[PATCH v3 0/9] Add ghost messages and fix thread linking

[PATCH v3 0/9] Add ghost messages and fix thread linking

[Austin Clements]

This is v3 of
id:1412637438-4821-1-git-send-email-aclements@csail.mit.edu.
This fixes some comments, as suggested by Mark.  There are no
code changes relative to v2.  The diff from v2 is below.

diff --git a/lib/database.cc b/lib/database.cc
index 6e51a72..3601f9d 100644
--- a/lib/database.cc
+++ b/lib/database.cc
@@ -2121,10 +2121,13 @@ _consume_metadata_thread_id (void *ctx, notmuch_database_t *notmuch,
 /* Given a blank or ghost 'message' and its corresponding
  * 'message_file' link it to existing threads in the database.
  *
- * The first check is in the metadata of the database to see if we
- * have pre-allocated a thread_id in advance for this message, (which
- * would have happened if a message was previously added that
- * referenced this one).
+ * First, if is_ghost, this retrieves the thread ID already stored in
+ * the message (which will be the case if a message was previously
+ * added that referenced this one).  If the message is blank
+ * (!is_ghost), it doesn't have a thread ID yet (we'll generate one
+ * later in this function).  If the database does not support ghost
+ * messages, this checks for a thread ID stored in database metadata
+ * for this message ID.
  *
  * Second, we look at 'message_file' and its link-relevant headers
  * (References and In-Reply-To) for message IDs.
@@ -2132,12 +2135,12 @@ _consume_metadata_thread_id (void *ctx, notmuch_database_t *notmuch,
  * Finally, we look in the database for existing message that
  * reference 'message'.
  *
- * In all cases, we assign to the current message the first thread_id
- * found (through either parent or child). We will also merge any
- * existing, distinct threads where this message belongs to both,
- * (which is not uncommon when messages are processed out of order).
+ * In all cases, we assign to the current message the first thread ID
+ * found. We will also merge any existing, distinct threads where this
+ * message belongs to both, (which is not uncommon when messages are
+ * processed out of order).
  *
- * Finally, if no thread ID has been found through parent or child, we
+ * Finally, if no thread ID has been found through referenced messages, we
  * call _notmuch_message_generate_thread_id to generate a new thread
  * ID. This should only happen for new, top-level messages, (no
  * References or In-Reply-To header in this message, and no previously

[PATCH v3 1/9] lib: Add a ghost messages database feature

[Austin Clements]

From: Austin Clements <amdragon@mit.edu>

This will be implemented over the next several patches.  The feature
is not yet "enabled" (this does not add it to
NOTMUCH_FEATURES_CURRENT).
---
 lib/database-private.h | 7 +++++++
 lib/database.cc        | 2 ++
 2 files changed, 9 insertions(+)

diff --git a/lib/database-private.h b/lib/database-private.h
index ca0751c..e2e4bc8 100644
--- a/lib/database-private.h
+++ b/lib/database-private.h
@@ -85,6 +85,13 @@ enum _notmuch_features {
      *
      * Introduced: version 2. */
     NOTMUCH_FEATURE_BOOL_FOLDER = 1 << 3,
+
+    /* If set, missing messages are stored in ghost mail documents.
+     * If unset, thread IDs of ghost messages are stored as database
+     * metadata instead of in ghost documents.
+     *
+     * Introduced: version 3. */
+    NOTMUCH_FEATURE_GHOSTS = 1 << 4,
 };
 
 /* In C++, a named enum is its own type, so define bitwise operators
diff --git a/lib/database.cc b/lib/database.cc
index 1c6ffc5..8fd7fad 100644
--- a/lib/database.cc
+++ b/lib/database.cc
@@ -286,6 +286,8 @@ static const struct {
       "from/subject/message-ID in database", "w" },
     { NOTMUCH_FEATURE_BOOL_FOLDER,
       "exact folder:/path: search", "rw" },
+    { NOTMUCH_FEATURE_GHOSTS,
+      "mail documents for missing messages", "w"},
 };
 
 const char *
-- 
2.1.0

[PATCH v3 2/9] lib: Update database schema doc for ghost messages

[Austin Clements]

From: Austin Clements <amdragon@mit.edu>

This describes the structure of ghost mail documents.  Ghost messages
are not yet implemented.
---
 lib/database.cc | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/lib/database.cc b/lib/database.cc
index 8fd7fad..c641bcd 100644
--- a/lib/database.cc
+++ b/lib/database.cc
@@ -50,8 +50,8 @@ typedef struct {
 
 /* Here's the current schema for our database (for NOTMUCH_DATABASE_VERSION):
  *
- * We currently have two different types of documents (mail and
- * directory) and also some metadata.
+ * We currently have three different types of documents (mail, ghost,
+ * and directory) and also some metadata.
  *
  * Mail document
  * -------------
@@ -109,6 +109,15 @@ typedef struct {
  *
  * The data portion of a mail document is empty.
  *
+ * Ghost mail document [if NOTMUCH_FEATURE_GHOSTS]
+ * -----------------------------------------------
+ * A ghost mail document is like a mail document, but where we don't
+ * have the message content.  These are used to track thread reference
+ * information for messages we haven't received.
+ *
+ * A ghost mail document has type: ghost; id and thread fields that
+ * are identical to the mail document fields; and a MESSAGE_ID value.
+ *
  * Directory document
  * ------------------
  * A directory document is used by a client of the notmuch library to
@@ -172,6 +181,13 @@ typedef struct {
  *			generated is 1 and the value will be
  *			incremented for each thread ID.
  *
+ * Obsolete metadata
+ * -----------------
+ *
+ * If ! NOTMUCH_FEATURE_GHOSTS, there are no ghost mail documents.
+ * Instead, the database has the following additional database
+ * metadata:
+ *
  *	thread_id_*	A pre-allocated thread ID for a particular
  *			message. This is actually an arbitrarily large
  *			family of metadata name. Any particular name is
-- 
2.1.0

[PATCH v3 3/9] lib: Introduce macros for bit operations

[Austin Clements]

These macros help clarify basic bit-twiddling code and are written to
be robust against C undefined behavior of shift operators.
---
 lib/message.cc        |  6 +++---
 lib/notmuch-private.h | 11 +++++++++++
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/lib/message.cc b/lib/message.cc
index 38bc929..55d2ff6 100644
--- a/lib/message.cc
+++ b/lib/message.cc
@@ -869,7 +869,7 @@ notmuch_bool_t
 notmuch_message_get_flag (notmuch_message_t *message,
 			  notmuch_message_flag_t flag)
 {
-    return message->flags & (1 << flag);
+    return NOTMUCH_TEST_BIT (message->flags, flag);
 }
 
 void
@@ -877,9 +877,9 @@ notmuch_message_set_flag (notmuch_message_t *message,
 			  notmuch_message_flag_t flag, notmuch_bool_t enable)
 {
     if (enable)
-	message->flags |= (1 << flag);
+	NOTMUCH_SET_BIT (&message->flags, flag);
     else
-	message->flags &= ~(1 << flag);
+	NOTMUCH_CLEAR_BIT (&message->flags, flag);
 }
 
 time_t
diff --git a/lib/notmuch-private.h b/lib/notmuch-private.h
index 36cc12b..7250291 100644
--- a/lib/notmuch-private.h
+++ b/lib/notmuch-private.h
@@ -63,6 +63,17 @@ NOTMUCH_BEGIN_DECLS
 #define STRNCMP_LITERAL(var, literal) \
     strncmp ((var), (literal), sizeof (literal) - 1)
 
+/* Robust bit test/set/reset macros */
+#define NOTMUCH_TEST_BIT(val, bit) \
+    ((bit < 0 || bit >= CHAR_BIT * sizeof (unsigned long long)) ? 0	\
+     : !!((val) & (1ull << bit)))
+#define NOTMUCH_SET_BIT(valp, bit) \
+    ((bit < 0 || bit >= CHAR_BIT * sizeof (unsigned long long)) ? *(valp) \
+     : (*(valp) |= (1ull << bit)))
+#define NOTMUCH_CLEAR_BIT(valp,  bit) \
+    ((bit < 0 || bit >= CHAR_BIT * sizeof (unsigned long long)) ? *(valp) \
+     : (*(valp) &= ~(1ull << bit)))
+
 #define unused(x) x __attribute__ ((unused))
 
 #ifdef __cplusplus
-- 
2.1.0

Re: [PATCH v3 3/9] lib: Introduce macros for bit operations

[Jani Nikula]

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On Oct 23, 2014 3:31 PM, "Austin Clements" <aclements@csail.mit.edu> wrote:
>
> These macros help clarify basic bit-twiddling code and are written to
> be robust against C undefined behavior of shift operators.
> ---
>  lib/message.cc        |  6 +++---
>  lib/notmuch-private.h | 11 +++++++++++
>  2 files changed, 14 insertions(+), 3 deletions(-)
>
> diff --git a/lib/message.cc b/lib/message.cc
> index 38bc929..55d2ff6 100644
> --- a/lib/message.cc
> +++ b/lib/message.cc
> @@ -869,7 +869,7 @@ notmuch_bool_t
>  notmuch_message_get_flag (notmuch_message_t *message,
>                           notmuch_message_flag_t flag)
>  {
> -    return message->flags & (1 << flag);
> +    return NOTMUCH_TEST_BIT (message->flags, flag);
>  }
>
>  void
> @@ -877,9 +877,9 @@ notmuch_message_set_flag (notmuch_message_t *message,
>                           notmuch_message_flag_t flag, notmuch_bool_t
enable)
>  {
>      if (enable)
> -       message->flags |= (1 << flag);
> +       NOTMUCH_SET_BIT (&message->flags, flag);
>      else
> -       message->flags &= ~(1 << flag);
> +       NOTMUCH_CLEAR_BIT (&message->flags, flag);
>  }
>
>  time_t
> diff --git a/lib/notmuch-private.h b/lib/notmuch-private.h
> index 36cc12b..7250291 100644
> --- a/lib/notmuch-private.h
> +++ b/lib/notmuch-private.h
> @@ -63,6 +63,17 @@ NOTMUCH_BEGIN_DECLS
>  #define STRNCMP_LITERAL(var, literal) \
>      strncmp ((var), (literal), sizeof (literal) - 1)
>
> +/* Robust bit test/set/reset macros */
> +#define NOTMUCH_TEST_BIT(val, bit) \
> +    ((bit < 0 || bit >= CHAR_BIT * sizeof (unsigned long long)) ? 0    \
> +     : !!((val) & (1ull << bit)))
> +#define NOTMUCH_SET_BIT(valp, bit) \
> +    ((bit < 0 || bit >= CHAR_BIT * sizeof (unsigned long long)) ?
*(valp) \
> +     : (*(valp) |= (1ull << bit)))
> +#define NOTMUCH_CLEAR_BIT(valp,  bit) \
> +    ((bit < 0 || bit >= CHAR_BIT * sizeof (unsigned long long)) ?
*(valp) \
> +     : (*(valp) &= ~(1ull << bit)))

bit should be in braces in the above, like valp.

Jani.

> +
>  #define unused(x) x __attribute__ ((unused))
>
>  #ifdef __cplusplus
> --
> 2.1.0
>
> _______________________________________________
> notmuch mailing list
> notmuch@notmuchmail.org
> http://notmuchmail.org/mailman/listinfo/notmuch

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[PATCH v3.1 3/9] lib: Introduce macros for bit operations

[Austin Clements]

These macros help clarify basic bit-twiddling code and are written to
be robust against C undefined behavior of shift operators.
---
 lib/message.cc        |  6 +++---
 lib/notmuch-private.h | 11 +++++++++++
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/lib/message.cc b/lib/message.cc
index 38bc929..55d2ff6 100644
--- a/lib/message.cc
+++ b/lib/message.cc
@@ -869,7 +869,7 @@ notmuch_bool_t
 notmuch_message_get_flag (notmuch_message_t *message,
 			  notmuch_message_flag_t flag)
 {
-    return message->flags & (1 << flag);
+    return NOTMUCH_TEST_BIT (message->flags, flag);
 }
 
 void
@@ -877,9 +877,9 @@ notmuch_message_set_flag (notmuch_message_t *message,
 			  notmuch_message_flag_t flag, notmuch_bool_t enable)
 {
     if (enable)
-	message->flags |= (1 << flag);
+	NOTMUCH_SET_BIT (&message->flags, flag);
     else
-	message->flags &= ~(1 << flag);
+	NOTMUCH_CLEAR_BIT (&message->flags, flag);
 }
 
 time_t
diff --git a/lib/notmuch-private.h b/lib/notmuch-private.h
index 36cc12b..b86897c 100644
--- a/lib/notmuch-private.h
+++ b/lib/notmuch-private.h
@@ -63,6 +63,17 @@ NOTMUCH_BEGIN_DECLS
 #define STRNCMP_LITERAL(var, literal) \
     strncmp ((var), (literal), sizeof (literal) - 1)
 
+/* Robust bit test/set/reset macros */
+#define NOTMUCH_TEST_BIT(val, bit) \
+    (((bit) < 0 || (bit) >= CHAR_BIT * sizeof (unsigned long long)) ? 0	\
+     : !!((val) & (1ull << (bit))))
+#define NOTMUCH_SET_BIT(valp, bit) \
+    (((bit) < 0 || (bit) >= CHAR_BIT * sizeof (unsigned long long)) ? *(valp) \
+     : (*(valp) |= (1ull << (bit))))
+#define NOTMUCH_CLEAR_BIT(valp,  bit) \
+    (((bit) < 0 || (bit) >= CHAR_BIT * sizeof (unsigned long long)) ? *(valp) \
+     : (*(valp) &= ~(1ull << (bit))))
+
 #define unused(x) x __attribute__ ((unused))
 
 #ifdef __cplusplus
-- 
2.1.0

[PATCH v3 4/9] lib: Internal support for querying and creating ghost messages

[Austin Clements]

From: Austin Clements <amdragon@mit.edu>

This updates the message abstraction to support ghost messages: it
adds a message flag that distinguishes regular messages from ghost
messages, and an internal function for initializing a newly created
(blank) message as a ghost message.
---
 lib/message.cc        | 52 +++++++++++++++++++++++++++++++++++++++++++++++++--
 lib/notmuch-private.h |  4 ++++
 lib/notmuch.h         |  9 ++++++++-
 3 files changed, 62 insertions(+), 3 deletions(-)

diff --git a/lib/message.cc b/lib/message.cc
index 55d2ff6..a7a13cc 100644
--- a/lib/message.cc
+++ b/lib/message.cc
@@ -39,6 +39,9 @@ struct visible _notmuch_message {
     notmuch_message_file_t *message_file;
     notmuch_message_list_t *replies;
     unsigned long flags;
+    /* For flags that are initialized on-demand, lazy_flags indicates
+     * if each flag has been initialized. */
+    unsigned long lazy_flags;
 
     Xapian::Document doc;
     Xapian::termcount termpos;
@@ -99,6 +102,7 @@ _notmuch_message_create_for_document (const void *talloc_owner,
 
     message->frozen = 0;
     message->flags = 0;
+    message->lazy_flags = 0;
 
     /* Each of these will be lazily created as needed. */
     message->message_id = NULL;
@@ -192,7 +196,7 @@ _notmuch_message_create (const void *talloc_owner,
  *
  *     There is already a document with message ID 'message_id' in the
  *     database. The returned message can be used to query/modify the
- *     document.
+ *     document. The message may be a ghost message.
  *
  *   NOTMUCH_PRIVATE_STATUS_NO_DOCUMENT_FOUND:
  *
@@ -305,6 +309,7 @@ _notmuch_message_ensure_metadata (notmuch_message_t *message)
     const char *thread_prefix = _find_prefix ("thread"),
 	*tag_prefix = _find_prefix ("tag"),
 	*id_prefix = _find_prefix ("id"),
+	*type_prefix = _find_prefix ("type"),
 	*filename_prefix = _find_prefix ("file-direntry"),
 	*replyto_prefix = _find_prefix ("replyto");
 
@@ -337,10 +342,25 @@ _notmuch_message_ensure_metadata (notmuch_message_t *message)
 	message->message_id =
 	    _notmuch_message_get_term (message, i, end, id_prefix);
 
+    /* Get document type */
+    assert (strcmp (id_prefix, type_prefix) < 0);
+    if (! NOTMUCH_TEST_BIT (message->lazy_flags, NOTMUCH_MESSAGE_FLAG_GHOST)) {
+	i.skip_to (type_prefix);
+	/* "T" is the prefix "type" fields.  See
+	 * BOOLEAN_PREFIX_INTERNAL. */
+	if (*i == "Tmail")
+	    NOTMUCH_CLEAR_BIT (&message->flags, NOTMUCH_MESSAGE_FLAG_GHOST);
+	else if (*i == "Tghost")
+	    NOTMUCH_SET_BIT (&message->flags, NOTMUCH_MESSAGE_FLAG_GHOST);
+	else
+	    INTERNAL_ERROR ("Message without type term");
+	NOTMUCH_SET_BIT (&message->lazy_flags, NOTMUCH_MESSAGE_FLAG_GHOST);
+    }
+
     /* Get filename list.  Here we get only the terms.  We lazily
      * expand them to full file names when needed in
      * _notmuch_message_ensure_filename_list. */
-    assert (strcmp (id_prefix, filename_prefix) < 0);
+    assert (strcmp (type_prefix, filename_prefix) < 0);
     if (!message->filename_term_list && !message->filename_list)
 	message->filename_term_list =
 	    _notmuch_database_get_terms_with_prefix (message, i, end,
@@ -371,6 +391,11 @@ _notmuch_message_invalidate_metadata (notmuch_message_t *message,
 	message->tag_list = NULL;
     }
 
+    if (strcmp ("type", prefix_name) == 0) {
+	NOTMUCH_CLEAR_BIT (&message->flags, NOTMUCH_MESSAGE_FLAG_GHOST);
+	NOTMUCH_CLEAR_BIT (&message->lazy_flags, NOTMUCH_MESSAGE_FLAG_GHOST);
+    }
+
     if (strcmp ("file-direntry", prefix_name) == 0) {
 	talloc_free (message->filename_term_list);
 	talloc_free (message->filename_list);
@@ -869,6 +894,10 @@ notmuch_bool_t
 notmuch_message_get_flag (notmuch_message_t *message,
 			  notmuch_message_flag_t flag)
 {
+    if (flag == NOTMUCH_MESSAGE_FLAG_GHOST &&
+	! NOTMUCH_TEST_BIT (message->lazy_flags, flag))
+	_notmuch_message_ensure_metadata (message);
+
     return NOTMUCH_TEST_BIT (message->flags, flag);
 }
 
@@ -880,6 +909,7 @@ notmuch_message_set_flag (notmuch_message_t *message,
 	NOTMUCH_SET_BIT (&message->flags, flag);
     else
 	NOTMUCH_CLEAR_BIT (&message->flags, flag);
+    NOTMUCH_SET_BIT (&message->lazy_flags, flag);
 }
 
 time_t
@@ -989,6 +1019,24 @@ _notmuch_message_delete (notmuch_message_t *message)
     return NOTMUCH_STATUS_SUCCESS;
 }
 
+/* Transform a blank message into a ghost message.  The caller must
+ * _notmuch_message_sync the message. */
+notmuch_private_status_t
+_notmuch_message_initialize_ghost (notmuch_message_t *message,
+				   const char *thread_id)
+{
+    notmuch_private_status_t status;
+
+    status = _notmuch_message_add_term (message, "type", "ghost");
+    if (status)
+	return status;
+    status = _notmuch_message_add_term (message, "thread", thread_id);
+    if (status)
+	return status;
+
+    return NOTMUCH_PRIVATE_STATUS_SUCCESS;
+}
+
 /* Ensure that 'message' is not holding any file object open. Future
  * calls to various functions will still automatically open the
  * message file as needed.
diff --git a/lib/notmuch-private.h b/lib/notmuch-private.h
index 7250291..2f43c1d 100644
--- a/lib/notmuch-private.h
+++ b/lib/notmuch-private.h
@@ -308,6 +308,10 @@ _notmuch_message_sync (notmuch_message_t *message);
 notmuch_status_t
 _notmuch_message_delete (notmuch_message_t *message);
 
+notmuch_private_status_t
+_notmuch_message_initialize_ghost (notmuch_message_t *message,
+				   const char *thread_id);
+
 void
 _notmuch_message_close (notmuch_message_t *message);
 
diff --git a/lib/notmuch.h b/lib/notmuch.h
index dae0416..92594b9 100644
--- a/lib/notmuch.h
+++ b/lib/notmuch.h
@@ -1221,7 +1221,14 @@ notmuch_message_get_filenames (notmuch_message_t *message);
  */
 typedef enum _notmuch_message_flag {
     NOTMUCH_MESSAGE_FLAG_MATCH,
-    NOTMUCH_MESSAGE_FLAG_EXCLUDED
+    NOTMUCH_MESSAGE_FLAG_EXCLUDED,
+
+    /* This message is a "ghost message", meaning it has no filenames
+     * or content, but we know it exists because it was referenced by
+     * some other message.  A ghost message has only a message ID and
+     * thread ID.
+     */
+    NOTMUCH_MESSAGE_FLAG_GHOST,
 } notmuch_message_flag_t;
 
 /**
-- 
2.1.0

[PATCH v3 5/9] lib: Implement ghost-based thread linking

[Austin Clements]

From: Austin Clements <amdragon@mit.edu>

This updates the thread linking code to use ghost messages instead of
user metadata to link messages into threads.

In contrast with the old approach, this is actually correct.
Previously, thread merging updated only the thread IDs of message
documents, not thread IDs stored in user metadata.  As originally
diagnosed by Mark Walters [1] and as demonstrated by the broken
T260-thread-order test, this can cause notmuch to fail to link
messages even though they're in the same thread.  In principle the old
approach could have been fixed by updating the user metadata thread
IDs as well, but these are not indexed and hence this would have
required a full scan of all stored thread IDs.  Ghost messages solve
this problem naturally by reusing the exact same thread ID and message
ID representation and indexing as regular messages.

Furthermore, thanks to this greater symmetry, ghost messages are also
algorithmically simpler.  We continue to support the old user metadata
format, so this patch can't delete any code, but when we do remove
support for the old format, several functions can simply be deleted.

[1] id:8738h7kv2q.fsf@qmul.ac.uk
---
 lib/database.cc | 99 +++++++++++++++++++++++++++++++++++++++++++++++----------
 1 file changed, 83 insertions(+), 16 deletions(-)

diff --git a/lib/database.cc b/lib/database.cc
index c641bcd..92a92d9 100644
--- a/lib/database.cc
+++ b/lib/database.cc
@@ -1752,6 +1752,12 @@ _get_metadata_thread_id_key (void *ctx, const char *message_id)
 			    message_id);
 }
 
+static notmuch_status_t
+_resolve_message_id_to_thread_id_old (notmuch_database_t *notmuch,
+				      void *ctx,
+				      const char *message_id,
+				      const char **thread_id_ret);
+
 /* Find the thread ID to which the message with 'message_id' belongs.
  *
  * Note: 'thread_id_ret' must not be NULL!
@@ -1760,9 +1766,9 @@ _get_metadata_thread_id_key (void *ctx, const char *message_id)
  *
  * Note: If there is no message in the database with the given
  * 'message_id' then a new thread_id will be allocated for this
- * message and stored in the database metadata, (where this same
+ * message ID and stored in the database metadata so that the
  * thread ID can be looked up if the message is added to the database
- * later).
+ * later.
  */
 static notmuch_status_t
 _resolve_message_id_to_thread_id (notmuch_database_t *notmuch,
@@ -1770,6 +1776,49 @@ _resolve_message_id_to_thread_id (notmuch_database_t *notmuch,
 				  const char *message_id,
 				  const char **thread_id_ret)
 {
+    notmuch_private_status_t status;
+    notmuch_message_t *message;
+
+    if (! (notmuch->features & NOTMUCH_FEATURE_GHOSTS))
+	return _resolve_message_id_to_thread_id_old (notmuch, ctx, message_id,
+						     thread_id_ret);
+
+    /* Look for this message (regular or ghost) */
+    message = _notmuch_message_create_for_message_id (
+	notmuch, message_id, &status);
+    if (status == NOTMUCH_PRIVATE_STATUS_SUCCESS) {
+	/* Message exists */
+	*thread_id_ret = talloc_steal (
+	    ctx, notmuch_message_get_thread_id (message));
+    } else if (status == NOTMUCH_PRIVATE_STATUS_NO_DOCUMENT_FOUND) {
+	/* Message did not exist.  Give it a fresh thread ID and
+	 * populate this message as a ghost message. */
+	*thread_id_ret = talloc_strdup (
+	    ctx, _notmuch_database_generate_thread_id (notmuch));
+	if (! *thread_id_ret) {
+	    status = NOTMUCH_PRIVATE_STATUS_OUT_OF_MEMORY;
+	} else {
+	    status = _notmuch_message_initialize_ghost (message, *thread_id_ret);
+	    if (status == 0)
+		/* Commit the new ghost message */
+		_notmuch_message_sync (message);
+	}
+    } else {
+	/* Create failed. Fall through. */
+    }
+
+    notmuch_message_destroy (message);
+
+    return COERCE_STATUS (status, "Error creating ghost message");
+}
+
+/* Pre-ghost messages _resolve_message_id_to_thread_id */
+static notmuch_status_t
+_resolve_message_id_to_thread_id_old (notmuch_database_t *notmuch,
+				      void *ctx,
+				      const char *message_id,
+				      const char **thread_id_ret)
+{
     notmuch_status_t status;
     notmuch_message_t *message;
     string thread_id_string;
@@ -2007,13 +2056,16 @@ _consume_metadata_thread_id (void *ctx, notmuch_database_t *notmuch,
     }
 }
 
-/* Given a (mostly empty) 'message' and its corresponding
+/* Given a blank or ghost 'message' and its corresponding
  * 'message_file' link it to existing threads in the database.
  *
- * The first check is in the metadata of the database to see if we
- * have pre-allocated a thread_id in advance for this message, (which
- * would have happened if a message was previously added that
- * referenced this one).
+ * First, if is_ghost, this retrieves the thread ID already stored in
+ * the message (which will be the case if a message was previously
+ * added that referenced this one).  If the message is blank
+ * (!is_ghost), it doesn't have a thread ID yet (we'll generate one
+ * later in this function).  If the database does not support ghost
+ * messages, this checks for a thread ID stored in database metadata
+ * for this message ID.
  *
  * Second, we look at 'message_file' and its link-relevant headers
  * (References and In-Reply-To) for message IDs.
@@ -2021,7 +2073,7 @@ _consume_metadata_thread_id (void *ctx, notmuch_database_t *notmuch,
  * Finally, we look in the database for existing message that
  * reference 'message'.
  *
- * In all cases, we assign to the current message the first thread_id
+ * In all cases, we assign to the current message the first thread ID
  * found (through either parent or child). We will also merge any
  * existing, distinct threads where this message belongs to both,
  * (which is not uncommon when messages are processed out of order).
@@ -2035,16 +2087,22 @@ _consume_metadata_thread_id (void *ctx, notmuch_database_t *notmuch,
 static notmuch_status_t
 _notmuch_database_link_message (notmuch_database_t *notmuch,
 				notmuch_message_t *message,
-				notmuch_message_file_t *message_file)
+				notmuch_message_file_t *message_file,
+				notmuch_bool_t is_ghost)
 {
     void *local = talloc_new (NULL);
     notmuch_status_t status;
-    const char *thread_id;
+    const char *thread_id = NULL;
 
     /* Check if the message already had a thread ID */
-    thread_id = _consume_metadata_thread_id (local, notmuch, message);
-    if (thread_id)
-	_notmuch_message_add_term (message, "thread", thread_id);
+    if (notmuch->features & NOTMUCH_FEATURE_GHOSTS) {
+	if (is_ghost)
+	    thread_id = notmuch_message_get_thread_id (message);
+    } else {
+	thread_id = _consume_metadata_thread_id (local, notmuch, message);
+	if (thread_id)
+	    _notmuch_message_add_term (message, "thread", thread_id);
+    }
 
     status = _notmuch_database_link_message_to_parents (notmuch, message,
 							message_file,
@@ -2079,6 +2137,7 @@ notmuch_database_add_message (notmuch_database_t *notmuch,
     notmuch_message_t *message = NULL;
     notmuch_status_t ret = NOTMUCH_STATUS_SUCCESS, ret2;
     notmuch_private_status_t private_status;
+    notmuch_bool_t is_ghost = false;
 
     const char *date, *header;
     const char *from, *to, *subject;
@@ -2171,12 +2230,20 @@ notmuch_database_add_message (notmuch_database_t *notmuch,
 
 	_notmuch_message_add_filename (message, filename);
 
-	/* Is this a newly created message object? */
-	if (private_status == NOTMUCH_PRIVATE_STATUS_NO_DOCUMENT_FOUND) {
+	/* Is this a newly created message object or a ghost
+	 * message?  We have to be slightly careful: if this is a
+	 * blank message, it's not safe to call
+	 * notmuch_message_get_flag yet. */
+	if (private_status == NOTMUCH_PRIVATE_STATUS_NO_DOCUMENT_FOUND ||
+	    (is_ghost = notmuch_message_get_flag (
+		message, NOTMUCH_MESSAGE_FLAG_GHOST))) {
 	    _notmuch_message_add_term (message, "type", "mail");
+	    if (is_ghost)
+		/* Convert ghost message to a regular message */
+		_notmuch_message_remove_term (message, "type", "ghost");
 
 	    ret = _notmuch_database_link_message (notmuch, message,
-						  message_file);
+						  message_file, is_ghost);
 	    if (ret)
 		goto DONE;
 
-- 
2.1.0

[PATCH v3 6/9] lib: Implement upgrade to ghost messages feature

[Austin Clements]

From: Austin Clements <amdragon@mit.edu>

Somehow this is the first upgrade pass that actually does *any* error
checking, so this also adds the bit of necessary infrastructure to
handle that.
---
 lib/database.cc | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 64 insertions(+), 2 deletions(-)

diff --git a/lib/database.cc b/lib/database.cc
index 92a92d9..b673718 100644
--- a/lib/database.cc
+++ b/lib/database.cc
@@ -1231,6 +1231,7 @@ notmuch_database_upgrade (notmuch_database_t *notmuch,
     notmuch_bool_t timer_is_active = FALSE;
     enum _notmuch_features target_features, new_features;
     notmuch_status_t status;
+    notmuch_private_status_t private_status;
     unsigned int count = 0, total = 0;
 
     status = _notmuch_database_ensure_writable (notmuch);
@@ -1275,6 +1276,13 @@ notmuch_database_upgrade (notmuch_database_t *notmuch,
 	for (t = db->allterms_begin ("XTIMESTAMP"); t != t_end; t++)
 	    ++total;
     }
+    if (new_features & NOTMUCH_FEATURE_GHOSTS) {
+	/* The ghost message upgrade converts all thread_id_*
+	 * metadata values into ghost message documents. */
+	t_end = db->metadata_keys_end ("thread_id_");
+	for (t = db->metadata_keys_begin ("thread_id_"); t != t_end; ++t)
+	    ++total;
+    }
 
     /* Perform the upgrade in a transaction. */
     db->begin_transaction (true);
@@ -1378,10 +1386,64 @@ notmuch_database_upgrade (notmuch_database_t *notmuch,
 	}
     }
 
+    /* Perform metadata upgrades. */
+
+    /* Prior to NOTMUCH_FEATURE_GHOSTS, thread IDs for missing
+     * messages were stored as database metadata. Change these to
+     * ghost messages.
+     */
+    if (new_features & NOTMUCH_FEATURE_GHOSTS) {
+	notmuch_message_t *message;
+	std::string message_id, thread_id;
+
+	t_end = db->metadata_keys_end (NOTMUCH_METADATA_THREAD_ID_PREFIX);
+	for (t = db->metadata_keys_begin (NOTMUCH_METADATA_THREAD_ID_PREFIX);
+	     t != t_end; ++t) {
+	    if (do_progress_notify) {
+		progress_notify (closure, (double) count / total);
+		do_progress_notify = 0;
+	    }
+
+	    message_id = (*t).substr (
+		strlen (NOTMUCH_METADATA_THREAD_ID_PREFIX));
+	    thread_id = db->get_metadata (*t);
+
+	    /* Create ghost message */
+	    message = _notmuch_message_create_for_message_id (
+		notmuch, message_id.c_str (), &private_status);
+	    if (private_status == NOTMUCH_PRIVATE_STATUS_SUCCESS) {
+		/* Document already exists; ignore the stored thread ID */
+	    } else if (private_status ==
+		       NOTMUCH_PRIVATE_STATUS_NO_DOCUMENT_FOUND) {
+		private_status = _notmuch_message_initialize_ghost (
+		    message, thread_id.c_str ());
+		if (! private_status)
+		    _notmuch_message_sync (message);
+	    }
+
+	    if (private_status) {
+		fprintf (stderr,
+			 "Upgrade failed while creating ghost messages.\n");
+		status = COERCE_STATUS (private_status, "Unexpected status from _notmuch_message_initialize_ghost");
+		goto DONE;
+	    }
+
+	    /* Clear saved metadata thread ID */
+	    db->set_metadata (*t, "");
+
+	    ++count;
+	}
+    }
+
+    status = NOTMUCH_STATUS_SUCCESS;
     db->set_metadata ("features", _print_features (local, notmuch->features));
     db->set_metadata ("version", STRINGIFY (NOTMUCH_DATABASE_VERSION));
 
-    db->commit_transaction ();
+ DONE:
+    if (status == NOTMUCH_STATUS_SUCCESS)
+	db->commit_transaction ();
+    else
+	db->cancel_transaction ();
 
     if (timer_is_active) {
 	/* Now stop the timer. */
@@ -1397,7 +1459,7 @@ notmuch_database_upgrade (notmuch_database_t *notmuch,
     }
 
     talloc_free (local);
-    return NOTMUCH_STATUS_SUCCESS;
+    return status;
 }
 
 notmuch_status_t
-- 
2.1.0

[PATCH v3 7/9] lib: Enable ghost messages feature

[Austin Clements]

From: Austin Clements <amdragon@mit.edu>

This fixes the broken thread order test.
---
 lib/database-private.h    | 2 +-
 test/T260-thread-order.sh | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/database-private.h b/lib/database-private.h
index e2e4bc8..15e03cc 100644
--- a/lib/database-private.h
+++ b/lib/database-private.h
@@ -166,7 +166,7 @@ struct _notmuch_database {
  * databases will have it). */
 #define NOTMUCH_FEATURES_CURRENT \
     (NOTMUCH_FEATURE_FILE_TERMS | NOTMUCH_FEATURE_DIRECTORY_DOCS | \
-     NOTMUCH_FEATURE_BOOL_FOLDER)
+     NOTMUCH_FEATURE_BOOL_FOLDER | NOTMUCH_FEATURE_GHOSTS)
 
