OHDSI#2916 - Improvements to Docker Configurability of Atlas Applicat…

…ion (OHDSI#2917)

* OHDSI#2916
- added configuration via environment variables to Dockerfile
- amended authors list on container metadata
- amended envsubst command to include all environment variables
- extended config-local.js to include the majority of configuration options available in app.js
- Added comment to app.js to remind future contributors to add configuration to Dockerfile and config-local.js

* OHDSI#2916
- amended variables that exist to match those on Broadsea implementation

.github/workflows/ci.yaml

@@ -92,7 +92,7 @@ jobs:
           labels: |
             ${{ steps.docker_meta.outputs.labels }}
             maintainer=Joris Borgdorff <[email protected]>, Lee Evans - www.ltscomputingllc.com
-            org.opencontainers.image.authors=Joris Borgdorff <[email protected]>, Lee Evans - www.ltscomputingllc.com
+            org.opencontainers.image.authors=Joris Borgdorff <[email protected]>, Lee Evans - www.ltscomputingllc.com, Shaun Turner <[email protected]>
             org.opencontainers.image.vendor=OHDSI
 
       # If the image was pushed, we need to pull it again to inspect it

Dockerfile

@@ -29,16 +29,114 @@ RUN find . -type f "(" \
 FROM docker.io/nginxinc/nginx-unprivileged:1.23.3-alpine@sha256:c748ba587e7436aaa8729b64d4e0412410a486f0c592f0eec100fb3804ff9afd
 
 LABEL org.opencontainers.image.title="OHDSI-Atlas"
-LABEL org.opencontainers.image.authors="Joris Borgdorff <[email protected]>, Lee Evans - www.ltscomputingllc.com"
+LABEL org.opencontainers.image.authors="Joris Borgdorff <[email protected]>, Lee Evans - www.ltscomputingllc.com, Shaun Turner<[email protected]>"
 LABEL org.opencontainers.image.description="ATLAS is an open source software tool for researchers to \
 conduct scientific analyses on standardized observational data"
 LABEL org.opencontainers.image.licenses="Apache-2.0"
 LABEL org.opencontainers.image.vendor="OHDSI"
 LABEL org.opencontainers.image.source="https://github.com/OHDSI/Atlas"
 
