Merge pull request #66 from pepkit/dev

0.2.2 release

docs/api_docs.md

@@ -1,4 +1,4 @@
-Final targets: convert_project, get_available_pep_filters, inspect_project, read_schema, validate_config, validate_project, validate_sample
+Final targets: EidoValidationError, convert_project, get_available_pep_filters, get_input_files_size, inspect_project, read_schema, validate_config, validate_input_files, validate_project, validate_sample
 <script>
 document.addEventListener('DOMContentLoaded', (event) => {
   document.querySelectorAll('h3 code').forEach((block) => {
@@ -8,7 +8,7 @@ document.addEventListener('DOMContentLoaded', (event) => {
 </script>
 
 <style>
-h3 .content {
+h3 .content { 
     padding-left: 22px;
     text-indent: -15px;
  }
@@ -19,7 +19,7 @@ h3 .hljs .content {
     martin-bottom: 0px;
 }
 h4 .content, table .content, p .content, li .content { margin-left: 30px; }
-h4 .content {
+h4 .content { 
     font-style: italic;
     font-size: 1em;
     margin-bottom: 0px;
@@ -33,22 +33,33 @@ h4 .content {
 
 Project configuration
 
+## <a name="EidoValidationError"></a> Class `EidoValidationError`
+Object was not validated successfully according to schema.
+
+
 ```python
-def validate_project(project, schema, exclude_case=False)
+def __init__(self, message, errors_by_type)
+```
+
+Initialize self.  See help(type(self)) for accurate signature.
+
+
+
+```python
+def validate_project(project, schema)
 ```
 
 Validate a project object against a schema
 #### Parameters:
 
-- `project` (`peppy.Sample`):  a project object to validate
-- `schema` (`str | dict`):  schema dict to validate against or a path to one
-- `exclude_case` (`bool`):  whether to exclude validated objectsfrom the error. Useful when used ith large projects
+- `project` (`peppy.Project`):  a project object to validate
+- `schema` (`str | dict`):  schema dict to validate against or a path to onefrom the error. Useful when used ith large projects
 
 
 
 
 ```python
-def validate_sample(project, sample_name, schema, exclude_case=False)
+def validate_sample(project, sample_name, schema)
 ```
 
 Validate the selected sample object against a schema
@@ -57,21 +68,19 @@ Validate the selected sample object against a schema
 - `project` (`peppy.Project`):  a project object to validate
 - `sample_name` (`str | int`):  name or index of the sample to validate
 - `schema` (`str | dict`):  schema dict to validate against or a path to one
-- `exclude_case` (`bool`):  whether to exclude validated objectsfrom the error. Useful when used ith large projects
 
 
 
 
 ```python
-def validate_config(project, schema, exclude_case=False)
+def validate_config(project, schema)
 ```
 
 Validate the config part of the Project object against a schema
 #### Parameters:
 
 - `project` (`peppy.Project`):  a project object to validate
 - `schema` (`str | dict`):  schema dict to validate against or a path to one
-- `exclude_case` (`bool`):  whether to exclude validated objectsfrom the error. Useful when used ith large projects
 
 
 
@@ -145,7 +154,61 @@ Convert a `peppy.Project` object to a selected format
 
 
 
+```python
+def validate_input_files(project, schemas, sample_name=None)
+```
+
+Determine which of the required and optional files are missing.
+
+The names of the attributes that are required and/or deemed as inputs
+are sourced from the schema, more specifically from `required_files`
+and `files` sections in samples section:
+- If any of the required files are missing, this function raises an error.
+- If any of the optional files are missing, the function raises a warning.
+Note, this function also performs Sample object validation with jsonschema.
+#### Parameters:
+
+- `project` (`peppy.Project`):  project that defines the samples to validate
+- `schema` (`str | dict`):  schema dict to validate against or a path to one
+- `sample_name` (`str | int`):  name or index of the sample to validate. If None,validate all samples in the project
+
+
+#### Raises:
+
+- `PathAttrNotFoundError`:  if any required sample attribute is missing
+
+
+
+
+```python
+def get_input_files_size(sample, schema)
+```
+
+Determine which of this Sample's required attributes/files are missing and calculate sizes of the files (inputs).
+
+The names of the attributes that are required and/or deemed as inputs
+are sourced from the schema, more specifically from required_input_attrs
+and input_attrs sections in samples section. Note, this function does
+perform actual Sample object validation with jsonschema.
+#### Parameters:
+
+- `sample` (`peppy.Sample`):  sample to investigate
+- `schema` (`list[dict] | str`):  schema dict to validate against or a path to one
+
+
+#### Returns:
+
+- `dict`:  dictionary with validation data, i.e missing,required_inputs, all_inputs, input_file_size
+
+
+#### Raises:
+
+- `ValidationError`:  if any required sample attribute is missing
+
+
+
+
 
