def test_cli_validate_exec(
trace_gdf,
assume_error: rules.ValidationResults,
pandera_valid: bool,
database,
tmp_path_factory,
metadata_json: Path,
):
"""
Test tracerepo validate command with a set up of invalidated data.
"""
assert metadata_json.exists() and metadata_json.is_file()
area_gdf: gpd.GeoDataFrame = tests.kb11_area
tmp_path = tmp_path_factory.mktemp(basename="test_cli_validate_exec", numbered=True)
assert len(list(tmp_path.glob("*"))) == 0
# Make default directories
repo.scaffold(tmp_path)
organizer = tests.set_up_repo_with_invalids_organized(
database=database,
trace_gdf=trace_gdf,
area_gdf=area_gdf,
tracerepository_path=tmp_path,
)
database_csv_path: Path = tmp_path / rules.DATABASE_CSV
if database_csv_path.exists():
database_csv_path.unlink()
repo.write_database_csv(path=database_csv_path, database=organizer.database)
# Test if all column headers are in csv
database_text = database_csv_path.read_text()
database_first_line = database_text.splitlines()[0]
for column_enum in rules.ColumnNames:
assert column_enum.value in database_first_line.split(",")
result = runner.invoke(
app=app,
args=[
"validate",
"--report",
f"--metadata-json={metadata_json}",
f"--tracerepository-path={tmp_path}",
],
)
reports_path = Path(tmp_path) / Path(rules.PathNames.REPORTS.value)
if not pandera_valid:
assert reports_path.exists()
assert reports_path.is_dir()
assert len(list(reports_path.glob("*.html"))) > 0
# TODO: Inconsistent results here
if not "html" in result.output:
warn(f"Unknown error, html not found in result.output.")
tests.click_error_print(result)
# TODO: Inconsistent results here
if assume_error.value not in database_csv_path.read_text():
warn(f"Expected {assume_error.value} to be in {database_csv_path}.")
def test_fractopo_network_cli(traces_path, area_path, tmp_path):
"""
Test fractopo network cli entrypoint.
"""
tmp_path.mkdir(exist_ok=True)
result = typer_cli_runner.invoke(
cli.app,
[
"network",
str(traces_path),
str(area_path),
"--general-output",
str(tmp_path),
],
)
click_error_print(result)
output_files = list(tmp_path.glob("*"))
assert len(output_files) > 0
assert "branches" in str(output_files)
assert "nodes" in str(output_files)
assert len(list(tmp_path.glob("*.svg"))) > 0
def test_fractopo_network_cli(traces_path, area_path, determine_branches_nodes,
tmp_path):
"""
Test fractopo network cli entrypoint.
"""
tmp_path.mkdir(exist_ok=True)
result = typer_cli_runner.invoke(
cli.app,
[
"network",
str(traces_path),
str(area_path),
"--general-output",
str(tmp_path),
] + ([] if determine_branches_nodes else
["--no-determine-branches-nodes"]),
)
click_error_print(result)
output_files = list(tmp_path.glob("*"))
output_files_names = [path.name for path in output_files]
assert len(output_files) > 0
assert "branches" in str(output_files) or not determine_branches_nodes
assert "nodes" in str(output_files) or not determine_branches_nodes
assert len(list(tmp_path.glob("*.svg"))) > 0
assert "additional_numerical_data.json" in output_files_names
# Sanity check
assert "adddditional_numerical_data.json" not in output_files_names
def test_cli_app_help(subcommand: str):
"""
Test tracerepo cli help cmd.
"""
args = ["--help"]
if len(subcommand) > 0:
args.insert(0, subcommand)
assert isinstance(subcommand, str)
result: Result = runner.invoke(app=app, args=args)
tests.click_error_print(result=result)
def test_tracevalidate_only_area(args, tmp_path):
"""
Test tracevalidate script with --only-area-validation.
"""
outputs_cmds = ["--output", str(tmp_path / "output_traces")]
clirunner = TyperCliRunner()
result = clirunner.invoke(cli.app, ["tracevalidate"] + args + outputs_cmds)
# Check that exit code is 0 (i.e. ran successfully.)
click_error_print(result)
assert Path(outputs_cmds[1]).exists()
assert Validation.ERROR_COLUMN in gpd.read_file(outputs_cmds[1]).columns
def test_fractopo_callback(logging_level_str: str):
"""
Test .
"""
result = typer_cli_runner.invoke(
cli.app,
[
"--logging-level",
logging_level_str,
"info",
],
)
click_error_print(result=result)
def test_fractopo_callback_error(logging_level_str: str):
"""
Test .
