Docs and test

josemduarte · josemduarte · commit 100705d8b243 · 2021-10-01T14:19:23.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
@@ -101,10 +101,10 @@ public static void setServerBaseUrl(String serverBaseUrl) {
     /**
      * Set the path to append to the serverBaseUrl (settable in {@link #setServerBaseUrl(String)}).
      * The string can contain placeholders that will be expanded at runtime:
-     * <li>{ccd_id} to be replaced by the chemical component identifier, in capitals</li>
-     * <li>{ccd_id:beginIndex-endIndex} to be replaced by a substring of the chemical component identifier in capitals,
+     * <li>"{ccd_id}" to be replaced by the chemical component identifier, in capitals</li>
+     * <li>"{ccd_id:beginIndex-endIndex}" to be replaced by a substring of the chemical component identifier in capitals,
      * with indices following the same convention as {@link String#substring(int, int)} </li>
-     * <li>{ccd_id:index} to be replaced by a substring of the chemical component identifier in capitals,
+     * <li>"{ccd_id:index}" to be replaced by a substring of the chemical component identifier in capitals,
      * with index either a positive or negative integer to substring from left or right of the string respectively.</li>
      * If any of the indices are off-bounds, then the full chemical component identifier is replaced
      */
@@ -314,6 +314,13 @@ private static boolean fileIsAbsent(String recordName) {
         return !f.exists();
     }
 
+    /**
+     * Expands the given path URL template, replacing the placeholders as specified in {@link #setChemCompPathUrlTemplate(String)}
+     * by the ccdId given (or its substrings, if indices are present in the template)
+     * @param templateStr the template string with placeholders for ccd ids
+     * @param ccdId the ccd id to replace (in full or a substring)
+     * @return the input templateStr with placeholders replaced
+     */
     static String expandPathUrlTemplate(String templateStr, String ccdId) {
         Matcher m = CCD_ID_TEMPLATE_REGEX.matcher(templateStr);
         StringBuilder output = new StringBuilder();
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/chem/TestDownloadChemCompProvider.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/chem/TestDownloadChemCompProvider.java
@@ -136,6 +136,13 @@ public void testPathUrlTemplateExpansion() {
 		String e2 = "/my/path/D/hello/D/dir/abcdef/D/12345/D.cif";
 		String r2 = DownloadChemCompProvider.expandPathUrlTemplate(templateStr,"D");
 		assertEquals(e2, r2);
+
+		String e3 = "/my/path//hello//dir/abcdef//12345/.cif";
+		String r3 = DownloadChemCompProvider.expandPathUrlTemplate(templateStr,"");
+		assertEquals(e3, r3);
+
+		templateStr = "/my/fixed/dir";
+		assertEquals(templateStr, DownloadChemCompProvider.expandPathUrlTemplate(templateStr, "" ));
 	}
 
 }

Original file line number	Diff line number	Diff line change
`@@ -136,6 +136,13 @@ public void testPathUrlTemplateExpansion() {`
`136`	`136`	`String e2 = "/my/path/D/hello/D/dir/abcdef/D/12345/D.cif";`
`137`	`137`	`String r2 = DownloadChemCompProvider.expandPathUrlTemplate(templateStr,"D");`
`138`	`138`	`assertEquals(e2, r2);`
	`139`	`+`
	`140`	`+ String e3 = "/my/path//hello//dir/abcdef//12345/.cif";`
	`141`	`+ String r3 = DownloadChemCompProvider.expandPathUrlTemplate(templateStr,"");`
	`142`	`+ assertEquals(e3, r3);`
	`143`	`+`
	`144`	`+ templateStr = "/my/fixed/dir";`
	`145`	`+ assertEquals(templateStr, DownloadChemCompProvider.expandPathUrlTemplate(templateStr, "" ));`
`139`	`146`	`}`
`140`	`147`
`141`	`148`	`}`