Update schema dependency and update sample data files accordingly

CONTRIBUTING.md

@@ -103,6 +103,15 @@ Run the tests:
 docker compose up test
 ```
 
+If you plan to run the tests multiple times, we'd recommend running a shell within the `test` container and—from there—running the tests (as many times as you want). That will also enable syntax highlighting of the test results.
+
+```sh
+docker compose run --rm -it test bash
+
+# In the container:
+uv run --active pytest -v
+```
+
 <details>
 <summary>Show/hide FAQ about the ingest script's role in testing</summary>
 

mongodb/ingest_data.py

@@ -5,7 +5,7 @@
 import logging
 import os
 import sys
-from datetime import datetime
+from datetime import datetime, UTC
 from typing import Dict, Optional
 from schema.datamodel.bertron_schema_pydantic import Entity
 
@@ -100,7 +100,7 @@ def insert_entity(self, entity: Dict) -> Optional[str]:
         try:
             # Add metadata
             entity["_metadata"] = {
-                "ingested_at": datetime.utcnow(),
+                "ingested_at": datetime.now(UTC),
                 "schema_version": self.schema.get("version", "unknown"),
             }
 
@@ -198,7 +198,7 @@ def main():
     parser.add_argument("--db-name", default="bertron", help="MongoDB database name")
     parser.add_argument(
         "--schema-path",
-        default="https://raw.githubusercontent.com/ber-data/bertron-schema/96cbe257717d44137440be369a8414d153579926/src/schema/jsonschema/bertron_schema.json",
+        default="https://raw.githubusercontent.com/ber-data/bertron-schema/82498f5f5cbc71ed7abf71b8e2c01d15c003f8d8/src/schema/jsonschema/bertron_schema.json",
         help="Path or URL to the BERtron schema JSON file",
     )
     parser.add_argument(

pyproject.toml

@@ -17,11 +17,23 @@ version = "0.0.0"
 authors = [
   {name = "Chuck Parker", email = "ctparker@lbl.gov"},
 ]
-description = " Cross-BER Data Integration"
+description = "Cross-BER Data Integration"
 readme = "README.md"
 requires-python = ">=3.10.0,<3.14"
 dependencies = [
-  "bertron-schema @ git+https://github.com/ber-data/bertron-schema.git",
+  # Note: To depend upon the package built from the contents of the _latest commit_
+  #       on the _default branch_ in the `bertron-schema` repository, use:
+  #       ```
+  #       "bertron-schema @ git+https://github.com/ber-data/bertron-schema.git"
+  #       ```
+  #       To depend upon the package built from the contents of a _specific commit_
+  #       in the `bertron-schema` repository, use:
+  #       ```
+  #       "bertron-schema @ git+https://github.com/ber-data/bertron-schema.git@{COMMIT_HASH}"
+  #       ```
+  #       Reference: https://pip.pypa.io/en/stable/topics/vcs-support/
+  #
+  "bertron-schema @ git+https://github.com/ber-data/bertron-schema.git@82498f5f5cbc71ed7abf71b8e2c01d15c003f8d8",
   # "dtspy @ https://github.com/kbase/dtspy/archive/730828cff3924fc4b2215fe5c1b67bc04aad377f.tar.gz",
   "fastapi[standard]>=0.115.12",
   # `httpx` is a dependency of FastAPI's `TestClient` class, which we use

tests/data/gold-example.json

@@ -6,8 +6,8 @@
         "altitude": null,
         "depth": null,
         "elevation": {
-            "has_numeric_value": 2280,
-            "has_unit": "meter (UO:0000008)"
+            "numeric_value": 2280,
+            "unit": "meter (UO:0000008)"
         }
     },
     "entity_type": [

tests/data/monet-example.json

@@ -6,8 +6,8 @@
         "altitude": null,
         "depth": null,
         "elevation": {
-            "has_numeric_value": 722.613,
-            "has_unit": "unknown"
+            "numeric_value": 722.613,
+            "unit": "unknown"
         }
     },
     "entity_type": [

tests/data/nmdc-example.json

@@ -5,14 +5,14 @@
         "longitude": -81.434174,
         "altitude": null,
         "depth": {
-             "has_minimum_numeric_value": 0,
-             "has_maximum_numeric_value": 0.1,
-             "has_unit": "m",
-             "has_raw_value": "0 - 0.1m"
+             "minimum_numeric_value": 0,
+             "maximum_numeric_value": 0.1,
+             "unit": "m",
+             "raw_value": "0 - 0.1m"
          },
         "elevation": {
-            "has_numeric_value": 24,
-            "has_unit": "m"
+            "numeric_value": 24,
+            "unit": "m"
         }
     },
     "entity_type": [