CLI improvements take 2

[eboileau]

A clear and concise description of todo items.

• [ ] flask metadata cannot handle CSV entries incl. header with blank spaces, etc.

• [ ] flask delete (FileService) should except/pass FileNotFoundError when removing a gene cache file if it does not exists.

• [ ] The "selection" handling in the CLI is relegated to cli.dataset, but in services this is under project, and delete_selection cannot be properly tested now, being in the CLI only. Maybe we should have it under project or dataset service, or eventually selection service or move this to utilities (where it would be accessible for project, dataset, CLI and tests).

• [ ] The order in which tables are deleted should matter, but if I change ProjectService.delete_project e.g. to delete project first, test_delete_project still completes successfuly, whereas it shoud not... Using on cascade would probably be more robust, but do we need to set it up in the model?

• [ ] Handle graceful exit on failure e.g. if annotating dataset with nonexistent taxa_id and version, see also below:

• flask project with e.g. nonexistent combination of taxa_id and cto

  Failed to create project: (MySQLdb.IntegrityError) (1452, 'Cannot add or update a child row: a foreign key constraint fails (`scimodom`.`organism`, CONSTRAINT `fk_organism_taxa_id_ncbi_taxa` FOREIGN KEY (`taxa_id`) REFERENCES `ncbi_taxa` (`id`))')
  [SQL: INSERT INTO organism (taxa_id, cto) VALUES (%s, %s)]
  [parameters: (10900, 'Cell')]
  (Background on this error at: https://sqlalche.me/e/20/gkpj)... skipping t1!

• FileNotFoundError: [Errno 2] No such file or directory: '/data/metadata/project_requests/bla.json'

• [ ] Is logging-level CLI-specific configurable? Check click-logging.

• [ ] When done, update CLI docs.

[eboileau]

We would also like to add CLI tests, something like

from scimodom.app import create_app
# w/ a redefinition of the config for testing
@pytest.fixture
def app():
    app = create_app()
    yield app

does not work for testing, because of setup_service.upsert_all() which does not work with sqlite

sqlalchemy.exc.UnsupportedCompilationError: Compiler <sqlalchemy.dialects.sqlite.base.SQLiteCompiler object at 0x7fa1256e2fd0> can't render element of type <class 'sqlalchemy.dialects.mysql.dml.OnDuplicateClause'> (Background on this error at: https://sqlalche.me/e/20/l7de)

We could try registering-commands-with-blueprints, this might work then with

@pytest.fixture()
def runner(app):
    return app.test_cli_runner()

but this needs to be tested (we want to have the application context pushed). Otherwise, we might just as well try custom scripts.