Adding Testing Suite

.github/workflows/testing.yml

@@ -28,7 +28,7 @@ jobs:
 
       - name: Run tests
         env:
-          ELINK_REVIEW_API_TOKEN: ${{ secrets.ELINK_REVIEW_API_TOKEN }}
+          elink_api_PRODUCTION_key: ${{ secrets.ELINK_PRODUCTION_API_TOKEN }}
+          elink_review_api_token: ${{ secrets.ELINK_REVIEW_API_TOKEN }}
           ELINK_REVIEW_ENDPOINT: ${{ secrets.ELINK_REVIEW_ENDPOINT }}
-        run: uv run pytest tests
-# codecov?
+        run: uv run pytest tests

pyproject.toml

@@ -5,7 +5,7 @@ description = "Add your description here"
 readme = "README.md"
 authors = [
     { name = "The Materials Project", email = "feedback@materialsproject.org" },
-    { name = "Hugo Onghai", email = "" },
+    { name = "Hugo Onghai", email = "hugoonghai@g.ucla.edu" },
     { name = "Tyler Mathis", email = "35553152+tsmathis@users.noreply.github.com" },
 ]
 maintainers = [
@@ -14,9 +14,10 @@ maintainers = [
 ]
 requires-python = ">=3.11"
 dependencies = [
-    "elinkapi>=0.4.9",
+    "elinkapi>=0.5.2",
     "pydantic>=2.11.7",
     "pymongo>=4.13.2",
+    "python-dotenv>=1.1.1",
 ]
 
 [dependency-groups]

src/mp_cite/core.py

@@ -1,16 +1,12 @@
-from typing import TypeAlias
+from typing import Literal, TypeAlias
 
+import requests
 from elinkapi import Elink
 from elinkapi.record import RecordResponse
-from pymongo import MongoClient
-
-import requests
 from elinkapi.utils import Validation
+from pymongo import MongoClient
 
-
-from mp_cite.doi_builder import MinimumDARecord
-
-from typing import Literal
+from mp_cite.models import MinimumDARecord
 
 OstiID: TypeAlias = int
 
@@ -69,7 +65,10 @@ def find_out_of_date_doi_entries(
 
 
 def update_existing_osti_record(
-    elinkapi: Elink, osti_id: OstiID, new_values: dict
+    elinkapi: Elink,
+    osti_id: OstiID,
+    new_values: dict,
+    new_state: Literal["save", "submit"],
 ) -> RecordResponse:
     """
     update_existing_osti_record allows users to provide a dictionary of keywords and new values, which will replace the old values under the same keywords in the record with the given osti id
@@ -97,9 +96,16 @@ def update_existing_osti_record(
     for keyword in new_values:
         setattr(record_on_elink, keyword, new_values[keyword])
 
-    return elinkapi.update_record(
-        osti_id, record_on_elink, state="save"
-    )  # user should use update_state_of_osti_record to submit instead
+    if new_state == "submit":
+        # due to bug in elinkapi version<=0.5.2, new_state passing does not update workflow status.
+        # for now, it is updated manually to 'SO' submitted to OSTI, which is should do itself.
+        record_on_elink.workflow_status = "SO"
+
+    return elinkapi.update_record(osti_id, record_on_elink, state=new_state)
+
+    # due to bug in elinkapi version<=0.5.2, elinkapi.patch_record fails due to bad casting of dict to str.
+    # when the next release fixes this, we can change it to this again below.
+    # elinkapi.patch_record(osti_id, new_values, new_state)
 
 
 def submit_new_osti_record(

src/mp_cite/models.py

@@ -1,10 +1,9 @@
 from pydantic import BaseModel, Field, model_validator
 
-from datetime import datetime
+from datetime import datetime, timezone, date
 from elinkapi import Record, Organization, Person
 
 from typing import List, Any
-import pytz
 
 
 class DOIModel(BaseModel):
@@ -78,7 +77,7 @@ class MinimumDARecord(Record):
     )
     site_ownership_code: str = Field(default="LBNL-MP")
     access_limitations: List[str] = Field(default_factory=lambda: ["UNL"])
-    publication_date: datetime = Field(
-        default_factory=lambda: datetime.now(tz=pytz.UTC)
+    publication_date: date = Field(
+        default_factory=lambda: datetime.now(timezone.utc).date()
     )
     site_url: str = Field(default="https://next-gen.materialsproject.org/materials")

tests/conf_test.py

@@ -0,0 +1,27 @@
+import os
+import pytest
+from elinkapi import Elink
+from dotenv import load_dotenv
+
+load_dotenv()
+
+
+@pytest.fixture
+def elink_review_client():
+    """
+    tests whether or not the elink review client can be properly retrieved.
+    returns the elink review client
+    """
+    elink_review_api_key = os.getenv("elink_review_api_token")
+    review_endpoint = os.getenv("ELINK_REVIEW_ENDPOINT")
+    return Elink(token=elink_review_api_key, target=review_endpoint)
+
+
+@pytest.fixture
+def elink_production_client():
+    """
+    tests whether or not the elink review client can be properly retrieved.
+    returns the elink review client
+    """
+    elink_prod_api_key = os.getenv("elink_api_PRODUCTION_key")
+    return Elink(token=elink_prod_api_key)

tests/elink_service_test.py

@@ -1,16 +1,137 @@
+from elinkapi import exceptions, Person, Organization, Record
 from elinkapi.record import RecordResponse
+import pytest
+from dotenv import load_dotenv
 
