Add new FhirContactPoints domain #253

mherman22 · 2023-10-20T08:27:13Z

No description provided.

.../src/main/java/org/openmrs/module/initializer/api/fhir/cpm/FhirContactPointMapCsvParser.java

.../test/java/org/openmrs/module/initializer/api/FhirPatientContactPointMapIntegrationTest.java

ibacher · 2023-10-30T13:48:58Z

@mherman22 Is there no way to get this to work without shifting to 2.0.0 of the FHIR2 module? I would prefer to support older versions.

mherman22 · 2023-10-30T14:06:16Z

@mherman22 Is there no way to get this to work without shifting to 2.0.0 of the FHIR2 module? I would prefer to support older versions.

I was trying this out. I'm pushing it back to 1.11.0 however the challenge there has to do with the location type translator not being got as a bean i.e NoSuchBeanException

omod/src/main/resources/config.xml

ibacher · 2023-11-15T15:20:05Z

It looks like we're going to need to make 2.6 the minimum version for the LoaderTest and probably the validator too for this to work. @Ruhanga Do you have an opinion on that? Otherwise, we maybe add something to the Loader to not try to run a domain if a valid version of a loader isn't available.

mherman22 · 2023-11-15T15:28:25Z

It looks like we're going to need to make 2.6 the minimum version for the LoaderTest and probably the validator too for this to work. @Ruhanga Do you have an opinion on that? Otherwise, we maybe add something to the Loader to not try to run a domain if a valid version of a loader isn't available.

Fyi, I have done this locally though it is now not loading the loader for QUEUE so I am still looking for a workaround around that.

Ruhanga · 2023-11-16T07:48:23Z

It looks like we're going to need to make 2.6 the minimum version for the LoaderTest and probably the validator too for this to work.

@ibacher, @mherman22 concerning the above, upgrading to OpenMRS Core greater than 2.4.0 might require refactoring on the part of the Validator to accommodate new changes + upgraded libraries on Core. This will consequently need some extensive testing of the Validator itself.

ibacher · 2023-11-27T17:48:31Z

First bit looks like we need to change the calls like:

executeChangelog("changelog", null);

To:

executeChangelog("changelog", (ChangeSetExecutorCallback) null);

In ConfigTester...

mks-d

@mherman22 could you provide a detailed description to this PR so as to provide more context? Or @ibacher could you speak to it?

ibacher · 2023-11-15T14:02:37Z

.../src/main/java/org/openmrs/module/initializer/api/fhir/cpm/FhirContactPointMapCsvParser.java

+import org.springframework.stereotype.Component;
+
+@Component
+@OpenmrsProfile(modules = { "fhir2:1.11.* - 9.*" }, openmrsPlatformVersion = "2.6.3 - 2.6.*, 2.7.* - 9.*")


Suggested change

@OpenmrsProfile(modules = { "fhir2:1.11.* - 9.*" }, openmrsPlatformVersion = "2.6.3 - 2.6.*, 2.7.* - 9.*")

@OpenmrsProfile(modules = { "fhir2:1.11.* - 9.*" }, openmrsPlatformVersion = "2.6.3 - 9.*")

@ibacher is this (namely → modules = { "fhir2:1.11.* - 9.*" }) used because there is no way to say "1.11.* and above"?

Actually, I think we could just use fhir2:1.11.0 and possibly the same for openmrsPlatformVersion. I always forget how these get parsed.

Let's try these, here and elsewhere:

Suggested change

@OpenmrsProfile(modules = { "fhir2:1.11.* - 9.*" }, openmrsPlatformVersion = "2.6.3 - 2.6.*, 2.7.* - 9.*")

@OpenmrsProfile(modules = { "fhir2:1.11.0" }, openmrsPlatformVersion = "2.6.3")

ibacher · 2024-06-28T14:55:56Z

@mks-d This PR adds support for a feature that allows mapping between OMRS Attributes and FHIR ContactPoints. It populates a table that we use in the FHIR2 module to map between them. So, if you have an attribute that represents something covered by FHIR's ContactPoints type (phone number, email, website, etc.) as either a PersonAttribute or standard OMRS attribute, it will show up in the FHIR2 output for Patient, Provider, Location, etc. in the appropriate semantic field rather than as an OMRS-specific extension.

mks-d

@ibacher will you re-review this then?

mks-d · 2024-06-28T15:08:36Z

README.md

 1. [Cohort Attribute Types (CSV files)](readme/cohort.md#domain-cohortattributetypes)
 1. [FHIR Concept Sources (CSV files)](readme/fhir.md#domain-fhirconceptsources)
 1. [FHIR Patient Identifier Systems (CSV Files)](readme/fhir.md#domain-fhirpatientidentifiersystems)
+2. [FHIR ContactPointMap (CSV Files)](https://github.com/mherman22/openmrs-module-initializer/blob/ContactPointMap-impl/readme/fhir.md#domain-fhircontactpointmap)


The path is wrong here.

