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From Peter Klügl <peter.klu...@averbis.com>
Subject Re: Very long Ruta stream initialization
Date Thu, 07 Jan 2016 09:40:08 GMT
Here's the description of the UIMA site:

Here's the description of general apache process:

A short summary of what is to do:
- complete the ICLA (http://www.apache.org/licenses/icla.pdf), print it,
sign it and scan it
- maybe do the same for the CCLA
(http://www.apache.org/licenses/cla-corporate.txt) if your employer
requires it and you did the contribution/implementation during work time
- send the scanned document (or both) to secretary@apache.org

"apache id" and "notify project" are optional but I would add it (so
that we get informed that the documents have been processed, and you
already have an id in case you would gain comitter rights).

I hope I have not forgotten something...



Am 07.01.2016 um 10:22 schrieb Mario Gazzo:
> Yes, where do we sign this?
> :-)
>> On 07 Jan 2016, at 10:16 , Peter Klügl <peter.kluegl@averbis.com> wrote:
>> :-) let me know if you need help or have any questions.
>> Am 07.01.2016 um 10:12 schrieb Mario Gazzo:
>>> Yes, let us just sign and submit it.
>>>> On 07 Jan 2016, at 10:11 , Peter Klügl <peter.kluegl@averbis.com>
>>>> Hi,
>>>> thanks, that would be great. Patches are simply attached to the issue.
>>>> Non-trivial changes require an ICLA. Do you want to sign and submit it?
>>>> Best,
>>>> Peter
>>>> Am 07.01.2016 um 10:08 schrieb Mario Gazzo:
>>>>> Thanks,
>>>>> I just added the JIRA issue: https://issues.apache.org/jira/browse/UIMA-4729
>>>>> If you like, then we can also implement it and submit a patch, just let
us know what the process is.
>>>>> Cheers
>>>>> Mario
>>>>>> On 07 Jan 2016, at 09:08 , Peter Klügl <peter.kluegl@averbis.com>
>>>>>> Hi,
>>>>>> Am 06.01.2016 um 14:48 schrieb Mario Gazzo:
>>>>>>> Hi Peter,
>>>>>>> I had a look at the test cases and I think there are many interesting
and useful features that cover many of our use cases but I will have to experiment with them
before I know what might be missing. I have a few questions though:
>>>>>>> 1) It appears that we would then also be able to assign annotations
to lists, which is nice. I am not sure from looking at the tests whether it is possible to
use ADD with the annotation lists but I assume so.
>>>>>> Not yet, but I will implement it. It's still work in progress. But
>>>>>> thanks for pointing it out, I would probably have forgotten about
>>>>>>> 2) The use of addresses is unclear to me just from reading the
test, maybe you could explain them.? This concept is very new to me.
>>>>>> It's not intented be to utilized directly in a rule file. It's rather
>>>>>> just a way to combine logic in java with ruta rules or use ruta
>>>>>> functionality in java code.
>>>>>> Let's say we have a new method like
>>>>>> boolean Ruta.matches(CAS cas, String rule, AnnotationFS... annotations)
>>>>>> and you call it with something like (syntax is not yet specified)
>>>>>> Ruta.matches(cas, "${PARTOF(Headline)} Keyword;", annotation)
>>>>>> Then, the "$" would be replaced by the address of the annotation
and the
>>>>>> method would return whether the annotation is covered by a Headline
>>>>>> annotation and is followed by a Keyword annotation.
>>>>>>> 3) The annotation feature expression looks nice but I wonder
whether an array element can also be referenced using an int expression and not just a constant
e.g. Struct.as[intVar+1]{->T1};
>>>>>> Yes, without allowing number expressions, it would not really be
>>>>>> The current implementation is just a test in order to check whether
>>>>>> internal object model is good enough to cover it. The complete
>>>>>> functionality will probably not be included in the next release since
>>>>>> there is still much work left in order to get it up and running.
>>>>>> semantics of such expressions (Struct.as) are resolved on the fly,
>>>>>> the code odes not support expressions at all. I still have to think
>>>>>> about a way to implement it.
>>>>>>> The label expressions are also useful and will make some of our
rules more readable.
>>>>>>> Finally I have one additional question to the MARKUP initialisation.
I have a case where I need the token seeds coming from the default seeder but I don’t want
to run the markup initialisation. Is there a separate seeder defined for this somewhere? Right
now I have my own copy of the default seeder without the MARKUP initialisation but obviously
I do not want to maintain this. It looks as if they could also be split in two seeders with
both added as default and then I could overwrite with my own seeder list containing only the
token seeder.
>>>>>> Yes, we can split them or just add another one that ignores markup.
>>>>>> was also always thinking about adding a DetailedSeeder that creates
>>>>>> more finegrained types like different brackets and quotes... but
it was
>>>>>> never on top of my todo list.
>>>>>> Do you want to open a jira issue for it?
>>>>>> Best,
>>>>>> Peter
>>>>>>> Cheers
>>>>>>> Mario
>>>>>>>> On 04 Jan 2016, at 17:06 , Peter Klügl <peter.kluegl@averbis.com>
>>>>>>>> Hi,
>>>>>>>> Am 04.01.2016 um 16:13 schrieb Mario Gazzo:
>>>>>>>>> Hi Peter,
>>>>>>>>> No problem, I was anyway pretty much offline myself during
Christmas holidays.
>>>>>>>>> The term “overhead” is probably an exaggeration in
this context especially after I disabled the MARKUP initialisation. We implemented earlier
our own XML markup annotator tailored to better fit our needs with additional annotation types
and properties, so the Ruta MARKUP is currently not used. It just happens that we don’t
directly use RutaBasic in any of our rules in this particular case so I was curious to know