 /* Return the list of terms from the given iterator matching a prefix.
  * The prefix will be stripped from the strings in the returned list.
diff --git a/test/T260-thread-order.sh b/test/T260-thread-order.sh
index b435d79..99f5833 100755
--- a/test/T260-thread-order.sh
+++ b/test/T260-thread-order.sh
@@ -30,7 +30,6 @@ expected=$(for ((i = 0; i < $nthreads; i++)); do
 test_expect_equal "$output" "$expected"
 
 test_begin_subtest "Messages with all parents get linked in all delivery orders"
-test_subtest_known_broken
 # Here we do the same thing as the previous test, but each message
 # references all of its parents.  Since every message references the
 # root of the thread, each thread should always be fully joined.  This
-- 
2.1.0

[PATCH v3 8/9] test: Test upgrade to ghost messages feature

[Austin Clements]

---
 test/T530-upgrade.sh | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/test/T530-upgrade.sh b/test/T530-upgrade.sh
index c4c4ac8..6b42a69 100755
--- a/test/T530-upgrade.sh
+++ b/test/T530-upgrade.sh
@@ -116,4 +116,25 @@ MAIL_DIR/bar/new/21:2,
 MAIL_DIR/bar/new/22:2,
 MAIL_DIR/cur/51:2,"
 
+# Ghost messages are difficult to test since they're nearly invisible.
+# However, if the upgrade works correctly, the ghost message should
+# retain the right thread ID even if all of the original messages in
+# the thread are deleted.  That's what we test.  This won't detect if
+# the upgrade just plain didn't happen, but it should detect if
+# something went wrong.
+test_begin_subtest "ghost message retains thread ID"
+# Upgrade database
+notmuch new
+# Get thread ID of real message
+thread=$(notmuch search --output=threads id:4EFC743A.3060609@april.org)
+# Delete all real messages in that thread
+rm $(notmuch search --output=files $thread)
+notmuch new
+# "Deliver" ghost message
+add_message '[subject]=Ghost' '[id]=4EFC3931.6030007@april.org'
+# If the ghost upgrade worked, the new message should be attached to
+# the existing thread ID.
+nthread=$(notmuch search --output=threads id:4EFC3931.6030007@april.org)
+test_expect_equal "$thread" "$nthread"
+
 test_done
-- 
2.1.0

[PATCH v3 9/9] lib: Remove unnecessary thread linking steps when using ghost messages

[Austin Clements]

From: Austin Clements <amdragon@mit.edu>

Previously, it was necessary to link new messages to children to work
around some (though not all) problems with the old metadata-based
approach to stored thread IDs.  With ghost messages, this is no longer
necessary, so don't bother with child linking when ghost messages are
in use.
---
 lib/database.cc | 29 +++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diff --git a/lib/database.cc b/lib/database.cc
index b673718..3601f9d 100644
--- a/lib/database.cc
+++ b/lib/database.cc
@@ -2136,11 +2136,11 @@ _consume_metadata_thread_id (void *ctx, notmuch_database_t *notmuch,
  * reference 'message'.
  *
  * In all cases, we assign to the current message the first thread ID
- * found (through either parent or child). We will also merge any
- * existing, distinct threads where this message belongs to both,
- * (which is not uncommon when messages are processed out of order).
+ * found. We will also merge any existing, distinct threads where this
+ * message belongs to both, (which is not uncommon when messages are
+ * processed out of order).
  *
- * Finally, if no thread ID has been found through parent or child, we
+ * Finally, if no thread ID has been found through referenced messages, we
  * call _notmuch_message_generate_thread_id to generate a new thread
  * ID. This should only happen for new, top-level messages, (no
  * References or In-Reply-To header in this message, and no previously
@@ -2172,10 +2172,23 @@ _notmuch_database_link_message (notmuch_database_t *notmuch,
     if (status)
 	goto DONE;
 
-    status = _notmuch_database_link_message_to_children (notmuch, message,
-							 &thread_id);
-    if (status)
-	goto DONE;
+    if (! (notmuch->features & NOTMUCH_FEATURE_GHOSTS)) {
+	/* In general, it shouldn't be necessary to link children,
+	 * since the earlier indexing of those children will have
+	 * stored a thread ID for the missing parent.  However, prior
+	 * to ghost messages, these stored thread IDs were NOT
+	 * rewritten during thread merging (and there was no
+	 * performant way to do so), so if indexed children were
+	 * pulled into a different thread ID by a merge, it was
+	 * necessary to pull them *back* into the stored thread ID of
+	 * the parent.  With ghost messages, we just rewrite the
+	 * stored thread IDs during merging, so this workaround isn't
+	 * necessary. */
+	status = _notmuch_database_link_message_to_children (notmuch, message,
+							     &thread_id);
+	if (status)
+	    goto DONE;
+    }
 
     /* If not part of any existing thread, generate a new thread ID. */
     if (thread_id == NULL) {
-- 
2.1.0

Re: [PATCH v3 0/9] Add ghost messages and fix thread linking

[David Bremner]

Austin Clements <aclements@csail.mit.edu> writes:

> This is v3 of
> id:1412637438-4821-1-git-send-email-aclements@csail.mit.edu.
> This fixes some comments, as suggested by Mark.  There are no
> code changes relative to v2.  The diff from v2 is below.

because I thought things were a little quiet today, I pushed this series
as well.

d