Merge pull request #197 from UW-Macrostrat/auth-fixes

Small fixes for local auth

Author: davenquinn

cli/macrostrat/cli/database/migrations/column_builder/__init__.py

@@ -12,3 +12,5 @@ class ColumnBuilderMigration(Migration):
     depends_on = ["macrostrat-core-v2"]
 
     postconditions = [schema_exists("macrostrat_api")]
+
+    always_apply = True

cli/macrostrat/cli/database/migrations/map_sources/__init__.py

@@ -8,7 +8,7 @@ class MapsSourcesMetadataMigration(Migration):
     Create views for sources_metadata and ingest_process in the maps and macrostrat_api schemas
     """
 
-    depends_on = ["api-v3", "column-builder"]
+    depends_on = ["api-v3"]
 
     postconditions = [
         view_exists("maps", "sources_metadata", "ingest_process"),

cli/macrostrat/cli/database/migrations/update_macrostrat/__init__.py

@@ -18,5 +18,5 @@ class MacrostratCoreMigration(Migration):
 
     postconditions = [
         exists("macrostrat", "units", "sections"),
-        has_fks("macrostrat", "units", "sections"),
+        has_fks("macrostrat", "units", "sections", "strat_names"),
     ]

cli/macrostrat/cli/entrypoint.py

@@ -1,17 +1,16 @@
 from os import environ
-from pathlib import Path
 
 import typer
+from macrostrat.app_frame import CommandBase
+from macrostrat.utils.shell import run
+from pathlib import Path
 from rich import print
 from rich.traceback import install
 from typer import Argument, Typer
 
-from macrostrat.app_frame import CommandBase
 from macrostrat.core import app
 from macrostrat.core.exc import MacrostratError
 from macrostrat.core.main import env_text, set_app_state
-from macrostrat.utils.shell import run
-
 from .database import db_app, db_subsystem
 from .subsystems.macrostrat_api import MacrostratAPISubsystem
 from .subsystems.paleogeography import (
@@ -380,6 +379,14 @@ def inspect():
     IPython.embed()
 
 
+# Print the environment variables
+@self_app.command()
+def printenv():
+    """Print the environment variables"""
+    for k, v in environ.items():
+        print(f"[bold cyan]{k}[/]: {v}")
+
+
 main.add_typer(
     self_app,
     name="self",

core/macrostrat/core/config.py

@@ -1,15 +1,14 @@
 from os import environ
-from pathlib import Path
 
 from dotenv import load_dotenv
 from dynaconf import Dynaconf, Validator
+from macrostrat.app_frame.control_command import BackendType
+from macrostrat.utils import get_logger
+from pathlib import Path
 from sqlalchemy.engine import make_url
 from sqlalchemy.engine.url import URL
 from toml import load as load_toml
 
-from macrostrat.app_frame.control_command import BackendType
-from macrostrat.utils import get_logger
-
 from .resolvers import cast_sources, setup_source_roots_environment
 from .utils import convert_to_string, find_macrostrat_config, path_list_resolver
 
@@ -89,6 +88,9 @@ def get(self, key, default=None):
 if env_files := getattr(settings, "env_files", None):
     for env in env_files:
         log.info(f"Loading environment variables from {env}")
+        # Resolve env file from settings path
+        if not Path(env).is_absolute():
+            env = settings.config_file.parent / env
         load_dotenv(env)
 
 # Validate settings