Add scripts and commands for radread and listmode warning emails (#6)

README.md

@@ -175,4 +175,4 @@ commands will be available on subject pages.
 
 ## Licence
 
-See [LICENSE.txt](`./LICENSE.txt`)
+See [LICENSE.txt](./LICENSE.txt)

email_listmode.json

@@ -0,0 +1,60 @@
+{
+  "name": "email-listmode",
+  "description": "Send email with listmode warnings",
+  "label": "Send email with listmode warnings",
+  "version": "1.0",
+  "schema-version": "1.0",
+  "type": "docker",
+  "command-line": "email_listmode #PROJECTID# #EMAILLIST#",
+  "image": "ghcr.io/ucl-mirsg/drc-containers:latest",
+  "override-entrypoint": true,
+  "mounts": [],
+  "inputs": [
+    {
+      "name": "PROJECTID",
+      "description": "Project ID",
+      "type": "string",
+      "user-settable": false,
+      "required": true,
+      "replacement-key": "#PROJECTID#"
+    },
+    {
+      "name": "EMAILLIST",
+      "description": "Comma separated list of email addresses",
+      "type": "string",
+      "user-settable": true,
+      "required": true,
+      "replacement-key": "#EMAILLIST#"
+    }
+  ],
+  "outputs": [],
+  "xnat": [
+    {
+      "name": "project-email-listmode",
+      "label": "Send email with listmode warnings",
+      "description": "Send email with listmode warnings",
+      "contexts": ["xnat:projectData"],
+      "external-inputs": [
+        {
+          "name": "project",
+          "description": "Input project",
+          "type": "Project",
+          "required": true,
+          "load-children": false
+        }
+      ],
+      "derived-inputs": [
+        {
+          "name": "project-id",
+          "type": "string",
+          "derived-from-wrapper-input": "project",
+          "derived-from-xnat-object-property": "id",
+          "provides-value-for-command-input": "PROJECTID",
+          "user-settable": false,
+          "required": true
+        }
+      ],
+      "output-handlers": []
+    }
+  ]
+}

email_radreads.json

@@ -0,0 +1,60 @@
+{
+  "name": "email-radreads",
+  "description": "Send email listing sessions without radreads",
+  "label": "Send email listing sessions without radreads",
+  "version": "1.0",
+  "schema-version": "1.0",
+  "type": "docker",
+  "command-line": "email_radreads #PROJECTID# #EMAILLIST#",
+  "image": "ghcr.io/ucl-mirsg/drc-containers:latest",
+  "override-entrypoint": true,
+  "mounts": [],
+  "inputs": [
+    {
+      "name": "PROJECTID",
+      "description": "Project ID",
+      "type": "string",
+      "user-settable": false,
+      "required": true,
+      "replacement-key": "#PROJECTID#"
+    },
+    {
+      "name": "EMAILLIST",
+      "description": "Comma separated list of email addresses",
+      "type": "string",
+      "user-settable": true,
+      "required": true,
+      "replacement-key": "#EMAILLIST#"
+    }
+  ],
+  "outputs": [],
+  "xnat": [
+    {
+      "name": "project-email-radreads",
+      "label": "Send email listing sessions without radreads",
+      "description": "Send email listing sessions without radreads",
+      "contexts": ["xnat:projectData"],
+      "external-inputs": [
+        {
+          "name": "project",
+          "description": "Input project",
+          "type": "Project",
+          "required": true,
+          "load-children": false
+        }
+      ],
+      "derived-inputs": [
+        {
+          "name": "project-id",
+          "type": "string",
+          "derived-from-wrapper-input": "project",
+          "derived-from-xnat-object-property": "id",
+          "provides-value-for-command-input": "PROJECTID",
+          "user-settable": false,
+          "required": true
+        }
+      ],
+      "output-handlers": []
+    }
+  ]
+}

pyproject.toml

@@ -6,9 +6,11 @@ dependencies = [
 ]
 name = "drc-containers"
 requires-python = ">3.10"
-version = "0.0.1"
+version = "0.0.2"
 
 [project.scripts]
+email_listmode = "drc_containers:email_listmode.main"
+email_radreads = "drc_containers:email_radreads.main"
 share_subject_to_genetic_project = "drc_containers:share_subject_to_genetic_project.main"
 
 [tool.setuptools.packages.find]

