def test_quast_complete_run_through():
app = app_helper.setup_app_state('quast', 'execute')
image_helper.execute_image(app)
file_helper.assert_is_file(
fs.get_task_file_path(app, 'outputs/assembly_metrics/684281f282'))
file_helper.assert_is_file(
fs.get_task_file_path(app, 'outputs/container_log/86bbc499b0'))
def test_gaet_complete_run_through():
app = app_helper.setup_app_state('gaet', 'execute')
image_helper.execute_image(app)
file_helper.assert_is_file(
fs.get_task_file_path(app, 'outputs/assembly_metrics/d70c163200'))
file_helper.assert_is_file(
fs.get_task_file_path(app, 'outputs/container_log/1661337965'))
def test_fetch_short_read_assembler_input_files():
db_helper.reset_database()
app = app_helper.setup_app_state('sra', 'task')
fetch.create_input_files(app)
file_helper.assert_is_file(
app["path"] +
"/inputs/short_read_fastq/24b5b01b08482053d7d13acd514e359fb0b726f1e8ae36aa194b6ddc07335298.fq.gz"
)
def test_fetch_reference_assembler_input_files():
db_helper.reset_database()
app = app_helper.setup_app_state('quast', 'task')
fetch.create_input_files(app)
file_helper.assert_is_file(
app["path"] +
"/inputs/reference_fasta/6bac51cc35ee2d11782e7e31ea1bfd7247de2bfcdec205798a27c820b2810414.fa.gz"
)
file_helper.assert_is_file(
app["path"] +
"/inputs/contig_fasta/57601ff10b7faf7fcf53a7268e3615db58088db34eb8e8bf31cb475c24381451.fa"
)
def test_failing_image_with_no_outputs():
image = {
"name": "bioboxes/crash-test-biobox",
"sha256":
"eaf1ab35314712db9d3fff0d265613629fe628ed9b058a9a4fe94424184f8c41",
"task": "exit-1",
"type": "short_read_assembler"
}
app = app_helper.setup_app_state('sra', 'inputs')
app["task"]["image"] = image
app_helper.rewrite_app_task(app)
image_helper.execute_image(app)
file_helper.assert_is_file(
fs.get_task_file_path(
app, 'outputs/container_runtime_metrics/metrics.json.gz'))
def test_fetch_reference_assembler_input_files_with_short_contigs():
db_helper.reset_database()
app = app_helper.setup_app_state('quast_short_contigs', 'task')
fetch.create_input_files(app)
# If the short contig are filtered as part of the download process, the input
# file should have the same SHA256 as the contig.fa without the short contigs.
file_helper.assert_is_file(
app["path"] +
"/inputs/contig_fasta/de3d9f6d31285985139aedd9e3f4b4ad04dadb4274c3c0ce28261a8e8e542a0f.fa"
)
file_helper.assert_is_not_file(
app["path"] +
"/inputs/contig_fasta/1ff29bcb6940b7d629d2d070fd67b23604e3459c9fd0167cdb6d1dcb26966c87.fa"
)
file_helper.assert_is_not_file(
app["path"] +
"/inputs/contig_fasta/1ff29bcb6940b7d629d2d070fd67b23604e3459c9fd0167cdb6d1dcb26966c87.fa.fai"
)
def test_complete_run_through():
app = app_helper.setup_app_state('sra', 'inputs')
image_helper.execute_image(app)
file_helper.assert_is_file(fs.get_task_file_path(app, 'outputs/contig_fasta/01eb7cec61'))
file_helper.assert_is_file(fs.get_task_file_path(app, 'outputs/container_runtime_metrics/metrics.json.gz'))
file_helper.assert_is_file(fs.get_task_file_path(app, 'outputs/container_log/1099992390'))
def test_fetch_file():
src = "s3://nucleotides-testing/short-read-assembler/6bac51cc35ee2d11782e7e31ea1bfd7247de2bfcdec205798a27c820b2810414"
dst = os.path.join(tempfile.mkdtemp(), 'dummy_file')
s3.fetch_file(src, dst)
file_helper.assert_is_file(dst)
def test_copy_output_files():
app = app_helper.setup_app_state('sra', 'intermediates')
run.copy_output_files(app)
file_helper.assert_is_file(fs.get_task_file_path(app, 'outputs/container_log/e0e8af3790'))
file_helper.assert_is_file(fs.get_task_file_path(app, 'outputs/contig_fasta/de3d9f6d31'))
def test_get_task_metadata_with_no_metadata_json():
app = app_helper.setup_app_state('sra')
metadata = util.get_task_metadata("1", app)
nose.assert_in("id", metadata)
file_helper.assert_is_file(app["path"] + "/metadata.json")