IRC Chat : 2011-12-06 - OpenMRS

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01:37:52 <OpenMRSBot> Recent updates in the world of openmrs: On Twitter: OpenMRS: RT @downeym: Google Open Source Blog: #GSoC Students write code and save lives with @OpenMRS - http://t.co/g81b4k2u #ICT4D <http://twitter.com/OpenMRS/statuses/143858640623910912>
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02:53:49 <deadpool> djazayeri1: is there an extension point user profiles?
02:54:07 <djazayeri1> deadpool: I don't know, look at the source code
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02:54:47 <deadpool> djazayeri1: what would tell me that there is an extension point for that?
02:55:02 <djazayeri1> the jsp page for viewing user profiles
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08:31:28 <bwolfe> dkayiwa, forgot that extra commit again? :-)
08:31:35 <bwolfe> dkayiwa, did you backport my comments too?
08:31:45 <dkayiwa> bwolfe: yes i did :)
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11:00:20 <rafa_> hi bwolfe
11:00:27 <bwolfe> hey
11:01:17 <rafa_> I've just tried an update from 1.6 to 1.9
11:01:29 <rafa_> after a few problems finally got it running
11:01:37 <rafa_> but now I see in logs something like:
11:01:38 <rafa_> INFO - LoggingAdvice.invoke(117) |2011-12-06 11:59:59,266| In method ConceptServ
11:01:38 <rafa_> ice.updateConceptIndex. Arguments: Concept=11,
11:01:38 <rafa_> INFO - LoggingAdvice.invoke(142) |2011-12-06 12:00:04,782| Exiting method update
11:01:38 <rafa_> ConceptIndex
11:01:38 <rafa_> INFO - LoggingAdvice.invoke(117) |2011-12-06 12:00:06,128| In method Administrat
11:01:39 <rafa_> ionService.saveGlobalProperty. Arguments: GlobalProperty=property: conceptIndexU
11:01:39 <rafa_> pdateTask.lastConceptUpdated value: 11,
11:01:40 <rafa_> INFO - LoggingAdvice.invoke(142) |2011-12-06 12:00:07,573| Exiting method saveGl
11:01:40 <rafa_> obalProperty
11:01:41 <rafa_> INFO - LoggingAdvice.invoke(117) |2011-12-06 12:00:09,505| In method ConceptServ
11:01:41 <rafa_> ice.updateConceptIndex. Arguments: Concept=12,
11:01:42 <rafa_> INFO - LoggingAdvice.invoke(142) |2011-12-06 12:00:19,206| Exiting method update
11:01:42 <rafa_> ConceptIndex
11:01:56 <rafa_> the server runs fine and this thing is executed in background
11:02:04 <rafa_> do you know what that is? :)
11:02:20 <rafa_> it's really slow and I have a few thousands of concepts
11:02:38 <rafa_> should I wait for that to complete before trying to validate concepts?
11:03:14 <rafa_> (I hope not)
11:03:31 <rafa_> bwolfe:
11:05:29 <bwolfe> rafa?
11:05:29 <bwolfe> oh, above, one sec
11:10:02 <rafa_> bwolfe: ok
11:10:41 <bwolfe> it is updating the concept_word table
11:11:19 <rafa_> bwolfe: yeah so it should be safe to run validators
11:11:20 <bwolfe> its a scheduled task that runs one time
11:11:20 <bwolfe> its needed before you created your dump for the demo sql, but you should be ablet o validate while its going on
11:11:30 <bwolfe> rafa, is it only doing one at a time?!
11:11:41 <rafa_> bwolfe: seems like that
11:11:48 <bwolfe> how long for each?
11:11:54 <rafa_> bwolfe: and it's eating up one of my cores entirely
11:12:05 <rafa_> bwolfe: about 2 secs each
11:12:09 <bwolfe> mmm, cores
11:12:12 <bwolfe> sheesh
11:12:13 <rafa_> bwolfe: I'm only at 83 now
11:12:14 <bwolfe> very very slow
11:12:20 <bwolfe> 83 of 60000 ??
11:12:28 <rafa_> something like that :D
11:12:40 <bwolfe> that needs to be optimized. it should at least be doing 100 or so at a time before flushing and changing the gp for the last one done
11:12:41 <rafa_> no maybe not that drastic
11:13:42 <rafa_> I've got only 48275 concepts :D
11:13:53 <bwolfe> ha
11:14:05 <bwolfe> so sometime next year it'll finish...
11:14:19 <rafa_> haha that's right :D
11:17:24 <bwolfe> rafa, wouldn't hurt for you to take a look at that after doing the validating. because the concept_word stuff def needs to be done before you dump for the standalone
11:18:04 <rafa_> bwolfe: actually Darius idea was not to dump rather use Andy's dict every time
11:18:31 <rafa_> bwolfe: so that when he updates, we can get updated version for the standalone automatically
11:18:48 <rafa_> bwolfe: but I'm not sure if that's even possible
11:19:37 <djazayeri> rafa_, bwolfe: I don't want the dictionary to be automatically downloaded. (Well, I do, but that's not possible.)
11:20:11 <rafa_> djazayeri: yeah you want to point it to a zip with his dict right?
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11:20:54 <djazayeri> rather I want it to be such that the only thing we need to do when building the standalone distro is that we fetch the latest file from his dropbox, and then run the standalone-package-builder
11:20:55 <rafa_> djazayeri: (btw still awake?)
11:21:04 <djazayeri> yes, but pretend I'm not. :-P
11:21:30 <rafa_> djazayeri: :D
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11:22:01 <djazayeri> rafa_: I mean that a zip file is the *input* to building the standalone. (or, whatever format he distributes the dictionary in)
11:22:13 <djazayeri> a different zip file is the output.
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11:22:24 <rafa_> djazayeri: yeah I got it
11:22:48 <djazayeri> cool, okay, then i'm back to my other window
11:22:53 <djazayeri> tty in the morning :-)
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13:38:05 <rafa_> bwolfe: I'm running validators and it's not good
13:38:26 <rafa_> bwolfe: I tested around 1000 concepts now and 250 is not valid
13:38:44 <rafa_> bwolfe: due to DuplicateConceptNameException
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14:09:35 <bwolfe> rafa_, thats crappy
14:09:55 <bwolfe> its your call when you think its going to take too much work to clean it up
14:16:50 <rafa_> bwolfe: I don't feel like I'm the righ person to do that. It's not that I can just remove duplicates without thinking.
