCOL.equals(this.protocol)) {
+        	return this.protocol + ':' + this.protocol + "://" + this.authority + this.identifier;
+        } else {
+            return this.protocol + ':' + this.authority + '/' + this.identifier;
+        }
     }
 
     public URL toURL() {
@@ -120,67 +221,43 @@ public URL toURL() {
 					return new URL(DOI_RESOLVER_URL + this.authority + '/' + this.identifier);
 				} else if (HDL_PROTOCOL.equals(this.protocol)) {
 					return new URL(HDL_RESOLVER_URL + this.authority + '/' + this.identifier);
-				} 
+				} else if(HTTP_PROTOCOL.equals(this.protocol) || HTTPS_PROTOCOL.equals(this.protocol)) {
+					return new URL(this.protocol, this.authority, this.identifier);
+				}
 			} catch (final MalformedURLException ex) {
 				logger.log(SEVERE, null, ex);
 			}
 		}
 		return null;
     }
+
+    public String getStoragePath() {
+    	return this.authority.replace(':', '_') + '/' + 
+    			stripLeadingSlashes(this.identifier.replace(':', '_'));
+    }
+
+    private static String stripLeadingSlashes(final String s) {
+    	int index = 0;
+    	while(s.charAt(index) == '/') {
+    		++index;
+    	}
+    	return s.substring(index);
+    }
 
-
-    /**
-     * Parse a Persistent Id and set the protocol, authority, and identifier
-     * <p>
-     * Example 1: doi:10.5072/FK2/BYM3IW
-     * protocol: doi
-     * authority: 10.5072
-     * identifier: FK2/BYM3IW
-     * <p>
-     * Example 2: hdl:1902.1/111012
-     * protocol: hdl
-     * authority: 1902.1
-     * identifier: 111012
-     *
-     * @param identifierString
-     * @param separator        the string that separates the authority from the identifier.
-     * @param destination      the global id that will contain the parsed data.
-     * @return {@code destination}, after its fields have been updated, or
-     * {@code null} if parsing failed.
-     */
-    private boolean parsePersistentId(final String identifierString) {
-
-        final int index1 = identifierString.indexOf(':');
-        if (index1 > 0) { // ':' found with one or more characters before it
-            final int index2 = identifierString.indexOf('/', index1 + 1);
-            if (index2 > 0 && (index2 + 1) < identifierString.length()) { // '/' found with one or more characters
-                // between ':'
-                this.protocol = identifierString.substring(0, index1); // and '/' and there are characters after '/'
-                if (!DOI_PROTOCOL.equals(this.protocol) && !HDL_PROTOCOL.equals(this.protocol)) {
-                    return false;
-                }
-                //Strip any whitespace, ; and ' from authority (should finding them cause a failure instead?)
-                this.authority = formatIdentifierString(identifierString.substring(index1 + 1, index2));
-                if (testforNullTerminator(this.authority)) {
-                    return false;
-                }
-                if (this.protocol.equals(DOI_PROTOCOL) && !this.checkDOIAuthority(this.authority)) {
-                    return false;
-                }
-                // Passed all checks
-                //Strip any whitespace, ; and ' from identifier (should finding them cause a failure instead?)
-                this.identifier = formatIdentifierString(identifierString.substring(index2 + 1));
-                return !testforNullTerminator(this.identifier);
-            } else {
-                logger.log(INFO, "Error parsing identifier: {0}: '':<authority>/<identifier>'' not found in string", 
-                		identifierString);
-                return false;
-            }
-        } else {
-            logger.log(INFO, "Error parsing identifier: {0}: ''<protocol>:'' not found in string", 
-            		identifierString);
-            return false;
-        }
+    public static boolean isDOI(final String id) {
+    	return id.startsWith(DOI_RESOLVER_URL) || id.startsWith(DOI_RESOLVER_URL2);
+    }
+
+    public static boolean isHDL(final String id) {
+    	return id.startsWith(HDL_RESOLVER_URL) || id.startsWith(HDL_RESOLVER_URL2);
+    }
+
+    public static boolean isHTTP(final String id) {
+    	return id.startsWith(HTTP_RESOLVER_URL);
+    }
+
+    public static boolean isHTTPS(final String id) {
+    	return id.startsWith(HTTPS_RESOLVER_URL);
     }
 
     private static String formatIdentifierString(final String str) {
@@ -202,7 +279,7 @@ private static String formatIdentifierString(final String str) {
         // http://www.doi.org/doi_handbook/2_Numbering.html
     }
 
-    private static boolean testforNullTerminator(final String str) {
+    private static boolean conainsNullTerminator(final String str) {
     	return str != null ? str.indexOf('\u0000') > 0 : false;
     }