[InterMine Dev] tomcat restart deletes query templates

Joe Carlson jwcarlson at lbl.gov
Thu Aug 27 02:05:46 BST 2015


Hi Chen,

They are all tagged with im:aspect:Genomics. This is part of the mystery.

I don’t know yet, but when I was reviewing them I saw that some had aspect tags for non-existent aspects.

I’m going to do some experiments and tag things im:aspect:bogus to see what happens.

Joe


> On Aug 26, 2015, at 5:59 PM, Chen, Yian <chenyian at nibiohn.go.jp> wrote:
> 
> Hi Joe,
> 
> In your figure of the Templates tab, there is a filter "Genomics".
> Either remove the filter or tag your templates with "im:aspect:Genomics <im:aspect:Genomics>", to get them shown in the Templates tab.
> 
> Chen
> 
> On 2015/08/27 4:56, Joe Carlson wrote:
>> Hi Sergio,
>> 
>> After a few distractions, I’m finally getting back to the looking into why my templates are getting deleted. I’ll let you know what I find if and when I see something interesting.
>> 
>> In the meantime, I had another issue with template queries that I don’t understand.
>> 
>> If I tag a template with public, frontpage and an aspect, it appears in the 'Home’ tab on the front page, and this is good. I thought they should also show up in the ‘Templates’ tab. But I’m only seeing one of my templates from the home tab showing up in the templates tab:
>> 
>> <Mail Attachment.png>  
>> 
>> and, for what it’s worth, when I have the problem of the templates disappearing, it is only the 1 template that shows up in the templates tab that does not disappear.
>> 
>> All im:frontpage <im:frontpage> templates should also appear in template tab, correct?
>> 
>> maybe there is something amiss with my tagging.
>> 
>> thanks,
>> 
>> Joe
>> 
>>> On Aug 10, 2015, at 2:06 AM, sergio contrino <sergio at modencode.org <mailto:sergio at modencode.org>> wrote:
>>> 
>>> dear joe,
>>> thank you for all the info.
>>> i need to try it, but a couple of notes on your test so far:
>>> - you are right, the invalid templates should be ok
>>> - i was not expecting the behaviour you describe when updating a template (all templates deleted and then copied): at a first check the code seems fine and and only the affected template should be dealt with.
>>> is it possible that there is some configuration issues? (but you write that your 2 instances use different userprofiles, so i am not sure where to look at)
>>> - we usually don't force the shut down of tomcat (unless it is becoming annoyingly long..)
>>> please let me know if you have any news
>>> thanks
>>> sergio
>>> 
>>> 
>>> On 08/08/15 00:54, Joe Carlson wrote:
>>>> One last thing I just thought about.
>>>> 
>>>> I’m trying to understand why we’re just starting to see this now and it
>>>> has not been a problem before. One thing that is different is that we’re
>>>> running 2 instances of intermine on this server. They’re at different
>>>> paths (phytomine/ and phytomine-dev/) and using different back end
>>>> databases - both for the mine and for the user profile db - on different
>>>> postgres servers. I would expect that should not create any issues. But
>>>> thought it was worth mentioning.
>>>> 
>>>> Joe
>>>> 
>>>> On Aug 7, 2015, at 4:32 PM, Joe Carlson < <mailto:jwcarlson at lbl.gov>jwcarlson at lbl.gov <mailto:jwcarlson at lbl.gov>
>>>> <mailto:jwcarlson at lbl.gov <mailto:jwcarlson at lbl.gov>>> wrote:
