Match API

.gitignore

@@ -1,3 +1,5 @@
 .venv
 __pycache__
-macrostrat.toml
+macrostrat.toml
+*.egg-info
+*.pyc

README.md

@@ -46,6 +46,10 @@ Setting the `MACROSTRAT_PYROOT` environment variable allows a different root
 Python version to be installed. This can be used to add new plugins
 or application dependencies.
 
+### Debugging the installation
+
+- Run `macrostrat uv sync` to ensure that all dependencies are installed.
+
 ## Usage
 
 Once a Macrostrat configuration file is defined, the Macrostrat command-line app

bin/macrostrat

@@ -72,7 +72,7 @@ if [ "$1" = "uv" ]; then
     echo -e "MACROSTRAT_PYROOT is set to \033[36m$BASE_DIR\033[0m"
     echo ""
   fi
-  $_uv --directory "$BASE_DIR" "$@"
+  $_uv --project "$BASE_DIR" "$@"
   exit $?
 fi
 

cli/macrostrat/cli/__init__.py

@@ -1,3 +1 @@
 __version__ = "2.0.0"
-
-from .entrypoint import main

cli/macrostrat/cli/__main__.py

@@ -1,3 +1,3 @@
-from . import main
+from .entrypoint import main
 
 main()

cli/macrostrat/cli/database/migrations/composite_projects/projects-evolution.sql

@@ -0,0 +1,73 @@
+
+ALTER TABLE macrostrat.projects ADD COLUMN IF NOT EXISTS is_composite BOOLEAN DEFAULT FALSE;
+
+
+CREATE TABLE IF NOT EXISTS macrostrat.project_composite (
+  id integer PRIMARY KEY GENERATED ALWAYS AS IDENTITY,
+  parent_project_id integer REFERENCES macrostrat.projects(id) ON DELETE CASCADE,
+  child_project_id integer REFERENCES macrostrat.projects(id) ON DELETE CASCADE,
+  UNIQUE (parent_project_id, child_project_id)
+);
+
+-- Ensure that only composite projects can be parent of other projects
+CREATE OR REPLACE FUNCTION macrostrat.check_composite_parent()
+RETURNS TRIGGER AS $$
+BEGIN
+  IF NOT (SELECT is_composite FROM macrostrat.projects WHERE id = NEW.parent_project_id) THEN
+    RAISE EXCEPTION 'Parent project must be a composite project';
+  END IF;
+  RETURN NEW;
+END;
+$$ LANGUAGE plpgsql;
+
+-- Create the trigger on the project_composite table
+CREATE TRIGGER trg_check_composite_parent
+BEFORE INSERT OR UPDATE ON macrostrat.project_composite
+FOR EACH ROW EXECUTE FUNCTION macrostrat.check_composite_parent();
+
+/**
+  Ensure that only non-composite projects can have columns as children.
+  This is probably not strictly necessary, but it makes the composite project
+  system a bit more straightforward at the start.
+*/
+CREATE OR REPLACE FUNCTION macrostrat.check_column_project_non_composite()
+RETURNS TRIGGER AS $$
+BEGIN
+  IF (SELECT is_composite FROM macrostrat.projects WHERE id = NEW.project_id)
+  THEN
+    RAISE EXCEPTION 'A composite project cannot itself contain columns. We may relax this restriction in the future.';
+  END IF;
+  RETURN NEW;
+END;
+$$ LANGUAGE plpgsql;
+
+-- Add the trigger on the macrostrat.cols table
+CREATE TRIGGER trg_check_column_project_non_composite
+BEFORE INSERT OR UPDATE ON macrostrat.cols
+FOR EACH ROW EXECUTE FUNCTION macrostrat.check_column_project_non_composite();
+
+
+/** Take the opportunity to add a slug for nicer URLs **/
+ALTER TABLE macrostrat.projects ADD COLUMN IF NOT EXISTS slug TEXT UNIQUE;
+
+/** Function to generate slugs from project names **/
+CREATE OR REPLACE FUNCTION macrostrat.generate_project_slug()
+RETURNS VOID AS $$
+DECLARE
+  proj RECORD;
+  base_slug TEXT;
+  unique_slug TEXT;
+  suffix INT;
+BEGIN
+  FOR proj IN SELECT id, name FROM macrostrat.projects WHERE slug IS NULL LOOP
+    base_slug := lower(regexp_replace(proj.name, '[^a-zA-Z0-9]+', '-', 'g'));
+    unique_slug := base_slug;
+    suffix := 1;
+    WHILE EXISTS (SELECT 1 FROM macrostrat.projects WHERE slug = unique_slug) LOOP
+      suffix := suffix + 1;
+      unique_slug := base_slug || '-' || suffix;
+    END LOOP;
+    UPDATE macrostrat.projects SET slug = unique_slug WHERE id = proj.id;
+  END LOOP;
+END;
+$$ LANGUAGE plpgsql;

cli/macrostrat/cli/entrypoint.py

@@ -341,8 +341,9 @@ def update_weaver(db):
     main.add_typer(
         mariadb_app,
         name="mariadb",
-        rich_help_panel="Subsystems",
+        rich_help_panel="Legacy",
         short_help="Manage the MariaDB database",
+        deprecated=True,
     )
 
 # Knowledge graph CLI

cli/macrostrat/cli/subsystems/sgp/__init__.py

@@ -36,11 +36,18 @@ def import_sgp_data():
     print("Importing SGP data...")
     print(sgp_db.engine.url)
 
+    host = sgp_db.engine.url.host
+    port = sgp_db.engine.url.port or 5432
+
+    if host == "localhost":
+        # Use an internal port for connectivity.
+        port = "5432"
+
     db.run_sql(
         sql_dir / "create-fdw.sql",
         dict(
-            sgp_host=sgp_db.engine.url.host,
-            sgp_port=str(sgp_db.engine.url.port or 5432),
+            sgp_host=host,
+            sgp_port=str(port),
             sgp_database=sgp_db.engine.url.database,
             sgp_user=sgp_db.engine.url.username,
             sgp_password=sgp_db.engine.url.password,