Merge pull request #241 from samply/develop

feat: add focus tags in ccp and bbmri (#240)

.github/scripts/rename_inactive_branches.py

@@ -0,0 +1,39 @@
+import os
+import requests
+from datetime import datetime, timedelta
+
+# Configuration
+GITHUB_TOKEN = os.getenv('GITHUB_TOKEN')
+REPO = 'samply/bridgehead'
+HEADERS = {'Authorization': f'token {GITHUB_TOKEN}', 'Accept': 'application/vnd.github.v3+json'}
+API_URL = f'https://api.github.com/repos/{REPO}/branches'
+INACTIVE_DAYS = 365
+CUTOFF_DATE = datetime.now() - timedelta(days=INACTIVE_DAYS)
+
+# Fetch all branches
+def get_branches():
+    response = requests.get(API_URL, headers=HEADERS)
+    response.raise_for_status()
+    return response.json() if response.status_code == 200 else []
+
+# Rename inactive branches
+def rename_branch(old_name, new_name):
+    rename_url = f'https://api.github.com/repos/{REPO}/branches/{old_name}/rename'
+    response = requests.post(rename_url, json={'new_name': new_name}, headers=HEADERS)
+    response.raise_for_status()
+    print(f"Renamed branch {old_name} to {new_name}" if response.status_code == 201 else f"Failed to rename {old_name}: {response.status_code}")
+
+# Check if the branch is inactive
+def is_inactive(commit_url):
+    last_commit_date = requests.get(commit_url, headers=HEADERS).json()['commit']['committer']['date']
+    return datetime.strptime(last_commit_date, '%Y-%m-%dT%H:%M:%SZ') < CUTOFF_DATE
+
+# Rename inactive branches
+def main():
+    for branch in get_branches():
+        if is_inactive(branch['commit']['url']):
+            #rename_branch(branch['name'], f"archived/{branch['name']}")
+            print(f"[LOG] Branch '{branch['name']}' is inactive and would be renamed to 'archived/{branch['name']}'")
+
+if __name__ == "__main__":
+    main()

.github/workflows/rename-inactive-branches.yml

@@ -0,0 +1,27 @@
+name: Cleanup - Rename Inactive Branches
+
+on:
+  schedule:
+    - cron: '0 0 * * 0'  # Runs every Sunday at midnight
+
+jobs:
+  archive-stale-branches:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - name: Install Libraries
+        run: pip install requests
+
+      - name: Run Script to Rename Inactive Branches
+        run: |
+          python .github/scripts/rename_inactive_branches.py
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

bbmri/docker-compose.yml

@@ -4,7 +4,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-bbmri-blaze
     environment:
       BASE_URL: "http://bridgehead-bbmri-blaze:8080"

bbmri/modules/eric-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   focus-eric:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
     container_name: bridgehead-focus-eric
     environment:
       API_KEY: ${ERIC_FOCUS_BEAM_SECRET_SHORT}

bbmri/modules/gbn-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   focus-gbn:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-bbmri
     container_name: bridgehead-focus-gbn
     environment:
       API_KEY: ${GBN_FOCUS_BEAM_SECRET_SHORT}

bbmri/vars

@@ -7,7 +7,6 @@
 FOCUS_RETRY_COUNT=${FOCUS_RETRY_COUNT:-64}
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
-source versions
 for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"

bridgehead

@@ -64,7 +64,7 @@ loadVars() {
 	fetchVarsFromVaultByFile /etc/bridgehead/$PROJECT.conf || fail_and_report 1 "Unable to fetchVarsFromVaultByFile"
 	setHostname
 	optimizeBlazeMemoryUsage
-	[ -e ./$PROJECT/vars ] && source ./versions ./$PROJECT/vars
+	[ -e ./$PROJECT/vars ] && source ./$PROJECT/vars
 	set +a
 
 	OVERRIDE=${OVERRIDE:=""}

cce/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-cce-blaze
     environment:
       BASE_URL: "http://bridgehead-cce-blaze:8080"

cce/vars

@@ -7,7 +7,6 @@ SUPPORT_EMAIL=manoj.waikar@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-source versions
 for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"

ccp/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-ccp-blaze
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze:8080"
@@ -22,7 +22,7 @@ services:
       - "traefik.http.routers.blaze_ccp.tls=true"
 
   focus:
-    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/focus:${FOCUS_TAG}-dktk
     container_name: bridgehead-focus
     environment:
       API_KEY: ${FOCUS_BEAM_SECRET_SHORT}

ccp/modules/blaze-secondary-compose.yml

@@ -2,14 +2,13 @@ version: "3.7"
 
 services:
   blaze-secondary:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-ccp-blaze-secondary
     environment:
       BASE_URL: "http://bridgehead-ccp-blaze-secondary:8080"
       JAVA_TOOL_OPTIONS: "-Xmx${BLAZE_MEMORY_CAP:-4096}m"
       DB_RESOURCE_CACHE_SIZE: ${BLAZE_RESOURCE_CACHE_CAP:-2500000}
-      DB_BLOCK_CACHE_SIZE: ${BLAZE_MEMORY_CAP}
-      CQL_EXPR_CACHE_SIZE: ${BLAZE_CQL_CACHE_CAP:-32}
+      DB_BLOCK_CACHE_SIZE: $BLAZE_MEMORY_CAP
       ENFORCE_REFERENTIAL_INTEGRITY: "false"
     volumes:
       - "blaze-secondary-data:/app/data"

ccp/vars

@@ -18,7 +18,8 @@ OIDC_URL="https://login.verbis.dkfz.de"
 OIDC_ISSUER_URL="${OIDC_URL}/realms/${OIDC_REALM}"
 OIDC_GROUP_CLAIM="groups"
 
