Merge remote-tracking branch 'remotes/upstream/master' into ATL-29

.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/components/authorship.html

@@ -1,14 +1,12 @@
 <!-- ko if: createdBy && createdDate -->
 <div data-bind="css: classes('container')">
-	<span data-bind="text: createdText"></span>
-	<span data-bind="visible: createdBy, text: ko.i18nformat('components.authorship.byCreated', 'by <%=createdBy%>', {createdBy: createdBy})"></span>
-	<span data-bind="text: ko.i18n('components.authorship.on', 'on')"></span>
-	<span data-bind="text: createdDate"></span><span data-bind="visible: modifiedDate">,</span>
-	<span data-bind="visible: modifiedDate">
-		<span data-bind="text: ko.i18n('components.authorship.modified', 'modified')"></span>
-		<span data-bind="visible: createdBy, text: ko.i18nformat('components.authorship.byModified', 'by <%=modifiedBy%>', {modifiedBy: modifiedBy})"></span>
-		<span data-bind="text: ko.i18n('components.authorship.on', 'on')"></span>
-		<span data-bind="text: modifiedDate"></span>
-	</span>
+	<span data-bind="visible: createdBy,
+	    text: ko.i18nformat('components.authorship.createdLabel',
+						'created by <%=createdBy%> on <%=cratedDate%>',
+						{createdBy: createdBy, createdDate: createdDate})"></span><span data-bind="visible: modifiedDate">,</span>
+    <span data-bind="visible: modifiedDate,
+	    text: ko.i18nformat('components.authorship.modifiedLabel',
+						'modified by <%=modifiedBy%> on <%=modifiedDate%>',
+						{modifiedBy: modifiedBy, modifiedDate: modifiedDate})"></span>
 </div>
-<!-- /ko -->
+<!-- /ko -->

js/components/cohortbuilder/components/CensoringCriteriaEditor.js

@@ -140,6 +140,20 @@ define([
                     });
                 },
             },
+            {
+                ...constants.censoringEventList.addObservationPeriod,
+                selected: false,
+                action: function () {
+                    var unwrappedExpression = ko.utils.unwrapObservable(self.expression);
+                    unwrappedExpression
+                        .CensoringCriteria.push({
+                        ObservationPeriod: new criteriaTypes.ObservationPeriod(
+                            null,
+                            unwrappedExpression.ConceptSets
+                        ),
+                    });
+                },
+            },
             {
                 ...constants.censoringEventList.addPayerPlanPeriod,
                 selected: false,

js/components/cohortbuilder/const.js

@@ -95,7 +95,9 @@ define(["knockout"], function (ko) {
       title: 'const.eventsList.addObservationPeriod.title',
       defaultTitle: 'Add Observation Period',
       descriptionInitial: 'const.eventsList.addObservationPeriod.desc_initial',
-      defaultDescriptionInitial: 'Find patients based on observations.',
+      defaultDescriptionInitial: 'Find patients based on observation period.',
+      descriptionCensoring: 'const.eventsList.addObservationPeriod.desc_censoring',
+      defaultDescriptionCensoring: 'Exit cohort based on observaton period.',
       descriptionGroup: 'const.eventsList.addObservationPeriod.desc_group',
       defaultDescriptionGroup: 'Find patients based on observation periods.',
     },
@@ -1112,6 +1114,7 @@ define(["knockout"], function (ko) {
     'addDrugExposure',
     'addMeasurement',
     'addObservation',
+    'addObservationPeriod',
     'addPayerPlanPeriod',
     'addProcedureOccurrence',
     'addSpecimen',

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 = {};
 

js/pages/configuration/configuration.html

@@ -135,6 +135,11 @@
 							<span data-bind="text:ko.i18n('configuration.buttons.clearServerCache', 'Clear Server Cache')"></span>
 						</a>
 					</div>
+					<div class="configuration__padded">
+						<a href="#" class="btn btn-sm btn-primary" data-bind="click: runDiagnostics">
+							<span data-bind="text: 'Run Diagnostics'"></span>
+						</a>
+					</div>
 				</div>
 			</div>
 		</div>

js/pages/configuration/configuration.js

@@ -260,6 +260,24 @@ define([
         buttonClass,
       }
     }
+
+    runDiagnostics() {
+
+      const startTime = performance.now();
+
+      // get the list of isPermitted functions, except the literal isPermitted
+      for (const key in authApi) {
+        if (typeof authApi[key] === 'function' && key.startsWith('isPermitted') && key != 'isPermitted') {
+          authApi[key](); // Invoke the function
+        }
+      }
+
+      const endTime = performance.now();
+
+      const elapsedTime = endTime - startTime;
+      console.log(`Script execution time: ${elapsedTime} milliseconds`);
+
+    }
   }
 
   return commonUtils.build('ohdsi-configuration', Configuration, view);