Also let's use normal Title Case: "Contact Point Map".

Suggested change

2. [FHIR ContactPointMap (CSV Files)](https://github.com/mherman22/openmrs-module-initializer/blob/ContactPointMap-impl/readme/fhir.md#domain-fhircontactpointmap)

2. [FHIR Contact Point Map (CSV Files)](readme/fhir.md#domain-fhircontactpointmap)

ibacher

@mherman22 Are you able to wrap up the necessary changes here?

ibacher · 2024-06-28T15:11:20Z

README.md

  ├── encounterroles/
  ├── fhirconceptsources/
  ├── fhirpatientidentifiersystems/
+  ├── fhirContactPointMap/


Suggested change

├── fhirContactPointMap/

├── fhircontactpointmaps/

ibacher · 2024-06-28T15:12:13Z

README.md

 1. [Cohort Attribute Types (CSV files)](readme/cohort.md#domain-cohortattributetypes)
 1. [FHIR Concept Sources (CSV files)](readme/fhir.md#domain-fhirconceptsources)
 1. [FHIR Patient Identifier Systems (CSV Files)](readme/fhir.md#domain-fhirpatientidentifiersystems)
+2. [FHIR ContactPointMap (CSV Files)](https://github.com/mherman22/openmrs-module-initializer/blob/ContactPointMap-impl/readme/fhir.md#domain-fhircontactpointmap)


Suggested change

2. [FHIR ContactPointMap (CSV Files)](https://github.com/mherman22/openmrs-module-initializer/blob/ContactPointMap-impl/readme/fhir.md#domain-fhircontactpointmap)

2. [FHIR Contact Point Map (CSV Files)](readme/fhir.md#domain-fhircontactpointmap)

ibacher · 2024-06-28T15:14:07Z

.../src/main/java/org/openmrs/module/initializer/api/fhir/cpm/FhirContactPointMapCsvParser.java

+import org.springframework.stereotype.Component;
+
+@Component
+@OpenmrsProfile(modules = { "fhir2:1.11.* - 9.*" }, openmrsPlatformVersion = "2.6.3 - 2.6.*, 2.7.* - 9.*")


Let's try these, here and elsewhere:

Suggested change

@OpenmrsProfile(modules = { "fhir2:1.11.* - 9.*" }, openmrsPlatformVersion = "2.6.3 - 2.6.*, 2.7.* - 9.*")

@OpenmrsProfile(modules = { "fhir2:1.11.0" }, openmrsPlatformVersion = "2.6.3")

ibacher · 2024-06-28T15:14:13Z

.../main/java/org/openmrs/module/initializer/api/fhir/cpm/FhirContactPointMapLineProcessor.java

+import static org.openmrs.module.initializer.api.fhir.cpm.FhirContactPointMapCsvParser.ATTRIBUTE_TYPE_DOMAIN_HEADER;
+
+@Component
+@OpenmrsProfile(modules = { "fhir2:1.11.* - 9.*" }, openmrsPlatformVersion = "2.6.3 - 2.6.*, 2.7.* - 9.*")


See previous

ibacher · 2024-06-28T15:15:07Z

.../main/java/org/openmrs/module/initializer/api/fhir/cpm/FhirContactPointMapLineProcessor.java

+	private static final String SYSTEM_HEADER = "system";
+
+	private static final String USE_HEADER = "use";
+
+	private static final String RANK_HEADER = "rank";


I think headers are normally capitalized, e.g. "System", etc.

ibacher · 2024-06-28T15:15:47Z

.../src/main/java/org/openmrs/module/initializer/api/fhir/cpm/FhirContactPointMapCsvParser.java

+	public static final String ATTRIBUTE_TYPE_DOMAIN_HEADER = "Entity name";
+
+	public static final String ATTRIBUTE_TYPE = "Attribute Type";


Headers at least should be like "Entity name", so, e.g., "Attribute type", etc.

ibacher · 2024-06-28T15:19:53Z

readme/fhir.md

+| Uuid                                 | Void/Retire | Entity name | Attribute Type                       | System | Use  | Rank | _order:1000 |
+|--------------------------------------|-------------|-------------|--------------------------------------|--------|------|------|-------------|
+| fa48acc4-ef1f-46d6-b0af-150b00ddee9d |             | person      | 717ec942-3c4a-11ea-b024-ffc81a23382e | PHONE  | WORK | 1    |             |
+|                                      |             | person      | PAT_RENAME_NEW_NAME                  | PHONE  | HOME |      |             |


Is the Attribute Type field here correct?

mherman22 · 2024-06-29T06:48:37Z

@mherman22 Are you able to wrap up the necessary changes here?

