Implemented a simple method to attach() provenance to the BaseFile.

JasperVanDenBosch · Feb 4, 2015 · ca63ad4 · ca63ad4
1 parent 4f9485d
commit ca63ad4
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Showing 5 changed files with 42 additions and 5 deletions.
diff --git a/niprov/basefile.py b/niprov/basefile.py
@@ -2,16 +2,19 @@
 from niprov.dependencies import Dependencies
 from niprov.filesystem import Filesystem
 from niprov.hashing import Hasher
+from niprov.jsonserializing import JsonSerializer
 
 
 class BaseFile(object):
 
     def __init__(self, fpath, listener=Commandline(), 
-            filesystem=Filesystem(), hasher=Hasher()):
+            filesystem=Filesystem(), hasher=Hasher(), 
+            serializer=JsonSerializer()):
         self.path = fpath
         self.listener = listener
         self.filesystem = filesystem
         self.hasher = hasher
+        self.serializer = serializer
 
     def inspect(self):
         provenance = {}
@@ -20,3 +23,14 @@ def inspect(self):
         provenance['created'] = self.filesystem.getctime(self.path)
         provenance['hash'] = self.hasher.digest(self.path)
         return provenance
+
+    def attach(self):
+        """
+        Attach the current provenance to the file by saving it encoded 
+        in a small textfile alongside it.
+
+        The resulting file's name is like the file it describes,
+        but with the .provenance extension.
+        """
+        provstr = self.serializer.serialize(self.provenance)
+        self.filesystem.write(self.path+'.provenance', provstr)
diff --git a/tests/basefile.py b/tests/basefile.py
@@ -8,10 +8,11 @@ def setUp(self):
         self.log = Mock()
         self.hasher = Mock()
         self.filesys = Mock()
+        self.json = Mock()
         self.path = 'example.abc'
         from niprov.basefile import BaseFile
         self.file = BaseFile(self.path, listener=self.log, 
-            filesystem=self.filesys, hasher=self.hasher)
+            filesystem=self.filesys, hasher=self.hasher, serializer=self.json)
 
     def test_Saves_file_path_along_with_provenance(self):
         out = self.file.inspect()
@@ -28,3 +29,22 @@ def test_Saves_file_creation_time_along_with_provenance(self):
     def test_Asks_hasher_for_digest_of_file(self):
         out = self.file.inspect()
         self.assertEqual(out['hash'], self.hasher.digest(self.path))
+
+    def test_Attach_writes_provenance_to_a_file(self):
+        self.file.provenance = {'foo':'bar'}
+        self.file.attach()
+        self.json.serialize.assert_called_with(self.file.provenance)
+        self.filesys.write.assert_called_with(
+            self.path+'.provenance', self.json.serialize(self.file.provenance))
+
+
+#ATTACH
+# check if we have provenance to attach
+# call method for type-specific attachment behavior (file or insert)
+
+
+
+#READATTACHED
+# call method for type-specific attachment behavior (file or insert)
+# return provenance
+# save provenance to instance
diff --git a/tests/dicomfile.py b/tests/dicomfile.py
@@ -12,7 +12,8 @@ def setUp(self):
         self.setupPydicom()
         from niprov.dcm import DicomFile
         self.file = DicomFile(self.path, listener=self.log, 
-            filesystem=self.filesys, hasher=self.hasher, dependencies=self.libs)
+            filesystem=self.filesys, hasher=self.hasher, dependencies=self.libs,
+            serializer=self.json)
 
     def test_Gets_basic_info_from_pydicom_and_returns_it(self):
         out = self.file.inspect()

diff --git a/tests/test_fif.py b/tests/test_fif.py
@@ -12,7 +12,8 @@ def setUp(self):
         self.setupMne()
         from niprov.fif import FifFile
         self.file = FifFile(self.path, listener=self.log, 
-            filesystem=self.filesys, hasher=self.hasher, dependencies=self.libs)
+            filesystem=self.filesys, hasher=self.hasher, dependencies=self.libs,
+            serializer=self.json)
 
     def test_If_error_during_inspection_tells_listener_and_returns_None(self):
         self.libs.mne.io.Raw.side_effect = ValueError

diff --git a/tests/test_parrec.py b/tests/test_parrec.py
@@ -12,7 +12,8 @@ def setUp(self):
         self.setupNibabel()
         from niprov.parrec import ParrecFile
         self.file = ParrecFile(self.path, listener=self.log, 
-            filesystem=self.filesys, hasher=self.hasher, dependencies=self.libs)
+            filesystem=self.filesys, hasher=self.hasher, dependencies=self.libs,
+            serializer=self.json)
 
     def test_If_error_during_inspection_tells_listener_and_returns_None(self):
         self.libs.nibabel.load.side_effect = ValueError