From c33f378461cc617d47f30d6e4bb426724d338d8f Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 6 Nov 2024 12:13:53 +0000
Subject: [PATCH] JAL-4485 Extracted the whitelist/blacklist fileglob finding
 code into FileUtils for more generic use

---
 src/jalview/util/FileUtils.java |  121 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 121 insertions(+)

diff --git a/src/jalview/util/FileUtils.java b/src/jalview/util/FileUtils.java
index 7950de4..5f58903 100644
--- a/src/jalview/util/FileUtils.java
+++ b/src/jalview/util/FileUtils.java
@@ -36,7 +36,9 @@ import java.nio.file.attribute.BasicFileAttributes;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.EnumSet;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import jalview.bin.Console;
@@ -368,4 +370,123 @@ public class FileUtils
       return hasExtension ? filename0.substring(0, dot + 1) : filename0;
     }
   }
+
+  /**
+   * Look for files that use a template, with two "%s" formatting entries, to
+   * look for files with the template substituted with combinations of root and
+   * version. If versionWhitelist is not null then these paths will be added. If
+   * versionBlacklist is not null then globbed versions will be looked for and
+   * these versions excluded. If both are given then both will be included. If
+   * separator is not null then it will be added before the version number, and
+   * additionally a path without the separator and version will be looked for or
+   * added if the whitelist or blacklist are supplied respectively.
+   * 
+   * @param templates
+   * @param roots
+   * @param versionWhitelist
+   * @param versionBlacklist
+   * @param separator
+   * @return
+   */
+  public static List<File> getMatchingVersionedFiles(String[] templates,
+          String[] roots, String[] versionWhitelist,
+          String[] versionBlacklist, String separator)
+  {
+    Set<File> matchingFiles = new HashSet<>();
+    if (templates == null)
+    {
+      Console.debug(
+              "getMatchingVersionedFiles called with a null template array");
+      List<File> files = new ArrayList<File>();
+      files.addAll(matchingFiles);
+      return files;
+    }
+
+    Console.debug("Looking for all versions with a blacklist of size "
+            + versionBlacklist.length);
+    for (String template : templates)
+    {
+      Console.debug("Using template '" + template + "'");
+      for (String root : roots)
+      {
+        Console.debug("Using root '" + root + "'");
+        if (versionBlacklist != null)
+        {
+          String globMatch = String.format(template, root, "*");
+          Console.debug("Using glob '" + globMatch + "'");
+          List<File> foundFiles = FileUtils.getFilesFromGlob(globMatch,
+                  false);
+          for (File found : foundFiles)
+          {
+            Console.debug("Checking " + found.getPath() + " is okay");
+            boolean add = true;
+            for (String notVersion : versionBlacklist)
+            {
+              StringBuilder vSB = new StringBuilder();
+              if (separator != null)
+              {
+                vSB.append(separator);
+              }
+              vSB.append(notVersion);
+              String versionString = vSB.toString();
+              if (String.format(template, root, versionString)
+                      .equals(found.getPath()))
+              {
+                add = false;
+                Console.debug(
+                        "Not adding " + found.getPath() + ": version '"
+                                + notVersion + "' is in the blacklist");
+                break;
+              }
+            }
+            if (add)
+            {
+              Console.debug("Adding " + found.getPath() + " to list");
+              matchingFiles.add(found);
+            }
+          }
+
+          if (separator != null)
+          {
+            // try without a version number too
+            String nonVersioned = String.format(template, root, "");
+            matchingFiles.addAll(
+                    FileUtils.getFilesFromGlob(nonVersioned, false));
+          }
+        }
+
+        if (versionWhitelist != null)
+        {
+          Console.debug("Adding " + versionWhitelist.length
+                  + " whitelist versions");
+          for (String addVersion : versionWhitelist)
+          {
+            StringBuilder vSB = new StringBuilder();
+            if (separator != null)
+            {
+              vSB.append(separator);
+            }
+            vSB.append(addVersion);
+            String versionString = vSB.toString();
+            String versionPath = String.format(template, root,
+                    versionString);
+            Console.debug("Adding whitelist path '" + versionPath + "'");
+            matchingFiles.add(new File(versionPath));
+          }
+
+          if (separator != null)
+          {
+            // try without a version number too
+            String nonVersioned = String.format(template, root, "");
+            matchingFiles.add(new File(nonVersioned));
+          }
+        }
+      }
+    }
+
+    List<File> files = new ArrayList<File>();
+    files.addAll(matchingFiles);
+    return files;
+  }
+
 }
-- 
1.7.10.2