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05:52:57
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<irfn> Hi all
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05:53:40
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<irfn> anyone faced MySQLIntegrityConstraintViolationException: Column 'uuid' cannot be null
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05:53:48
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<irfn> while using openmrs api jar
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06:01:47
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06:05:21
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<irfn> @bwolfe while using openmrs api jar i get Column 'uuid' cannot be null
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06:05:32
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<irfn> constraint voilation
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06:05:42
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<bwolfe> irfn, how are you using it?
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06:05:52
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<bwolfe> for which object?
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06:06:07
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<irfn> userService.saveUser(user, "Openmr5xy");
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06:06:35
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<irfn> i see this kind of code in the openmrs unit tests
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06:06:53
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<irfn> i have practically just copied this from unit test code
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06:07:06
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<irfn> i want to use the openmrs api jar
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06:07:15
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<irfn> 1.8
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06:08:01
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<irfn> i am able to call api correctly for reading records
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06:08:19
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<irfn> such as userService.getUserByUsername("admin")
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06:08:23
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<irfn> works as expected
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06:08:32
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<irfn> all the saves to db
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06:08:43
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<irfn> for any object are failing with same exceptions
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06:09:10
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<irfn> database is essentially a blank installation of openmrs
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06:11:30
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<irfn> bwolfe, any ideas
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06:44:51
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<irfn> bwolfe: i am still stuck with the issue :(
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06:45:34
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<bwolfe> irfn, did you answer my questions? seems I got disconnected before I saw them
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06:45:45
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<bwolfe> last thing I see in my logs is my link to the "how to use the api" page
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06:45:57
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<irfn> oops
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06:46:01
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<irfn> i didnt see that one
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06:46:21
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<irfn> ill paste what i think u missed out
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06:46:28
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<irfn> userService.saveUser(user, "Openmr5xy");
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06:46:29
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<irfn> irfn
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06:46:29
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<irfn> i see this kind of code in the openmrs unit tests
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06:46:30
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<irfn> irfn
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06:46:32
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<irfn> i have practically just copied this from unit test code
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06:46:34
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<irfn> irfn
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06:46:36
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<irfn> i want to use the openmrs api jar
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06:46:38
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<irfn> irfn
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06:46:40
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<irfn> 1.8
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06:46:42
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<irfn> irfn
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06:46:44
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<irfn> i am able to call api correctly for reading records
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06:46:46
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<irfn> irfn
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06:46:48
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<irfn> such as userService.getUserByUsername("admin")
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06:46:50
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<irfn> irfn
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06:46:52
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<irfn> works as expected
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06:46:54
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<irfn> irfn
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06:46:56
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<irfn> all the saves to db
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06:46:58
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<irfn> irfn
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06:47:00
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<irfn> for any object are failing with same exceptions
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06:47:02
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<irfn> irfn
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06:47:04
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<irfn> database is essentially a blank installation of openmrs
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06:47:06
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<irfn> 11:41 irfn
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06:47:07
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<bwolfe> I got tall fo that
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06:47:08
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<irfn> bwolfe, any ideas
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06:47:12
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<bwolfe> *I got all of that
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06:47:22
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<bwolfe> irfn, so any call to any save method is giving you that error?
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06:47:22
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<bwolfe> did you start the transactions correctly?
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06:47:23
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<bwolfe> https://wiki.openmrs.org/display/docs/How+To+Use+the+OpenMRS+API
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06:47:24
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<bwolfe> did you see that?
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06:47:30
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<OpenMRSBot> <http://ln-s.net/9CYJ> (at wiki.openmrs.org)
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06:47:48
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<irfn> yes
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06:48:08
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<irfn> i am able to make calls that read data from db
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06:48:18
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<irfn> but not the ones that write data to db
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06:57:21
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<irfn> is it possible that Context isnt wired up with all necessary handlers
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06:57:36
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<bwolfe> irfn, probably
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06:57:52
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<bwolfe> irfn, was your "yes" meaning that you have seen that wiki page?
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06:57:57
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<bwolfe> you have to do an open session
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06:58:00
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<bwolfe> and a close session
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06:58:07
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<irfn> i have done that
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06:58:09
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<bwolfe> and make sure that all the right spring application context files are started
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06:58:16
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<irfn> eh
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06:58:24
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<irfn> what does that mean
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07:00:42
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<irfn> bwolfe: i have a sample code at https://github.com/irfn/openmrs-api-example
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07:01:20
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<bwolfe> irfn, can you link me right to your openmrs api startup code?
