Commits now update the sha1's so we know the data is changed

client/cli/bam.py

@@ -203,7 +203,8 @@ class bam_session:
 
     @staticmethod
     def status(session_rootdir,
-               paths_add, paths_remove, paths_modified, paths_remap_subset_add):
+               paths_add, paths_remove, paths_modified, paths_remap_subset_add,
+               paths_uuid_update=None):
 
         assert(isinstance(paths_add, dict))
         assert(isinstance(paths_remove, dict))
@@ -223,7 +224,7 @@ class bam_session:
             os.path.join(session_rootdir, ".bam_tmp.zip"),
             }
 
-        with open(os.path.join(session_rootdir, ".bam_paths_uuid.json")) as f:
+        with open(os.path.join(session_rootdir, ".bam_paths_uuid.json"), 'r') as f:
             import json
             paths_uuid = json.load(f)
             del json
@@ -231,9 +232,11 @@ class bam_session:
         for fn_rel, sha1 in paths_uuid.items():
             fn_abs = os.path.join(session_rootdir, fn_rel)
             if os.path.exists(fn_abs):
-                if sha1_from_file(fn_abs) != sha1:
+                sha1_modified = sha1_from_file(fn_abs)
+                if sha1_modified != sha1:
                     paths_modified[fn_rel] = fn_abs
-
+                if paths_uuid_update is not None:
+                    paths_uuid_update[fn_rel] = sha1_modified
                 paths_used.add(fn_abs)
             else:
                 paths_remove[fn_rel] = fn_abs
@@ -266,6 +269,9 @@ class bam_session:
                 # remap paths of added files
                 paths_add[fn_rel] = fn_abs
 
+                if paths_uuid_update is not None:
+                    paths_uuid_update[fn_rel] = sha1_from_file(fn_abs)
+
                 # TESTING ONLY
                 fn_abs_remote = fn_rel
                 paths_remap_subset_add[fn_rel] = fn_abs_remote
@@ -475,10 +481,12 @@ class bam_commands:
         paths_modified = {}
         paths_remove = {}
         paths_remap_subset_add = {}
+        paths_uuid_update = {}
 
         bam_session.status(
                 session_rootdir,
                 paths_add, paths_remove, paths_modified, paths_remap_subset_add,
+                paths_uuid_update,
                 )
 
         if not any((paths_add, paths_modified, paths_remove)):
@@ -578,8 +586,19 @@ class bam_commands:
         except Exception:
             print(r.text)
 
-        # TODO(cam)
-        # if all goes well, rewrite sha1's
+        # TODO, handle error cases
+        ok = True
+        if ok:
+            # NOTE, we may want to generalize the 'update uuid' code & share it.
+
+            paths_uuid.update(paths_uuid_update)
+            with open(os.path.join(session_rootdir, ".bam_paths_uuid.json"), 'w') as f:
+                json.dump(
+                        paths_uuid_update, f, ensure_ascii=False,
+                        check_circular=False,
+                        # optional (pretty)
+                        sort_keys=True, indent=4, separators=(',', ': '),
+                        )
 
     @staticmethod
     def status(paths, use_json=False):
@@ -594,7 +613,10 @@ class bam_commands:
         paths_remove = {}
         paths_remap_subset_add = {}
 
-        bam_session.status(session_rootdir, paths_add, paths_remove, paths_modified, paths_remap_subset_add)
+        bam_session.status(
+                session_rootdir,
+                paths_add, paths_remove, paths_modified, paths_remap_subset_add,
+                )
 
         if use_json:
             for fn in sorted(paths_add):

tests/test_cli.py

@@ -15,6 +15,8 @@ Run a single test:
 
 import os
 VERBOSE = os.environ.get("VERBOSE", False)
+if VERBOSE == "0":
+    VERBOSE = None
 if VERBOSE:
     # for the server subprocess
     os.environ["BAM_VERBOSE"] = "1"
@@ -743,6 +745,48 @@ class BamCommitTest(BamSessionTestCase):
         stdout, stderr = bam_run(["commit", "-m", "test message"], session_path)
         self.assertEqual("", stderr)
 
+    def test_commit_partial(self):
+        """Checks the commit is only writing the modified files,
+        across multiple commits and changes.
+        """
+        session_name = "mysession"
+        files = (
+            "a.data",
+            os.path.join("b_dir", "b.data"),
+            os.path.join("c_dir", "c_subdir", "c.data"),
+            os.path.join("d_dir", "d_subdir", "d_nested", "d.data"),
+            )
+        proj_path, session_path = self.init_session(session_name)
+
+        # ------
+        # Commit
+        # arbitrary data so this is seen as binary data
+        file_binary_chunk = b'\x89'
+        for f in files:
+            file_quick_write(session_path, f, file_binary_chunk + f.encode('ascii'))
+
+        stdout, stderr = bam_run(["commit", "-m", "test 1"], session_path)
+        self.assertEqual("", stderr)
+
+        # now check that status reads there are no changes
+        ret = bam_run_as_json(["status", "--json"], session_path)
+        self.assertEqual([], ret)
+
+        # ------
+        # Modify
+        # check the status now shows modified
+        for f in files:
+            file_quick_write(session_path, f, b'_foo', append=True)
+
+        ret = bam_run_as_json(["status", "--json"], session_path)
+        ret.sort()
+        self.assertEqual(
+                [["M", "a.data"],
+                 ["M", "b_dir/b.data"],
+                 ["M", "c_dir/c_subdir/c.data"],
+                 ["M", "d_dir/d_subdir/d_nested/d.data"],
+                 ], ret)
+
     def test_checkout(self):
         session_name = "mysession"
         file_name = "other_file.txt"