import copy
from pathlib import Path
from immuneML.dsl.instruction_parsers.LabelHelper import LabelHelper
from immuneML.dsl.symbol_table.SymbolTable import SymbolTable
from immuneML.dsl.symbol_table.SymbolType import SymbolType
from immuneML.encodings.kmer_frequency.KmerFreqSequenceEncoder import KmerFreqSequenceEncoder
from immuneML.encodings.kmer_frequency.KmerFrequencyEncoder import KmerFrequencyEncoder
from immuneML.encodings.word2vec.Word2VecEncoder import Word2VecEncoder
from immuneML.environment.LabelConfiguration import LabelConfiguration
from immuneML.ml_methods.dim_reduction.DimRedMethod import DimRedMethod
from immuneML.util.ParameterValidator import ParameterValidator
from immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisInstruction import ExploratoryAnalysisInstruction
from immuneML.workflows.instructions.exploratory_analysis.ExploratoryAnalysisUnit import ExploratoryAnalysisUnit
[docs]
class ExploratoryAnalysisParser:
"""
The specification consists of a list of analyses that need to be performed;
Each analysis is defined by a dataset identifier, a report identifier and optionally encoding and labels
and are loaded into ExploratoryAnalysisUnit objects;
DSL example for ExploratoryAnalysisInstruction assuming that d1, p1, r1, r2, e1, w1 are defined previously in definitions section:
.. highlight:: yaml
.. code-block:: yaml
instruction_name:
type: ExploratoryAnalysis
number_of_processes: 4
analyses:
my_first_analysis: # simple analysis running a report on a dataset
dataset: d1
report: r1
my_second_analysis: # more complicated analysis; including preprocessing, encoding, example weighting and running a report
dataset: d1
preprocessing_sequence: p1
encoding: e1
example_weighting: w1
report: r2
labels:
- CD
- CMV
"""
[docs]
def parse(self, key: str, instruction: dict, symbol_table: SymbolTable, path: Path = None) -> ExploratoryAnalysisInstruction:
exp_analysis_units = {}
ParameterValidator.assert_keys(instruction, ["analyses", "type", "number_of_processes"],
"ExploratoryAnalysisParser", "ExploratoryAnalysis")
ParameterValidator.assert_type_and_value(instruction["number_of_processes"], int,
ExploratoryAnalysisParser.__name__, "number_of_processes")
for analysis_key, analysis in instruction["analyses"].items():
params = self._prepare_params(analysis, symbol_table, f"{key}/{analysis_key}")
params["number_of_processes"] = instruction["number_of_processes"]
exp_analysis_units[analysis_key] = ExploratoryAnalysisUnit(**params)
process = ExploratoryAnalysisInstruction(exploratory_analysis_units=exp_analysis_units, name=key)
return process
def _prepare_params(self, analysis: dict, symbol_table: SymbolTable, yaml_location: str) -> dict:
valid_keys = ["dataset", "report", "preprocessing_sequence", "labels", "encoding", "example_weighting", "dim_reduction"]
ParameterValidator.assert_keys(list(analysis.keys()), valid_keys, "ExploratoryAnalysisParser", "analysis", False)
params = {"dataset": symbol_table.get(analysis["dataset"]), "report": copy.deepcopy(symbol_table.get(analysis["report"]))}
optional_params = self._prepare_optional_params(analysis, symbol_table, yaml_location)
params = {**params, **optional_params}
return params
def _prepare_optional_params(self, analysis: dict, symbol_table: SymbolTable, yaml_location: str) -> dict:
params = {}
dataset = symbol_table.get(analysis["dataset"])
loc = ExploratoryAnalysisParser.__name__
if "encoding" in analysis:
params["encoder"] = symbol_table.get(analysis["encoding"]).build_object(dataset, **symbol_table.get_config(analysis["encoding"])["encoder_params"])
if "labels" in analysis:
params["label_config"] = LabelHelper.create_label_config(analysis["labels"], dataset, loc, yaml_location)
else:
params["label_config"] = LabelConfiguration()
if "preprocessing_sequence" in analysis:
params["preprocessing_sequence"] = symbol_table.get(analysis["preprocessing_sequence"])
if "example_weighting" in analysis:
params["example_weighting"] = symbol_table.get(analysis["example_weighting"]).build_object(dataset, **symbol_table.get_config(analysis["example_weighting"])["example_weighting_params"])
if "dim_reduction" in analysis:
valid_dim_reductions = {el.symbol: el.item for el in symbol_table.get_by_type(SymbolType.ML_METHOD)
if isinstance(el.item, DimRedMethod)}
ParameterValidator.assert_in_valid_list(analysis["dim_reduction"], list(valid_dim_reductions.keys()),
ExploratoryAnalysisParser.__name__, "dim_reduction")
params["dim_reduction"] = copy.deepcopy(valid_dim_reductions[analysis['dim_reduction']])
assert isinstance(params["encoder"], (KmerFreqSequenceEncoder, Word2VecEncoder)), \
(f"{loc}: {yaml_location}: Only KmerFrequency and Word2Vec are valid encoders when doing dimensionality"
f" reduction.")
return params