 # URL where WebAPI can be queried by the client
-ENV WEBAPI_URL=http://localhost:8080/WebAPI/ \
-  CONFIG_PATH=/etc/atlas/config-local.js
+ENV USE_DYNAMIC_WEBAPI_URL="false"
+ENV DYNAMIC_WEBAPI_SUFFIX="/WebAPI/"
+ENV WEBAPI_URL="http://localhost:8080/WebAPI/"
+ENV CONFIG_PATH="/etc/atlas/config-local.js"
+ENV ATLAS_INSTANCE_NAME="OHDSI"
+ENV ATLAS_COHORT_COMPARISON_RESULTS_ENABLED="false"
+ENV ATLAS_USER_AUTH_ENABLED="false"
+ENV ATLAS_PLP_RESULTS_ENABLED="false"
+ENV ATLAS_CLEAR_LOCAL_STORAGE="false"
+ENV ATLAS_DISABLE_BROWSER_CHECK="false"
+ENV ATLAS_ENABLE_PERMISSIONS_MGMT="true"
+ENV ATLAS_CACHE_SOURCES="false"
+ENV ATLAS_POLL_INTERVAL="60000"
+ENV ATLAS_SKIP_LOGIN="false"
+ENV ATLAS_USE_EXECUTION_ENGINE="false"
+ENV ATLAS_VIEW_PROFILE_DATES="false"
+ENV ATLAS_ENABLE_COSTS="false"
+ENV ATLAS_SUPPORT_URL="https://github.com/ohdsi/atlas/issues"
+ENV ATLAS_SUPPORT_MAIL="[email protected]"
+ENV ATLAS_FEEDBACK_CONTACTS="For access or questions concerning the Atlas application please contact:"
+ENV ATLAS_FEEDBACK_HTML=""
+ENV ATLAS_COMPANYINFO_HTML=""
+ENV ATLAS_COMPANYINFO_SHOW="true"
+ENV ATLAS_DEFAULT_LOCALE="en"
+
+ENV ATLAS_SECURITY_WIN_PROVIDER_ENABLED="false"
+ENV ATLAS_SECURITY_WIN_PROVIDER_NAME="Windows"
+ENV ATLAS_SECURITY_WIN_PROVIDER_URL="user/login/windows"
+ENV ATLAS_SECURITY_WIN_PROVIDER_AJAX="true"
+ENV ATLAS_SECURITY_WIN_PROVIDER_ICON="fab fa-windows"
+
+ENV ATLAS_SECURITY_KERB_PROVIDER_ENABLED="false"
+ENV ATLAS_SECURITY_KERB_PROVIDER_NAME="Kerberos"
+ENV ATLAS_SECURITY_KERB_PROVIDER_URL="user/login/kerberos"
+ENV ATLAS_SECURITY_KERB_PROVIDER_AJAX="true"
+ENV ATLAS_SECURITY_KERB_PROVIDER_ICON="fab fa-windows"
+
+ENV ATLAS_SECURITY_OID_PROVIDER_ENABLED="false"
+ENV ATLAS_SECURITY_OID_PROVIDER_NAME="OpenID Connect"
+ENV ATLAS_SECURITY_OID_PROVIDER_URL="user/login/openid"
+ENV ATLAS_SECURITY_OID_PROVIDER_AJAX="false"
+ENV ATLAS_SECURITY_OID_PROVIDER_ICON="fa fa-openid"
+
+ENV ATLAS_SECURITY_GGL_PROVIDER_ENABLED="false"
+ENV ATLAS_SECURITY_GGL_PROVIDER_NAME="Google"
+ENV ATLAS_SECURITY_GGL_PROVIDER_URL="user/oauth/google"
+ENV ATLAS_SECURITY_GGL_PROVIDER_AJAX="false"
+ENV ATLAS_SECURITY_GGL_PROVIDER_ICON="fab fa-google"
+
+ENV ATLAS_SECURITY_FB_PROVIDER_ENABLED="false"
+ENV ATLAS_SECURITY_FB_PROVIDER_NAME="Facebook"
+ENV ATLAS_SECURITY_FB_PROVIDER_URL="user/oauth/facebook"
+ENV ATLAS_SECURITY_FB_PROVIDER_AJAX="false"
+ENV ATLAS_SECURITY_FB_PROVIDER_ICON="fab fa-facebook-f"
+
+ENV ATLAS_SECURITY_GH_PROVIDER_ENABLED="false"
+ENV ATLAS_SECURITY_GH_PROVIDER_NAME="Github"
+ENV ATLAS_SECURITY_GH_PROVIDER_URL="user/oauth/github"
+ENV ATLAS_SECURITY_GH_PROVIDER_AJAX="false"
+ENV ATLAS_SECURITY_GH_PROVIDER_ICON="fab fa-github"
+
+ENV ATLAS_SECURITY_DB_PROVIDER_ENABLED="false"
+ENV ATLAS_SECURITY_DB_PROVIDER_NAME="DB"
+ENV ATLAS_SECURITY_DB_PROVIDER_URL="user/login/db"
+ENV ATLAS_SECURITY_DB_PROVIDER_AJAX="true"
+ENV ATLAS_SECURITY_DB_PROVIDER_ICON="fa fa-database"
+ENV ATLAS_SECURITY_DB_PROVIDER_CREDFORM="true"
+
+ENV ATLAS_SECURITY_LDAP_PROVIDER_ENABLED="false"
+ENV ATLAS_SECURITY_LDAP_PROVIDER_NAME="LDAP"
+ENV ATLAS_SECURITY_LDAP_PROVIDER_URL="user/login/ldap"
+ENV ATLAS_SECURITY_LDAP_PROVIDER_AJAX="true"
+ENV ATLAS_SECURITY_LDAP_PROVIDER_ICON="fa fa-cubes"
+ENV ATLAS_SECURITY_LDAP_PROVIDER_CREDFORM="true"
+
+ENV ATLAS_SECURITY_SAML_PROVIDER_ENABLED="false"
+ENV ATLAS_SECURITY_SAML_PROVIDER_NAME="SAML"
+ENV ATLAS_SECURITY_SAML_PROVIDER_URL="user/login/saml"
+ENV ATLAS_SECURITY_SAML_PROVIDER_AJAX="false"
+ENV ATLAS_SECURITY_SAML_PROVIDER_ICON="fab fa-openid"
+
+ENV ATLAS_SECURITY_AD_PROVIDER_ENABLED="false"
+ENV ATLAS_SECURITY_AD_PROVIDER_NAME="Active Directory LDAP"
+ENV ATLAS_SECURITY_AD_PROVIDER_URL="user/login/ad"
+ENV ATLAS_SECURITY_AD_PROVIDER_AJAX="true"
+ENV ATLAS_SECURITY_AD_PROVIDER_ICON="fa fa-cubes"
+ENV ATLAS_SECURITY_AD_PROVIDER_CREDFORM="true"
+
+# for existing broadsea implementations
+ENV ATLAS_SECURITY_PROVIDER_ENABLED="true"
+ENV ATLAS_SECURITY_PROVIDER_NAME="none"
+ENV ATLAS_SECURITY_PROVIDER_TYPE="none"
+ENV ATLAS_SECURITY_USE_AJAX="false"
+ENV ATLAS_SECURITY_PROVIDER_ICON="fa-cubes"
+ENV ATLAS_SECURITY_USE_FORM="false"
+
+ENV ATLAS_ENABLE_TANDCS="true"
+ENV ATLAS_ENABLE_PERSONCOUNT="true"
+ENV ATLAS_ENABLE_TAGGING_SECTION="false"
+ENV ATLAS_REFRESH_TOKEN_THRESHOLD="240"
 