14:25:48 <r_friedman> bwolfe: hi ben, please ping me when your conversation with rafa is over
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15:36:53 <OpenMRSBot> Recent updates in the world of openmrs: OpenMRS Modules: HTML Form Entry 1.8.0 uploaded to OpenMRS Module Repository <https://dev.openmrs.org/modules/view.jsp?module=htmlformentry&ampversion=&amp1.8.0>
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16:56:44 <suranga> heloo james_regen
16:56:54 <suranga> james_regen, terriblly sorry, I had missed you yesterday :-(
17:01:39 <james_regen> suranga: hi
17:02:05 <suranga> james_regen, sorry about yesterday
17:02:33 <suranga> Dr. shaun taked to be about MI scoring stuff, and I totally forgot to et back to you :(
17:03:44 <james_regen> suranga: that's okay, i think talking to shaun was more important. what's the status with MI?
17:04:26 <suranga> basically Dr. Shaun said that he will re check the MI data and get back to me, and that I can commit it based on his feedback :-)
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17:05:17 <suranga> he said he would check it last night, but I guess he got caught up with something...
17:05:31 <suranga> james_regen, no hurry, lets see how it goes
17:06:02 <suranga> james_regen, in the meanwhile, Ada got back to me saying that the last omod I sent her is working fine...
17:06:18 <suranga> so I guess her problems with AMPATH are ending...
17:06:57 <james_regen> that's great news
17:08:23 <suranga> now, I can focuss more on improvements etc. I guess
17:08:55 <suranga> other that what Ada had proposed (the db changes) have you anything else in mind that needed to be done ?
17:10:08 <james_regen> suranga: not right now. i think the db changes are complicated enough
17:12:27 <suranga> james_regen, I need to take a closer look at what Ada had requested, and maybe ask her to eloberate
17:12:55 <suranga> I'll try to get back to you on this maybe tomorrow (wednesday) before you go off on leave :P
17:13:04 <suranga> and we'll see how we can start off...
17:13:50 <james_regen> suranga: ok, i'll be here
17:15:13 <suranga> james_regen, I'll go try contacting Ada regarding this, will report back tomorrow, if possible :-)
17:15:19 <suranga> james_regen, happy holidays...
17:15:40 <james_regen> suranga: thanks, good luck with your busy schedule
17:15:55 <suranga> james_regen, :P
17:43:43 <r_friedman> me tests connectivity
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19:00:12 <dawn> !scrumon dawn
19:00:12 * OpenMRSBot says the DAILY SCRUM MEETING is STARTING. This meeting should not last longer than 15 minutes. Please hold other comments until the end of the meeting, or message someone privately. Thank you! ScrumMaster dawn- you may begin when ready.
19:00:47 <dawn> djazayeri: bwolfe_ rafa_ wyclif : hi
19:01:07 <rafa_> hello
19:01:11 <dawn> Today's order: rafa_ bwolfe_ wyclif djazayeri
19:01:14 <dawn> :)
19:01:23 <rafa_> ready? :)
19:01:32 <djazayeri> yup
19:01:37 <rafa_> Today:
19:01:37 <rafa_> * Worked on STAND-36: Automatically create MVP/CIEL dictionary-based dataset as part of the standalone build process
19:01:37 <rafa_> https://tickets.openmrs.org/browse/STAND-36
19:01:37 <rafa_> Tomorrow:
19:01:37 <rafa_> * Continue to work on STAND-36 or move to something else
19:01:37 <rafa_> Blockers:
19:01:37 <rafa_> * STAND-36: Hundreds of duplicate concept names in the MVP dicionary
19:02:00 <wyclif> hey
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19:02:13 <bwolfe> I'm second again? *sigh* always the bridesmaid...
19:02:39 <rafa_> haha I wonder what is the algorithm ;)
19:02:43 <djazayeri> rafa_: I don't remember getting nearly that many validation errors when upgrading the MVP dictionary to 1.8.x. I wonder if we made some aspect of validation _stricter_.
19:02:58 <djazayeri> http://xkcd.com/221/
19:03:11 <bwolfe> rafa, lets discuss that after the scrum
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19:03:24 <dawn> bwolfe: your turn
19:03:30 <bwolfe> today:
19:03:30 <bwolfe> uploaded hibernate jar to maven repo
19:03:30 <bwolfe> applied hibernate patch
19:03:30 <bwolfe> added formentry docs
19:03:30 <bwolfe> emails
19:03:31 <bwolfe> rest tutorial with ampath devs
19:03:33 <bwolfe> scrum reviews
19:03:35 <bwolfe> set up next week's sprint
19:03:37 <bwolfe> wednesday:
19:03:39 <bwolfe> design call
19:03:41 <bwolfe> pm call
19:03:43 <bwolfe> sprint setup
19:03:45 <bwolfe> sprint reviews
19:04:12 <bwolfe> (no blockers)
19:04:29 <dawn> wyclif: your turn
19:04:35 <wyclif> yesterday:
19:04:35 <wyclif> -Completed STAND-35 - Fixing the standalone build support to include the demo data and testing the entire build process.
19:04:36 <wyclif> -Made changes as per review comments for - STAND-31
19:04:36 <wyclif> -Code reviews for TRUNK-2639 and TRUNK-2821
19:04:36 <wyclif> today:
19:04:37 <wyclif> -Code reviews for TRUNK-2903 - AuditableInterceptor throw NPE
19:04:39 <wyclif> -SMART-22 - Simplify mapping of concepts to terminologies
19:04:41 <wyclif> -Fix TODOs for TRUNK-2844 - Auto-created visits populate end time
19:04:43 <wyclif> -more sprint tickets
19:05:00 <djazayeri> !ticket trunk-2639
19:05:02 <OpenMRSBot> djazayeri: [#TRUNK-2639] Drugs are not showing up in the concept search in the concept dictionary - OpenMRS JIRA - https://tickets.openmrs.org/browse/trunk-2639
19:05:08 <djazayeri> !ticket trunk-2821
19:05:09 <OpenMRSBot> djazayeri: [#TRUNK-2821] Merge Patients page should be displayed on a separate pop-up screen - OpenMRS JIRA - https://tickets.openmrs.org/browse/trunk-2821
19:05:14 <wyclif> i will talk about some things i ran into with the standalone builder
19:05:17 <wyclif> later
19:05:17 <djazayeri> !ticket trunk-2903
19:05:18 <OpenMRSBot> djazayeri: [#TRUNK-2903] AuditableInterceptor fails with a NPE at startup if there are scheduled tasks to run at startup - OpenMRS JIRA - https://tickets.openmrs.org/browse/trunk-2903
19:05:44 <djazayeri> okay
19:05:52 <bwolfe> no other blockers wyclif?
