IRC Chat : 2012-02-13 - OpenMRS

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02:00:35 <harshadura> hi
02:00:39 <harshadura> anyone thr
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05:50:28 <suranga> wondering if any experts who are familiar with the use of R statistial module hang out here :P
05:50:34 <suranga> (but some rare chance :-)
05:53:43 <dkayiwa> suranga: for that, you would need to get to your knees and pray to God. :)
05:54:09 <suranga> dkayiwa, by some chance, have u tried working with it ?
05:54:21 <suranga> based on your tone, I feel tjhat you have prior experiance with it :)
05:54:35 <dkayiwa> suranga: i do not even know what it is used for :D
05:54:51 <suranga> ooops :D
05:55:32 <suranga> looks like praying may be my only option :-)
05:55:43 <suranga> dkayiwa, any news on Bens reapperance ?
05:55:59 <dkayiwa> suranga: still taking care of the little one :)
05:56:34 <suranga> I dont think I'll raise a family... it seems too much commitment to me :P
05:56:57 <dkayiwa> suranga: if it did not require so, it would cease to be enjoyable
05:57:07 <dkayiwa> suranga: is more than just coding :)
05:57:15 <dkayiwa> life is
05:57:50 <dkayiwa> suranga: the day you will fall in love with a young gal, you will forget all about what you have said :)
05:59:19 <suranga> dkayiwa, dear god, I hope that doesnt happen until Im too old to code :P
05:59:49 <dkayiwa> suranga: you do not plan for it. it just happens :)
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07:21:09 <ibewes> hello!
07:22:15 <ibewes> I'm getting up to speed on the openmrs codebase, is svn still the most current version or is there has the github repo replaced it?
07:22:44 <dkayiwa> ibewes: svn is the most current as far as i know
07:23:16 <ibewes> ok, looking through the wiki it seems like some things are being moved to github, is that correct?
07:24:48 <dkayiwa> ibewes: some modules. as for core, still under discussion
07:25:07 <ibewes> gotcha, thanks for the info!
07:25:14 <dkayiwa> yo welcome
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08:39:14 <allan_> just downloaded 1.8.3 and have existing database how do i update my database
08:40:07 <dkayiwa> allan_: first of all do a database backup
08:41:44 <allan_> ok
08:41:57 <allan_> finished
08:42:16 <dkayiwa> allan_: one of the ways is
08:43:16 <dkayiwa> allan_: 1) stop tomcat 2) delete the openmrs expanded folder under ../tomcat/webapps 3)overwrite the war file in ../tomcat/webapps with the one you have just downloaded 4) then start tomcat
08:46:56 <allan_> is ../tomcat/webapps in c:/m drive
08:58:41 <dkayiwa> allan_: it is wherever you installed tomcat
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09:24:24 <allan_> please someone help me
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09:28:55 <suranga> allan_, the webaopps folder is inside your tomcat folder
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09:29:10 <suranga> u need to go into that folder .
09:29:18 <suranga> oops, he has left already :(
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09:34:12 <harshadura> suranga ayya u thr
09:36:08 <suranga> hello hello
09:36:32 <suranga> Wellcome to our humble IRC channel
09:38:36 <harshadura> hi ayya :)
09:39:06 <suranga> so hows it going ? looked at any bugs lately ?
09:41:21 <harshadura> im started working on a intro ticket ayya > https://tickets.openmrs.org/browse/TRUNK-2768 but the thing is i cant jz figure out whr to start
09:41:26 <harshadura> pls can u help me ayya
09:48:15 <suranga> hi.. its like this...
09:48:30 <suranga> the aim of that ticket is to add an extra parameter to the model class and the database
09:48:54 <harshadura> okay yes
09:49:18 <suranga> so they want us to add a boolean value to the model class, and reflect that in the hbm, and finally add a column to the database...
09:49:27 <suranga> what part are u specifically stuck with ?