"""
with pytest.raises(Exception):
result = typer_cli_runner.invoke(
cli.app,
[
"--logging-level",
logging_level_str,
"info",
],
)
click_error_print(result=result)
def test_cli_organize(database, trace_gdf, other_args, tmp_path_factory):
"""
Test cli_organize click entrypoint.
"""
area_gdf: gpd.GeoDataFrame = tests.kb11_area
tmp_path = tmp_path_factory.mktemp(basename="test_cli_organize", numbered=True)
other_args.append(f"--tracerepository-path={tmp_path}")
args = ["organize"] + other_args
# make default directories
repo.scaffold(tmp_path)
organizer = tests.set_up_repo_with_invalids_organized(
database=database,
trace_gdf=trace_gdf,
area_gdf=area_gdf,
organized=False,
tracerepository_path=tmp_path,
)
repo.write_database_csv(
path=tmp_path / rules.DATABASE_CSV, database=organizer.database
)
result = runner.invoke(app=app, args=args)
if "--simulate" not in args:
organizer.check()
if "--report" in args:
assert len(result.stdout) > 0
elif "--no-report" in args:
assert len(result.stdout) == 0
tests.click_error_print(result)
def test_tracevalidate_typer(
trace_path: Path,
area_path: Path,
auto_fix: str,
tmp_path: Path,
snap_threshold: float,
):
"""
Tests tracevalidate typer functionality.
"""
clirunner = TyperCliRunner()
output_file = tmp_path / f"{trace_path.stem}.{trace_path.suffix}"
cli_args = [
"tracevalidate",
str(trace_path),
str(area_path),
auto_fix,
"--output",
str(output_file),
"--summary",
"--snap-threshold",
# should be valid for both 0.01 and 0.001
str(snap_threshold),
]
result = clirunner.invoke(cli.app, cli_args)
# Check that exit code is 0 (i.e. ran successfully.)
click_error_print(result)
# Checks if output is saved
assert output_file.exists()
output_gdf = gpd.read_file(output_file)
assert isinstance(output_gdf, gpd.GeoDataFrame)
assert output_gdf.crs == gpd.read_file(trace_path).crs
assert Validation.ERROR_COLUMN in output_gdf.columns
if "--summary" in cli_args:
assert "Out of" in result.output
assert "There were" in result.output
def test_all_cli(ready_tracerepository: Path):
"""
Test all cli tools in ready-made tracerepository.
"""
metadata_json_path = ready_tracerepository / Path(rules.PathNames.METADATA.value)
database_csv_path = ready_tracerepository / Path(rules.DATABASE_CSV)
reports_path = ready_tracerepository / Path(rules.PathNames.REPORTS.value)
assert (metadata_json_path).exists()
assert (database_csv_path).exists()
# Read database.csv before execution
csv_text_before = database_csv_path.read_text()
# Assert that that what we expect is in database
assert rules.ValidationResults.VALID.value in csv_text_before
assert rules.ValidationResults.INVALID.value in csv_text_before
assert rules.ValidationResults.CRITICAL.value not in csv_text_before
# Run help and subcommands without arguments
for cmd in ("--help", "check", "organize", "format-geojson"):
# Run tracerepo --help
help_result = runner.invoke(
app=app,
args=[
cmd,
f"--tracerepository-path={ready_tracerepository}"
if "--help" not in cmd
else "",
],
)
tests.click_error_print(help_result)
# Run tracerepo validate
# Validate kb* and hastholmen infinity traces
validate_result = runner.invoke(
app=app,
args=[
"validate",
"--traces-filter=kb",
"--traces-filter=hastholmen",
"--report",
f"--metadata-json={metadata_json_path}",
f"--tracerepository-path={ready_tracerepository}",
],
)
# Make sure pandera error was caught
assert "Reported" in validate_result.stdout
assert "html" in validate_result.stdout
assert reports_path.exists()
assert len(list(reports_path.glob("*.html"))) > 0
# Test that there were no changes to database
csv_text_after = database_csv_path.read_text()
assert csv_text_after == csv_text_before
assert rules.ValidationResults.VALID.value in csv_text_after
assert rules.ValidationResults.INVALID.value in csv_text_after
assert rules.ValidationResults.CRITICAL.value not in csv_text_after
# Run tracerepo export
validate_result = runner.invoke(
app=app,
args=[
"export",
str(ready_tracerepository),
f"--tracerepository-path={ready_tracerepository}",
],
)
# Find export directory and check contents
found = []
for directory in ready_tracerepository.glob(f"{utils.EXPORT_DIR_PREFIX}*"):
found.append(directory)
if directory.is_dir():
# Verify contents
assert len(list(directory.rglob("*.shp"))) > 0
assert len(found) > 0