whether we could avoid creating them in the first place since there seems to be quite a few.
However, overall processing required by our Ruta scripts compared to other processing steps
is now small and sub-optimising this further by making RutaBasic optional would currently
be of very low priority to us. We would prioritise other features higher e.g. being able to
assign annotations to variables as we discussed previously in another thread.
>>>>>>>> I am working on this right now and there is finally some
first progress :-)
>>>>>>>> I fear that I won't catch all use cases (combinations with
>>>>>>>> elements) with the first attempt. If you are interested (and
wanna take
>>>>>>>> care I do not miss your use case), feel free to take a look
at the new
>>>>>>>> unit tests:
>>>>>>>> https://svn.apache.org/repos/asf/uima/ruta/trunk/ruta-core/src/test/java/org/apache/uima/ruta/expression/annotation
>>>>>>>> It's still work in progress. Proposals for more unit tests
are very welcome.
>>>>>>>>> We haven’t processed documents as large as those you
mention since books have so far been divided into chapters and processing could therefore
be parallelised accordingly. We also drop extreme outliers above a certain size if we encounter
them and then we batch process them later in smaller chunks but this has so far not been necessary
with our current data sets. Like you, our processing bottlenecks are now in different components.
>>>>>>>> Ah, that's nice to hear that ruta is not the bottleneck :-D
>>>>>>>> Best,
>>>>>>>> Peter
>>>>>>>>> Cheers
>>>>>>>>> Mario
>>>>>>>>>> On 30 Dec 2015, at 16:44 , Peter Klügl <peter.kluegl@averbis.com>
>>>>>>>>>> Hi,
>>>>>>>>>> sorry for the delayed reply.
>>>>>>>>>> RutaEngine::initializeStream:
>>>>>>>>>> The special treatment of MARKUPs that causes the
increased time required for initialization is just a workaround because I was to lazy to write
a working jflex rule. Well, I tried but failed. It shouldn't be hard be to improve this code...
I will create an issue for it. When I did the last performance optimization, uima did not
check the indexes yet and my test set did not contain markups.
>>>>>>>>>> Deactivate creation of RutaBasic:
>>>>>>>>>> Short answer is no. I was already thinking about
making RutaBasic optional in future so that the user can configure if they are used. However,
right now, they are required for rule inference and make the rule inference "fast" in the
first place. RutaBasic is just an internal annotation like RutaAnnotation (for SCORE, MARKSCORE)
and RutaFrame, and rules should not match on them at all.
>>>>>>>>>> Some background information:
>>>>>>>>>> RutaBasics are used for three things:
>>>>>>>>>> - store additional information in order to avoid
index operations. Some useful conditions would require many index operations, e.g., PARTOF
or ENDSWITH. RutaBasic is utilized as a cache what annotations start and end at which position,
and which positions are covered by which types.
>>>>>>>>>> - provide a container to make this information available
across analysis engines. Information shared by analysis engine is normally stored in the CAS,
e.g. in annotations, (or in external resources). This is the role of RutaBasic. It is not
really implemented right now as it should be but I will improve it soon. Then, there is no
performance decrease when a pipeline is spammed with small ruta engines.
>>>>>>>>>> - a basic minimal disjunct partitioning of the document
for the coverage based visibility concept.
>>>>>>>>>> Making RutaBasic optional is possible. If there is
a real need for it, e.g., in order to reduce the memory footprint or when processing large
documents where parts are simply not interesting, then I will put it on my TODO list. I am
also open for other/new ideas how to solve the challenges (and for incremental usage of internal
>>>>>>>>>> What is your experience with the processing overhead
concerning RutaBasic? Is it the rule matching or rather the initialization? I myself had already
some performance problems with the initalization and memory consumption in large CAS (500+
pages pdfs). However, other components, serialization and the CAS editor were the actual bottlenecks.
>>>>>>>>>> Best,
>>>>>>>>>> Peter
>>>>>>>>>> Am 22.12.2015 um 17:26 schrieb Mario Gazzo:
>>>>>>>>>>> I got around it by removing the default seeders
by specifying an empty seeders list since we don’t need the MARKUP annotations anymore.
>>>>>>>>>>> I still don’t know why it created so much overhead
but it sometimes seemed to rival the POS tagger in processing time.
>>>>>>>>>>> Anyway, this leads me to the next question. Can
I disable the creation of Ruta basic annotations entirely to save processing overhead and
only apply Ruta rules to other annotation types created by other AEs such as our own?
>>>>>>>>>>> Cheers
>>>>>>>>>>> Mario
>>>>>>>>>>>> On 21 Dec 2015, at 16:09 , Mario Juric <mario.juric.dk@gmail.com>
>>>>>>>>>>>> Hi Peter,
>>>>>>>>>>>> I noticed that occasionally the initialisation
in RutaEngine::initializeStream can tak very long time. I can’t really explain them and
it seems independent of document length since I have seen this with even very small XML documents.
>>>>>>>>>>>> The method seems to spend much time in the
DefaultSeeder when creating MARKUP annotations during subiterator.moveToNext calls (line 89)
and inside Subiterator it seems to be the while loop inside adjustForStrictForward (line 232),
which is inside UIMA core classes. I haven’t gone into any deeper analysis yet but I first
like to hear whether you have an idea what could be the main cause(s) for this?
>>>>>>>>>>>> We use Ruta 2.3.1 with UIMA 2.8.1
>>>>>>>>>>>> Cheers
>>>>>>>>>>>> Mario

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