Implement Entity editing commands

cli/medperf/commands/benchmark/benchmark.py

@@ -6,10 +6,21 @@
 from medperf.entities.benchmark import Benchmark
 from medperf.commands.list import EntityList
 from medperf.commands.view import EntityView
+from medperf.commands.edit import EntityEdit
 from medperf.commands.benchmark.submit import SubmitBenchmark
 from medperf.commands.benchmark.associate import AssociateBenchmark
 from medperf.commands.result.create import BenchmarkExecution
 
+NAME_HELP = "Name of the benchmark"
+DESC_HELP = "Description of the benchmark"
+DOCS_HELP = "URL to documentation"
+DEMO_URL_HELP = """Identifier to download the demonstration dataset tarball file.\n
+    See `medperf mlcube submit --help` for more information"""
+DEMO_HASH_HELP = "SHA1 of demonstration dataset tarball file"
+DATA_PREP_HELP = "Data Preparation MLCube UID"
+MODEL_HELP = "Reference Model MLCube UID"
+EVAL_HELP = "Evaluator MLCube UID"
+
 app = typer.Typer()
 
 
@@ -31,31 +42,61 @@ def list(
 @app.command("submit")
 @clean_except
 def submit(
-    name: str = typer.Option(..., "--name", "-n", help="Name of the benchmark"),
-    description: str = typer.Option(
-        ..., "--description", "-d", help="Description of the benchmark"
+    name: str = typer.Option(..., "--name", "-n", help=NAME_HELP),
+    description: str = typer.Option(..., "--description", "-d", help=DESC_HELP),
+    docs_url: str = typer.Option("", "--docs-url", "-u", help=DOCS_HELP),
+    demo_url: str = typer.Option("", "--demo-url", help=DEMO_URL_HELP),
+    demo_hash: str = typer.Option("", "--demo-hash", help=DEMO_HASH_HELP),
+    data_preparation_mlcube: int = typer.Option(
+        ..., "--data-preparation-mlcube", "-p", help=DATA_PREP_HELP
     ),
-    docs_url: str = typer.Option("", "--docs-url", "-u", help="URL to documentation"),
-    demo_url: str = typer.Option(
-        "",
-        "--demo-url",
-        help="""Identifier to download the demonstration dataset tarball file.\n
-        See `medperf mlcube submit --help` for more information""",
+    reference_model_mlcube: int = typer.Option(
+        ..., "--reference-model-mlcube", "-m", help=MODEL_HELP
     ),
-    demo_hash: str = typer.Option(
-        "", "--demo-hash", help="SHA1 of demonstration dataset tarball file"
+    evaluator_mlcube: int = typer.Option(
+        ..., "--evaluator-mlcube", "-e", help=EVAL_HELP
     ),
+):
+    """Submits a new benchmark to the platform"""
+    benchmark_info = {
+        "name": name,
+        "description": description,
+        "docs_url": docs_url,
+        "demo_dataset_tarball_url": demo_url,
+        "demo_dataset_tarball_hash": demo_hash,
+        "data_preparation_mlcube": data_preparation_mlcube,
+        "reference_model_mlcube": reference_model_mlcube,
+        "data_evaluator_mlcube": evaluator_mlcube,
+    }
+    SubmitBenchmark.run(benchmark_info)
+    config.ui.print("✅ Done!")
+
+
+@app.command("edit")
+@clean_except
+def edit(
+    entity_id: int = typer.Argument(..., help="Benchmark ID"),
+    name: str = typer.Option(None, "--name", "-n", help=NAME_HELP),
+    description: str = typer.Option(None, "--description", "-d", help=DESC_HELP),
+    docs_url: str = typer.Option(None, "--docs-url", "-u", help=DOCS_HELP),
+    demo_url: str = typer.Option(None, "--demo-url", help=DEMO_URL_HELP),
+    demo_hash: str = typer.Option(None, "--demo-hash", help=DEMO_HASH_HELP),
     data_preparation_mlcube: int = typer.Option(
-        ..., "--data-preparation-mlcube", "-p", help="Data Preparation MLCube UID"
+        None, "--data-preparation-mlcube", "-p", help=DATA_PREP_HELP
     ),
     reference_model_mlcube: int = typer.Option(
-        ..., "--reference-model-mlcube", "-m", help="Reference Model MLCube UID"
+        None, "--reference-model-mlcube", "-m", help=MODEL_HELP
     ),
     evaluator_mlcube: int = typer.Option(
-        ..., "--evaluator-mlcube", "-e", help="Evaluator MLCube UID"
+        None, "--evaluator-mlcube", "-e", help=EVAL_HELP
+    ),
+    is_valid: bool = typer.Option(
+        None,
+        "--valid/--invalid",
+        help="Flags a dataset valid/invalid. Invalid datasets can't be used for experiments",
     ),
 ):
-    """Submits a new benchmark to the platform"""
+    """Edits a benchmark"""
     benchmark_info = {
         "name": name,
         "description": description,
@@ -65,8 +106,9 @@ def submit(
         "data_preparation_mlcube": data_preparation_mlcube,
         "reference_model_mlcube": reference_model_mlcube,
         "data_evaluator_mlcube": evaluator_mlcube,
+        "is_valid": is_valid,
     }
-    SubmitBenchmark.run(benchmark_info)
+    EntityEdit.run(Benchmark, entity_id, benchmark_info)
     config.ui.print("✅ Done!")
 
 
@@ -84,11 +126,12 @@ def associate(
     ),
     approval: bool = typer.Option(False, "-y", help="Skip approval step"),
     no_cache: bool = typer.Option(
-        False, "--no-cache", help="Execute the test even if results already exist",
+        False,
+        "--no-cache",
+        help="Execute the test even if results already exist",
     ),
 ):
-    """Associates a benchmark with a given mlcube or dataset. Only one option at a time.
-    """
+    """Associates a benchmark with a given mlcube or dataset. Only one option at a time."""
     AssociateBenchmark.run(
         benchmark_uid, model_uid, dataset_uid, approved=approval, no_cache=no_cache
     )
@@ -118,11 +161,12 @@ def run(
         help="Ignore failing model cubes, allowing for possibly submitting partial results",
     ),
     no_cache: bool = typer.Option(
-        False, "--no-cache", help="Execute even if results already exist",
+        False,
+        "--no-cache",
+        help="Execute even if results already exist",
     ),
 ):
-    """Runs the benchmark execution step for a given benchmark, prepared dataset and model
-    """
+    """Runs the benchmark execution step for a given benchmark, prepared dataset and model"""
     BenchmarkExecution.run(
         benchmark_uid,
         data_uid,
@@ -163,6 +207,5 @@ def view(
         help="Output file to store contents. If not provided, the output will be displayed",
     ),
 ):
-    """Displays the information of one or more benchmarks
-    """
+    """Displays the information of one or more benchmarks"""
     EntityView.run(entity_id, Benchmark, format, local, mine, output)

cli/medperf/commands/dataset/dataset.py

@@ -6,10 +6,16 @@
 from medperf.entities.dataset import Dataset
 from medperf.commands.list import EntityList
 from medperf.commands.view import EntityView
+from medperf.commands.edit import EntityEdit
 from medperf.commands.dataset.create import DataPreparation
 from medperf.commands.dataset.submit import DatasetRegistration
 from medperf.commands.dataset.associate import AssociateDataset
 
+NAME_HELP = "Name of the dataset"
+DESC_HELP = "Description of the dataset"
+LOC_HELP = "Location or Institution the data belongs to"
+LOC_OPTION = typer.Option(..., "--location", help=LOC_HELP)
+
 app = typer.Typer()
 
