Simulation validation (#246)

* Added simulation config schema validation
* Added tests for simulation schema validation
* Add simulation validation as click command
* Update docs
* deprecated 'validate' -> 'validate-circuit'

CHANGELOG.rst

@@ -1,6 +1,23 @@
 Changelog
 =========
 
+Version v2.1.0
+--------------
+
+New Features
+~~~~~~~~~~~~
+- Added simulation config validation
+- Added a new  commandline subcommand: ``validate-simulation``
+- Added an alias ``validate-circuit`` for the old ``validate`` subcommand
+
+  - deprecated ``validate``
+
+
+Breaking Changes
+~~~~~~~~~~~~~~~~
+- Deprecated the commandline subcommand ``validate`` in favor of new ``validate-circuit`` command
+
+
 Version v2.0.2
 --------------
 

README.rst

@@ -62,7 +62,7 @@ This functionality is provided by either the cli function:
 
 .. code-block:: shell
 
-    bluepysnap validate my/circuit/path/circuit_config.json
+    bluepysnap validate-circuit my/circuit/path/circuit_config.json
 
 
 Or a python free function:
@@ -73,6 +73,31 @@ Or a python free function:
     errors = validate("my/circuit/path/circuit_config.json")
 
 
+Simulation Validation
+~~~~~~~~~~~~~~~~~~~~~
+
+Similarly to circuit validation, Blue Brain SNAP also provides a SONATA simulation validator for verifying simulation configs.
+
+Currently, the validator only verifies that:
+
+- all the mandatory fields are present in the config file
+- all the properties in the `simulation config specification <https://sonata-extension.readthedocs.io/en/latest/sonata_simulation.html>`__ have correct data types and accepted values
+
+This functionality is provided by either the cli function:
+
+.. code-block:: shell
+
+    bluepysnap validate-simulation my/circuit/path/simulation_config.json
+
+
+Or a python free function:
+
+.. code-block:: python3
+
+    from bluepysnap.simulation_validation import validate
+    errors = validate("my/circuit/path/simulation_config.json")
+
+
 Acknowledgements
 ----------------
 

bluepysnap/circuit_validation.py

@@ -5,7 +5,6 @@
 import logging
 from pathlib import Path
 
-import click
 import h5py
 import numpy as np
 import pandas as pd
@@ -15,7 +14,7 @@
 from bluepysnap.exceptions import BluepySnapValidationError
 from bluepysnap.morph import EXTENSIONS_MAPPING
 from bluepysnap.sonata_constants import DEFAULT_EDGE_TYPE, DEFAULT_NODE_TYPE
-from bluepysnap.utils import load_json
+from bluepysnap.utils import load_json, print_validation_errors
 
 L = logging.getLogger("brainbuilder")
 MAX_MISSING_FILES_DISPLAY = 10
@@ -73,21 +72,6 @@ def _check_files(name, files):
     return []
 
 
-def _print_errors(errors):
-    """Some fancy errors printing."""
-    colors = {
-        BluepySnapValidationError.WARNING: "yellow",
-        BluepySnapValidationError.FATAL: "red",
-        BluepySnapValidationError.INFO: "green",
-    }
-
-    if not errors:
-        print(click.style("No Error: Success.", fg=colors[BluepySnapValidationError.INFO]))
-
-    for error in errors:
-        print(click.style(error.level + ": ", fg=colors[error.level]) + str(error))
-
-
 def _check_duplicate_populations(networks, key):
     """Check that that for key = nodes|edges, no duplicate populations names exists."""
     seen = set()
@@ -599,7 +583,7 @@ def validate(config_file, skip_slow, only_errors=False, print_errors=True):
         print_errors (bool): print errors
 
     Returns:
-        list: List of errors, empty if no errors
+        set: set of errors, empty if no errors
     """
     config = Parser.parse(load_json(config_file), str(Path(config_file).parent))
     errors = schemas.validate_circuit_schema(config_file, config)
@@ -618,6 +602,6 @@ def validate(config_file, skip_slow, only_errors=False, print_errors=True):
         errors = [e for e in errors if e.level == BluepySnapValidationError.FATAL]
 
     if print_errors:
-        _print_errors(errors)
+        print_validation_errors(errors)
 
     return set(errors)

bluepysnap/cli.py

@@ -1,9 +1,14 @@
 """The project's command line launcher."""
+import functools
 import logging
+import warnings
 
 import click
 
-from bluepysnap import circuit_validation
+from bluepysnap import circuit_validation, simulation_validation
+from bluepysnap.utils import Deprecate
+
+CLICK_EXISTING_FILE = click.Path(exists=True, file_okay=True, dir_okay=False)
 
 
 @click.group()
@@ -18,23 +23,66 @@ def cli(verbose):
     )
 
 
+def circuit_validation_params(func):
+    """Small helper to have shared params."""
+
+    @click.argument("config_file", type=CLICK_EXISTING_FILE)
+    @click.option(
+        "--skip-slow/--no-skip-slow",
+        default=True,
+        help=(
+            "Skip slow checks; checking all edges refer to existing node ids, "
+            "edge indices are correct, etc"
+        ),
+    )
+    @click.option("--only-errors", is_flag=True, help="Only print fatal errors (ignore warnings)")
+    @functools.wraps(func)
+    def wrapper(*args, **kwargs):
+        return func(*args, **kwargs)
+
+    return wrapper
+
+
 @cli.command()
-@click.argument("config_file", type=click.Path(exists=True, file_okay=True, dir_okay=False))
-@click.option(
-    "--skip-slow/--no-skip-slow",
-    default=True,
-    help=(
-        "Skip slow checks; checking all edges refer to existing node ids, "
-        "edge indices are correct, etc"
-    ),
-)
-@click.option("--only-errors", is_flag=True, help="Only print fatal errors (ignore warnings)")
+@circuit_validation_params
 def validate(config_file, skip_slow, only_errors):
-    """Validate of Sonata circuit based on config file.
+    """[DEPRECATED] Validate Sonata circuit based on config file.
 
     Args:
         config_file (str): path to Sonata circuit config file
         skip_slow (bool): skip slow tests
         only_errors (bool): only print fatal errors
     """
+    with warnings.catch_warnings():
+        # Making sure the warning is shown
+        warnings.simplefilter("always", DeprecationWarning)
+        Deprecate.warn(
+            "Calling circuit validation with 'validate' is deprecated. "
+            "Please use 'validate-circuit' instead."
+        )
+
     circuit_validation.validate(config_file, skip_slow, only_errors)
+
+
+@cli.command()
+@circuit_validation_params
+def validate_circuit(config_file, skip_slow, only_errors):
+    """Validate Sonata circuit based on config file.
+
+    Args:
+        config_file (str): path to Sonata circuit config file
+        skip_slow (bool): skip slow tests
+        only_errors (bool): only print fatal errors
+    """
+    circuit_validation.validate(config_file, skip_slow, only_errors)
+
+
+@cli.command()
+@click.argument("config_file", type=CLICK_EXISTING_FILE)
+def validate_simulation(config_file):
+    """Validate Sonata simulation based on config file.
+
+    Args:
+        config_file (str): path to Sonata simulation config file
+    """
+    simulation_validation.validate(config_file)

bluepysnap/schemas/__init__.py

@@ -3,4 +3,5 @@
     validate_circuit_schema,
     validate_edges_schema,
     validate_nodes_schema,
+    validate_simulation_schema,
 )