Fix tar2db breaking with --tar-include/exclude #561

We were not correctly updating the position in the tar file, when files were skipped
soedinglab · Jul 4, 2022 · 7be78c8 · 7be78c8
1 parent d155586
commit 7be78c8
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diff --git a/lib/microtar/microtar.c b/lib/microtar/microtar.c
@@ -151,6 +151,15 @@ int mtar_read_header(mtar_t *tar, mtar_header_t *h) {
   return MTAR_ESUCCESS;
 }
 
+int mtar_skip_data(mtar_t *tar) {
+  int n = round_up(tar->curr_size, 512);
+  int err = tar->seek(tar, n, SEEK_CUR);
+  if (err) {
+      return err;
+  }
+  return MTAR_ESUCCESS;
+}
+
 int mtar_read_data(mtar_t *tar, void *ptr, size_t size) {
   /* Read data */
   int err = tar->read(tar, ptr, size);

diff --git a/lib/microtar/microtar.h b/lib/microtar/microtar.h
@@ -73,6 +73,7 @@ int mtar_close(mtar_t *tar);
 
 int mtar_read_header(mtar_t *tar, mtar_header_t *h);
 int mtar_read_data(mtar_t *tar, void *ptr, size_t size);
+int mtar_skip_data(mtar_t *tar);
 
 #ifdef __cplusplus
 }

diff --git a/src/util/tar2db.cpp b/src/util/tar2db.cpp
@@ -177,6 +177,10 @@ int tar2db(int argc, const char **argv, const Command& command) {
                         }
                         if (header.type == MTAR_TREG || header.type == MTAR_TCONT || header.type == MTAR_TOLDREG) {
                             if (include.isMatch(name.c_str()) == false || exclude.isMatch(name.c_str()) == true) {
+                                if (header.size > 0 && mtar_skip_data(&tar) != MTAR_ESUCCESS) {
+                                    Debug(Debug::ERROR) << "Cannot skip entry " << name << "\n";
+                                    EXIT(EXIT_FAILURE);
+                                }
                                 __sync_fetch_and_add(&(globalKey), 1);
                                 proceed = true;
                                 writeEntry = false;
@@ -194,6 +198,10 @@ int tar2db(int argc, const char **argv, const Command& command) {
                                 currentKey = __sync_fetch_and_add(&(globalKey), 1);
                             }
                         } else {
+                            if (header.size > 0 && mtar_skip_data(&tar) != MTAR_ESUCCESS) {
+                                Debug(Debug::ERROR) << "Cannot skip entry " << name << "\n";
+                                EXIT(EXIT_FAILURE);
+                            }
                             proceed = true;
                             writeEntry = false;
                         }