BAH-460 Add search similar patients API [WIP] #33

eyalgo · 2018-05-16T06:16:30Z

Add API for search similar patients in BahmniPatientService
Add API for similar patients in PatientDao
The search is done using Lucene

eyalgo · 2018-05-16T08:31:41Z

There was previously a discussion to create a special class (or use existing one) instead of sending parameters.
We didn't add it now, as we preferred to do the minimal necessary code changes.
Not to add code "in case we need it in the future".

teleivo · 2018-05-17T15:41:18Z

@eyalgo please merge the commits into one (we do not need the commits in between as the state was not clean)

eyalgo · 2018-05-17T19:51:11Z

@angshu @djazayeri
hi,
can you please review the PR (I think I don't have permission to add reviewers).

Thanks !

/cc @teleivo , @mduemcke

djazayeri

Made some comments. The high level comment is also captured in this JIRA comment:
https://bahmni.atlassian.net/browse/BAH-460?focusedCommentId=12001&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#comment-12001

djazayeri · 2018-05-18T19:29:07Z

bahmnicore-api/src/main/java/org/bahmni/module/bahmnicore/dao/PatientDao.java

@@ -19,6 +20,12 @@
                                                       String programAttributeFieldName, String[] addressSearchResultFields,
                                                       String[] patientSearchResultFields, String loginLocationUuid, Boolean filterPatientsByLocation, Boolean filterOnAllIdentifiers);

+    List<PatientResponse> getSimilarPatientsUsingLuceneSearch(String identifer, String name, String gender, String customAttribute,


Do we really have to add another method here? The DAO isn't an external-facing interface so we should just be able to add a parameter to the above, right?

djazayeri · 2018-05-18T19:32:48Z

...pi/src/test/java/org/bahmni/module/bahmnicore/service/impl/BahmniPatientServiceImplTest.java

@@ -67,4 +69,5 @@ public void shouldGetPatientByPartialIdentifier() throws Exception {
        bahmniPatientService.get("partial_identifier", shouldMatchExactPatientId);
        verify(patientDao).getPatients("partial_identifier", shouldMatchExactPatientId);
    }
+


spurious change

djazayeri · 2018-05-18T19:34:32Z

bahmnicore-api/src/main/java/org/bahmni/module/bahmnicore/dao/impl/PatientDaoImpl.java

+    @Override
+    public List<PatientResponse> getSimilarPatientsUsingLuceneSearch(String identifier, String name, String gender, String customAttribute,
+                                                              String addressFieldName, String addressFieldValue, Integer length,
+                                                              Integer offset, String[] customAttributeFields, String programAttributeFieldValue,


I didn't look closely but I think you're ignoring the length and offset parameters.

djazayeri · 2018-05-18T19:36:08Z

...api/src/main/java/org/bahmni/module/bahmnicore/contract/patient/PatientSearchParameters.java

@@ -71,6 +73,14 @@ public void setName(String name) {
        this.name = name;
    }

+    public String getGender() {


If we add this field here we also need to make sure it's respected by existing API methods that use PatientSearchParameters.
(It would be okay to skip the gender field when searching for similar patients, if your timeline to finish this is tight.)

@djazayeri what do you mean by respected?

djazayeri · 2018-05-18T19:40:17Z

...re-api/src/test/java/org/bahmni/module/bahmnicore/dao/impl/BahmniPatientDaoImplLuceneIT.java

+        PatientResponse patient1 = patients.get(0);
+
+        for(PatientResponse response: patients) {
+            System.out.println(response.getGivenName() + " " + response.getMiddleName() + " " + response.getFamilyName());


Remove this before merging.

djazayeri · 2018-05-18T19:44:44Z

...a/org/bahmni/module/bahmnicore/web/v1_0/controller/search/BahmniPatientSearchController.java

+
+    @RequestMapping(value="similar", method = RequestMethod.GET)
+    @ResponseBody
+    public ResponseEntity<AlreadyPaged<PatientResponse>> searchSimilarPerson(HttpServletRequest request,


I'm not convinced that this is the right place to add this search (and that would have a big impact on the rest of the code).

See this comment: https://bahmni.atlassian.net/browse/BAH-460?focusedCommentId=12001&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#comment-12001

This code needs to be called from the Register New Patient screen, asking the question "are there any similar patients to this one that I'm about to create?" Therefor I would expect that the client is allowed to submit an incomplete version of the patient creation object, instead of needing to construct a search that's in a different format.

If you prefer not to do it that for some reason, please give a justification.

Hey Darius, I might be missing some context (just joined the team) but I thought that this search needs to be called as the user inputs first name / last name, and wouldn't require them to hit the submit button before checking for matches.
Did I misunderstand your comment? Do you still think we should change this?

@djazayeri cc @mduemcke

Therefor I would expect that the client is allowed to submit an incomplete version of the patient creation object, instead of needing to construct a search that's in a different format

Hi Darius, I'm trying to figure this out (I've also just joined and took over from Martina). If we were to send an incomplete patient representation to the, say BahmniPatientProfileResource we'd still have to construct input from that representation in order to be able to search for the potentially similar patient using Lucene. As far as I understood it was suggested/agreed upon that Lucene is to be utilized for this search. Ultimately we don't want to create new patients from the lookup, but just aid the creation process, trying to avoid creation of duplicates, no?

Thus, wouldn't that mean adding a responsibility to BahmniPatientProfileResource which it shouldn't have? As is, the responsibilities of patient creation and searching seem more properly separated.

Though a different approach just came to mind while writing this — when creating a new patient object from the given, incomplete data, said object could obtain a new functionality searchSimilar() and conduct a Lucene search from there, e.g. something along BahmniPatient::searchSimilar()... was that what you're after? I'd probably still would want to keep that in the search controller.

