old_contents: import pytest
  
  
  @pytest.fixture
  def file_no_replicate(testapp, experiment, award, lab):
      item = {
          'dataset': experiment['@id'],
          'lab': lab['@id'],
          'award': award['@id'],
          'file_format': 'bam',
          'md5sum': 'e002cd204df36d93dd070ef0712b8eed',
          'output_type': 'alignments',
          'status': 'in progress',  # avoid s3 upload codepath
      }
      return testapp.post_json('/file', item).json['@graph'][0]
  
  
  @pytest.fixture
  def file_with_replicate(testapp, experiment, award, lab, replicate):
      item = {
          'dataset': experiment['@id'],
          'replicate': replicate['@id'],
          'lab': lab['@id'],
          'award': award['@id'],
          'file_format': 'bam',
          'md5sum': 'e003cd204df36d93dd070ef0712b8eed',
          'output_type': 'alignments',
          'status': 'in progress',  # avoid s3 upload codepath
      }
      return testapp.post_json('/file', item).json['@graph'][0]
  
  
  @pytest.fixture
  def file_with_derived(testapp, experiment, award, lab, file_with_replicate):
      item = {
          'dataset': experiment['@id'],
          'lab': lab['@id'],
          'award': award['@id'],
          'file_format': 'bam',
          'md5sum': 'e004cd204df36d93dd070ef0712b8eed',
          'output_type': 'alignments',
          'status': 'in progress',  # avoid s3 upload codepath
          'derived_from': [file_with_replicate['@id']],
      }
      return testapp.post_json('/file', item).json['@graph'][0]
  
  
  def test_file_post(file_no_replicate):
      assert file_no_replicate['biological_replicates'] == []
  
  
  def test_file_with_replicate_post(file_with_replicate):
      assert file_with_replicate['biological_replicates'] == [1]
  
  
  def test_file_with_derived_from_post(testapp, file_with_derived):
      assert file_with_derived['biological_replicates'] == [1]
  
new_contents: import pytest
  
  
  @pytest.fixture
  def file_no_replicate(testapp, experiment, award, lab):
      item = {
          'dataset': experiment['@id'],
          'lab': lab['@id'],
          'award': award['@id'],
          'file_format': 'bam',
          'assembly': 'hg19',
          'md5sum': 'e002cd204df36d93dd070ef0712b8eed',
          'output_type': 'alignments',
          'status': 'in progress',  # avoid s3 upload codepath
      }
      return testapp.post_json('/file', item).json['@graph'][0]
  
  
  @pytest.fixture
  def file_with_replicate(testapp, experiment, award, lab, replicate):
      item = {
          'dataset': experiment['@id'],
          'replicate': replicate['@id'],
          'lab': lab['@id'],
          'award': award['@id'],
          'file_format': 'bam',
          'assembly': 'hg19',
          'md5sum': 'e003cd204df36d93dd070ef0712b8eed',
          'output_type': 'alignments',
          'status': 'in progress',  # avoid s3 upload codepath
      }
      return testapp.post_json('/file', item).json['@graph'][0]
  
  
  @pytest.fixture
  def file_with_derived(testapp, experiment, award, lab, file_with_replicate):
      item = {
          'dataset': experiment['@id'],
          'lab': lab['@id'],
          'award': award['@id'],
          'file_format': 'bam',
          'assembly': 'hg19',
          'md5sum': 'e004cd204df36d93dd070ef0712b8eed',
          'output_type': 'alignments',
          'status': 'in progress',  # avoid s3 upload codepath
          'derived_from': [file_with_replicate['@id']],
      }
      return testapp.post_json('/file', item).json['@graph'][0]
  
  
  def test_file_post(file_no_replicate):
      assert file_no_replicate['biological_replicates'] == []
  
  
  def test_file_with_replicate_post(file_with_replicate):
      assert file_with_replicate['biological_replicates'] == [1]
  
  
  def test_file_with_derived_from_post(testapp, file_with_derived):
      assert file_with_derived['biological_replicates'] == [1]
  
subject: Update audit fixtures to have assembly in bams