src/drc_containers/email_listmode.py

@@ -0,0 +1,232 @@
+import sys
+from dataclasses import dataclass
+from datetime import datetime, timedelta
+
+from pyxnat import Interface
+from pyxnat.core.resources import Experiments
+
+from drc_containers.xnat_utils.email import send_email
+from drc_containers.xnat_utils.xnat_credentials import (
+    open_pyxnat_session,
+    XnatContainerCredentials,
+    XnatCredentials,
+)
+
+
+@dataclass(frozen=True)
+class ListModeRecord:
+    """Store data from sessions with listmode errors
+    The frozen dataclass allows this to be used in a set to ensure no sessions
+    are repeated"""
+
+    id: str
+    label: str
+    subject_id: str
+    date: str
+    errors: str
+
+
+def get_recent_sessions(
+    pyxnat_interface: Interface, datatype: str, threshold_days: int, project_name: str
+) -> Experiments:
+    threshold_date = datetime.now() - timedelta(threshold_days)
+    str_threshold_date = threshold_date.strftime("%Y-%m-%d")
+    columns = [
+        datatype + "/SESSION_ID",
+        datatype + "/SUBJECT_ID",
+        datatype + "/DATE",
+        datatype + "/LABEL",
+        datatype + "/PROJECT",
+    ]
+    constraints = [
+        (datatype + "/project", "=", project_name),
+        (datatype + "/date", ">=", str_threshold_date),
+        "AND",
+    ]
+    return pyxnat_interface.select(datatype, columns).where(constraints)
+
+
+def check_session(
+    pyxnat_interface: Interface, session_id: str, project_name: str
+) -> [str]:
+    resources = (
+        pyxnat_interface.select.project(project_name).experiment(session_id).resources()
+    )
+
+    num_lm_files = 0
+    num_norm_files = 0
+    lm_found = False
+    norm_found = False
+    errors = []
+
+    for resource in resources:
+        res_label = resource.label()
+        if res_label == "LM":
+            lm_found = True
+            for file in resource.files():
+                num_lm_files += 1
+                file_label = file.label()
+                try:
+                    if ".bf" in file_label:
+                        file_size = file.size()
+                        if int(file_size) < 1000000:
+                            errors.append(
+                                f"LM File is too small " f"{file_label} - {file_size}"
+                            )
+                except:  # noqa: E722
+                    pass
+        elif res_label == "Norm":
+            norm_found = True
+            for _ in resource.files():
+                num_norm_files += 1
+
+    if not lm_found:
+        errors.append("LM does not exist")
+    elif num_lm_files != 2:
+        errors.append(f"Wrong number of LM files {num_lm_files}")
+
+    if not norm_found:
+        errors.append("Norm does not exist")
+    elif num_norm_files != 2:
+        errors.append(f"Wrong number of Norm files: {num_lm_files}")
+    return errors
+
+
+def get_listmode_issues(
+    pyxnat_interface: Interface, threshold_days: int, project_name: str
+) -> set[ListModeRecord]:
+    session_datatypes = [
+        "xnat:crSessionData",
+        "xnat:mrSessionData",
+        "xnat:otherDicomSessionData",
+        "xnat:petSessionData",
+        "xnat:petmrSessionData",
+        "xnat:srSessionData",
+    ]
+    issue_list = set()
+
+    for datatype in session_datatypes:
+        sessions = get_recent_sessions(
+            pyxnat_interface=pyxnat_interface,
+            datatype=datatype,
+            threshold_days=threshold_days,
+            project_name=project_name,
+        )
+        for session in sessions.data:
+            session_id = session["session_id"]
+            session_label = session["label"]
+            subject_id = session["subject_id"]
+            session_date = session["date"]
+
+            errors = check_session(
+                pyxnat_interface=pyxnat_interface,
+                session_id=session_id,
+                project_name=project_name,
+            )
+            if len(errors) > 0:
+                error_string = ", ".join(errors)
+                message = (
+                    f"Subject ID: {subject_id}   "
+                    f"Scan Date: {session_date}   "
+                    f"Errors: {error_string}<br>"
+                )
+                issue_list.add(
+                    ListModeRecord(
+                        id=session_id,
+                        label=session_label,
+                        subject_id=subject_id,
+                        date=session_date,
+                        errors=message,
+                    )
+                )
+
+    return issue_list
+
+
+def construct_email(list_mode_records: set[ListModeRecord]) -> str:
+    body = "<p>"
+
+    for session in list_mode_records:
+        body += f"Subject ID:{session.subject_id}   Scan Date:{session.date} Errors:{session.errors}<br>"
+    return body
+
+
+def email_listmode(
+    credentials: XnatCredentials,
+    project_name: str,
+    email_subject: str,
+    to_emails: list[str],
+    cc_emails: list[str] = None,
+    bcc_emails: list[str] = None,
+    debug_output: bool = True,
+):
+    """Email notification about image sessions with listmode errors
+
+    Args:
+        credentials: XNAT host name and user login details
+        project_name: The project to search for sessions
+        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
+        cc_emails: list of email addresses for cc. XNAT will only send emails
+            to addresses which already correspond to XNAT users on the server
+        bcc_emails: list of email addresses for bcc. XNAT will only send emails
+            to addresses which already correspond to XNAT users on the server
+        debug_output: set to True to output debugging data to the console
+    """
+
+    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
+        )
+
+        if debug_output:
+            print("Sessions failing listmode checks:")
+            if len(sessions_to_report) > 0:
+                for s in sessions_to_report:
+                    print(s)
+            else:
+                print("None found")
+
+        if len(sessions_to_report) > 0:
+            # Construct email html body
+            body_html = construct_email(list_mode_records=sessions_to_report)
+
+            # Print email content so it is visible in the container log
+            print("Sending email with the following content:")
+            print(f"To: {to_emails}")
+            print(f"cc: {cc_emails}")
+            print(f"bcc: {bcc_emails}")
+            print(f"Subject: {email_subject}")
+            print(body_html)
+
+            # Send the email via XNAT
+            send_email(
+                session=xnat_session,
+                subject=email_subject,
+                to=to_emails,
+                cc=cc_emails,
+                bcc=bcc_emails,
+                content_html=body_html,
+            )
+
+
+def main():
+    if len(sys.argv) < 3:
+        raise ValueError("No email list specified")
+    if len(sys.argv) < 2:
+        raise ValueError("No project name specified")
+
+    credentials = XnatContainerCredentials()
+
+    email_listmode(
+        credentials=credentials,
+        project_name=sys.argv[1],
+        email_subject="1946 Weekly Listmode Status Check",
+        to_emails=sys.argv[2].split(","),
+    )
+
+
+if __name__ == "__main__":
+    main()