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Revert "Raise a helpful error when a datatype cannot be found in a schema" #1300

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merged 1 commit into from
Sep 21, 2023
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Revert "Raise a helpful error when a datatype cannot be found in a schema" #1300

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21 changes: 5 additions & 16 deletions schematic/manifest/generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,11 +54,7 @@ def __init__(
self.creds = services_creds["creds"]

# schema root
if root:
self.root = root
# Raise an error if no DataType has been provided
else:
raise ValueError("No DataType has been provided.")
self.root = root

# alphabetize valid values
self.alphabetize = alphabetize_valid_values
Expand All @@ -83,19 +79,12 @@ def __init__(

# additional metadata to add to manifest
self.additional_metadata = additional_metadata

# Check if the class is in the schema
root_in_schema = self.sg.se.is_class_in_schema(self.root)

# If the class could not be found, give a notification
if not root_in_schema:
exception_message = f"The DataType entered ({self.root}) could not be found in the data model schema. " + \
"Please confirm that the datatype is in the data model and that the spelling matches the class label in the .jsonld file."
raise LookupError(exception_message)

# Determine whether current data type is file-based
self.is_file_based = "Filename" in self.sg.get_node_dependencies(self.root)

is_file_based = False
if self.root:
is_file_based = "Filename" in self.sg.get_node_dependencies(self.root)
self.is_file_based = is_file_based

def _attribute_to_letter(self, attribute, manifest_fields):
"""Map attribute to column letter in a google sheet"""
Expand Down
27 changes: 4 additions & 23 deletions tests/test_manifest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,34 +87,13 @@ def test_init(self, helpers):
generator = ManifestGenerator(
title="mock_title",
path_to_json_ld=helpers.get_data_path("example.model.jsonld"),
root = "Patient"
)

assert type(generator.title) is str
# assert generator.sheet_service == mock_creds["sheet_service"]
assert generator.root is "Patient"
assert generator.root is None
assert type(generator.sg) is SchemaGenerator

@pytest.mark.parametrize("data_type, exc, exc_message",
[("MissingComponent", LookupError, "could not be found in the data model schema"),
(None, ValueError, "No DataType has been provided.")],
ids = ["DataType not found in Schema", "No DataType provided"])
def test_missing_root_error(self, helpers, data_type, exc, exc_message):
"""
Test for errors when either no DataType is provided or when a DataType is provided but not found in the schema
"""

# A LookupError should be raised and include message when the component cannot be found
with pytest.raises(exc) as e:
generator = ManifestGenerator(
path_to_json_ld=helpers.get_data_path("example.model.jsonld"),
root=data_type,
use_annotations=False,
)

# Check message contents
assert exc_message in str(e)

@pytest.mark.google_credentials_needed
def test_get_manifest_first_time(self, manifest):

Expand Down Expand Up @@ -166,7 +145,7 @@ def test_get_manifest_first_time(self, manifest):
# An annotation merged with an attribute from the data model
if use_annotations:
assert output["File Format"].tolist() == ["txt", "csv", "fastq"]

@pytest.mark.parametrize("output_format", [None, "dataframe", "excel", "google_sheet"])
@pytest.mark.parametrize("sheet_url", [None, True, False])
@pytest.mark.parametrize("dataset_id", [None, "syn27600056"])
Expand Down Expand Up @@ -433,3 +412,5 @@ def test_populate_existing_excel_spreadsheet(self, simple_manifest_generator, si
# remove file
os.remove(dummy_output_path)



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