Merge branch 'master' of ssh://vcs.r3c.de:63022/till-software/labinform

labinform/datasafe/datasafe.py

@@ -5,6 +5,8 @@
 """
 
 import os
+import hashlib
+import shutil
 
 
 class Error(Exception):
@@ -253,7 +255,6 @@ def generate(self, experiment="", sample_id=""):
         dir_path = os.path.join(self.path, path_for_loi)
         if not self.has_dir(dir_path):
             self.add_directory(dir_path)
-        #print(dir_path)
         loi_complete = loi_basic + path_for_loi
         return loi_complete
 
@@ -271,7 +272,10 @@ def push(self, data="", loi=""):
             unique identifier providing a directory path
 
         """
-        pass
+        target_path = self.loi_to_path(loi)
+        print(target_path)
+        shutil.copy(data, target_path)
+
 
     def pull(self, loi=""):
         """Retrieve data from the datasafe.
@@ -312,6 +316,14 @@ def index(self, loi=""):
 
         """
         return dict()
+
+    def make_checksum_for_path(self, path=""):
+        md5 = hashlib.md5()
+        with open(path, "rb") as f:
+            for line in f.readlines():
+                md5.update(line)
+        checksum = md5.hexdigest()
+        return checksum
 
     def checksum(self, loi=""):
         """Create a cryptographic hash (MD5) for a file in the datasafe.

tests/datasafe/test_datasafe.py

@@ -30,6 +30,7 @@ def test_has_push_method(self):
         self.assertTrue(hasattr(self.datasafe, 'push'))
         self.assertTrue(callable(self.datasafe.push))
 
+    @unittest.skip
     def test_call_push_with_parameters(self):
         self.datasafe.push("", "42.1001/ds/cwepr/sa42/01/data/raw")
 
@@ -174,6 +175,19 @@ def test_has_dir_returns_bool(self):
         hasdir = self.datasafe.has_dir("")
         self.assertEqual(bool, type(hasdir))
 
+    def test_has_make_checksum_for_path_method(self):
+        self.assertTrue(hasattr(self.datasafe, 'make_checksum_for_path'))
+        self.assertTrue(callable(self.datasafe.make_checksum_for_path))
+
+    @unittest.skip
+    def test_call_make_checksum_for_path_with_parameters(self):
+        self.datasafe.make_checksum_for_path("")
+
+    @unittest.skip
+    def test_make_checksum_for_path_returns_str(self):
+        checksum = self.datasafe.make_checksum_for_path("")
+        self.assertEqual(str, type(checksum))
+
 
 class TestEmptyDir(unittest.TestCase):
     def setUp(self):
@@ -335,3 +349,46 @@ def test_find_highest(self):
         highest = self.datasafe.find_highest(self.target_directory[:-1])
         self.assertEqual(1, highest)
 
+
+class TestChecksumPath(unittest.TestCase):
+    def setUp(self):
+        self.datasafe = datasafe.Datasafe()
+        top_level_directory = os.path.dirname(os.path.dirname(os.path.dirname(
+            os.path.dirname(__file__))))
+        self.target_directory = top_level_directory + "/datasafe-test/cwepr/sa571/1"
+        self.target_file = self.target_directory + "/data/raw/Manifest.yaml"
+
+    def test_correct_checksum_for_yaml(self):
+        md5 = self.datasafe.make_checksum_for_path(self.target_file)
+        self.assertEqual("48aa739357f70bd7694fcf0ebc3a2e24", md5)
+
+
+class TestChecksum(unittest.TestCase):
+    pass
+
+
+class TestPush(unittest.TestCase):
+    def setUp(self):
+        self.datasafe = datasafe.Datasafe()
+        top_level_directory = os.path.dirname(os.path.dirname(os.path.dirname(
+            os.path.dirname(__file__))))
+        self.common_directory = top_level_directory + "/datasafe-test"
+        self.target_directory = top_level_directory + "/datasafe-test/ds"
+        print(self.target_directory)
+        if not os.path.exists(self.target_directory):
+            os.makedirs(self.target_directory)
+        self.datasafe.set_path(self.target_directory)
+        self.target_file = self.common_directory + "/cwepr/sa571/1/data/raw/Manifest.yaml"
+
+    def tearDown(self):
+        shutil.rmtree(self.target_directory)
+
+    def test_push(self):
+        loi = self.datasafe.generate(experiment="cwepr", sample_id="sa571")
+        self.assertEqual(True, self.datasafe.has_dir(self.datasafe.path + "/cwepr/sa571/1/data/raw"))
+        self.datasafe.push(self.target_file, loi)
+        final_path = self.datasafe.path + "/cwepr/sa571/1/data/raw/Manifest.yaml"
+        self.assertEqual(True, os.path.isfile(final_path))
+
+
+