core: handle shared files and multilib

Not all files from an RPM are necessarily removed during pkg erasure.
For example, files which are shared between pkgs shouldn't be deleted.
Similarly, not all files in an RPM are necessarily copied during pkg
installs. This is the case for multilib handling, which is a mess in its
own right. But such is the cost of trying to replace major parts of a
long-standing foundational project like RPM.

This patch adds some smarts to the way we do overlays and overrides to
handle these cases by calculating beforehand which files we *should't*
checkout/delete.

Closes: #1217
Closes: #1145

Closes: #1227
Approved by: cgwalters

src/libpriv/rpmostree-core.c

@@ -2378,6 +2378,37 @@ rpmostree_context_consume_package (RpmOstreeContext  *self,
   return TRUE;
 }
 
+/* Builds a mapping from filename to rpm color */
+static void
+add_te_files_to_ht (rpmte        te,
+                    GHashTable  *ht)
+{
+#ifdef BUILDOPT_HAVE_RPMFILES /* use rpmfiles API if possible, rpmteFI is deprecated */
+  g_auto(rpmfiles) files = rpmteFiles (te);
+  g_auto(rpmfi) fi = rpmfilesIter (files, RPMFI_ITER_FWD);
+#else
+  rpmfi fi = rpmteFI (te); /* rpmfi owned by rpmte */
+#endif
+
+  while (rpmfiNext (fi) >= 0)
+    {
+      const char *fn = rpmfiFN (fi);
+      rpm_color_t color = rpmfiFColor (fi);
+      g_hash_table_insert (ht, g_strdup (fn), GUINT_TO_POINTER (color));
+    }
+}
+
+static char*
+canonicalize_rpmfi_path (const char *path)
+{
+  /* this is a bit awkward; we relativize for the translation, but then make it absolute
+   * again to match libostree */
+  path += strspn (path, "/");
+  g_autofree char *translated =
+    rpmostree_translate_path_for_ostree (path) ?: g_strdup (path);
+  return g_build_filename ("/", translated, NULL);
+}
+
 /* Convert e.g. lib/foo/bar → usr/lib/foo/bar */
 static char *
 canonicalize_non_usrmove_path (RpmOstreeContext  *self,
@@ -2393,12 +2424,151 @@ canonicalize_non_usrmove_path (RpmOstreeContext  *self,
   return g_build_filename (link, slash + 1, NULL);
 }
 
