Merge branch 'master' into dependabot/npm_and_yarn/compose/neurosynth…

…-frontend/tough-cookie-and-cypress/request-4.1.3

.codespellrc

@@ -0,0 +1,5 @@
+[codespell]
+skip = .git,*.pdf,*.svg,*.ts,*.tsx,package-lock.json,data-*vocabulary.txt,sample_*.csv
+# regexes
+ignore-regex = r"\(\?i\).*\\\\1
+ignore-words-list = te,fwe,connexion,zoon,covert,rime

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/workflow.yml

@@ -182,7 +182,7 @@ jobs:
             -e "AUTH0_AUTH_URL=${AUTH0_AUTH_URL}" \
             --rm -w /neurostore \
             neurostore \
-            python -m pytest neurostore/tests
+            bash -c "python -m pytest neurostore/tests && python -m pytest --auth neurostore/tests/test_auth.py"
 
   neurosynth_compose_backend_tests:
     runs-on: ubuntu-latest

compose/README.md

@@ -9,7 +9,7 @@ First, set up the main environment variables in `.env` (see: `.env.example`).
 
 Edit the `.env` template to set the correct variables
 
-## Initalizing backend
+## Initializing backend
 Create the network, build the containers, and start services using the development configuration:
 
     docker network create nginx-proxy  # if this does not already exist

compose/neurosynth-frontend/src/assets/config/meta_analysis_params.json

@@ -155,7 +155,7 @@
                     "default": 10000
                 },
                 "xyz": {
-                    "description": "Tab-delimited file of coordinates from database or numpy array with XYZ coordinates. Voxels are rows and x, y, z (meaning coordinates) values are the three columnns.",
+                    "description": "Tab-delimited file of coordinates from database or numpy array with XYZ coordinates. Voxels are rows and x, y, z (meaning coordinates) values are the three columns.",
                     "type": "str",
                     "default": null
                 },

compose/neurosynth_compose/schemas/analysis.py

@@ -197,7 +197,7 @@ class MetaAnalysisResultSchema(BaseSchema):
 
     @post_load
     def process_data(self, data, **kwargs):
-        # propogate meta-analysis id to the neurovault collection
+        # propagate meta-analysis id to the neurovault collection
         if data.get("neurovault_collection", None):
             data["neurovault_collection"]["meta_analysis_id"] = data["meta_analysis_id"]
 

compose/neurosynth_compose/tests/conftest.py

@@ -155,7 +155,7 @@ def mock_ns(monkeysession):
 
 
 """
-Session / db managment tools
+Session / db management tools
 """
 
 

docs/taxonomy.md

@@ -45,7 +45,7 @@ The study is connected to the original journal it was published in.
 
 ### Functions
 
-Studies can be created, cloned, and edited to accomodate your needs for your meta-analysis
+Studies can be created, cloned, and edited to accommodate your needs for your meta-analysis
 
 ## Analysis
 

docs/typical-workflows.md

@@ -12,7 +12,7 @@ If the study does indeed use a finger tapping task, she wants to keep track of t
 To the left of the study there is a plus button.
 She clicks on the plus button and sees she can add the study to a "study-set".
 She names the studyset "finger tapping" and adds the selected study.
-When she is done reading and adding all relevent studies, she notices
+When she is done reading and adding all relevant studies, she notices
 that the finger tapping task typically falls under three categories:
 1) right handed index finger,
 2) right handed multiple fingers, and

store/README.md

@@ -9,7 +9,7 @@ First, set up the main environment variables in `.env` (see: `.env.example`).
 
 Edit the `.env` template to set the correct variables
 
-## Initalizing backend
+## Initializing backend
 Create the network, build the containers, and start services using the development configuration:
 
     docker network create nginx-proxy

store/neurostore/ingest/__init__.py

@@ -221,7 +221,7 @@ def ingest_neurosynth(max_rows=None):
                     base_study = base_studies[0]
                 elif len(base_studies) > 1:
                     source_base_study = base_studies[0]
-                    # do not overwrite the verions column
+                    # do not overwrite the versions column
                     # we want to append to this column
                     columns = [
                         c
@@ -484,7 +484,7 @@ def ace_ingestion_logic(coordinates_df, metadata_df, text_df):
                     other_base_studies = [
                         bs for bs in base_studies if bs.id != source_base_study.id
                     ]
-                    # do not overwrite the verions column
+                    # do not overwrite the versions column
                     # we want to append to this column
                     columns = [
                         c.name

store/neurostore/resources/base.py

@@ -32,6 +32,24 @@
 from . import data as viewdata
 
 
+def create_user():
+    from auth0.v3.authentication.users import Users
+    auth = request.headers.get("Authorization", 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
+
+
 class BaseView(MethodView):
     _model = None
     _nested = {}
@@ -64,9 +82,8 @@ def update_or_create(cls, data, id=None, commit=True):
 
         current_user = get_current_user()
         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"])
+            current_user = create_user()
+
             db.session.add(current_user)
             db.session.commit()
 

store/neurostore/tests/api/test_analyses.py

@@ -3,7 +3,7 @@
 from ...schemas import AnalysisSchema
 
 
-def test_get_nested_and_not_nested_analyses(auth_client, ingest_neurosynth):
+def test_get_nested_and_not_nested_analyses(auth_client, ingest_neurosynth, session):
     analysis_id = Analysis.query.first().id
     non_nested = auth_client.get(f"/api/analyses/{analysis_id}?nested=false")
     nested = auth_client.get(f"/api/analyses/{analysis_id}?nested=true")
@@ -12,7 +12,7 @@ def test_get_nested_and_not_nested_analyses(auth_client, ingest_neurosynth):
     assert isinstance(nested.json["points"][0], dict)
 
