File size now in provenance

niprov/filesystem.py

@@ -1,7 +1,10 @@
 import os
 
 
-class Filesystem():
+class Filesystem(object):
+    """Wrapper of filesystem access functionality such as that implemented by 
+    the os package in the standard library.
+    """
 
     def __init__(self):
         self.open = open
@@ -30,3 +33,6 @@ def read(self, path):
             contents = fhandle.read()
         return contents
 
+    def getsize(self, path):
+        return os.path.getsize(path)
+

niprov/html.py

@@ -32,7 +32,7 @@ class HtmlExporter(object):
 """
     _footer = '</html>'
     _expectedFields = ['acquired','subject','protocol']
-    _allfields = ['path','ancestor','acquired','subject','protocol','transformation','code','logtext']
+    _allfields = ['path','ancestor','acquired','subject','protocol','transformation','code','logtext','size']
 
     def __init__(self, filesys, listener, externals):
         self.filesys = filesys

niprov/inspection.py

@@ -4,12 +4,14 @@
 from datetime import datetime
 from niprov.commandline import Commandline
 from niprov.dependencies import Dependencies
+from niprov.filesystem import Filesystem
 
 formats = {'.PAR':'nibabel',
            '.dcm':'dicom'}
 
 
-def inspect(fpath, listener=Commandline(), libs=Dependencies()):
+def inspect(fpath, listener=Commandline(), libs=Dependencies(), 
+        filesystem=Filesystem()):
     provenance = {}
     extension = os.path.splitext(fpath)[1]
     if not extension in formats:
@@ -19,6 +21,7 @@ def inspect(fpath, listener=Commandline(), libs=Dependencies()):
         listener.missingDependencyForImage(formats[extension], fpath)
         return None
     provenance['path'] = fpath
+    provenance['size'] = filesystem.getsize(fpath)
     if formats[extension] == 'nibabel':
         try:
             img = libs.nibabel.load(fpath)

tests/htmlexporting.py

@@ -89,9 +89,11 @@ def test_Exporting_a_single_item(self):
         item1['acquired'] = datetime(2014, 8, 5, 12, 23, 46)
         item1['code'] = 'private static void'
         item1['logtext'] = 'Hello World!'
+        item1['size'] = 45678
         html.export(item1)
         filehandle.write.assert_any_call('<dt>code</dt><dd>private static void</dd>\n')
         filehandle.write.assert_any_call('<dt>logtext</dt><dd>Hello World!</dd>\n')
+        filehandle.write.assert_any_call('<dt>size</dt><dd>45678</dd>\n')
 
     def setupFilesys(self):
         filesys = Mock()

tests/inspection.py

@@ -9,15 +9,17 @@ def test_Loads_file_with_nibabel(self):
         log = Mock()
         libs = self.setupNibabel()
         libs.hasDependency.return_value = True
-        niprov.inspection.inspect('/p/f1.PAR', listener=log, libs=libs)
+        filesys = Mock()
+        niprov.inspection.inspect('/p/f1.PAR', listener=log, libs=libs, filesystem=filesys)
         libs.nibabel.load.assert_any_call('/p/f1.PAR')
 
     def test_Doesnt_use_nibabel_if_not_installed(self):
         import niprov.inspection
         log = Mock()
         libs = self.setupNibabel()
         libs.hasDependency.return_value = False
-        provenance = niprov.inspection.inspect('/p/f1.PAR', listener=log, libs=libs)
+        filesys = Mock()
+        provenance = niprov.inspection.inspect('/p/f1.PAR', listener=log, libs=libs, filesystem=filesys)
         self.assertRaises(AssertionError,
             libs.nibabel.load.assert_any_call, '/p/f1.PAR')
 
