Merge pull request #30 from medizininformatik-initiative/release-v0.2.2

Release v0.2.2
medizininformatik-initiative · Sep 17, 2024 · 401a6d0 · 401a6d0
2 parents 358c555 + 3e6e593
commit 401a6d0
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Showing 12 changed files with 496 additions and 96 deletions.
diff --git a/.env.default b/.env.default
@@ -15,7 +15,9 @@ HISTORY_TABLE_LEN=14
 EXECUTE_FEAS_TEST=false
 CONFLUENCE_PAGE_ID_FEAS=""
 EXECUTE_DSF_PING_TEST=false
+EXECUTE_ACTIVITY_DEF_COLLECTION=false
+EXECUTE_COLLECT_REPORT_OVERVIEW=false
 CONFLUENCE_PAGE_ID_PING=""
 LOCAL_DSF_CERT_PATH=
 LOCAL_DSF_KEY_PATH=
-LOG_LEVEL=INFO
+LOG_LEVEL=INFO
diff --git a/.gitignore b/.gitignore
@@ -2,7 +2,9 @@
 feasibility-results.json
 dev-call.sh
 reports/*.json
+reports/*.csv
+venv
 certs/
 temp/
 __pycache__/
-config/config.yml
+config/config.yml
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Fixed
 ### Security
 
+
+## [0.2.2] - 2024-09-17
+
+### Fixed
+
+### Added
+
+- Added new loinc code ([#28](https://github.com/medizininformatik-initiative/feasibility-monitoring/issues/28))
+- Added new ATC and changed specimen code ([#26](https://github.com/medizininformatik-initiative/feasibility-monitoring/issues/26))
+- Added ActivityDefinition query ([#25](https://github.com/medizininformatik-initiative/feasibility-monitoring/pull/25))
+- Added collection of kds report overview
+
 ## [0.2.1] - 2024-02-16
 
 ### Fixed

diff --git a/config/input-queries.json b/config/input-queries.json
@@ -96,6 +96,21 @@
                 "display": "Laboruntersuchung"
               }
             },
+            {
+              "termCodes": [
+                {
+                  "code": "59260-0",
+                  "system": "http://loinc.org",
+                  "display": "Hemoglobin [Moles/volume] in Blood"
+                }
+              ],
+              "context": {
+                "code": "Laboruntersuchung",
+                "system": "fdpg.mii.cds",
+                "version": "1.0.0",
+                "display": "Laboruntersuchung"
+              }
+            },
             {
               "termCodes": [
                 {
@@ -199,6 +214,22 @@
                 "version": "1.0.0",
                 "display": "Verabreichung von Medikamenten"
               }
+            },
+            {
+              "termCodes": [
+                {
+                  "code": "L03AA02",
+                  "system": "http://fhir.de/CodeSystem/bfarm/atc",
+                  "version": "2022",
+                  "display": "Filgrastim"
+                }
+              ],
+              "context": {
+                "code": "Medikamentenverabreichung",
+                "system": "fdpg.mii.cds",
+                "version": "1.0.0",
+                "display": "Verabreichung von Medikamenten"
+              }
             }
           ]
         ]
@@ -263,7 +294,7 @@
                 {
                   "code": "119297000",
                   "system": "http://snomed.info/sct",
-                  "version": "http://snomed.info/sct/900000000000207008/version/20220930",
+                  "version": "http://snomed.info/sct/900000000000207008/version/20240501",
                   "display": "Blood specimen"
                 }
               ],
@@ -279,7 +310,7 @@
                 {
                   "code": "119361006",
                   "system": "http://snomed.info/sct",
-                  "version": "http://snomed.info/sct/900000000000207008/version/20220930",
+                  "version": "http://snomed.info/sct/900000000000207008/version/20240501",
                   "display": "Plasma specimen"
                 }
               ],
@@ -295,7 +326,7 @@
                 {
                   "code": "119376003",
                   "system": "http://snomed.info/sct",
-                  "version": "http://snomed.info/sct/900000000000207008/version/20220930",
+                  "version": "http://snomed.info/sct/900000000000207008/version/20240501",
                   "display": "Tissue specimen"
                 }
               ],
@@ -311,7 +342,7 @@
                 {
                   "code": "441652008",
                   "system": "http://snomed.info/sct",
-                  "version": "http://snomed.info/sct/900000000000207008/version/20220930",
+                  "version": "http://snomed.info/sct/900000000000207008/version/20240501",
                   "display": "Formalin-fixed paraffin-embedded tissue specimen"
                 }
               ],
@@ -327,7 +358,7 @@
                 {
                   "code": "441479001",
                   "system": "http://snomed.info/sct",
-                  "version": "http://snomed.info/sct/900000000000207008/version/20220930",
+                  "version": "http://snomed.info/sct/900000000000207008/version/20240501",
                   "display": "Fresh tissue specimen"
                 }
               ],
@@ -341,25 +372,9 @@
             {
               "termCodes": [
                 {
-                  "code": "420135007",
+                  "code": "258580003",
                   "system": "http://snomed.info/sct",
-                  "version": "http://snomed.info/sct/900000000000207008/version/20220930",
-                  "display": "Whole blood"
-                }
-              ],
-              "context": {
-                "code": "Specimen",
-                "system": "fdpg.mii.cds",
-                "version": "1.0.0",
-                "display": "Bioprobe"
-              }
-            },
-            {
-              "termCodes": [
-                {
-                  "code": "404798000",
-                  "system": "http://snomed.info/sct",
-                  "version": "http://snomed.info/sct/900000000000207008/version/20220930",
+                  "version": "http://snomed.info/sct/900000000000207008/version/20240501",
                   "display": "Whole blood"
                 }
               ],
@@ -375,8 +390,8 @@
                 {
                   "code": "119342007",
                   "system": "http://snomed.info/sct",
-                  "version": "http://snomed.info/sct/900000000000207008/version/20220930",
-                  "display": "Whole blood"
+                  "version": "http://snomed.info/sct/900000000000207008/version/20240501",
+                  "display": "Saliva Specimen"
                 }
               ],
               "context": {

diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -5,6 +5,8 @@ RUN mkdir -p /opt/reportclient
 COPY src/py/feasibility-monitoring.py /opt/reportclient/src/py/feasibility-monitoring.py
 COPY src/py/execute_ping_test.py /opt/reportclient/src/py/execute_ping_test.py
 COPY src/py/execute_feasibility_test.py /opt/reportclient/src/py/execute_feasibility_test.py
+COPY src/py/execute_collect_activity_definitions.py /opt/reportclient/src/py/execute_collect_activity_definitions.py
+COPY src/py/execute_collect_report_overview.py /opt/reportclient/src/py/execute_collect_report_overview.py
 COPY config/input-queries.json /opt/reportclient/config/input-queries.json
 COPY config/history-query.json /opt/reportclient/config/history-query.json
 COPY config/config.yml /opt/reportclient/config/config.yml

diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
     feasibility-test-client:
-        image: ghcr.io/medizininformatik-initiative/feasibility-monitoring:0.2.1
+        image: ghcr.io/medizininformatik-initiative/feasibility-monitoring:0.2.2
         environment:
             - BACKEND_BASE_URL=${BACKEND_BASE_URL:-"https://localhost/api/v1"} 
             - BACKEND_CLIENT_ID=${BACKEND_CLIENT_ID:-""} 
@@ -22,6 +22,8 @@ services:
             - EXECUTE_DSF_PING_TEST=${EXECUTE_DSF_PING_TEST:-"false"}
             - CONFLUENCE_PAGE_ID_PING=${CONFLUENCE_PAGE_ID_PING:-""}
             - LOG_LEVEL=${LOG_LEVEL:-"INFO"}
+            - EXECUTE_ACTIVITY_DEF_COLLECTION=${EXECUTE_ACTIVITY_DEF_COLLECTION:-"false"}
+            - EXECUTE_COLLECT_REPORT_OVERVIEW=${EXECUTE_COLLECT_REPORT_OVERVIEW:-"false"}
         volumes:
             - ${LOCAL_DSF_CERT_PATH:-./cert/dsf-cert.cer}:/opt/reportclient/certs/dsf-cert.cer
             - ${LOCAL_DSF_KEY_PATH:-./cert/dsf-key.key}:/opt/reportclient/certs/dsf-key.key

diff --git a/docker/docker-entrypoint.sh b/docker/docker-entrypoint.sh
@@ -20,13 +20,17 @@ CONFLUENCE_PAGE_ID_HIST=${CONFLUENCE_PAGE_ID_HIST:-""}
 HISTORY_TABLE_LEN=${HISTORY_TABLE_LEN:-14}
 EXECUTE_DSF_PING_TEST=${EXECUTE_DSF_PING_TEST:-"false"}
 CONFLUENCE_PAGE_ID_PING=${CONFLUENCE_PAGE_ID_PING:-""}
+EXECUTE_ACTIVITY_DEF_COLLECTION=${EXECUTE_ACTIVITY_DEF_COLLECTION:-"false"}
+EXECUTE_COLLECT_REPORT_OVERVIEW=${EXECUTE_COLLECT_REPORT_OVERVIEW:-"false"}
 LOG_LEVEL=${LOG_LEVEL:-"INFO"}
 
