Minor Adjustments

medizininformatik-initiative · Dec 10, 2024 · 6532eb4 · 6532eb4
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Showing 18 changed files with 127 additions and 123 deletions.
diff --git a/.github/integration-test/basic-auth/Dockerfile b/.github/integration-test/basic-auth/Dockerfile
@@ -1,4 +1,4 @@
-# Image is uses as base for a dummy container from which curl can request data within the same network as the other containers
+# Image is used as base for a dummy container from which curl can request data within the same network as the other containers
 FROM alpine
 RUN apk add --no-cache curl
 CMD ["sh", "-c", "while true; do sleep 3600; done"]
diff --git a/.github/integration-test/basic-auth/docker-compose.yml b/.github/integration-test/basic-auth/docker-compose.yml
@@ -22,9 +22,9 @@ services:
       FHIR_SOURCE_SERVER: "http://proxy:8080/fhir"
       FHIR_SOURCE_USER: "test"
       FHIR_SOURCE_PASSWORD: "bar"
-      FHIR_DESTINATION_SERVER: "http://proxy:8080/fhir"
-      FHIR_DESTINATION_USER: "test"
-      FHIR_DESTINATION_PASSWORD: "bar"
+      FHIR_REPORT_SERVER: "http://proxy:8080/fhir"
+      FHIR_REPORT_USER: "test"
+      FHIR_REPORT_PASSWORD: "bar"
       SEND_REPORT_TO_SERVER: ${FDE_SEND_REPORT_TO_SERVER:-false}
       AUTHOR_IDENTIFIER_SYSTEM: ${FDE_AUTHOR_IDENTIFIER_SYSTEM:-}
       AUTHOR_IDENTIFIER_VALUE: ${FDE_AUTHOR_IDENTIFIER_VALUE:-}

diff --git a/.github/integration-test/evaluate-and-post-different-doc-ref.sh b/.github/integration-test/evaluate-and-post-different-doc-ref.sh
@@ -38,12 +38,12 @@ get_response() {
                       -d 'grant_type=client_credentials' \
                       -d 'client_id=account' \
                       -d 'client_secret=test'")
-    FHIR_DESTINATION_BEARER_TOKEN=$(echo "$oauth_response" | jq -r '.access_token')
+    FHIR_REPORT_BEARER_TOKEN=$(echo "$oauth_response" | jq -r '.access_token')
 
     response=$(docker exec "$CURL_TESTER_ID" sh -c "
                   curl -s 'https://secure-fhir-server:8443/fhir/$URL' \
                            -H 'Content-Type: application/fhir+json' \
-                           -H 'Authorization: Bearer $FHIR_DESTINATION_BEARER_TOKEN'")
+                           -H 'Authorization: Bearer $FHIR_REPORT_BEARER_TOKEN'")
 
     echo "$response"
   fi

diff --git a/.github/integration-test/evaluate-and-post-report.sh b/.github/integration-test/evaluate-and-post-report.sh
@@ -39,12 +39,12 @@ get_response() {
                       -d 'grant_type=client_credentials' \
                       -d 'client_id=account' \
                       -d 'client_secret=test'")
-    FHIR_DESTINATION_BEARER_TOKEN=$(echo "$oauth_response" | jq -r '.access_token')
+    FHIR_REPORT_BEARER_TOKEN=$(echo "$oauth_response" | jq -r '.access_token')
 
     response=$(docker exec "$CURL_TESTER_ID" sh -c "
                   curl -s 'https://secure-fhir-server:8443/fhir/$URL' \
                            -H 'Content-Type: application/fhir+json' \
-                           -H 'Authorization: Bearer $FHIR_DESTINATION_BEARER_TOKEN'")
+                           -H 'Authorization: Bearer $FHIR_REPORT_BEARER_TOKEN'")
 