>>>> 
>>>>> Hi Sergio,
>>>>> 
>>>>> I looked at this a little bit more. I haven’t stepped through this in
>>>>> the debugger (yet), but here is what I see in my black box testing.
>>>>> 
>>>>> I checked that the proper number of template queries were in the user
>>>>> profile database:
>>>>> 
>>>>>> userprofile-phytomine-dev=# select count(*) from savedtemplatequery;
>>>>>> count
>>>>>> -------
>>>>>>    51
>>>>>> (1 row)
>>>>> 
>>>>> Of these, 47 are owned by the intermine superuser. The others are user
>>>>> templates.
>>>>> 
>>>>> Then, became the intermine superuser and “modified" a template query.
>>>>> I actually did nothing, just hit the ‘edit’, then ‘save and run’. I
>>>>> was monitoring the postgres log files with log_statement set to ‘mod’:
>>>>> 
>>>>> 
>>>>>> 2015-08-07 16:00:13.818 PDT,,,98659,"",55c5387d.18163,1,"",2015-08-07
>>>>>> 16:00:13 PDT,,0,LOG,00000,"connection received: host=128.55.71.54
>>>>>> port=47823",,,,,,,,,""
>>>>>> 2015-08-07 16:00:13.820
>>>>>> PDT,"jcarlson","phytomine-dev",98659,"128.55.71.54:47823",55c5387d.18163,2,"authentication",2015-08-07
>>>>>> 16:00:13 PDT,25/97515,0,LOG,00000,"connection authorized:
>>>>>> user=jcarlson database=phytomine-dev",,,,,,,,,""
>>>>>> 2015-08-07 16:01:05.619
>>>>>> PDT,"jcarlson","userprofile-phytomine-dev",98620,"128.55.71.54:47757",55c53860.1813c,5,"DELETE",2015-08-07
>>>>>> 15:59:44 PDT,15/20715,0,LOG,00000,"execute <unnamed>: DELETE FROM
>>>>>> SavedTemplateQuery WHERE id IN (1135000000)",,,,,,,,,""
>>>>>> 2015-08-07 16:01:05.672
>>>>>> PDT,"jcarlson","userprofile-phytomine-dev",98620,"128.55.71.54:47757",55c53860.1813c,6,"DELETE",2015-08-07
>>>>>> 15:59:44 PDT,15/20716,0,LOG,00000,"execute <unnamed>: DELETE FROM
>>>>>> SavedTemplateQuery WHERE id IN (1135000001)",,,,,,,,,""
>>>>>> 2015-08-07 16:01:05.680
>>>>>> PDT,"jcarlson","userprofile-phytomine-dev",98620,"128.55.71.54:47757",55c53860.1813c,7,"DELETE",2015-08-07
>>>>>> 15:59:44 PDT,15/20717,0,LOG,00000,"execute <unnamed>: DELETE FROM
>>>>>> SavedTemplateQuery WHERE id IN (1135000002)",,,,,,,,,""
>>>>>> 2015-08-07 16:01:05.689
>>>>>> PDT,"jcarlson","userprofile-phytomine-dev",98620,"128.55.71.54:47757",55c53860.1813c,8,"DELETE",2015-08-07
>>>>>> 15:59:44 PDT,15/20718,0,LOG,00000,"execute <unnamed>: DELETE FROM
>>>>>> SavedTemplateQuery WHERE id IN (1135000003)",,,,,,,,,""
>>>>>> <lines deleted >
>>>>>> 2015-08-07 16:01:06.047
>>>>>> PDT,"jcarlson","userprofile-phytomine-dev",98620,"128.55.71.54:47757",55c53860.1813c,51,"DELETE",2015-08-07
>>>>>> 15:59:44 PDT,15/20761,0,LOG,00000,"execute <unnamed>: DELETE FROM
>>>>>> SavedTemplateQuery WHERE id IN (1135000046)",,,,,,,,,""
>>>>>> 2015-08-07 16:01:06.058
>>>>>> PDT,"jcarlson","userprofile-phytomine-dev",98620,"128.55.71.54:47757",55c53860.1813c,52,"idle
>>>>>> in transaction",2015-08-07 15:59:44
>>>>>> PDT,15/20762,0,LOG,00000,"statement: COPY SavedTemplateQuery (id,
>>>>>> templateQuery, userProfileId) FROM STDIN BINARY",,,,,,,,,""
>>>>>> 2015-08-07 16:01:06.077
>>>>>> PDT,"jcarlson","userprofile-phytomine-dev",98620,"128.55.71.54:47757",55c53860.1813c,53,"DELETE",2015-08-07
>>>>>> 15:59:44 PDT,15/20763,0,LOG,00000,"execute <unnamed>: DELETE FROM
>>>>>> UserProfile WHERE id IN (1000000)",,,,,,,,,""
>>>>>> 2015-08-07 16:01:06.078
>>>>>> PDT,"jcarlson","userprofile-phytomine-dev",98620,"128.55.71.54:47757",55c53860.1813c,54,"idle
