Merge branch 'main' of https://github.com/CDCgov/phdi into robert/add…

…-baseclass-to-containers

.github/workflows/buildReleaseContainers.yaml

@@ -47,6 +47,7 @@ jobs:
         id: meta
         uses: docker/metadata-action@v4
         with:
+          ref: ${{ inputs.container-tag }}
           images: ghcr.io/${{ github.repository }}/${{matrix.container-to-build}}
           # this sets the version for tags and labels for each of the containers to be
           # be the same as the version/tag where the code was pulled from

.github/workflows/createNewRelease.yaml

@@ -55,9 +55,27 @@ jobs:
           git config --local user.email "action@github.com"
           git config --local user.name "GitHub Action"
       - name: Tag Release
+        uses: EndBug/latest-tag@latest
+        with:
+          ref: ${{ steps.get_version.outputs.version }}
+      # Generate release notes
+      - name: Generate release notes
+        id: release_notes
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          git tag ${{ steps.get_version.outputs.version }}
-          git push origin ${{ steps.get_version.outputs.version }}
+          latest_release_date=$(gh release list --limit 1 --json createdAt -q ".[0].createdAt")
+          prs=$(gh pr list --base main --state closed --json title,number,url,closedAt -q ".[] | select(.closedAt > \"$latest_release_date\")")
+
+          release_notes="# Release Notes\n\n"
+          for pr in "$prs"; do
+            pr_title=$(echo "$pr" | jq -r ".title")
+            pr_number=$(echo "$pr" | jq -r ".number")
+            pr_url=$(echo "$pr" | jq -r ".url")
+            release_notes+="- $pr_title ([PR#$pr_number]($pr_url))\n"
+          done
+
+          echo "RELEASE_NOTES=$release_notes" >> $GITHUB_OUTPUT
       # Create new release based upon the latest created tag
       - name: Create Release
         id: create_release
@@ -66,7 +84,8 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           tag_name: ${{ steps.get_version.outputs.version }}
-          release_name: Release ${{ steps.get_version.outputs.version }} 
+          release_name: ${{ steps.get_version.outputs.version }} 
+          body: ${{ steps.release_notes.outputs.RELEASE_NOTES }}
 
   release-to-pypi:
     name: Build and publish PHDI to PyPI
@@ -164,6 +183,15 @@ jobs:
           ref: ${{ needs.tag-release.outputs.version }}
 
       - name: Update Container Documenation
+        env:
+          MPI_DBNAME: testdb
+          MPI_PASSWORD: pw
+          MPI_DB_TYPE: postgres
+          MPI_HOST: localhost
+          MPI_USER: postgres
+          MPI_PORT: 5432
+          MPI_PATIENT_TABLE: patient
+          MPI_PERSON_TABLE: person
         run: |
           npm i -g redoc-cli
           CONTAINER=${{ matrix.container }}

containers/message-parser/tests/test_parse_message_endpoint.py

@@ -11,6 +11,7 @@
     Path(__file__).parent.parent.parent.parent
     / "tests"
     / "assets"
+    / "general"
     / "patient_bundle.json"
 )
 

containers/tabulation/tests/test_tabulation.py

@@ -13,6 +13,7 @@
     pathlib.Path(__file__).parent.parent.parent.parent
     / "tests"
     / "assets"
+    / "tabulation"
     / "valid_schema.json"
 )
 

containers/tabulation/tests/test_utils.py

@@ -77,6 +77,7 @@ def test_check_schema_validity_valid_schema():
         pathlib.Path(__file__).parent.parent.parent.parent
         / "tests"
         / "assets"
+        / "tabulation"
         / "valid_schema.json"
     )
     valid_schema = json.load(open(valid_schema_path))

containers/validation/config/ecr_config_LAC.yaml

@@ -83,14 +83,14 @@ fields:
   textRequired: 'True'
 - fieldName: City
   cdaPath: "//hl7:ClinicalDocument/hl7:recordTarget/hl7:patientRole/hl7:addr/hl7:city"
-  errorType: "fatal"
+  errorType: "errors"
   textRequired: 'True'
-  relatives:
-    - name: addr
-      cdaPath: "//hl7:ClinicalDocument/hl7:recordTarget/hl7:patientRole/hl7:addr"
-      attributes:
-      - attributeName: use
-        regEx: "H"
+  # relatives:
+  #   - name: addr
+  #     cdaPath: "//hl7:ClinicalDocument/hl7:recordTarget/hl7:patientRole/hl7:addr"
+  #     attributes:
+  #     - attributeName: use
+  #       regEx: "H"
 - fieldName: State
   cdaPath: "//hl7:ClinicalDocument/hl7:recordTarget/hl7:patientRole/hl7:addr/hl7:state"
   errorType: "errors"

containers/validation/config/sample_ecr_config.yaml

@@ -27,15 +27,15 @@ fields:
 #   - attributeName: value
 - fieldName: First Name
   cdaPath: "//hl7:ClinicalDocument/hl7:recordTarget/hl7:patientRole/hl7:patient/hl7:name/hl7:given"
-  errorType: "fatal"
+  errorType: "errors"
   textRequired: 'True'
   validateOne: False
-  relatives:
-    - name: name
-      cdaPath: "//hl7:ClinicalDocument/hl7:recordTarget/hl7:patientRole/hl7:patient/hl7:name"
-      attributes:
-      - attributeName: use
-        regEx: "L"
+  # relatives:
+  #   - name: name
+  #     cdaPath: "//hl7:ClinicalDocument/hl7:recordTarget/hl7:patientRole/hl7:patient/hl7:name"
+  #     attributes:
+  #     - attributeName: use
+  #       regEx: "L"
 - fieldName: Middle Name
   cdaPath: "//hl7:ClinicalDocument/hl7:recordTarget/hl7:patientRole/hl7:patient/hl7:name/hl7:given"
   errorType: "errors"

containers/validation/tests/test_utils.py

@@ -43,6 +43,7 @@ def test_validate_config_bad():
         pathlib.Path(__file__).parent.parent.parent.parent
         / "tests"
         / "assets"
+        / "validation"
         / "sample_ecr_config_bad.yaml",
         "r",
     ) as file:
@@ -56,6 +57,7 @@ def test_validate_config_good():
         pathlib.Path(__file__).parent.parent.parent.parent
         / "tests"
         / "assets"
+        / "validation"
         / "sample_ecr_config.yaml",
         "r",
     ) as file:

containers/validation/tests/test_validation.py

@@ -17,6 +17,7 @@
     pathlib.Path(__file__).parent.parent.parent.parent
     / "tests"
     / "assets"
+    / "validation"
     / "ecr_sample_input_good.xml"
 ).read()
 
@@ -25,6 +26,7 @@
     pathlib.Path(__file__).parent.parent.parent.parent
     / "tests"
     / "assets"
+    / "validation"
     / "ecr_sample_input_bad.xml"
 ).read()
 
@@ -33,6 +35,7 @@
     pathlib.Path(__file__).parent.parent.parent.parent
     / "tests"
     / "assets"
+    / "validation"
     / "ecr_sample_input_good_with_RR.xml"
 ).read()
 
@@ -94,9 +97,6 @@ def test_validate_ecr_invalid():
                 + "'Conditions' Attributes: attribute #1: 'code' "
                 + "with the required value pattern: '[0-9]+',"
                 + " attribute #2: 'codeSystem'",
-                "Could not find field. Field name: 'City' Related"
-                + " elements: Field name: 'addr' Attributes: attribute"
-                + " #1: 'use' with the required value pattern: 'H'",
                 "The field value does not exist or doesn't match "
                 + "the following pattern: "
                 + "'[0-9]{5}(?:-[0-9]{4})?'. For the Field name: 'Zip' value: '9999'",

tests/assets/example_eicr_with_rr_data.xml → tests/assets/fhir-converter/ecr/example_eicr_with_rr_data.xml

@@ -2650,7 +2650,7 @@
         <entry>
             <act classCode="ACT" moodCode="EVN">
                 <templateId extension="2017-04-01" root="2.16.840.1.113883.10.20.15.2.3.29"/>
-                <id root="39d966b9-8a3a-4024-93d8-138e97d5898a"/>
+                <id root="8675309a-7754-r2d2-c3p0-973d9f777777"/>
                 <code code="RRVS19" codeSystem="2.16.840.1.114222.4.5.274" codeSystemName="PHIN VS (CDC Local Coding System)" displayName="eICR processed"/>
             </act>
         </entry>