nmdc-runtime 2.8.0__tar.gz → 2.9.0__tar.gz

{nmdc_runtime-2.8.0 → nmdc_runtime-2.9.0}/.env.example

@@ -71,4 +71,12 @@ DEV_STACK_HOST_MACHINE_PORT_FASTAPI=8000
 DEV_STACK_HOST_MACHINE_PORT_MONGO=27018
 TEST_STACK_HOST_MACHINE_PORT_DAGIT=3005
 TEST_STACK_HOST_MACHINE_PORT_FASTAPI=8005
-TEST_STACK_HOST_MACHINE_PORT_MONGO=27022
+TEST_STACK_HOST_MACHINE_PORT_MONGO=27022
+
+# Feature flag that can be used to enable/disable the `/nmdcschema/related_ids`
+# endpoint and the tests that target it. Valid values: {`true`, `false`}
+IS_RELATED_IDS_ENDPOINT_ENABLED=true
+
+# Feature flag that can be used to enable/disable the `/scalar` endpoint.
+# Valid values: {`true`, `false`}
+IS_SCALAR_ENABLED=true

{nmdc_runtime-2.8.0 → nmdc_runtime-2.9.0}/.gitignore

@@ -17,6 +17,7 @@ eggs/
 lib/
 !/tests/lib/
 !/nmdc_runtime/api/endpoints/lib/
+!/nmdc_runtime/api/models/lib/
 lib64/
 parts/
 sdist/

{nmdc_runtime-2.8.0/nmdc_runtime.egg-info → nmdc_runtime-2.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nmdc_runtime
-Version: 2.8.0
+Version: 2.9.0
 Summary: A runtime system for NMDC data management and orchestration
 Home-page: https://github.com/microbiomedata/nmdc-runtime
 Author: Donny Winston

nmdc_runtime-2.9.0/db/migrations/README.md

@@ -0,0 +1,8 @@
+# Migrations
+
+This directory contains files related to migrating the MongoDB database.
+
+It has the following subdirectories:
+
+- `./notebooks`: Python notebooks related to migrating the MongoDB database between versions of the NMDC Schema.
+- `./ad_hoc_scripts`: MongoDB (`mongosh`) scripts—and maybe, eventually, other kinds of scripts—related to migrating parts of the MongoDB database that aren't described by the NMDC Schema.

nmdc_runtime-2.9.0/db/migrations/ad_hoc_scripts/migrate_jobs_collection_from_schema_11.8.0_to_11.9.1.mongosh.js

@@ -0,0 +1,38 @@
+// Note: The `use("nmdc");` syntax works in MongoDB Compass, but not in Studio 3T.
+//       The `use nmdc;` syntax works in Studio 3T, but not in MongoDB Compass.
+use("nmdc");
+
+/**
+ * This MongoDB shell script updates the `jobs` collection so that any
+ * documents where `config.was_informed_by` is a string are updated so that
+ * `config.was_informed_by` is a single-element array containing that string.
+ */
+
+// 🔍 Define the filter for the documents we will be updating.
+const filter = { "config.was_informed_by": { $type: "string" } };
+
+// 🧮 Before: Print the total number of documents.
+let numDocsTotal = db.getCollection("jobs").countDocuments({});
+console.log(`Number of documents: ${numDocsTotal}`);
+
+// 🧮 Before: Print the number of documents that match the filter.
+let numDocsMatchingFilter = db.getCollection("jobs").countDocuments(filter);
+console.log(`Number of documents matching filter: ${numDocsMatchingFilter}`);
+
+// ✏️ Update the documents that match the filter.
+//    Reference: https://www.mongodb.com/docs/manual/reference/method/db.collection.updateMany/
+db.jobs.updateMany(filter, [
+  {
+    $set: {
+      "config.was_informed_by": ["$config.was_informed_by"],
+    },
+  }
+]);
+
+// 🧮 After: Print the total number of documents.
+numDocsTotal = db.getCollection("jobs").countDocuments({});
+console.log(`Number of documents (expecting same as before): ${numDocsTotal}`);
+
+// 🧮 After: Print the number of documents that match the filter.
+numDocsMatchingFilter = db.getCollection("jobs").countDocuments(filter);
+console.log(`Number of documents matching filter (expecting 0): ${numDocsMatchingFilter}`);