set HOME env variable; handle SENDGRID_API_KEY env variable

src/utils/studies_functions.py

@@ -9,11 +9,12 @@
 
 import httpx
 from google.cloud import firestore
-from google.cloud.firestore_v1 import AsyncDocumentReference, DocumentReference, FieldFilter
+from google.cloud.firestore_v1 import AsyncDocumentReference, FieldFilter
 from python_http_client.exceptions import HTTPError
 from quart import current_app, g
 from sendgrid import SendGridAPIClient
 from sendgrid.helpers.mail import Email, Mail
+from werkzeug.exceptions import BadRequest
 
 from src.api_utils import APIException
 from src.auth import get_service_account_headers
@@ -41,7 +42,11 @@ async def email(inviter: str, recipient: str, invitation_message: str, study_tit
     :return: The status code of the email sending operation.
     """
     doc_ref_dict: dict = (await current_app.config["DATABASE"].collection("meta").document("sendgrid").get()).to_dict()
-    sg = SendGridAPIClient(api_key=doc_ref_dict.get("api_key", ""))
+
+    api_key = os.getenv("SENDGRID_API_KEY") or doc_ref_dict.get("api_key")
+    if not api_key:
+        raise BadRequest("No SendGrid API key found")
+    sg = SendGridAPIClient(api_key=api_key)
 
     html_content = email_template.substitute(
         inviter=escape(inviter),

src/vm_scripts/startup-script.sh

@@ -12,6 +12,7 @@ handle_error() {
 }
 
 trap handle_error ERR
+export HOME=/root
 
 sudo -s
 

src/vm_scripts/startup-script_user_cp0.sh

@@ -1,6 +1,7 @@
 #!/bin/bash
 
 sudo -s
+export HOME=/root
 
 if [[ -f startup_was_launched ]]; then exit 0; fi
 touch startup_was_launched

src/web/study.py

@@ -57,16 +57,17 @@ async def restart_study() -> Response:
     doc_ref = db.collection("studies").document(study_id)
     doc_ref_dict: dict = (await doc_ref.get()).to_dict() or {}
 
-    for role, v in enumerate(doc_ref_dict["participants"]):
-        participant = doc_ref_dict["personal_parameters"][v]
-        if (gcp_project := participant.get("GCP_PROJECT").get("value")) != "":
-            google_cloud_compute = GoogleCloudCompute(study_id, gcp_project)
-            for instance in google_cloud_compute.list_instances():
-                if instance == format_instance_name(google_cloud_compute.study_id, str(role)):
-                    google_cloud_compute.delete_instance(instance)
-
-            google_cloud_compute.delete_firewall("")
-    logger.info("Successfully Deleted gcp instances and firewalls")
+    if not constants.TERRA:  # TODO: add equivalent for terra
+        for role, v in enumerate(doc_ref_dict["participants"]):
+            participant = doc_ref_dict["personal_parameters"][v]
+            if (gcp_project := participant.get("GCP_PROJECT").get("value")) != "":
+                google_cloud_compute = GoogleCloudCompute(study_id, gcp_project)
+                for instance in google_cloud_compute.list_instances():
+                    if instance == format_instance_name(google_cloud_compute.study_id, str(role)):
+                        google_cloud_compute.delete_instance(instance)
+
+                google_cloud_compute.delete_firewall("")
+        logger.info("Successfully Deleted gcp instances and firewalls")
 
     for participant in doc_ref_dict["participants"]:
         doc_ref_dict["status"][participant] = "ready to begin protocol" if participant == get_cp0_id() else ""
@@ -141,12 +142,12 @@ async def delete_study() -> Response:
     doc_ref = db.collection("studies").document(study_id)
     doc_ref_dict: dict = (await doc_ref.get()).to_dict() or {}
 
-    for participant in doc_ref_dict["personal_parameters"].values():
-        if (gcp_project := participant.get("GCP_PROJECT").get("value")) != "":
-            google_cloud_compute = GoogleCloudCompute(study_id, gcp_project)
-            google_cloud_compute.delete_everything()
-
-    logger.info("Successfully deleted GCP instances and other related resources")
+    if not constants.TERRA:  # TODO: add equivalent for terra
+        for participant in doc_ref_dict["personal_parameters"].values():
+            if (gcp_project := participant.get("GCP_PROJECT").get("value")) != "":
+                google_cloud_compute = GoogleCloudCompute(study_id, gcp_project)
+                google_cloud_compute.delete_everything()
+        logger.info("Successfully deleted GCP instances and other related resources")
 
     for participant in doc_ref_dict["personal_parameters"].values():
         if (auth_key := participant.get("AUTH_KEY").get("value")) != "":