remove alpha_cased altogether

peppy/project.py

@@ -68,7 +68,7 @@
 from .exceptions import PeppyError
 from .sample import merge_sample, Sample
 from .utils import \
-    add_project_sample_constants, alpha_cased, copy, fetch_samples, is_url, \
+    add_project_sample_constants, copy, fetch_samples, is_url, \
     non_null_value, warn_derived_cols, warn_implied_cols
 
 
@@ -571,15 +571,15 @@ def build_sheet(self, *protocols):
             given, else all of this Project's samples
         """
         # Use all protocols if none are explicitly specified.
-        protocols = {alpha_cased(p) for p in (protocols or self.protocols)}
+        protocols = {p for p in (protocols or self.protocols)}
         include_samples = []
         for s in self.samples:
             try:
                 proto = s.protocol
             except AttributeError:
                 include_samples.append(s)
                 continue
-            check_proto = alpha_cased(proto)
+            check_proto = proto
             if check_proto in protocols:
                 include_samples.append(s)
             else:

peppy/utils.py

@@ -41,20 +41,6 @@ def add_project_sample_constants(sample, project):
 
 
 
-def alpha_cased(text, lower=False):
-    """
-    Filter text to just letters and homogenize case.
-
-    :param str text: what to filter and homogenize.
-    :param bool lower: whether to convert to lowercase; default uppercase.
-    :return str: input filtered to just letters, with homogenized case.
-    """
-    text = "".join(filter(
-            lambda c: c.isalpha() or c == GENERIC_PROTOCOL_KEY, text))
-    return text.lower() if lower else text.upper()
-
-
-
 def check_bam(bam, o):
     """
     Check reads in BAM file for read type and lengths.

tests/models/integration/test_Project_Sample_interaction.py

@@ -13,8 +13,6 @@
 from peppy import \
         Project, Sample, \
         SAMPLE_ANNOTATIONS_KEY, SAMPLE_NAME_COLNAME
-from peppy.utils import alpha_cased
-
 
 __author__ = "Vince Reuter"
 __email__ = "[email protected]"
@@ -199,9 +197,9 @@ def test_multiple_samples(
         sheet = p.build_sheet(*protocols)
         assert exp_num_samples == len(sheet)
         if protocols:
-            fuzzy_protos = {alpha_cased(p) for p in protocols}
+            fuzzy_protos = {p for p in protocols}
             for _, sample_data in sheet.iterrows():
-                assert alpha_cased(sample_data.protocol) in fuzzy_protos
+                assert sample_data.protocol in fuzzy_protos