Allows multiple batch insertions in one loop

The following changes to offset insertion script:

- Adds a loop to complete multiple batch insertions (the whole
  table) in a single execution of the script
- Fixes indentation errors (convert to spaces)
- Improves debugging outputs with item and batch counts

submission_offsets.py

@@ -12,57 +12,77 @@
 @cli.command(name='add-offsets')
 @click.option("--limit", "-l", default=10000)
 def add_offsets(limit):
-	"""Update lowlevel submission offsets with a specified limit."""
-	incremental_add_offset(limit)
+    """Update lowlevel submission offsets with a specified limit."""
+    incremental_add_offset(limit)
 
 def incremental_add_offset(limit):
-	with db.engine.connect() as connection:
-		# Find the next batch of items to update
-		batch_query = text("""
-			SELECT id, gid
-			  FROM lowlevel
-			 WHERE submission_offset IS NULL
-			 LIMIT :limit
-		""")
-		batch_result = connection.execute(batch_query, { "limit": limit })
-
-		# Find max existing offsets
-		offset_query = text("""
-			SELECT gid, MAX(submission_offset)
-			  FROM lowlevel
-			 WHERE submission_offset IS NOT NULL
-		      GROUP BY gid
-		""")
-		offset_result = connection.execute(offset_query)
-
-		max_offsets = defaultdict(int)
-		for gid, max_offset in offset_result.fetchall():
-			max_offsets[gid] = max_offset
-
-		print("Starting batch insertions...")
-		print("============================")
-		count = 0
-		for id, gid in batch_result.fetchall():
-			print("Finished {}/{} items".format(count, limit))
-			print("Current lowlevel.id: {}".format(id)) 
-			print("Inserting...")
-			if gid in max_offsets:
-				# Current offset exists
-				max_offsets[gid] += 1
-			else:
-				# No existing offset
-				max_offsets[gid] = 0
-			offset = max_offsets[gid]
-
-			query = text("""
-				UPDATE lowlevel
-				   SET submission_offset = :offset
-				 WHERE id = :id
-			""")
-			connection.execute(query, { "id": id, "offset": offset })
-			count += 1
-
-		print("============================")
-		print("Batch insertions finished.")
+    with db.engine.connect() as connection:
+
+        # Find number of items in table
+        size_query = text("""
+            SELECT MAX(id) AS size
+              FROM lowlevel
+        """)
+        size_result = connection.execute(size_query)
+        table_size = size_result.fetchone()["size"]
+
+        # Find max existing offsets
+        offset_query = text("""
+            SELECT gid, MAX(submission_offset)
+              FROM lowlevel
+             WHERE submission_offset IS NOT NULL
+          GROUP BY gid
+        """)
+        offset_result = connection.execute(offset_query)
+
+        max_offsets = defaultdict(int)
+        for gid, max_offset in offset_result.fetchall():
+            max_offsets[gid] = max_offset
+
+        # Find the next batch of items to update
+        batch_query = text("""
+            SELECT id, gid
+              FROM lowlevel
+             WHERE submission_offset IS NULL
+          ORDER BY id
+             LIMIT :limit
+        """)
+
+        batch_count = 0
+        item_count = 0
+        print("Starting batch insertions...")
+        print("============================")
+        while True:
+            batch_result = connection.execute(batch_query, { "limit": limit })
+            if not batch_result.rowcount:
+                print("\nSubmission offset exists for all items. Exiting...")
+                break
+
+            batch_count += 1
+            print("\nUpdating batch {}:".format(batch_count))
+            with connection.begin() as transaction:
+                for id, gid in batch_result.fetchall():
+                    if gid in max_offsets:
+                        # Current offset exists
+                        max_offsets[gid] += 1
+                    else:
+                        # No existing offset
+                        max_offsets[gid] = 0
+                    offset = max_offsets[gid]
+
+                    query = text("""
+                        UPDATE lowlevel
+                           SET submission_offset = :offset
+                         WHERE id = :id
+                    """)
+                    connection.execute(query, { "id": id, "offset": offset })
+                    item_count += 1
+                    print("\r   Inserted {}/{} items...".format(item_count, table_size)),
+        print("")
+
+
+        print("============================")
+        print("Batch insertions finished.")
+