[ENH] add usernames to compose (#588)

* run test in ci

* run black

* undo changes to test_auth in neurostore

* add new test file

.github/workflows/workflow.yml

@@ -254,7 +254,7 @@ jobs:
           -e "NEUROVAULT_ACCESS_TOKEN=${NEUROVAULT_ACCESS_TOKEN}" \
           --rm -w /compose \
           compose \
-          bash -c "python -m pytest neurosynth_compose/tests && python -m pytest --celery neurosynth_compose/tests/api/celery_tests"
+          bash -c "python -m pytest neurosynth_compose/tests && python -m pytest --celery neurosynth_compose/tests/api/celery_tests && python -m pytest --auth neurosynth_compose/tests/api/test_auth.py"
 
   style_check:
     runs-on: ubuntu-latest

compose/neurosynth_compose/resources/analysis.py

@@ -44,6 +44,26 @@
 from .singular import singularize
 
 
+def create_user():
+    from auth0.v3.authentication.users import Users
+
+    auth = request.headers.get("Authorization", None)
+    if auth is None:
+        return None
+    token = auth.split()[1]
+    profile_info = Users(
+        current_app.config["AUTH0_BASE_URL"].removeprefix("https://")
+    ).userinfo(access_token=token)
+
+    # user signed up with auth0, but has not made any queries yet...
+    # should have endpoint to "create user" after sign on with auth0
+    current_user = User(
+        external_id=connexion.context["user"], name=profile_info.get("name", "Unknown")
+    )
+
+    return current_user
+
+
 def get_current_user():
     user = connexion.context.get("user")
     if user:
@@ -81,9 +101,10 @@ def update_or_create(cls, data, id=None, commit=True):
         if not current_user:
             # user signed up with auth0, but has not made any queries yet...
             # should have endpoint to "create user" after sign on with auth0
-            current_user = User(external_id=connexion.context["user"])
-            db.session.add(current_user)
-            db.session.commit()
+            current_user = create_user()
+            if current_user:
+                db.session.add(current_user)
+                db.session.commit()
 
         id = id or data.get("id", None)  # want to handle case of {"id": "asdfasf"}
 
@@ -446,7 +467,9 @@ def put(self, id):
             access_token = request.headers.get("Authorization")
             neurostore_analysis_upload = create_or_update_neurostore_analysis.si(
                 ns_analysis_id=ns_analysis.id,
-                cluster_table=str(cluster_table_fnames[0]) if cluster_table_fnames else None,
+                cluster_table=str(cluster_table_fnames[0])
+                if cluster_table_fnames
+                else None,
                 nv_collection_id=result.neurovault_collection.id,
                 access_token=access_token,
             )

compose/neurosynth_compose/resources/tasks.py

@@ -88,6 +88,7 @@ def create_or_update_neurostore_analysis(
     from auth0.v3.authentication.get_token import GetToken
     import pandas as pd
     from .neurostore import neurostore_session
+
     ns_analysis = NeurostoreAnalysis.query.filter_by(id=ns_analysis_id).one()
     nv_collection = NeurovaultCollection.query.filter_by(id=nv_collection_id).one()
 
@@ -126,7 +127,7 @@ def create_or_update_neurostore_analysis(
                         "value": row["Peak Stat"],
                     }
                 ],
-                "order": point_idx
+                "order": point_idx,
             }
             if not pd.isna(row["Cluster Size (mm3)"]):
                 point["subpeak"] = True

compose/neurosynth_compose/schemas/analysis.py

@@ -119,6 +119,7 @@ class BaseSchema(Schema):
     created_at = fields.DateTime()
     updated_at = fields.DateTime(allow_none=True)
     user_id = fields.String(data_key="user")
+    username = fields.String(attribute="user.name", dump_only=True)
 
 
 class EstimatorSchema(Schema):

compose/neurosynth_compose/tests/api/celery_tests/test_meta_analysis_result.py

@@ -7,14 +7,17 @@
     NeurostoreStudy,
     NeurostoreAnalysis,
 )
-from ....resources.tasks import file_upload_neurovault, create_or_update_neurostore_analysis
+from ....resources.tasks import (
+    file_upload_neurovault,
+    create_or_update_neurostore_analysis,
+)
 from ....resources.analysis import (
     create_or_update_neurostore_study,
 )
 
 
 @celery_test
-def test_file_upload_neurovault(app, db, mock_pynv):
+def test_file_upload_neurovault(session, app, db, mock_pynv):
     import os
     from pathlib import Path
     import shutil
@@ -35,7 +38,7 @@ def test_file_upload_neurovault(app, db, mock_pynv):
 
 @celery_test
 def test_create_or_update_neurostore_analysis(
-    auth_client, app, db, mock_pynv, meta_analysis_cached_result_files
+    session, auth_client, app, db, mock_pynv, meta_analysis_cached_result_files
 ):
     cluster_tables = [
         f for f in meta_analysis_cached_result_files["tables"] if "clust.tsv" in f.name
@@ -78,7 +81,9 @@ def test_create_or_update_neurostore_analysis(
 
