Move code from jpa to key branch of new main #7

garrettlew · 2021-03-09T18:06:52Z

Set patient id back to 0 as the default
Pass composite key to ebean
Sql: set patient id back to asc
Generate patient id in the application
Gets the largest patient id
adds 1 to it and makes that the new patient's id
this patient can now be passed around and inserted into the table
ZZS-70

ZZS-70

elenarfowler

the scala tests are currently failing, so we should fix those before merge
this doesn't look like it will work with patient matching query

elenarfowler · 2021-03-09T21:52:16Z

app/femr/data/daos/system/PatientRepository.java

@@ -268,7 +269,8 @@ public IPatient retrievePatientById(Integer id) {

            RawSql rawSql = RawSqlBuilder
                    .parse(sql)
-                    .columnMapping("id", "patient.id")
+                    .columnMapping("id", "patient_id")


The column mappings for id and kit id do not work with the new key, you need to use patient.patientKey...

elenarfowler · 2021-03-09T21:55:23Z

app/femr/data/daos/system/PatientRepository.java

+                savedSafely = true;
+            } catch (io.ebean.DuplicateKeyException ex) {
+                // id must have just been taken, try again
+                System.out.println("duplicate key exception, try to get a valid id again");


If this is an error message you should use log not println

It's not totally an error as this case is just when two devices running on the same try to add a patient at the same time. This is basically a bottle neck to make sure each time a patient is added, each patient gets assigned a unique patient id (for the kit its on). I can change it to a log though, since that makes sense whether or not this is an error. Do we have a logger though?

yes there is a logger

elenarfowler · 2021-03-09T21:56:41Z

app/femr/data/daos/system/PatientRepository.java

+        Optional<Patient> maxIdPatient;
+        Boolean savedSafely = false;
+        while (!(savedSafely)) {
+            try {


this is a lot of logic for one function, maybe we should split this up so the queries especially are in their own functions

like line 356 to 373 should be pulled out

There is only one query here: lines 360 to 364 to get back the largest patient id for that kit. So I could move the query to its own new supportive function, but lines 356 to 373 is basically the whole function.

right, it should be pulled out into one or maybe two

elenarfowler · 2021-03-09T21:59:37Z

app/femr/data/models/mysql/Patient.java

-        return id;
+        return patientKey.getPatientId();
+    }
+


setters and getters for kit id are missing, if you include them for id then you should include them for kit id too

elenarfowler · 2021-03-09T22:01:12Z

app/femr/data/models/mysql/RankedPatientMatch.java

@@ -7,7 +7,11 @@
 @Sql
 public class RankedPatientMatch implements IRankedPatientMatch {

-    @OneToOne
+    @OneToOne //(fetch = FetchType.EAGER)


remove these comments

Ya this is a work in progress. If you look at patientEncounter, one of its member variables is patients. I was hoping what worked in patientEncounter would also work with RankedPatientMatch class.

elenarfowler · 2021-03-09T22:02:31Z

app/femr/data/models/mysql/keys/PatientKey.java

+    /**
+     * Getter for patient id.
+     *
+     * @return int patient id is the number patients are assigned for identification


this comment is misleading, patients are not uniquely identifiable anymore just by id

elenarfowler · 2021-03-09T22:04:16Z

conf/evolutions/default/4.sql

  `first_name` VARCHAR(255) NOT NULL ,
  `last_name` VARCHAR(255) NOT NULL ,
  `age` INT NOT NULL ,
  `sex` VARCHAR(10) NOT NULL ,
  `address` VARCHAR(255) NOT NULL ,
  `city` VARCHAR(255) NOT NULL ,
-  PRIMARY KEY  (`id`) ,
+  PRIMARY KEY  (`id`, `kit_id`) ,
  UNIQUE INDEX `id_UNIQUE` (`id` ASC))
 DEFAULT CHARACTER SET = utf8;


dont we usually want to create a new evolutions file for db changes? if we were to push this the existing kits would have to rebuild starting at this evolution instead of only adding the new one

Ya I believe you are right. These changes happened before we understood evolutions. I can go back and make new sql files.