>>>>>> in transaction",2015-08-07 15:59:44
>>>>>> PDT,15/20763,8548697,LOG,00000,"statement: COPY UserProfile
>>>>>> (superuser, id, password, username, apiKey, localAccount) FROM STDIN
>>>>>> BINARY",,,,,,,,,""
>>>>>> 2015-08-07 16:01:06.091
>>>>>> PDT,"jcarlson","userprofile-phytomine-dev",98622,"128.55.71.54:47759",55c53860.1813e,3,"UPDATE",2015-08-07
>>>>>> 15:59:44 PDT,17/89534,0,LOG,00000,"execute <unnamed>: UPDATE
>>>>>> templatetrack SET templatename = 'All_Gene_Homolog' WHERE
>>>>>> templatename = 'All_Gene_Homolog'",,,,,,,,,""
>>>>>> 2015-08-07 16:01:06.118
>>>>>> PDT,"jcarlson","userprofile-phytomine-dev",98621,"128.55.71.54:47758",55c53860.1813d,4,"INSERT",2015-08-07
>>>>>> 15:59:44 PDT,16/24559,0,LOG,00000,"execute <unnamed>: INSERT INTO
>>>>>> querytrack VALUES ( 'Homolog',' <mailto:jwcarlson at lbl.gov>jwcarlson at lbl.gov <mailto:jwcarlson at lbl.gov>
>>>>>> <mailto:jwcarlson at lbl.gov <mailto:jwcarlson at lbl.gov>>','0DB198E8114D7C8002343A200AE9CBDA','2015-08-07
>>>>>> 16:01:06.111')",,,,,,,,,""
>>>>>> 2015-08-07 16:01:39.083 PDT,,,99209,"",55c538d3.18389,1,"",2015-08-07
>>>>>> 16:01:39 PDT,,0,LOG,00000,"connection received: host=128.55.64.67
>>>>>> port=37744",,,,,,,,,""
>>>>>> 2015-08-07 16:01:39.083
>>>>>> PDT,,,99209,"128.55.64.67:37744",55c538d3.18389,2,"",2015-08-07
>>>>>> 16:01:39 PDT,,0,LOG,08P01,"incomplete startup packet",,,,,,,,,""
>>>>> 
>>>>> 
>>>>> So all 47 template queries are getting deleted one-by-one before COPY
>>>>> to SavedTemplateQuery is getting executed. When I check the db:
>>>>> 
>>>>>> 
>>>>>> userprofile-phytomine-dev=# select count(*) from savedtemplatequery;
>>>>>> count
>>>>>> -------
>>>>>>     5
>>>>>> (1 row)
>>>>> 
>>>>> The 5 queries are the 4 user templates and the one 1 edited. But this
>>>>> isn’t the whole story. Even though the user profile db says I only
>>>>> have 1 template, all 47 template queries still appear on the front page.
>>>>> 
>>>>> But: if I execute a tomcat restart (stopping is done with
>>>>> “$CATALINA_HOME/bin/shutdown.sh -force"), 46 queries are no longer on
>>>>> the front page nor are they in the template page of the superuser
>>>>> MyMine page. Only one remains.
>>>>> 
>>>>> So my questions are: is this to be expected? Are the
>>>>> savedtemplatequeries supposed to be flushed back into the user profile
>>>>> db with some secondary operation? Is there are better way to bring
>>>>> down the web app for a clean shutdown that I need to do?
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Joe
>>>>> 
>>>>> 
>>>>> On Aug 7, 2015, at 10:01 AM, Joe Carlson < <mailto:jwcarlson at lbl.gov>jwcarlson at lbl.gov <mailto:jwcarlson at lbl.gov>
>>>>> <mailto:jwcarlson at lbl.gov <mailto:jwcarlson at lbl.gov>>> wrote:
>>>>> 
>>>>>> Hi Sergio,
>>>>>> 
>>>>>> I’m running tomcat 7.0.62 and postgres server 9.4.1 and 9.4.2. I’ve
>>>>>> seen the behavior on two different installs.
>>>>>> 
>>>>>> I know I have a couple of old templates in the db that do not work
>>>>>> anymore. These appear with red lines through them with I become
>>>>>> superuser and look at the templates. I was assuming (or maybe just
>>>>>> hoping) that this could be ignored. Whether or not this is related,
>>>>>> I’m also seeing NotSerializableException from
>>>>>> org.intermine.api.template.ApiTemplate in the log files. I’m starting
