add cache_root_dir attribute & behavior (#216)

* add cache_root_dir attribute & behavior

* add cache_dir_kwargs

* modify default value

* fix returns & add logger

* dont use get_logger here (not sure it matters)

* bad edit

cohorts/cohort.py

@@ -48,7 +48,7 @@
 from tqdm import tqdm
 
 from .dataframe_loader import DataFrameLoader
-from .utils import DataFrameHolder, first_not_none_param, filter_not_null, InvalidDataError, strip_column_names as _strip_column_names, get_logger
+from .utils import DataFrameHolder, first_not_none_param, filter_not_null, InvalidDataError, strip_column_names as _strip_column_names, get_logger, get_cache_dir
 from .provenance import compare_provenance
 from .survival import plot_kmf
 from .plot import mann_whitney_plot, fishers_exact_plot, roc_curve_plot, stripboxplot, CorrelationResults
@@ -72,6 +72,10 @@ class Cohort(Collection):
         A list of `Patient`s for this cohort.
     cache_dir : str
         Path to store cached results, e.g. cached variant effects.
+    cache_root_dir : str
+        (optional) directory in which cache_dir should be created
+    cache_dir_kwargs : dict
+        (optional) dictionary of name=value data to use when formatting cache_dir str
     show_progress : bool
         Whether or not to show DataFrame application progress as an increasing percentage.
     kallisto_ensembl_version : int
@@ -118,6 +122,8 @@ class Cohort(Collection):
     def __init__(self,
                  patients,
                  cache_dir,
+                 cache_root_dir=None,
+                 cache_dir_kwargs=dict(),
                  show_progress=True,
                  kallisto_ensembl_version=None,
                  cache_results=True,
@@ -146,7 +152,8 @@ def __init__(self,
         # this when patient-specific functions all live in Patient.
         for patient in patients:
             patient.cohort = self
-        self.cache_dir = cache_dir
+        self.cache_dir = get_cache_dir(cache_dir=cache_dir, cache_root_dir=cache_root_dir, **cache_dir_kwargs)
+        self.cache_root_dir = cache_root_dir
         self.show_progress = show_progress
         self.cache_results = cache_results
         self.kallisto_ensembl_version = kallisto_ensembl_version

cohorts/utils.py

@@ -17,6 +17,29 @@
 from collections import namedtuple
 import sys
 import logging
+from os import path
+
+logger = logging.getLogger(__name__)
+
+def get_cache_dir(cache_dir, cache_root_dir=None, *args, **kwargs):
+    """
+    Return full cache_dir, according to following logic:
+        - if cache_dir is a full path (per path.isabs), return that value
+        - if not and if cache_root_dir is not None, join two paths
+        - otherwise, log warnings and return None
+    Separately, if args or kwargs are given, format cache_dir using kwargs
+    """
+    cache_dir = cache_dir.format(*args, **kwargs)
+    if path.isabs(cache_dir):
+        if cache_root_dir is not None:
+            logger.warning('cache_dir ({}) is a full path; ignoring cache_root_dir'.format(cache_dir))
+        return cache_dir
+    if cache_root_dir is not None:
+        return path.join(cache_root_dir, cache_dir)
+    else:
+        logger.warning("cache dir is not full path & cache_root_dir not given. Caching may not work as expected!")
+    return None
+
 
 class DataFrameHolder(namedtuple("DataFrameHolder", ["cols", "df"])):
     """Holds a DataFrame along with associated columns of interest."""