+/* This is a lighter version of calculations that librpm calls "file disposition".
+ * Essentially, we determine which file removals/installations should be skipped. The librpm
+ * functions and APIs for these are unfortunately private since they're just run as part of
+ * rpmtsRun(). XXX: see if we can make the rpmfs APIs public, but we'd still need to support
+ * RHEL/CentOS anyway. */
+static gboolean
+handle_file_dispositions (RpmOstreeContext *self,
+                          int           tmprootfs_dfd,
+                          rpmts         ts,
+                          GHashTable  **out_files_skip_add,
+                          GHashTable  **out_files_skip_delete,
+                          GCancellable *cancellable,
+                          GError      **error)
+{
+  g_autoptr(GHashTable) pkgs_deleted = g_hash_table_new (g_direct_hash, g_direct_equal);
+
+  /* note these entries are *not* canonicalized for ostree conventions */
+  g_autoptr(GHashTable) files_deleted =
+    g_hash_table_new_full (g_str_hash, g_str_equal, g_free, NULL);
+  g_autoptr(GHashTable) files_added =
+    g_hash_table_new_full (g_str_hash, g_str_equal, g_free, NULL);
+
+  const guint n_rpmts_elements = (guint)rpmtsNElements (ts);
+  for (guint i = 0; i < n_rpmts_elements; i++)
+    {
+      rpmte te = rpmtsElement (ts, i);
+      rpmElementType type = rpmteType (te);
+      if (type == TR_REMOVED)
+        g_hash_table_add (pkgs_deleted, GUINT_TO_POINTER (rpmteDBInstance (te)));
+      add_te_files_to_ht (te, type == TR_REMOVED ? files_deleted : files_added);
+    }
+
+  /* this we *do* canonicalize since we'll be comparing against ostree paths */
+  g_autoptr(GHashTable) files_skip_add =
+    g_hash_table_new_full (g_str_hash, g_str_equal, g_free, NULL);
+  /* this one we *don't* canonicalize since we'll be comparing against rpmfi paths */
+  g_autoptr(GHashTable) files_skip_delete =
+    g_hash_table_new_full (g_str_hash, g_str_equal, g_free, NULL);
+
+  /* we deal with color similarly to librpm (compare with skipInstallFiles()) */
+  rpm_color_t ts_color = rpmtsColor (ts);
+  rpm_color_t ts_prefcolor = rpmtsPrefColor (ts);
+
+  /* ignore colored files not in our rainbow */
+  GLNX_HASH_TABLE_FOREACH_IT (files_added, it, const char*, fn, gpointer, colorp)
+    {
+      rpm_color_t color = GPOINTER_TO_UINT (colorp);
+      if (color && ts_color && !(ts_color & color))
+        g_hash_table_add (files_skip_add, canonicalize_rpmfi_path (fn));
+    }
+
+  g_auto(rpmdbMatchIterator) it = rpmtsInitIterator (ts, RPMDBI_PACKAGES, NULL, 0);
+  Header h;
+  while ((h = rpmdbNextIterator (it)) != NULL)
+    {
+      /* is this pkg to be deleted? */
+      guint off = rpmdbGetIteratorOffset (it);
+      if (g_hash_table_contains (pkgs_deleted, GUINT_TO_POINTER (off)))
+        continue;
+
+      /* try to only load what we need: filenames and colors */
+      rpmfiFlags flags = RPMFI_FLAGS_QUERY;
+#ifdef BUILDOPT_HAVE_RPMFILES /* we're using this more as a "if not on CentOS" switch */
+      /* this is even more restrictive that QUERY */
+      flags = RPMFI_FLAGS_ONLY_FILENAMES;
+#endif
+      flags &= ~RPMFI_NOFILECOLORS;
+
+      g_auto(rpmfi) fi = rpmfiNew (ts, h, RPMTAG_BASENAMES, flags);
+
+      fi = rpmfiInit (fi, 0);
+      while (rpmfiNext (fi) >= 0)
+        {
+          const char *fn = rpmfiFN (fi);
+          g_assert (fn != NULL);
+
+          /* check if one of the pkgs to delete wants to delete our file */
+          if (g_hash_table_contains (files_deleted, fn))
+            g_hash_table_add (files_skip_delete, g_strdup (fn));
+
+          rpm_color_t color = (rpmfiFColor (fi) & ts_color);
+
+          /* let's make the safe assumption that the color mess is only an issue for /usr */
+          const char *fn_rel = fn + strspn (fn, "/");
+
+          /* be sure we've canonicalized usr/ */
+          g_autofree char *fn_rel_owned = canonicalize_non_usrmove_path (self, fn_rel);
+          if (fn_rel_owned)
+            fn_rel = fn_rel_owned;
+
+          if (!g_str_has_prefix (fn_rel, "usr/"))
+            continue;
+
+          /* check if one of the pkgs to install wants to overwrite our file */
+          rpm_color_t other_color =
+            GPOINTER_TO_UINT (g_hash_table_lookup (files_added, fn));
+          other_color &= ts_color;
+
+          /* see handleColorConflict() */
+          if (color && other_color && (color != other_color))
+            {
+              /* do we already have the preferred color installed? */
+              if (color & ts_prefcolor)
+                g_hash_table_add (files_skip_add, canonicalize_rpmfi_path (fn));
+              else if (other_color & ts_prefcolor)
+                {
+                  /* the new pkg is bringing our favourite color, give way now so we let
+                   * checkout silently write into it */
+                  if (!glnx_shutil_rm_rf_at (tmprootfs_dfd, fn_rel, cancellable, error))
+                    return FALSE;
+                }
+            }
+        }
+    }
+
+  *out_files_skip_add = g_steal_pointer (&files_skip_add);
+  *out_files_skip_delete = g_steal_pointer (&files_skip_delete);
+  return TRUE;
+}
+
+static OstreeRepoCheckoutFilterResult
+checkout_filter (OstreeRepo         *self,
+                 const char         *path,
+                 struct stat        *st_buf,
+                 gpointer            user_data)
+{
+  GHashTable *files_skip = user_data;
+  if (g_hash_table_contains (files_skip, path))
+    return OSTREE_REPO_CHECKOUT_FILTER_SKIP;
+  /* Hack for nsswitch.conf: the glibc.i686 copy is identical to the one in glibc.x86_64,
+   * but because we modify it at treecompose time, UNION_IDENTICAL wouldn't save us here. A
+   * better heuristic here might be to skip all /etc files which have a different digest
+   * than the one registered in the rpmdb */
+  if (g_str_equal (path, "/usr/etc/nsswitch.conf"))
+    return OSTREE_REPO_CHECKOUT_FILTER_SKIP;
+  return OSTREE_REPO_CHECKOUT_FILTER_ALLOW;
+}
+
 static gboolean
 checkout_package (OstreeRepo   *repo,
                   int           dfd,
                   const char   *path,
                   OstreeRepoDevInoCache *devino_cache,
                   const char   *pkg_commit,
+                  GHashTable   *files_skip,
                   OstreeRepoCheckoutOverwriteMode ovwmode,
                   GCancellable *cancellable,
                   GError      **error)
@@ -2415,6 +2585,12 @@ checkout_package (OstreeRepo   *repo,
   /* Always want hardlinks */
   opts.no_copy_fallback = TRUE;
 