 
 
-*Version Information: `eido` v0.1.5-dev, generated by `lucidoc` v0.4.2*
+*Version Information: `eido` v0.2.2-dev, generated by `lucidoc` v0.4.4*

docs/autodoc_build/eido.md

@@ -30,21 +30,19 @@ h4 .content {
 # Package `eido` Documentation
 
 ```python
-def validate_project(project, schema, exclude_case=False)
+def validate_project(project, schema)
 ```
 
 Validate a project object against a schema
 #### Parameters:
 
 - `project` (`peppy.Sample`):  a project object to validate
 - `schema` (`str | dict`):  schema dict to validate against or a path to one
-- `exclude_case` (`bool`):  whether to exclude validated objectsfrom the error. Useful when used ith large projects
-
 
 
 
 ```python
-def validate_sample(project, sample_name, schema, exclude_case=False)
+def validate_sample(project, sample_name, schema)
 ```
 
 Validate the selected sample object against a schema
@@ -53,23 +51,17 @@ Validate the selected sample object against a schema
 - `project` (`peppy.Project`):  a project object to validate
 - `sample_name` (`str | int`):  name or index of the sample to validate
 - `schema` (`str | dict`):  schema dict to validate against or a path to one
-- `exclude_case` (`bool`):  whether to exclude validated objectsfrom the error. Useful when used ith large projects
-
-
 
 
 ```python
-def validate_config(project, schema, exclude_case=False)
+def validate_config(project, schema)
 ```
 
 Validate the config part of the Project object against a schema
 #### Parameters:
 
 - `project` (`peppy.Project`):  a project object to validate
 - `schema` (`str | dict`):  schema dict to validate against or a path to one
-- `exclude_case` (`bool`):  whether to exclude validated objectsfrom the error. Useful when used ith large projects
-
-
 
 
 ```python

docs/changelog.md

@@ -2,6 +2,11 @@
 
 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.
 
+## [0.2.2] - 2023-11-16
+
+### Changed
+- remove unused `exclude-case` from CLI. Fixes #65
+
 ## [0.2.1] - 2023-07-05
 
 ### Changed

docs/plugin_api_docs.md

@@ -1,5 +1,3 @@
-**The PEP filters are an experimental feature and may change in feature versions of `eido`**
-
 Final targets: basic_pep_filter, csv_pep_filter, yaml_pep_filter, yaml_samples_pep_filter
 <script>
 document.addEventListener('DOMContentLoaded', (event) => {
@@ -10,7 +8,7 @@ document.addEventListener('DOMContentLoaded', (event) => {
 </script>
 
 <style>
-h3 .content {
+h3 .content { 
     padding-left: 22px;
     text-indent: -15px;
  }
@@ -21,7 +19,7 @@ h3 .hljs .content {
     martin-bottom: 0px;
 }
 h4 .content, table .content, p .content, li .content { margin-left: 30px; }
-h4 .content {
+h4 .content { 
     font-style: italic;
     font-size: 1em;
     margin-bottom: 0px;
@@ -30,11 +28,13 @@ h4 .content {
 </style>
 
 
-# Built-in `eido` Plugins Documentation
+# Package `eido` Documentation
+
 
+Project configuration
 