     echo "$response"
   fi

diff --git a/.github/integration-test/evaluate-and-post-update.sh b/.github/integration-test/evaluate-and-post-update.sh
@@ -36,12 +36,12 @@ get_response() {
                       -d 'grant_type=client_credentials' \
                       -d 'client_id=account' \
                       -d 'client_secret=test'")
-    FHIR_DESTINATION_BEARER_TOKEN=$(echo "$oauth_response" | jq -r '.access_token')
+    FHIR_REPORT_BEARER_TOKEN=$(echo "$oauth_response" | jq -r '.access_token')
 
     response=$(docker exec "$CURL_TESTER_ID" sh -c "
                   curl -s 'https://secure-fhir-server:8443/fhir/$URL' \
                            -H 'Content-Type: application/fhir+json' \
-                           -H 'Authorization: Bearer $FHIR_DESTINATION_BEARER_TOKEN'")
+                           -H 'Authorization: Bearer $FHIR_REPORT_BEARER_TOKEN'")
 
     echo "$response"
   fi

diff --git a/.github/integration-test/no-auth/Dockerfile b/.github/integration-test/no-auth/Dockerfile
@@ -1,4 +1,4 @@
-# Image is uses as base for a dummy container from which curl can request data within the same network as the other containers
+# Image is used as base for a dummy container from which curl can request data within the same network as the other containers
 FROM alpine
 RUN apk add --no-cache curl
 CMD ["sh", "-c", "while true; do sleep 3600; done"]
diff --git a/.github/integration-test/no-auth/docker-compose.yml b/.github/integration-test/no-auth/docker-compose.yml
@@ -15,7 +15,7 @@ services:
     environment:
       CONVERT_TO_CSV: ${FDE_CONVERT_TO_CSV:-true}
       FHIR_SOURCE_SERVER: "http://fhir-server:8080/fhir"
-      FHIR_DESTINATION_SERVER: "http://fhir-server:8080/fhir"
+      FHIR_REPORT_SERVER: "http://fhir-server:8080/fhir"
       SEND_REPORT_TO_SERVER: ${FDE_SEND_REPORT_TO_SERVER:-false}
       AUTHOR_IDENTIFIER_SYSTEM: ${FDE_AUTHOR_IDENTIFIER_SYSTEM:-}
       AUTHOR_IDENTIFIER_VALUE: ${FDE_AUTHOR_IDENTIFIER_VALUE:-}

diff --git a/.github/integration-test/oauth/Dockerfile b/.github/integration-test/oauth/Dockerfile
@@ -1,4 +1,4 @@
-# Image is uses as base for a dummy container from which curl can request data within the same network as the other containers
+# Image is used as base for a dummy container from which curl can request data within the same network as the other containers
 FROM alpine
 RUN apk add --no-cache curl
 CMD ["sh", "-c", "while true; do sleep 3600; done"]
diff --git a/.github/integration-test/oauth/docker-compose.yml b/.github/integration-test/oauth/docker-compose.yml
@@ -111,10 +111,10 @@ services:
       FHIR_SOURCE_OAUTH_ISSUER_URI: "https://secure-keycloak:8443/realms/test"
       FHIR_SOURCE_OAUTH_CLIENT_ID: "account"
       FHIR_SOURCE_OAUTH_CLIENT_SECRET: "test"
-      FHIR_DESTINATION_SERVER: "https://secure-fhir-server:8443/fhir"
-      FHIR_DESTINATION_OAUTH_ISSUER_URI: "https://secure-keycloak:8443/realms/test"
-      FHIR_DESTINATION_OAUTH_CLIENT_ID: "account"
-      FHIR_DESTINATION_OAUTH_CLIENT_SECRET: "test"
+      FHIR_REPORT_SERVER: "https://secure-fhir-server:8443/fhir"
+      FHIR_REPORT_OAUTH_ISSUER_URI: "https://secure-keycloak:8443/realms/test"
+      FHIR_REPORT_OAUTH_CLIENT_ID: "account"
+      FHIR_REPORT_OAUTH_CLIENT_SECRET: "test"
       SEND_REPORT_TO_SERVER: ${FDE_SEND_REPORT_TO_SERVER:-false}
       AUTHOR_IDENTIFIER_SYSTEM: ${FDE_AUTHOR_IDENTIFIER_SYSTEM:-}
       AUTHOR_IDENTIFIER_VALUE: ${FDE_AUTHOR_IDENTIFIER_VALUE:-}

