Add user roles to patient's contact and update conftest file (#383)

* Add user roles to patient's contact and update conftest file

* Reformat

* Simplify code

* tiny fix in test

---------

Co-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>

Author: northwestwitch

CHANGELOG.md

@@ -1,9 +1,11 @@
 ## [unpublished]
 ### Added
 - `email` and `additionalContacts` in API reference json schema (#380)
+- Allow assigning contact `roles` using the cli (#383)
 ### Changed
 - Updated versions of external actions and MongoDB in GitHub workflows (#374)
 - Allow updating contact's email and href separately using the command line (#381)
+- Conftest file to reflect a patient's contact with email, roles and additionalContacts (#383)
 ### Fixed
 - Fixed typo on conda installation docs (#373)
 

patientMatcher/cli/update.py

@@ -27,23 +27,26 @@ def update():
 @click.option("--new-email", type=click.STRING, required=False, help="New email")
 @click.option("--new-name", type=click.STRING, required=False, help="New name")
 @click.option("--new-institution", type=click.STRING, required=False, help="New institution")
-def contact(href, email, new_href, new_email, new_name, new_institution):
+@click.option("--new-role", multiple=True, help="New role(s)")
+def contact(href, email, new_href, new_email, new_name, new_institution, new_role):
     """Update contact person for a group of patients."""
 
     # Validate exactly one identifier
     if bool(href) == bool(email):
         raise click.UsageError("You must provide EITHER --href or --email")
 
     # Validate at least one field to update
-    if not any([new_href, new_email, new_name, new_institution]):
+    if not any([new_href, new_email, new_name, new_institution, new_role]):
         click.echo(
             "Provide at least a field you wish to update: "
             "--new-href / --new-email / --new-name / --new-institution"
         )
         return
 
     # Build query
-    query = {HREF_FIELD: {"$regex": href}} if href else {"contact.email": email}
+    query = {"contact.email": email}
+    if href:
+        query = {HREF_FIELD: {"$regex": href}}
 
     database = current_app.db
     matching_patients = patients(database=database, match_query=query)
@@ -64,7 +67,7 @@ def contact(href, email, new_href, new_email, new_name, new_institution):
     if new_href:
         if EMAIL_REGEX.match(new_href) and not new_href.startswith("mailto:"):
             new_href = f"mailto:{new_href}"
-        if not href_validate(new_href):
+        elif not href_validate(new_href):
             LOG.error(
                 "Provided href does not have a valid schema. Provide either a URL (http://.., https://..) or an email address (mailto:..)"
             )
@@ -76,6 +79,8 @@ def contact(href, email, new_href, new_email, new_name, new_institution):
         set_options["contact.name"] = new_name
     if new_institution:
         set_options["contact.institution"] = new_institution
+    if new_role:
+        set_options["contact.roles"] = list(new_role)
 
     # Confirm and update
     patient_count = len(list(matching_patients))

tests/cli/test_update.py

@@ -8,6 +8,7 @@
 NEW_EMAIL = "new.email@mail.com"
 NEW_NAME = "New Name"
 TEST_INST = "Test Institution"
+TEST_ROLES = ["clinician", "researcher"]
 
 
 @responses.activate
@@ -67,6 +68,10 @@ def test_update_contact_success(mock_app, gpx4_patients, monkeypatch):
             NEW_NAME,
             "--new-institution",
             TEST_INST,
+            "--new-role",
+            TEST_ROLES[0],
+            "--new-role",
+            TEST_ROLES[1],
         ],
     )
 
@@ -80,6 +85,7 @@ def test_update_contact_success(mock_app, gpx4_patients, monkeypatch):
     assert updated_patient[0]["contact"]["email"] == NEW_EMAIL
     assert updated_patient[0]["contact"]["name"] == NEW_NAME
     assert updated_patient[0]["contact"]["institution"] == TEST_INST
+    assert updated_patient[0]["contact"]["roles"] == TEST_ROLES
 
 
 def test_update_contact_validation(mock_app, gpx4_patients):

tests/conftest.py

@@ -38,6 +38,14 @@
     "SGOL1": "ENSG00000129810",
 }
 
+PATIENT_CONTACT = {
+    "href": "https://someurl.com",
+    "email": "user@mail.com",
+    "institution": "Test institution",
+    "name": "Test User",
+    "roles": ["clinician", "researcher"],
+}
+
 
 @pytest.fixture
 def mock_symbol_2_ensembl():
@@ -126,11 +134,8 @@ def test_node():
 def entrez_gene_patient():
     """Returns a test patient with an entrez gene ID"""
     patient = {
-        "contact": {
-            "href": "mailto:someuser@mail.com",
-            "institution": "Test institution",
-            "name": "Test user",
-        },
+        "contact": PATIENT_CONTACT,
+        "additionalContacts": [PATIENT_CONTACT],
         "disorders": [],
         "features": [
             {"id": "HP:0001263", "label": "Global developmental delay", "observed": "yes"},