Merge branch 'measurements' of https://github.com/UW-Macrostrat/macrostrat into measurements

Author: davidsklar99

.github/workflows/build-usage-stats.yaml

@@ -0,0 +1,64 @@
+name: Build usage-stats
+on:
+  push:
+    # Branches and paths are exclusive
+    branches: ["main"]
+    paths:
+      - services/usage-stats/**
+    tags:
+      - usage-stats-v[0-9]+.[0-9]+.[0-9]+ # Semver Release (non-prerelease)
+      - usage-stats-v[0-9]+.[0-9]+.[0-9]+-** # Semver release (prerelease)
+  pull_request:
+    branches: [main]
+    paths:
+      - services/usage-stats/**
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: "recursive"
+      # Set up python and poetry
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+      - name: Install Poetry
+        run: python3 -m pip install poetry==2.1.1
+      - name: Build and stage local packages
+        run: scripts/prepare-services
+      - name: Get the version from the tag, if it exists
+        run: |
+          TAG=${{ github.event.release.tag_name }}
+          VERSION=$(echo "${TAG}" | sed -E 's/usage-stats-v//')
+          echo "VERSION=${VERSION}" >> $GITHUB_ENV
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: hub.opensciencegrid.org/macrostrat/usage-stats
+          tags: |
+            type=ref,event=pr,suffix=-{{date 'YYYYMMDDHHmmss'}}
+            type=ref,event=branch,suffix=-{{date 'YYYYMMDDHHmmss'}}
+            type=semver,pattern={{version}}
+            type=raw,value=latest,enable={{is_default_branch}}
+            type=raw,value=sha-{{sha}}
+      - name: Set up Docker BuildX
+        uses: docker/setup-buildx-action@v2
+      - name: Login to OSG DockerHub
+        uses: docker/login-action@v2
+        with:
+          registry: hub.opensciencegrid.org
+          username: ${{ vars.HARBOR_CLI_NAME }}
+          password: ${{ secrets.HARBOR_CLI_SECRET }}
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: services/usage-stats
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.idea/dataSources.xml

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

.idea/sqldialects.xml

@@ -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"),

.idea/vcs.xml

@@ -0,0 +1,54 @@
+-- SCHEMA
+CREATE SCHEMA IF NOT EXISTS ecosystem;
+
+-- PEOPLE
+CREATE TABLE IF NOT EXISTS ecosystem.people (
+    id serial PRIMARY KEY,
+    name text NOT NULL,
+    email text NOT NULL UNIQUE,
+    title text NOT NULL,
+    website text,
+    img_id text,
+    active_start timestamp with time zone NOT NULL DEFAULT now(),
+    active_end timestamp with time zone
+);
+
+-- ROLES
+CREATE TABLE IF NOT EXISTS ecosystem.roles (
+    id serial PRIMARY KEY,
+    name text NOT NULL UNIQUE,
+    description text NOT NULL
+);
+
+-- PEOPLE-ROLES MAPPING
+CREATE TABLE IF NOT EXISTS ecosystem.people_roles (
+    person_id integer NOT NULL REFERENCES ecosystem.people(id) ON DELETE CASCADE,
+    role_id integer NOT NULL REFERENCES ecosystem.roles(id) ON DELETE CASCADE,
+    PRIMARY KEY (person_id, role_id)
+);
+
+-- CONTRIBUTIONS
+CREATE TABLE IF NOT EXISTS ecosystem.contributions (
+    id serial PRIMARY KEY,
+    person_id integer NOT NULL REFERENCES ecosystem.people(id) ON DELETE CASCADE,
+    contribution text NOT NULL,
+    description text,
+    date timestamp with time zone NOT NULL DEFAULT now(),
+    url text
+);
+
+-- PEOPLE-CONTRIBUTIONS MAPPING
+CREATE TABLE IF NOT EXISTS ecosystem.people_contributions (
+    person_id integer NOT NULL REFERENCES ecosystem.people(id) ON DELETE CASCADE,
+    contribution_id integer NOT NULL REFERENCES ecosystem.contributions(id) ON DELETE CASCADE,
+    PRIMARY KEY (person_id, contribution_id)
+);
+
+-- PREPOPULATE ROLES
+INSERT INTO ecosystem.roles (name, description) VALUES
+  ('Student', 'Currently enrolled in an academic program'),
+  ('Researcher', 'Conducts academic or applied research'),
+  ('Developer', 'Writes and maintains software code'),
+  ('Leader', 'Leads research or development projects and mentors others'),
+  ('Collaborator', 'Contributes to joint projects'),
+ON CONFLICT (name) DO NOTHING;

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

@@ -380,6 +380,14 @@ 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",

cli/macrostrat/cli/database/migrations/people/main.sql

@@ -4,7 +4,10 @@
 
 from typer import Typer
 
+from macrostrat.cli.database import get_db
+
 from .match import import_sgp_data, log_matches
+from .migrations import *
 from .paleogeography import compute_paleo_positions
 
 sgp = Typer(
@@ -15,3 +18,17 @@
 sgp.command(name="match-units")(import_sgp_data)
 sgp.command(name="paleogeography")(compute_paleo_positions)
 sgp.command(name="log-matches")(log_matches)
+
+
+@sgp.command("import-data")
+def import_sgp_data():
+    """
+    Import SGP sample and analysis data.
+    """
+
+    db = get_db()
+
+    sql_dir = Path(__file__).parent / "sql"
+
+    db.run_sql(sql_dir / "create-fdw.sql")
+    db.run_sql(sql_dir / "copy-sgp-data.sql")