implement divvy config validation, add schema; #54

pepkit · Feb 26, 2021 · d40bfeb · d40bfeb
1 parent 5973700
commit d40bfeb
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Showing 4 changed files with 35 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -2,6 +2,7 @@
 
 [![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
 [![Build Status](https://travis-ci.org/pepkit/divvy.svg?branch=master)](https://travis-ci.org/pepkit/divvy)
-[![Coverage Status](https://coveralls.io/repos/github/pepkit/divvy/badge.svg?branch=master)](https://coveralls.io/github/pepkit/divvy?branch=master)
+[![codecov](https://codecov.io/gh/pepkit/divvy/branch/master/graph/badge.svg?token=AO0I7HA2YL)](https://codecov.io/gh/pepkit/divvy)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 `divvy` is a python package for reading portable computing environment configuration files, which we call *divvy configuration files*. Complete documentation and API for the `divvy` python package is at [divvy.databio.org](http://divvy.databio.org).
diff --git a/divvy/compute.py b/divvy/compute.py
@@ -17,6 +17,7 @@
     DEFAULT_COMPUTE_RESOURCES_NAME,
     NEW_COMPUTE_KEY,
     DEFAULT_CONFIG_FILEPATH,
+    DEFAULT_CONFIG_SCHEMA,
 )
 from .utils import write_submit_script
 from . import __version__
@@ -45,7 +46,12 @@ def __init__(self, entries=None, filepath=None):
             # Handle the case of an empty one, when we'll use the default
             filepath = select_divvy_config(None)
 
-        super(ComputingConfiguration, self).__init__(entries, filepath)
+        super(ComputingConfiguration, self).__init__(
+            entries=entries,
+            filepath=filepath,
+            schema_source=DEFAULT_CONFIG_SCHEMA,
+            write_validate=True,
+        )
 
         if not hasattr(self, "compute_packages"):
             raise Exception(
@@ -63,7 +69,7 @@ def __init__(self, entries=None, filepath=None):
         self.config_file = self.file_path
 
     def write(self, filename=None):
-        super(ComputingConfiguration, self).write(filename)
+        super(ComputingConfiguration, self).write(filepath=filename, exclude_case=True)
         filename = filename or getattr(self, yacman.FILEPATH_KEY)
         filedir = os.path.dirname(filename)
         # For this object, we *also* have to write the template files

diff --git a/divvy/const.py b/divvy/const.py
@@ -9,11 +9,15 @@
 DEFAULT_CONFIG_FILEPATH = os.path.join(
     os.path.dirname(__file__), "default_config", "divvy_config.yaml"
 )
+DEFAULT_CONFIG_SCHEMA = os.path.join(
+    os.path.dirname(__file__), "schemas", "divvy_config_schema.yaml"
+)
 COMPUTE_CONSTANTS = [
     "COMPUTE_SETTINGS_VARNAME",
     "DEFAULT_COMPUTE_RESOURCES_NAME",
     "NEW_COMPUTE_KEY",
     "DEFAULT_CONFIG_FILEPATH",
+    "DEFAULT_CONFIG_SCHEMA",
 ]
 
 __all__ = COMPUTE_CONSTANTS + ["DEFAULT_COMPUTE_RESOURCES_NAME"]
diff --git a/divvy/schemas/divvy_config_schema.yaml b/divvy/schemas/divvy_config_schema.yaml
@@ -0,0 +1,21 @@
+description: "divvy configuration file schema"
+version: "0.1"
+required:
+  - compute_packages
+properties:
+  compute_packages:
+    type: object
+    additionalProperties: false
+    patternProperties:
+      ^.*$:
+        type: object
+        additionalProperties: false
+        patternProperties:
+          ^.*$:
+            type: string
+  adapters:
+    type: object
+    additionalProperties: false
+    patternProperties:
+      ^.*$:
+        type: string