 ```python
-def basic_pep_filter(p, **kwargs)
+def basic_pep_filter(p, **kwargs) -> Dict[str, str]
 ```
 
 Basic PEP filter, that does not convert the Project object.
@@ -48,7 +48,7 @@ This filter can save the PEP representation to file, if kwargs include `path`.
 
 
 ```python
-def yaml_pep_filter(p, **kwargs)
+def yaml_pep_filter(p, **kwargs) -> Dict[str, str]
 ```
 
 YAML PEP filter, that returns Project object representation.
@@ -62,7 +62,7 @@ This filter can save the YAML to file, if kwargs include `path`.
 
 
 ```python
-def csv_pep_filter(p, **kwargs)
+def csv_pep_filter(p, **kwargs) -> Dict[str, str]
 ```
 
 CSV PEP filter, that returns Sample object representations
@@ -77,7 +77,7 @@ This filter can save the CSVs to files, if kwargs include
 
 
 ```python
-def yaml_samples_pep_filter(p, **kwargs)
+def yaml_samples_pep_filter(p, **kwargs) -> Dict[str, str]
 ```
 
 YAML samples PEP filter, that returns only Sample object representations.
@@ -93,4 +93,4 @@ This filter can save the YAML to file, if kwargs include `path`.
 
 
 
-*Version Information: `eido` v0.1.5-dev, generated by `lucidoc` v0.4.2*
+*Version Information: `eido` v0.2.2-dev, generated by `lucidoc` v0.4.4*

eido/_version.py

@@ -1 +1 @@
-__version__ = "0.2.1"
+__version__ = "0.2.2"

eido/argparser.py

@@ -88,16 +88,6 @@ def build_argparser():
         metavar="S",
     )
 
-    sps[VALIDATE_CMD].add_argument(
-        "-e",
-        "--exclude-case",
-        default=False,
-        action="store_true",
-        help="Whether to exclude the validation case from an error. "
-        "Only the human readable message explaining the error will "
-        "be raised. Useful when validating large PEPs.",
-    )
-
     sps[INSPECT_CMD].add_argument(
         "-n",
         "--sample-name",

eido/cli.py

@@ -142,19 +142,19 @@ def main():
                 f"against a schema: {args.schema}"
             )
             validator = validate_sample
-            arguments = [p, args.sample_name, args.schema, args.exclude_case]
+            arguments = [p, args.sample_name, args.schema]
         elif args.just_config:
             _LOGGER.debug(
                 f"Comparing Project ('{args.pep}') against a schema: {args.schema}"
             )
             validator = validate_config
-            arguments = [p, args.schema, args.exclude_case]
+            arguments = [p, args.schema]
         else:
             _LOGGER.debug(
                 f"Comparing Project ('{args.pep}') against a schema: {args.schema}"
             )
             validator = validate_project
-            arguments = [p, args.schema, args.exclude_case]
+            arguments = [p, args.schema]
         try:
             validator(*arguments)
         except EidoValidationError as e:

eido/exceptions.py

@@ -43,3 +43,7 @@ class EidoValidationError(EidoException):
     def __init__(self, message, errors_by_type):
         super().__init__(message)
         self.errors_by_type = errors_by_type
+        self.message = message
+
+    def __str__(self):
+        return f"EidoValidationError ({self.message}): {self.errors_by_type}"

eido/inspection.py

@@ -77,7 +77,11 @@ def get_input_files_size(sample, schema):
         all_inputs.update(required_inputs)
     with catch_warnings(record=True) as w:
         input_file_size = sum(
-            [size(f, size_str=False) or 0.0 for f in all_inputs if f != ""]
+            [
+                size(f, size_str=False) or 0.0
+                for f in all_inputs
+                if f != "" and f != None
+            ]
         ) / (1024**3)
         if w:
             _LOGGER.warning(

eido/validation.py

@@ -21,19 +21,19 @@
 _LOGGER = getLogger(__name__)
 
 
-def _validate_object(object, schema, sample_name_colname=False):
+def _validate_object(obj, schema, sample_name_colname=False):
     """
     Generic function to validate object against a schema
 
-    :param Mapping object: an object to validate
+    :param Mapping obj: an object to validate
     :param str | dict schema: schema dict to validate against or a path to one
         from the error. Useful when used ith large projects
     :raises EidoValidationError: if validation is unsuccessful
     """
     validator = Draft7Validator(schema)
-    _LOGGER.debug(f"{object},\n {schema}")
-    if not validator.is_valid(object):
-        errors = sorted(validator.iter_errors(object), key=lambda e: e.path)
+    _LOGGER.debug(f"{obj},\n {schema}")
+    if not validator.is_valid(obj):
+        errors = sorted(validator.iter_errors(obj), key=lambda e: e.path)
         errors_by_type = {}
 
         # Accumulate and restructure error objects by error type

requirements/requirements-all.txt

@@ -1,5 +1,5 @@
 jsonschema>=3.0.1
 logmuse>=0.2.5
 pandas
-peppy>=0.35.5
+peppy>=0.35.7
 ubiquerg>=0.5.2

webeido/webeido/main.py

@@ -112,7 +112,7 @@ async def validate_pep(request: Request, files: List[UploadFile] = File(...)):
     def vwrap(p, schema):
         x = None
         try:
-            eido.validate_project(project=p, schema=schema, exclude_case=True)
+            eido.validate_project(project=p, schema=schema)
         except Exception as e:
             x = e
             print(x)