19:05:58 <wyclif> no blockers
19:07:36 <bwolfe> djazayeri, your turn
19:07:45 <djazayeri> oh, my turn. (I was waiting for daniel, I just knew I was last!)
19:08:18 <djazayeri> Monday 5-Dec-2011
19:08:18 <djazayeri> * Updated patch and committed TRUNK-2588
19:08:18 <djazayeri> * Created a blocker TRUNK-2917 (AuditableInterceptor throws NPE at startup)
19:08:18 <djazayeri> * Reviewed UI and created some tickets: TRUNK-2909, TRUNK-2910, TRUNK-2911, TRUNK-2912, TRUNK-2913, TRUNK-2914, TRUNK-2915, TRUNK-2916
19:08:18 <djazayeri> * Noticed a problem with TRUNK-422 (Edit/View forms should merge)
19:08:19 <djazayeri> * Discuss current sprint tickets with Wyclif
19:08:19 <djazayeri> * Prepare for TW meeting on Friday
19:08:20 <djazayeri> Tuesday 6-Dec-2011
19:08:21 <djazayeri> * Review tickets created by TW BA
19:08:21 <djazayeri> * Prepare for TW meeting on Friday
19:08:22 <djazayeri> * Some code reviews
19:08:22 <djazayeri> * Comment on TRUNK-422 (Edit/View forms should merge) for Rafal
19:08:31 <djazayeri> no blockers, because I created tickets for everything that was bothering me.
19:08:57 <djazayeri> We need to figure out the startup +/- daemon issues
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19:09:07 <wyclif> true
19:09:24 <djazayeri> either now, or we leave that for design time tomorrow
19:09:39 <wyclif> i would vote for design call
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19:09:51 <r_friedman> bwolfe: hi ben pls ping me when you're done
19:09:55 <dawn> connecton fail
19:09:58 <dawn> djazayeri: i missed your updates
19:10:15 <djazayeri> dawn: should I repaste them?
19:10:40 <dawn> djazayeri: if you don't mind...keeping a summary for what to discuss after
19:10:59 <djazayeri> did others see my updates?
19:11:06 <djazayeri> anyway, here they are again:
19:11:12 <djazayeri> Monday 5-Dec-2011
19:11:13 <djazayeri> * Updated patch and committed TRUNK-2588
19:11:13 <djazayeri> * Created a blocker TRUNK-2917 (AuditableInterceptor throws NPE at startup)
19:11:13 <djazayeri> * Reviewed UI and created some tickets: TRUNK-2909, TRUNK-2910, TRUNK-2911, TRUNK-2912, TRUNK-2913, TRUNK-2914, TRUNK-2915, TRUNK-2916
19:11:13 <djazayeri> * Noticed a problem with TRUNK-422 (Edit/View forms should merge)
19:11:13 <djazayeri> * Discuss current sprint tickets with Wyclif
19:11:13 <djazayeri> * Prepare for TW meeting on Friday
19:11:14 <djazayeri> Tuesday 6-Dec-2011
19:11:15 <djazayeri> * Review tickets created by TW BA
19:11:15 <djazayeri> * Prepare for TW meeting on Friday
19:11:16 <djazayeri> * Some code reviews
19:11:16 <djazayeri> * Comment on TRUNK-422 (Edit/View forms should merge) for Rafal
19:11:28 <bwolfe> I saw them (twice)
19:11:31 <djazayeri> no blockers, because I created tickets for everything that was bothering me. But we need to figure out the startup +/- daemon issues
19:11:48 <bwolfe> is the tw meeting a tw hackathon type thing?
19:12:23 <djazayeri> no
19:12:35 <djazayeri> I'll give you more details offline
19:12:58 <djazayeri> "tickets created by TW BA" and "TW meeting" are totally separate
19:13:21 <dawn> djazayeri: rafa_ wyclif bwolfe I have 2 discussion topics then: 1) STAND-36 and 2) startup +/- daemon issues
19:13:27 <dawn> !scrumoff dawn
19:13:27 * OpenMRSBot says the DAILY SCRUM MEETING has ENDED. This channel is now returned to normal hacking operations. Post-scrum meeting follow-up conversations may now begin.
19:14:15 <bwolfe> rafa, STAND-36: how many dupes of the 50k ?
19:14:19 <djazayeri> dawn: (3) wyclif wants to discuss something about the standalone builder
19:14:25 <wyclif> djazayeri, i have realise the empty DB with the standalone is actually empty
19:14:32 <rafa_> bwolfe: they're still running
19:14:33 <dawn> djazayeri: thnx, got it
19:14:41 <wyclif> djazayeri, i.e no empty tables
19:14:46 <rafa_> bwolfe: so far 16154/48275, errors: 394
19:14:53 <wyclif> djazayeri, i thought it should have emptyy tables
19:15:03 <bwolfe> wyclif, the tables ar ecreated by the init wizard
19:15:05 <wyclif> djazayeri, and core data
19:15:30 <wyclif> bwolfe, that is expert mode
19:15:31 <djazayeri> bwolfe, wyclif: emptydatabase.zip *is* supposed to contain tables and core data
19:15:40 <wyclif> djazayeri, and it isn't
19:15:50 <djazayeri> okay, that's a bug then
19:15:56 <djazayeri> It definitely did at some point.
19:16:00 <wyclif> djazayeri, but i guess i kow why
19:16:38 <djazayeri> wyclif: maybe an issue about having an old mysqld process?
