Fix mount permissions on input volumes (#492)

* Add Data Preparator cookiecutter template

* Rename cookiecutter folder

* Temporarily remove possibly offending files

* Remove cookicutter conditionals

* Inclube back missing pieces of template

* remove cookiecutter typo

* Use project_name attribute

* Change cookiecutter fields order

* Create empty directories on hook

* Fix empty folders paths

* Create evaluator mlcube cookiecutter template

* Fix JSON Syntax Error

* Update template default values

* Remove reference to undefined template variable

* Implement model mlcube cookiecutter template

* Update cookiecutter variable default values

* Create medperf CLI command for creating MLCubes

* Provide additional options for mlcube create

* Start working on tests

* Add tests for cube create

* Ignore invalid syntax on cookiecutter conditionals

* Ignore more flake8 errors

* Remove unused import

* Empty commit for cloudbuild

* Fix inconsistency with labels paths

* Update mlcube.yaml so it can be commented on docs

* Don't render noqa comments on template

* Remove flake8 specific ignores

* Exclude templates from lint checks

* Remove specific flake8 ignores

* Fix labels_paht being passed in he wrong situation

* Add requirements to cookiecutters

* Set separate labels as true by default

* Remove duplicate templates

* Abstract field-error dict formatting

* Reformat errors dictionary for printing

* Implement general read-only input permission

* Remove unnecessary permission definition

* Fix/implement ro tests

---------

Co-authored-by: hasan7n <[email protected]>

cli/medperf/commands/dataset/create.py

@@ -119,33 +119,22 @@ def run_cube_tasks(self):
             "output_path": out_datapath,
             "output_labels_path": out_labelspath,
         }
-        prepare_str_params = {
-            "Ptasks.prepare.parameters.input.data_path.opts": "ro",
-            "Ptasks.prepare.parameters.input.labels_path.opts": "ro",
-        }
 
         sanity_params = {
             "data_path": out_datapath,
             "labels_path": out_labelspath,
         }
-        sanity_str_params = {
-            "Ptasks.sanity_check.parameters.input.data_path.opts": "ro"
-        }
 
         statistics_params = {
             "data_path": out_datapath,
             "output_path": self.out_statistics_path,
             "labels_path": out_labelspath,
         }
-        statistics_str_params = {
-            "Ptasks.statistics.parameters.input.data_path.opts": "ro"
-        }
 
         # Run the tasks
         self.ui.text = "Running preparation step..."
         self.cube.run(
             task="prepare",
-            string_params=prepare_str_params,
             timeout=prepare_timeout,
             **prepare_params,
         )
@@ -154,7 +143,6 @@ def run_cube_tasks(self):
         self.ui.text = "Running sanity check..."
         self.cube.run(
             task="sanity_check",
-            string_params=sanity_str_params,
             timeout=sanity_check_timeout,
             **sanity_params,
         )
@@ -163,7 +151,6 @@ def run_cube_tasks(self):
         self.ui.text = "Generating statistics..."
         self.cube.run(
             task="statistics",
-            string_params=statistics_str_params,
             timeout=statistics_timeout,
             **statistics_params,
         )

cli/medperf/commands/execution.py

@@ -86,7 +86,6 @@ def run_inference(self):
                 timeout=infer_timeout,
                 data_path=data_path,
                 output_path=preds_path,
-                string_params={"Ptasks.infer.parameters.input.data_path.opts": "ro"},
             )
             self.ui.print("> Model execution complete")
 
@@ -113,10 +112,6 @@ def run_evaluation(self):
                 predictions=preds_path,
                 labels=labels_path,
                 output_path=results_path,
-                string_params={
-                    "Ptasks.evaluate.parameters.input.predictions.opts": "ro",
-                    "Ptasks.evaluate.parameters.input.labels.opts": "ro",
-                },
             )
         except ExecutionError as e:
             logging.error(f"Metrics MLCube Execution failed: {e}")

