Skip to content

mihcsme_py.writer#

mihcsme_py.writer #

Write MIHCSME metadata to Excel format.

write_metadata_to_excel(metadata: MIHCSMEMetadata, output_path: Union[Path, BinaryIO]) -> None #

Write MIHCSME metadata to Excel file.

All sheets are always written, even if empty, so the file can be used as a template. The AssayConditions sheet uses default column headers when no conditions are present.

:param metadata: MIHCSMEMetadata object to export :param output_path: Path to output Excel file, or a file-like object (e.g., BytesIO)

Source code in src/mihcsme_py/writer.py 
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
def write_metadata_to_excel(
    metadata: MIHCSMEMetadata, output_path: Union[Path, BinaryIO]
) -> None:
    """
    Write MIHCSME metadata to Excel file.

    All sheets are always written, even if empty, so the file can be used as
    a template. The AssayConditions sheet uses default column headers when no
    conditions are present.

    :param metadata: MIHCSMEMetadata object to export
    :param output_path: Path to output Excel file, or a file-like object (e.g., BytesIO)
    """
    wb = Workbook()
    # Remove default sheet
    if "Sheet" in wb.sheetnames:
        wb.remove(wb["Sheet"])

    # Write Investigation Information (always)
    groups = metadata.investigation_information.groups if metadata.investigation_information else {}
    _write_grouped_sheet(
        wb,
        "InvestigationInformation",
        groups,
        header_comment="# Investigation Information - Metadata about the overall investigation"
    )

    # Write Study Information (always)
    groups = metadata.study_information.groups if metadata.study_information else {}
    _write_grouped_sheet(
        wb,
        "StudyInformation",
        groups,
        header_comment="# Study Information - Metadata about the study design"
    )

    # Write Assay Information (always)
    groups = metadata.assay_information.groups if metadata.assay_information else {}
    _write_grouped_sheet(
        wb,
        "AssayInformation",
        groups,
        header_comment="# Assay Information - Metadata about the assay protocol"
    )

    # Write Assay Conditions (always)
    _write_assay_conditions(wb, metadata.assay_conditions)

    # Write Reference Sheets
    for ref_sheet in metadata.reference_sheets:
        _write_reference_sheet(wb, ref_sheet.name, ref_sheet.data)

    # Save workbook
    wb.save(output_path)