def test_export_run():
'''Test the NCBImetaExport application for run completion'''
# Use the test database
test_db = os.path.join(os.path.dirname(os.path.abspath(__file__)),"test.sqlite")
test_output_dir = os.path.dirname(os.path.abspath(__file__))
# If the test_db doesn't alread exist, run the test cmd from test_ncbimeta
if not os.path.exists(test_db): test_ncbimeta.test_ncbimeta_run()
test_cmd = ("ncbimeta/NCBImetaExport.py --database " + test_db +
" --outputdir " + test_output_dir)
# test NCBImetaExport through a subprocess
returned_value = subprocess.call(test_cmd, shell=True)
# If it returns a non-zero value, it failed
assert returned_value == 0
def test_annotatereplace_run():
'''Test the NCBImetaAnnotateReplace application for run completion'''
# Use the test database
test_db = os.path.join(os.path.dirname(os.path.abspath(__file__)),"test.sqlite")
test_annotfile = os.path.join(os.path.dirname(os.path.abspath(__file__)),'test_annot.txt')
# If the test_db doesn't alread exist, run the test cmd from test_ncbimeta
if not os.path.exists(test_db): test_ncbimeta.test_ncbimeta_run()
test_table = 'BioSample'
test_cmd = ("ncbimeta/NCBImetaAnnotateReplace.py --database " + test_db +
" --table " + test_table +
" --annotfile " + test_annotfile)
# test NCBImetaAnnotateReplace through a subprocess
returned_value = subprocess.call(test_cmd, shell=True)
# If it returns a non-zero value, it failed
assert returned_value == 0
def test_join_run():
'''Test the NCBImetaJoin application for run completion'''
# Use the test database
test_db = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"test.sqlite")
# If the test_db doesn't alread exist, run the test cmd from test_ncbimeta
if not os.path.exists(test_db): test_ncbimeta.test_ncbimeta_run()
test_anchor_table = 'BioSample'
test_final_table = 'Master'
test_accessory_table = "\'BioProject Assembly SRA Nucleotide\'"
test_unique_field = "\'BioSampleAccession BioSampleAccessionSecondary BioSampleBioProjectAccession\'"
test_cmd = ("ncbimeta/NCBImetaJoin.py --database " + test_db +
" --final " + test_final_table + " --anchor " +
test_anchor_table + " --accessory " + test_accessory_table +
" --unique " + test_unique_field)
# test NCBImetaJoin through a subprocess
returned_value = subprocess.call(test_cmd, shell=True)
# If it returns a non-zero value, it failed
assert returned_value == 0
def test_multi_match():
''' The ability to properly concatenate multiple matches'''
# Use the test database
test_db = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"test.sqlite")
# If the test_db doesn't alread exist, run the test cmd from test_ncbimeta
if not os.path.exists(test_db): test_ncbimeta.test_ncbimeta_run()
test_anchor_table = 'BioProject'
test_final_table = 'BioProjectNucleotide'
test_accessory_table = "Nucleotide"
test_unique_field = "BioProjectAccession"
test_cmd = ("ncbimeta/NCBImetaJoin.py --database " + test_db +
" --final " + test_final_table + " --anchor " +
test_anchor_table + " --accessory " + test_accessory_table +
" --unique " + test_unique_field)
# test NCBImetaJoin through a subprocess
returned_value = subprocess.call(test_cmd, shell=True)
# If it returns a non-zero value, it failed
assert returned_value == 0 #def test_join_ErrorDBNotExists():