nmdc-runtime 1.4.0__tar.gz → 1.4.1__tar.gz

{nmdc_runtime-1.4.0 → nmdc_runtime-1.4.1}/.github/workflows/python-app.yml

@@ -39,4 +39,4 @@ jobs:
     - name: Test with pytest
       run: |
         make up-test
-        make test-run
+        make test

{nmdc_runtime-1.4.0 → nmdc_runtime-1.4.1}/.gitignore

@@ -168,4 +168,8 @@ nmdc_runtime/site/changesheets/changesheets_output/
 mdb-nmdc-dev.tar.gz
 
 # superceded by .github/workflows/build-and-release-to-spin.yml
-docker-build.sh
+docker-build.sh
+
+neon.db
+neon_api_cache.sqlite
+nmdc-db.nt.gz

{nmdc_runtime-1.4.0 → nmdc_runtime-1.4.1}/Makefile

@@ -29,8 +29,7 @@ up-test:
 		up --build --force-recreate --detach --remove-orphans
 
 test-build:
-	docker compose --file docker-compose.test.yml \
-		up test --build --force-recreate --detach --remove-orphans
+	docker compose --file docker-compose.test.yml build test
 
 test-dbinit:
 	docker compose --file docker-compose.test.yml \

{nmdc_runtime-1.4.0 → nmdc_runtime-1.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nmdc_runtime
-Version: 1.4.0
+Version: 1.4.1
 Summary: A runtime system for NMDC data management and orchestration
 Home-page: https://github.com/microbiomedata/nmdc-runtime
 Author: Donny Winston

nmdc_runtime-1.4.1/demo/metadata_migration/notebooks/bookkeeper.py

@@ -0,0 +1,127 @@
+from typing import Optional
+from enum import Enum
+from datetime import datetime
+
+from pymongo import MongoClient
+from nmdc_schema.migrators.migrator_base import MigratorBase
+
+
+class MigrationEvent(str, Enum):
+    r"""
+    Enumeration of all migration events that can be recorded.
+    Reference: https://docs.python.org/3.10/library/enum.html#others
+
+    >>> MigrationEvent.MIGRATION_COMPLETED.value
+    'MIGRATION_COMPLETED'
+    >>> MigrationEvent.MIGRATION_STARTED.value
+    'MIGRATION_STARTED'
+    """
+
+    MIGRATION_STARTED = "MIGRATION_STARTED"
+    MIGRATION_COMPLETED = "MIGRATION_COMPLETED"
+
+
+class Bookkeeper:
+    r"""
+    A class you can use to record migration-related events in a Mongo database.
+    """
+
+    def __init__(
+        self,
+        mongo_client: MongoClient,
+        database_name: str = "nmdc",
+        collection_name: str = "_migration_events",
+        view_name: str = "_migration_latest_schema_version",
+    ):
+        self.database_name = database_name
+        self.collection_name = collection_name
+        self.view_name = view_name
+
+        # Store references to the database and collection.
+        self.db = mongo_client[self.database_name]
+        self.collection = self.db.get_collection(self.collection_name)
+
+        # Ensure the MongoDB view that indicates the current schema version, exists.
+        self.ensure_current_schema_version_view_exists()
+
+    @staticmethod
+    def get_current_timestamp() -> str:
+        r"""Returns an ISO 8601 timestamp (string) representing the current time in UTC."""
+        utc_now = datetime.utcnow()
+        iso_utc_now = utc_now.isoformat()
+        return iso_utc_now  # e.g. "2024-02-21T04:31:03.115107"
+
+    def record_migration_event(
+        self,
+        migrator: MigratorBase,
+        event: MigrationEvent,
+        to_schema_version: Optional[str] = None,
+    ) -> None:
+        r"""
+        Records a migration event in the collection.
+
+        The `to_schema_version` parameter is independent of the `migrator` parameter because, even though the migrator
+        does have a `.get_destination_version()` method, the string returned by that method is the one defined when the
+        migrator was _written_, which is sometimes more generic than the one used for data validation when the migrator
+        is _run_ (e.g. "1.2" as opposed to "1.2.3"). So, this method provides a means by which the calling code can,
+        optionally, specify a more precise version identifier.
+        """
+
+        # If a custom schema version identifier was specified, use that; otherwise, use the one built into the migrator.
+        to_schema_version_str = migrator.get_destination_version()
+        if to_schema_version is not None:
+            to_schema_version_str = to_schema_version
+
+        document = dict(
+            created_at=self.get_current_timestamp(),
+            event=event.value,
+            from_schema_version=migrator.get_origin_version(),
+            to_schema_version=to_schema_version_str,
+            migrator_module=migrator.__module__,  # name of the Python module in which the `Migrator` class is defined
+        )
+        self.collection.insert_one(document)
+
+    def ensure_current_schema_version_view_exists(self) -> None:
+        r"""
+        Ensures the MongoDB view that indicates the current schema version, exists.
+
+        References:
+        - https://www.mongodb.com/community/forums/t/is-there-anyway-to-create-view-using-python/161363/2
+        - https://www.mongodb.com/docs/manual/reference/method/db.createView/#mongodb-method-db.createView
+        - https://pymongo.readthedocs.io/en/stable/api/pymongo/database.html#pymongo.database.Database.create_collection
+        """
+        if (
+            self.view_name not in self.db.list_collection_names()
+        ):  # returns list of names of both collections and views
+            agg_pipeline = [
+                # Sort the documents so the most recent one is first.
+                {"$sort": {"created_at": -1}},
+                # Only preserve the first document.
+                {"$limit": 1},
+                # Derive a simplified document for the view.
+                # Examples: `{ "schema_version": "1.2.3" }` or `{ "schema_version": null }`
+                {
+                    "$project": {
+                        "_id": 0,  # omit the `_id` field
+                        "schema_version": {  # add this field based upon the migration status
+                            "$cond": {
+                                "if": {
+                                    "$eq": [
+                                        "$event",
+                                        MigrationEvent.MIGRATION_COMPLETED.value,
+                                    ]
+                                },
+                                "then": "$to_schema_version",  # database conforms to this version of the NMDC Schema
+                                "else": None,  # database doesn't necessarily conform to any version of the NMDC Schema
+                            }
+                        },
+                    }
+                },
+            ]
+            self.db.create_collection(
+                name=self.view_name,
+                viewOn=self.collection_name,
+                pipeline=agg_pipeline,
+                check_exists=True,  # only create the view if it doesn't already exist
+                comment="The version of the NMDC Schema to which the database conforms.",
+            )