09:49:49 <suranga> first, u will need to add the variable into the model class, and write getters and setters
09:50:11 <suranga> next, u will need to add an Hibernate mapping to the hbm.xml file of the model class
09:50:42 <harshadura> okay ayya then
09:51:15 <harshadura> do i hv to edit the view
09:51:53 <suranga> thirdly, u will need to add a liquibase changeset so that the database table will be modified to include the new column
09:52:23 <suranga> and yep, u will also need to edit the jsp page (probably a tick box) so users can set it manually
09:52:43 <suranga> mm... how are u planning to proceed with this one ? :-)
09:53:45 <harshadura> i never used liquibase before. is that too difficult to getting started ayya
09:53:58 <suranga> no, not very
09:54:20 <suranga> basically liquibase is an xml file.. when we need to modify a database table, we code it into the liquibase file
09:54:26 <suranga> its not that hard
09:54:41 <suranga> actually, this is a good ticket to start learning, it covers all the basic angls
09:55:23 <suranga> I dont have openmrs checked out with me right now, but i think theres an xml file called liquibasechangeset.xml (something like that)
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09:56:20 <harshadura> okay ayya thanks lot I will look into it inform u later if i got any probs
09:56:23 <harshadura> thx again
09:57:18 <suranga> sure, no problem... Ill come online later tonight
09:57:31 <suranga> no worries, all the best !
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10:40:36 <sthaiya> hi all
10:40:36 <sthaiya> Just compiled openmrs war file from latest repo code
10:40:36 <sthaiya> while trying to install, i get an error at the last step "updating database"
10:40:36 <sthaiya> The error is
10:40:36 <sthaiya> There was an error while updating the database to the latest. file: liquibase-update-to-latest.xml. Error: null Error while trying to update to the latest database version
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12:29:59 <dkayiwa> hi rafa
12:30:24 <dkayiwa> rafa: do you know where i can find instructions on how to install pentaho components for this sprint?
12:30:52 <rafa> dkayiwa: I haven't looked at it yet.
12:31:07 <dkayiwa> rafa: ok
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13:17:34 <rafa> dkayiwa: seems like no installation is required for the pentaho components just download and unpack
13:17:57 <rafa> dkayiwa: don't ask me how to use it though ;)
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14:29:22 <mvorobey> hi all
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14:33:04 <downeym> hey there mvorobey
14:33:17 <dkayiwa> rafa: hahahha
14:33:48 <dkayiwa> bwolfe: welcome back :D
14:34:08 <bwolfe> thanks dkayiwa
14:34:34 <dkayiwa> you are welcome :)
14:35:09 <downeym> bwolfe++
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14:39:45 <downeym> Hi 13WAAGHWE and welcome to the #openmrs IRC channel.
14:40:12 <13WAAGHWE> dkayiwa, have you ever run more than one standalone instance at the same time?
14:40:16 <dkayiwa> 13WAAGHWE: what a name!!!! :)
14:40:26 <13WAAGHWE> wow
14:40:28 <13WAAGHWE> hehe
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14:40:41 <dkayiwa> 13WAAGHWE: oh yes. all i do is change the mysql and tomcat ports for each
14:40:48 <downeym> I kind of like 13WAAGHWE.
14:41:00 <downeym> it's catchy.
14:41:02 <chopin> dkayiwa, strange ... seems like the second instance is picking up on the first instance's MySQL port
14:41:03 <chopin> :-/
14:41:04 <chopin> heh
14:41:09 <chopin> not sure how to pronounce it
14:41:13 <chopin> or make it happen again, for that matter
14:41:31 <dkayiwa> chopin: you need to change the port number from the runtime properties file before you run it
14:41:38 <chopin> dkayiwa, ah set it there?
14:41:43 * chopin tries that
14:42:03 <bwolfe> 13wwaaghwe rolls right off the tongue too
14:42:22 <dkayiwa> chopin: yes
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14:59:17 <djazayeri> dkayiwa, rafa, bwolfe, mvorobey, Gretchie, join us at breeze.iu.edu/openmrsdev
14:59:27 <dkayiwa> djazayeri: ok
14:59:28 <djazayeri> (I see Gretchie and mvorobey there already.)
14:59:43 <rafa> ok
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15:59:22 <dawn_> djazayeri: is there no sprint dashboard for Pentaho yet?
15:59:33 <djazayeri> dawn_: no
15:59:52 <djazayeri> dawn_: no scrum today—we're in the middle of an intro presentation from gretchen
15:59:59 <dawn_> k
16:00:07 <bwolfe> or delayed scrum?