 # Configure webserver
 COPY ./docker/nginx-default.conf /etc/nginx/conf.d/default.conf

docker/30-atlas-env-subst.sh

@@ -26,7 +26,7 @@ if [ -n "${WEBAPI_URL}" ]; then
   TFILE=`mktemp`
   trap "rm -f $TFILE" 0 1 2 3 15
   # Don't copy but rewrite so that permissions are not changed.
-  envsubst '$WEBAPI_URL' < "$CONFIG_TARGET_PATH" > "$TFILE"
+  envsubst < "$CONFIG_TARGET_PATH" > "$TFILE"
   cat "$TFILE" > "$CONFIG_TARGET_PATH"
   rm -f "$TFILE"
 fi

docker/config-local.js

@@ -1,15 +1,141 @@
 define([], function () {
 	var configLocal = {};
 
+	if ("${ATLAS_CLEAR_LOCAL_STORAGE}" == "true") {
+		localStorage.clear();
+	}
+
+	var webapi_url = "${WEBAPI_URL}";
+
+	if ("${USE_DYNAMIC_WEBAPI_URL}" == "true") {
+		var getUrl = window.location;
+	    webapi_url = getUrl.protocol + "//" + getUrl.hostname + "${DYNAMIC_WEBAPI_SUFFIX}";
+	}
+
 	// WebAPI
 	configLocal.api = {
-		name: 'OHDSI',
-		url: '${WEBAPI_URL}'
+		name: '${ATLAS_INSTANCE_NAME}',
+		url: webapi_url
 	};
 
