account for time-/state-dependence of column naming

vreuter · Jun 4, 2019 · 4aa8341 · 4aa8341
1 parent 578355d
commit 4aa8341
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Showing 2 changed files with 11 additions and 4 deletions.
diff --git a/peppy/sample.py b/peppy/sample.py
@@ -719,7 +719,12 @@ def merge_sample(sample, sample_subann, data_sources=None,
         return merged_attrs
 
     if sample_colname not in sample_subann.columns:
-        raise KeyError("Subannotation requires column '{}'.".format(sample_colname))
+        alternative = SAMPLE_NAME_COLNAME
+        _LOGGER.debug("'{}' is not a subannotation column; trying {}".
+                      format(sample_colname, alternative))
+        if alternative not in sample_subann.columns:
+            raise KeyError("Subannotation requires column '{}'.".format(sample_colname))
+        sample_colname = alternative
 
     _LOGGER.debug("Merging Sample with data sources: {}".
                   format(data_sources))

diff --git a/peppy/snake_project.py b/peppy/snake_project.py
@@ -1,8 +1,7 @@
 """ Adapting Project for interop with Snakemake """
 
 from copy import deepcopy
-from .const import *
-from .const import SNAKEMAKE_SAMPLE_COL
+from .const import SAMPLE_NAME_COLNAME, SNAKEMAKE_SAMPLE_COL
 from .project import Project, sample_table, subsample_table, MAIN_INDEX_KEY, \
     SUBS_INDEX_KEY
 from .utils import count_repeats, get_logger, type_check_strict
@@ -73,7 +72,10 @@ def _finalize_subsample_table(self, t):
     def _get_sample_ids(df):
         """ Return the sample identifiers in the given table. """
         type_check_strict(df, DataFrame)
-        return df[SNAKEMAKE_SAMPLE_COL]
+        try:
+            return df[SNAKEMAKE_SAMPLE_COL]
+        except KeyError:
+            return df[SAMPLE_NAME_COLNAME]
 
 
 def _rename_columns(t):