from pathlib import Path
from immuneML.data_model.dataset.Dataset import Dataset
from immuneML.data_model.dataset.ReceptorDataset import ReceptorDataset
from immuneML.data_model.dataset.RepertoireDataset import RepertoireDataset
from immuneML.data_model.dataset.SequenceDataset import SequenceDataset
from immuneML.reports.ReportOutput import ReportOutput
from immuneML.reports.ReportResult import ReportResult
from immuneML.reports.data_reports.DataReport import DataReport
from immuneML.util.PathBuilder import PathBuilder
[docs]class SimpleDatasetOverview(DataReport):
"""
Generates a simple text-based overview of the properties of any dataset, including the dataset name, size, and metadata labels.
YAML specification:
.. indent with spaces
.. code-block:: yaml
reports:
my_overview: SimpleDatasetOverview
"""
UNKNOWN_CHAIN = "unknown"
def __init__(self, dataset: Dataset = None, result_path: Path = None, number_of_processes: int = 1, name: str = None):
super().__init__(dataset=dataset, result_path=result_path, number_of_processes=number_of_processes, name=name)
[docs] @classmethod
def build_object(cls, **kwargs):
return SimpleDatasetOverview(**kwargs)
def _generate(self) -> ReportResult:
PathBuilder.build(self.result_path)
text_path = self.result_path / "dataset_description.txt"
dataset_name = self.dataset.name if self.dataset.name is not None else self.dataset.identifier
output_text = self._get_generic_dataset_text()
if isinstance(self.dataset, RepertoireDataset):
output_text += self._get_repertoire_dataset_text()
elif isinstance(self.dataset, ReceptorDataset):
output_text += self._get_receptor_dataset_text()
elif isinstance(self.dataset, SequenceDataset):
output_text += self._get_sequence_dataset_text()
text_path.write_text(output_text)
return ReportResult(name=self.name,
info="A simple text-based overview of the properties of any dataset, including the dataset name, size, and metadata labels.",
output_text=[ReportOutput(text_path, f"Description of dataset {dataset_name}")])
def _get_generic_dataset_text(self):
element_name = type(self.dataset).__name__.replace("Dataset", "s").lower()
output_text = f"Dataset name: {self.dataset.name}\n" \
f"Dataset identifier: {self.dataset.identifier}\n" \
f"Dataset type: {type(self.dataset).__name__}\n" \
f"Dataset size: {self.dataset.get_example_count()} {element_name}\n" \
f"Labels available for classification:"
if len(self.dataset.get_label_names()) == 0:
output_text += " None"
else:
for label in self.dataset.get_label_names():
output_text += "\n - " + label
return output_text
def _get_repertoire_dataset_text(self):
output_text = f"\nmetadata file location: {self.dataset.metadata_file}\n"
output_text += "\n\nProperties per repertoire:\n"
for repertoire in self.dataset.repertoires:
output_text += f"- Name: {repertoire.data_filename.name}\n"
output_text += f" Number of sequences: {repertoire.get_element_count()}\n"
chains = [chain.value if chain else SimpleDatasetOverview.UNKNOWN_CHAIN for chain in set(repertoire.get_chains())]
if len(chains) == 1:
output_text += f" Chain type: {chains[0]}\n"
else:
output_text += f" Chain types: {','.join(chains)}\n"
return output_text
def _get_receptor_dataset_text(self):
receptor_types = list(set([type(receptor).__name__ for receptor in self.dataset.get_data()]))
if len(receptor_types) > 1:
output_text = "\nReceptor types: " + ",".join(receptor_types)
else:
output_text = "\nReceptor type: " + receptor_types[0]
return output_text
def _get_sequence_dataset_text(self):
chains = list(set([sequence.get_attribute("chain") for sequence in self.dataset.get_data()]))
chains = [chain.value if chain else SimpleDatasetOverview.UNKNOWN_CHAIN for chain in chains]
if len(chains) > 1:
output_text = "\nChain types: " + ",".join(chains)
else:
output_text = "\nChain type: " + chains[0]
return output_text