nmdc_runtime-1.4.1/demo/metadata_migration/notebooks/manual_test_bookkeeper.py

@@ -0,0 +1,186 @@
+# Note: This module's name starts with `manual_test_` instead of `test_` to signify that its author (currently) expects
+#       people to run it manually as opposed to via automated test infrastructure. Its author chose that route after a
+#       GitHub Actions workflow that runs tests in `test_` modules kept failing due to a database access issue.
+
+from typing import Optional
+import unittest
+import re
+import os
+from datetime import datetime, timedelta
+
+from pymongo import MongoClient, timeout
+from pymongo.database import Database
+from nmdc_schema.migrators.migrator_base import MigratorBase
+
+from demo.metadata_migration.notebooks.bookkeeper import Bookkeeper, MigrationEvent
+
+# Consume environment variables.
+MONGO_HOST: str = os.getenv("MONGO_HOST", "localhost")
+MONGO_USER: Optional[str] = os.getenv("MONGO_USERNAME", None)
+MONGO_PASS: Optional[str] = os.getenv("MONGO_PASSWORD", None)
+MONGO_DATABASE_NAME: str = os.getenv("MONGO_TEST_DBNAME", "test-migration-bookkeeper")
+
+MONGO_TIMEOUT_DURATION: int = 3  # seconds
+
+
+class FakeMigrator(MigratorBase):
+    _to_version = "A.B.C"
+    _from_version = "X.Y.Z"
+
+    def upgrade(self):
+        pass
+
+
+class TestBookkeeper(unittest.TestCase):
+    r"""
+    Tests targeting the `Bookkeeper` class.
+
+    You can format this file like this:
+    $ python -m black demo/metadata_migration/notebooks/manual_test_bookkeeper.py
+
+    You can start up a containerized MongoDB server like this:
+    $ docker run --rm --detach --name mongo-test-migration-bookkeeper -p 27017:27017 mongo
+
+    One that's running, other containers will be able to access it via:
+    - host.docker.internal:27017
+
+    You can run these tests like this:
+    $ python -m unittest -v demo/metadata_migration/notebooks/manual_test_bookkeeper.py
+
+    Reference: https://docs.python.org/3/library/unittest.html#basic-example
+    """
+
+    mongo_client: Optional[MongoClient] = None
+    db: Optional[Database] = None
+
+    def setUp(self) -> None:
+        r"""
+        Connects to the MongoDB server and gets a reference to the database.
+
+        Note: This function runs before each test starts.
+        """
+
+        # Connect to the MongoDB server and store a reference to the connection.
+        self.mongo_client = MongoClient(
+            host=MONGO_HOST,
+            username=MONGO_USER,
+            password=MONGO_PASS,
+        )
+        with timeout(MONGO_TIMEOUT_DURATION):
+            # Try connecting to the database server.
+            _ = self.mongo_client.server_info()
+            db = self.mongo_client[MONGO_DATABASE_NAME]
+
+            # Ensure the database contains no collections.
+            if len(db.list_collection_names()):
+                raise KeyError(f"Database is not empty: {MONGO_DATABASE_NAME}")
+
+        # Store a reference to the database.
+        self.db = db
+
+    def tearDown(self) -> None:
+        r"""
+        Drops all collections in the database and closes the connection to the MongoDB server.
+
+        Note: This function runs after each test finishes.
+        """
+
+        # Drop all collections in the database.
+        for collection_name in self.db.list_collection_names():
+            self.db.drop_collection(collection_name)
+
+        # Close the connection to the server.
+        self.mongo_client.close()
+
+    def test_get_current_timestamp(self):
+        pattern = r"^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}\.\d{6}$"
+        ts_str = Bookkeeper.get_current_timestamp()
+
