added NOTICE file

.github/trivy_scan.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+#Install Trivy
+sudo apt-get install wget apt-transport-https gnupg lsb-release
+wget -qO - https://aquasecurity.github.io/trivy-repo/deb/public.key | sudo apt-key add -
+echo deb https://aquasecurity.github.io/trivy-repo/deb $(lsb_release -sc) main | sudo tee -a /etc/apt/sources.list.d/trivy.list
+sudo apt-get update
+sudo apt-get install trivy
+
+#Make an array of input paths
+TARGETS=("$@")
+#Count number of inputs
+NUMBER_OF_PATHS=${#args[@]} 
+#If no input given scan all
+if [ -z "$TARGETS" ]; then
+    TARGETS=(".")
+fi
+#Trivy scan the elements of array
+for TARGET_PATH in "${TARGETS[@]}";
+do
+echo "scanning $TARGET_PATH"
+trivy fs --severity "MEDIUM,HIGH,CRITICAL" --exit-code 1 $TARGET_PATH
+done

.github/workflows/atomfeed_console_build_publish.yaml

@@ -0,0 +1,52 @@
+name: Build and Publish atomfeed-console Image
+on:
+  push:
+    branches: [master]
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+    paths:
+      - 'atomfeed-console/**'
+      - '.github/workflows/atomfeed_console_build_publish.yaml'
+  repository_dispatch:
+    types: 
+      - atomfeed-console-trigger
+jobs:
+  Trivy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Trivy Scan
+        run: ./.github/trivy_scan.sh atomfeed-console .github/workflows/atomfeed_console_build_publish.yaml
+
+  docker-build-publish:
+    name: Docker Build & Publish
+    runs-on: ubuntu-latest
+    needs: Trivy
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set env.ARTIFACT_VERSION
+        run: |
+          wget -q https://raw.githubusercontent.com/Bahmni/bahmni-infra-utils/main/setArtifactVersion.sh && chmod +x setArtifactVersion.sh
+          ./setArtifactVersion.sh atomfeed-console/.appversion
+          rm setArtifactVersion.sh
+      - name: Download atomfeed-console jar
+        run: |
+          curl -H "Accept: application/vnd.github.v3+json" \
+          https://api.github.com/repos/ICT4H/atomfeed-console/actions/artifacts | \
+          jq -r '.artifacts[0].archive_download_url' | \
+          xargs curl -L -o atomfeed-console-SNAPSHOT.zip -H "Authorization: token ${{secrets.BAHMNI_PAT}}"
+          unzip atomfeed-console-SNAPSHOT.zip  -d atomfeed-console/resources/
+      - name: Login to DockerHub
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_TOKEN }}
+      - name: Docker Build and push
+        uses: docker/build-push-action@v2
+        with:
+          context: atomfeed-console/
+          no-cache: true
+          push: true
+          tags: bahmni/atomfeed-console:${{env.ARTIFACT_VERSION}},bahmni/atomfeed-console:latest
+

.github/workflows/tomcat_build_upload.yml

@@ -0,0 +1,65 @@
+name: Build and Upload Embedded Tomcat
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - "bahmni-embedded-tomcat/**"
+      - "bahmni-embedded-tomcat-10/**"
+      - "gradle.properties"
+      - ".github/workflows/tomcat_build_upload.yml"
+  workflow_dispatch:
+
+jobs:
+  trivy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+      - name: Trivy Scan
+        run: ./.github/trivy_scan.sh bahmni-embedded-tomcat
+
+  build-upload-artifact:
+    name: Build and upload embedded Tomcat Server artifact
+    runs-on: ubuntu-latest
+    needs: trivy
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v4
+        with:
+          distribution: "corretto"
+          java-version: "8"
+      - name: Generate Artifact for bahmni-embedded-tomcat
+        run: ./gradlew :bahmni-embedded-tomcat:clean :bahmni-embedded-tomcat:build
+      - name: Configure AWS Credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.S3_MVN_ACCESS_KEY }}
+          aws-secret-access-key: ${{ secrets.S3_MVN_SECRET_KEY }}
+          aws-region: ap-southeast-1
+      - name: Upload Artifact for bahmni-embedded-tomcat
+        run: aws s3 cp bahmni-embedded-tomcat/build/libs/bahmni-embedded-tomcat-*.jar s3://repo.mybahmni.org/packages/build/
+
+  build-upload-artifact-10:
+    name: Build and upload embedded Tomcat 10 Server artifact
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          distribution: "corretto"
+          java-version: "17"
+      - name: Generate Artifact for bahmni-embedded-tomcat-10
+        run: |
+          cd bahmni-embedded-tomcat-10
+          ./gradlew clean build
+      - name: Configure AWS Credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.S3_MVN_ACCESS_KEY }}
+          aws-secret-access-key: ${{ secrets.S3_MVN_SECRET_KEY }}
+          aws-region: ap-southeast-1
+      - name: Upload Artifact for bahmni-embedded-tomcat-10
+        run: aws s3 cp bahmni-embedded-tomcat-10/build/libs/bahmni-embedded-tomcat-10-*.jar s3://repo.mybahmni.org/packages/build/