elenarfowler · 2021-03-09T22:10:53Z

app/femr/data/daos/system/EncounterRepository.java

@@ -48,10 +49,11 @@ public IPatientEncounter createPatientEncounter(int patientID, DateTime date, in


        try{
-
+            // testing


this comment doesn't provide info about what would need to change for not testing

This was just here because I'm not sure if I should be creating this patientKey here or maybe instead I should pass one in from patient Item or something

elenarfowler · 2021-03-09T22:11:13Z

app/femr/data/daos/system/PatientRepository.java

        }

+        //io.ebean.DuplicateKeyException
+
        return patient;


general note for this file, there is a get patient by id function. This may now return more than one patient since they are not uniquely identified by id anymore. There should also be a function for get patient by kek

Ya i think you mean get patient by id will need to be changed to get patient by id and kit id?

no, we need get by id for the search bar, so we need to make sure we can handle getting multiple patients back. it would also make sense to have a get by key, but we still need get by id for search bar

elenarfowler · 2021-03-09T22:12:19Z

app/femr/data/models/mysql/keys/PatientKey.java

+        this.kitId = kitId;
+    }
+
+    public PatientKey() {}


is this needed?

To create a compound key in ebean, an embeddable key is required. This is the class for the embeddable key which represents a patients primary compound key. So I would say this is needed. The other option for a compound key is to do something like @IdClass, but ebean doesn't support that sadly. If it did, that would have been way easier because it wouldn't require a new class and key object.

Program doesn't crash because commented out onetoone columnMapping uses patient.patient_id etc. Add join columns to RankedPatientMatch to reference compound key Use logger Add kit id setter and getters Change patientKey comments Remove un-needed constructor Split savePatient into smaller functions ZZS-70

Add transitionary class CompoundKeyRankedPatientMatch that goes in place of RankedPatientMatch which includes the new kit id to map to. Then these objects are used to create a list of mapped matches which are used to create a list of RankedPatientItems that are displayed in the UI matches. The new class shouldn't be a long term solution and is just to get the feature under test as it just takes all the attributes from rankedpatientmatch and patient and puts them in a class to map the sql database too. ZZS-96

Add kitId as an attribute Add getters and setters ZZS-101

Move code from jpa to key branch of new main

1b3ffed

ZZS-70

garrettlew requested a review from elenarfowler March 9, 2021 18:09

elenarfowler reviewed Mar 9, 2021

View reviewed changes

garrettlew force-pushed the key branch from 9fd5bde to e8adfd3 Compare March 13, 2021 06:25

garrettlew added 6 commits April 6, 2021 10:44

Possibly fixed column mapping but response is a list of null patients

afd012a

trying stuff

3139600

Fix complilation error

8510590

add comment

1142887

Add kitId to PatientItem

51b7327

Add kitId as an attribute Add getters and setters ZZS-101

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Move code from jpa to key branch of new main #7

Move code from jpa to key branch of new main #7

garrettlew commented Mar 9, 2021

elenarfowler left a comment

elenarfowler Mar 9, 2021

elenarfowler Mar 9, 2021

garrettlew Mar 9, 2021

elenarfowler Mar 9, 2021

elenarfowler Mar 9, 2021

elenarfowler Mar 9, 2021

garrettlew Mar 9, 2021

elenarfowler Mar 9, 2021

elenarfowler Mar 9, 2021

elenarfowler Mar 9, 2021

garrettlew Mar 9, 2021

elenarfowler Mar 9, 2021

elenarfowler Mar 9, 2021

garrettlew Mar 9, 2021

elenarfowler Mar 9, 2021

garrettlew Mar 9, 2021

elenarfowler Mar 9, 2021

garrettlew Mar 9, 2021

elenarfowler Mar 9, 2021

elenarfowler Mar 9, 2021

garrettlew Mar 9, 2021 •

edited

Loading

		@@ -48,10 +49,11 @@ public IPatientEncounter createPatientEncounter(int patientID, DateTime date, in


		try{

		// testing

Move code from jpa to key branch of new main #7

Are you sure you want to change the base?

Move code from jpa to key branch of new main #7

Conversation

garrettlew commented Mar 9, 2021

elenarfowler left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

garrettlew Mar 9, 2021 • edited Loading

Choose a reason for hiding this comment

garrettlew Mar 9, 2021 •

edited

Loading