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07:01:38
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<bwolfe> (sorry, am on a slow connection and am trying to pay attention to the training I'm currently in) :-)
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07:01:50
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<irfn> its very similar to this https://github.com/irfn/openmrs-api-example/blob/master/src/main/java/org/openmrs/api/example/Example.java
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07:01:57
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<OpenMRSBot> <http://ln-s.net/9CYO> (at github.com)
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07:02:41
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<irfn> except i am doing
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07:02:45
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<irfn> User user = new User();
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07:02:45
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<irfn> user.setPerson(new Person());
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07:02:45
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<irfn> user.addName(new PersonName("Benjamin", "A", "Wolfe"));
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07:02:47
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<irfn> user.setUsername("bwolfe");
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07:02:49
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<irfn> user.getPerson().setGender("M");
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07:02:51
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<irfn> user.getPerson().setPersonDateCreated(new Date());
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07:02:53
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<irfn> userService.saveUser(user, "Openmr5xy");
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07:03:26
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<bwolfe> irfn, yeah, that code is ok. its all about whether the hibernate interceptor and the aop classes are set up right
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07:03:48
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<irfn> how do i ensure that
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07:04:00
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<bwolfe> irfn, whats in your startup method?
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07:04:11
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<bwolfe> (from the code you just linked me to)
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<irfn> logger.warn(format("connecting to openmrs instance at %s", url));
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07:04:36
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<irfn> Properties properties = new Properties();
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07:04:36
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<irfn> properties.setProperty(AUTO_UPDATE_DATABASE_RUNTIME_PROPERTY, String.valueOf(true));
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07:04:37
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<irfn> String path = getClass().getClassLoader().getResource("openmrs-data").toURI().getPath();
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07:04:39
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<irfn> logger.warn(format("openmrs data folder is set to %s", path));
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07:04:41
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<irfn> properties.setProperty(APPLICATION_DATA_DIRECTORY_RUNTIME_PROPERTY, path);
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07:04:43
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<irfn> startup(url, user, password, properties);
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07:04:45
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<irfn> openSession();
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07:04:47
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<irfn> authenticate(openmrsUser, openmrsPassword);
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07:04:49
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<irfn> logger.warn(format("loaded %d modules", ModuleFactory.getLoadedModules().size()));
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07:05:17
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<irfn> essentially just
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07:05:18
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<irfn> startup(url, user, password, properties);
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07:05:24
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<irfn> openSession();
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07:05:30
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<irfn> authenticate(openmrsUser, openmrsPassword);
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07:05:59
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<bwolfe> oh, you're doing a static import of Context methods?
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07:06:00
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<bwolfe> boo
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07:06:09
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<irfn> hehe
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07:06:12
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<bwolfe> makes code less readable for me :-p
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07:06:18
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<irfn> sorry if that was confusing
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07:08:28
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<bwolfe> ok, so you're calling the openmrs startup methods
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07:09:41
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<irfn> i am
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07:10:33
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<irfn> could it be related to the idgen.omod in any way
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07:10:58
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<bwolfe> I dunno
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07:11:01
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<bwolfe> are you loading that in as well?
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07:11:09
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<bwolfe> try without any modules (other than logic)
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07:11:44
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<irfn> ok ill try
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07:12:56
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<irfn> doesnt work
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07:13:02
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<irfn> same issue Column 'uuid' cannot be null
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07:13:17
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<irfn> even when i explicitly setUuid
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07:13:36
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<bwolfe> ha
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07:13:42
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<bwolfe> now thats even weirded
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07:13:51
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<bwolfe> it says no uuid for the user?
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07:14:11
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<irfn> could not insert: [org.openmrs.Person]
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07:14:24
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<irfn> : Column 'uuid' cannot be null
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07:14:30
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<bwolfe> hmm, so its not putting the uuid on the person object
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07:14:39
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<bwolfe> this might be a bug
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07:14:48
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<bwolfe> although it works in the unit test??
