updating comparison exampleo

Author: vsoch

examples/reproducibility/assess_replication.py

@@ -1,8 +1,14 @@
 from glob import glob
 
+from singularity.reproduce import (
+    assess_replication, 
+    assess_differences
+)
+
 image_files=glob('*.img')
-from singularity.reproduce import *
-Environment message level found to be DEBUG
+
+# ASSESS REPLICATION #######################################
+# returns booleans for if the hashes for levels are the same
 
 assess_replication(image_files[0],image_files[1])
 
@@ -23,3 +29,32 @@
  'RECIPE': True,
  'REPLICATE': True,
  'RUNSCRIPT': True}
+
+# ASSESS DIFFERENCES #######################################
+# returns dictionary with 
+
+report = assess_differences(image_files[0],image_files[1])
+
+report.keys()
+# dict_keys(['different', 'missing', 'same'])
+
+# These files are equivalent between the images
+print(len(report['same']))
+5663
+
+# These files are present in both, but different
+print(report['different'])
+['./etc/hosts', 
+ './.exec', 
+ './environment', 
+ './etc/mtab', 
+ './etc/resolv.conf', 
+ './.run', 
+ './.shell', 
+ './singularity']
+
+# These files are found in the first image, but not the second
+print(report['missing'])
+['./var/lib/apt/lists/.wh.archive.ubuntu.com_ubuntu_dists_xenial-updates_main_i18n_Translation-en', 
+ './bin/gunzip']
+

singularity/reproduce.py

@@ -37,31 +37,38 @@ def assess_replication(image_file1,image_file2,version=None):
     return report
 
 
-def assess_differences(image_file1,image_file2,version=None):
+def assess_differences(image_file1,image_file2,level=None,version=None):
     '''assess_replications will compare two images on each level of 
     reproducibility,
     '''
     levels = get_levels(version=version)
+    if level is None:
+        level = "IDENTICAL"
+
+    if level not in list(levels.keys()):
+        bot.logger.error("%s is not a valid level. See get_levels().",level)
+        sys.exit(1)
+
     different = []
     same = []
     setdiff = []
-    for level_name, values in levels.items():
-        hashes1 = get_content_hashes(image_path=image_file1,
-                                     level=level_name)
-        hashes2 = get_content_hashes(image_path=image_file2,
-                                     level=level_name)
-        for file_name,hash_value in hashes1.items():
-            if file_name in hashes2:
-                if hashes2[file_name] == hashes1[file_name]:
-                    same.append(file_name)
-                else:
-                    different.append(file_name)
+
+    # Compare the dictionary of file:hash between two images
+    hashes1 = get_content_hashes(image_path=image_file1,level=level)
+    hashes2 = get_content_hashes(image_path=image_file2,level=level)
+    for file_name,hash_value in hashes1.items():
+        if file_name in hashes2:
+            if hashes2[file_name] == hashes1[file_name]:
+                same.append(file_name)
             else:
-                setdiff.append(file_name)
+                different.append(file_name)
+        else:
+            setdiff.append(file_name)
 
     report = {'missing':setdiff,
               'same':same,
               'different':different}
+
     return report
 
 
@@ -214,7 +221,7 @@ def get_content_hashes(image_path,level=None,regexp=None,include_files=None,skip
     digest = dict()
     for member in tar:
         if member.isfile():
-            if include_file(member.name,file_filters):
+            if include_file(member.name,file_filter):
                 buf = member.tobuf()
                 hasher = hashlib.sha1()
                 hasher.update(buf)