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HomeHomeUsing EPPI-Revi...Using EPPI-Revi...Questions about...Questions about...Searching in Titles and Abstracts - timeout error encounteredSearching in Titles and Abstracts - timeout error encountered
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31/03/2015 11:55
 

 Hi,

I am trying to screen abstracts and titles of 1200 records imported into EPPI 4 Reviewer, but I frequently encounter a "Timeout expired" error ("the timeout period elapsed prior to completion of the operation or the server is not responding").

I noticed that the error occurs usually when complex search queries are used (trying to find documents containing any of ca. 10 keywords, using the OR operator), but even as simple search query as "intox*" triggers this error (whereas for examplet search query "tox*" was OK). 

I am using the free trial version so far, but me and my colleagues will need to use EPPI 4 Reviewer intensively for the next 18 months, so I would like to make sure that this issue is not relevant for the full version of the tool.

Thank you for any advice, Tomas.

 
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31/03/2015 16:17
 

Dear Tomáš,

thanks for letting us know, it is important for us to receive this sort of feedback. The issue you report isn't new, we do know that searches can timeout. The first bit of (bad) news is that the behaviour you see isn't due to the Trial version, trial accounts are functionally the same as paid-for accounts, they just start with a default one-month free trial.

Back on the main issue:
First of all, if you are getting timeouts only when using (full-text) searches, but not elsewhere, then this is a known (and somewhat difficult to tackle) problem. If you are frequently getting timeouts elsewhere, then we are dealing with (also) another problem, and I would really like to learn the details.

On the issue with searches: I have good reasons to believe that the problem can be solved, but so far I've been unable to get in the right conditions to actually find a solution. We know for sure that there is plenty of room for improvement (e.g. we can speed up the searching algorithms), however, the subject is tricky because the malfunctioning mechanism is tightly linked to the automatic 'optimisation' routines of the database engine itself. We know that this is the case because the timeouts have the bad habit of disappearing when we start looking: whenever I probe inside the query engine, this triggers more optimisations, searches don't time out anymore, and I'm left with nothing to optimise explicitly.

Hopefully you may experience the same kind of behaviour: it is normal to find that a particular search that was reliably timing out yesterday is working perfectly today (the other way round may also happen, but it's more rare). Also: as full-text searches rely on the creation of full text indexes, and this in turn eventually triggers more internal adjustments, it is also known that recent changes on the overall list of items makes timeouts more likely. If the list hasn't changed in the last 24 hours, the timeouts should be far less common.

The way forward: in order to properly tackle the issue, I can re-design some mid-level logic in ways that nudge the autmatic "optimisations" in the right direction. So far, in other areas, this approach has always worked. However, full-text searches come with some additional complications, so I wouldn't promise that it will be possible to make them work each time without exceptions. On the other hand, in order to do this work, I need to have a long-ish and diverse list of searches that do time out regularly (your examples seem perfect, but I'd need more!). Once I have that (unfortunately all examples I've tried so far "fixed" themselves soon after I've started looking), I would apply the known solutions I mention above. That is to say: I may need your help to identify enough unreliable search queries, without that I don't have a starting point.

Furthermore: we are already moving in new directions with our full-text (and machine learning) facilities, so I do hope that we will eventually implement entirely new "full-text search" facilities, thus side-stepping the issue altogether.

Take-home message is that you can assume the situation will improve, but this might require you to give us a little more feedback in the near future.

Finally: have you looked into the "keyword" highlighting features that can be found in the "document details" window (more details here)? They may provide an alternative strategy to the heavy usage of searches.

 
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03/04/2015 14:00
 

 Dear Sergio,

first of all, thank you for your complex answer.

Thanks to you, I have finally found out how to use the "Show terms" button (keyword highlighting tool), which I was wondering about for a while already :-)

Unfortunatelly, unless I am mistaken, using this tool, I still have to go through my list of references one by one to discover whether the title or abstract contains a keyword in question. Since I have 1200 records in a single review (and I need to do about 1000 reviews), I am looking for automatic keyword search.

So I am definitely interested in optimisation of the search tools and I will gladly provide all details on searches giving the timeout error. 

So for starters, my list of keywords I use for the searches:

poison*

tox*

intox*

adverse

safe*

side effect*

harm*

hazard*

risk*

bioactiv*

biolog* activ*

lethal*

sublethal*

sub-lethal*

 

acut*

First I tried to search using all these keywords with the OR operator, i.e. "poison* OR tox* OR intox* , ..."

This complex search returned the timeout error. So I started simplyfying the search query to shorten the search time. I ended up searching for individual keywords one by one, because most of the combined searches crashed with the timeout error. Even when using individual single keywords, the search crashed for keywords „intox*“, „side effect*“, „risk*“ and „biolog* activ*“. I tried it again today to make sure that the situation is still the same (especially referring to the indexing you mentioned. I haven't made any modifications to the list in the past 48 hours). Result - situation is still the same (the search crashes for most combined keyword search terms as well as for the four individual single keywords mentioned above).

Just to make sure we are on the same page - I perform the search using the operator "containing this text" and I search in "Title / abstract". As I mentioned the list I search contains 1200 references. If it helps, I can send you the list of references in RIS or any other format.

Thank you for your help and do not hesitate to contact me at novotny@techemcz.cz if I can help to solve this issue.

Regards, Tomáš. 

 
New Post
09/04/2015 11:44
 

Dear Tomáš,

Apologies for the late reply (was away for a few days).
Yes, the "highlighting tool" does not find the items for you, it's designed around the very common requirement to actually look at all the items found in the searching phase: the aim is to cut down the amount of time it takes to screen by title and abstract a single item. With the aid of the "auto advance" option and of keyboard shortcuts, I believe some people are able to screen an item in just a few seconds...

What you are trying to achieve should be possible, and I've set aside some time today to have a look at it. 1200 references should count as small amounts (it's not uncommon to have review with 40,000+ references to screen), I am determined to make this work for you. I must add that since the structure of your searches is fairly repetitive, I might hit the usual obstacle: after a bit of poking, searches will start to work, but you certainly gave me a good reason and enough material to start trying again.

Will let you know how I proceed.
Best wishes,
Sergio

 
New Post
09/04/2015 16:46
 

Hi again,

I've given this an exploratory look, and, as feared, couldn't do much: all the searches I've tried (both from the standard interface and via direct SQL access) worked at the first attempt, giving me little or no scope to try and improve how they work. As usual, the problem disappears when the mechanic is looking.
You will find some new searches "created by" me in your review (ID = 6078), please have a try yourself and let me know if searches are still timing out for you.

In the process I did develop some fairly sketchy ideas on how to modify what happens behind the scenes, but without having a way to verify their reliability (they may be prone to the same kind of problem, and fail in an intermittent way) I hesitate to implement them on the public version of EPPI-Reviewer.

I will give it a second try next week and report back here.
Sergio

 
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