From af2ec9a21875d64586958dcc7e28b4a678501570 Mon Sep 17 00:00:00 2001
From: Monique Rio <mrio@umich.edu>
Date: Thu, 31 Oct 2024 18:09:57 +0000
Subject: [PATCH 1/5] adds pagination to items endpoint

---
 aim/digifeeds/database/crud.py        | 36 +++++++++++++++++++----
 aim/digifeeds/database/main.py        | 13 +++++++--
 aim/digifeeds/database/schemas.py     |  8 ++++++
 tests/digifeeds/database/test_crud.py | 41 ++++++++++++++-------------
 tests/digifeeds/database/test_main.py | 28 ++++++++++++------
 5 files changed, 89 insertions(+), 37 deletions(-)

diff --git a/aim/digifeeds/database/crud.py b/aim/digifeeds/database/crud.py
index 887b799..a5a8b3d 100644
--- a/aim/digifeeds/database/crud.py
+++ b/aim/digifeeds/database/crud.py
@@ -3,6 +3,7 @@
 
 Operations that act on the digifeeds database
 """
+
 from sqlalchemy.orm import Session
 from aim.digifeeds.database import schemas
 from aim.digifeeds.database import models
@@ -23,7 +24,28 @@ def get_item(db: Session, barcode: str):
     return db.query(models.Item).filter(models.Item.barcode == barcode).first()
 
 
-def get_items(db: Session, in_zephir: bool | None):
+def get_item_total(db: Session, in_zephir: bool | None):
+    if in_zephir is True:
+        return (
+            db.query(models.Item)
+            .filter(
+                models.Item.statuses.any(models.ItemStatus.status_name == "in_zephir")
+            )
+            .count()
+        )
+    elif in_zephir is False:
+        return (
+            db.query(models.Item)
+            .filter(
+                ~models.Item.statuses.any(models.ItemStatus.status_name == "in_zephir")
+            )
+            .count()
+        )
+
+    return db.query(models.Item).count()
+
+
+def get_items(db: Session, in_zephir: bool | None, limit: int, offset: int):
     """
     Get Digifeed items from the database
 
@@ -38,22 +60,24 @@ def get_items(db: Session, in_zephir: bool | None):
         return (
             db.query(models.Item)
             .filter(
-                models.Item.statuses.any(
-                    models.ItemStatus.status_name == "in_zephir")
+                models.Item.statuses.any(models.ItemStatus.status_name == "in_zephir")
             )
+            .offset(offset)
+            .limit(limit)
             .all()
         )
     elif in_zephir is False:
         return (
             db.query(models.Item)
             .filter(
-                ~models.Item.statuses.any(
-                    models.ItemStatus.status_name == "in_zephir")
+                ~models.Item.statuses.any(models.ItemStatus.status_name == "in_zephir")
             )
+            .offset(offset)
+            .limit(limit)
             .all()
         )
 
-    return db.query(models.Item).all()
+    return db.query(models.Item).offset(offset).limit(limit).all()
 
 
 def add_item(db: Session, item: schemas.ItemCreate):
diff --git a/aim/digifeeds/database/main.py b/aim/digifeeds/database/main.py
index 1122c4b..86280e6 100644
--- a/aim/digifeeds/database/main.py
+++ b/aim/digifeeds/database/main.py
@@ -41,11 +41,13 @@ def get_db():  # pragma: no cover
 
 @app.get("/items/", response_model_by_alias=False, tags=["Digifeeds Database"])
 def get_items(
+    offset: int = Query(0, ge=0, description="Requested offset from the list of pages"),
+    limit: int = Query(50, ge=1, description="Requested number of items per page"),
     in_zephir: bool | None = Query(
         None, description="Filter for items that do or do not have metadata in Zephir"
     ),
     db: Session = Depends(get_db),
-) -> list[schemas.Item]:
+) -> schemas.PageOfItems:  # list[schemas.Item]:
     """
     Get the digifeeds items.
 