On it

ibacher · 2024-07-01T16:05:40Z

api-2.6/pom.xml

+    <parent>
+        <groupId>org.openmrs.module</groupId>
+        <artifactId>initializer</artifactId>
+        <version>2.7.0-SNAPSHOT</version>


We should update this now that 2.7.0 is released. I guess this should be 2.8.0-SNAPSHOT.

mherman22 mentioned this pull request Oct 20, 2023

Add Domain for FhirContactPoints #246

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mherman22 changed the title ~~Add Domain for FhirContactPoints~~ Add new FhirContactPoints domain. Oct 20, 2023

mherman22 force-pushed the ContactPointMap-impl branch from 93423e2 to 2ded69e Compare October 20, 2023 08:43

mherman22 commented Oct 20, 2023

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.../src/main/java/org/openmrs/module/initializer/api/fhir/cpm/FhirContactPointMapCsvParser.java Show resolved Hide resolved

ibacher reviewed Oct 20, 2023

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.../test/java/org/openmrs/module/initializer/api/FhirPatientContactPointMapIntegrationTest.java Outdated Show resolved Hide resolved

mherman22 force-pushed the ContactPointMap-impl branch from 5d7bd68 to 3aa66b2 Compare October 30, 2023 17:52

mherman22 mentioned this pull request Oct 31, 2023

Change openmrs version on locationTypeTranslatorImpl openmrs/openmrs-module-fhir2#527

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5 tasks

mherman22 force-pushed the ContactPointMap-impl branch from 3aa66b2 to f778a03 Compare October 31, 2023 07:19

Ruhanga reviewed Nov 14, 2023

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omod/src/main/resources/config.xml Outdated Show resolved Hide resolved

mherman22 force-pushed the ContactPointMap-impl branch 2 times, most recently from 825acb5 to 8bc7331 Compare November 14, 2023 15:15

mherman22 requested a review from ibacher November 15, 2023 10:01

mherman22 force-pushed the ContactPointMap-impl branch from 6761356 to a18324e Compare November 16, 2023 05:53

mherman22 force-pushed the ContactPointMap-impl branch from f3907bf to 07f2377 Compare November 24, 2023 19:46

mks-d reviewed Jun 28, 2024

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ibacher reviewed Jun 28, 2024

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mks-d requested a review from ibacher June 28, 2024 15:07

mks-d requested changes Jun 28, 2024

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ibacher requested changes Jun 28, 2024

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mherman22 added 3 commits July 1, 2024 18:32

add fhir contact point map to initializer

4ca8ddc

suggestions from talk post

1922f29

mimick what is happening in api-2.5 pom

84f445b

mherman22 added 3 commits July 1, 2024 18:43

fix build in validator

fa1360f

change encoding class

c372bae

fix according to reviews

55f1658

mherman22 force-pushed the ContactPointMap-impl branch from 88cc779 to 55f1658 Compare July 1, 2024 15:49

ibacher changed the title ~~Add new FhirContactPoints domain.~~ Add new FhirContactPoints domain Jul 1, 2024

ibacher reviewed Jul 1, 2024

View reviewed changes

change to 2.8.0-snapshot

0b5dac5

mks-d assigned mherman22 Jul 3, 2024

	@OpenmrsProfile(modules = { "fhir2:1.11.* - 9." }, openmrsPlatformVersion = "2.6.3 - 2.6., 2.7.* - 9.*")
	@OpenmrsProfile(modules = { "fhir2:1.11.* - 9." }, openmrsPlatformVersion = "2.6.3 - 9.")

	2. [FHIR ContactPointMap (CSV Files)](https://github.com/mherman22/openmrs-module-initializer/blob/ContactPointMap-impl/readme/fhir.md#domain-fhircontactpointmap)
	2. [FHIR Contact Point Map (CSV Files)](readme/fhir.md#domain-fhircontactpointmap)

	├── fhirContactPointMap/
	├── fhircontactpointmaps/

		public static final String ATTRIBUTE_TYPE_DOMAIN_HEADER = "Entity name";

		public static final String ATTRIBUTE_TYPE = "Attribute Type";

Add new FhirContactPoints domain #253

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mherman22 commented Oct 20, 2023

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ibacher commented Oct 30, 2023

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ibacher commented Jun 28, 2024

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mherman22 commented Jun 29, 2024

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ibacher commented Nov 27, 2023 •

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