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07:15:03
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<irfn> i see that unitest in openmrs codebase
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07:15:03
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<bwolfe> irfn, trying creating/saving something simple like an EncounterType to see if it saves the uuid for you
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07:15:09
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<bwolfe> irfn, which class?
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07:15:12
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<bwolfe> UserServerTest?
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07:15:16
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<bwolfe> *Service
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07:15:42
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<irfn> UserServiceTest
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07:15:44
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<irfn> yes
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07:15:47
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<bwolfe> ok, I see that
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07:15:49
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<bwolfe> very strange
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07:16:04
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<bwolfe> irfn, try with an encountertype
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07:16:11
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<irfn> ok
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07:20:49
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<irfn> ok bwolfe, just did
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07:20:52
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<irfn> EncounterType encounterType = new EncounterType("foo", "bar");
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07:20:52
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<irfn> encounterType.setDateCreated(new Date());
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07:20:52
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<irfn> encounterType.setCreator(userService.getUserByUsername("admin"));
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07:20:53
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<irfn> encounterService.saveEncounterType(encounterType);
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07:21:08
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<irfn> i get same error
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07:21:20
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<bwolfe> hmm
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07:21:29
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<irfn> onstraintViolationException: could not insert: [org.openmrs.EncounterType]
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07:21:36
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<bwolfe> so the RequiredDataAdvice interceptor is not getting called
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07:21:37
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<irfn> Column 'uuid' cannot be null
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07:21:43
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<irfn> oh ok
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07:21:47
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<bwolfe> very strange
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07:21:55
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<irfn> hmm
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07:21:58
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<bwolfe> the applicationContext-service.xml spring config file is supposed to set that on all services
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07:22:13
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<irfn> i am getting all the services
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07:22:19
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<bwolfe> and the Context.startup() is calling that
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07:22:24
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<irfn> yes
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07:23:00
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<irfn> anyways thanks bwolfe
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07:23:17
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<irfn> will keep u posted on if i find any solution
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07:23:21
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<bwolfe> irfn, ok
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07:23:55
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<bwolfe> irfn, if you're good with debugging you might want to check to see what interceptors are called around those save methods. you can tell from the stacktrace
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<irfn> we should push source zip's for api jar to maven repo
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08:08:51
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<irfn> for ide integration
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08:09:16
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<irfn> Intellij offers to download zipped source from maven repo
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12:08:51
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<surangak> hi james_regen
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12:09:02
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<surangak> james_regen, you're really early, right :-)
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12:10:56
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<bwolfe> 8am isn't that early
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12:11:10
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<bwolfe> I think james usually gets to the office at 7am
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12:12:55
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<surangak> bwolfe, 7 am ?? wow, Im usualy in by 8 am, but thats only becoz I wanna do downloads :P
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12:13:27
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<surangak> one of these days Im gonna get caught :-)
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12:13:43
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<bwolfe> who says you haven't been caught already?
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12:13:51
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<bwolfe> this channel is publicly logged you know ;-)
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12:13:52
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<james_regen> hi surangak. i'm here before the other people who sit around me
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12:14:04
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<surangak> bwolfe, :D
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12:14:19
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<surangak> james_regen, good morning !
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12:14:26
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<surangak> james_regen, same here :-)
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12:14:45
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<surangak> james_regen, r u busy ?
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12:15:18
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<james_regen> i can answer any questions you have. i don't have any meetings this morning
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12:15:32
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<surangak> james_regen, thats great... let me go in point form...
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12:16:41
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<surangak> james_regen, 1. Im thinking that the MI should be calculated before the record linkage process is run, because we r going to need the MI values to determine the scores...
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12:17:07
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<surangak> james_regen, therefore, I put the check box on the sessions tab...
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12:18:55
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<surangak> dkayiwa, thanks, that was a really old bug you closed :-)
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12:19:19
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<dkayiwa> more to you for fixing it surangak :D
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12:20:29
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<james_regen> surangak: so at what time will it be run with the check box?
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12:21:18
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<surangak> james_regen, when the user clickes on the 'run linkage process' button, itll check if the check box was ticked, and work accordingly...
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12:21:26
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<surangak> james_regen, is that behavior correct ?