16:00:24 <djazayeri> bwolfe: we can do it delayed. in 1 hour maybe?
16:00:26 <dawn_> djazayeri: will there be a dashboard after this meeting with gretchen?
16:00:51 <bwolfe> lunch time, perfect. :-)
16:00:53 <djazayeri> dawn_: I'm not creating a dashboard until I'm more clear what's going to go on it. (This sprint is unusual)
16:01:11 <dkayiwa> :D
16:01:35 <dawn_> djazayeri: bwolfe : i have meetings after this time until 12:30. If you have a scrum, I'll check the logs on the wiki
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16:02:51 <downeym> Hi harshadura and welcome to the #openmrs IRC channel.
16:03:56 <harshadura> hi thx :)
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16:48:45 <MarkG> djazayeri: do you know where/how in HFE we enforce that encounter form submission actions are handled before other tags?
16:48:54 <MarkG> i've got a form that works if I define it this way:
16:48:57 <djazayeri> MarkG: I don't hink we do.
16:49:10 <djazayeri> they happen sequentially based on where they live in the file
16:49:17 <MarkG> <htmlform>
16:49:17 <MarkG> Encounter Date: <encounterDate/>
16:49:17 <MarkG> Encounter Location: <encounterLocation/>
16:49:17 <MarkG> Encounter Provider: <encounterProvider role="Provider"/>
16:49:17 <MarkG> <enrollInProgram programId="10" />
16:49:17 <MarkG> <submit/>
16:49:17 <MarkG> </htmlform>
16:50:00 <MarkG> but fails if defined with "enrollInProgram" before encounterDate, since the enroll in program tag doesn't have a valid encounter date?
16:50:27 <djazayeri> Something we ought to do is add an <encounter></encounter> tag, and also make tag handlers have a tagStarted and tagEnded callbacks...
16:50:30 <MarkG> djazayeri: are you saying you think this is a known/existing limitation, and not a regression?
16:50:38 <djazayeri> MarkG: yes
16:50:49 <MarkG> djazayeri: okay, cool, that makes it easier... thanks...
16:51:20 <MarkG> djazayeri: i will enter a ticket/note about this somewhere...
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17:05:39 <mseaton> wyclif - have you started looking at logic today?
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17:17:04 <downeym> Hi ploerch and welcome to the #openmrs IRC channel.
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17:41:58 <djazayeri> wyclif: have you and mseaton caught up yet?
17:56:00 <wyclif> djazayeri, mike just responded to the email thread i started
17:56:22 <djazayeri> wyclif: okay, you should also feel free to talk by phone, etc.
17:59:58 <wyclif> djazayeri, sure
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18:57:49 <wyclif> mseaton, djazayeri am calling the module rule
18:58:17 <djazayeri> wyclif: I don't like that because rule implies an "action", not just a calculation, at least to me as a computer guy
18:58:25 <djazayeri> but it does have the advantage of being shrot
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19:11:46 <chopin> djazayeri, (or any other ws person): when you do not include a field in someone's name or address (for example), is it because the value of that field (address4 for example) is "" or null?
19:12:16 <chopin> djazayeri, also do you have plans on exposing relationships in ws?
19:12:23 <djazayeri> chopin: it *should* be null, but I don't know how we coded it.
19:12:31 <djazayeri> chopin: yes, we'll do that eventually.
19:12:33 <djazayeri> chopin: busy now
19:12:39 <chopin> djazayeri, thought so ... k
19:12:43 <bwolfe> chopin, correct, to save bandwidth those are excluded from the output
19:12:50 <bwolfe> chopin, make a ticket for it
19:12:56 <bwolfe> (for the relationships)
19:13:22 <chopin> bwolfe, ah k ... i think i might be working with a slightly older version of ws on one instance because it is showing me nulls
19:13:30 <wyclif> bwolfe, mseaton djazayeri what version of the core should the new logic module require?
19:16:03 <bwolfe> wyclif, 1.15, since thats when it will be done ;-)
19:16:32 <wyclif> bwolfe, hmm
19:17:01 <bwolfe> chopin, hmm, maybe that wasn't implemented? :-/
19:17:20 <chopin> bwolfe, it does not show them in the most recent version
19:17:34 <chopin> bwolfe, i think the 1.8.1-with-ws standalone might have an older version?
