Add Golden Copy Tests

.github/workflows/automated-staging-test-run.yml

@@ -6,23 +6,10 @@ on:
   workflow_dispatch:
 
 jobs:
-  test_files:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Check out the repository
-        uses: actions/checkout@v4
-
-      - name: Run automated tests
-        env:
-          AZURE_STORAGE_CONNECTION_STRING: ${{ secrets.AUTOMATED_TEST_AZURE_STORAGE_CONNECTION_STRING }}
-        run: ./gradlew rs-e2e:clean rs-e2e:automatedTest
-
-      - name: Send slack notification on test failure
-        if: failure()
-        uses: slackapi/[email protected]
-        with:
-          webhook: ${{ secrets.SLACK_WEBHOOK_URL }}
-          webhook-type: incoming-webhook
-          payload: |
-            text: "Automated Staging RS Integration Test Failed!: https://github.com/CDCgov/trusted-intermediary/actions/runs/${{ github.run_id }}"
+  call-staging-test-run:
+    uses: ./.github/workflows/staging-test-run_reusable.yml
+    with:
+      FILE_PATH: '../examples/Test/Automated/Assertion/'
+      NAME: 'Automated'
+      TEST_TYPE: 'automatedTest'
+    secrets: inherit # pragma: allowlist secret

.github/workflows/automated-staging-test-submit.yml

@@ -18,8 +18,8 @@ jobs:
 
       - name: Install jwt-cli
         run: |
-            curl --silent --location https://github.com/mike-engel/jwt-cli/releases/latest/download/jwt-linux.tar.gz | tar xvz -C /usr/local/bin/
-            sudo chmod +x /usr/local/bin/jwt
+          curl --silent --location https://github.com/mike-engel/jwt-cli/releases/latest/download/jwt-linux.tar.gz | tar xvz -C /usr/local/bin/
+          sudo chmod +x /usr/local/bin/jwt
 
       - name: Write private key to file
         run: |
@@ -28,32 +28,33 @@ jobs:
 
       - name: Send HL7 sample messages to staging RS
         run: |
-            host=https://staging.prime.cdc.gov:443
-            client_id=flexion
-            client_sender=simulated-sender
-            jwt=$(jwt encode --exp='+5min' --jti $(uuidgen) --alg RS256 \
-                -k $client_id.$client_sender -i $client_id.$client_sender \
-                -s $client_id.$client_sender -a $host --no-iat -S @/tmp/staging_private_key.pem)
-
-            token=$(curl \
-                    --header "Content-Type: application/x-www-form-urlencoded" \
-                    --data "scope=$client_id.*.report" \
-                    --data "client_assertion=$jwt" \
-                    --data "client_assertion_type=urn:ietf:params:oauth:client-assertion-type:jwt-bearer" \
-                    --data "grant_type=client_credentials" \
-                    --silent \
-                    "$host/api/token" | jq -r ".access_token")
-
-            for file in $(pwd)/examples/Test/Automated/*.hl7; do
-                echo "Sending $file"
-                curl \
-                    --header "Content-Type: application/hl7-v2" \
-                    --header "Client: $client_id.$client_sender" \
-                    --header "Authorization: Bearer $token" \
-                    --data-binary "@$file" \
-                    --silent \
-                    "$host/api/waters"
-            done
+          shopt -s globstar
+          host=https://staging.prime.cdc.gov:443
+          client_id=flexion
+          client_sender=simulated-sender
+          jwt=$(jwt encode --exp='+5min' --jti $(uuidgen) --alg RS256 \
+              -k $client_id.$client_sender -i $client_id.$client_sender \
+              -s $client_id.$client_sender -a $host --no-iat -S @/tmp/staging_private_key.pem)
+
+          token=$(curl \
+                  --header "Content-Type: application/x-www-form-urlencoded" \
+                  --data "scope=$client_id.*.report" \
+                  --data "client_assertion=$jwt" \
+                  --data "client_assertion_type=urn:ietf:params:oauth:client-assertion-type:jwt-bearer" \
+                  --data "grant_type=client_credentials" \
+                  --silent \
+                  "$host/api/token" | jq -r ".access_token")
+
+          for file in $(pwd)/examples/Test/Automated/**/*.hl7; do
+              echo "Sending $file"
+              curl \
+                  --header "Content-Type: application/hl7-v2" \
+                  --header "Client: $client_id.$client_sender" \
+                  --header "Authorization: Bearer $token" \
+                  --data-binary "@$file" \
+                  --silent \
+                  "$host/api/waters"
+          done
 