 
-def test_get_analyses(auth_client, ingest_neurosynth):
+def test_get_analyses(auth_client, ingest_neurosynth, session):
     # List of analyses
     resp = auth_client.get("/api/analyses/")
     assert resp.status_code == 200

store/neurostore/tests/api/test_annotations.py

@@ -3,7 +3,7 @@
 from ...models import Studyset, User
 
 
-def test_post_blank_annotation(auth_client, ingest_neurosynth):
+def test_post_blank_annotation(auth_client, ingest_neurosynth, session):
     dset = Studyset.query.first()
     payload = {
         "studyset": dset.id,
@@ -17,7 +17,7 @@ def test_post_blank_annotation(auth_client, ingest_neurosynth):
     )
 
 
-def test_post_annotation(auth_client, ingest_neurosynth):
+def test_post_annotation(auth_client, ingest_neurosynth, session):
     dset = Studyset.query.first()
     # y for x in non_flat for y in x
     data = [
@@ -37,7 +37,7 @@ def test_post_annotation(auth_client, ingest_neurosynth):
 
 # for some reason output is no longer valid
 @pytest.mark.xfail
-def test_get_annotations(auth_client, ingest_neurosynth):
+def test_get_annotations(auth_client, ingest_neurosynth, session):
     import pandas as pd
     from io import StringIO
 
@@ -59,7 +59,7 @@ def test_get_annotations(auth_client, ingest_neurosynth):
     assert isinstance(df, pd.DataFrame)
 
 
-def test_clone_annotation(auth_client, simple_neurosynth_annotation):
+def test_clone_annotation(auth_client, simple_neurosynth_annotation, session):
     annotation_entry = simple_neurosynth_annotation
     resp = auth_client.post(
         f"/api/annotations/?source_id={annotation_entry.id}", data={}
@@ -71,7 +71,7 @@ def test_clone_annotation(auth_client, simple_neurosynth_annotation):
     assert data["source"] == "neurostore"
 
 
-def test_single_analysis_delete(auth_client, user_data):
+def test_single_analysis_delete(auth_client, user_data, session):
     user = User.query.filter_by(name="user1").first()
     # get relevant studyset
     studysets = auth_client.get(f"/api/studysets/?user_id={user.external_id}")
@@ -215,7 +215,7 @@ def test_analysis_addition_to_studyset(auth_client, session, user_data):
     )
 
 
-def test_mismatched_notes(auth_client, ingest_neurosynth):
+def test_mismatched_notes(auth_client, ingest_neurosynth, session):
     dset = Studyset.query.first()
     # y for x in non_flat for y in x
     data = [
@@ -249,7 +249,7 @@ def test_mismatched_notes(auth_client, ingest_neurosynth):
 
 # test push analysis id that does not exist
 # Handle error better
-def test_put_nonexistent_analysis(auth_client, ingest_neurosynth):
+def test_put_nonexistent_analysis(auth_client, ingest_neurosynth, session):
     dset = Studyset.query.first()
     # y for x in non_flat for y in x
     data = [
@@ -281,7 +281,7 @@ def test_put_nonexistent_analysis(auth_client, ingest_neurosynth):
     )
 
 
-def test_correct_note_overwrite(auth_client, ingest_neurosynth):
+def test_correct_note_overwrite(auth_client, ingest_neurosynth, session):
     dset = Studyset.query.first()
     # y for x in non_flat for y in x
     data = [

store/neurostore/tests/api/test_base_studies.py

@@ -1,7 +1,7 @@
 """Test Base Study Endpoint"""
 
 
-def test_flat_base_study(auth_client, ingest_neurosynth):
+def test_flat_base_study(auth_client, ingest_neurosynth, session):
     flat_resp = auth_client.get("/api/base-studies/?flat=true")
     reg_resp = auth_client.get("/api/base-studies/?flat=false")
 
@@ -11,7 +11,7 @@ def test_flat_base_study(auth_client, ingest_neurosynth):
     assert "versions" in reg_resp.json["results"][0]
 
 
-def test_info_base_study(auth_client, ingest_neurosynth):
+def test_info_base_study(auth_client, ingest_neurosynth, session):
     info_resp = auth_client.get("/api/base-studies/?info=true")
 
     assert info_resp.status_code == 200

store/neurostore/tests/api/test_conditions.py

@@ -1,11 +1,11 @@
-def test_get_conditions(auth_client, ingest_neurovault):
+def test_get_conditions(auth_client, ingest_neurovault, session):
     resp = auth_client.get("/api/conditions/")
     assert resp.status_code == 200
     assert len(resp.json["results"]) > 1
 
