Workflow to send HL7 messages to RS staging (#1274)

* Added inital workflow to send hl7 files to staging * Added option for manual testing * Added trigger to test * Fixed installation * Fixed path * Fixed hurl command call and added test sample files * Testing workflow * Testing workflow * Added env variable * Seems like the jwt cli has a limitation that requires the private key to be read from a file * Added required pem extension * Fixed path to hurl script * Changed sender name for testing * Testing getting token from RS * Fixed variable name * Added request to waters api * Cleaned up and reverted to correct sender name * Remved temp files and updated file path * Clean up * Removed pr trigger * Changed to use Azure storage blob instead of repository to store files * Added back pr trigger for testing purposes * Added required permissions * Changed source for az command and formatted * Changed back to use repository-stored files instead of Azure container * Renamed workflow * Testing uploading to azure storage container * Testing uploading to azure storage container (cont.) * Testing uploading to azure storage container (cont.) * Reverted steps used for testing * Removed pull_request trigger used for testing * Added test order based on AL sample file * Added pull_request trigger for testing * Small change to trigger gh action * Changed public/private keypair for RS sender * Removed pull_request trigger used for testing * Changed schedule to run from Tuesday to Saturday, after changes in the repositories are expected to happen * Added ORU sample file
CDCgov · Sep 6, 2024 · 01e27b0 · 01e27b0
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diff --git a/.github/workflows/automated-staging-test-submit.yml b/.github/workflows/automated-staging-test-submit.yml
@@ -0,0 +1,61 @@
+name: Automated Staging Test - Submit Messages
+
+on:
+  schedule:
+    - cron: "0 0 * * 2-6"  # Tuesday to Saturday at Midnight UTC
+  workflow_dispatch:
+
+jobs:
+  send_files:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@v4
+
+      - name: Install jq
+        run: sudo apt-get install -y jq
+
+      - 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
+
+      - name: Write private key to file
+        run: |
+          echo "${{ secrets.AUTOMATED_STAGING_RS_INTEGRATION_PRIVATE_KEY }}" > /tmp/staging_private_key.pem
+          chmod 600 /tmp/staging_private_key.pem
+
+      - name: Send HL7 sample messages to staging RS
+        run: |
+            host=https://staging.prime.cdc.gov:443
+            client_id=flexion
+            client_sender=automated-staging-test-sender
+            jwt=$(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()
+        run: |
+          rm -f /tmp/staging_private_key.pem
diff --git a/examples/Test/Automated/001_Staging_ORM_O01_short_linked_to_002_ORU.hl7 b/examples/Test/Automated/001_Staging_ORM_O01_short_linked_to_002_ORU.hl7
@@ -0,0 +1,6 @@
+MSH|^~\&|Sender Application^sender.test.com^DNS|Sender Facility^0.0.0.0.0.0.0.0^ISO|Receiver Application^0.0.0.0.0.0.0.0^ISO|Receiver Facility^automated-staging-test-receiver-id^DNS|20230101010000-0000||ORM^O01^ORM_O01|111111|T|2.5.1||||||||||
+PID|1||1300974^^^Baptist East^MR||ONE^TESTCASE||202402210152-0500|F^Female^HL70001||2106-3^White^HL70005|1234 GPCS WAY^^MONTGOMERY^Alabama^36117^USA^home^^Montgomery|||||||2227600015||||N^Not Hispanic or Latino^HL70189|||1|||||
+NK1|1|ONE^MOMFIRST|MTH^Mother^HL70063||^^^^^804^5693861||||||||||||||||||||||||||||123456789^^^Medicaid&2.16.840.1.113883.4.446&ISO^MD||||000-00-0000^^^ssn&2.16.840.1.113883.4.1&ISO^SS
+ORC|NW|4560411583^ORDERID||||||||||12345^^^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L|||||||||
+OBR|1|4560411583^ORDERID||54089-8^Newborn screening panel AHIC^LN|||202402221854-0500|||||||||12345^^^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L||||||||
+OBX|1|ST|57723-9^Unique bar code number of Current sample^LN||123456||||||F|||202402221854-0500
diff --git a/examples/Test/Automated/002_Staging_ORU_O01_short_linked_to_001_ORM.hl7 b/examples/Test/Automated/002_Staging_ORU_O01_short_linked_to_001_ORM.hl7
@@ -0,0 +1,7 @@
+MSH|^~\&|Sender Application^sender.test.com^DNS|Sender Facility^0.0.0.0.0.0.0.0^ISO|Receiver Application^0.0.0.0.0.0.0.0^ISO|Receiver Facility^automated-staging-test-receiver-id^DNS|20230101010000-0000||ORU^R01^ORU_R01|111111|T|2.5.1||||||||||
+PID|1||1300974^^^Baptist East^MR||ONE^TESTCASE||20230504131000|F^Female^HL70001||2106-3^White^HL70005|1234 GPCS WAY^^MONTGOMERY^Alabama^36117^USA^home^^Montgomery|||||||2227600015||||N^Not Hispanic or Latino^HL70189|||1|||||N|
+NK1|1|ONE^MOMFIRST|MTH^Mother^HL70063^^^^^^Mother||^^^^^804^5693861||||||||||||||||||||||||||||123456789^^^Medicaid&2.16.840.1.113883.4.446&ISO^MD||||000-00-0000^^^ssn&2.16.840.1.113883.4.1&ISO^SS|||||||
+ORC|RE|4560411583^ORDERID|20231561137^ALPHL|||||||||1174911127^SMITH^SAMANTHA^^^^^^NPI^L^^^NPI|||||||||BAPTIST EAST^L^^^^CMS^NPI^^^1043269798~BAPTIST EAST^L^^^^AL Public Health Lab^Submitter ID^^^739||||||||||54089-8^Newborn screening panel American Health Information Community (AHIC)^LN|
+OBR|1|4560411583^ORDERID|20231561137^ALPHL|57128-1^Newborn Screening Report summary panel^LN|||20230603045000||||O|||||1174911127^SMITH^SAMANTHA^^^^^^NPI^L^^^NPI||||||20230606191613|||F||||423787478&EPIC&1.2.840.114350.1.13.145.2.7.2.695071&ISO^20231561137&AL Public Health Lab&2.16.840.1.114222.4.1.10080&ISO|||||||||||||||||||||54089-8^Newborn screening panel American Health Information Community (AHIC)^LN|
+OBX|1|CWE|57718-9^Sample quality of Dried blood spot^LN|^1^1|LA12432-3^Acceptable^LN||||||F|||20230603045000|||||20230606191613||||AL PHL Newborn Screening Laboratory^^^^^|204 Legends Court^^Prattville^AL^36066|^Miller^Marie^^^^^^||||RSLT|UNSP|
+SPM|1|423787478&EPIC&1.2.840.114350.1.13.145.2.7.2.695071&ISO^20231561137&AL Public Health Lab&2.16.840.1.114222.4.1.10080&ISO||440500007^Blood spot specimen^SCT|||||||||||||20230603045000^20230603045000|20230605102300|