 
@@ -43,16 +49,11 @@ def create(
     labels_path: str = typer.Option(
         ..., "--labels_path", "-l", help="Labels file location"
     ),
-    name: str = typer.Option(..., "--name", help="Name of the dataset"),
-    description: str = typer.Option(
-        ..., "--description", help="Description of the dataset"
-    ),
-    location: str = typer.Option(
-        ..., "--location", help="Location or Institution the data belongs to"
-    ),
+    name: str = typer.Option(..., "--name", help=NAME_HELP),
+    description: str = typer.Option(..., "--description", help=DESC_HELP),
+    location: str = typer.Option(..., "--location", help=LOC_HELP),
 ):
-    """Runs the Data preparation step for a specified benchmark and raw dataset
-    """
+    """Runs the Data preparation step for a specified benchmark and raw dataset"""
     ui = config.ui
     data_uid = DataPreparation.run(
         benchmark_uid,
@@ -77,8 +78,7 @@ def register(
     ),
     approval: bool = typer.Option(False, "-y", help="Skip approval step"),
 ):
-    """Submits an unregistered Dataset instance to the backend
-    """
+    """Submits an unregistered Dataset instance to the backend"""
     ui = config.ui
     uid = DatasetRegistration.run(data_uid, approved=approval)
     ui.print("✅ Done!")
@@ -87,6 +87,30 @@ def register(
     )
 
 
+@app.command("edit")
+@clean_except
+def edit(
+    entity_id: int = typer.Argument(..., help="Dataset ID"),
+    name: str = typer.Option(None, "--name", help=NAME_HELP),
+    description: str = typer.Option(None, "--description", help=DESC_HELP),
+    location: str = typer.Option(None, "--location", help=LOC_HELP),
+    is_valid: bool = typer.Option(
+        None,
+        "--valid/--invalid",
+        help="Flags a dataset valid/invalid. Invalid datasets can't be used for experiments",
+    ),
+):
+    """Edits a Dataset"""
+    dset_info = {
+        "name": name,
+        "description": description,
+        "location": location,
+        "is_valid": is_valid,
+    }
+    EntityEdit.run(Dataset, entity_id, dset_info)
+    config.ui.print("✅ Done!")
+
+
 @app.command("associate")
 @clean_except
 def associate(
@@ -98,7 +122,9 @@ def associate(
     ),
     approval: bool = typer.Option(False, "-y", help="Skip approval step"),
     no_cache: bool = typer.Option(
-        False, "--no-cache", help="Execute the test even if results already exist",
+        False,
+        "--no-cache",
+        help="Execute the test even if results already exist",
     ),
 ):
     """Associate a registered dataset with a specific benchmark.
@@ -137,6 +163,5 @@ def view(
         help="Output file to store contents. If not provided, the output will be displayed",
     ),
 ):
-    """Displays the information of one or more datasets
-    """
+    """Displays the information of one or more datasets"""
     EntityView.run(entity_id, Dataset, format, local, mine, output)

cli/medperf/commands/edit.py

@@ -0,0 +1,40 @@
+from medperf.entities.interface import Updatable
+from medperf.exceptions import InvalidEntityError
+
+
+class EntityEdit:
+    @staticmethod
+    def run(entity_class, id: str, fields: dict):
+        """Edits and updates an entity both locally and on the server if possible
+
+        Args:
+            entity (Editable): Entity to modify
+            fields (dict): Dicitonary of fields and values to modify
+        """
+        editor = EntityEdit(entity_class, id, fields)
+        editor.prepare()
+        editor.validate()
+        editor.edit()
+
+    def __init__(self, entity_class, id, fields):
+        self.entity_class = entity_class
+        self.id = id
+        self.fields = fields
+
+    def prepare(self):
+        self.entity = self.entity_class.get(self.id)
+        # Filter out empty fields
+        self.fields = {k: v for k, v in self.fields.items() if v is not None}
+
+    def validate(self):
+        if not isinstance(self.entity, Updatable):
+            raise InvalidEntityError("The passed entity can't be edited")
+
+    def edit(self):
+        entity = self.entity
+        entity.edit(**self.fields)
+
+        if isinstance(entity, Updatable) and entity.is_registered:
+            entity.update()
+
+        entity.write()