+  if (files_skip && g_hash_table_size (files_skip) > 0)
+    {
+      opts.filter = checkout_filter;
+      opts.filter_user_data = files_skip;
+    }
+
   return ostree_repo_checkout_at (repo, &opts, dfd, path,
                                   pkg_commit, cancellable, error);
 }
@@ -2426,6 +2602,7 @@ checkout_package_into_root (RpmOstreeContext *self,
                             const char   *path,
                             OstreeRepoDevInoCache *devino_cache,
                             const char   *pkg_commit,
+                            GHashTable   *files_skip,
                             OstreeRepoCheckoutOverwriteMode ovwmode,
                             GCancellable *cancellable,
                             GError      **error)
@@ -2447,7 +2624,7 @@ checkout_package_into_root (RpmOstreeContext *self,
     }
 
   if (!checkout_package (pkgcache_repo, dfd, path,
-                         devino_cache, pkg_commit, ovwmode,
+                         devino_cache, pkg_commit, files_skip, ovwmode,
                          cancellable, error))
     return glnx_prefix_error (error, "Checkout %s", dnf_package_get_nevra (pkg));
 
@@ -2516,20 +2693,21 @@ static gboolean
 delete_package_from_root (RpmOstreeContext *self,
                           rpmte         pkg,
                           int           rootfs_dfd,
+                          GHashTable   *files_skip,
                           GCancellable *cancellable,
                           GError      **error)
 {
 #ifdef BUILDOPT_HAVE_RPMFILES /* use rpmfiles API if possible, rpmteFI is deprecated */
   g_auto(rpmfiles) files = rpmteFiles (pkg);
+  /* NB: new librpm uses RPMFI_ITER_BACK here to empty out dirs before deleting them using
+   * unlink/rmdir. Older rpm doesn't support this API, so rather than doing some fancy
+   * compat, we just use shutil_rm_rf anyway since we now skip over shared dirs/files. */
   g_auto(rpmfi) fi = rpmfilesIter (files, RPMFI_ITER_FWD);
 #else
   rpmfi fi = rpmteFI (pkg); /* rpmfi owned by rpmte */
 #endif
 
-  g_autoptr(GPtrArray) deleted_dirs = g_ptr_array_new_with_free_func (g_free);
-
-  int i;
-  while ((i = rpmfiNext (fi)) >= 0)
+  while (rpmfiNext (fi) >= 0)
     {
       /* see also apply_rpmfi_overrides() for a commented version of the loop */
       const char *fn = rpmfiFN (fi);
@@ -2540,6 +2718,9 @@ delete_package_from_root (RpmOstreeContext *self,
             S_ISDIR (mode)))
         continue;
 
+      if (g_hash_table_contains (files_skip, fn))
+        continue;
+
       g_assert (fn != NULL);
       fn += strspn (fn, "/");
       g_assert (fn[0]);
@@ -2560,20 +2741,8 @@ delete_package_from_root (RpmOstreeContext *self,
       if (!g_str_has_prefix (fn, "usr/"))
         continue;
 
-      /* avoiding the stat syscall is worth a bit of userspace computation */
-      if (rpmostree_str_has_prefix_in_ptrarray (fn, deleted_dirs))
-        continue;
-
-      if (!glnx_fstatat_allow_noent (rootfs_dfd, fn, NULL, AT_SYMLINK_NOFOLLOW, error))
-        return FALSE;
-      if (errno == ENOENT)
-        continue; /* a job well done */
-
       if (!glnx_shutil_rm_rf_at (rootfs_dfd, fn, cancellable, error))
         return FALSE;
-
-      if (S_ISDIR (mode))
-        g_ptr_array_add (deleted_dirs, g_strconcat (fn, "/", NULL));
     }
 
   return TRUE;
@@ -2648,7 +2817,7 @@ relabel_in_thread_impl (RpmOstreeContext *self,
   g_autoptr(OstreeRepoDevInoCache) cache = ostree_repo_devino_cache_new ();
 
   if (!checkout_package (repo, tmpdir_dfd, pkg_dirname, cache,
-                         commit_csum, OSTREE_REPO_CHECKOUT_OVERWRITE_NONE,
+                         commit_csum, NULL, OSTREE_REPO_CHECKOUT_OVERWRITE_NONE,
                          cancellable, error))
     return FALSE;
 