-	configLocal.cohortComparisonResultsEnabled = false;
-	configLocal.userAuthenticationEnabled = false;
-	configLocal.plpResultsEnabled = false;
+	configLocal.cohortComparisonResultsEnabled = ("${ATLAS_COHORT_COMPARISON_RESULTS_ENABLED}" == "true");
+	configLocal.plpResultsEnabled = ("${ATLAS_PLP_RESULTS_ENABLED}" === "true");
+	configLocal.userAuthenticationEnabled = ("${ATLAS_USER_AUTH_ENABLED}" === "true");
+	configLocal.authProviders = [];
+	configLocal.disableBrowserCheck = ("${ATLAS_DISABLE_BROWSER_CHECK}" === "true");
+	configLocal.enablePermissionManagement = ("${ATLAS_ENABLE_PERMISSIONS_MGMT}" === "true");
+	configLocal.cacheSources = ("${ATLAS_CACHE_SOURCES}" === "true");
+	configLocal.enableSkipLogin = ("${ATLAS_SKIP_LOGIN}" === "true"); // automatically opens login window when user is not authenticated
+	configLocal.useExecutionEngine = ("${ATLAS_USE_EXECUTION_ENGINE}" === "true");
+	configLocal.viewProfileDates = ("${ATLAS_VIEW_PROFILE_DATES}" === "true");
+	configLocal.enableCosts = ("${ATLAS_ENABLE_COSTS}" === "true");
+	configLocal.supportUrl = "${ATLAS_SUPPORT_URL}";
+	configLocal.supportMail = "${ATLAS_SUPPORT_MAIL}";
+	configLocal.feedbackContacts = "${ATLAS_FEEDBACK_CONTACTS}";
+	configLocal.feedbackCustomHtmlTemplate = "${ATLAS_FEEDBACK_HTML}";
+	configLocal.companyInfoCustomHtmlTemplate = "${ATLAS_COMPANYINFO_HTML}";
+	configLocal.showCompanyInfo = ("${ATLAS_COMPANYINFO_SHOW}" === "true");
+	configLocal.defaultLocale = "${ATLAS_DEFAULT_LOCALE}";
+	configLocal.pollInterval = parseInt("${ATLAS_POLL_INTERVAL}");
+
+
+	if ("${ATLAS_SECURITY_WIN_PROVIDER_ENABLED}" === "true") {
+		configLocal.authProviders.push(openIdProvider = {
+			name: "${ATLAS_SECURITY_WIN_PROVIDER_NAME}",
+			url: "${ATLAS_SECURITY_WIN_PROVIDER_URL}",
+			ajax: ("${ATLAS_SECURITY_WIN_PROVIDER_AJAX}" === "true"),
+			icon: "${ATLAS_SECURITY_WIN_PROVIDER_ICON}",
+		});
+	}
+
+	if ("${ATLAS_SECURITY_KERB_PROVIDER_ENABLED}" === "true") {
+		configLocal.authProviders.push(openIdProvider = {
+			name: "${ATLAS_SECURITY_KERB_PROVIDER_NAME}",
+			url: "${ATLAS_SECURITY_KERB_PROVIDER_URL}",
+			ajax: ("${ATLAS_SECURITY_KERB_PROVIDER_AJAX}" === "true"),
+			icon: "${ATLAS_SECURITY_KERB_PROVIDER_ICON}",
+		});
+	}
+
+	if ("${ATLAS_SECURITY_OID_PROVIDER_ENABLED}" === "true") {
+		configLocal.authProviders.push(openIdProvider = {
+			name: "${ATLAS_SECURITY_OID_PROVIDER_NAME}",
+			url: "${ATLAS_SECURITY_OID_PROVIDER_URL}",
+			ajax: ("${ATLAS_SECURITY_OID_PROVIDER_AJAX}" === "true"),
+			icon: "${ATLAS_SECURITY_OID_PROVIDER_ICON}",
+		});
+	}
+
+	if ("${ATLAS_SECURITY_GGL_PROVIDER_ENABLED}" === "true") {
+		configLocal.authProviders.push(openIdProvider = {
+			name: "${ATLAS_SECURITY_GGL_PROVIDER_NAME}",
+			url: "${ATLAS_SECURITY_GGL_PROVIDER_URL}",
+			ajax: ("${ATLAS_SECURITY_GGL_PROVIDER_AJAX}" === "true"),
