Replace -debug by -verbose

ebi-pf-team · Nov 5, 2024 · 71c3edb · 71c3edb
1 parent 6097d48
commit 71c3edb
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Showing 2 changed files with 19 additions and 16 deletions.
diff --git a/...main/java/uk/ac/ebi/interpro/scan/precalc/berkeley/iprscan/CreateMatchesDBFromOracle.java b/...main/java/uk/ac/ebi/interpro/scan/precalc/berkeley/iprscan/CreateMatchesDBFromOracle.java
@@ -30,7 +30,7 @@ public class CreateMatchesDBFromOracle {
                     "EVALUE, SEQ_FEATURE " +
                     "FROM " + USER + ".LOOKUP_MATCH PARTITION (?)";
 
-    void buildDatabase(String url, String password, int fetchSize, File outputDirectory, boolean debug) {
+    void buildDatabase(String url, String password, int fetchSize, File outputDirectory, boolean verbose) {
         System.err.println(Utilities.getTimeAlt() + ": starting");
 
         try (BerkeleyDBJE bdbje = new BerkeleyDBJE(outputDirectory)) {
@@ -40,10 +40,13 @@ void buildDatabase(String url, String password, int fetchSize, File outputDirect
             try (Connection connection = DriverManager.getConnection(url, USER, password)) {
                 List<String> partitions = getPartitions(connection);
 
-                long proteinCount = 0;
+                int proteinCount = 0;
+                int milestone = 1_000_000;
+                int step = 1_000_000;
                 int partitionDone = 0;
                 Map<String, KVSequenceEntry> matches = new HashMap<>();
-                for (String partition: partitions) {
+                for (int i = 0; i < partitions.size(); i++) {
+                    String partition = partitions.get(i);
                     String query = QUERY.replace("?", partition);
 
                     try (PreparedStatement ps = connection.prepareStatement(query)) {
@@ -157,14 +160,14 @@ void buildDatabase(String url, String password, int fetchSize, File outputDirect
                     matches.clear();
                     partitionDone++;
 
-                    String msg = String.format("%s: %,d proteins processed (%d/%d)",
-                            Utilities.getTimeAlt(),
-                            proteinCount,
-                            partitionDone,
-                            partitions.size());
-                    System.err.println(msg);
-                    if (debug) {
-                        System.err.println(bdbje.getStats());
+                    if (verbose || i + 1 == partitions.size() || proteinCount >= milestone) {
+                        String msg = String.format("%s: %,d proteins processed (%d/%d)",
+                                Utilities.getTimeAlt(),
+                                proteinCount,
+                                partitionDone,
+                                partitions.size());
+                        System.err.println(msg);
+                        milestone += step;
                     }
                 }
             } catch (SQLException e) {

diff --git a/.../berkeley/src/main/java/uk/ac/ebi/interpro/scan/precalc/berkeley/iprscan/IprscanMain.java b/.../berkeley/src/main/java/uk/ac/ebi/interpro/scan/precalc/berkeley/iprscan/IprscanMain.java
@@ -5,7 +5,7 @@ public class IprscanMain {
     private static String databaseType = null;
     private static String databasePath = null;
     private static String databaseUrl = null;
-    private static boolean debug = false;
+    private static boolean verbose = false;
 
     public static void main(String[] args) {
         parseArgs(args);
@@ -48,7 +48,7 @@ public static void main(String[] args) {
             }
             case "matches": {
                 CreateMatchesDBFromOracle builder = new CreateMatchesDBFromOracle();
-                builder.buildDatabase(databaseUrl, databasePassword, fetchSize, outputDir, debug);
+                builder.buildDatabase(databaseUrl, databasePassword, fetchSize, outputDir, verbose);
                 break;
             }
             case "sites": {
@@ -76,8 +76,8 @@ private static void parseArgs(String[] args) {
                     case "url":
                         databaseUrl = args[++i];
                         break;
-                    case "debug":
-                        debug = true;
+                    case "verbose":
+                        verbose = true;
                         break;
                     default:
                         usage();
@@ -93,7 +93,7 @@ private static void usage() {
         System.out.println("  -type TYPE: type of database to build (md5, matches, sites)");
         System.out.println("  -dir PATH : output directory of the Berkeley DB");
         System.out.println("  -url URL  : Oracle connection URL, i.e. jdbc:oracle:thin:@//<host>:<port>/<service>");
-        System.out.println("  -debug    : show stats");
+        System.out.println("  -verbose  : increase frequency of progress messages");
         System.exit(1);
     }
 }