Avoid overwrite existing YAML files if no change has been made (#987)

Do not overwrite existing yaml files by default.

bindings/python/scripts/CMakeLists.txt

@@ -79,3 +79,13 @@ test_success(
   dlite-validate-empty
   dlite-validate Empty.json
 )
+# Test valid yaml
+test_success(
+  dlite-validate-valid1-yaml
+  dlite-validate ../tests/entities/ValidYaml1.yaml
+)
+# Test invalid yaml
+test_failure(
+  dlite-validate-invalid1-yaml
+  dlite-validate ../tests/entities/InvalidYaml1.yaml
+)

bindings/python/tests/entities/InvalidYaml1.yaml

@@ -0,0 +1,14 @@
+# An invalid version of datamodel Valid1.yaml
+uri: http://onto-ns.com/meta/0.1/InvalidYaml1
+description: An datamodel for an item with float type and invalid shape name.
+dimensions:
+  nf: Number of eigen-frequencies.
+properties:
+  name:
+    type: str
+    description: Name of the item.
+  f:
+    type: float64
+    shape: [nf_MISPELLED]
+    unit: Hz
+    description: The magic eigen-frequencies of the item.

bindings/python/tests/entities/ValidYaml1.yaml

@@ -0,0 +1,14 @@
+# An valid version of datamodel Invalid1.yaml
+uri: http://onto-ns.com/meta/0.1/ValidYaml1
+description: An datamodel for an item with float type and invalid shape name.
+dimensions:
+  nf: Number of eigen-frequencies.
+properties:
+  name:
+    type: str
+    description: Name of the item.
+  f:
+    type: float64
+    shape: [nf]
+    unit: Hz
+    description: The magic eigen-frequencies of the item.

bindings/python/tests/test_storage.py

@@ -127,9 +127,9 @@
             location: Path to YAML file.
             options: Supported options:
             - `mode`: Mode for opening.  Valid values are:
-                - `a`: Append to existing file or create new file (default).
-                - `r`: Open existing file for read-only.
-                - `w`: Truncate existing file or create new file.
+                - `a`: Open for writing, add to existing `location` (default).
+                - `r`: Open existing `location` for reading.
+                - `w`: Open for writing. If `location` exists, it is truncated.
             - `soft7`: Whether to save using SOFT7 format.
             - `single`: Whether the input is assumed to be in single-entity form.
               If "auto" (default) the form will be inferred automatically.

storages/python/python-storage-plugins/yaml.py

@@ -24,9 +24,9 @@ def open(self, location: str, options=None):
             location: Path to YAML file.
             options: Supported options:
             - `mode`: Mode for opening.  Valid values are:
-                - `a`: Append to existing file or create new file (default).
-                - `r`: Open existing file for read-only.
-                - `w`: Truncate existing file or create new file.
+                - `a`: Open for writing, add to existing `location` (default).
+                - `r`: Open existing `location` for reading.
+                - `w`: Open for writing. If `location` exists, it is truncated.
             - `soft7`: Whether to save using SOFT7 format.
             - `single`: Whether the input is assumed to be in single-entity form.
               If "auto" (default) the form will be inferred automatically.
@@ -35,13 +35,13 @@ def open(self, location: str, options=None):
         self.options = Options(
             options, defaults="mode=a;soft7=true;single=auto;with_uuid=false"
         )
-        self.readable = "r" in self.options.mode
-        self.writable = "r" != self.options.mode
+        mode = self.options.mode
+        self.writable = "w" in mode or "a" in mode
         self.generic = True
         self.location = location
-        self.flushed = False  # whether buffered data has been written to file
+        self.flushed = True  # whether buffered data has been written to file
         self._data = {}  # data buffer
-        if self.options.mode in ("r", "a", "append"):
+        if "r" in mode or "a" in mode:
             with open(location, "r") as f:
                 data = pyyaml.safe_load(f)
             if data: