Support for SPARQL IN and NOT IN, the new class signals

I made some documentation about our SPARQL-IN feature that we recently added. I added some interesting use-cases like doing an insert and a delete based on in values.

For the new class signal API that we’re developing this and next week, we’ll probably emit the IDs that tracker:id() would give you if you’d use that on a resource. This means that IN is very useful for the purpose of giving you metadata of resources that are in the list of IDs that you just received from the class signal.

We never documented tracker:id() very much, as it’s not an RDF standard; rather it’s something Tracker specific. But neither are the class signals a RDF standard; they are Tracker specific too. I guess here that makes it usable in combo and turns the status of ‘internal API’, irrelevant.

We’re right now prototyping the new class signals API. It’ll probably be a “sa(iii)a(iii)”:

That’s class-name and two arrays of subject-id, predicate-id, object-id. The class-name is to allow D-Bus filtering. The first array are the deletes and the second are the inserts. We’ll only give you object-ids of non-literal objects (literal objects have no internal object-id). This means that we don’t throw literals to you in the signal (you need to make a query to get them, we’ll throw 0 to you in the signal).

We give you the object-ids because of a use-case that we didn’t cover yet:

Given triple <a> nie:isLogicalPartOf <b>. When <a> is deleted, how do you know <b> during the signal? So the feature request was to do a select ?b { <a> nie:isLogicalPartOf ?b } when <a> is deleted (so the client couldn’t do that query anymore).

With the new signal we’ll give you the ID of <b> when <a> is deleted. We’ll also implement a tracker:uri(integer id) allowing you to get <b> out of that ID. It’ll do something like this, but then much faster: select ?subject { ?subject a rdfs:Resource . FILTER (tracker:id(?subject) IN (%d)) }

I know there will be people screaming for all objects, also literals, in the signals, but we don’t want to flood your D-Bus daemon with all that data. Scream all you want. Really, we don’t. Just do a roundtrip query.

Domain indexes finished, technical conclusions

The support for domain specific indexes is, awaiting review / finished. Although we can further optimize it now. More on that later in this post. Image that you have this ontology:

nie:InformationElement a rdfs:Class .

nie:title a rdf:Property ;
  nrl:maxCardinality 1 ;
  rdfs:domain nie:InformationElement ;
  rdfs:range xsd:string .

nmm:MusicPiece a rdfs:Class ;
  rdfs:subClassOf nie:InformationElement .

nmm:beatsPerMinute a rdf:Property ;
  nrl:maxCardinality 1 ;
  rdfs:domain nmm:MusicPiece ;
  rdfs:range xsd:integer .

With that ontology there are three tables called “Resource”, “nmo:MusicPiece” and “nie:InformationElement” in SQLite’s schema:

  • The “Resource” table has ID and the subject string
  • The “nie:InformationElement” has ID and “nie:title”
  • The “nmm:MusicPiece” one has ID and “nmm:beatsPerMinute”

That’s fairly simple, right? The problem is that when you ORDER BY “nie:title” that you’ll cause a full table scan on “nie:InformationElement”. That’s not good, because there are less “nmm:MusicPiece” records than “nie:InformationElement” ones.

Imagine that we do this SPARQL query:

SELECT ?title WHERE {
   ?resource a nmm:MusicPiece ;
             nie:title ?title
} ORDER BY ?title

We translate that, for you, to this SQL on our schema:

SELECT   "title_u" FROM (
  SELECT "nmm:MusicPiece1"."ID" AS "resource_u",
         "nie:InformationElement2"."nie:title" AS "title_u"
  FROM   "nmm:MusicPiece" AS "nmm:MusicPiece1",
         "nie:InformationElement" AS "nie:InformationElement2"
  WHERE  "nmm:MusicPiece1"."ID" = "nie:InformationElement2"."ID"
  AND    "title_u" IS NOT NULL
) ORDER BY "title_u"

OK, so with support for domain indexes we change the ontology like this:

nmm:MusicPiece a rdfs:Class ;
  rdfs:subClassOf nie:InformationElement ;
  tracker:domainIndex nie:title .

Now we’ll have the three tables called “Resource”, “nmo:MusicPiece” and “nie:InformationElement” in SQLite’s schema. But they will look like this:

  • The “Resource” table has ID and the subject string
  • The “nie:InformationElement” has ID and “nie:title”
  • The “nmm:MusicPiece” table now has three columns called ID, “nmm:beatsPerMinute” and “nie:title”

The same data, for titles of music pieces, will be in both “nie:InformationElement” and “nmm:MusicPiece”. We copy to the mirror column during ontology change coping, and when new inserts happen.

When now the rdf:type is known in the SPARQL query as a nmm:MusicPiece, like in the query mentioned earlier, we know that we can use the “nie:title” from the “nmm:MusicPiece” table in SQLite. That allows us to generate you this SQL query:

SELECT   "title_u" FROM (
  SELECT "nmm:MusicPiece1"."ID" AS "resource_u",
         "nmm:MusicPiece1"."nie:title" AS "title_u"
  FROM   "nmm:MusicPiece" AS "nmm:MusicPiece1"
  WHERE  "title_u" IS NOT NULL
) ORDER BY "title_u"

A remaining optimization is when you request a rdf:type that is a subclass of nmm:MusicPiece, like this:

SELECT ?title WHERE {
  ?resource a nmm:MusicPiece, nie:InformationElement ;
            nie:title ?title
} ORDER BY ?title

It’s still not as bad as now the “nie:title” is still taken from the “nmm:MusicPiece” table. But the join with “nie:InformationElement” is still needlessly there (we could just do the earlier SQL query in this case):

SELECT   "title_u" FROM (
  SELECT "nmm:MusicPiece1"."ID" AS "resource_u",
         "nmm:MusicPiece1"."nie:title" AS "title_u"
  FROM   "nmm:MusicPiece" AS "nmm:MusicPiece1",
         "nie:InformationElement" AS "nie:InformationElement2"
  WHERE  "nmm:MusicPiece1"."ID" = "nie:InformationElement2"."ID"
  AND    "title_u" IS NOT NULL
) ORDER BY "title_u"

We will probably optimize this specific use-case further later this week.

Friday’s performance improvements in Tracker

The crawler’s modification time queries

Yesterday we optimized the crawler’s query that gets the modification time of files. We use this timestamp to know whether or not a file must be reindexed.

Originally, we used a custom SQLite function called tracker:uri-is-parent() in SPARQL. This, however, caused a full table scan. As long as your SQL table for nfo:FileDataObjects wasn’t too large, that wasn’t a huge problem. But it didn’t scale linear. I started with optimizing the function itself. It was using a strlen() so I replaced that with a sqlite3_value_bytes(). We only store UTF-8, so that worked fine. It gained me ~ 10%; not enough.

So this commit was a better improvement. First it makes nfo:belongsToContainer an indexed property. The x nfo:belongsToContainer p means x is in a directory p for file resources. The commit changes the query to use the property that is now indexed.

The original query before we started with this optimization took 1.090s when you had ~ 300,000 nfo:FileDataObject resources. The new query takes about 0.090s. It’s of course an unfair comparison because now we use an indexed property. Adding the index only took a total of 10s for a ~ 300,000 large table and the table is being queried while we index (while we insert into it). Do the math, it’s a huge win in all situations. For the SQLite freaks; the SQLite database grew by 4 MB, with all items in the table indexed.

PDF extractor

Another optimization I did earlier was the PDF extractor. Originally, we used the poppler-glib library. This library doesn’t allow us to set the OutputDev at runtime. If compiled with Cairo, the OutputDev is in some versions a CairoOutputDev. We don’t want all images in the PDF to be rendered to a Cairo surface. So I ported this back to C++ and made it always use a TextOutputDev instead. In poppler-glib master this appears to have improved (in git master poppler_page_get_text_page is always using a TextOutputDev).

Another major problem with poppler-glib is the huge amount of copying strings in heap. The performance to extract metadata and content text for a 70 page PDF document without any images went from 1.050s to 0.550s. A lot of it was caused by copying strings and GValue boxing due to GObject properties.

Table locked problem

Last week I improved D-Bus marshaling by using a database cursor. I forgot to handle SQLITE_LOCKED while Jürg and Carlos had been introducing multithreaded SELECT support. Not good. I fixed this; it was causing random Table locked errors.

Performance DBus handling of the query results in Tracker’s RDF service

Before

For returning the results of a SPARQL SELECT query we used to have a callback like this. I removed error handling, you can find the original here.

We need to marshal a database result_set to a GPtrArray because dbus-glib fancies that. This is a lot of boxing the strings into GValue and GStrv. It does allocations, so not good.

static void
query_callback(TrackerDBResultSet *result_set,GError *error,gpointer user_data)
{
  TrackerDBusMethodInfo *info = user_data;
  GPtrArray *values = tracker_dbus_query_result_to_ptr_array (result_set);
  dbus_g_method_return (info->context, values);
  tracker_dbus_results_ptr_array_free (&values);
}

void
tracker_resources_sparql_query (TrackerResources *self, const gchar *query,
                                DBusGMethodInvocation *context, GError **error)
{
  TrackerDBusMethodInfo *info = ...; guint request_id;
  TrackerResourcesPrivate *priv= ...; gchar *sender;
  info->context = context;
  tracker_store_sparql_query (query, TRACKER_STORE_PRIORITY_HIGH,
                              query_callback, ...,
                              info, destroy_method_info);
}

After

Last week I changed the asynchronous callback to return a database cursor. In SQLite that means an sqlite3_step(). SQLite returns const pointers to the data in the cell with its sqlite3_column_* APIs.

This means that now we’re not even copying the strings out of SQLite. Instead, we’re using them as const to fill in a raw DBusMessage:

static void
query_callback(TrackerDBCursor *cursor,GError *error,gpointer user_data)
{
  TrackerDBusMethodInfo *info = user_data;
  DBusMessage *reply; DBusMessageIter iter, rows_iter;
  guint cols; guint length = 0;
  reply = dbus_g_method_get_reply (info->context);
  dbus_message_iter_init_append (reply, &iter);
  cols = tracker_db_cursor_get_n_columns (cursor);
  dbus_message_iter_open_container (&iter, DBUS_TYPE_ARRAY,
                                    "as", &rows_iter);
  while (tracker_db_cursor_iter_next (cursor, NULL)) {
    DBusMessageIter cols_iter; guint i;
    dbus_message_iter_open_container (&rows_iter, DBUS_TYPE_ARRAY,
                                      "s", &cols_iter);
    for (i = 0; i < cols; i++, length++) {
      const gchar *result_str = tracker_db_cursor_get_string (cursor, i);
      dbus_message_iter_append_basic (&cols_iter,
                                      DBUS_TYPE_STRING,
                                      &result_str);
    }
    dbus_message_iter_close_container (&rows_iter, &cols_iter);
  }
  dbus_message_iter_close_container (&iter, &rows_iter);
  dbus_g_method_send_reply (info->context, reply);
}

Results

The test is a query on 13500 resources where we ask for two strings, repeated eleven times. I removed a first repeat from each round, because the first time the sqlite3_stmt still has to be created. This means that our measurement would get a few more milliseconds. I also directed the standard out to /dev/null to avoid the overhead created by the terminal. The results you see below are the value for “real”.

There is of course an overhead created by the “tracker-sparql” program. It does demarshaling using normal dbus-glib. If your application uses DBusMessage directly, then it can avoid the same overhead. But since for both rounds I used the same “tracker-sparql” it doesn’t matter for the measurement.

$ time tracker-sparql -q "SELECT ?u  ?m { ?u a rdfs:Resource ;
          tracker:modified ?m }" > /dev/null

Without the optimization:

0.361s, 0.399s, 0.327s, 0.355s, 0.340s, 0.377s, 0.346s, 0.380s, 0.381s, 0.393s, 0.345s

With the optimization:

0.279s, 0.271s, 0.305s, 0.296s, 0.295s, 0.294s, 0.295s, 0.244s, 0.289s, 0.237s, 0.307s

The improvement ranges between 7% and 40% with average improvement of 22%.

Focus on query performance

Every (good) developer knows that copying of memory and boxing, especially when dealing with a large amount of pieces like members of collections and the cells in a table, are a bad thing for your performance.

More experienced developers also know that novice developers tend to focus on just their algorithms to improve performance, while often the single biggest bottleneck is needless boxing and allocating. Experienced developers come up with algorithms that avoid boxing and copying; they master clever pragmatical engineering and know how to improve algorithms. A lot of newcomers use virtual machines and script languages that are terrible at giving you the tools to control this and then they start endless religious debates about how great their programming language is (as if it matters). (Anti-.NET people don’t get on your horses too soon: if you know what you are doing, C# is actually quite good here).

We were of course doing some silly copying ourselves. Apparently it had a significant impact on performance.

Once Jürg and Carlos have finished the work on parallelizing SELECT queries we plan to let the code that walks the SQLite statement fill in the DBusMessage directly without any memory copying or boxing (for marshalling to DBus). We found the get_reply and send_reply functions; they sound useful for this purpose.

I still don’t really like DBus as IPC for data transfer of Tracker’s RDF store’s query results. Personally I think I would go for a custom Unix socket here. But Jürg so far isn’t convinced. Admittedly he’s probably right; he’s always right. Still, DBus to me doesn’t feel like a good IPC for this data transfer..

We know about the requests to have direct access to the SQLite database from your own process. I explained in the bug that SQLite3 isn’t MVCC and that this means that your process will often get blocked for a long time on our transaction. A longer time than any IPC overhead takes.

Supporting ontology changes in Tracker

It used to be in Tracker that you couldn’t just change the ontology. When you did, you had to reboot the database. This means loosing all the non-embedded data. For example your tags or other such information that’s uniquely stored in Tracker’s RDF store.