@@ -53,8 +55,13 @@ def get_items(
     all of them can be fetched.
     """
 
-    db_items = crud.get_items(in_zephir=in_zephir, db=db)
-    return db_items
+    db_items = crud.get_items(in_zephir=in_zephir, db=db, offset=offset, limit=limit)
+    return {
+        "limit": limit,
+        "offset": offset,
+        "total": crud.get_item_total(in_zephir=in_zephir, db=db),
+        "items": db_items,
+    }
 
 
 @app.get(
diff --git a/aim/digifeeds/database/schemas.py b/aim/digifeeds/database/schemas.py
index c2a43fb..af4e76b 100644
--- a/aim/digifeeds/database/schemas.py
+++ b/aim/digifeeds/database/schemas.py
@@ -1,4 +1,5 @@
 """Digifeeds Pydantic Models"""
+
 from pydantic import BaseModel, Field, ConfigDict
 from datetime import datetime
 
@@ -39,6 +40,12 @@ class Item(ItemBase):
     )
 
 
+class PageOfItems(BaseModel):
+    items: list[Item]
+    limit: int = 10
+    offset: int = 0
+    total: int = 15
+
 
 class ItemCreate(ItemBase):
     pass
@@ -67,6 +74,7 @@ class Response400(Response):
         }
     )
 
+
 class Response404(Response):
     model_config = ConfigDict(
         json_schema_extra={
diff --git a/tests/digifeeds/database/test_crud.py b/tests/digifeeds/database/test_crud.py
index ae9de03..d6f6484 100644
--- a/tests/digifeeds/database/test_crud.py
+++ b/tests/digifeeds/database/test_crud.py
@@ -4,63 +4,64 @@
     add_item,
     get_status,
     get_statuses,
-    add_item_status
+    add_item_status,
 )
 from aim.digifeeds.database.schemas import ItemCreate
 
+
 class TestCrud:
     def test_get_item(self, db_session):
         item = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode"))
         barcode = item.barcode
         item_in_db = get_item(barcode=barcode, db=db_session)
-        assert(item_in_db.barcode) == "valid_barcode"
+        assert (item_in_db.barcode) == "valid_barcode"
 
     def test_get_item_that_does_not_exist(self, db_session):
         item_in_db = get_item(barcode="does not exist", db=db_session)
-        assert(item_in_db) is None
+        assert (item_in_db) is None
 
     def test_get_items_all(self, db_session):
         item1 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode"))
         item2 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode2"))
         status = get_status(db=db_session, name="in_zephir")
-        add_item_status(db=db_session,item=item1, status=status)
-        items = get_items(db=db_session, in_zephir=None)
+        add_item_status(db=db_session, item=item1, status=status)
+        items = get_items(db=db_session, in_zephir=None, limit=2, offset=0)
         db_session.refresh(item1)
         db_session.refresh(item2)
-        assert(items[0]) == item1
-        assert(items[1]) == item2
-        
+        assert (items[0]) == item1
+        assert (items[1]) == item2
+
     def test_get_items_in_zephir(self, db_session):
         item1 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode"))
         item2 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode2"))
         status = get_status(db=db_session, name="in_zephir")
-        add_item_status(db=db_session,item=item1, status=status)
-        items = get_items(db=db_session, in_zephir=True)
+        add_item_status(db=db_session, item=item1, status=status)
+        items = get_items(db=db_session, in_zephir=True, limit=2, offset=0)
         db_session.refresh(item1)
         db_session.refresh(item2)
-        assert(len(items)) == 1
-        assert(items[0]) == item1
+        assert (len(items)) == 1
+        assert (items[0]) == item1
 