19:17:54 <bwolfe> chopin, thats a pre-alpha, for sure
19:18:17 <chopin> k
19:18:26 <bwolfe> chopin, what version of openmrs are you using with the latest?
19:18:36 <chopin> 1.8.2
19:18:58 <wyclif> djazayeri, if we are having things like Rule, RuleContext, RuleService etc why not call them Calculation etc
19:18:59 <bwolfe> ok
19:19:11 <djazayeri> wyclif: you and mseaton can decide on the name
19:19:21 <djazayeri> I agree that if we call the module calculation, we should name things Calculaiton instead
19:19:32 <djazayeri> you two just decide something, and the rest of us will have to deal with it
19:20:48 <wyclif> djazayeri, i think renaming things things an an IDE is trivial, so i will use rule in the meantime and will rename them once i come to an agreement with mike
19:20:49 <mseaton> wyclif: yes, see the wiki page. it says basically if we change the name rule, everything that has rule in it should be changed to have the new thing in it
19:21:07 <wyclif> mseaton, are you fine with rule?
19:21:15 <wyclif> mseaton, sorry calculation
19:21:27 <mseaton> wyclif: my suggestion in my last email was calculation.patient, but no one responded.
19:21:34 <mseaton> this was last week
19:22:21 <wyclif> i think calculation is more inclusive than calculation.patient
19:22:21 <mseaton> this way, if we decide to have encounter-based calculations (like number of encounters per day at location x), then we can do that with calculation.encounter
19:22:39 <mseaton> yes it is, but we are only writing code for patient calculations here.
19:23:22 <wyclif> mseaton, then why not patientcalculation rather then calculation.patient
19:23:30 <mseaton> i'm happy if the module is called calculation, as long as the specific packages we write for the logic replacement are in the "patient" org.openmrs.module.calculation.patient subpackage
19:24:04 <mseaton> that way we keep all of the code in the one module, but we leave the door open for other types of calculations.
19:24:19 <mseaton> so i think using the moduleid "calculation" is good.
19:24:46 <wyclif> mseaton, i will take care of the packages, am using org.openmrs namespace and not org.openmrs.module
19:31:01 <mseaton> oh right. org.openmrs.calculation is great.
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19:31:37 <mseaton> thanks wyclif! i'm about to go offline. email me if you want to connect today.
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19:32:31 <wyclif> mseaton. ok, so you are fine with the package name not including module as you initially suggested on the project design page?
19:33:05 <wyclif> djazayeri, did we agree that wer are using the org.openmrs namespace rather than the org.openmrs.module?
19:33:31 <djazayeri> wyclif: do it the way mseaton says
19:33:46 <djazayeri> yes, don't use .module, since we intend to pull this into core when it's ready
19:33:55 <wyclif> djazayeri, ok
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20:00:16 <dkayiwa> anyone familiar with this? ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
20:02:18 <r0bby_> hey all!
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20:18:21 <mvorobey> bye all!!!
20:18:34 <mvorobey> gotta sleeep :)
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21:02:17 <rafa> djazayeri: btw removing select min(obs_datetime) from that query makes it execute in 1,5 sec ;)
21:02:25 <MarkG> fyi, if anyone has been trying to reach anyone at PIH, our email has been down for most of the day
21:03:00 <rafa> djazayeri: I suppose we could execute that part as a separate query or some transformation
21:03:36 <djazayeri> rafa: maybe for something that (we know) very rarely recurs, we can flatten to one-per-patient manually in java faster
21:05:02 <rafa> djazayeri: right doing this kind of filter on 4k rows should be fast in java
21:05:44 <djazayeri> rafa: but I don't know how we'll represent that as we try to generalize for OpenMRS...
21:06:08 <djazayeri> I guess as "obs that should only happen once per patient"
21:06:24 <djazayeri> have you tried running the 1.6 webapp against this database?
21:06:37 <rafa> djazayeri: nope
21:06:41 <djazayeri> okay
21:07:03 <djazayeri> I was just trying the same query in the reporting module, but I'm getting an error with something about the location_tag table being misformed
21:07:27 <djazayeri> oh well, never mind that...