This was of course utterly unacceptable and this was among the reasons why we kept 0.8 from being released for so long: we were afraid that we would need to make ontology changes during the 0.8 series.

So during 0.7 I added support for what I call modest ontology changes. This means adding a class, adding a property. But just that. Not changing an existing property. This was sufficient for 0.8 because now we could at least do some changes like adding a property to a class, or adding a new class. You know, making implementing the standard feature requests possible.

Last two weeks I worked on supporting more intrusive ontology changes. The branch that I’m working on currently supports changing tracker:notify for the signals on changes feature, tracker:writeback for the writeback features and tracker:indexed which controls the indexes in the SQLite tables.

But also certain range changes are supported. For example integer to string, double and boolean. String to integer, double and boolean. Double to integer, string and boolean. Range changes will sometimes of course mean data loss.

Plenty of code was also added to detect an unsupported ontology change and to ensure that we just abort the process and don’t do any changes in that case.

It’s all quite complex so it might take a while before the other team members have tested and reviewed all this. It should probably take even longer before it hits the stable 0.8 branch.

We wont yet open the doors to custom ontologies. Several reasons:

  • We want more testing on the support for ontology changes. We know that once we open the doors to custom ontologies that we’ll see usage of this rather sooner than later.
  • We don’t yet support removing properties and classes. This would be easy (drop the table and columns away and log the event in the journal) but it’s not yet supported. Mostly because we don’t need it ourselves (which is a good reason).
  • We don’t want you to meddle with the standard ontologies (we’ll do that, don’t worry). So we need a bit of ontology management code to also look in other directories, etc.
  • The error handling of unsupported ontology changes shouldn’t abort like mentioned above. Another piece of software shouldn’t make Tracker unusable just because they install junk ontologies.
  • We actually want to start using OSCAF‘s ontology format. Perhaps it’s better that we wait for this instead of later asking everybody to convert their custom ontologies?
  • We’re a bunch of pussies who are afraid of the can of worms that you guys’ custom ontologies will open.

But yes, you could say that the basics are being put in place as we speak.

Zürichsee

Today after I brought Tinne to the airport I drove around Zürichsee. She can’t stay in Switzerland the entire month; she has to go back to school on Monday.

While driving on the Seestrasse I started counting luxury cars. After I reached two for Lamborgini and three for Ferrari I started thinking: Zimmerberg Sihltal and Pfannenstiel must be expensive districts tooAnd yes, they are.

I was lucky today that it was nice weather. But wow, what a nice view on the mountain tops when you look south over Zürichsee. People from Zürich, you guys are so lucky! Such immense calming feeling the view gives me! For me, it beats sauna. And I’m a real sauna fan.

I’m thinking to check it out south of Zürich. But not the canton. I think the house prices are just exaggerated high in the canton of Zürich. I was thinking Sankt Gallen, Toggenburg. I’ve never been there; I’ll check it out tomorrow.

Hmmr, meteoswiss gives rain for tomorrow. Doesn’t matter.

Actually, when I came back from the airport the first thing I really did was fix coping with property changes in ontologies for Tracker. Yesterday it wasn’t my day, I think. I couldn’t find this damn problem in my code! And in the evening I lost three chess games in a row against Tinne. That’s really a bad score for me. Maybe after two weeks of playing chess almost every evening, she got better than me? Hmmrr, that’s a troubling idea.

Anyway, so when I got back from the airport I couldn’t resist beating the code problem that I didn’t find on Friday. I found it! It works!

I guess I’m both a dreamer and a realist programmer. But don’t tell my customers that I’m such a dreamer.

Bern, an idyllic capital city

Today Tinne and I visited Switzerland’s capital, Bern.

We were really surprised; we’d never imagined that a capital city could offer so much peace and calm. It felt good to be there.

The fountains, the old houses, the river and the snowy mountain peaks give the city an idyllic image.

Standing on the bridge, you see the roofs of all these lovely small houses.

The bear is the symbol of Bern. Near the House of Parliament there was this statue of a bear. Tinne just couldn’t resist to give it a hug. Bern has also got real bears. Unfortunately, Tinne was not allowed to cuddle those bears.

The House of Parliament is a truly impressive building. It looks over the snowy mountains, its people and its treasury, the National Bank of Switzerland.


As you can imagine, the National Bank building is a master piece as well. And even more impressive; it issues a world leading currency.

On the market square in Oerlikon we first saw this chess board on the street; black and white stones and giant chess pieces. In Bern there was also a giant chess board in the backyard of the House of Parliament. Tinne couldn’t resist to challenge me for a game of chess. (*edit*, Armin noted in a comment that the initial position of knight and bishop are swapped. And OMG, he’s right!)

And she won!

At the House of Parliament you get a stunning, idyllic view on the mountains of Switzerland.