Let me know what you think (or had in mind).. thanks!

teleivo · 2018-05-22T18:51:33Z

bahmnicore-api/src/main/java/org/bahmni/module/bahmnicore/dao/impl/PatientDaoImpl.java

-
-import static java.util.stream.Collectors.reducing;
+
+import java.util.*;


please dont use star imports

teleivo · 2018-05-22T18:53:51Z

bahmnicore-api/src/main/java/org/bahmni/module/bahmnicore/dao/impl/PatientDaoImpl.java

+        String query = LuceneQuery.escapeQuery(name);
+        PersonLuceneQuery personLuceneQuery = new PersonLuceneQuery(sessionFactory);
+        LuceneQuery<PersonName> nameQuery = personLuceneQuery.getPatientNameQueryWithOrParser(query, false);
+        /* person.gender does not work somehow in LuceneQuery, so the dirty way is to filter result with person's gender */


please remove this comment, we should explain in the JIRA ticket that we decided to go this route as to not have to adapt the openmrs lucene index (since this is where gender would need to be included in the index)

teleivo · 2018-05-22T18:56:07Z

...re-api/src/test/java/org/bahmni/module/bahmnicore/dao/impl/BahmniPatientDaoImplLuceneIT.java

+    @Test
+    public void shouldSearchSimilarPatientByPatientName() {
+        List<PatientResponse> patients = patientDao.getSimilarPatientsUsingLuceneSearch("Peet", "", "c36006e5-9fbb-4f20-866b-0ece245615a1", 5);
+        PatientResponse patient1 = patients.get(0);


these 2 lines should move below the assertEquals(2, patients.size()), so we get a clean error message in case the patients returned are empty or only of length 1

teleivo · 2018-05-22T18:57:49Z

...pi/src/test/java/org/bahmni/module/bahmnicore/service/impl/BahmniPatientServiceImplTest.java

-import static org.mockito.Mockito.anyInt;
-import static org.mockito.Mockito.verify;
-import static org.mockito.Mockito.when;
+import static org.mockito.Mockito.*;


we do not use star imports, please replace

teleivo · 2018-05-22T18:57:52Z

...re-api/src/test/java/org/bahmni/module/bahmnicore/dao/impl/BahmniPatientDaoImplLuceneIT.java

+        assertEquals(patient1.getFamilyName(), "Sinha");
+    }
+
+    //TODO missing tests: by limit, parameters verification


remove the TODO/replace it with missing tests.
you tested limit in shouldSearchSimilarPatientByPatientNameAndUseLimitResult

what do you want to test in parameters verification ?

teleivo · 2018-05-22T18:58:18Z

...pi/src/test/java/org/bahmni/module/bahmnicore/service/impl/BahmniPatientServiceImplTest.java

+        patientSearchParameters.setName("John");
+        patientSearchParameters.setGender("M");
+        patientSearchParameters.setLoginLocationUuid("someUUid");
+


remove newline

mduemcke · 2018-06-08T08:31:47Z

amended the pull request - still work in progress! Going to hand over to next pair

…h similar name, gender and birthdate/age

CLAassistant · 2019-07-23T12:26:44Z

All committers have signed the CLA.

eyalgo force-pushed the master branch from ee21dca to 6d1d72a Compare May 17, 2018 12:57

eyalgo force-pushed the master branch 2 times, most recently from 5a04180 to 114c540 Compare May 17, 2018 16:03

djazayeri requested changes May 18, 2018

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eyalgo force-pushed the master branch 2 times, most recently from 767f916 to 5a04180 Compare May 22, 2018 10:00

eyalgo changed the title ~~BAH-460 Add search similar patients API~~ BAH-460 Add search similar patients API [WIP] May 22, 2018

teleivo mentioned this pull request May 22, 2018

Jian | BAH-460 | add api for search similar patient using PersonService #29

Closed

teleivo reviewed May 22, 2018

View reviewed changes

mduemcke force-pushed the master branch 2 times, most recently from 23f941d to 7ee46a5 Compare May 24, 2018 09:11

mduemcke force-pushed the master branch from 9ea15aa to a88cb84 Compare June 8, 2018 07:32

carhartl mentioned this pull request Jun 13, 2018

Simplify getPatientsByNameAndGender() method eyalgo/bahmni-core#1

Merged

mduemcke force-pushed the master branch 4 times, most recently from 170944c to 331580d Compare August 9, 2018 07:20

Martina, Roni, Eyal, Klaus | BAH-460 | add api to search patients wit…

117df8f

…h similar name, gender and birthdate/age

mduemcke force-pushed the master branch from da52d51 to 117df8f Compare August 20, 2018 06:51

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BAH-460 Add search similar patients API [WIP] #33

BAH-460 Add search similar patients API [WIP] #33

eyalgo commented May 16, 2018

eyalgo commented May 16, 2018

teleivo commented May 17, 2018

eyalgo commented May 17, 2018

djazayeri left a comment

djazayeri May 18, 2018

djazayeri May 18, 2018

djazayeri May 18, 2018

djazayeri May 18, 2018

teleivo May 22, 2018

djazayeri May 18, 2018

djazayeri May 18, 2018

rgrnwd May 23, 2018

carhartl Jun 13, 2018

teleivo May 22, 2018

teleivo May 22, 2018

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teleivo May 22, 2018

mduemcke commented Jun 8, 2018

CLAassistant commented Jul 23, 2019 •

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		import static java.util.stream.Collectors.reducing;

		import java.util.*;

BAH-460 Add search similar patients API [WIP] #33

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BAH-460 Add search similar patients API [WIP] #33

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eyalgo commented May 16, 2018

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