text: from argparse import Namespace
  import pytest
  from bifrostlib import common
  from bifrostlib import datahandling
  from bifrostlib import database_interface
  from bifrostlib.datahandling import ComponentReference
  from bifrostlib.datahandling import Component
  from bifrostlib.datahandling import SampleReference
  from bifrostlib.datahandling import Sample
  from bifrostlib.datahandling import RunReference
  from bifrostlib.datahandling import Run
  from bifrost_ssi_stamper import launcher
  import pymongo
  import os
  import shutil
  
  
  @pytest.fixture
  def test_connection():
      assert datahandling.has_a_database_connection()
      assert "TEST" in os.environ['BIFROST_DB_KEY'].upper()  # A very basic piece of protection ensuring the word test is in the DB
  
  class TestBifrostMinReadCheck:
      component_name = "ssi_stamper__v2_2_12"
      current_dir = os.getcwd()
      test_dir = "/bifrost/test_data/output/test__ssi_stamper/"
      json_entries = [
          {
              "_id": {"$oid": "000000000000000000000001"}, 
              "name": "S1", 
              "components": [], 
              "categories": {
                  "paired_reads": {
                      "summary": {
                          "data": ["/bifrost/test_data/samples/S1_R1.fastq.gz",
                                   "/bifrost/test_data/samples/S1_R2.fastq.gz"]
                      }
                  },
                  'species_detection': {
                      'summary': {
                          'species': 'Staphylococcus aureus', "detected_species": "Staphylococcus aureus"
                          }
                  }
              }
          }
      ]
      bson_entries = [database_interface.json_to_bson(i) for i in json_entries]
  
      @classmethod
      def setup_class(cls):
          client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
          db = client.get_database()
          cls.clear_all_collections(db)
          col = db["samples"]
          col.insert_many(cls.bson_entries)
          launcher.initialize()
          os.chdir(cls.current_dir)
  
      @classmethod
      def teardown_class(cls):
          client = pymongo.MongoClient(os.environ['BIFROST_DB_KEY'])
          db = client.get_database()
          cls.clear_all_collections(db)
  
      @staticmethod
      def clear_all_collections(db):
          db.drop_collection("components")
          db.drop_collection("hosts")
          db.drop_collection("run_components")
          db.drop_collection("runs")
          db.drop_collection("sample_components")
          db.drop_collection("samples")
  
      def test_info(self):
          launcher.run_pipeline(["--info"])
  
      def test_help(self):
          launcher.run_pipeline(["--help"])
  
      def test_pipeline(self):
          if os.path.isdir(self.test_dir):
              shutil.rmtree(self.test_dir)
  
          os.mkdir(self.test_dir)
          test_args = [
              "--sample_name", "S1",
              "--outdir", self.test_dir
          ]
          launcher.main(args=test_args)
          assert os.path.isfile(f"{self.test_dir}/{self.component_name}/datadump_complete")
          shutil.rmtree(self.test_dir)
          assert not os.path.isdir(f"{self.test_dir}/{self.component_name}")
  
  
  