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12:23:17
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<james_regen> i think it'd be easiest to add a button on the analysis tab. 'run linkage process' starts something that the user doesn't interact with. it uses the existing m and u values to score pairs and write the results to a file. if MI is calculated as part of that, i don't think there's an opportunity to inform the user how to modify anything
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12:24:27
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<james_regen> also, i'm not clear on how MI will be used. some things, like entropy of a field, doesn't directly result in values being changed in the program. it does let the user know, maybe, that a field is useless, and to not waste time and effor including in
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12:25:12
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<surangak> james_regen, give me a minue to think on that ....
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12:25:27
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<james_regen> this contrasts with something like random sampling, which directly calculates new u-values to use, meaning the results are stored and things change. do you know if MI will be descriptive and informative, or if it'll be a calculation that modifies something?
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12:28:09
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<surangak> james_regen, there are two ways we can use the MI score. a) if the user knows the MI score, he can decide which columns to include / block on. or b) the user is not told the MI score, but it it used to score pairs...
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12:29:20
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<james_regen> ok, i wasn't aware of option b. in that case, the score would be shifted, depending on the MI analysis results?
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12:30:04
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<surangak> james_regen, yeps, thats what I had in mind....
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12:30:22
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<surangak> james_regen, based on what Dr. Shaun told me..
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12:30:57
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<james_regen> that makes sense, we've done something like that before.
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12:31:12
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<surangak> as in, is column A and b match, we score 2 points. But if their MI value is high, then we should not score 2 points, but lower, because they're already similar
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12:32:25
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<surangak> james_regen, does this match with what u had in mind ?
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12:33:23
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<james_regen> the first idea that comes to mind is to keep the checkbox, but make it an option like "Use analysis results to modify scores" the analysis and creating the object that modifies the score can be done previously, so the results can inform the user, and i fthe results aren't as useful as expected, it doesn't have to be a part of the scoring process
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12:35:59
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<surangak> james_regen, sorry, didnt get that properly... u mean that the MI calculation should take place before the "Run linkage process' and that scored are modified based on the usuful ness of the results generated, it is ?
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12:38:22
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<james_regen> the analysis panel is a mess in the program, but it's kind of the place where things that do math are placed. i think MI can be calculated from a button there, and the user can see the output. thse results can be saved. if the user wants to use the MI results to modify the scores, then the checkbox you've added already can be selected.
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12:39:05
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<surangak> james_regen, ah, I get it...
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12:39:11
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<surangak> will do it that way...
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12:40:11
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<surangak> james_regen, you referrd to the 'check box' mmm.......... where should I have that ?
|
12:42:04
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<james_regen> i think it makes sense in the "Linkage Process" group of options, along with "perform grouping" and "include XML"
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12:42:28
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<surangak> james_regen, I get it.. will do that way....
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12:43:10
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<james_regen> there's a simple framework for modifying the scores. there's no exposed way in the GUI to use it, though. this will make it possible, though.
|
12:43:33
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<surangak> james_regen, the analysys tab is a place for us to run math tests on the data after the scoring has been done right ?
|
12:44:02
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<surangak> ah, mm.. can u remember the name of the score modification class ? that'd be really helpful....
|
12:44:43
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<james_regen> in the analysis package, there's a Modifier interface.
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12:44:57
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<james_regen> i'm trying to find an example of where it's used . . .
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12:45:34
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* surangak is excited...
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12:46:45
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<james_regen> there's ScaleWeightModifier. it's older code, and it's a bit messy, and a lot of the stuf fin the constructor and other methods probably no longer apply
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12:47:09
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<james_regen> the getModifiedMatchResult method looks to be helpful, though
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12:48:03
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<surangak> james_regen, thanks a lot... Ill be working on this today...
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12:48:16
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<surangak> james_regen, there will be something for you to look at tomorrow :-)
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12:48:51
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<james_regen> it adjusted the score based on the frequency of the value in the records. so if the records had a common name, the score went down, a rare name, the score went up. ScaleWeightAnalyzer was used to make it. that's also more complcated than it needs to be, i think, and more complicated than what you should end up writing
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12:50:12
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<surangak> james_regen, and thus we return to the hardest part, the math...
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12:50:41
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<surangak> james_regen, I've been trying out things, not much progress, but definitely getting somewhere...