cli/medperf/entities/cube.py

@@ -277,6 +277,7 @@ def run(
         output_logs: str = None,
         string_params: Dict[str, str] = {},
         timeout: int = None,
+        read_protected_input: bool = True,
         **kwargs,
     ):
         """Executes a given task on the cube instance
@@ -286,6 +287,7 @@ def run(
             string_params (Dict[str], optional): Extra parameters that can't be passed as normal function args.
                                                  Defaults to {}.
             timeout (int, optional): timeout for the task in seconds. Defaults to None.
+            read_protected_input (bool, optional): Wether to disable write permissions on input volumes. Defaults to True.
             kwargs (dict): additional arguments that are passed directly to the mlcube command
         """
         kwargs.update(string_params)
@@ -294,6 +296,8 @@ def run(
         cmd += f" --mlcube={self.cube_path} --task={task} --platform={config.platform} --network=none"
         if config.gpus is not None:
             cmd += f" --gpus={config.gpus}"
+        if read_protected_input:
+            cmd += " --mount=ro"
         for k, v in kwargs.items():
             cmd_arg = f'{k}="{v}"'
             cmd = " ".join([cmd, cmd_arg])

cli/medperf/tests/commands/dataset/test_create.py

@@ -116,25 +116,19 @@ def test_run_cube_tasks_runs_required_tasks(self, mocker, preparation):
             labels_path=LABELS_PATH,
             output_path=OUT_DATAPATH,
             output_labels_path=OUT_LABELSPATH,
-            string_params={
-                "Ptasks.prepare.parameters.input.data_path.opts": "ro",
-                "Ptasks.prepare.parameters.input.labels_path.opts": "ro",
-            },
         )
         check = call(
             task="sanity_check",
             timeout=None,
             data_path=OUT_DATAPATH,
             labels_path=OUT_LABELSPATH,
-            string_params={"Ptasks.sanity_check.parameters.input.data_path.opts": "ro"},
         )
         stats = call(
             task="statistics",
             timeout=None,
             data_path=OUT_DATAPATH,
             labels_path=OUT_LABELSPATH,
             output_path=STATISTICS_PATH,
-            string_params={"Ptasks.statistics.parameters.input.data_path.opts": "ro"},
         )
         calls = [prepare, check, stats]
 

cli/medperf/tests/commands/test_execution.py

@@ -178,7 +178,6 @@ def test_cube_run_are_called_properly(mocker, setup):
         timeout=config.infer_timeout,
         data_path=INPUT_DATASET.data_path,
         output_path=exp_preds_path,
-        string_params={"Ptasks.infer.parameters.input.data_path.opts": "ro"},
     )
     exp_eval_call = call(
         task="evaluate",
@@ -187,10 +186,6 @@ def test_cube_run_are_called_properly(mocker, setup):
         predictions=exp_preds_path,
         labels=INPUT_DATASET.labels_path,
         output_path=ANY,
-        string_params={
-            "Ptasks.evaluate.parameters.input.predictions.opts": "ro",
-            "Ptasks.evaluate.parameters.input.labels.opts": "ro",
-        },
     )
     # Act
     Execution.run(INPUT_DATASET, INPUT_MODEL, INPUT_EVALUATOR)

cli/medperf/tests/entities/test_cube.py

@@ -162,7 +162,7 @@ def test_cube_runs_command(self, mocker, timeout, setup, task):
         )
         expected_cmd = (
             f"mlcube run --mlcube={self.manifest_path} --task={task} "
-            + f"--platform={self.platform} --network=none"
+            + f"--platform={self.platform} --network=none --mount=ro"
         )
 
         # Act
@@ -172,13 +172,29 @@ def test_cube_runs_command(self, mocker, timeout, setup, task):
         # Assert
         spy.assert_any_call(expected_cmd, timeout=timeout)
 
+    def test_cube_runs_command_with_rw_access(self, mocker, setup, task):
+        # Arrange
+        mpexpect = MockPexpect(0, "expected_hash")
+        spy = mocker.patch("pexpect.spawn", side_effect=mpexpect.spawn)
+        expected_cmd = (
+            f"mlcube run --mlcube={self.manifest_path} --task={task} "
+            + f"--platform={self.platform} --network=none"
+        )
+
+        # Act
+        cube = Cube.get(self.id)
+        cube.run(task, read_protected_input=False)
+
+        # Assert
+        spy.assert_any_call(expected_cmd, timeout=None)
+
     def test_cube_runs_command_with_extra_args(self, mocker, setup, task):
         # Arrange
         mpexpect = MockPexpect(0, "expected_hash")
         spy = mocker.patch("pexpect.spawn", side_effect=mpexpect.spawn)
         expected_cmd = (
             f"mlcube run --mlcube={self.manifest_path} --task={task} "
-            + f'--platform={self.platform} --network=none test="test"'
+            + f'--platform={self.platform} --network=none --mount=ro test="test"'
         )
 
         # Act