 
 @celery_test
-def test_result_upload(auth_client, app, db, meta_analysis_cached_result_files):
+def test_result_upload(
+    session, auth_client, app, db, meta_analysis_cached_result_files
+):
     data = {}
     data["statistical_maps"] = [
         (open(m, "rb"), m.name) for m in meta_analysis_cached_result_files["maps"]

compose/neurosynth_compose/tests/api/test_annotation.py

@@ -1,4 +1,4 @@
-def test_get_annotations(auth_client, user_data):
+def test_get_annotations(session, auth_client, user_data):
     get_all = auth_client.get("/api/annotations")
     assert get_all.status_code == 200
     id_ = get_all.json["results"][0]["id"]

compose/neurosynth_compose/tests/api/test_auth.py

@@ -0,0 +1,30 @@
+from ..conftest import auth_test
+import pytest
+
+
+@auth_test
+def test_decode_token(add_users):
+    from ...resources.auth import decode_token, AuthError
+
+    with pytest.raises(AuthError):
+        decode_token("improper_token")
+
+    for user in add_users.values():
+        decode_token(user["token"])
+
+
+@auth_test
+def test_creating_new_user_on_db(add_users):
+    from ..request_utils import Client
+
+    token_info = add_users
+    user_name = "user1"  # user1 was not entered into database
+
+    client = Client(
+        token=token_info[user_name]["token"],
+        username=token_info[user_name]["external_id"],
+    )
+
+    resp = client.post("/api/projects", data={"name": "my project"})
+
+    assert resp.status_code == 200

compose/neurosynth_compose/tests/api/test_crud.py

@@ -21,7 +21,7 @@
         ("projects", Project, ProjectSchema),
     ],
 )
-def test_create(auth_client, user_data, endpoint, model, schema):
+def test_create(session, auth_client, user_data, endpoint, model, schema):
     user = User.query.filter_by(name="user1").first()
     examples = model.query.filter_by(user=user).all()
     for example in examples:
@@ -42,6 +42,8 @@ def test_create(auth_client, user_data, endpoint, model, schema):
             del payload["neurostore_url"]
         if "neurostore_study" in payload:
             del payload["neurostore_study"]
+        if "username" in payload:
+            del payload["username"]
 
         if isinstance(example, MetaAnalysis):
             del payload["neurostore_analysis"]
@@ -75,7 +77,7 @@ def test_create(auth_client, user_data, endpoint, model, schema):
         ("projects", Project, ProjectSchema),
     ],
 )
-def test_read(auth_client, user_data, endpoint, model, schema):
+def test_read(session, auth_client, user_data, endpoint, model, schema):
     user = User.query.filter_by(name="user1").first()
     if hasattr(model, "public"):
         query = (model.user == user) | (model.public == True)  # noqa E712
@@ -107,7 +109,7 @@ def test_read(auth_client, user_data, endpoint, model, schema):
         ("projects", Project, ProjectSchema, {"name": "my project"}),
     ],
 )
-def test_update(auth_client, db, session, user_data, endpoint, model, schema, update):
+def test_update(session, auth_client, db, user_data, endpoint, model, schema, update):
     user = User.query.filter_by(name="user1").first()
     record = model.query.filter_by(user=user).first()
 

compose/neurosynth_compose/tests/api/test_meta_analysis.py

@@ -1,4 +1,4 @@
-def test_get_meta_analyses(app, auth_client, user_data):
+def test_get_meta_analyses(session, app, auth_client, user_data):
     get_all = auth_client.get("/api/meta-analyses")
     assert get_all.status_code == 200
 
@@ -15,5 +15,5 @@ def test_get_meta_analyses(app, auth_client, user_data):
         assert data[key] is None or isinstance(data[key], dict)
 
 
-def test_ingest_neurostore(neurostore_data):
+def test_ingest_neurostore(session, neurostore_data):
     pass

compose/neurosynth_compose/tests/api/test_meta_analysis_result.py

@@ -1,7 +1,7 @@
 from neurosynth_compose.models import MetaAnalysis
 
 
-def test_create_meta_analysis_result(app, auth_client, user_data):
+def test_create_meta_analysis_result(session, app, auth_client, user_data):
     meta_analysis = MetaAnalysis.query.first()
     headers = {"Compose-Upload-Key": meta_analysis.run_key}
     data = {
@@ -20,7 +20,9 @@ def test_create_meta_analysis_result(app, auth_client, user_data):
     assert meta_resp.status_code == 200
 
 
-def test_create_meta_analysis_result_no_snapshots(app, db, auth_client, user_data):
+def test_create_meta_analysis_result_no_snapshots(
+    session, app, db, auth_client, user_data
+):
     meta_analysis = MetaAnalysis.query.first()
     meta_analysis.studyset.snapshot = None
     meta_analysis.annotation.snapshot = None

compose/neurosynth_compose/tests/api/test_specification.py

@@ -1,3 +1,3 @@
-def test_get_specification(app, auth_client, user_data):
+def test_get_specification(session, app, auth_client, user_data):
     get = auth_client.get("/api/specifications")
     assert get.status_code == 200

compose/neurosynth_compose/tests/api/test_studyset.py

@@ -2,17 +2,18 @@
 from ...schemas import StudysetSchema
 
 
-def test_get_studysets(auth_client, user_data):
+def test_get_studysets(session, auth_client, user_data):
     get = auth_client.get("/api/studysets")
     assert get.status_code == 200
 
 
-def test_post_studyset_with_new_neurostore_id(auth_client, user_data):
+def test_post_studyset_with_new_neurostore_id(session, auth_client, user_data):
     user = User.query.filter_by(name="user1").first()
     example = Studyset.query.filter_by(user=user).first()
     schema = StudysetSchema()
     payload = schema.dump(example)
     payload.pop("url")
+    payload.pop("username")
     # payload["neurostore_id"] = ""
 
     resp = auth_client.post("/api/studysets", data=payload)