.github/workflows/trivy_scan.yaml

@@ -0,0 +1,24 @@
+name: Trivy Scan
+on:
+  push:
+    branches: [ '*' ]
+    paths-ignore:
+      - 'atomfeed-console/**'
+      - '.github/workflows/atomfeed_console_build_publish.yaml'
+      - "core/**"
+      - 'bahmni-pacs/**'
+      - '.github/workflows/dcm4chee_build_publish.yml'
+      - 'bahmni-proxy/**'
+  pull_request:
+    branches: [ '*' ]
+    types: [opened, synchronize, reopened]
+
+
+jobs:
+  Trivy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+      - name: Trivy Scan
+        run:  ./.github/trivy_scan.sh

.gitignore

@@ -25,6 +25,9 @@ Thumbs.db
 ################
 *~
 *.swp
+*.project
+*.classpath
+*.settings
 
 # Gradle Files #
 ################
@@ -54,4 +57,8 @@ bahmni-web/resources/bahmni_config
 bahmni-installer/resources/bahmni-playbooks
 bahmni-installer/resources/bahmni-command-line-tool/bahmni.egg-info/
 bahmni-pacs/resources/dcm4chee/oviyam2.war
-*.pyc
+*.pyc
+*.class
+bahmni-lab/resources/openelis_demo_dump.sql
+bahmni-erp/resources/odoo_demo_dump.sql
+bahmni-proxy/resources/client_side_logging

NOTICE

@@ -0,0 +1,7 @@
+Copyright (C) 2013 OpenMRS, Inc
+
+This product includes software developed under the stewardship of the Bahmni Coalition, under fiscal sponsorship of OpenMRS, Inc. (http://www.openmrs.org/)
+
+This product includes software developed at ThoughtWorks, Inc. (http://www.thoughtworks.com/)
+
+

atomfeed-console/.appversion

@@ -0,0 +1 @@
+1.1.0

atomfeed-console/Dockerfile

@@ -0,0 +1,8 @@
+FROM amazoncorretto:8
+COPY resources/application.yml.template .
+COPY resources/start.sh .
+COPY resources/*.jar .
+RUN yum install -y gettext
+EXPOSE 9080
+RUN chmod +x start.sh 
+ENTRYPOINT ["./start.sh"]

atomfeed-console/README.md

@@ -0,0 +1,14 @@
+# atomfeed-console
+
+This directory contains resources for building Docker image for atomfeed-console. The atomfeed-console container is used to show the failed events that happened in an atomfeed client.
+
+Atomfeed console is useful when you are facing some sync issues with components like OpenMRS, OpenELIS, Odoo, etc. Issues can be like patients not getting created, orders not getting synced, pacs orders not getting synced etc.,
+
+## Building the image locally
+
+1. Checkout the [atomfeed-console](https://github.com/ICT4H/atomfeed-console) repository.
+2. Generate the jar file by running `mvn clean install -DskipTests`.
+3. Navigate into bahmni-package directory and copy the above generated jar file to `bahmni-package/atomfeed-console/resources`.
+4. Build the docker image `docker build -t atomfeed-console:latest .` from `bahmni-package/atomfeed-console`
+
+[application.yml.template](resources/application.yml.template) contains list of atom feeds that we want to configure in Atomfeed Console. To add/remove the feed sources, update the [list](resources/application.yml.template#L4) accordingly.

