Pull Request for 10-31-2023 release (#102)

* [ALS-5150] Add Google tag manager to infrastructure (#92) * [ALS-5150] Add Google tag manager to infrastructure (#92) * [ALS-5123] Banner open leaving (#95) * [ALS-5134] Update banner_config.json Update banner to display message about Open Access leaving * [ALS-5128] Add fence mapping file to dictionary resource (#96) * Get fence metadata file * add dataset-s3-object-key * Update fence mapping path * remove source_dictionary_s3_object_key (#101) # source_dictionary_s3_object_key is not declared or used. Terraform will fail. * removing source_dictionary_s3_object_key Co-authored-by: Tom <[email protected]> --------- Co-authored-by: gcolon021 <[email protected]> Co-authored-by: Gcolon021 <[email protected]> Co-authored-by: James <[email protected]> Co-authored-by: Tom <[email protected]>
hms-dbmi · Nov 9, 2023 · dd148d3 · dd148d3
1 parent 7c02e08
commit dd148d3
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Showing 6 changed files with 40 additions and 17 deletions.
diff --git a/app-infrastructure/configs/banner_config.json b/app-infrastructure/configs/banner_config.json
@@ -7,6 +7,14 @@
       "styles": "background-color: #C0143C; color: #fff; font-size: 1.1em; padding: 10px;",
       "isDismissible": false,
       "disabled": true
+    },
+    {
+      "text": "Open PIC-SURE without login is now live! Users can search, query, and build cohorts using data in BDC, with no login required. Check out this new feature <a href='https://openpicsure.biodatacatalyst.nhlbi.nih.gov/picsureui/' target='_blank' style='color: #fff; text-decoration: underline;'>here</a>.<br />The “Open Access” tab will no longer be accessible from this site starting December 2023. Please use the <a href='http://openpicsure.biodatacatalyst.nhlbi.nih.gov/' target='_blank' style='color: #fff; text-decoration: underline;'>Open PIC-SURE site</a> to continue using the Open Access functionality.",
+      "startDate": "2023-11-01T00:00:00Z",
+      "endDate": "2024-12-23T00:00:00Z",
+      "styles": "background-color: #1a568c; color: #fff; font-size: 1.1em; padding: 10px;",
+      "isDismissible": true,
+      "disabled": false
     }
   ]
-}
+}
diff --git a/app-infrastructure/configs/picsureui_settings.json b/app-infrastructure/configs/picsureui_settings.json
@@ -87,17 +87,19 @@
 	    "phs002383": "Walk-PHaSST",
 	    "phs002348": "MSH"
 	},
-        "categorySearchResultList" : [
-            "DCC_Harmonized_data_set",
-            "Coronary_Artery_Risk_Development_in_Young_Adults_CARDIA",
-            "Framingham_Cohort",
-            "Genetic_Epidemiology_of_COPD_COPDGene_",
-            "Multi_Ethnic_Study_of_Atherosclerosis_MESA_Cohort",
-            "The_Jackson_Heart_Study_JHS_",
-            "_Consents"
-             ],
-  "idp_provider":"fence",
-  "idp_provider_uri":"https://gen3.biodatacatalyst.nhlbi.nih.gov",
-	"fence_client_id":"${fence_client_id}",
-	"analyticsId":"${analytics_id}"
+	"categorySearchResultList" : [
+		"DCC_Harmonized_data_set",
+		"Coronary_Artery_Risk_Development_in_Young_Adults_CARDIA",
+		"Framingham_Cohort",
+		"Genetic_Epidemiology_of_COPD_COPDGene_",
+		"Multi_Ethnic_Study_of_Atherosclerosis_MESA_Cohort",
+		"The_Jackson_Heart_Study_JHS_",
+		"_Consents"
+	],
+	"idp_provider": "fence",
+	"idp_provider_uri": "https://gen3.biodatacatalyst.nhlbi.nih.gov",
+	"fence_client_id": "${fence_client_id}",
+	"fence_redirect_url": "https://biodatacatalyst.integration.hms.harvard.edu/psamaui/login/",
+	"analyticsId": "${analytics_id}",
+	"tagManagerId": "${tag_manager_id}"
 }
diff --git a/app-infrastructure/dictionary-instance.tf b/app-infrastructure/dictionary-instance.tf
@@ -59,6 +59,6 @@ resource "aws_instance" "dictionary-ec2" {
   metadata_options {
   	http_endpoint = "enabled"
   	http_tokens = "required"
-	  instance_metadata_tags = "enabled"  
+	  instance_metadata_tags = "enabled"
   }
 }
diff --git a/app-infrastructure/httpd-instance.tf b/app-infrastructure/httpd-instance.tf
@@ -83,6 +83,7 @@ data "template_file" "picsureui_settings" {
   vars = {
     fence_client_id = var.fence_client_id
     analytics_id = var.analytics_id
+    tag_manager_id = var.tag_manager_id
   }
 }
 

diff --git a/app-infrastructure/scripts/dictionary-user_data.sh b/app-infrastructure/scripts/dictionary-user_data.sh
@@ -207,6 +207,13 @@ for i in 1 2 3 4 5; do sudo /usr/local/bin/aws --region us-east-1 s3 cp s3://${s
 sudo bash /root/domain-join.sh
 
 sudo mkdir -p /var/log/dictionary-docker-logs
+for i in 1 2 3 4 5 6 7 8 9; do sudo /usr/local/bin/aws --region us-east-1 s3 cp s3://${stack_s3_bucket}/releases/jenkins_pipeline_build_${stack_githash}/pic-sure-hpds-dictionary-resource.tar.gz . && break || sleep 45; done
+
+for i in 1 2 3 4 5; do echo "trying to download fence mapping from s3://${stack_s3_bucket}/data/${dataset_s3_object_key}/fence_mapping.json" && sudo /usr/local/bin/aws --region us-east-1 s3 cp s3://${stack_s3_bucket}/data/${dataset_s3_object_key}/fence_mapping.json /home/centos/fence_mapping.json && break || sleep 45; done
+echo "pulled fence mapping"
+#sudo mkdir -p /usr/local/docker-config/search/
+#for i in 1 2 3 4 5 6 7 8 9; do sudo /usr/local/bin/aws --region us-east-1 s3 cp s3://${stack_s3_bucket}/data/${stack_githash}/dictionary.javabin.tar.gz /usr/local/docker-config/search/dictionary.javabin.tar.gz && break || sleep 45; done
+#sudo tar -xvzf /usr/local/docker-config/search/dictionary.javabin.tar.gz -C /usr/local/docker-config/search/
 for i in 1 2 3 4 5 6 7 8 9; do sudo /usr/local/bin/aws --region us-east-1 s3 cp s3://${stack_s3_bucket}/releases/jenkins_pipeline_build_${stack_githash}/pic-sure-hpds-dictionary-resource.tar.gz /home/centos/pic-sure-hpds-dictionary-resource.tar.gz && break || sleep 45; done
 sudo mkdir -p /usr/local/docker-config/search/
 

diff --git a/app-infrastructure/variables.tf b/app-infrastructure/variables.tf
@@ -56,6 +56,11 @@ variable "allowed_hosts" {
 }
 
 variable "analytics_id" {
-  type        = string
-  default     = "__ANALYTICS_ID__"
+  type    = string
+  default = "__ANALYTICS_ID__"
+}
+
+variable "tag_manager_id" {
+  type    = string
+  default = "__TAG_MANAGER_ID__"
 }