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -155,13 +155,13 @@ jobs:
       - name: Run Integration Test to check if it correctly exits when there are insufficient writing permissions
         run: .github/integration-test/missing-permissions-test.sh
 
-      - name: Run Integration Test for Posting the MeasureReport to the FHIR server
+      - name: Run Integration Test for Posting the MeasureReport to the Report FHIR server
         run: .github/integration-test/evaluate-and-post-report.sh ${{ matrix.test }} Test_PROJECT_Evaluation_1
 
-      - name: Run Integration Test for Posting the MeasureReport to the FHIR server with the Same Project Identifier
+      - name: Run Integration Test for Posting the MeasureReport to the Report FHIR server with the Same Project Identifier
         run: .github/integration-test/evaluate-and-post-update.sh ${{ matrix.test }} Test_PROJECT_Evaluation_1
 
-      - name: Run Integration Test for Posting the MeasureReport to the FHIR server with a Different Project Identifier
+      - name: Run Integration Test for Posting the MeasureReport to the Report FHIR server with a Different Project Identifier
         run: .github/integration-test/evaluate-and-post-different-doc-ref.sh ${{ matrix.test }} Test_PROJECT_Evaluation_2
 
       - name: Remove Blaze volumes

diff --git a/README.md b/README.md
@@ -31,8 +31,9 @@ For a more detailed Documentation see: * [Documentation](Documentation/Documenta
 
 ## Run
 
-When running the Fhir Data Evaluator with Docker, it will require a Measure resource file as input and save the resulting
-MeasureReport into a Directory named after the current date combined with the Measure's name (specified in the 'name' field).
+When running the Fhir Data Evaluator with Docker, it will require a Measure resource file as input. The resulting
+MeasureReport will be saved inside `/app/output/` of the Docker container into a new Directory named after the current 
+date combined with the Measure's name (specified in the 'name' field of the Measure).
 If specified, additional CSV files will be created that represent the MeasureReport.
 
 An example of a Measure can be found [here](Documentation/example-measures/example-measure-1.json).
@@ -83,7 +84,7 @@ docker run -v <your/measurefile.json>:/app/measure.json -v <your/output/dir>:/ap
 
 ### Sending the MeasureReport to a FHIR Server
 
-If `SEND_REPORT_TO_SERVER` is set to true, the MeasureReport is sent to the `FHIR_DESTINATION_SERVER` along with a 
+If `SEND_REPORT_TO_SERVER` is set to true, the MeasureReport is sent to the `FHIR_REPORT_SERVER` along with a
 DocumentReference that is configured with the following environment variables:
 * `AUTHOR_IDENTIFIER_SYSTEM` (example: `http://dsf.dev/sid/organization-identifier`)
 * `AUTHOR_IDENTIFIER_VALUE` (example: `Test_DIC1`)
@@ -92,35 +93,35 @@ DocumentReference that is configured with the following environment variables:
 
