From b3840422fb6196a5b59d073c5cb29e4814c1a456 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 5 Feb 2018 16:32:13 -0500
Subject: [PATCH] better handling of default class1 models configuration
---
mhcflurry/class1_affinity_predictor.py | 4 +--
mhcflurry/downloads.py | 36 +++++++++++++++++++++++++-
mhcflurry/downloads_command.py | 6 ++---
mhcflurry/predict_command.py | 6 ++---
4 files changed, 42 insertions(+), 10 deletions(-)
diff --git a/mhcflurry/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
index 3eb2bfb6..fb19b09f 100644
--- a/mhcflurry/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -18,7 +18,7 @@ from six import string_types
from .class1_neural_network import Class1NeuralNetwork
from .common import random_peptides
-from .downloads import get_path
+from .downloads import get_default_class1_models_dir
from .encodable_sequences import EncodableSequences
from .percent_rank_transform import PercentRankTransform
from .regression_target import to_ic50
@@ -283,7 +283,7 @@ class Class1AffinityPredictor(object):
`Class1AffinityPredictor` instance
"""
if models_dir is None:
- models_dir = get_path("models_class1", "models")
+ models_dir = get_default_class1_models_dir()
manifest_path = join(models_dir, "manifest.csv")
manifest_df = pandas.read_csv(manifest_path, nrows=max_models)
diff --git a/mhcflurry/downloads.py b/mhcflurry/downloads.py
index e88675ed..b3b7e9d3 100644
--- a/mhcflurry/downloads.py
+++ b/mhcflurry/downloads.py
@@ -9,7 +9,7 @@ from __future__ import (
)
import logging
import yaml
-from os.path import join, exists
+from os.path import join, exists, relpath
from pipes import quote
from os import environ
from collections import OrderedDict
@@ -20,11 +20,14 @@ ENVIRONMENT_VARIABLES = [
"MHCFLURRY_DATA_DIR",
"MHCFLURRY_DOWNLOADS_CURRENT_RELEASE",
"MHCFLURRY_DOWNLOADS_DIR",
+ "MHCFLURRY_DEFAULT_CLASS1_MODELS"
]
_DOWNLOADS_DIR = None
_CURRENT_RELEASE = None
_METADATA = None
+_MHCFLURRY_DEFAULT_CLASS1_MODELS_DIR = environ.get(
+ "MHCFLURRY_DEFAULT_CLASS1_MODELS_DIR")
def get_downloads_dir():
@@ -51,6 +54,37 @@ def get_downloads_metadata():
return _METADATA
+def get_default_class1_models_dir(test_exists=True):
+ """
+ Return the absolute path to the default class1 models dir.
+
+ If environment variable MHCFLURRY_DEFAULT_CLASS1_MODELS_DIR is set to an
+ absolute path, return that path. If it's set to a relative path (i.e. does
+ not start with /) then return that path taken to be relative to the mhcflurry
+ downloads dir.
+
+ If environment variable MHCFLURRY_DEFAULT_CLASS1_MODELS_DIR is NOT set,
+ then return the path to downloaded models in the "models_class1" download.
+
+ Parameters
+ ----------
+
+ test_exists : boolean, optional
+ Whether to raise an exception of the path does not exist
+
+ Returns
+ -------
+ string : absolute path
+ """
+ if _MHCFLURRY_DEFAULT_CLASS1_MODELS_DIR:
+ result = join(get_downloads_dir(), _MHCFLURRY_DEFAULT_CLASS1_MODELS_DIR)
+ if test_exists and not exists(result):
+ raise IOError("No such directory: %s" % result)
+ return result
+ else:
+ return get_path("models_class1", "models", test_exists=test_exists)
+
+
def get_current_release_downloads():
"""
Return a dict of all available downloads in the current release.
diff --git a/mhcflurry/downloads_command.py b/mhcflurry/downloads_command.py
index 08648a99..3af2fa3e 100644
--- a/mhcflurry/downloads_command.py
+++ b/mhcflurry/downloads_command.py
@@ -229,15 +229,13 @@ def info_subcommand(args):
downloads = get_current_release_downloads()
- format_string = "%-40s %-12s %-12s %-20s "
- print(format_string % (
- "DOWNLOAD NAME", "DOWNLOADED?", "DEFAULT?", "URL"))
+ format_string = "%-40s %-12s %-20s "
+ print(format_string % ("DOWNLOAD NAME", "DOWNLOADED?", "URL"))
for (item, info) in downloads.items():
print(format_string % (
item,
yes_no(info['downloaded']),
- yes_no(info['metadata']['default']),
info['metadata']["url"]))
diff --git a/mhcflurry/predict_command.py b/mhcflurry/predict_command.py
index ab07cfac..aea742d3 100644
--- a/mhcflurry/predict_command.py
+++ b/mhcflurry/predict_command.py
@@ -33,7 +33,7 @@ import logging
import pandas
-from .downloads import get_path
+from .downloads import get_default_class1_models_dir
from .class1_affinity_predictor import Class1AffinityPredictor
@@ -122,7 +122,7 @@ model_args.add_argument(
metavar="DIR",
default=None,
help="Directory containing models. "
- "Default: %s" % get_path("models_class1", "models", test_exists=False))
+ "Default: %s" % get_default_class1_models_dir(test_exists=False))
model_args.add_argument(
"--include-individual-model-predictions",
action="store_true",
@@ -143,7 +143,7 @@ def run(argv=sys.argv[1:]):
# The reason we set the default here instead of in the argument parser is that
# we want to test_exists at this point, so the user gets a message instructing
# them to download the models if needed.
- models_dir = get_path("models_class1", "models")
+ models_dir = get_default_class1_models_dir(test_exists=True)
predictor = Class1AffinityPredictor.load(models_dir)
# The following two are informative commands that can come
--
GitLab