def test_get_product(snapshot: Snapshot) -> None:
post_item: PostItem = {
"url": "tests/product_page.html",
"type": "silver-black/140 \" ″'MM",
"qty": 1,
"pa": "",
}
html = load_test_product_page_html(post_item["url"])
document = lxml.html.document_fromstring(html)
product = bc.get_product(document, post_item)
snapshot.assert_match(product)
def test_parse_config(snapshot: Snapshot, config_raw: dict):
"""
tests the function parse_config against a snapshot
"""
# GIVEN the raw MIP analysis config file
# WHEN getting the files used to build the bundle
mip_rna_parse_config = store_mip.parse_config(config_raw)
# THEN the result should contain the data to be stored in Housekeeper
snapshot.assert_match(mip_rna_parse_config)
def test_dry_sample(cli_runner, base_context, microbial_sample_id,
snapshot: Snapshot):
"""Test working dry command for sample"""
# GIVEN
# WHEN dry running a sample name
result = cli_runner.invoke(config_case, ["--dry", microbial_sample_id],
obj=base_context)
# THEN command should give us a json dump
assert result.exit_code == EXIT_SUCCESS
snapshot.assert_match(result.output)
def test_parse_files(mock_missing, snapshot: Snapshot, deliverables_raw: dict):
"""
tests the function parse_files against a snapshot
"""
# GIVEN the a MIP analysis deliverables file
mock_missing.return_value = False, []
pipeline = "wts"
# WHEN getting the files used to build the bundle
mip_files = store_base.parse_files(deliverables_raw, pipeline)
# THEN the result should contain the data to be stored in Housekeeper
snapshot.assert_match(mip_files)
def test_parse_sampleinfo_data(snapshot: Snapshot, files_raw):
"""
tests the function parse_sampleinfo_data against a snapshot
"""
# GIVEN the raw MIP sample info file
rna_sampleinfo = files_raw["rna_sampleinfo"]
# WHEN getting the smaple info used to build the bundle
mip_rna_parse_sampleinfo = store_mip.parse_sampleinfo(rna_sampleinfo)
# THEN the result should contain the data to be stored in Housekeeper
snapshot.assert_match(mip_rna_parse_sampleinfo)
def test_sample(cli_runner, base_context, microbial_sample_id, queries_path,
snapshot: Snapshot):
"""Test working command for sample"""
# GIVEN an existing queries path
Path(queries_path).mkdir(exist_ok=True)
# WHEN dry running a sample name
result = cli_runner.invoke(config_case, [microbial_sample_id],
obj=base_context)
# THEN command should give us a json dump
assert result.exit_code == EXIT_SUCCESS
outfilename = queries_path / microbial_sample_id
outfilename = outfilename.with_suffix(".json")
with open(outfilename, "r") as outputfile:
snapshot.assert_match(outputfile.readlines())
def test_parse_sampleinfo_rna_result_contents(snapshot: Snapshot,
files_raw: dict):
"""test parse_sampleinfo_rna using snapshot
Note: to retake all snapshots run `pytest --snapshot-update`
Args:
snapshot (Snapshot): a file with a snapshot of the correct test result, see
cg/cg/tests/snapshots/snap_test_apps_mip_files.py
files_raw (dict): dict of raw .yaml files
"""
# GIVEN an RNA sample info file
sampleinfo_raw = files_raw["rna_sampleinfo"]
# WHEN parsing the file
sampleinfo_data = files.parse_sampleinfo_rna(sampleinfo_raw)
# THEN the result should contains the data as specified by the MIP team
snapshot.assert_match(sampleinfo_data)
def test_build_bundle(
mock_missing,
mock_parse_files,
snapshot: Snapshot,
config_data: dict,
sampleinfo_data: dict,
deliverables_raw: dict,
):
"""
tests the function_build bundle against a snapshot
"""
# GIVEN the MIP analysis config data, the sampleinfo data and the deliverables file
# WHEN building the bundle
mock_missing.return_value = False, []
mock_parse_files.return_value = ["mock of parsed files"]
mip_rna_bundle = store_base.build_bundle(config_data, sampleinfo_data,
deliverables_raw)
# THEN the result should contain the data to be stored in Housekeeper
snapshot.assert_match(mip_rna_bundle)
def test_get_cells(snapshot: Snapshot) -> None:
order_items_per_user = load_test_order_items_per_user()
cells = spreadsheet.get_cells(order_items_per_user)
snapshot.assert_match(cells)
def test_get_post_items_per_user(snapshot: Snapshot) -> None:
bc_number = 150
posts = load_test_posts()
post_items_per_user = wtos.get_post_items_per_user(bc_number, posts)
snapshot.assert_match(post_items_per_user)