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12:51:30
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<james_regen> yeah, it's easy doing something, not so easy doing the right thing. at least you should be able to get your objects made, get it working in the right places, and if the numbers are a bit wrong, it's just going back to fix a bit of code
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12:53:35
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<surangak> james_regen, yep, ill have to do some designing too.. but we'll ultimately get there, I guess
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13:03:09
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<surangak> james_regen, would it help if I write up the math equation stuff, my planned solution, and have it on a wiki page, so that people can ckeck it out if they like ?
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13:04:46
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<james_regen> it couldn't hurt. providing a simple test case, expected results, and eventually results from the code would provide evidence we're doing it correctly
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13:05:42
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<surangak> james_regen, yeps, I'll do that
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13:05:54
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<surangak> james_regen, thanks for everything, you've been a great help... :-)
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<james_regen> no problem
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14:11:25
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<rafa> hey bwolfe, wluyima
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14:11:46
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<bwolfe> hi rafa
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14:11:56
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<rafa> scrum?
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14:11:59
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<bwolfe> I'm about to sign off so I can drive home. were you starting the scrum?
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14:12:03
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<bwolfe> ah yes
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14:12:06
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<bwolfe> where is daniel?
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14:12:16
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<bwolfe> rafa, you can copy yours in
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14:12:21
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<bwolfe> I only have about 5 mins!
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14:12:23
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<rafa> *** Rafal ***
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14:12:23
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<rafa> Today:
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14:12:23
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<rafa> * Continued to work on TRUNK-2710: Create Encounters by Visit portlet
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14:12:23
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<rafa> https://tickets.openmrs.org/browse/TRUNK-2710
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14:12:23
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<rafa> QUESTION: Do I need to replace the Visits Tab on the Patient Dashboard with this new Encounters By Visits Tab?
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14:12:24
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<rafa> Tomorrow:
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14:12:24
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<rafa> * Finish TRUNK-2710
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14:12:25
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<rafa> No blockers.
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14:12:47
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<wluyima> hi
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14:14:08
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<bwolfe> rafa, your mockup looks better. I'd say "yes, replace it"
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14:14:31
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<bwolfe> wluyima, can you paste in your scrum log quickly?>
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14:14:32
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<bwolfe> :-)
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14:14:39
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<rafa> it's Darius who made the mockup ;)
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14:14:47
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<rafa> I'll confirm with him too
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14:15:53
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<bwolfe> rafa, commit first, ask questions later ;-)
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14:16:13
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<wluyima> today:
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14:16:13
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<wluyima> - TRUNK-2447 - Add Show Verbose to the new jquery search widgets
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14:16:13
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<wluyima> - Created TRUNK-2712 - Encounter form is broken
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14:16:13
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<wluyima> - TRUNK-2717 - Display a meaningful message when a scheduled task with no repeat interval fails to start
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14:16:13
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<wluyima> - TRUNK-2099 - Update Concept Index task should be able to pick up where it left off if it's interrupted
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14:16:14
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<wluyima> today:
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14:16:16
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<wluyima> TRUNK-2716 - Cannot submit an encounter form
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14:16:18
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<wluyima> - other Sprint tickets
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14:16:24
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<rafa> bwolfe: hmm if you say so :D
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14:16:59
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<wluyima> TRUNK-2717 - Created it, didn't work on it
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14:18:35
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<rafa> !ticket trunk-2717
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14:18:36
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<OpenMRSBot> rafa: [#TRUNK-2717] Display a meaningful message when a scheduled task with no repeat interval fails to start - OpenMRS JIRA - https://tickets.openmrs.org/browse/trunk-2717
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14:19:20
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<rafa> !ticket trunk-2712
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14:19:21
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<OpenMRSBot> rafa: [#TRUNK-2712] Encounter form is broken - OpenMRS JIRA - https://tickets.openmrs.org/browse/trunk-2712
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14:20:16
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<rafa> wluyima: 2712 would help me out with my ticket too :)
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14:22:17
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<rafa> wluyima: I need to enter test encounters with SQLs :/
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14:22:39
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14:24:19
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<wluyima> !ticket TRUNK-2712
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14:24:20
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<OpenMRSBot> wluyima: [#TRUNK-2712] Encounter form is broken - OpenMRS JIRA - https://tickets.openmrs.org/browse/TRUNK-2712
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14:24:30
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<wluyima> ok i will work on it
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14:24:50
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<rafa> thanks in advance :D
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14:24:58
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<wluyima> acttualli will start with that
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14:25:06
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<rafa> cool
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14:25:21
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<wluyima> rafa, have you managed to reproduce the bug?