@@ -3479,7 +3648,7 @@ rpmostree_context_assemble (RpmOstreeContext      *self,
       if (!checkout_package_into_root (self, filesystem_package,
                                        tmprootfs_dfd, ".", self->devino_cache,
                                        g_hash_table_lookup (pkg_to_ostree_commit,
-                                                            filesystem_package),
+                                                            filesystem_package), NULL,
                                        OSTREE_REPO_CHECKOUT_OVERWRITE_UNION_IDENTICAL,
                                        cancellable, error))
         return FALSE;
@@ -3487,13 +3656,11 @@ rpmostree_context_assemble (RpmOstreeContext      *self,
       rpmostree_output_progress_n_items ("Building filesystem", n_rpmts_done, n_rpmts_elements);
     }
 
-  /* We're completely disregarding how rpm normally does upgrades/downgrade here. rpm
-   * usually calculates the fate of each file and then installs the new files first, then
-   * removes the obsoleted files. So the TR_ADDED element for the new pkg comes *before* the
-   * TR_REMOVED element for the old pkg. This makes sense when operating on the live system.
-   * Though that's not the case here, so let's just take the easy way out and first nuke
-   * TR_REMOVED pkgs, then checkout the TR_ADDED ones. This will probably start to matter
-   * though when we start handling e.g. file triggers. */
+  g_autoptr(GHashTable) files_skip_add = NULL;
+  g_autoptr(GHashTable) files_skip_delete = NULL;
+  if (!handle_file_dispositions (self, tmprootfs_dfd, ordering_ts, &files_skip_add,
+                                 &files_skip_delete, cancellable, error))
+    return FALSE;
 
   for (guint i = 0; i < n_rpmts_elements; i++)
     {
@@ -3504,7 +3671,8 @@ rpmostree_context_assemble (RpmOstreeContext      *self,
         continue;
       g_assert_cmpint (type, ==, TR_REMOVED);
 
-      if (!delete_package_from_root (self, te, tmprootfs_dfd, cancellable, error))
+      if (!delete_package_from_root (self, te, tmprootfs_dfd, files_skip_delete,
+                                     cancellable, error))
         return FALSE;
       n_rpmts_done++;
       rpmostree_output_progress_n_items ("Building filesystem", n_rpmts_done, n_rpmts_elements);
@@ -3533,7 +3701,7 @@ rpmostree_context_assemble (RpmOstreeContext      *self,
 
       if (!checkout_package_into_root (self, pkg, tmprootfs_dfd, ".", self->devino_cache,
                                        g_hash_table_lookup (pkg_to_ostree_commit, pkg),
-                                       ovwmode, cancellable, error))
+                                       files_skip_add, ovwmode, cancellable, error))
         return FALSE;
       n_rpmts_done++;
       rpmostree_output_progress_n_items ("Building filesystem", n_rpmts_done, n_rpmts_elements);

tests/vmcheck/test-layering-rpmdb.sh

@@ -127,3 +127,41 @@ if vm_rpmostree upgrade; then
   assert_not_reached "upgrade succeeded but new base has conflicting pkg foo"
 fi
 echo "ok can't upgrade with conflicting layered pkg"
+
+vm_rpmostree cleanup -p
+
+check_bloop_color() {
+  color=$1; shift
+  root=$(vm_get_deployment_root 0)
+  vm_cmd file $root/usr/bin/bloop > file.txt
+  assert_file_has_content file.txt $color
+}
+
+# now let's build two pkgs with different colors
+# we use -nostdlib so we don't pull in glibc.i686
+vm_build_rpm bloop arch i686 build 'echo "void main() {}" | gcc -m32 -nostdlib -o bloop -xc -'
+vm_build_rpm bloop arch x86_64 build 'echo "void main() {}" | gcc -m64 -nostdlib -o bloop -xc -'
+# now embed the x86_64 version into it
+vm_rpmostree install bloop.x86_64
+vm_cmd ostree commit -b vmcheck --tree=ref=$(vm_get_pending_csum) --fsync=no
+vm_rpmostree cleanup -p
+vm_rpmostree upgrade
+check_bloop_color 64-bit
+# now let's pkglayer the i686 version
+vm_rpmostree install bloop.i686
+# check that the x86_64 version won
+check_bloop_color 64-bit
+echo "ok coloring skip"
+
+# now embed the 32-bit version instead
+vm_rpmostree cleanup -p
+vm_rpmostree install bloop.i686
+vm_cmd ostree commit -b vmcheck --tree=ref=$(vm_get_pending_csum) --fsync=no
+vm_rpmostree cleanup -p
+vm_rpmostree upgrade
+check_bloop_color 32-bit
+# now let's pkglayer the x86_64 version
+vm_rpmostree install bloop.x86_64
+# and check that the x86_64 version won
+check_bloop_color 64-bit
+echo "ok coloring replace"