19:16:59 <wyclif> djazayeri, the database you set in the connection urls in the pom files is diffrent from what is being used by the builder
19:17:03 <djazayeri> rafa: percentage-wise that's small. :-)
19:17:34 <rafa_> djazayeri: % at the beginning it looked very bad, now is getting bettter
19:17:58 <djazayeri> rafa_: can you give an example of one of those invalid concepts?
19:18:05 <wyclif> djazayeri, the urls are pointing to emtydatabase in project root yet the builder looks in target
19:18:09 <djazayeri> also, did you do a full upgrade, and now you're validating? or something else?
19:18:29 <djazayeri> wyclif: ah, okay. want to create a ticket then?
19:18:36 <wyclif> djazayeri, sure
19:19:00 <rafa_> djazayeri: I stared with the latest 1.6 fresh install, imported mvp and upgraded to the latest 1.9
19:19:14 <rafa_> djazayeri: I mean the latest trunk
19:19:22 <rafa_> djazayeri: example: org.openmrs.api.DuplicateConceptNameException: 'PRE-ECLAMPSIA' is a duplicate name in locale 'en' at
19:19:29 <wyclif> djazayeri, the builder takes up excessive memory
19:19:29 <rafa_> org.openmrs.api.DuplicateConceptNameException: 'Pruritus' is a duplicate name in locale 'en' at
19:19:36 <rafa_> org.openmrs.api.DuplicateConceptNameException: 'MEASLES' is a duplicate name in locale 'en' at
19:19:45 <rafa_> and so on...
19:19:56 <rafa_> other langs too
19:19:56 <rafa_> org.openmrs.api.DuplicateConceptNameException: 'gastritis' is a duplicate name in locale 'es' at
19:20:04 <djazayeri> rafa_: I mean, are these messages happening during the upgrade script? Or afterwards if you validate?
19:20:21 <rafa_> the upgrade was sucessful
19:20:21 <wyclif> rafa, we made a change in 1.9/trunk where short names and i think retired names are ignores, make sure these aren't the reasons
19:20:31 <rafa_> now I'm running validators with a small module I wrote
19:21:02 <wyclif> djazayeri, rafa is concept_reference_source.hl7_code intended to be nullable?
19:21:17 <djazayeri> wyclif: one thing at a time!
19:21:17 <djazayeri> :-)
19:21:24 <bwolfe> wyclif, thats the problem I had: emptydatabase was being put in the wrong place. deleting/renaming that seemed ot fix it on mine (not sure why)
19:21:25 <wyclif> ok
19:21:34 <djazayeri> I'm looking into one of those duplicate concepts
19:22:03 <wyclif> bwolfe, the problem is the locations the urls in the pom.xml are pointing to
19:22:35 <djazayeri> rafa_: by the way, will you get irc notifications on "rafa" even though you're "rafa_"?
19:22:48 <rafa_> djazayeri: yeah both work
19:22:55 <djazayeri> okay, good
19:22:56 <bwolfe> r_friedman, whats up?
19:23:02 <wyclif> bwolfe, you need to make it target/emptydatabase rather than emptydatabase, this is what i did for demodata and it works
19:23:40 <bwolfe> ok, so just commit that. problem solved. no need for discussion. :-)
19:23:46 <r_friedman> hi ben, from your e-mail today about my rest compilation problem, i was thinking we were talking past each other and that we should talk virtually face to face, bwolfe
19:24:07 <bwolfe> r_friedman, or nick to nick as it is in irc? :-)
19:24:33 <djazayeri> rafa: measles is also a dup for me
19:24:36 <djazayeri> (there are two concepts...)
19:24:40 <r_friedman> bwolfe: i have 3 projects in my workspace -- my jsslab module, omrs 1.8.x, restws 0.9-SNAPSHOT
19:24:54 <rafa_> yeah org.openmrs.api.DuplicateConceptNameException: 'MEASLES' is a duplicate name in locale 'en' at
19:24:56 <rafa_> got it
19:25:26 <rafa_> djazayeri: I'll have all of them by tomorrow probably :)
19:25:47 <r_friedman> bwolfe: i worked with rafa on the problem and compiled restws. that results in a message that i was out of synch with maven repo and maven would recheck after repo refresh period
19:26:13 <djazayeri> grr, maternalconceptlab.com search is hanging. :-(
19:26:30 <r_friedman> bwolfe: for that one day, I had no errors except the omod pom with that message
19:27:08 <r_friedman> bwolfe: but the next day i was back to having all my references not found due to lack of restws in maven repo
19:27:54 <djazayeri> rafa: can you make a complete list of them, in some csv format, so we can somehow get it to Andy to look at / clean up?
19:28:23 <djazayeri> also, can you spot check one or two of them by looking at them in the 1.6.x dictionary, to see if it's an upgrade bug, or a problem in the source dictionary?
19:28:24 <rafa_> r_friedman: have you tried switching back to restws 1.0 version?
19:28:29 <rafa_> djazayeri: sure
19:28:39 <bwolfe> djazayeri, rafa: I propose if it takes more than 2-3 days to get it cleaned up with just take that MVP option out for the time being.
19:28:53 <rafa_> djazayeri: I've done the spot check already
19:28:54 <djazayeri> bwolfe: completely agree
19:29:13 <djazayeri> we want to include the MVP dictionary option in the final release in Q1, but it's not required for the beta.
19:29:41 <r_friedman> rafa: no, i have posted ITSM-2167 to put restws in the maven repo
19:29:55 <bwolfe> r_friedman, that isn't the solution
19:30:13 <djazayeri> rafa: and they're problems in the source?
19:30:17 <bwolfe> (and we won't do that)
19:30:23 <bwolfe> r_friedman, make sure all your projects reference the same version
19:30:31 <r_friedman> ben: cool, solve me
19:30:33 <bwolfe> if you're mucking with the versions in the poms you need ot muck with all of them
19:30:35 <djazayeri> wyclif: okay, about concept_reference_source
19:30:45 <r_friedman> yes, i muck with all of them
19:30:47 <djazayeri> rafa: do you remember the details of that?
