RF: reproin - remove binding of fixup data structures in function signatures

Binding in signatured forbided easy rebinding of them to new values at the module level.

Author: yarikoptic

heudiconv/heuristics/reproin.py

@@ -372,14 +372,14 @@ def get_study_hash(seqinfo):
     return md5sum(get_study_description(seqinfo))
 
 
-def fix_canceled_runs(seqinfo, accession2run=fix_accession2run):
+def fix_canceled_runs(seqinfo):
     """Function that adds cancelme_ to known bad runs which were forgotten
     """
     accession_number = get_unique(seqinfo, 'accession_number')
-    if accession_number in accession2run:
+    if accession_number in fix_accession2run:
         lgr.info("Considering some runs possibly marked to be "
                  "canceled for accession %s", accession_number)
-        badruns = accession2run[accession_number]
+        badruns = fix_accession2run[accession_number]
         badruns_pattern = '|'.join(badruns)
         for i, s in enumerate(seqinfo):
             if re.match(badruns_pattern, s.series_id):
@@ -391,13 +391,9 @@ def fix_canceled_runs(seqinfo, accession2run=fix_accession2run):
     return seqinfo
 
 
-def fix_dbic_protocol(seqinfo, keys=None, subsdict=None):
+def fix_dbic_protocol(seqinfo):
     """Ad-hoc fixup for existing protocols
     """
-    if subsdict is None:
-        subsdict = protocols2fix
-    if keys is None:
-        keys = series_spec_fields
 
     study_hash = get_study_hash(seqinfo)
 
@@ -408,14 +404,14 @@ def fix_dbic_protocol(seqinfo, keys=None, subsdict=None):
         ('global', ''),
     )
     for subs_scope, subs_key in candidate_substitutions:
-        if subs_key not in subsdict:
+        if subs_key not in protocols2fix:
             continue
-        substitutions = subsdict[subs_key]
+        substitutions = protocols2fix[subs_key]
         lgr.info("Considering %s substitutions", subs_scope)
         for i, s in enumerate(seqinfo):
             fixed_kwargs = dict()
             # need to replace both protocol_name series_description
-            for key in keys:
+            for key in series_spec_fields:
                 value = getattr(s, key)
                 # replace all I need to replace
                 for substring, replacement in substitutions:

heudiconv/heuristics/test_reproin.py

@@ -2,6 +2,9 @@
 # Tests for reproin.py
 #
 from collections import OrderedDict
+from mock import patch
+
+from . import reproin
 from .reproin import (
     filter_files,
     fix_canceled_runs,
@@ -78,7 +81,8 @@ def test_fix_canceled_runs():
         'accession1': ['^01-', '^03-']
     }
 
-    seqinfo_ = fix_canceled_runs(seqinfo, fake_accession2run)
+    with patch.object(reproin, 'fix_accession2run', fake_accession2run):
+        seqinfo_ = fix_canceled_runs(seqinfo)
 
     for i, s in enumerate(seqinfo_, 1):
         output = runname
@@ -108,14 +112,15 @@ def test_fix_dbic_protocol():
 
 
     seqinfos = [seq1, seq2]
-    keys = ['field1']
-    subsdict = {
+    protocols2fix = {
         md5sum('mystudy'):
             [('scout_run\+', 'scout'),
              ('run-life[0-9]', 'run+_task-life')],
     }
 
-    seqinfos_ = fix_dbic_protocol(seqinfos, keys=keys, subsdict=subsdict)
+    with patch.object(reproin, 'protocols2fix', protocols2fix), \
+            patch.object(reproin, 'series_spec_fields', ['field1']):
+        seqinfos_ = fix_dbic_protocol(seqinfos)
     assert(seqinfos[1] == seqinfos_[1])
     # field2 shouldn't have changed since I didn't pass it
     assert(seqinfos_[0] == FakeSeqInfo(accession_number,
@@ -124,8 +129,9 @@ def test_fix_dbic_protocol():
                                        seq1.field2))
 
     # change also field2 please
-    keys = ['field1', 'field2']
-    seqinfos_ = fix_dbic_protocol(seqinfos, keys=keys, subsdict=subsdict)
+    with patch.object(reproin, 'protocols2fix', protocols2fix), \
+            patch.object(reproin, 'series_spec_fields', ['field1', 'field2']):
+        seqinfos_ = fix_dbic_protocol(seqinfos)
     assert(seqinfos[1] == seqinfos_[1])
     # now everything should have changed
     assert(seqinfos_[0] == FakeSeqInfo(accession_number,