Dynamic errors

[siberianisaev]

import cap_upload_validator.errors as err


def main():
    e = err.CapMultiException()

    # File errors
    e.append(err.BadAnnDataFile())

    # X
    e.append(err.AnnDataMissingCountMatrix())
    e.append(err.AnnDataInvalidCountMatrix())
    e.append(err.CSCMatrixInX(locations=["adata.X", "adata.raw.X"]))

    # Embeddings
    e.append(err.AnnDataMissingEmbeddings())

    # Obs
    e.append(err.AnnDataMissingObs())

    e.append(
        err.AnnDataMissingObsColumns(
            missing_columns=["organism", "assay", "tissue"]
        )
    )

    e.append(
        err.AnnDataEmptyOrNoneInGeneralMetadata(
            none_columns=["organism", "assay"],
            empty_columns=["tissue"],
        )
    )

    # Var
    e.append(err.AnnDataMissingVarIndex())
    e.append(err.AnnDataNumericVarIndex())
    e.append(err.AnnDataVarNotSubsetOfRawVar())
    e.append(err.AnnDataGeneIndexIsNotUnique())

    e.append(err.AnnDataNonStandardVarError())
    e.append(err.AnnDataUnsupportedGenes(missing_genes_count=42))

    if e.have_errors():
        raise e


if __name__ == "__main__":
    try:
        main()
    except err.CapMultiException as ex:
        print("\n=================================\n")
        print(str(ex))
        print("\n=================================\n")

CapMultiException:

BadAnnDataFile: The file format is not supported!

AnnDataMissingCountMatrix: Matrix is missing in both `.X` and `.raw.X`.

AnnDataInvalidCountMatrix: Raw counts matrix values must be non-negative integers.

CSCMatrixInX: A CSC matrix is found in adata.X and adata.raw.X. The gene expression matrix must be stored in CSR or dense format!

AnnDataMissingEmbeddings: Embeddings are missing or incorrectly formatted. They must be stored in `.obsm` as [n_cells × 2] datasets with names starting with 'X_' (e.g., X_umap, X_tsne).

AnnDataMissingObs: The `.obs` is missing.

AnnDataMissingObsColumns: Required `.obs` metadata is missing. The file must contain 'assay', 'disease', 'organism', 'tissue' or corresponding '<x>_ontology_term_id' fields.
Missing columns: organism, assay, tissue

AnnDataEmptyOrNoneInGeneralMetadata: Required `.obs` metadata contains missing or invalid values.
All required fields must be filled with valid values.
Columns with None / NaN values: assay, organism
Columns with empty values: tissue

AnnDataMissingVarIndex: The `.var.index` is missing or empty.

AnnDataNumericVarIndex: The `.var.index` contains numeric values instead of gene identifiers.

AnnDataVarNotSubsetOfRawVar: `var.index` must be a subset of `raw.var.index`.

AnnDataGeneIndexIsNotUnique: `var.index` must not contain duplicates.

AnnDataNonStandardVarError: Generic CAP exception

AnnDataUnsupportedGenes: File does not contain valid ENSEMBL terms in var.
We currently support only Homo sapiens and Mus musculus.
In the case of multiple species in the dataset, orthologous Homo sapiens genes are required.
If there are other species you wish to upload to CAP, please contact support@celltype.info and we will work to accommodate your request.
Number of unsupported genes found: 42

For details visit:
	https://github.com/cellannotation/cap-validator/wiki/Validation-Errors