     def test_get_items_not_in_zephir(self, db_session):
         item1 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode"))
         item2 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode2"))
         status = get_status(db=db_session, name="in_zephir")
-        add_item_status(db=db_session,item=item1, status=status)
-        items = get_items(db=db_session, in_zephir=False)
+        add_item_status(db=db_session, item=item1, status=status)
+        items = get_items(db=db_session, in_zephir=False, limit=2, offset=0)
         db_session.refresh(item1)
         db_session.refresh(item2)
-        assert(len(items)) == 1
-        assert(items[0]) == item2
+        assert (len(items)) == 1
+        assert (items[0]) == item2
 
     def test_get_status_that_exists(self, db_session):
         status = get_status(db=db_session, name="in_zephir")
-        assert(status.name) == "in_zephir"
+        assert (status.name) == "in_zephir"
 
     def test_get_status_that_does_not_exist(self, db_session):
         status = get_status(db=db_session, name="does_not_exist")
-        assert(status) is None 
+        assert (status) is None
 
     def test_get_statuses(self, db_session):
         statuses = get_statuses(db=db_session)
-        assert(len(statuses)) > 1
-        assert(statuses[0].name) == "in_zephir"
+        assert (len(statuses)) > 1
+        assert (statuses[0].name) == "in_zephir"
diff --git a/tests/digifeeds/database/test_main.py b/tests/digifeeds/database/test_main.py
index 3996f6d..4e36a05 100644
--- a/tests/digifeeds/database/test_main.py
+++ b/tests/digifeeds/database/test_main.py
@@ -2,10 +2,12 @@
 from aim.digifeeds.database.schemas import ItemCreate
 import pytest
 
+
 @pytest.fixture()
 def valid_item(db_session):
     return crud.add_item(db=db_session, item=ItemCreate(barcode="valid_barcode"))
 
+
 @pytest.fixture()
 def valid_in_zephir_item(db_session):
     item = crud.add_item(db=db_session, item=ItemCreate(barcode="in_zephir_item"))
@@ -14,32 +16,36 @@ def valid_in_zephir_item(db_session):
     db_session.refresh(item)
     return item
 
+
 def test_get_statuses(client):
     response = client.get("/statuses")
     assert response.status_code == 200, response.text
 
+
 def test_get_items(client, valid_item, valid_in_zephir_item, db_session):
     valid_item
     valid_in_zephir_item
     response = client.get("/items")
     assert response.status_code == 200, response.text
-    assert len(response.json()) == 2
+    assert len(response.json()["items"]) == 2
+
 
 def test_get_items_with_in_zephir_true(client, valid_item, valid_in_zephir_item):
     valid_item
     valid_in_zephir_item
-    response = client.get("/items", params={"in_zephir":True})
+    response = client.get("/items", params={"in_zephir": True})
     assert response.status_code == 200, response.text
-    assert len(response.json()) == 1
-    assert response.json()[0]["barcode"] == valid_in_zephir_item.barcode
+    assert len(response.json()["items"]) == 1
+    assert response.json()["items"][0]["barcode"] == valid_in_zephir_item.barcode
+
 
 def test_get_items_with_in_zephir_false(client, valid_item, valid_in_zephir_item):
     valid_item
     valid_in_zephir_item
-    response = client.get("/items", params={"in_zephir":False})
+    response = client.get("/items", params={"in_zephir": False})
     assert response.status_code == 200, response.text
-    assert len(response.json()) == 1
-    assert response.json()[0]["barcode"] == valid_item.barcode
+    assert len(response.json()["items"]) == 1
+    assert response.json()["items"][0]["barcode"] == valid_item.barcode
 
 
 def test_get_item(client, valid_item, valid_in_zephir_item):
@@ -48,30 +54,36 @@ def test_get_item(client, valid_item, valid_in_zephir_item):
     response = client.get(f"/items/{valid_item.barcode}")
     assert response.status_code == 200, response.text
 
+
 def test_get_item_not_found(client):
     response = client.get("/items/some_barcode_that_does_not_exist")
     assert response.status_code == 404
     assert response.json() == {"detail": "Item not found"}
 
+
 def test_create_item(client):
     response = client.post("items/new_barcode")
     assert response.status_code == 200, response.text
 
