Merge pull request #248 from UW-Macrostrat/files_v3

modifying object s3 routes and refactoring

Author: amyfromandi

py-modules/map-integration/macrostrat/map_integration/utils/s3_file_management.py

@@ -102,7 +102,7 @@ def get_existing_object_id(db, *, host: str, bucket: str, key: str) -> int | Non
     return db.run_query(
         """
         SELECT id
-        FROM storage.object
+        FROM storage.objects 
         WHERE scheme = 's3'
           AND host = :host
           AND bucket = :bucket
@@ -123,7 +123,7 @@ def insert_storage_object(
 ) -> int:
     db.run_sql(
         """
-        INSERT INTO storage.object
+        INSERT INTO storage.objects 
           (scheme, host, bucket, key, source, sha256_hash, mime_type)
         VALUES
           ('s3', :host, :bucket, :key, :source, :sha256, :mime_type)
@@ -139,7 +139,7 @@ def insert_storage_object(
     )
     object_id = get_existing_object_id(db, host=host, bucket=bucket, key=key)
     if object_id is None:
-        raise RuntimeError("Failed to retrieve storage.object id after insert")
+        raise RuntimeError("Failed to retrieve storage.objects  id after insert")
     return object_id
 
 
@@ -187,7 +187,7 @@ def staging_upload_dir(
     ingest_process_id: int,
 ) -> dict:
     """
-    Upload local files to S3 via MinIO and register them in storage.object.
+    Upload local files to S3 via MinIO and register them in storage.objects.
     Always uploads a single zip archive for the provided data_path.
     """
     if ingest_process_id is None:
@@ -278,7 +278,7 @@ def get_objects_for_slug(db, *, host: str, bucket: str, slug: str) -> list[dict]
         db.run_query(
             """
         SELECT id, key
-        FROM storage.object
+        FROM storage.objects 
         WHERE scheme = 's3'
           AND host = :host
           AND bucket = :bucket
@@ -309,7 +309,7 @@ def unlink_object_from_ingests(db, *, object_id: int) -> None:
 def delete_storage_object(db, *, object_id: int) -> None:
     db.run_sql(
         """
-        DELETE FROM storage.object
+        DELETE FROM storage.objects 
         WHERE id = :id
         """,
         dict(id=object_id),
@@ -409,7 +409,7 @@ def staging_list_dir(
             db.run_query(
                 """
             SELECT id, key
-            FROM storage.object
+            FROM storage.objects 
             WHERE scheme = 's3'
               AND host = :host
               AND bucket = :bucket
@@ -460,7 +460,7 @@ def staging_download_dir(db, slug: str, dest_path: Path) -> dict:
             db.run_query(
                 """
             SELECT id, key
-            FROM storage.object
+            FROM storage.objects 
             WHERE scheme = 's3'
               AND host = :host
               AND bucket = :bucket

py-modules/map-integration/tests/test_map_staging.py

@@ -111,7 +111,7 @@ def test_map_staging(test_db, test_maps):
     )
 
     # object_group_id is a foreign key into the storage schema where the curr user postgres does not have access to.
-    # the storage.sql ALTER TABLE storage.object OWNER TO macrostrat is switching the owner.
+    # the storage.sql ALTER TABLE storage.objects  OWNER TO macrostrat is switching the owner.
     # we are temporarily using macrostrat to run the query below
     object_group_id = db.run_query(
         "INSERT INTO storage.object_group DEFAULT VALUES RETURNING id"

schema/_migrations/api_v3/08-storage.sql

@@ -13,7 +13,7 @@ CREATE TYPE storage.scheme AS ENUM (
 
 ALTER TYPE storage.scheme OWNER TO macrostrat;
 
-CREATE TABLE IF NOT EXISTS storage.object (
+CREATE TABLE IF NOT EXISTS storage.objects (
     id integer GENERATED ALWAYS AS IDENTITY PRIMARY KEY,
     scheme storage.scheme NOT NULL,
     host character varying(255) NOT NULL,
@@ -28,7 +28,7 @@ CREATE TABLE IF NOT EXISTS storage.object (
 );
 
 
-ALTER TABLE storage.object OWNER TO macrostrat;
+ALTER TABLE storage.objects OWNER TO macrostrat;
 
 GRANT ALL ON DATABASE macrostrat TO postgrest;
 

schema/_migrations/file_storage_updates/__init__.py

@@ -17,7 +17,7 @@ class FileStorageUpdates(Migration):
         exists("maps_metadata", "ingest_process"),
     ]
     postconditions = [
-        # storage.object no longer has object_group_id
+        # storage.objects no longer has object_group_id
         has_columns(
             "storage",
             "object",

schema/_migrations/file_storage_updates/map-files-table.sql

@@ -1,4 +1,4 @@
-ALTER TABLE storage.object DROP COLUMN IF EXISTS object_group_id;
+ALTER TABLE storage.objects DROP COLUMN IF EXISTS object_group_id;
 DROP TABLE IF EXISTS storage.object_group CASCADE;
 CREATE TABLE IF NOT EXISTS maps_metadata.map_files (
             id serial PRIMARY KEY,

schema/_migrations/storage_schema.py

@@ -16,9 +16,9 @@ def apply(self, db: Database):
         ALTER TYPE storage.scheme ADD VALUE 'http' AFTER 'https';
 
         -- Lock the table to prevent concurrent updates
-        LOCK TABLE storage.object IN ACCESS EXCLUSIVE MODE;
+        LOCK TABLE storage.objects  IN ACCESS EXCLUSIVE MODE;
 
-        ALTER TABLE storage.object
+        ALTER TABLE storage.objects 
         ALTER COLUMN scheme
               TYPE storage.scheme USING scheme::text::storage.scheme;
 

schema/core/0002-storage.sql

@@ -11,7 +11,7 @@ ALTER TYPE storage.scheme OWNER TO macrostrat;
 SET default_tablespace = '';
 SET default_table_access_method = heap;
 
-CREATE TABLE storage.object (
+CREATE TABLE storage.objects (
     id integer NOT NULL,
     scheme storage.scheme NOT NULL,
     host character varying(255) NOT NULL,
@@ -24,7 +24,7 @@ CREATE TABLE storage.object (
     updated_on timestamp with time zone DEFAULT now() NOT NULL,
     deleted_on timestamp with time zone
 );
-ALTER TABLE storage.object OWNER TO macrostrat;
+ALTER TABLE storage.objects OWNER TO macrostrat;
 
 CREATE SEQUENCE storage.object_id_seq
     AS integer
@@ -37,11 +37,11 @@ ALTER TABLE storage.object_id_seq OWNER TO macrostrat;
 
 ALTER SEQUENCE storage.object_id_seq OWNED BY storage.object.id;
 
-ALTER TABLE ONLY storage.object ALTER COLUMN id SET DEFAULT nextval('storage.object_id_seq'::regclass);
+ALTER TABLE ONLY storage.objects ALTER COLUMN id SET DEFAULT nextval('storage.objects _id_seq'::regclass);
 
-ALTER TABLE ONLY storage.object
+ALTER TABLE ONLY storage.objects
     ADD CONSTRAINT object_pkey PRIMARY KEY (id);
 
-ALTER TABLE ONLY storage.object
+ALTER TABLE ONLY storage.objects
     ADD CONSTRAINT unique_file UNIQUE (scheme, host, bucket, key);