19:30:58 <wyclif> hm
19:30:59 <rafa_> djazayeri: yes, they are
19:31:20 <rafa_> djazayeri: the MVP doesn't include any hl7 codes
19:31:21 <wyclif> djazayeri, should hl7_code be nullable
19:31:22 <djazayeri> wyclif, rafa: IIRC we decided either that hl7_code should be nullable
19:31:44 <djazayeri> wyclif, rafa: or else that we'd need to do 99_SOMETHING automatically
19:32:00 <rafa_> djazayeri: so the upgrade from 1.6 to 1.9 originally failed for me
19:32:08 <rafa_> djazayeri: because it relied on them being not null
19:32:11 <wyclif> djazayeri, i have a problem with making it nullable
19:32:26 <wyclif> djazayeri, what is the reason for making it nullable?
19:32:26 <bwolfe> r_friedman, are you running at commandline or in eclipse?
19:32:44 <r_friedman> bwolfe: eclipse
19:32:50 <rafa_> wyclif: I guess 50k concepts in the MVP dict is a good reason
19:32:51 <rafa_> :)
19:33:08 <djazayeri> wyclif, rafa: the reason is that not every concept_reference_source has an hl7 code
19:33:34 <djazayeri> e.g. SNOMED does, but "PIH Rwanda dictionary" does not.
19:33:49 <bwolfe> r_friedman, running the "install" target or just the "compile" target on api?
19:33:52 <wyclif> but concept reference term uuids are generated by concating the code with the hl7 code
19:34:08 <djazayeri> wyclif: well, we'd need to fix/workaround that
19:34:17 <djazayeri> !ticket TRUNK-2516
19:34:19 <r_friedman> bwolfe: clean install ... let me try again, just found a discrepancy between the POMs
19:34:19 <OpenMRSBot> djazayeri: [#TRUNK-2516] Add unique constraint to concept_source.hl7_code column - OpenMRS JIRA - https://tickets.openmrs.org/browse/TRUNK-2516
19:34:22 <wyclif> djazayeri, then would have to change this to be either the concept source id or uuid
19:34:44 <djazayeri> wyclif: hold up, let's figure out what we decided about hl7 code back in the day
19:34:45 <bwolfe> r_friedman, version or artifact discrepancy?
19:35:18 <rafa_> wyclif: it's what I did to force it to upgrade
19:36:10 <wyclif> ok
19:36:13 <r_friedman> bwolfe: main project was 0.8, omod was 0.9-SNAPSHOT
19:36:18 <r_friedman> bwolfe: made them both 0.8
19:36:31 <bwolfe> r_friedman, I see success in your future
19:36:38 <bwolfe> or rather "SUCCESS"
19:36:46 <r_friedman> bwolfe: wrong, failure --
19:36:49 <r_friedman> Failed to execute goal on project JSSLab-omod: Could not resolve dependencies for project org.openmrs.module:JSSLab-omod:omod:1.0-SNAPSHOT: The following artifacts could not be resolved: org.openmrs.module:webservices.rest-api:jar:0.8, org.openmrs.module:webservices.rest:jar:0.8: Could not find artifact org.openmrs.module:webservices.rest-api:jar:0.8 in openmrs-repo (http://mavenrepo.openmrs.org/nexus/content/repositories/public
19:36:50 <OpenMRSBot> <http://ln-s.net/8-2X> (at mavenrepo.openmrs.org)
19:36:56 <rafa_> r_friedman: I feel it should be 0.9-SNAPSHOT :)
19:37:19 <r_friedman> rafa, i know, i will try again. as i was saying earlier, it only worked for 1 day
19:37:31 <djazayeri> !ticket TRUNK-1273
19:37:32 <OpenMRSBot> djazayeri: [#TRUNK-1273] ConceptSource needs voided notNull=true, and hl7_code Null - OpenMRS JIRA - https://tickets.openmrs.org/browse/TRUNK-1273
19:38:04 <djazayeri> wyclif: ^^ back in OpenMRS 1.6.0 we allowed nullable hl7_code
19:38:18 <wyclif> djazayeri, ok and is it still the case?
19:38:33 <djazayeri> we haven't changed that, so yes, it's still the case
19:38:56 <wyclif> then we will have to change how set reference term uuids
19:40:12 <r_friedman> bwolfe: rafa: so i changed to 0.9-SNAPSHOT and got the same message
19:40:26 <djazayeri> wyclif: the final word was 23-sept-2009, in a conversation with subject "concept map method + hl7 code
19:40:26 <djazayeri> " when Burke said "+1 for making concept_source.hl7_code optional"
19:41:01 <r_friedman> bwolfe: rafa_ and here's the crazy part -- when I tried to recompile restws, it tried to compile jsslab yet again
19:41:39 <rafa_> r_friedman: does restws compile for you?
19:41:41 <bwolfe> r_friedman, it tried jsslab after trying restws, right? probably just an eclipse trigger because it sees them linked
19:41:57 <djazayeri> wyclif: so, you need a uuid for what then?
19:42:02 <r_friedman> bwolfe: rafa_ no sign that restws compiled
19:42:11 <bwolfe> right, make sure restws is "install"ed to your maven local repo
19:42:20 <wyclif> djazayeri, am fine with that, but then we should not have used it to generate reference term uuids
19:42:33 <wyclif> djazayeri, if it is nullable
19:42:56 <djazayeri> wyclif: why did we manually generate reference term uuids?
19:42:58 <wyclif> bwolfe, why didnt we assign 'normal' uuids to reference terms
19:43:06 <djazayeri> :-)
19:43:15 <wyclif> djazayeri, im trying to get that from bwolfe and burke
19:43:32 <djazayeri> wyclif: what liquibase changeset and/or ticket was it? does that help?
19:43:55 <bwolfe> about why we did calculated uuids? because we were generating the tables in a sql script
19:44:22 <wyclif> djazayeri, there is a custom changeset, an xml changeset and the ConceptReferenceTermSaveHandler
19:44:24 <djazayeri> instead of liquibase?
19:44:44 <wyclif> bwolfe, can't a sql script generate uuids
19:44:53 <bwolfe> if the conversion was done in a java changeset theres no reason not to use a standard uuid
19:45:02 <djazayeri> wyclif: what table exactly?
