hiv_workflow.lib.utils.project_data module

exception hiv_workflow.lib.utils.project_data.UnsupportedFileFormat

Bases: Exception

exception hiv_workflow.lib.utils.project_data.MissingRequiredWorksheet

Bases: Exception

exception hiv_workflow.lib.utils.project_data.IncompleteParameterSpecification

Bases: Exception

exception hiv_workflow.lib.utils.project_data.IncompleteAnalyzerSpecification

Bases: Exception

exception hiv_workflow.lib.utils.project_data.IncompleteDataSpecification

Bases: Exception

exception hiv_workflow.lib.utils.project_data.ParameterOutOfRange

Bases: Exception

exception hiv_workflow.lib.utils.project_data.InvalidAnalyzerWeight

Bases: Exception

exception hiv_workflow.lib.utils.project_data.AnalyzerSheetException

Bases: Exception

exception hiv_workflow.lib.utils.project_data.SiteNodeMappingException

Bases: Exception

exception hiv_workflow.lib.utils.project_data.ObsMetadataException

Bases: Exception

hiv_workflow.lib.utils.project_data.get_ingest_information(ingest_filename: str) → Tuple[dict, hiv_workflow.lib.analysis.hiv_calib_site.HIVCalibSite]

Returns a dictionary and a HIVCalibSite drawn from parsing the given ingest xlsm file :param ingest_filename: xlsm file to parse for ingest info

Returns: a dict of parsed ingest information and a HIVCalibSite object

hiv_workflow.lib.utils.project_data.get_sheet_from_workbook(wb: openpyxl.workbook.workbook.Workbook, sheet_name: str, wb_path: str) → openpyxl.worksheet.worksheet.Worksheet

Obtains a Worksheet from the given Workbook by name :param wb: a Workbook to get a Worksheet from :param sheet_name: name of sheet to retrieve :param wb_path: path of workbook (for error reporting)

Returns: the requested Worksheet

hiv_workflow.lib.utils.project_data.parse_ingest_data_from_xlsm(filename: str) → Tuple[List[dict], dict, hiv_workflow.lib.analysis.population_obs.PopulationObs, List[dict], List[hiv_workflow.lib.analysis.channel.Channel]]

Parses an ingest xlsm file into various types of information :param filename: xlsm file to parse for ingest info

Returns: parsed ingest information