@@ -26,7 +28,8 @@ def test_If_dcm_passed_uses_pydicom_to_open(self):
         log = Mock()
         libs = self.setupPydicom()
         libs.hasDependency.return_value = True
-        provenance = niprov.inspection.inspect('/p/f1.dcm', listener=log, libs=libs)
+        filesys = Mock()
+        provenance = niprov.inspection.inspect('/p/f1.dcm', listener=log, libs=libs, filesystem=filesys)
         # doesnt complain about missing pydicom        
         self.assertRaises(AssertionError,
             log.missingDependencyForImage.assert_any_call, 'dicom','/p/f1.dcm')
@@ -38,7 +41,8 @@ def test_If_dcm_passed_but_pydicom_not_installed_tells_listener(self):
         log = Mock()
         libs = self.setupPydicom()
         libs.hasDependency.return_value = False
-        provenance = niprov.inspection.inspect('/p/f1.dcm', listener=log, libs=libs)
+        filesys = Mock()
+        provenance = niprov.inspection.inspect('/p/f1.dcm', listener=log, libs=libs, filesystem=filesys)
         self.assertRaises(AssertionError,
             libs.dicom.read_file.assert_any_call, '/p/f1.dcm')
         log.missingDependencyForImage.assert_any_call('dicom','/p/f1.dcm')
@@ -48,15 +52,17 @@ def test_If_nothing_inspected_returns_None(self):
         log = Mock()
         libs = self.setupNibabel()
         libs.hasDependency.return_value = False
-        provenance = niprov.inspection.inspect('/p/f1.PAR', listener=log, libs=libs)
+        filesys = Mock()
+        provenance = niprov.inspection.inspect('/p/f1.PAR', listener=log, libs=libs, filesystem=filesys)
         self.assertIsNone(provenance)
 
     def test_Gets_basic_info_from_nibabel_and_returns_it(self):
         import niprov.inspection
         log = Mock()
         libs = self.setupNibabel()
         libs.hasDependency.return_value = True
-        out = niprov.inspection.inspect('/p/f1.PAR', listener=log, libs=libs)
+        filesys = Mock()
+        out = niprov.inspection.inspect('/p/f1.PAR', listener=log, libs=libs, filesystem=filesys)
         self.assertEqual(out['subject'], 'John Doeish')
         self.assertEqual(out['protocol'], 'T1 SENSE')
         self.assertEqual(out['acquired'], datetime(2014, 8, 5, 11, 27, 34))
@@ -66,7 +72,8 @@ def test_Gets_basic_info_from_pydicom_and_returns_it(self):
         log = Mock()
         libs = self.setupPydicom()
         libs.hasDependency.return_value = True
-        out = niprov.inspection.inspect('/p/f1.dcm', listener=log, libs=libs)
+        filesys = Mock()
+        out = niprov.inspection.inspect('/p/f1.dcm', listener=log, libs=libs, filesystem=filesys)
         self.assertEqual(out['subject'], 'John Doeish')
         self.assertEqual(out['protocol'], 'T1 SENSE')
         self.assertEqual(out['acquired'], datetime(2014, 8, 5, 12, 19, 14))
@@ -76,16 +83,27 @@ def test_Saves_file_path_along_with_provenance(self):
         log = Mock()
         libs = self.setupPydicom()
         libs.hasDependency.return_value = True
-        out = niprov.inspection.inspect('/p/f1.dcm', listener=log, libs=libs)
+        filesys = Mock()
+        out = niprov.inspection.inspect('/p/f1.dcm', listener=log, libs=libs, filesystem=filesys)
         self.assertEqual(out['path'], '/p/f1.dcm')
 
+    def test_Saves_filesize_along_with_provenance(self):
+        import niprov.inspection
+        log = Mock()
+        libs = self.setupPydicom()
+        libs.hasDependency.return_value = True
+        filesys = Mock()
+        out = niprov.inspection.inspect('/p/f1.dcm', listener=log, libs=libs, filesystem=filesys)
+        self.assertEqual(out['size'], filesys.getsize('/p/f1.dcm'))
+
     def test_If_error_during_inspection_tells_listener_and_returns_None(self):
         import niprov.inspection
         log = Mock()
         libs = Mock()
         libs.hasDependency.return_value = True
         libs.nibabel.load.side_effect = ValueError
-        out = niprov.inspection.inspect('/p/f1.PAR', listener=log, libs=libs)
+        filesys = Mock()
+        out = niprov.inspection.inspect('/p/f1.PAR', listener=log, libs=libs, filesystem=filesys)
         self.assertIsNone(out)
         log.fileError.assert_any_call('/p/f1.PAR')