19:45:07 <bwolfe> not all DBs can generate uuids
19:45:15 <wyclif> bwolfe, hmm
19:45:29 <wyclif> djazayeri, concept_reference_term
19:47:07 <djazayeri> so, here's the changeset
19:47:08 <djazayeri> <changeSet id="20110301-1030k" author="wyclif">
19:47:08 <djazayeri> <preConditions onFail="MARK_RAN">
19:47:08 <djazayeri> <and>
19:47:08 <djazayeri> <not><sqlCheck expectedResult="0">SELECT count(*) FROM concept_reference_map</sqlCheck></not>
19:47:08 <djazayeri> <dbms type="mysql" />
19:47:09 <djazayeri> </and>
19:47:09 <djazayeri> </preConditions>
19:47:10 <djazayeri> <comment>Creating concept reference terms from existing rows in the concept_map table(For MySQL)</comment>
19:47:10 <djazayeri> <sql>
19:47:11 <djazayeri> INSERT INTO concept_reference_term (concept_reference_term_id, concept_source_id, code, description, creator, date_created, uuid)
19:47:11 <djazayeri> SELECT cm.concept_map_id, cm.source, cm.source_code, cm.comment, cm.creator, cm.date_created, CONCAT(crs.hl7_code, "-",cm.source_code)
19:47:12 <djazayeri> FROM concept_reference_map cm, concept_reference_source crs
19:47:12 <djazayeri> WHERE cm.source = crs.concept_source_id
19:47:13 <djazayeri> </sql>
19:47:13 <djazayeri> </changeSet>
19:47:35 <r_friedman> bwolfe: no sign of restws in either of my repositories -- I have 2, one that I put in a special place while installing maven standalone, the other got created while installing maven eclipse addons
19:48:17 <djazayeri> r_friedman: (surely you've done "mvn install" on the project, right? not just maven build, or mvn package?)
19:48:50 <r_friedman> djazayeri: clean install
19:48:59 <r_friedman> many times
19:49:04 <djazayeri> ok
19:49:25 <djazayeri> bwolfe, wyclif: it doesn't seem like the uuid there is meaningful
19:49:52 <bwolfe> r_friedman, can you create a patch of the changes you have to restws and put it on pastebin?
19:50:13 <djazayeri> so I guess we should switch this to autogenerate a uuid in the annoying old one-for-mysql and one-for-other-dbs approach
19:50:29 <r_friedman> bwolfe: i have no changes to restws, i only keep it around to clone from
19:51:01 <bwolfe> r_friedman, but you were mucking with versions in it...
19:51:07 <djazayeri> fwiw, the changeset's comment say "(For MySQL)"
19:51:15 <wyclif> djazayeri, this changest only runs for mysql, so it ok to switch to generate uuids for mysql
19:51:16 <r_friedman> no, only in the poms in my project, bwolfe
19:51:33 <djazayeri> wyclif: yes, I think so. bwolfe, do you agree?
19:51:40 <wyclif> djazayeri, then we edit the custom changeset to generate them via java
19:51:57 <wyclif> bwolfe, ?
19:51:58 <djazayeri> since saptarshi's work this changeset now has <dbms type="mysql"/>
19:52:10 <djazayeri> actually I don't think you even need another custom changeset.
19:52:14 <bwolfe> r_friedman, in your jss project?
19:52:22 <r_friedman> bwolfe: yes
19:52:22 <djazayeri> just switch the concat(…) to uuid()
19:52:24 <bwolfe> djazayeri, wyclif, yes, do that
19:52:46 <wyclif> djazayeri, so we dont need the custom changeset, right?
19:52:48 <bwolfe> wyclif, was there anything in code that generated the uuids like this? I /think/ it was only in the changeset, but I'm not certain
19:52:55 <wyclif> bwolfe, yes
19:53:14 <wyclif> i will have to remove that code from the ConceptReferenceTermSaveHandler
19:53:17 <djazayeri> wyclif: correct, if it currently only runs for mysql, it's okay to switch it to use uuid()
19:53:35 <djazayeri> bwolfe, wyclif, rafa: there's also this question about stuff happening at startup, and the daemon user.
19:53:39 <djazayeri> should we discuss now or not?
19:54:12 <bwolfe> wyclif, djazayeri, hmm, yes, I guess we can just add that
19:55:06 <rafa_> djazayeri: Burke is misssing and he's got opinions :)
19:55:18 <djazayeri> yeah, so maybe table this until tomorrow's design call
19:55:24 <djazayeri> and/or mail the dev list
19:55:49 <rafa_> djazayeri: godd. I didn't really look into the details of that.
19:56:12 <djazayeri> (the fact that we save the last executed timestamp in the db for scheduled tasks has only caused heartache and pain, btw)
19:56:38 <bwolfe> wyclif, the savehandler did it to? If we had it in code then there might have been a larger reason...
19:57:23 <r_friedman> ben, rafa: realized why my restws compile didn't work, i keep forgetting that selecting the node to compile from the tree does no good, you have to select it from inside the maven run config
19:58:08 <r_friedman> Could not resolve dependencies for project org.openmrs.module:JSSLab-omod:omod:1.0-SNAPSHOT: Failure to find org.openmrs.module:webservices.rest:jar:0.9-SNAPSHOT in http://mavenrepo.openmrs.org/nexus/content/repositories/public was cached in the local repository, resolution will not be reattempted until the update interval of openmrs-repo has elapsed or updates are forced
19:58:09 <r_friedman> ben, rafa_ so i set my POMs to 0.9-SNAPSHOT and ran against the compiled version and got the same message I got Sunday --
19:58:09 <OpenMRSBot> <http://ln-s.net/8-2X> (at mavenrepo.openmrs.org)
20:00:12 <rafa_> r_friedman: you need to run mvn -U clean install
20:00:40 <r_friedman> what is -U, and against what, rafa?
