Merge pull request #41 from pepkit/dev

Release `0.1.7`

.gitignore

@@ -89,4 +89,8 @@ webeido/webeido/uploads
 # virtual env's
 .env
 env
-venv
+venv
+.venv
+
+# tests
+out/

docs/changelog.md

@@ -2,6 +2,10 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.1.7] - 2022-08-11
+### Changed
+- When a validation fails, `eido` will now return all errors instead of just the first one it finds.
+
 ## [0.1.6] - 2022-05-16
 ### Added
 - a possibility to set a custom sample table index with `-s/--st-index` option

eido/_version.py

@@ -1 +1 @@
-__version__ = "0.1.6"
+__version__ = "0.1.7"

eido/exceptions.py

@@ -30,3 +30,11 @@ class EidoFilterError(EidoException):
 
     def __init__(self, key):
         super(EidoFilterError, self).__init__(key)
+
+
+class EidoValidationError(EidoException):
+    """Object was not validated successfully according to schema."""
+
+    def __init__(self, message, errors):
+        super().__init__(message)
+        self.errors = errors

eido/validation.py

@@ -2,11 +2,13 @@
 from copy import deepcopy as dpcpy
 from logging import getLogger
 from warnings import catch_warnings as cw
+from .exceptions import EidoValidationError
 
-import jsonschema
 from pandas.core.common import flatten
 from ubiquerg import size
 
+from jsonschema import Draft7Validator
+
 from .const import (
     ALL_INPUTS_KEY,
     FILES_KEY,
@@ -30,12 +32,13 @@ def _validate_object(object, schema, exclude_case=False):
     :param bool exclude_case: whether to exclude validated objects
         from the error. Useful when used ith large projects
     """
-    try:
-        jsonschema.validate(object, schema)
-    except jsonschema.exceptions.ValidationError as e:
-        if not exclude_case:
-            raise
-        raise jsonschema.exceptions.ValidationError(e.message)
+
+    validator = Draft7Validator(schema)
+    if not validator.is_valid(object):
+        errors = sorted(validator.iter_errors(object), key=lambda e: e.path)
+        raise EidoValidationError(
+            f"Validation unsuccessful. {len(errors)} errors found.", errors
+        )
 
 
 def validate_project(project, schema, exclude_case=False):

tests/data/schemas/test_schema_imports.yaml

@@ -1,5 +1,5 @@
 imports:
-    - https://schema.databio.org/pep/2.0.0.yaml
+    - http://schema.databio.org/pep/2.0.0.yaml
 description: Schema for a more restrictive PEP
 properties:
   samples:

tests/test_validations.py

@@ -6,6 +6,7 @@
 from peppy.utils import load_yaml
 
 from eido import *
+from eido.exceptions import EidoValidationError
 
 
 def _check_remote_file_accessible(url):
@@ -23,13 +24,13 @@ def test_validate_works(self, project_object, schema_file_path):
         validate_project(project=project_object, schema=schema_file_path)
 
     def test_validate_detects_invalid(self, project_object, schema_invalid_file_path):
-        with pytest.raises(ValidationError):
+        with pytest.raises(EidoValidationError):
             validate_project(project=project_object, schema=schema_invalid_file_path)
 
     def test_validate_detects_invalid_imports(
         self, project_object, schema_imports_file_path
     ):
-        with pytest.raises(ValidationError):
+        with pytest.raises(EidoValidationError):
             validate_project(project=project_object, schema=schema_imports_file_path)
 
     def test_validate_converts_samples_to_private_attr(
@@ -80,7 +81,7 @@ def test_validate_raises_error_for_incorrect_sample_name(
     def test_validate_detects_invalid(
         self, project_object, sample_name, schema_sample_invalid_file_path
     ):
-        with pytest.raises(ValidationError):
+        with pytest.raises(EidoValidationError):
             validate_sample(
                 project=project_object,
                 sample_name=sample_name,
@@ -96,9 +97,7 @@ def test_validate_succeeds_on_invalid_sample(
 
 
 class TestRemoteValidation:
-    @pytest.mark.parametrize(
-        "schema_url", ["https://schema.databio.org/pep/2.0.0.yaml"]
-    )
+    @pytest.mark.parametrize("schema_url", ["http://schema.databio.org/pep/2.0.0.yaml"])
     def test_validate_works_with_remote_schemas(self, project_object, schema_url):
         _check_remote_file_accessible(schema_url)
         validate_project(project=project_object, schema=schema_url)
@@ -135,7 +134,7 @@ def test_validate_works(self, schema_file_path, remote_pep_cfg):
     )
     def test_validate_detects_invalid(self, schema_invalid_file_path, remote_pep_cfg):
         _check_remote_file_accessible(remote_pep_cfg)
-        with pytest.raises(ValidationError):
+        with pytest.raises(EidoValidationError):
             validate_project(
                 project=Project(remote_pep_cfg),
                 schema=schema_invalid_file_path,