-source versions
+POSTGRES_TAG=15.6-alpine
+
 for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"

dhki/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-dhki-blaze
     environment:
       BASE_URL: "http://bridgehead-dhki-blaze:8080"
@@ -39,7 +39,7 @@ services:
       - "blaze"
 
   beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}

dhki/vars

@@ -8,7 +8,8 @@ PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-source versions
+POSTGRES_TAG=15.6-alpine
+
 for module in ccp/modules/*.sh
 do
     log DEBUG "sourcing $module"

itcc/docker-compose.yml

@@ -2,7 +2,7 @@ version: "3.7"
 
 services:
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-itcc-blaze
     environment:
       BASE_URL: "http://bridgehead-itcc-blaze:8080"

itcc/vars

@@ -7,7 +7,6 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-source versions
 for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"

kr/docker-compose.yml

@@ -6,7 +6,7 @@ services:
       replicas: 0 #deactivate landing page
 
   blaze:
-    image: docker.verbis.dkfz.de/cache/samply/blaze:${BLAZE_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/blaze:0.28
     container_name: bridgehead-kr-blaze
     environment:
       BASE_URL: "http://bridgehead-kr-blaze:8080"
@@ -40,7 +40,7 @@ services:
       - "blaze"
 
   beam-proxy:
-    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:${BEAM_TAG}
+    image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
     container_name: bridgehead-beam-proxy
     environment:
       BROKER_URL: ${BROKER_URL}

kr/modules/exporter.md

@@ -0,0 +1,15 @@
+# Exporter and Reporter
+
+
+## Exporter
+The exporter is a REST API that exports the data of the different databases of the bridgehead in a set of tables.
+It can accept different output formats as CSV, Excel, JSON or XML. It can also export data into Opal.
+
+## Exporter-DB
+It is a database to save queries for its execution in the exporter. 
+The exporter manages also the different executions of the same query in through the database.
+
+## Reporter
+This component is a plugin of the exporter that allows to create more complex Excel reports described in templates.
+It is compatible with different template engines as Groovy, Thymeleaf,...
+It is perfect to generate a document as our traditional CCP quality report.

kr/modules/teiler.md

@@ -0,0 +1,19 @@
+# Teiler
+This module orchestrates the different microfrontends of the bridgehead as a single page application.  
+
+## Teiler Orchestrator
+Single SPA component that consists on the root HTML site of the single page application and a javascript code that
+gets the information about the microfrontend calling the teiler backend and is responsible for registering them. With the
+resulting mapping, it can initialize, mount and unmount the required microfrontends on the fly. 
+
+The microfrontends run independently in different containers and can be based on different frameworks (Angular, Vue, React,...)
+This microfrontends can run as single alone but need an extension with Single-SPA (https://single-spa.js.org/docs/ecosystem).
+There are also available three templates (Angular, Vue, React) to be directly extended to be used directly in the teiler.
+
+## Teiler Dashboard
+It consists on the main dashboard and a set of embedded services.
+### Login
+user and password in ccp.local.conf
+
+## Teiler Backend
+In this component, the microfrontends are configured.

kr/vars

@@ -7,7 +7,6 @@ SUPPORT_EMAIL=arturo.macias@dkfz-heidelberg.de
 PRIVATEKEYFILENAME=/etc/bridgehead/pki/${SITE_ID}.priv.pem
 BROKER_URL_FOR_PREREQ=$BROKER_URL
 
-source versions
 for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"

lib/functions.sh

@@ -170,11 +170,11 @@ optimizeBlazeMemoryUsage() {
 		available_system_memory_chunks=$((BLAZE_MEMORY_CAP / 1000))
 		if [ $available_system_memory_chunks -eq 0 ]; then
 			log WARN "Only ${BLAZE_MEMORY_CAP} system memory available for Blaze. If your Blaze stores more than 128000 fhir ressources it will run significally slower."
-			export BLAZE_RESOURCE_CACHE_CAP=128000
-			export BLAZE_CQL_CACHE_CAP=32
+			export BLAZE_RESOURCE_CACHE_CAP=128000;
+			export BLAZE_CQL_CACHE_CAP=32;
 		else
 			export BLAZE_RESOURCE_CACHE_CAP=$((available_system_memory_chunks * 312500))
-			export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16))
+			export BLAZE_CQL_CACHE_CAP=$((($system_memory_in_mb/4)/16));
 		fi
 	fi
 }

lib/prepare-system.sh

@@ -57,9 +57,9 @@ case "$PROJECT" in
 		;;
 	itcc)
 		site_configuration_repository_middle="git.verbis.dkfz.de/itcc-sites/"
-    ;;
-  dhki)
-    site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
+        ;;
+    dhki)
+        site_configuration_repository_middle="git.verbis.dkfz.de/dhki/"
 		;;
 	kr)
 		site_configuration_repository_middle="git.verbis.dkfz.de/krebsregister-sites/"

lib/prerequisites.sh

@@ -67,7 +67,7 @@ fi
 log INFO "Checking network access ($BROKER_URL_FOR_PREREQ) ..."
 
 source "${CONFIG_DIR}${PROJECT}".conf
-source ${PROJECT}/vars vars
+source ${PROJECT}/vars
 
 if [ "${PROJECT}" != "minimal" ]; then
   set +e

minimal/vars

@@ -1,5 +1,3 @@
-
-source versions
 for module in $PROJECT/modules/*.sh
 do
     log DEBUG "sourcing $module"

versions

@@ -1,2 +0,0 @@
-BLAZE_TAG=0.28
-POSTGRES_TAG=15.6-alpine