20:00:58 <rafa_> r_friedman: -U forces updates in local repository
20:01:14 <rafa_> r_friedman: run it against your module
20:01:58 <rafa_> r_friedman: (anyway I wonder why mvn clean install on wsrest didn't do that for you)
20:03:33 <rafa_> r_friedman: if it fails paste your omod pom.xml again
20:03:57 <r_friedman> rafa_ The only U option I could find in Eclipse was Update Snapshots and I selected it and now am back to the normal can't resolve dependencies bcs not in openmrs repo
20:06:01 <r_friedman> rafa_: bwolfe http://pastebin.com/yxAMNFVf
20:07:34 <r_friedman> rafa_: bwolfe sorry that's the main jsslab pom, try this one from the omod: http://pastebin.com/q9g6EXP4
20:10:18 * r_friedman tests connectivity
20:10:19 <rafa_> r_friedman, bwolfe I ran out of ideas, looks good to me
20:13:22 <bwolfe> r_friedman, the artifactId for the wsrest module omod is now webservices.rest-omod. the parent is just webservices.rest
20:15:20 <r_friedman> bwolfe: i'm sorry ben, i don't follow
20:15:38 <rafa_> bwolfe: ha! when did you change that? :)
20:16:00 <bwolfe> r_friedman, the dependencies in your pom point at just webservices.rest, not webservices.rest-omod
20:16:17 <r_friedman> bwolfe: ok, will change and try again
20:16:27 <bwolfe> I changed it last week. I sent an email to the dev list saying "I changed all the projects in my workspace". restws was one of them
20:16:45 <bwolfe> sorry r_friedman, I didn't think of this type of repercussion
20:17:26 <OpenMRSBot> Recent updates in the world of openmrs: On Twitter: OpenMRS: @MrMarkStewart Sorry about that - seems someone had a bit too much fun! We just ran the regular rebuild of the @OpenMRS demo & it's usable. <http://twitter.com/OpenMRS/statuses/144143822018969600>
20:19:42 <r_friedman> bwolfe: must have to do something more, it's still failing for inability to locate BaseCRUDController but somehow the error messages look different
20:21:55 <r_friedman> bwolfe: all the error flags are gone from my methods
20:22:13 <bwolfe> r_friedman, do a clean in eclipse?
20:22:25 <bwolfe> menu-->project-->clean
20:23:16 <r_friedman> bwolfe: cleaning... my last comment was wrong, plenty of errors in omod, i was looking at root
20:23:41 <r_friedman> bwolfe: how am i getting to your workspace anyway?
20:24:07 <bwolfe> r_friedman, to my workspace? huh?
20:24:30 <bwolfe> r_friedman, did you change the pom in both the parent and the omod projects in jss?
20:25:15 <r_friedman> yes, i changed both poms, clean did a lot of good, now i only have an error on the jsslab omod pom
20:26:07 <bwolfe> error on the pom just means its hiding other things
20:26:12 <bwolfe> edit error ?
20:26:27 <r_friedman> bwolfe: yes, it's all back again. here's this:
20:26:30 <r_friedman> Plugin execution not covered by lifecycle configuration: org.openmrs.maven.plugins:maven-openmrs-plugin:1.0.1:initialize-module (execution: default-initialize-module, phase: initialize)
20:27:11 <bwolfe> r_friedman, did your jss module ever work? or has it been compiling wrong from the start?
20:27:30 <r_friedman> bwolfe: never has compiled
20:27:49 <r_friedman> bwolfe: but only errors are referencing restws
20:28:52 <bwolfe> r_friedman, does it compile at commandline? if so, its an eclipse project error. perhaps the .project and .classpath files are missing in th eomod project?
20:31:07 <r_friedman> bwolfe: have both .project and .classpath in -api and -omod
20:33:21 <r_friedman> bwolfe: should i have both standalone and plugin maven installed? could they be confusing each other?
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20:35:14 <bwolfe> r_friedman, those shouldn't matter.
20:35:26 <bwolfe> I'm not sure what you mean by installed on those anyway
20:36:12 <r_friedman> bwolfe: need to do a phone call brb
20:41:29 <djazayeri> rafa: you there?
20:41:39 <rafa_> djazayeri: ye
20:41:49 <rafa_> s
20:42:10 <djazayeri> I looked at "measles" in my mvp dictionary (probably 6 months old) and noticed that one of the two measles concepts is retired.
20:43:10 <djazayeri> my dictionary doesn't have dups for pruritus or for preeclampsia
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20:43:55 <rafa_> hmm let me check them
20:44:03 <djazayeri> rafa: though both of my measles concepts seem to be retired when I search on MCL:search
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20:44:35 <djazayeri> rafa: perhaps the validation we're doing used to ignore dup names on retired concepts, but now catches them?
20:45:24 <rafa_> djazayeri: it might be a problem that names are acutally not voided
20:45:35 <rafa_> djazayeri: but concepts are?
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20:46:05 <djazayeri> rafa: might be
20:46:14 <djazayeri> I don't know how the validation code is written
20:46:35 <rafa_> ha that's right
20:46:43 <rafa_> I just run SQL queries
20:46:58 <rafa_> I have three concept_names with measles
20:47:07 <rafa_> none of them is voided
20:47:12 <djazayeri> the names or the concepts?
20:47:20 <djazayeri> I'm doing this
20:47:20 <djazayeri> select c.concept_id, c.retired, cn.name
20:47:21 <djazayeri> from concept c
20:47:21 <djazayeri> inner join concept_name cn on c.concept_id = cn.concept_id
20:47:21 <djazayeri> where lower(cn.name) like '%measles%'
20:47:29 <rafa_> have 3 concepts, 2 of which are retired
20:48:33 <rafa_> djazayeri: so it seems that we don't void concept_names when retiring concepts?
20:48:41 <djazayeri> rafa: intentionally no
20:48:51 <r_friedman> haha
20:48:52 <rafa_> djazayeri: and validators rely on that...
20:49:19 <rafa_> djazayeri: it's actually doesn't make sense not to void names since they can't be used by two concepts
20:49:32 <djazayeri> rafa: retire != void
20:49:46 <djazayeri> retire means stop using this going forwards, but past data may still refer to it
20:50:05 <rafa_> djazayeri: yeah sorry :P
20:50:44 <djazayeri> it appears that ConceptValidator skips retired concepts...
20:51:17 <djazayeri> but I do not really trust the code in ConceptValidator
20:51:17 <rafa_> it skips concepts but still tests for duplicate names
20:51:37 <rafa_> and does not check if they belong to retired concepts
20:51:40 <djazayeri> oh, you mean that if the concept itself is retired, it shouldn't be checking
20:51:49 <rafa_> yes
20:52:04 <rafa_> it makes sense I guess
20:52:12 <djazayeri> that seems to be the issue
20:52:33 <djazayeri> i.e. if concepts R and NR have the same name, and R is retired
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20:52:50 <djazayeri> you would want both validate(R) and validate(NR) to both pass
20:53:03 <djazayeri> however currently validate(NR) will pass, but validate(R) will fail
20:53:18 <djazayeri> rafa: that's how it's behaving now, right?
