Add a starter CLI for a self-check script

augur/application/cli/_cli_util.py

@@ -4,6 +4,7 @@
 import psutil
 import signal
 from urllib.parse import urlparse
+import sqlalchemy as s
 
 from augur.tasks.init.redis_connection import get_redis_connection
 
@@ -69,4 +70,21 @@ def raise_open_file_limit(num_files):
 
     resource.setrlimit(resource.RLIMIT_NOFILE, (num_files, current_hard))
 
-    return
+    return
+
+def get_db_version(engine):
+    """ a helper function to return the database version
+    used in print_db_version and upgrade_db_version in the db cli module
+    """
+
+    db_version_sql = s.sql.text(
+        """
+        SELECT * FROM augur_operations.augur_settings WHERE setting = 'augur_data_version'
+        """
+    )
+
+    with engine.connect() as connection:
+        result = int(connection.execute(db_version_sql).fetchone()[2])
+
+    engine.dispose()
+    return result

augur/application/cli/db.py

@@ -29,6 +29,8 @@
     process_repo_group_csv,
 )
 
+from ._cli_util import get_db_version
+
 logger = logging.getLogger(__name__)
 
 
@@ -258,21 +260,6 @@ def add_github_org(ctx, organization_name):
         controller.add_cli_org(organization_name)
 
 
-# get_db_version is a helper function to print_db_version and upgrade_db_version
-def get_db_version(engine):
-    db_version_sql = s.sql.text(
-        """
-        SELECT * FROM augur_operations.augur_settings WHERE setting = 'augur_data_version'
-        """
-    )
-
-    with engine.connect() as connection:
-        result = int(connection.execute(db_version_sql).fetchone()[2])
-
-    engine.dispose()
-    return result
-
-
 @cli.command("print-db-version")
 @test_connection
 @test_db_connection

augur/application/cli/selftest.py

@@ -0,0 +1,51 @@
+# SPDX-License-Identifier: MIT
+import logging
+import click
+import sqlalchemy as s
+from sqlalchemy import select, func
+
+from augur.application.cli import (
+    test_connection,
+    test_db_connection,
+    with_database,
+    DatabaseContext,
+)
+from augur.application.db.models.augur_data import Commit
+
+# from augur.application.db.session import DatabaseSession
+from datetime import datetime
+from augur.application.db.models import Repo
+
+from ._cli_util import get_db_version
+
+
+logger = logging.getLogger(__name__)
+
+
+@click.group("selftest", short_help="Augur self-testing utilities")
+@click.pass_context
+def cli(ctx):
+    ctx.obj = DatabaseContext()
+
+
+@cli.command("report")
+@test_connection
+@test_db_connection
+@with_database
+@click.pass_context
+def run_selftest_report(ctx):
+    """
+    Run queries to evaluate various aspects of the augur system's functioning and produce a report
+    """
+    click.echo('Generating Augur selftest report....')
+
+    cmt_author_name_issue_3740_query = (
+        select(func.count())
+        .select_from(Commit)
+        .where(Commit.cmt_author_name == '')
+    )
+    cmt_author_name_issue_3740_count = None
+
+    with ctx.obj.engine.begin() as connection:
+        cmt_author_name_issue_3740_count = connection.execute(cmt_author_name_issue_3740_query).scalar_one()
+        click.echo(f'Issue 3740 count: {cmt_author_name_issue_3740_count} commit files in the `commits` table contain authors with an empty string as their name')