atomfeed-console/resources/application.yml.template

@@ -0,0 +1,24 @@
+server:
+  port: 9080
+  contextPath: /atomfeed-console
+appConfigs:
+-
+   appName: OpenMRS
+   dbUrl: jdbc:mysql://${OPENMRS_DB_HOST}/${OPENMRS_DB_NAME}
+   dbUser: ${OPENMRS_DB_USERNAME}
+   dbPassword: ${OPENMRS_DB_PASSWORD}
+-
+   appName: Odoo
+   dbUrl: jdbc:postgresql://${ODOO_DB_HOST}/${ODOO_DB_NAME}
+   dbUser: ${ODOO_DB_USER}
+   dbPassword: ${ODOO_DB_PASSWORD}
+-
+   appName: OpenELIS
+   dbUrl: jdbc:postgresql://${OPENELIS_DB_HOST}/clinlims?currentSchema=clinlims
+   dbUser: ${OPENELIS_DB_USER}
+   dbPassword: ${OPENELIS_DB_PASSWORD}
+-
+   appName: Pacs Integration
+   dbUrl: jdbc:postgresql://${PACS_INTEGRATION_DB_HOST}/${PACS_INTEGRATION_DB_NAME}
+   dbUser: ${PACS_INTEGRATION_DB_USERNAME}
+   dbPassword: ${PACS_INTEGRATION_DB_PASSWORD}

atomfeed-console/resources/start.sh

@@ -0,0 +1,7 @@
+#!/bin/sh
+set -e
+
+echo "[INFO] Substituting Environment Variables"
+envsubst < application.yml.template > application.yml
+echo "[INFO] Starting Application"
+java -jar *.jar --spring.config.location=appilcation.yml

bahmni-docker/README.md

@@ -0,0 +1,2 @@
+# 🚧 Migration Notice 🚧
+### 🚀 The contents from here has been migrated to [bahmni-docker](https://github.com/Bahmni/bahmni-docker) repository. Please use the artifacts from [bahmni-docker](https://github.com/Bahmni/bahmni-docker) repository.

bahmni-embedded-tomcat-10/.gitignore

@@ -0,0 +1,38 @@
+target/
+!.mvn/wrapper/maven-wrapper.jar
+!**/src/main/**/target/
+!**/src/test/**/target/
+
+### IntelliJ IDEA ###
+.idea/modules.xml
+.idea/jarRepositories.xml
+.idea/compiler.xml
+.idea/libraries/
+*.iws
+*.iml
+*.ipr
+
+### Eclipse ###
+.apt_generated
+.classpath
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/
+
+### Mac OS ###
+.DS_Store

bahmni-embedded-tomcat-10/build.gradle

@@ -0,0 +1,63 @@
+plugins {
+    id 'java'
+}
+group 'org.bahmni.deployment'
+version '1.0-SNAPSHOT'
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(17)
+    }
+}
+
+repositories {
+    mavenCentral()
+    jcenter()
+    maven {
+        url 'https://mavenrepo.openmrs.org/nexus/content/repositories/public' // Use HTTPS instead of HTTP
+    }
+    maven {
+        url 'https://oss.sonatype.org/content/repositories' // Use HTTPS
+    }
+}
+
+def tomcatVersion = '10.1.24'  // Define Tomcat version here
+
+dependencies {
+    implementation "org.apache.tomcat.embed:tomcat-embed-core:${tomcatVersion}"
+    implementation "org.apache.tomcat.embed:tomcat-embed-jasper:${tomcatVersion}"
+    implementation "org.apache.tomcat:tomcat-jasper:${tomcatVersion}"
+    implementation "org.apache.tomcat:tomcat-jasper-el:${tomcatVersion}"
+    implementation "org.apache.tomcat:tomcat-jsp-api:${tomcatVersion}"
+    implementation "ch.qos.logback:logback-classic:1.5.0"
+    implementation 'javax.servlet:javax.servlet-api:4.0.1'
+}
+
+jar {
+    duplicatesStrategy = 'exclude'
+
+    manifest {
+        attributes 'Main-Class': 'org.bahmni.deployment.launch.Main'
+    }
+
+    from {
+        configurations.runtimeClasspath.collect {
+            it.isDirectory() ? it : zipTree(it)
+        }
+    }
+
+    exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA'
+}
+
+configurations {
+    all {
+        exclude group: 'com.sun.jdmk', module: 'jmxtools'
+        exclude group: 'com.sun.jmx', module: 'jmxri'
+        exclude group: 'javax.jms', module: 'jms'
+        exclude group: 'javax.mail', module: 'mail'
+    }
+}
+
+// Print Tomcat version after project configuration
+gradle.afterProject { project ->
+    println "Built with Apache Tomcat version: ${tomcatVersion}"
+}

bahmni-embedded-tomcat-10/gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,7 @@
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.8-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists