Merge branch 'main' of github.com:UW-Macrostrat/macrostrat

Author: amyfromandi

map-integration/macrostrat/map_integration/__init__.py

@@ -5,9 +5,11 @@
 os.environ["USE_PYGEOS"] = "0"
 
 import re
+from pathlib import Path
 from sys import stdin
 
 from psycopg2.sql import Identifier
+from rich.console import Console
 from typer import Option
 
 from macrostrat.core import app
@@ -17,6 +19,7 @@
 from macrostrat.map_integration.process.geometry import create_rgeom, create_webgeom
 from macrostrat.map_integration.utils.file_discovery import find_gis_files
 from macrostrat.map_integration.utils.map_info import get_map_info
+from macrostrat.map_integration.utils.staging_upload_dir import *
 
 from . import pipeline
 from .commands.copy_sources import copy_macrostrat_sources
@@ -28,23 +31,19 @@
 from .commands.sources import map_sources
 from .database import get_database
 from .migrations import run_migrations
+from .pipeline import upload_file
 from .process import cli as _process
 from .process.insert import _delete_map_data
 from .utils import IngestionCLI, MapInfo, table_exists
-from rich.console import Console
-
-from pathlib import Path
-from .pipeline import upload_file
-from macrostrat.map_integration.utils.file_discovery import find_gis_files
-from macrostrat.map_integration.utils.staging_upload_dir import *
 
 help_text = f"""Ingest maps into Macrostrat.
 
 Active map: [bold cyan]{app.state.get("active_map")}[/]
 """
-console =Console()
+console = Console()
 cli = IngestionCLI(no_args_is_help=True, name="map-ingestion", help=help_text)
 
+
 @cli.command(name="set-active")
 def set_active_map(map: MapInfo = None):
     """Set the active map for the current session."""
@@ -256,6 +255,7 @@ def _run_migrations(database: str = None):
 staging_cli = IngestionCLI(no_args_is_help=True, help="Staging pipeline & storage")
 cli.add_typer(staging_cli, name="staging")
 
+
 def staging(
     slug: str,
     data_path: str,
@@ -382,11 +382,13 @@ def staging(
         f"\nFinished staging setup for {slug}. View map here: https://dev.macrostrat.org/maps/ingestion/{source_id}/ \n"
     )
 
+
 staging_cli.add_command(staging, name="ingest")
 
-#------------------------------------------
+# ------------------------------------------
 # commands nested under 'macrostrat maps staging...'
 
+
 @staging_cli.command("upload-dir")
 def cmd_upload_dir(
     slug: str = ...,
@@ -395,40 +397,52 @@ def cmd_upload_dir(
     """Upload a local directory to the staging bucket under SLUG/."""
     res = staging_upload_dir(slug, data_path)
     pretty_res = json.dumps(res, indent=2)
-    console.print(f'[green] Upload successful! \n {pretty_res} [/green]')
+    console.print(f"[green] Upload successful! \n {pretty_res} [/green]")
+
 
 @staging_cli.command("delete-dir")
 def cmd_delete_dir(
     slug: str = ...,
-    file_name: str = Option(None, help="deletes a specified file within the slug directory.")
+    file_name: str = Option(
+        None, help="deletes a specified file within the slug directory."
+    ),
 ):
     """Delete all objects under SLUG/ in the staging bucket."""
     staging_delete_dir(slug, file_name)
-    console.print(f"[green] Delete successful! \n Deleted objects under slug: {slug} [/green]")
+    console.print(
+        f"[green] Delete successful! \n Deleted objects under slug: {slug} [/green]"
+    )
+
 
 @staging_cli.command("list")
 def cmd_list_dir(
     slug: str = ...,
     page_token: int = Option(0, "--page-token", "-t", help="Offset to start from"),
     page_size: int = Option(10, "--page-size", "-s", help="Items per page"),
-    more: bool = Option(False, "--more", "-m", help="Interactively page through results"),
+    more: bool = Option(
+        False, "--more", "-m", help="Interactively page through results"
+    ),
 ):
     """List paginated files under SLUG."""
     if not more:
         page = staging_list_dir(slug, page_token=page_token, page_size=page_size)
         files = json.dumps(page, indent=2)
-        console.print(f'[green] {files} [/green]')
+        console.print(f"[green] {files} [/green]")
         return
 
     token = page_token
     while True:
         page = staging_list_dir(slug, page_token=token, page_size=page_size)
         for f in page["files"]:
-            console.print(f'[green]{f}[/green]')
+            console.print(f"[green]{f}[/green]")
         if page["next_page_token"] is None:
             print("\n-- End of list --")
             break
-        resp = input("\nPress Enter for next page, or type 'exit' to stop: ").strip().lower()
+        resp = (
+            input("\nPress Enter for next page, or type 'exit' to stop: ")
+            .strip()
+            .lower()
+        )
         if resp in ("exit", "quit", "q"):
             break
         token = page["next_page_token"]