tests/vmcheck/test-override-remove.sh

@@ -43,9 +43,19 @@ vm_cmd ostree refs $(vm_get_booted_csum) \
 # foo has files in /lib, to test our re-canonicalization to /usr
 vm_build_rpm foo \
              files "%dir /lib/foo
-                    /lib/foo/foo.txt" \
-             install 'mkdir -p %{buildroot}/lib/foo && echo %{name} > %{buildroot}/lib/foo/foo.txt'
-vm_build_rpm bar
+                    /lib/foo/foo.txt
+                    /lib/foo/shared.txt" \
+             install 'mkdir -p %{buildroot}/lib/foo && \
+                      echo %{name} > %{buildroot}/lib/foo/foo.txt && \
+                      echo shared > %{buildroot}/lib/foo/shared.txt'
+# make bar co-own /lib/foo and /lib/foo/shared.txt
+vm_build_rpm bar \
+             files "%dir /lib/foo
+                    /lib/foo/bar.txt
+                    /lib/foo/shared.txt" \
+             install 'mkdir -p %{buildroot}/lib/foo && \
+                      echo %{name} > %{buildroot}/lib/foo/bar.txt && \
+                      echo shared > %{buildroot}/lib/foo/shared.txt'
 vm_rpmostree install foo bar
 vm_cmd ostree refs $(vm_get_deployment_info 0 checksum) \
   --create vmcheck_tmp/with_foo_and_bar
@@ -70,7 +80,23 @@ vm_cmd mv /tmp/vmcheck/yumrepo{,.bak}
 # this works. the only difference here is the [.0] which we use to access the
 # nevra of each gv_nevra element.
 
-vm_rpmostree override remove foo bar
+# remove just bar first to check deletion handling
+vm_rpmostree override remove bar
+vm_assert_status_jq \
+  '.deployments[0]["base-removals"]|length == 1' \
+  '[.deployments[0]["base-removals"][][.0]]|index("bar-1.0-1.x86_64") >= 0' \
+  '.deployments[0]["requested-base-removals"]|length == 1' \
+  '.deployments[0]["requested-base-removals"]|index("bar") >= 0'
+newroot=$(vm_get_deployment_root 0)
+# And test that we removed fully owned files, but not shared files
+vm_cmd "test -d ${newroot}/usr/lib/foo && \
+        test -f ${newroot}/usr/lib/foo/foo.txt && \
+        test -f ${newroot}/usr/lib/foo/shared.txt && \
+        test ! -f ${newroot}/usr/lib/foo/bar.txt"
+echo "ok override remove bar"
+
+# now also remove foo
+vm_rpmostree override remove foo
 vm_assert_status_jq \
   '.deployments[0]["base-removals"]|length == 2' \
   '[.deployments[0]["base-removals"][][.0]]|index("foo-1.0-1.x86_64") >= 0' \
@@ -79,8 +105,10 @@ vm_assert_status_jq \
   '.deployments[0]["requested-base-removals"]|index("foo") >= 0' \
   '.deployments[0]["requested-base-removals"]|index("bar") >= 0'
 newroot=$(vm_get_deployment_root 0)
-# And this tests handling /lib -> /usr/lib
-vm_cmd "test -d ${newroot}/usr/lib && test '!' -f ${newroot}/usr/lib/foo/foo.txt && \
+# And this tests handling /lib -> /usr/lib as well as removal of shared files
+vm_cmd "test -d ${newroot}/usr/lib && \
+        test '!' -f ${newroot}/usr/lib/foo/foo.txt && \
+        test '!' -f ${newroot}/usr/lib/foo/shared.txt && \
         test '!' -d ${newroot}/usr/lib/foo"
 echo "ok override remove foo and bar"