immuneML.presentation.html package

Submodules

immuneML.presentation.html.DatasetExportHTMLBuilder module

class immuneML.presentation.html.DatasetExportHTMLBuilder.DatasetExportHTMLBuilder[source]

Bases: object

CSS_PATH = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/immuneML/presentation/html/templates/css/custom.css')
static build_from_objects(state: immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState) → pathlib.Path[source]

Function that builds the HTML files based on the Simulation state. :param state: SimulationState object including all details of the Simulation instruction

Returns

path to the main HTML file (which is located under state.result_path)

static make_html_map(state: immuneML.workflows.instructions.dataset_generation.DatasetExportState.DatasetExportState, base_path: pathlib.Path) → dict[source]

immuneML.presentation.html.ExploratoryAnalysisHTMLBuilder module

class immuneML.presentation.html.ExploratoryAnalysisHTMLBuilder.ExploratoryAnalysisHTMLBuilder[source]

Bases: object

A class that will make a HTML file(s) out of ExploratoryAnalysisState object to show what analysis took place in the ExploratoryAnalysisInstruction.

CSS_PATH = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/immuneML/presentation/html/templates/css/custom.css')
static build_from_objects(state: immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState.ExploratoryAnalysisState) → pathlib.Path[source]

Function that builds the HTML files based on the ExploratoryAnalysis state. :param state: ExploratoryAnalysisState object with details and results of the instruction

Returns

path to the main HTML file (which is located under state.result_path)

static make_html_map(state: immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisState.ExploratoryAnalysisState, base_path: pathlib.Path) → dict[source]

immuneML.presentation.html.HPHTMLBuilder module

class immuneML.presentation.html.HPHTMLBuilder.HPHTMLBuilder[source]

Bases: object

A class that will make HTML file(s) out of TrainMLModelState object to show what analysis took place in the TrainMLModel.

CSS_PATH = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/immuneML/presentation/html/templates/css/custom.css')
NUM_DIGITS = 3
static build_from_objects(state: Optional[immuneML.hyperparameter_optimization.states.TrainMLModelState.TrainMLModelState] = None) → pathlib.Path[source]

Function that builds the HTML files based on the HPOptimization state. :param state: HPOptimizationState object with all details on the optimization

Returns

path to the main HTML file (index.html which is located under state.result_path)

immuneML.presentation.html.HTMLBuilder module

class immuneML.presentation.html.HTMLBuilder.HTMLBuilder[source]

Bases: object

Outputs HTML results of the analysis. This is currently the only defined format of presentation of results.

YAML specification:

definitions:
    ...
instructions:
    ...
output: # the output format
    format: HTML
static build_from_objects(states: list, path: pathlib.Path) → pathlib.Path[source]

immuneML.presentation.html.MLApplicationHTMLBuilder module

class immuneML.presentation.html.MLApplicationHTMLBuilder.MLApplicationHTMLBuilder[source]

Bases: object

CSS_PATH = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/immuneML/presentation/html/templates/css/custom.css')
static build_from_objects(state: Optional[immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState] = None) → str[source]
static make_html_map(state: immuneML.workflows.instructions.ml_model_application.MLApplicationState.MLApplicationState, base_path: pathlib.Path) → dict[source]

immuneML.presentation.html.MultiDatasetBenchmarkHTMLBuilder module

class immuneML.presentation.html.MultiDatasetBenchmarkHTMLBuilder.MultiDatasetBenchmarkHTMLBuilder[source]

Bases: object

CSS_PATH = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/immuneML/presentation/html/templates/css/custom.css')
static build_from_objects(report_results: dict, result_path: pathlib.Path, instruction_result_paths: dict) → pathlib.Path[source]

immuneML.presentation.html.SimulationHTMLBuilder module

class immuneML.presentation.html.SimulationHTMLBuilder.SimulationHTMLBuilder[source]

Bases: object

A class that will make a HTML file(s) out of SimulationState object to show what analysis took place in the SimulationInstruction.

CSS_PATH = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/immuneML/presentation/html/templates/css/custom.css')
static build_from_objects(state: immuneML.simulation.SimulationState.SimulationState) → str[source]

Function that builds the HTML files based on the Simulation state. :param state: SimulationState object including all details of the Simulation instruction

Returns

path to the main HTML file (which is located under state.result_path)

static make_html_map(state: immuneML.simulation.SimulationState.SimulationState, base_path: pathlib.Path) → dict[source]

immuneML.presentation.html.SubsamplingHTMLBuilder module

class immuneML.presentation.html.SubsamplingHTMLBuilder.SubsamplingHTMLBuilder[source]

Bases: object

A class that will make a HTML file(s) out of SubsamplingState object to show what analysis took place in the SubsamplingInstruction.

CSS_PATH = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/immuneML/presentation/html/templates/css/custom.css')
static build_from_objects(state: immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState) → str[source]

Function that builds the HTML files based on the Subsampling state. :param state: SubsamplingState object including all details of the Subsampling instruction

Returns

path to the main HTML file (which is located under state.result_path)

static make_html_map(state: immuneML.workflows.instructions.subsampling.SubsamplingState.SubsamplingState, base_path: pathlib.Path) → dict[source]

immuneML.presentation.html.Util module

class immuneML.presentation.html.Util.Util[source]

Bases: object

static get_css_content(css_path: pathlib.Path)[source]
static get_full_specs_path(base_path) → str[source]
static get_table_string_from_csv(csv_path: pathlib.Path, separator: str = ',', has_header: bool = True) → str[source]
static get_table_string_from_csv_string(csv_string: str, separator: str = ',', has_header: bool = True) → str[source]
static make_downloadable_zip(base_path: pathlib.Path, path_to_zip: pathlib.Path, filename: str = '') → str[source]
static to_dict_recursive(obj, base_path: pathlib.Path)[source]
static update_report_paths(report_result: immuneML.reports.ReportResult.ReportResult, path: pathlib.Path) → immuneML.reports.ReportResult.ReportResult[source]

Module contents