 ## Environment Variables
 
-| Name                                 | Default                                                       | Description                                                                                                |
-|:-------------------------------------|:--------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------|
-| FHIR_SOURCE_SERVER                   | http://localhost:8080/fhir                                    | The base URL of the FHIR server to use for downloading the resources.                                      |
-| FHIR_SOURCE_USER                     |                                                               | The username to use for HTTP Basic Authentication for the source FHIR server.                              |
-| FHIR_SOURCE_PASSWORD                 |                                                               | The password to use for HTTP Basic Authentication for the source FHIR server.                              |
-| FHIR_SOURCE_MAX_CONNECTIONS          | 4                                                             | The maximum number of connections to open towards the source FHIR server.                                  |
-| FHIR_SOURCE_MAX_QUEUE_SIZE           | 500                                                           | The maximum number FHIR server requests at the source FHIR server to queue before returning an error.      |
-| FHIR_SOURCE_PAGE_COUNT               | 1000                                                          | The number of resources per page to request from the source FHIR server.                                   |
-| FHIR_SOURCE_BEARER_TOKEN             |                                                               | Bearer token for authentication for the source FHIR server.                                                |
-| FHIR_SOURCE_OAUTH_ISSUER_URI         |                                                               | The issuer URI of the OpenID Connect provider for the source FHIR server.                                  |
-| FHIR_SOURCE_OAUTH_CLIENT_ID          |                                                               | The client ID to use for authentication with OpenID Connect provider for the source FHIR server.           |
-| FHIR_SOURCE_OAUTH_CLIENT_SECRET      |                                                               | The client secret to use for authentication with OpenID Connect provider for the source FHIR server.       |
-| FHIR_DESTINATION_SERVER              | http://localhost:8080/fhir                                    | The base URL of the FHIR server to use for (optionally) uploading the MeasureReport.                       |
-| FHIR_DESTINATION_USER                |                                                               | The username to use for HTTP Basic Authentication for the destination FHIR server.                         |
-| FHIR_DESTINATION_PASSWORD            |                                                               | The password to use for HTTP Basic Authentication for the destination FHIR server.                         |
-| FHIR_DESTINATION_MAX_CONNECTIONS     | 4                                                             | The maximum number of connections to open towards the destination FHIR server.                             |
-| FHIR_DESTINATION_MAX_QUEUE_SIZE      | 500                                                           | The maximum number FHIR server requests at the destination FHIR server to queue before returning an error. |
-| FHIR_DESTINATION_BEARER_TOKEN        |                                                               | Bearer token for authentication for the destination FHIR server.                                           |
-| FHIR_DESTINATION_OAUTH_ISSUER_URI    |                                                               | The issuer URI of the OpenID Connect provider for the destination FHIR server.                             |
-| FHIR_DESTINATION_OAUTH_CLIENT_ID     |                                                               | The client ID to use for authentication with OpenID Connect provider for the destination FHIR server.      |
-| FHIR_DESTINATION_OAUTH_CLIENT_SECRET |                                                               | The client secret to use for authentication with OpenID Connect provider for the destination FHIR server.  |
-| MAX_IN_MEMORY_SIZE_MIB               | 10                                                            | The maximum in-memory buffer size for each webclient in MiB.                                               |
-| TZ                                   | Europe/Berlin                                                 | The time zone used to create the output directory and set the date in the DocumentReference.               |
-| CONVERT_TO_CSV                       | false                                                         | Whether for the MeasureReport should be generated CSV files.                                               |
-| SEND_REPORT_TO_SERVER                | false                                                         | Whether the MeasureReport should be sent to a FHIR server.                                                 |
-| AUTHOR_IDENTIFIER_SYSTEM             | http://dsf.dev/sid/organization-identifier                    | The system of the author organization used when uploading the report.                                      |
-| AUTHOR_IDENTIFIER_VALUE              |                                                               | The code of the author organization used when uploading the report.                                        |
-| PROJECT_IDENTIFIER_SYSTEM            | http://medizininformatik-initiative.de/sid/project-identifier | The system of the master identifier used when uploading the report.                                        |
-| PROJECT_IDENTIFIER_VALUE             |                                                               | The value of the master identifier used when uploading the report.                                         |