+        # Verify the timestamp is a string having a valid format.
+        self.assertIsInstance(ts_str, str)
+        self.assertTrue(re.match(pattern, ts_str))
+
+        # Verify the moment represented by the timestamp was within the past minute.
+        ts = datetime.fromisoformat(ts_str)
+        now_ts = datetime.now()
+        time_difference = now_ts - ts
+        self.assertLess(time_difference, timedelta(minutes=1))
+
+    def test_init_method(self):
+        # Confirm the view does not exist yet.
+        view_name = "test_view"
+        self.assertFalse(view_name in self.db.list_collection_names())
+
+        # Instantiate the class-under-test.
+        _ = Bookkeeper(
+            mongo_client=self.mongo_client,
+            database_name=MONGO_DATABASE_NAME,
+            view_name=view_name,
+        )
+
+        # Confirm the view exists now.
+        self.assertTrue(view_name in self.db.list_collection_names())
+
+    def test_record_migration_event(self):
+        # Instantiate a bookkeeper.
+        bk = Bookkeeper(
+            mongo_client=self.mongo_client,
+            database_name=MONGO_DATABASE_NAME,
+        )
+
+        # Verify the collection is empty.
+        collection = self.db.get_collection(bk.collection_name)
+        self.assertTrue(collection.count_documents({}) == 0)
+
+        # Record a "migration started" event.
+        migrator = FakeMigrator()
+        bk.record_migration_event(
+            migrator=migrator, event=MigrationEvent.MIGRATION_STARTED
+        )
+
+        # Verify the migration event was recorded.
+        self.assertTrue(collection.count_documents({}) == 1)
+        doc = collection.find({})[0]
+        self.assertIsInstance(doc["created_at"], str)
+        self.assertIsInstance(doc["event"], str)
+        self.assertEqual(doc["event"], MigrationEvent.MIGRATION_STARTED)
+        self.assertIsInstance(doc["from_schema_version"], str)
+        self.assertEqual(doc["from_schema_version"], migrator.get_origin_version())
+        self.assertIsInstance(doc["to_schema_version"], str)
+        self.assertEqual(doc["to_schema_version"], migrator.get_destination_version())
+        self.assertIsInstance(doc["migrator_module"], str)
+
+        # Verify the document in the view says the schema version is `null`.
+        # Note: That's what I expect, since no "migration complete" events have been recorded yet.
+        view = self.db.get_collection(bk.view_name)
+        self.assertTrue(view.count_documents({}) == 1)
+        view_doc = view.find({})[0]
+        self.assertIsNone(view_doc["schema_version"])
+
+        # Record a "migration completed" event.
+        bk.record_migration_event(
+            migrator=migrator, event=MigrationEvent.MIGRATION_COMPLETED
+        )
+
+        # Verify the migration event was recorded.
+        self.assertTrue(collection.count_documents({}) == 2)
+
+        # Verify the document in the view says the schema version matches the one recorded.
+        view = self.db.get_collection(bk.view_name)
+        self.assertTrue(view.count_documents({}) == 1)
+        view_doc = view.find({})[0]
+        self.assertEqual(view_doc["schema_version"], migrator.get_destination_version())
+
+        # Finally, record another "migration started" event.
+        bk.record_migration_event(
+            migrator=migrator, event=MigrationEvent.MIGRATION_STARTED
+        )
+
+        # Confirm the document in the view once again says the schema version is `null`.
+        self.assertTrue(view.count_documents({}) == 1)
+        view_doc = view.find({})[0]
+        self.assertIsNone(view_doc["schema_version"])
+
+
+if __name__ == "__main__":
+    unittest.main()