+			icon: "${ATLAS_SECURITY_GGL_PROVIDER_ICON}",
+		});
+	}
+
+	if ("${ATLAS_SECURITY_FB_PROVIDER_ENABLED}" === "true") {
+		configLocal.authProviders.push(openIdProvider = {
+			name: "${ATLAS_SECURITY_FB_PROVIDER_NAME}",
+			url: "${ATLAS_SECURITY_FB_PROVIDER_URL}",
+			ajax: ("${ATLAS_SECURITY_FB_PROVIDER_AJAX}" === "true"),
+			icon: "${ATLAS_SECURITY_FB_PROVIDER_ICON}",
+		});
+	}
+
+	if ("${ATLAS_SECURITY_GH_PROVIDER_ENABLED}" === "true") {
+		configLocal.authProviders.push(openIdProvider = {
+			name: "${ATLAS_SECURITY_GH_PROVIDER_NAME}",
+			url: "${ATLAS_SECURITY_GH_PROVIDER_URL}",
+			ajax: ("${ATLAS_SECURITY_GH_PROVIDER_AJAX}" === "true"),
+			icon: "${ATLAS_SECURITY_GH_PROVIDER_ICON}",
+		});
+	}
+
+	if ("${ATLAS_SECURITY_DB_PROVIDER_ENABLED}" === "true") {
+		configLocal.authProviders.push(openIdProvider = {
+			name: "${ATLAS_SECURITY_DB_PROVIDER_NAME}",
+			url: "${ATLAS_SECURITY_DB_PROVIDER_URL}",
+			ajax: ("${ATLAS_SECURITY_DB_PROVIDER_AJAX}" === "true"),
+			icon: "${ATLAS_SECURITY_DB_PROVIDER_ICON}",
+			isUseCredentialsForm: ("${ATLAS_SECURITY_DB_PROVIDER_CREDFORM}" === "true")
+		});
+	}
+
+	if ("${ATLAS_SECURITY_LDAP_PROVIDER_ENABLED}" === "true") {
+		configLocal.authProviders.push(openIdProvider = {
+			name: "${ATLAS_SECURITY_LDAP_PROVIDER_NAME}",
+			url: "${ATLAS_SECURITY_LDAP_PROVIDER_URL}",
+			ajax: ("${ATLAS_SECURITY_LDAP_PROVIDER_AJAX}" === "true"),
+			icon: "${ATLAS_SECURITY_LDAP_PROVIDER_ICON}",
+			isUseCredentialsForm: ("${ATLAS_SECURITY_LDAP_PROVIDER_CREDFORM}" === "true")
+		});
+	}
+
+	if ("${ATLAS_SECURITY_SAML_PROVIDER_ENABLED}" === "true") {
+		configLocal.authProviders.push(openIdProvider = {
+			name: "${ATLAS_SECURITY_SAML_PROVIDER_NAME}",
+			url: "${ATLAS_SECURITY_SAML_PROVIDER_URL}",
+			ajax: ("${ATLAS_SECURITY_SAML_PROVIDER_AJAX}" === "true"),
+			icon: "${ATLAS_SECURITY_SAML_PROVIDER_ICON}",
+		});
+	}
+
+	// For existing broadsea implementations
+	if ("${ATLAS_SECURITY_PROVIDER_ENABLED}" === "true") {
+		configLocal.authProviders.push(openIdProvider = {
+			name: "${ATLAS_SECURITY_PROVIDER_NAME}",
+			url: "user/login/${ATLAS_SECURITY_PROVIDER_TYPE}",
+			ajax: ("${ATLAS_SECURITY_PROVIDER_AJAX}" === "true"),
+			icon: "${ATLAS_SECURITY_PROVIDER_ICON}",
+		});
+	}
+
+	configLocal.enableTermsAndConditions = ("${ATLAS_ENABLE_TANDCS}" === "true");
+	configLocal.enablePersonCount = ("${ATLAS_ENABLE_PERSONCOUNT}" === "true");
+	configLocal.enableTaggingSection = ("${ATLAS_ENABLE_TAGGING_SECTION}" === "true");
+	configLocal.refreshTokenThreshold = 1000 * 60 * parseInt("${ATLAS_REFRESH_TOKEN_THRESHOLD}");
 
 	return configLocal;
 });

js/config/app.js

@@ -1,3 +1,6 @@
+// Please remember to update the environmental variables in the Dockerfile and the docker config-local.js to reflect
+// any new settings introduced here
+
 define(function () {
   var appConfig = {};