import datetime
from pathlib import Path
from immuneML.util.ReflectionHandler import ReflectionHandler
from immuneML.workflows.instructions.Instruction import Instruction
[docs]class SemanticModel:
def __init__(self, instructions: list, result_path: Path, output=None):
assert all(isinstance(instruction, Instruction) for instruction in instructions), \
"SemanticModel: error occurred in parsing: check instruction definitions in the configuration file."
self.instructions = instructions
self.result_path = result_path
self.output = output
[docs] def run(self):
instruction_states = self.run_instructions()
if self.output is not None:
self.build_reports(instruction_states)
return instruction_states
[docs] def build_reports(self, instruction_states):
report_builder = self.make_report_builder()
print(f"{datetime.datetime.now()}: Generating {self.output['format']} reports...", flush=True)
result_path = report_builder.build_from_objects(instruction_states, self.result_path)
print(f"{datetime.datetime.now()}: {self.output['format']} reports are generated.", flush=True)
return result_path
[docs] def run_instructions(self) -> list:
instruction_states = []
for index, instruction in enumerate(self.instructions):
print("{}: Instruction {}/{} has started.".format(datetime.datetime.now(), index+1, len(self.instructions)), flush=True)
result = instruction.run(result_path=self.result_path)
instruction_states.append(result)
print("{}: Instruction {}/{} has finished.".format(datetime.datetime.now(), index+1, len(self.instructions)), flush=True)
return instruction_states
[docs] def make_report_builder(self):
report_builder = ReflectionHandler.get_class_by_name(f"{self.output['format']}Builder", "presentation/")
return report_builder