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21:18:06 <rafa> djazayeri: still there?
21:18:12 <djazayeri> yes
21:18:26 <rafa> I've come up with such a query:
21:18:27 <rafa> select obs.person_id, person.birthdate, value_numeric, obs_datetime
21:18:27 <rafa> from obs
21:18:27 <rafa> left join person on obs.person_id = person.person_id
21:18:27 <rafa> left join patient on patient.patient_id = person.person_id
21:18:27 <rafa> where person.voided = 0 and obs.voided = 0 and patient.voided = 0
21:18:28 <rafa> and concept_id = 5916
21:18:28 <rafa> group by obs.person_id
21:18:29 <rafa> having min(obs_datetime) = obs_datetime;
21:19:18 <rafa> Ohh sorry thought it was faster, but it wasn't even started :P
21:19:40 <djazayeri> It's possible that turning the subquery into a join is faster. I think it is.
21:21:31 <rafa> djazayeri: okay it seems to be much faster
21:21:46 <rafa> djazayeri: I'm not sure if results are still good
21:22:18 <bwolfe> rafa: results probably arent good. the other columns will be random
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21:22:34 <bwolfe> they won't necessarily be the same as the values from the row with the min
21:23:23 <rafa> bwolfe: you're probabaly right
21:25:54 <bwolfe> rafa:
21:25:55 <bwolfe> SELECT o1.*
21:25:55 <bwolfe> from (
21:25:55 <bwolfe> select person_id, min(obs_datetime) as first_obs_date
21:25:55 <bwolfe> from obs
21:25:55 <bwolfe> group by person_id) as o2
21:25:56 <bwolfe> inner join obs as o1
21:25:58 <bwolfe> on
21:26:00 <bwolfe> (o1.person_id=o2.person_id and o1.obs_datetime=o2.first_obs_date)
21:26:02 <bwolfe> where
21:26:04 <bwolfe> o1.concept_id = 1234
21:26:37 <bwolfe> ada happened to be struggling with this same thing today, and got this to be the fastest way to select rows out of the encounter table with 3.8m rows in it. I adapted it to obs here
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21:29:39 <rafa> bwolfe: seems like what Darius originally suggested, but maybe there's some subtle difference that seeds it up :)
21:29:57 <bwolfe> is it faster?
21:30:16 <bwolfe> I don't see darius' suggestion
21:30:19 <rafa> bwolfe: I haven't tried
21:30:38 <djazayeri> rafa: bwolfe has done it subtly differently, so that the group by happens in the from, rather than the where. I think that may be faster
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21:37:13 <bwolfe> rafa, needs a voided = 0 in the inner from
21:41:13 <bwolfe> only took 90 seconds to get the birth weights
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22:33:46 <wyclif> hi djazayeri
22:34:00 <djazayeri> hi wyclif
22:35:29 <wyclif> so the persistent class is TokenRegistration, but i wanted to call it something else, i plan to edit the wiki page so as to keep it updated with changes in the domain objects and services
22:35:40 <wyclif> djazayeri, so the persistent class is TokenRegistration, but i wanted to call it something else, i plan to edit the wiki page so as to keep it updated with changes in the domain objects and services
22:35:53 <wyclif> djazayeri, probably Calculation
22:36:00 <djazayeri> wyclif: you don't strictly have to keep the wiki page up to date
22:36:05 <djazayeri> you could just comment.
22:36:14 <djazayeri> i.e. comment on the wiki page.
22:37:05 <djazayeri> wyclif: so as not to cost you lots of time
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23:25:24 <wyclif> djazayeri, was it agreed to use custom datatypes and handler interfaces?
23:25:33 <djazayeri> wyclif: we didn't discuss it
23:25:37 <djazayeri> I think it'd be too much of a pain
23:25:43 <wyclif> djazayeri, thought it seems like we want to support older versions
23:25:48 <djazayeri> exactly
23:26:31 <wyclif> djazayeri, ParameterDefinitionis an interface, what would be a typical implementation
23:26:46 <djazayeri> Oh, I thought ParameterDefinition was a class
23:26:55 <djazayeri> if it's an interface, make a BaseParameterDefinition
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