RF+ENH: reproin - allow for an empty key in protocols2fix to provide fixups for any study

For some data we cannot rely on reliable presence of consistent study_description
across scans.  That results in the necessity to duplicate the same protocols2fix
records for multiple (not known in advance) study descriptions (actually -- their
hashes, which makes it even more difficult).  But in the cases with custom
overloads of protocols2fix, it is desired to just provide global rewrite rules,
which could be applied to any collection since they did follow some convention.

Now, with an empty "hash", those rules would be applied last, i.e. after possible
study-specific fixups applied.

As part of the solution I removed preliminary check to skip a call to
fix_dbic_protocol altogether.  It should be better this way.

I also removed binding of series_spec_fields and protocols2fix within function
signature.  It should allow easier overloading at the module level when needed

Author: yarikoptic

heudiconv/heuristics/reproin.py

@@ -391,26 +391,38 @@ def fix_canceled_runs(seqinfo, accession2run=fix_accession2run):
     return seqinfo
 
 
-def fix_dbic_protocol(seqinfo, keys=series_spec_fields, subsdict=protocols2fix):
+def fix_dbic_protocol(seqinfo, keys=None, subsdict=None):
     """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)
 
-    if study_hash not in subsdict:
-        raise ValueError("I don't know how to fix {0}".format(study_hash))
-
-    # need to replace both protocol_name series_description
-    substitutions = subsdict[study_hash]
-    for i, s in enumerate(seqinfo):
-        fixed_kwargs = dict()
-        for key in keys:
-            value = getattr(s, key)
-            # replace all I need to replace
-            for substring, replacement in substitutions:
-                value = re.sub(substring, replacement, value)
-            fixed_kwargs[key] = value
-        # namedtuples are immutable
-        seqinfo[i] = s._replace(**fixed_kwargs)
+    # We will consider study specific (based on hash) and global (if key is "",
+    # ie empty string) and in that order substitutions
+    candidate_substitutions = (
+        ('study (%s) specific' % study_hash, study_hash),
+        ('global', ''),
+    )
+    for subs_scope, subs_key in candidate_substitutions:
+        if subs_key not in subsdict:
+            continue
+        substitutions = subsdict[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:
+                value = getattr(s, key)
+                # replace all I need to replace
+                for substring, replacement in substitutions:
+                    value = re.sub(substring, replacement, value)
+                fixed_kwargs[key] = value
+            # namedtuples are immutable
+            seqinfo[i] = s._replace(**fixed_kwargs)
 
     return seqinfo
 
@@ -420,10 +432,7 @@ def fix_seqinfo(seqinfo):
     """
     # add cancelme to known bad runs
     seqinfo = fix_canceled_runs(seqinfo)
-    study_hash = get_study_hash(seqinfo)
-    if study_hash in protocols2fix:
-        lgr.info("Fixing up protocol for {0}".format(study_hash))
-        seqinfo = fix_dbic_protocol(seqinfo)
+    seqinfo = fix_dbic_protocol(seqinfo)
     return seqinfo