+
 def test_create_existing_item(client, valid_item):
     response = client.post(f"items/{valid_item.barcode}")
     assert response.status_code == 400
     assert response.json() == {"detail": "Item already exists"}
 
+
 def test_update_item_success(client, valid_item):
     response = client.put(f"items/{valid_item.barcode}/status/in_zephir")
     assert response.status_code == 200, response.text
 
+
 def test_update_nonexisting_item(client):
     response = client.put("/items/some_barcode_that_does_not_exist/status/in_zephir")
     assert response.status_code == 404
     assert response.json() == {"detail": "Item not found"}
 
+
 def test_update_existing_item_with_nonexistent_status(client, valid_item):
     response = client.put(f"/items/{valid_item.barcode}/status/non_existent_status")
     assert response.status_code == 404
-    assert response.json() == {"detail": "Status not found"}
\ No newline at end of file
+    assert response.json() == {"detail": "Status not found"}

From 1cfba87096eb3e937e5aefd443b500746ad7f9e9 Mon Sep 17 00:00:00 2001
From: Monique Rio <mrio@umich.edu>
Date: Thu, 31 Oct 2024 18:36:28 +0000
Subject: [PATCH 2/5] adds test for count; refactors filter in_zephir

---
 aim/digifeeds/database/crud.py        | 51 ++++++++-------------------
 aim/digifeeds/database/main.py        |  2 +-
 tests/digifeeds/database/test_crud.py | 13 +++++--
 3 files changed, 25 insertions(+), 41 deletions(-)

diff --git a/aim/digifeeds/database/crud.py b/aim/digifeeds/database/crud.py
index a5a8b3d..f2979fb 100644
--- a/aim/digifeeds/database/crud.py
+++ b/aim/digifeeds/database/crud.py
@@ -24,25 +24,9 @@ def get_item(db: Session, barcode: str):
     return db.query(models.Item).filter(models.Item.barcode == barcode).first()
 
 
-def get_item_total(db: Session, in_zephir: bool | None):
-    if in_zephir is True:
-        return (
-            db.query(models.Item)
-            .filter(
-                models.Item.statuses.any(models.ItemStatus.status_name == "in_zephir")
-            )
-            .count()
-        )
-    elif in_zephir is False:
-        return (
-            db.query(models.Item)
-            .filter(
-                ~models.Item.statuses.any(models.ItemStatus.status_name == "in_zephir")
-            )
-            .count()
-        )
-
-    return db.query(models.Item).count()
+def get_items_total(db: Session, in_zephir: bool | None):
+    query = get_items_query(db=db, in_zephir=in_zephir)
+    return query.count()
 
 
 def get_items(db: Session, in_zephir: bool | None, limit: int, offset: int):
@@ -56,28 +40,21 @@ def get_items(db: Session, in_zephir: bool | None, limit: int, offset: int):
     Returns:
         aim.digifeeds.database.models.Item: Item object
     """
+    query = get_items_query(db=db, in_zephir=in_zephir)
+    return query.offset(offset).limit(limit).all()
+
+
+def get_items_query(db: Session, in_zephir: bool | None):
+    query = db.query(models.Item)
     if in_zephir is True:
-        return (
-            db.query(models.Item)
-            .filter(
-                models.Item.statuses.any(models.ItemStatus.status_name == "in_zephir")
-            )
-            .offset(offset)
-            .limit(limit)
-            .all()
+        query = query.filter(
+            models.Item.statuses.any(models.ItemStatus.status_name == "in_zephir")
         )
     elif in_zephir is False:
-        return (
-            db.query(models.Item)
-            .filter(
-                ~models.Item.statuses.any(models.ItemStatus.status_name == "in_zephir")
-            )
-            .offset(offset)
-            .limit(limit)
-            .all()
+        query = query.filter(
+            ~models.Item.statuses.any(models.ItemStatus.status_name == "in_zephir")
         )
-
-    return db.query(models.Item).offset(offset).limit(limit).all()
+    return query
 