 
-def test_post_conditions(auth_client, ingest_neurovault):
-    my_condition = {"name": "ice cream", "description": "suprise, it's rocky road!"}
+def test_post_conditions(auth_client, ingest_neurovault, session):
+    my_condition = {"name": "ice cream", "description": "surprise, it's rocky road!"}
     post_resp = auth_client.post("/api/conditions/", data=my_condition)
     assert post_resp.status_code == 200
     post_data = post_resp.json

store/neurostore/tests/api/test_crud.py

@@ -37,7 +37,7 @@
         ("points", Point, PointSchema),
     ],
 )
-def test_create(auth_client, user_data, endpoint, model, schema):
+def test_create(auth_client, user_data, endpoint, model, schema, session):
     user = User.query.filter_by(name="user1").first()
 
     rows = model.query.filter_by(user=user).all()
@@ -77,7 +77,7 @@ def test_create(auth_client, user_data, endpoint, model, schema):
         ("points", Point, PointSchema),
     ],
 )
-def test_read(auth_client, user_data, endpoint, model, schema):
+def test_read(auth_client, user_data, endpoint, model, schema, session):
     user = User.query.filter_by(name="user1").first()
     query = True
     if hasattr(model, "public"):
@@ -110,7 +110,7 @@ def test_read(auth_client, user_data, endpoint, model, schema):
         ("points", Point, PointSchema, {"space": "MNI"}),
     ],
 )
-def test_update(auth_client, user_data, endpoint, model, schema, update):
+def test_update(auth_client, user_data, endpoint, model, schema, update, session):
     user = User.query.filter_by(name="user1").first()
     record = model.query.filter_by(user=user).first()
 

store/neurostore/tests/api/test_images.py

@@ -2,7 +2,7 @@
 from ...models import Study, Analysis, User, Image
 
 
-def test_get_images(auth_client, ingest_neurovault):
+def test_get_images(auth_client, ingest_neurovault, session):
     # List of studysets
     resp = auth_client.get("/api/images/")
     assert resp.status_code == 200

store/neurostore/tests/api/test_points.py

@@ -4,7 +4,7 @@
 from ...models import User, Analysis, Study
 
 
-def test_get_points(auth_client, ingest_neurosynth):
+def test_get_points(auth_client, ingest_neurosynth, session):
     # Get an analysis
     resp = auth_client.get("/api/analyses/")
     analysis = decode_json(resp)["results"][0]

store/neurostore/tests/api/test_query_params.py

@@ -12,7 +12,7 @@
         ("analyses", AnalysisSchema()),
     ],
 )
-def test_nested(auth_client, ingest_neurosynth, nested, resource_schema):
+def test_nested(auth_client, ingest_neurosynth, nested, resource_schema, session):
     resource, schema = resource_schema
     resp = auth_client.get(f"/api/{resource}/?nested={nested}")
     fields = [
@@ -33,7 +33,7 @@ def test_nested(auth_client, ingest_neurosynth, nested, resource_schema):
                 continue
 
 
-def test_user_id(auth_client, user_data):
+def test_user_id(auth_client, user_data, session):
     from ...resources.users import User
 
     id_ = auth_client.username
@@ -43,7 +43,7 @@ def test_user_id(auth_client, user_data):
         assert study["user"] == user.external_id
 
 
-def test_source_id(auth_client, ingest_neurosynth):
+def test_source_id(auth_client, ingest_neurosynth, session):
     from ...resources.data import Study
 
     study = Study.query.first()
@@ -53,7 +53,7 @@ def test_source_id(auth_client, ingest_neurosynth):
     assert post.json == get.json["results"][0]
 
 
-def test_data_type(auth_client, ingest_neurosynth, ingest_neurovault):
+def test_data_type(auth_client, ingest_neurosynth, ingest_neurovault, session):
     get_coord = auth_client.get("/api/studies/?data_type=coordinate")
     assert get_coord.status_code == 200
     get_img = auth_client.get("/api/studies/?data_type=image")
@@ -67,12 +67,12 @@ def test_data_type(auth_client, ingest_neurosynth, ingest_neurovault):
     )
 
 
-def test_page_size(auth_client, ingest_neurosynth):
+def test_page_size(auth_client, ingest_neurosynth, session):
     get_page_size = auth_client.get("/api/studies/?page_size=5")
     assert get_page_size.status_code == 200
 
 
-def test_common_queries(auth_client, ingest_neurosynth):
+def test_common_queries(auth_client, ingest_neurosynth, session):
     study = Study.query.filter(Study.pmid.isnot(None)).first()
 
     pmid_search = auth_client.get(f"/api/studies/?pmid={study.pmid}")
@@ -83,7 +83,7 @@ def test_common_queries(auth_client, ingest_neurosynth):
     assert len(pmid_search.json["results"]) == len(total_search.json["results"])
 
 
-def test_multiword_queries(auth_client, ingest_neurosynth):
+def test_multiword_queries(auth_client, ingest_neurosynth, session):
     study = Study.query.first()
     name = study.name
     word_list = name.split(" ")