+
+
 python src/py/feasibility-monitoring.py --dsf_cert_path $DSF_CERT_PATH --dsf_key_path $DSF_KEY_PATH --backend_base_url "$BACKEND_BASE_URL" --backend_client_id "$BACKEND_CLIENT_ID" \
  --client_secret "$BACKEND_CLIENT_SECRET" --keycloak_token_url "$KEYCLOAK_TOKEN_URL" \
  --confluence_api_base_url "$CONFLUENCE_API_BASE_URL" --conf_user "$CONF_USER" --conf_pw "$CONF_PW"\
  --send_results_confluence $SEND_TO_CONFLUENCE  --wait_result_secs_feas "$WAIT_RESULT_SECS_FEAS"\
  --dsf_base_url $DSF_BASE_URL --execute_feas_test $EXECUTE_FEAS_TEST --confluence_page_id_feas $CONFLUENCE_PAGE_ID_FEAS\
  --execute_history_test $EXECUTE_HISTORY_TEST --confluence_page_id_hist $CONFLUENCE_PAGE_ID_HIST --history_table_len $HISTORY_TABLE_LEN\
  --execute_ping_test $EXECUTE_DSF_PING_TEST --confluence_page_id_ping $CONFLUENCE_PAGE_ID_PING  --wait_result_secs_ping "$WAIT_RESULT_SECS_PING"\
- --log_level "$LOG_LEVEL"
+ --execute_collect_activity_definition $EXECUTE_ACTIVITY_DEF_COLLECTION --log_level "$LOG_LEVEL" --execute_collect_report_overview $EXECUTE_COLLECT_REPORT_OVERVIEW
diff --git a/src/execute-local.sh b/src/execute-local.sh
@@ -20,11 +20,15 @@ CONFLUENCE_PAGE_ID_HIST=${CONFLUENCE_PAGE_ID_HIST:-""}
 HISTORY_TABLE_LEN=${HISTORY_TABLE_LEN:-14}
 EXECUTE_DSF_PING_TEST=${EXECUTE_DSF_PING_TEST:-"false"}
 CONFLUENCE_PAGE_ID_PING=$CONFLUENCE_PAGE_ID_PING
+EXECUTE_ACTIVITY_DEF_COLLECTION=${EXECUTE_ACTIVITY_DEF_COLLECTION:-"false"}
+EXECUTE_COLLECT_REPORT_OVERVIEW=${EXECUTE_COLLECT_REPORT_OVERVIEW:-"false"}
+LOG_LEVEL=${LOG_LEVEL:-"INFO"}
 
-python src/py/feasibility-monitoring.py --dsf_cert_path $DSF_CERT_PATH --dsf_key_path $DSF_KEY_PATH --backend_base_url "$BACKEND_BASE_URL" --backend_client_id "$BACKEND_CLIENT_ID" \
+python3 src/py/feasibility-monitoring.py --dsf_cert_path $DSF_CERT_PATH --dsf_key_path $DSF_KEY_PATH --backend_base_url "$BACKEND_BASE_URL" --backend_client_id "$BACKEND_CLIENT_ID" \
  --client_secret "$BACKEND_CLIENT_SECRET" --keycloak_token_url "$KEYCLOAK_TOKEN_URL" \
  --confluence_api_base_url "$CONFLUENCE_API_BASE_URL" --conf_user "$CONF_USER" --conf_pw "$CONF_PW"\
  --send_results_confluence $SEND_TO_CONFLUENCE  --wait_result_secs_feas "$WAIT_RESULT_SECS_FEAS"\
  --dsf_base_url $DSF_BASE_URL --execute_feas_test $EXECUTE_FEAS_TEST --confluence_page_id_feas $CONFLUENCE_PAGE_ID_FEAS\
  --execute_history_test $EXECUTE_HISTORY_TEST --confluence_page_id_hist $CONFLUENCE_PAGE_ID_HIST --history_table_len $HISTORY_TABLE_LEN\
- --execute_ping_test $EXECUTE_DSF_PING_TEST --confluence_page_id_ping $CONFLUENCE_PAGE_ID_PING  --wait_result_secs_ping "$WAIT_RESULT_SECS_PING"
+ --execute_ping_test $EXECUTE_DSF_PING_TEST --confluence_page_id_ping $CONFLUENCE_PAGE_ID_PING  --wait_result_secs_ping "$WAIT_RESULT_SECS_PING"\
+ --execute_collect_activity_definition $EXECUTE_ACTIVITY_DEF_COLLECTION --log_level $LOG_LEVEL  --execute_collect_report_overview $EXECUTE_COLLECT_REPORT_OVERVIEW