 
 def add_item(db: Session, item: schemas.ItemCreate):
diff --git a/aim/digifeeds/database/main.py b/aim/digifeeds/database/main.py
index 86280e6..c9f3d02 100644
--- a/aim/digifeeds/database/main.py
+++ b/aim/digifeeds/database/main.py
@@ -59,7 +59,7 @@ def get_items(
     return {
         "limit": limit,
         "offset": offset,
-        "total": crud.get_item_total(in_zephir=in_zephir, db=db),
+        "total": crud.get_items_total(in_zephir=in_zephir, db=db),
         "items": db_items,
     }
 
diff --git a/tests/digifeeds/database/test_crud.py b/tests/digifeeds/database/test_crud.py
index d6f6484..c9b06bd 100644
--- a/tests/digifeeds/database/test_crud.py
+++ b/tests/digifeeds/database/test_crud.py
@@ -5,6 +5,7 @@
     get_status,
     get_statuses,
     add_item_status,
+    get_items_total,
 )
 from aim.digifeeds.database.schemas import ItemCreate
 
@@ -20,38 +21,44 @@ def test_get_item_that_does_not_exist(self, db_session):
         item_in_db = get_item(barcode="does not exist", db=db_session)
         assert (item_in_db) is None
 
-    def test_get_items_all(self, db_session):
+    def test_get_items_and_total_any(self, db_session):
         item1 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode"))
         item2 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode2"))
         status = get_status(db=db_session, name="in_zephir")
         add_item_status(db=db_session, item=item1, status=status)
         items = get_items(db=db_session, in_zephir=None, limit=2, offset=0)
+        count = get_items_total(db=db_session, in_zephir=None)
         db_session.refresh(item1)
         db_session.refresh(item2)
         assert (items[0]) == item1
         assert (items[1]) == item2
+        assert (count) == 2
 
-    def test_get_items_in_zephir(self, db_session):
+    def test_get_items_and_total_in_zephir(self, db_session):
         item1 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode"))
         item2 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode2"))
         status = get_status(db=db_session, name="in_zephir")
         add_item_status(db=db_session, item=item1, status=status)
         items = get_items(db=db_session, in_zephir=True, limit=2, offset=0)
+        count = get_items_total(db=db_session, in_zephir=True)
         db_session.refresh(item1)
         db_session.refresh(item2)
         assert (len(items)) == 1
         assert (items[0]) == item1
+        assert count == 1
 
-    def test_get_items_not_in_zephir(self, db_session):
+    def test_get_items_and_total_not_in_zephir(self, db_session):
         item1 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode"))
         item2 = add_item(db=db_session, item=ItemCreate(barcode="valid_barcode2"))
         status = get_status(db=db_session, name="in_zephir")
         add_item_status(db=db_session, item=item1, status=status)
         items = get_items(db=db_session, in_zephir=False, limit=2, offset=0)
+        count = get_items_total(db=db_session, in_zephir=False)
         db_session.refresh(item1)
         db_session.refresh(item2)
         assert (len(items)) == 1
         assert (items[0]) == item2
+        assert count == 1
 
     def test_get_status_that_exists(self, db_session):
         status = get_status(db=db_session, name="in_zephir")

From 12ab4e4d3def16125c96da1b80d73551fff6fc24 Mon Sep 17 00:00:00 2001
From: Monique Rio <mrio@umich.edu>
Date: Thu, 31 Oct 2024 20:11:27 +0000
Subject: [PATCH 3/5] DBClient has a get_items method that pages through
 results from api

---
 aim/digifeeds/db_client.py              | 29 +++++++++
 tests/digifeeds/test_db_client.py       | 83 +++++++++++++++++++++++++
 tests/fixtures/digifeeds/item_list.json | 18 ++++++
 3 files changed, 130 insertions(+)
 create mode 100644 tests/fixtures/digifeeds/item_list.json

diff --git a/aim/digifeeds/db_client.py b/aim/digifeeds/db_client.py
index 6c6a3ed..d6f4538 100644
--- a/aim/digifeeds/db_client.py
+++ b/aim/digifeeds/db_client.py
@@ -68,5 +68,34 @@ def add_item_status(self, barcode: str, status: str):
             response.raise_for_status()
         return response.json()
 