       - name: Clean up private key
         if: always()

.github/workflows/golden-copy-staging-test-run.yml

@@ -0,0 +1,16 @@
+name: Golden Copy Staging Test - Run integration tests
+
+on:
+  pull_request:
+  schedule:
+    - cron: "10 7 * * 2-6"  # Tuesday to Saturday at 2am EST (7:10am UTC) - two hours after `automated-staging-test-submit` runs
+  workflow_dispatch:
+
+jobs:
+  call-staging-test-run:
+    uses: ./.github/workflows/staging-test-run_reusable.yml
+    with:
+      FILE_PATH: '../examples/Test/Automated/GoldenCopy/Expected/'
+      NAME: 'Golden Copy'
+      TEST_TYPE: 'goldenCopyTest'
+    secrets: inherit # pragma: allowlist secret

.github/workflows/staging-test-run_reusable.yml

@@ -0,0 +1,49 @@
+name: Staging Test - Run integration tests
+
+on:
+  workflow_call:
+    inputs:
+      TEST_TYPE:
+        type: string
+        description: The e2e test to run
+        required: true
+        default: 'automatedTest'
+      NAME:
+        type: string
+        description: The name of test
+        required: true
+        default: 'Automated'
+      FILE_PATH:
+        type: string
+        description: The path to local files
+        required: true
+        default: '../examples/Test/Automated/Assertion/'
+    secrets:
+        AUTOMATED_TEST_AZURE_STORAGE_CONNECTION_STRING:
+          required: true
+        SLACK_WEBHOOK_URL:
+          required: true
+
+jobs:
+  test_files:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@v4
+
+      - name: Run automated tests
+        env:
+          AZURE_STORAGE_CONNECTION_STRING: ${{ secrets.AUTOMATED_TEST_AZURE_STORAGE_CONNECTION_STRING }}
+          LOCAL_FILE_PATH: ${{ inputs.FILE_PATH }}
+        run: |
+          ./gradlew rs-e2e:clean rs-e2e:${{ inputs.TEST_TYPE }}
+
+      - name: Send slack notification on test failure
+        if: failure()
+        uses: slackapi/[email protected]
+        with:
+          webhook: ${{ secrets.SLACK_WEBHOOK_URL }}
+          webhook-type: incoming-webhook
+          payload: |
+            text: "${{ inputs.NAME }} Staging RS Integration Test Failed!: https://github.com/CDCgov/trusted-intermediary/actions/runs/${{ github.run_id }}"

examples/Test/Automated/GoldenCopy/Expected/008_CA_ORU_R01_CDPH_UCSD_MRN_80015955_pre_TI_TC007B.hl7

