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UCL-MIRSG · Oct 8, 2024 · e8c5937 · e8c5937
1 parent 0e06aa1
commit e8c5937
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Showing 3 changed files with 60 additions and 24 deletions.
diff --git a/email_listmode.json b/email_listmode.json
@@ -1,38 +1,47 @@
 {
   "name": "email-listmode",
-  "description": "Send email with listmode warnings",
-  "label": "Send email with listmode warnings",
-  "version": "1.0",
+  "description": "Send email listing subjects with missing listmode data",
+  "label": "Listmode email",
+  "version": "1.1",
   "schema-version": "1.0",
   "type": "docker",
-  "command-line": "email_listmode #PROJECTID# #EMAILLIST#",
+  "command-line": "email_listmode #PROJECTID# #THRESHOLDDAYS# #EMAILLIST#",
   "image": "ghcr.io/ucl-mirsg/drc-containers:latest",
   "override-entrypoint": true,
   "mounts": [],
   "inputs": [
     {
-      "name": "PROJECTID",
+      "name": "project-id",
       "description": "Project ID",
       "type": "string",
       "user-settable": false,
       "required": true,
       "replacement-key": "#PROJECTID#"
     },
     {
-      "name": "EMAILLIST",
+      "name": "email-list",
       "description": "Comma separated list of email addresses",
       "type": "string",
       "user-settable": true,
       "required": true,
       "replacement-key": "#EMAILLIST#"
+    },
+    {
+      "name": "threshold-days",
+      "description": "Only check sessions created within this number of days",
+      "type": "number",
+      "user-settable": true,
+      "required": true,
+      "replacement-key": "#THRESHOLDDAYS#",
+      "default-value": 90
     }
   ],
   "outputs": [],
   "xnat": [
     {
-      "name": "project-email-listmode",
-      "label": "Send email with listmode warnings",
-      "description": "Send email with listmode warnings",
+      "name": "email-listmode-project",
+      "label": "Send listmode email",
+      "description": "Send email listing subjects with missing listmode data",
       "contexts": ["xnat:projectData"],
       "external-inputs": [
         {
@@ -45,11 +54,11 @@
       ],
       "derived-inputs": [
         {
-          "name": "project-id",
+          "name": "project-identifier",
           "type": "string",
           "derived-from-wrapper-input": "project",
           "derived-from-xnat-object-property": "id",
-          "provides-value-for-command-input": "PROJECTID",
+          "provides-value-for-command-input": "project-id",
           "user-settable": false,
           "required": true
         }

diff --git a/email_radreads.json b/email_radreads.json
@@ -1,8 +1,8 @@
 {
   "name": "email-radreads",
   "description": "Send email listing sessions without radreads",
-  "label": "Send email listing sessions without radreads",
-  "version": "1.0",
+  "label": "Radreads email",
+  "version": "1.1",
   "schema-version": "1.0",
   "type": "docker",
   "command-line": "email_radreads #PROJECTID# #EMAILLIST#",
@@ -11,15 +11,15 @@
   "mounts": [],
   "inputs": [
     {
-      "name": "PROJECTID",
+      "name": "project-id",
       "description": "Project ID",
       "type": "string",
       "user-settable": false,
       "required": true,
       "replacement-key": "#PROJECTID#"
     },
     {
-      "name": "EMAILLIST",
+      "name": "email-list",
       "description": "Comma separated list of email addresses",
       "type": "string",
       "user-settable": true,
@@ -30,9 +30,9 @@
   "outputs": [],
   "xnat": [
     {
-      "name": "project-email-radreads",
-      "label": "Send email listing sessions without radreads",
-      "description": "Send email listing sessions without radreads",
+      "name": "email-radreads-project",
+      "label": "Send radreads email",
+      "description": "Send email listing sessions requiring radreads",
       "contexts": ["xnat:projectData"],
       "external-inputs": [
         {
@@ -45,11 +45,11 @@
       ],
       "derived-inputs": [
         {
-          "name": "project-id",
+          "name": "project-identifier",
           "type": "string",
           "derived-from-wrapper-input": "project",
           "derived-from-xnat-object-property": "id",
-          "provides-value-for-command-input": "PROJECTID",
+          "provides-value-for-command-input": "project-id",
           "user-settable": false,
           "required": true
         }

diff --git a/src/drc_containers/email_listmode.py b/src/drc_containers/email_listmode.py
@@ -95,6 +95,17 @@ def check_session(
 def get_listmode_issues(
     pyxnat_interface: Interface, threshold_days: int, project_name: str
 ) -> set[ListModeRecord]:
+    """
+
+    Args:
+        pyxnat_interface: current pyxnat session
+        threshold_days: check only sessions created within this number of days
+        project_name: name of project in which to check sessions
+
+    Returns:
+        set of ListModeRecords, each describing a session with missing listmode
+            data
+    """
     session_datatypes = [
         "xnat:crSessionData",
         "xnat:mrSessionData",
@@ -156,6 +167,7 @@ def email_listmode(
     project_name: str,
     email_subject: str,
     to_emails: list[str],
+    threshold_days: int = 90,
     cc_emails: list[str] = None,
     bcc_emails: list[str] = None,
     debug_output: bool = True,
@@ -165,6 +177,7 @@ def email_listmode(
     Args:
         credentials: XNAT host name and user login details
         project_name: The project to search for sessions
+        threshold_days: check only sessions created within this number of days
         email_subject: subject line of email
         to_emails: list of email addresses. XNAT will only send emails
             to addresses which already correspond to XNAT users on the server
@@ -178,7 +191,7 @@ def email_listmode(
     with open_pyxnat_session(credentials=credentials) as xnat_session:
         # Get list of ListModeRecords
         sessions_to_report = get_listmode_issues(
-            pyxnat_interface=xnat_session, threshold_days=90, project_name=project_name
+            pyxnat_interface=xnat_session, threshold_days=threshold_days, project_name=project_name
         )
 
         if debug_output:
@@ -213,18 +226,32 @@ def email_listmode(
 
 
 def main():
-    if len(sys.argv) < 3:
+    if len(sys.argv) < 4:
         raise ValueError("No email list specified")
+    to_emails = sys.argv[3].split(",")
+
+    if len(sys.argv) < 3:
+        raise ValueError("No threshold days specified")
+    threshold_days_str = sys.argv[2]
+
     if len(sys.argv) < 2:
         raise ValueError("No project name specified")
+    project_name = sys.argv[1]
+
+    try:
+        threshold_days = int(threshold_days_str)
+    except ValueError:
+        raise ValueError("Invalid input for threshold days: "
+                         "{threshold_days_str}")
 
     credentials = XnatContainerCredentials()
 
     email_listmode(
         credentials=credentials,
-        project_name=sys.argv[1],
+        project_name=project_name,
+        threshold_days=threshold_days,
         email_subject="1946 Weekly Listmode Status Check",
-        to_emails=sys.argv[2].split(","),
+        to_emails=to_emails,
     )