+| Name                            | Default                                                       | Description                                                                                           |
+|:--------------------------------|:--------------------------------------------------------------|:------------------------------------------------------------------------------------------------------|
+| FHIR_SOURCE_SERVER              | http://localhost:8080/fhir                                    | The base URL of the FHIR server to use for downloading the resources.                                 |
+| FHIR_SOURCE_USER                |                                                               | The username to use for HTTP Basic Authentication for the source FHIR server.                         |
+| FHIR_SOURCE_PASSWORD            |                                                               | The password to use for HTTP Basic Authentication for the source FHIR server.                         |
+| FHIR_SOURCE_MAX_CONNECTIONS     | 4                                                             | The maximum number of connections to open towards the source FHIR server.                             |
+| FHIR_SOURCE_MAX_QUEUE_SIZE      | 500                                                           | The maximum number FHIR server requests at the source FHIR server to queue before returning an error. |
+| FHIR_SOURCE_PAGE_COUNT          | 1000                                                          | The number of resources per page to request from the source FHIR server.                              |
+| FHIR_SOURCE_BEARER_TOKEN        |                                                               | Bearer token for authentication for the source FHIR server.                                           |
+| FHIR_SOURCE_OAUTH_ISSUER_URI    |                                                               | The issuer URI of the OpenID Connect provider for the source FHIR server.                             |
+| FHIR_SOURCE_OAUTH_CLIENT_ID     |                                                               | The client ID to use for authentication with OpenID Connect provider for the source FHIR server.      |
+| FHIR_SOURCE_OAUTH_CLIENT_SECRET |                                                               | The client secret to use for authentication with OpenID Connect provider for the source FHIR server.  |
+| FHIR_REPORT_SERVER              | http://localhost:8080/fhir                                    | The base URL of the FHIR server to use for (optionally) uploading the MeasureReport.                  |
+| FHIR_REPORT_USER                |                                                               | The username to use for HTTP Basic Authentication for the Report FHIR server.                         |
+| FHIR_REPORT_PASSWORD            |                                                               | The password to use for HTTP Basic Authentication for the Report FHIR server.                         |
+| FHIR_REPORT_MAX_CONNECTIONS     | 4                                                             | The maximum number of connections to open towards the Report FHIR server.                             |
+| FHIR_REPORT_MAX_QUEUE_SIZE      | 500                                                           | The maximum number FHIR server requests at the Report FHIR server to queue before returning an error. |
+| FHIR_REPORT_BEARER_TOKEN        |                                                               | Bearer token for authentication for the Report FHIR server.                                           |
+| FHIR_REPORT_OAUTH_ISSUER_URI    |                                                               | The issuer URI of the OpenID Connect provider for the Report FHIR server.                             |
+| FHIR_REPORT_OAUTH_CLIENT_ID     |                                                               | The client ID to use for authentication with OpenID Connect provider for the Report FHIR server.      |
+| FHIR_REPORT_OAUTH_CLIENT_SECRET |                                                               | The client secret to use for authentication with OpenID Connect provider for the Report FHIR server.  |
+| MAX_IN_MEMORY_SIZE_MIB          | 10                                                            | The maximum in-memory buffer size for each webclient in MiB.                                          |
+| TZ                              | Europe/Berlin                                                 | The time zone used to create the output directory and set the date in the DocumentReference.          |
+| CONVERT_TO_CSV                  | false                                                         | Whether for the MeasureReport should be generated CSV files.                                          |
+| SEND_REPORT_TO_SERVER           | false                                                         | Whether the MeasureReport should be sent to the FHIR Report server.                                   |
+| AUTHOR_IDENTIFIER_SYSTEM        | http://dsf.dev/sid/organization-identifier                    | The system of the author organization used when uploading the report.                                 |
+| AUTHOR_IDENTIFIER_VALUE         |                                                               | The code of the author organization used when uploading the report.                                   |
+| PROJECT_IDENTIFIER_SYSTEM       | http://medizininformatik-initiative.de/sid/project-identifier | The system of the master identifier used when uploading the report.                                   |
+| PROJECT_IDENTIFIER_VALUE        |                                                               | The value of the master identifier used when uploading the report.                                    |
 
 
 ## Documentation