20:53:29 <rafa_> djazayeri: yes it seems like that
20:53:50 <djazayeri> okay, if you're inspired enough, you could add a one-liner for this, and restart your module for its overnight run
20:54:01 <djazayeri> otherwise we can look at it tomorrow
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21:03:41 <rafa_> djazayeri: seems like validate_shouldPassIfTheConceptWithADuplicateNameIsRetired is testing for that?
21:03:50 <rafa_> djazayeri: or am I too tired to thing clear?
21:04:55 <djazayeri> rafa: no, that one is doing a validate on the non-retired concept
21:05:05 <djazayeri> i.e. it's validate(NR)
21:05:55 * r_friedman checks connectivity
21:05:57 <rafa_> djazayeri: right
21:06:54 <djazayeri> I just tweaked that unit test around a bit, and got this failing one:
21:06:54 <djazayeri> @Test
21:06:55 <djazayeri> public void validate_shouldPassIfAnotherConceptHasADuplicateNameButThisConceptIsRetired() throws Exception {
21:06:55 <djazayeri> Context.setLocale(new Locale("en"));
21:06:55 <djazayeri> Concept concept = Context.getConceptService().getConcept(5497);
21:06:55 <djazayeri> String duplicateName = concept.getFullySpecifiedName(Context.getLocale()).getName();
21:06:55 <djazayeri>
21:06:56 <djazayeri> Concept anotherConcept = Context.getConceptService().getConcept(5089);
21:06:56 <djazayeri> anotherConcept.getFullySpecifiedName(Context.getLocale()).setName(duplicateName);
21:06:57 <djazayeri> anotherConcept.setRetired(true);
21:06:58 <djazayeri> Errors errors = new BindException(anotherConcept, "concept");
21:06:58 <djazayeri> new ConceptValidator().validate(anotherConcept, errors);
21:06:59 <djazayeri> Assert.assertEquals(false, errors.hasErrors());
21:06:59 <djazayeri> }
21:07:16 <rafa_> djazayeri: what a pleasure to read :)
21:07:29 <rafa_> djazayeri: do we want to validate retired concepts at all?
21:07:54 <djazayeri> I think we do want to validate them for internal consistency, but not to compare them against other concepts
21:08:43 <djazayeri> I'll create a ticket, but if you want to temporarily put a one-liner in ConceptValidator that just returns no errors for any retired concept, and re-run your script, the results for that would be interesting to run overnight
21:09:29 <rafa_> yes, I'll do that
21:09:45 <djazayeri> rafa: btw, note
21:09:51 <djazayeri> !ticket TRUNK-2319
21:09:52 <OpenMRSBot> djazayeri: [#TRUNK-2319] A feature to validate all concept in the database, to ensure they are all legal - OpenMRS JIRA - https://tickets.openmrs.org/browse/TRUNK-2319
21:10:00 <djazayeri> you may have just done this :-)
21:10:32 <rafa_> djazayeri: yep :D
21:10:40 <rafa_> djazayeri: It's just that we have it as a module
21:10:48 <djazayeri> rafa: as a module seems fine to me
21:17:28 <djazayeri> created as TRUNK-2921
21:19:01 <rafa_> !ticket TRUNK-2921
21:19:02 <OpenMRSBot> rafa_: [#TRUNK-2921] ConceptValidator should not compare names of a retired concept against the names of other concepts - OpenMRS JIRA - https://tickets.openmrs.org/browse/TRUNK-2921
21:19:05 <rafa_> djazayeri: thanks
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21:30:29 <r_friedman> bwolfe: any more ideas?
21:31:57 <bwolfe> r_friedman, try running maven at command line in those the main folder. if it works there then its an eclipse problem
21:32:19 <r_friedman> bwolfe: how do i do that?
21:32:33 <bwolfe> install maven2 (mvn)
21:32:35 <bwolfe> go to the dir
21:32:39 <bwolfe> run "mvn clean install"
21:33:15 <r_friedman> what dir?
21:33:53 <bwolfe> the restws project dir
21:34:12 <bwolfe> somehow you aren't getting restws into your local maven repo and so your jss isn't finding it
21:34:12 <r_friedman> where's that?
21:34:24 <bwolfe> or maybe its just a jss compilation issue
21:34:32 <bwolfe> r_friedman, wherever you defined your eclipse workspace
21:34:49 <bwolfe> in windows I think the default is docsandsettings/username/workspace
21:34:49 <r_friedman> ok
21:34:53 <bwolfe> (not in my documents)
21:40:50 <r_friedman> bwolfe: compiled OK but had test erros
21:41:13 <bwolfe> r_friedman, which one?
21:41:18 <r_friedman> restws
21:41:28 <r_friedman> omod
21:41:40 <bwolfe> if it has test errors then it is not installing
21:41:48 <bwolfe> why are tests failing in it?
21:41:56 <bwolfe> I thought you didn't change the module? ;-)
21:42:09 <r_friedman> bwolfe: no, you changed the module :-)
21:42:20 <bwolfe> ha
21:42:29 <bwolfe> svn update on the root?
21:42:34 <bwolfe> r_friedman, tests pass for me...
21:43:00 <r_friedman> bwolfe: ok, will do svn update
21:47:38 <bwolfe> r_friedman, enough debugging from me for the night almost 1am. ttyl
21:48:04 <r_friedman> bwolfe: tks, maybe we'll chat tomorrow
21:48:16 <r_friedman> bwolfe: gotta keep you tired out, don't want any more kids
21:48:28 <bwolfe> too late
21:48:46 <bwolfe> and the 6000 miles between me and my wife make sure of that too
21:49:03 <r_friedman> would take quite a shot
21:49:09 <dkayiwa> only 6000?
21:49:12 <dkayiwa> :)
21:49:43 <dkayiwa> bwolfe: compare with my 10 metres :)
21:49:55 <r_friedman> is that erect or flaccid?
21:51:33 <r_friedman> bwolfe: all the tests are failing because it can't find the rest service
21:52:46 <r_friedman> bwolfe: ollerTest): Service not found: interface org.openmrs.module.webservices.rest.web.api.RestService
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21:53:33 <r_friedman> hah drove him away!!
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