+    def get_items(self, limit: int = 50, in_zephir: bool | None = None):
+        items = []
+        url = self._url(f"items")
+        params = {
+            "limit": limit,
+            "offset": 0,
+        }
+        if in_zephir != None:
+            params["in_zephir"] = in_zephir
+
+        response = requests.get(url, params=params)
+        if response.status_code != 200:
+            response.raise_for_status()
+
+        first_page = response.json()
+        total = first_page["total"]
+        for item in first_page["items"]:
+            items.append(item)
+
+        for offset in list(range(limit, total, limit)):
+            params["offset"] = offset
+            response = requests.get(url, params=params)
+            if response.status_code != 200:
+                response.raise_for_status()
+            for item in response.json()["items"]:
+                items.append(item)
+
+        return items
+
     def _url(self, path) -> str:
         return f"{self.base_url}/{path}"
diff --git a/tests/digifeeds/test_db_client.py b/tests/digifeeds/test_db_client.py
index df9b180..083b415 100644
--- a/tests/digifeeds/test_db_client.py
+++ b/tests/digifeeds/test_db_client.py
@@ -1,8 +1,18 @@
 import responses
+from responses import matchers
 import pytest
 from aim.services import S
 from aim.digifeeds.db_client import DBClient
 from requests.exceptions import HTTPError
+import json
+import copy
+
+
+@pytest.fixture
+def item_list():
+    with open("tests/fixtures/digifeeds/item_list.json") as f:
+        output = json.load(f)
+    return output
 
 
 @responses.activate
@@ -79,3 +89,76 @@ def test_add_item_status_failure():
     with pytest.raises(Exception) as exc_info:
         DBClient().add_item_status(barcode="my_barcode", status="in_zephir")
     assert exc_info.type is HTTPError
+
+
+@responses.activate
+def test_get_items_multiple_pages(item_list):
+    page_2 = copy.copy(item_list)
+    page_2["offset"] = 1
+    page_2["items"][0]["barcode"] = "some_other_barcode"
+    url = f"{S.digifeeds_api_url}/items"
+    responses.get(
+        url=url,
+        match=[matchers.query_param_matcher({"limit": 1, "offset": 0})],
+        json=item_list,
+    )
+    responses.get(
+        url=url,
+        match=[matchers.query_param_matcher({"limit": 1, "offset": 1})],
+        json=page_2,
+    )
+
+    items = DBClient().get_items(limit=1)
+    assert (len(items)) == 2
+
+
+@responses.activate
+def test_get_items_in_zephir_value(item_list):
+    item_list["total"] = 1
+    url = f"{S.digifeeds_api_url}/items"
+    responses.get(
+        url=url,
+        match=[
+            matchers.query_param_matcher({"limit": 1, "offset": 0, "in_zephir": False})
+        ],
+        json=item_list,
+    )
+    items = DBClient().get_items(limit=1, in_zephir=False)
+    assert (len(items)) == 1
+
+
+@responses.activate
+def test_get_items_fail_first_page():
+    url = f"{S.digifeeds_api_url}/items"
+    responses.get(
+        url=url,
+        status=500,
+        match=[matchers.query_param_matcher({"limit": 1, "offset": 0})],
+        json={},
+    )
+
+    with pytest.raises(Exception) as exc_info:
+        DBClient().get_items(limit=1)
+
+    assert exc_info.type is HTTPError
+
+
+@responses.activate
+def test_get_items_fail_later_page(item_list):
+    url = f"{S.digifeeds_api_url}/items"
+    responses.get(
+        url=url,
+        match=[matchers.query_param_matcher({"limit": 1, "offset": 0})],
+        json=item_list,
+    )
+    responses.get(
+        url=url,
+        status=500,
+        match=[matchers.query_param_matcher({"limit": 1, "offset": 1})],
+        json={},
+    )
+
+    with pytest.raises(Exception) as exc_info:
+        DBClient().get_items(limit=1)
+
+    assert exc_info.type is HTTPError
diff --git a/tests/fixtures/digifeeds/item_list.json b/tests/fixtures/digifeeds/item_list.json
new file mode 100644
index 0000000..b9c3502
--- /dev/null
+++ b/tests/fixtures/digifeeds/item_list.json
@@ -0,0 +1,18 @@
+{
+  "limit": 1,
+  "offset": 0,
+  "total": 2,
+  "items": [
+    {
+      "barcode": "some_barcode",
+      "created_at": "2024-09-25T17:12:39",
+      "statuses": [
+        {
+          "name": "added_to_digifeeds_set",
+          "description": "Item has been added to the digifeeds set",
+          "created_at": "2024-09-25T17:13:28"
+        }
+      ]
+    }
+  ]
+}
\ No newline at end of file