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14:25:39
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<rafa> wluyima: yes
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14:25:51
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<rafa> wluyima: it fails as you described
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14:28:26
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<dkayiwa> hi rafa
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14:28:37
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<rafa> hi dkayiwa
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14:28:45
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<dkayiwa> did you guys scrum?
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14:28:52
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<rafa> yes, a moment ago
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14:29:00
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<dkayiwa> oh sorry i missed that
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14:29:19
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<rafa> you can have a look at IRC logs :)
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14:29:46
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<dkayiwa> i had a network problem. and my other sim card which serves as backup had its credit expired
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14:29:46
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<dkayiwa> :)
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14:29:52
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<dkayiwa> just rushed to a shop and renewed it :)
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<rafa> haha
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14:31:11
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<rafa> I do the same when needed :)
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<rafa> but mostly while travelling
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<dkayiwa> lolll
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<wluyima> hi dkayiwa
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14:41:56
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<dkayiwa> hi wluyima
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17:33:53
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<Suranga> downeym, Hi michael
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17:34:04
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<Suranga> downeym, Got a minute ? :-)
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17:34:14
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<downeym> Suranga: I have 2 :)
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17:34:52
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<Suranga> downeym, I ment to ask about that presentation proposal I made for the conference
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17:35:16
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<Suranga> I wanted to ask you earlier, but I was too busy running aroud over the past few days :-(
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17:35:30
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<downeym> Suranga: looked good to me.
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17:35:51
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<downeym> Suranga: when do you arrive at the conference?
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17:35:57
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<Suranga> downeym, how should we plan for it ? that is, are they going to ask me to do it or... how prepared should I be ?
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17:35:59
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<Suranga> on the 9th
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17:36:27
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<downeym> Suranga: if you want to find me before things get started we can talk about it ⦠don't worry too much. :) also most of the mentors will be there and could help you understand how best to demo some of the other projects
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17:37:10
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<Suranga> downeym, Actually I was thinking of planning right away :P
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17:37:13
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<downeym> Suranga: what might be cool is to try to get volunteer mentors to all come to the same session and demo their own stuff :)
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17:37:22
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<downeym> and you can be the leader or moderator of the conversation
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17:37:48
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<Suranga> downeym, mm.. would I need any slides etc ?
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17:38:05
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<downeym> if you want. might be cool to do an overview of GSoC for the people who don't know about tit
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17:38:16
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<downeym> then maybe some demos, then Q&A ?
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17:38:34
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<downeym> i think the sessions will be 90 minutes this year so there's plenty of time to be relaxed
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17:39:59
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<Suranga> downeym, 90 minutes ?
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17:40:06
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<Suranga> wow, I better start reading up right awayyy
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17:40:22
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<downeym> Suranga: that's why i think it'd be good to get several people involved, so you don't have to do all the work
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17:40:30
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<downeym> at an unconference, there is really not a formal presentation usually
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17:40:43
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<Suranga> downeym, ah, I get it
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17:40:48
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<downeym> and lots of questions and conversation
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17:41:03
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<downeym> since there are several days, you could plan to go later in the event so you get the feel for how they go :)
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17:41:12
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<Suranga> downeym, I see
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17:42:03
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<Suranga> downeym, when will u be arriving ?
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17:42:15
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<downeym> i think i'll arrive the 9th too
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17:42:44
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<downeym> will probably hang around the hackathon on the 10th and do some helping with set up of the conference rooms
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17:42:56
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<downeym> we're going to *try* to do some live video streaming
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17:43:32
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<Suranga> downeym, :-O
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17:43:50
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<Suranga> downeym, Im not sure if network connections are that good in our countries :p
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17:44:12
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<downeym> Suranga: yeah ⦠we'll see about the place. we have some dedicated internet connectivity being donated
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17:44:45
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<downeym> will be trying the system used by barcamp nairobi which seemed to work pretty good there
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17:46:08
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<Suranga> downeym, that will be awesommeee
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17:46:23
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<downeym> http://www.livestream.com/OpenMRS
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