# quality: gold
import os
from pathlib import Path
from immuneML.caching.CacheType import CacheType
from immuneML.environment.Constants import Constants
from immuneML.environment.SequenceType import SequenceType
from immuneML.util.Logger import print_log
from immuneML.util.PathBuilder import PathBuilder
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class EnvironmentSettings:
"""
Class containing environment variables, like receptor_sequence type,
root path etc.
"""
sequence_type = SequenceType.AMINO_ACID
root_path = Path(os.path.normpath(os.path.dirname(os.path.abspath(__file__)) + "/../../") + "/")
default_params_path = root_path / "immuneML/config/default_params"
tmp_test_path = root_path / "test/tmp"
default_analysis_path = root_path / "analysis_runs"
cache_path = root_path / "cache"
tmp_cache_path = tmp_test_path / "cache"
html_templates_path = root_path / "immuneML/presentation/html/templates"
specs_docs_path = root_path / "docs/specs"
source_docs_path = root_path / "docs/source"
max_sequence_length = 20
low_memory = True
compairr_paths = [Path("/usr/local/bin/compairr"), Path("./compairr/src/compairr"), root_path / 'compairr/src/compairr']
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@staticmethod
def reset_cache_path():
EnvironmentSettings.cache_path = EnvironmentSettings.root_path / "cache"
del os.environ[Constants.CACHE_PATH]
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@staticmethod
def set_cache_path(path: Path):
EnvironmentSettings.cache_path = Path(path)
PathBuilder.build(path)
os.environ[Constants.CACHE_PATH] = str(EnvironmentSettings.cache_path)
print_log(f"Setting temporary cache path to {path}", include_datetime=True)
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@staticmethod
def get_cache_type():
if Constants.CACHE_TYPE not in os.environ:
os.environ[Constants.CACHE_TYPE] = CacheType.PRODUCTION.name
return CacheType[os.environ[Constants.CACHE_TYPE].upper()]
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@staticmethod
def get_cache_path(cache_type: CacheType = None):
cache_type = EnvironmentSettings.get_cache_type() if cache_type is None else cache_type
if cache_type == CacheType.PRODUCTION:
return EnvironmentSettings.cache_path if Constants.CACHE_PATH not in os.environ else Path(os.environ[Constants.CACHE_PATH])
elif cache_type == CacheType.TEST:
return EnvironmentSettings.tmp_cache_path
else:
raise RuntimeError("Cache is not set up.")
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@staticmethod
def set_sequence_type(sequence_type: SequenceType):
EnvironmentSettings.sequence_type = sequence_type
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@staticmethod
def get_sequence_type() -> SequenceType:
return EnvironmentSettings.sequence_type
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@staticmethod
def get_sequence_alphabet(sequence_type: SequenceType = None):
"""
:return: alphabetically sorted receptor_sequence alphabet
"""
seq_type = sequence_type if sequence_type is not None else EnvironmentSettings.sequence_type
if seq_type == SequenceType.AMINO_ACID:
alphabet = list("ACDEFGHIKLMNPQRSTVWY")
alphabet.sort()
elif seq_type == SequenceType.NUCLEOTIDE:
alphabet = list("ACGT")
alphabet.sort()
else:
raise RuntimeError("EnvironmentSettings: the sequence alphabet cannot be obtained if sequence_type was not set properly. "
f"Expected AMINO_ACID or NUCLEOTIDE, but got {seq_type} instead.")
return alphabet