Add Chenies email

email_chenies.json

@@ -0,0 +1,60 @@
+{
+  "name": "email-chenies",
+  "description": "Send email listing subjects with phase 3 data and no Chenies Mews MR data",
+  "label": "Chenies Mews email",
+  "version": "1.1",
+  "schema-version": "1.0",
+  "type": "docker",
+  "command-line": "email_chenies #PROJECTID# #EMAILLIST#",
+  "image": "ghcr.io/ucl-mirsg/drc-containers:latest",
+  "override-entrypoint": true,
+  "mounts": [],
+  "inputs": [
+    {
+      "name": "project-id",
+      "description": "Project ID",
+      "type": "string",
+      "user-settable": false,
+      "required": true,
+      "replacement-key": "#PROJECTID#"
+    },
+    {
+      "name": "email-list",
+      "description": "Comma separated list of email addresses",
+      "type": "string",
+      "user-settable": true,
+      "required": true,
+      "replacement-key": "#EMAILLIST#"
+    }
+  ],
+  "outputs": [],
+  "xnat": [
+    {
+      "name": "email-chenies-project",
+      "label": "Send Chenies Mews email",
+      "description": "Send email listing subjects with phase 3 data that are missing Chenies Mews MR data",
+      "contexts": ["xnat:projectData"],
+      "external-inputs": [
+        {
+          "name": "project",
+          "description": "Input project",
+          "type": "Project",
+          "required": true,
+          "load-children": false
+        }
+      ],
+      "derived-inputs": [
+        {
+          "name": "project-identifier",
+          "type": "string",
+          "derived-from-wrapper-input": "project",
+          "derived-from-xnat-object-property": "id",
+          "provides-value-for-command-input": "project-id",
+          "user-settable": false,
+          "required": true
+        }
+      ],
+      "output-handlers": []
+    }
+  ]
+}

pyproject.toml

@@ -6,11 +6,12 @@ dependencies = [
 ]
 name = "drc-containers"
 requires-python = ">3.10"
-version = "0.0.2"
+version = "0.0.3"
 
 [project.scripts]
 email_listmode = "drc_containers:email_listmode.main"
 email_radreads = "drc_containers:email_radreads.main"
+email_chenies = "drc_containers:email_chenies.main"
 share_subject_to_genetic_project = "drc_containers:share_subject_to_genetic_project.main"
 
 [tool.setuptools.packages.find]

src/drc_containers/email_chenies.py

@@ -0,0 +1,168 @@
+import sys
+
+from pyxnat import Interface
+
+from drc_containers.xnat_utils.email import send_email
+from drc_containers.xnat_utils.xnat_credentials import open_pyxnat_session, \
+    XnatContainerCredentials, XnatCredentials
+
+
+def get_subject_labels_for_phase(
+    pyxnat_interface: Interface,
+    datatype: str,
+    project_name: str,
+    phase: int
+) -> set[str]:
+    """Return list of sessions in this project for the specified datatype which
+    have a label matching the specified phase number
+
+    Args:
+        pyxnat_interface:  PyXnat session interface
+        datatype: data type to search for
+        project_name: project to search in
+        phase: phase number to search for in the session label
+
+    Returns:
+        set of subject labels
+    """
+    columns = [
+        datatype + "/SESSION_ID",
+        datatype + "/SUBJECT_LABEL",
+        datatype + "/DATE",
+        datatype + "/LABEL",
+        datatype + "/PROJECT"
+    ]
+    label_pattern = f'%\\_{phase:02d}\\_%'
+    constraints = [(datatype + '/project', '=', project_name),
+                   (datatype + '/label', 'LIKE', label_pattern),
+                   'AND']
+    sessions = pyxnat_interface.select(datatype, columns).where(constraints)
+    subject_labels = set(session['label'].split('_', 1)[0] for session in
+                      sessions.data)
+    return subject_labels
+
+
+def get_session_labels(
+    pyxnat_interface: Interface,
+    datatype: str,
+    project_name: str
+) -> set[str]:
+    """Return list of subject labels in this project
+
+    Args:
+        pyxnat_interface: PyXnat session interface
+        datatype: data type to search for
+        project_name: project to search in
+
+    Returns:
+        set of subject labels from datatypes in matching project
+    """
+    columns = [
+        datatype + "/LABEL",
+        datatype + "/SUBJECT_LABEL",
+        datatype + "/PROJECT"
+    ]
+    constraints = [(datatype + '/project', '=', project_name),
+                   'AND']
+    sessions = pyxnat_interface.select(datatype, columns).where(constraints)
+    subjects = set([session['subject_label'].split('_', 1)[0] for session in
+                    sessions.data])
+
+    return subjects
+
+
+def construct_email(
+        server_url: str, project: str, subjects_to_do: set[str]) -> str:
+    body_html = f'<p>The following subjects have phase 3 PET-MR sessions but ' \
+                f'do not have corresponding Chenies Mews MR data:'
+    body_html += '<p>'
+
+    for subject_label in subjects_to_do:
+        link_form = f'{server_url}/data/projects/{project}/subjects/{subject_label}'
+        body_html += f'Subject: <a href="{link_form}">{subject_label}</a> Project: {project}<br><br>'
+
+    return body_html
+
+
+def email_chenies(
+        credentials: XnatCredentials,
+        project_name: str,
+        email_subject: str,
+        to_emails: list[str],
+        cc_emails: list[str] = None,
+        bcc_emails: list[str] = None):
+    """Email notification about image sessions without radreads
+
+    Args:
+        credentials: XNAT host name and user login details
+        project_name: The project to search for PETMR 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
+    """
+
+    mr_projects = ['CHENIES_TRANSFER', 'CHENIES_MRI']
+    with open_pyxnat_session(credentials=credentials) as pyxnat_interface:
+
+        # Get list of subjects containing phase 3 PET-MR sessions
+        phase3_petmr_subjects = get_subject_labels_for_phase(
+            pyxnat_interface=pyxnat_interface,
+            datatype='xnat:petmrSessionData',
+            phase=3,
+            project_name=project_name
+        )
+        subjects_with_mr = set()
+        for mr_project in mr_projects:
+            subjects_with_mr = subjects_with_mr | get_session_labels(
+                pyxnat_interface=pyxnat_interface,
+                datatype='xnat:mrSessionData',
+                project_name=mr_project
+            )
+        subjects_to_do = set()
+        for subject_label in phase3_petmr_subjects:
+            if subject_label not in subjects_with_mr:
+                print(f'NOT FOUND: {subject_label}')
+                subjects_to_do.add(subject_label)
+
+        if len(subjects_to_do) > 0:
+
+            # Construct email html body
+            body_html = construct_email(
+                server_url=credentials.host,
+                project=project_name,
+                subjects_to_do=subjects_to_do
+            )
+
+            # Send the email via XNAT
+            send_email(
+                session=pyxnat_interface,
+                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_chenies(
+        credentials=credentials,
+        project_name=sys.argv[1],
+        email_subject="1946 update: Chenies Mews phase 3 data",
+        to_emails=sys.argv[2].split(","),
+    )
+
+
+if __name__ == '__main__':
+    main()