From 2194efb20e098d7d3bcbfca19d377837f638da22 Mon Sep 17 00:00:00 2001
From: Monique Rio <mrio@umich.edu>
Date: Mon, 18 Nov 2024 19:13:39 +0000
Subject: [PATCH 4/5] linting

---
 aim/cli/main.py                         |  1 +
 aim/digifeeds/db_client.py              |  4 ++--
 docs/conf.py                            | 13 ++++++++++---
 tests/conftest.py                       | 14 +++++++++-----
 tests/digifeeds/database/test_models.py | 14 +++++---------
 5 files changed, 27 insertions(+), 19 deletions(-)

diff --git a/aim/cli/main.py b/aim/cli/main.py
index 4124886..8c6df0a 100644
--- a/aim/cli/main.py
+++ b/aim/cli/main.py
@@ -3,6 +3,7 @@
 
 This hooks up the AIM CLI application. Nothing exciting happening here.
 """
+
 import typer
 import aim.cli.digifeeds as digifeeds
 
diff --git a/aim/digifeeds/db_client.py b/aim/digifeeds/db_client.py
index d6f4538..f08b0cd 100644
--- a/aim/digifeeds/db_client.py
+++ b/aim/digifeeds/db_client.py
@@ -70,12 +70,12 @@ def add_item_status(self, barcode: str, status: str):
 
     def get_items(self, limit: int = 50, in_zephir: bool | None = None):
         items = []
-        url = self._url(f"items")
+        url = self._url("items")
         params = {
             "limit": limit,
             "offset": 0,
         }
-        if in_zephir != None:
+        if in_zephir is not None:
             params["in_zephir"] = in_zephir
 
         response = requests.get(url, params=params)
diff --git a/docs/conf.py b/docs/conf.py
index fe52415..739c0a9 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -14,8 +14,15 @@
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = ["sphinx.ext.napoleon", "sphinx.ext.viewcode", "sphinx.ext.autosummary",
-              "sphinx.ext.autodoc", 'myst_parser', 'sphinxcontrib.mermaid', "sphinx_toolbox.more_autodoc.autonamedtuple"]
+extensions = [
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autodoc",
+    "myst_parser",
+    "sphinxcontrib.mermaid",
+    "sphinx_toolbox.more_autodoc.autonamedtuple",
+]
 autosummary_generate = True
 
 mermaid_d3_zoom = True
@@ -33,5 +40,5 @@
 html_theme_options = {
     "navigation_depth": 5,
     "collapse_navigation": False,
-    "titles_only": True
+    "titles_only": True,
 }
diff --git a/tests/conftest.py b/tests/conftest.py
index 8e71b08..99204f1 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -10,8 +10,10 @@
 
 engine = create_engine(
     S.test_database,
-    connect_args={ "check_same_thread": False,},
-    poolclass=StaticPool
+    connect_args={
+        "check_same_thread": False,
+    },
+    poolclass=StaticPool,
 )
 
 TestingSessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
@@ -25,10 +27,11 @@
 session.close()
 connection.close()
 
+
 # From: https://stackoverflow.com/questions/67255653/how-to-set-up-and-tear-down-a-database-between-tests-in-fastapi
 # These two event listeners are only needed for sqlite for proper
 # SAVEPOINT / nested transaction support. Other databases like postgres
-# don't need them. 
+# don't need them.
 # From: https://docs.sqlalchemy.org/en/14/dialects/sqlite.html#serializable-isolation-savepoints-transactional-ddl
 @sa.event.listens_for(engine, "connect")
 def do_connect(dbapi_connection, connection_record):
@@ -42,6 +45,7 @@ def do_begin(conn):
     # emit our own BEGIN
     conn.exec_driver_sql("BEGIN")
 
+
 # Handles rolling back the db after every test
 @pytest.fixture()
 def db_session(scope="module"):
@@ -49,7 +53,6 @@ def db_session(scope="module"):
     transaction = connection.begin()
     session = TestingSessionLocal(bind=connection)
 
-
     # Begin a nested transaction (using SAVEPOINT).
     nested = connection.begin_nested()
 
@@ -68,6 +71,7 @@ def end_savepoint(session, transaction):
     transaction.rollback()
     connection.close()
 
+
 # A fixture for the fastapi test client which depends on the
 # previous session fixture. Instead of creating a new session in the
 # dependency override as before, it uses the one provided by the
@@ -79,4 +83,4 @@ def override_get_db():
 
     app.dependency_overrides[get_db] = override_get_db
     yield TestClient(app)
-    del app.dependency_overrides[get_db]
\ No newline at end of file
+    del app.dependency_overrides[get_db]
diff --git a/tests/digifeeds/database/test_models.py b/tests/digifeeds/database/test_models.py
index e6d183d..23769cc 100644
--- a/tests/digifeeds/database/test_models.py
+++ b/tests/digifeeds/database/test_models.py
@@ -1,5 +1,6 @@
 from aim.digifeeds.database.models import Item, Status, ItemStatus
 
+
 class TestItem:
     def test_item_valid(self, db_session):
         valid_item = Item(barcode="valid_barcode")
@@ -15,19 +16,14 @@ def test_item_statuses(self, db_session):
         db_session.commit()
         status = db_session.query(Status).filter_by(name="in_zephir").first()
         db_session.refresh(item)
-        assert(len(item.statuses)) == 0
+        assert (len(item.statuses)) == 0
 
-        item_status = ItemStatus(item=item,status=status)
+        item_status = ItemStatus(item=item, status=status)
         db_session.add(item_status)
         db_session.commit()
         db_session.refresh(item)
 
         assert item.barcode == "valid_barcode"
-        assert(len(item.statuses)) == 1
-        assert(item.statuses[0].created_at)
+        assert (len(item.statuses)) == 1
+        assert item.statuses[0].created_at
         assert item.statuses[0].status_name == "in_zephir"
-
-    
-        
-      
-  
\ No newline at end of file

From 7407a683f7256cb3ef56df856bf501c033bb45fb Mon Sep 17 00:00:00 2001
From: Monique Rio <mrio@umich.edu>
Date: Mon, 18 Nov 2024 19:33:16 +0000
Subject: [PATCH 5/5] docs: make digifeeds pagination example make sense

---
 aim/digifeeds/database/schemas.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/aim/digifeeds/database/schemas.py b/aim/digifeeds/database/schemas.py
index af4e76b..657b83f 100644
--- a/aim/digifeeds/database/schemas.py
+++ b/aim/digifeeds/database/schemas.py
@@ -44,7 +44,7 @@ class PageOfItems(BaseModel):
     items: list[Item]
     limit: int = 10
     offset: int = 0
-    total: int = 15
+    total: int = 1
 
 
 class ItemCreate(ItemBase):