>>>>>> to look into that.
>>>>>> 
>>>>>> This morning I’ll try some experiments to see if loosing the
>>>>>> templates is reproducible. And if cleaning up the templates helps.
>>>>>> Unfortunately I don’t have access to the postgres log files so I
>>>>>> cannot track the db activity too closely. (but…I’m begging)
>>>>>> 
>>>>>> It is strange since we used to have a problem with tomcat restarts
>>>>>> quite often. And did not see the templates disappear then. As I
>>>>>> recall, there were bogus template queries at that time.
>>>>>> 
>>>>>> Joe
>>>>>> 
>>>>>> On Aug 7, 2015, at 4:25 AM, sergio contrino < <mailto:sergio at modencode.org>sergio at modencode.org <mailto:sergio at modencode.org>
>>>>>> <mailto:sergio at modencode.org <mailto:sergio at modencode.org>>> wrote:
>>>>>> 
>>>>>>> dear Joe,
>>>>>>> we have not experienced the issue of the disappearance of saved
>>>>>>> tamplates and it should not be linked to the tomcat restart.
>>>>>>> could you send us the postgres and tomcat versions, and anything
>>>>>>> else that seems relevant to you? i can try to replicate it here.
>>>>>>> thanks
>>>>>>> sergio
>>>>>>> 
>>>>>>> 
>>>>>>> On 06/08/15 17:42, Joe Carlson wrote:
>>>>>>>> Hi Julie and others,
>>>>>>>> 
>>>>>>>> I've seen a problem the past couple weeks. I'm just starting to figure
>>>>>>>> out what is going on here. What I'm seeing is that a tomcat restart
>>>>>>>> causes most of the saved templates to disappear. The savedtemplatequery
>>>>>>>> table in the userprofile db is almost cleaned out - it looks like there
>>>>>>>> are still some user-created queries, but only 1 template created by the
>>>>>>>> superuser. Of course they do not show up on the front page.
>>>>>>>> 
>>>>>>>> I think - but I'm not even sure about this - is that it happens with a
>>>>>>>> tomcat restart.
>>>>>>>> 
>>>>>>>> Most curious. Have you ever seen this behavior? I have a backup that I
>>>>>>>> can restore so it's not a catastrophe but annoying.
>>>>>>>> 
>>>>>>>> Thanks,
>>>>>>>> 
>>>>>>>> Joe
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> dev mailing list
>>>>>>>> dev at intermine.org <mailto:dev at intermine.org> <mailto:dev at intermine.org <mailto:dev at intermine.org>>
>>>>>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev <http://mail.intermine.org/cgi-bin/mailman/listinfo/dev>
>>>>>>>> 
>>>>>>> 
>>>>>>> --
>>>>>>> sergio contrino                  InterMine, University of Cambridge
>>>>>>> https://sergiocontrino.github.io <https://sergiocontrino.github.io/> <https://sergiocontrino.github.io/ <https://sergiocontrino.github.io/>>
>>>>>>> http://www.intermine.org <http://www.intermine.org/> <http://www.intermine.org/ <http://www.intermine.org/>>
>>>>>> 
>>>>> 
>>>> 
>>> 
>>> -- 
>>> sergio contrino                  InterMine, University of Cambridge
>>> https://sergiocontrino.github.io <https://sergiocontrino.github.io/>           http://www.intermine.org <http://www.intermine.org/>
>> 
>> 
>> 
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> 
> 
> -- 
> Chen, Yian
> chenyian at nibiohn.go.jp <mailto:chenyian at nibiohn.go.jp>
> Postdoctoral Fellow
> Bioinformatics project
> National Institutes of Biomedical Innovation, Health and Nutrition
> 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan

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