@@ -0,0 +1 @@
+MSH|^~\&|GOLDEN-COPY|CDPH|EPIC|R797|20241206093739||ORU^R01|008|N|2.5.1PID|1||80015955||INTERFACE^BOY A CDPHONE||202411180830|M||2131-1^Other Race||||||||||||UNK^Unknown||Y|1NK1|1|INTERFACE^CDPHONE|MTH^Mother|456 ST^^SAN DIEGO^CA^92123^USA|^^^^^858^2490016|||||||||||19921118ORC|RE|^HospOrdNumber||7902698491^FormNumber||||||||1427255868^JOHNSON^KATHRYN^^^^^^^^^^NPI|||||||||^^^^^^^^^R797|AG N 005EVA DLEIFR, F N 0037TERTS ONSER^^SAN DIEGO^CA^99999-9999OBR|1|^HospOrdNumber||54089-8^NB Screen Panel Patient AHIC^CDPHGSPEAP|||202411021023|||||||202411031023||1427255868^JOHNSON^KATHRYN^^^^^^^^^^NPI||||||20241206093739|||FOBX|1|TX|57724-7^Newborn screening short narrative summary^LN|1|ACTION REQUIRED\.br\\.br\Testing Lab - Quest \R\ S W 0094DVLB TESNU, SAN JUAN CAPISTRANO, CA 99999-9999\.br\\.br\Lab Director - Daisydoublek Toulousep, MD,PhD, Quest, (491)154-5445\.br\\.br\SCID Reviewer - Meadowsaffronpa Maxrm\.br\\.br\Lab Remarks: CD3/CD8/CD45RO, Percent:This test was developed and its analytical performance characteristics have been determined by Quest Diagnostics Nichols Institute San Juan Capistrano. It has not been cleared or approved by FDA. This assay has been validated pursuant to the CLIA regulations and is used for clinical purposes. \.br\\.br\Follow-up:\.br\\.br\Clinical Reviewer Comments: Testing\.br\\.br\Follow-up Recommendation: Refer to CCS-approved Immunology Center\.br\\.br\Disclaimer:\.br\\.br\This test was developed and its performance characteristics have been determined by Quest Diagnostics Nichols Institute, San Juan Capistrano. It has not been cleared or approved by the U.S. Food and Drug Administration. The FDA has determined that such clearance or approval is not necessary. Performance characteristics refer to the analytical performance of the test. \.br\\.br\|||N|||F|||20241206093739OBX|2|TM|57715-5^Time of birth^LN|1|0830|||N|||F|||20241206093739OBX|3|NM|73806-2^Newborn age in hours^LN|1|73|hour(s)||N|||F|||20241206093739OBX|4|TX|62327-2^Post-discharge provider practice address^LN|1|AG N 005EVA DLEIFR, F N 0037TERTS ONSER SAN DIEGO CA 99999-9999 USA|||N|||F|||20241206093739OBX|5|NM|6690-2^Leukocytes [#/volume] in Blood by Automated count^LN|1|45.1|Thousand/uL|9.0-30.0|H|||F|||20241206093739OBX|6|NM|789-8^Erythrocytes [#/volume] in Blood by Automated count^LN|1|4.25|Million/uL|3.90-5.90||||F|||20241206093739OBX|7|NM|718-7^Hemoglobin [Mass/volume] in Blood^LN|1|18.1|g/dL|13.4-19.9||||F|||20241206093739OBX|8|NM|4544-3^Hematocrit [Volume Fraction] of Blood by Automated count^LN|1|50.1|%|42.0-65.0||||F|||20241206093739OBX|9|NM|787-2^Erythrocyte mean corpuscular volume [Entitic volume] by Automated count^LN|1|100.0|fL|88.0-123.0||||F|||20241206093739OBX|10|NM|785-6^Erythrocyte mean corpuscular hemoglobin [Entitic mass] by Automated count^LN|1|35.1|pg|31.0-37.0||||F|||20241206093739OBX|11|NM|786-4^Erythrocyte mean corpuscular hemoglobin concentration [Mass/volume] by Automated count^LN|1|30.2|g/dL|28.0-36.0||||F|||20241206093739OBX|12|NM|777-3^Platelets [#/volume] in Blood by Automated count^LN|1|200|Thousand/uL|150-450||||F|||20241206093739OBX|13|NM|776-5^Platelet mean volume [Entitic volume] in Blood by Rees-Ecker^LN|1|11.1|fL|7.5-12.5||||F|||20241206093739OBX|14|NM|788-0^Erythrocyte distribution width [Ratio] by Automated count^LN|1|14.1|%|13.0-18.0||||F|||20241206093739OBX|15|NM|751-8^Neutrophils [#/volume] in Blood by Automated count^LN|1|7000|cells/uL|5000-21000||||F|||20241206093739OBX|16|NM|26507-4^Neutrophils.band form [#/volume] in Blood^LN^29153|1|3000|cells/uL|1500-4200||||F|||20241206093739OBX|17|NM|30433-7^Metamyelocytes [#/volume] in Blood^LN^29154|1|1|cells/uL|0|H|||F|||20241206093739OBX|18|NM|30446-9^Myelocytes [#/volume] in Blood^LN^29162|1|0|cells/uL|0||||F|||20241206093739OBX|19|NM|26523-1^Promyelocytes [#/volume] in Blood^LN^29163|1|0|cells/uL|0||||F|||20241206093739OBX|20|NM|731-0^Lymphocytes [#/volume] in Blood by Automated count^LN^29164|1|6000|cells/uL|2000-11500||||F|||20241206093739OBX|21|NM|742-7^Monocytes [#/volume] in Blood by Automated count^LN^29165|1|1200|cells/uL|300-2400||||F|||20241206093739OBX|22|NM|711-2^Eosinophils [#/volume] in Blood by Automated count^LN^29166|1|600|cells/uL|15-800||||F|||20241206093739OBX|23|NM|704-7^Basophils [#/volume] in Blood by Automated count^LN^29167|1|200|cells/uL|0-300||||F|||20241206093739OBX|24|NM|30376-8^Blasts [#/volume] in Blood^LN^29168|1|0|cells/uL|0||||F|||20241206093739OBX|25|NM|30392-5^Nucleated erythrocytes [#/volume] in Blood^LN^29169|1|300|cells/uL|0-5000||||F|||20241206093739OBX|26|NM|770-8^Neutrophils/100 leukocytes in Blood by Automated count^LN^29170|1|20|%|||||F|||20241206093739OBX|27|NM|26508-2^Neutrophils.band form/100 leukocytes in Blood^LN^29171|1|2|%|||||F|||20241206093739OBX|28|NM|28541-1^Metamyelocytes/100 leukocytes in Blood^LN^29172|1|1|%|||||F|||20241206093739OBX|29|NM|26498-6^Myelocytes/100 leukocytes in Blood^LN^29173|1|1|%|||||F|||20241206093739OBX|30|NM|26524-9^Promyelocytes/100 leukocytes in Blood^LN^29174|1|1|%|||||F|||20241206093739OBX|31|NM|736-9^Lymphocytes/100 leukocytes in Blood by Automated count^LN^29175|1|1|%|||||F|||20241206093739OBX|32|NM|13046-8^Lymphocytes Variant/100 leukocytes in Blood^LN^29176|1|1|%|0-10||||F|||20241206093739OBX|33|NM|5905-5^Monocytes/100 leukocytes in Blood by Automated count^LN^29177|1|1|%|||||F|||20241206093739OBX|34|NM|713-8^Eosinophils/100 leukocytes in Blood by Automated count^LN^29178|1|1|%|||||F|||20241206093739OBX|35|NM|706-2^Basophils/100 leukocytes in Blood by Automated count^LN^29179|1|1|%|||||F|||20241206093739OBX|36|NM|26446-5^Blasts/100 leukocytes in Blood^LN^29180|1|1|%|||||F|||20241206093739OBX|37|NM|19048-8^Nucleated erythrocytes/100 leukocytes [Ratio] in Blood^LN^29181|1|1|/100 WBC|0|H|||F|||20241206093739OBX|38|NM|8122-4^CD3 cells [#/volume] in Blood^LN^86007711^CD3+ T-Cells, Absolute^L|1|3000|cells/uL|2500-5500||||F|||20241206093739OBX|39|NM|8124-0^CD3 cells/100 cells in Blood^LN^86007712^CD3+ T-Cells, Percent^L|1|60|% of Lymphs|53-84||||F|||20241206093739OBX|40|NM|24467-3^CD3+CD4+ (T4 helper) cells [#/volume] in Blood^LN^86007713^CD3+/CD4+ T-Helper, Abs^L|1|2000|cells/uL|1600-4000||||F|||20241206093739OBX|41|NM|8123-2^CD3+CD4+ (T4 helper) cells/100 cells in Blood^LN^86007714^CD3+/CD4+ T-Helper,Percent^L|1|40|% of Lymphs|35-64||||F|||20241206093739OBX|42|NM|14135-8^CD3+CD8+ (T8 suppressor cells) cells [#/volume] in Blood^LN^86007715^CD3+/CD8+ T-Cytotoxic, Abs^L|1|1000|cells/uL|560-1700||||F|||20241206093739OBX|43|NM|8101-8^CD3+CD8+ (T8 suppressor cells) cells/100 cells in Blood^LN^86007716^CD3+/CD8+T-Cytotox,Percent^L|1|15|% of Lymphs|12-28||||F|||20241206093739OBX|44|NM|8116-6^CD19 cells [#/volume] in Blood^LN^86007717^CD19+ B-cells, Absolute^L|1|500|cells/uL|300-2000||||F|||20241206093739OBX|45|NM|8117-4^CD19 cells/100 cells in Blood^LN^86007718^CD19+ B-cells, Percent^L|1|10|% of Lymphs|6-32||||F|||20241206093739OBX|46|NM|9728-7^CD16C+CD56+ cells [#/volume] in Blood^LN^86007719^CD16/CD56 NK-cells, Abs^L|1|200|cells/uL|170-1100||||F|||20241206093739OBX|47|NM|8112-5^CD16+CD56+ cells/100 cells in Blood^LN^86007720^CD16/CD56 NK-cells,Percent^L|1|9|% of Lymphs|4-18||||F|||20241206093739OBX|48|NM|26759-1^CD4+CD45RA+cells [#/volume] in Blood^LN^86007721^CD3/CD4/CD45RA, Absolute^L|1|1500|cells/uL|1200-3700||||F|||20241206093739OBX|49|NM|13336-3^CD4+CD45RA+cells/100 cells in Blood^LN^^CD3/CD4/CD45RA, Percent^L|1|8|% CD4|||||F|||20241206093739OBX|50|NM|82743-6^CD8+CD45RA+ Cells # Bld^LN^86007723^CD3/CD8/CD45RA, Absolute^L|1|600|cells/uL|450-1500||||F|||20241206093739OBX|51|NM|82744-4^CD8+CD45RA+ Cells/100 CD8 NFr Bld^LN^86007724^CD3/CD8/CD45RA, Percent^L|1|10|% CD8|||||F|||20241206093739OBX|52|NM|85792-0^CD3+CD4+CD45RO+ # Bld^LN^86007725^CD3/CD4/CD45RO, Absolute^L|1|500|cells/uL|60-900||||F|||20241206093739OBX|53|NM|85791-2^CD3+CD4+CD45RO+/100 CD3 NFr Bld^LN^86007726^CD3/CD4/CD45RO, Percent^L|1|5|% CD4|2-22||||F|||20241206093739OBX|54|NM|85790-4^CD3+CD8+CD45RO+ # Bld^LN^86007727^CD3/CD8/CD45RO, Absolute^L|1|50|cells/uL|30-330||||F|||20241206093739OBX|55|NM|85789-6^CD3+CD8+CD45RO+/100 CD3 NFr Bld^LN^86007728^CD3/CD8/CD45RO, Percent^L|1|2|% CD8|1-9||||F|||20241206093739OBX|56|CE|62321-5^Severe combined immunodeficiency newborn screen interpretation^LN|1|LA18593-6^Out of range^LN|||A|||F|||20241206093739OBX|57|TX|62322-3^Severe combined immunodeficiency newborn screening comment-discussion^LN|1|Refer to CCS-approved Immunology Center|||A|||F|||20241206093739

examples/Test/Automated/GoldenCopy/Expected/011_CA_ORU_R01_CDPH_UCSD_MRN_80015981_pre_TI_TC008.hl7

@@ -0,0 +1 @@
+MSH|^~\&|GOLDEN-COPY|CDPH|EPIC|R508|20241211104422||ORU^R01|011|N|2.5.1PID|1||80015981||HIPPO^BOY B ALLIE||202412091336|M||2106-3^White||||||||||||2186-5^Not Hispanic or Latino||Y|2NK1|1|HIPPO^ALLIE|MTH^Mother|518 BIG BEN WAY^^OCEANSIDE^CA^92058^USA|^^^^^442^2885325|||||||||||19941209ORC|RE|189728238^HospOrdNumber||7322694174^FormNumber||||||||1427255868^JOHNSON^KATHRYN^^^^^^^^^^NPI|||||||||UC SAN DIEGO MEDICAL CENTER^^^^^^^^^R508|W 025TS HT71 , C #^^SAN DIEGO^CA^99999-9999OBR|1|189728238^HospOrdNumber||54089-8^NB Screen Panel Patient AHIC^CDPHGSPEAP|||202412101414|||||||||1427255868^JOHNSON^KATHRYN^^^^^^^^^^NPI||||||20241211104422|||FOBX|1|CE|57721-3^Reason for lab test in Dried blood spot^LN|1|LA12427-3^Subsequent screen - for clarification of initial results (not by law or protocol)^LN|||N|||F|||20241211104422OBX|2|CE|57718-9^Sample quality of Dried blood spot^LN|1|LA12443-0^Specimen quantity insufficient for testing^LN|||N|||F|||20241211104422OBX|3|CE|57131-5^Newborn conditions with positive markers [Identifier] in Dried blood spot^LN|1|LA137-2^None^LN|||N|||F|||20241211104422OBX|4|CE|57720-5^Newborn conditions with equivocal markers [Identifier] in Dried blood spot^LN|1|LA137-2^None^LN|||N|||F|||20241211104422OBX|5|TX|57724-7^Newborn screening short narrative summary^LN|1|ACTION REQUIRED\.br\\.br\Testing Lab - COMMUNITY REG MEDICAL CENTER LAB \R\ NAR 01303DR OJEIV OHC, TS513 E, FRESNO, CA 99999\.br\\.br\Lab Director - Genetic Disease Laboratory, (510) 231-1790\.br\\.br\** This specimen was inadequate for testing for the following reason: ** 13 - Specimen not collected on acceptable filter paper including expired form THE PHYSICIAN LISTED HAS BEEN NOTIFIED \.br\\.br\|||N|||F|||20241211104422OBX|6|TX|57129-9^Full newborn screening summary report for display or printing^LN|1||||N|||F|||20241211104422OBX|7|ST|57716-3^State printed on filter paper card [Identifier] in NBS card^LN|1|CA|||N|||F|||20241211104422OBX|8|NM|8339-4^Birthweight^LN|1|2812|grams||N|||F|||20241211104422OBX|9|TM|57715-5^Time of birth^LN|1|1336|||N|||F|||20241211104422OBX|10|CE|57722-1^Birth plurality of Pregnancy^LN|1|LA12412-5^Twins^LN|||N|||F|||20241211104422OBX|11|NM|73806-2^Newborn age in hours^LN|1|24|hour(s)||N|||F|||20241211104422OBX|12|CE|57713-0^Infant NICU factors that affect newborn screening interpretation^LN|1|LA137-2^None^LN|||N|||F|||20241211104422OBX|13|CE|67704-7^Feeding types^LN|1|LA16914-6^Breast milk^LN|||N|||F|||20241211104422OBX|14|TX|62324-9^Post-discharge provider name^LN|1|EUSTRATIA HUBBARD|||N|||F|||20241211104422OBX|15|TX|62327-2^Post-discharge provider practice address^LN|1|W 025TS HT71 , C # SAN DIEGO CA 99999-9999 USA|||N|||F|||20241211104422