-# TODO: Write tests that verify our usage of Elink is correct,
-#       and make sure any upstream breaking changes get caught
-#       here when version upgrades happen
+from .conf_test import elink_production_client, elink_review_client
 
-# 1. general query logic + params that we use regularly?
-# 2. make sure we can submit a correctly templated dataset submission
-# 3. make sure record updates work
-# 4. deleting records?
-# 5+. test any other surfaces of the Elink api that we interact with
+import sys
+import os
 
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
+import src.mp_cite.core as core
 
-def test_elink_query(elink_review_client):
-    # placeholder, just to verify gh actions until full test suite is done
+load_dotenv()
+
+
+def test_get_single_record(elink_production_client):
+    """
+    tried to use the production client to retrieve a record.
+    """
+    try:
+        record = elink_production_client.get_single_record(1190959)
+        assert record.title == "Materials Data on Si by Materials Project"
+        assert record.osti_id == 1190959
+    except exceptions.ForbiddenException as fe:
+        pytest.fail(
+            f"Forbidden: Check API key or permissions associated with provided API key. {fe}"
+        )
+    except exceptions.BadRequestException as ve:
+        pytest.fail(f"Bad Request: Possibly incorrect parameters. {ve}")
+    except Exception as e:
+        pytest.fail(f"Unexpected error: {e}")
+
+
+def test_query_records(elink_production_client):
+    """
+    tests the query functionality of the elinkapi on the production environment
+    """
+    try:
+        elink_production_client.query_records()
+    except exceptions.ForbiddenException as fe:
+        pytest.fail(
+            f"Forbidden: Check API key or permissions associated with provided API key. {fe}"
+        )
+    except exceptions.BadRequestException as ve:
+        pytest.fail(f"Bad Request: Possibly incorrect parameters. {ve}")
+    except Exception as e:
+        pytest.fail(f"Unexpected error: {e}")
+
+
+def test_query_exists(elink_review_client):
+    """
+    tests to see that the query does in fact resolve entries in the form of RecordResponse objects.
+    """
     assert isinstance(next(elink_review_client.query_records()), RecordResponse)
+
+
+def test_switching_states(elink_review_client):
+    """
+    This test repeats the tests done to demonstrate unexpected behavior or passing "save" and "submit" states present in Elinkapi 0.5.2.
+    """
+    my_record_dict = {
+        "product_type": "DA",
+        "title": "My Dataset",
+        "organizations": [
+            Organization(type="RESEARCHING", name="LBNL Materials Project (LBNL-MP)"),
+            Organization(
+                type="SPONSOR",
+                name="TEST SPONSOR ORG",
+                identifiers=[{"type": "CN_DOE", "value": "AC02-05CH11231"}],
+            ),  # sponsor org is necessary for submission
+        ],
+        "persons": [Person(type="AUTHOR", last_name="Persson")],
+        "site_ownership_code": "LBNL-MP",
+        "access_limitations": ["UNL"],
+        "publication_date": "2025-8-12",
+        "site_url": "https://next-gen.materialsproject.org/materials",
+    }
+
+    my_record = Record(**my_record_dict)
+
+    # save in post then update to submit
+    try:
+        my_rr = elink_review_client.post_new_record(my_record, "save")
+        osti_id = my_rr.osti_id
+        assert my_rr.workflow_status == "SA"
+        assert my_rr.revision == 1
+
+        got_record = elink_review_client.get_single_record(osti_id)
+        record_updated_state = elink_review_client.update_record(
+            osti_id, got_record, "submit"
+        )
+        assert record_updated_state.workflow_status == "SO"
+        assert record_updated_state.revision == 2
+        core.delete_osti_record(elink_review_client, osti_id, "Test completed!")
+    except Exception:
+        core.delete_osti_record(elink_review_client, osti_id, "Test failed!")
+        pytest.fail("Test failed!")
+
+    # submit in post then update to save
+    try:
+        record_submit_first = elink_review_client.post_new_record(my_record, "submit")
+        osti_id = record_submit_first.osti_id
+        assert record_submit_first.workflow_status == "SO"
+        assert record_submit_first.revision == 1
+
+        got_submitted_record = elink_review_client.get_single_record(osti_id)
+        record_updated_state = elink_review_client.update_record(
+            osti_id, got_submitted_record, "save"
+        )
+        assert (
+            record_updated_state.workflow_status == "SA"
+        )  # record was submitted but switched to save, so should be 'SA'
+        assert record_updated_state.revision == 2
+        core.delete_osti_record(elink_review_client, osti_id, "Test completed!")
+    except Exception:
+        core.delete_osti_record(elink_review_client, osti_id, "Test failed!")
+        pytest.fail("Test failed!")
+
+    # update the workflow_status manually?
+    try:
+        record_to_manual_update = elink_review_client.post_new_record(my_record, "save")
+        osti_id = record_to_manual_update.osti_id
+        assert record_to_manual_update.workflow_status == "SA"
+        assert record_to_manual_update.revision == 1
+
+        got_record_to_manual_update = elink_review_client.get_single_record(osti_id)
+        got_record_to_manual_update.workflow_status = "SO"
+        record_after_manual_update = elink_review_client.update_record(
+            osti_id, got_record_to_manual_update, "submit"
+        )
+        assert record_after_manual_update.workflow_status == "SO"
+        assert record_after_manual_update.revision == 2
+        core.delete_osti_record(elink_review_client, osti_id, "Test completed!")
+    except Exception:
+        core.delete_osti_record(elink_review_client, osti_id, "Test failed!")
+        pytest.fail("Test failed!")