eido 0.2.1__py3-none-any.whl → 0.2.3__py3-none-any.whl

eido/_version.py

@@ -1 +1 @@
-__version__ = "0.2.1"
+__version__ = "0.2.3"

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/const.py

@@ -14,8 +14,11 @@ SUBPARSER_MSGS = {
     CONVERT_CMD: "Convert PEP format using filters",
 }
 PROP_KEY = "properties"
-REQUIRED_FILES_KEY = "required_files"
-FILES_KEY = "files"
+
+SAMPLES_KEY = "samples"
+
+TANGIBLE_KEY = "tangible"
+SIZING_KEY = "sizing"
 
 # sample schema input validation key names, these values are required by looper
 # to refer to the dict values
@@ -34,7 +37,9 @@ GENERAL = [
     "FILTERS_CMD",
     "SUBPARSER_MSGS",
 ]
-SCHEMA_SECTIONS = ["PROP_KEY", "REQUIRED_FILES_KEY", "FILES_KEY"]
+
+SCHEMA_SECTIONS = ["PROP_KEY", "TANGIBLE_KEY", "SIZING_KEY"]
+
 SCHEMA_VALIDAION_KEYS = [
     "MISSING_KEY",
     "REQUIRED_INPUTS_KEY",

eido/conversion.py

@@ -1,12 +1,15 @@
-import inspect
 import sys
-import os
-from logging import getLogger
 
-from pkg_resources import iter_entry_points
+if sys.version_info < (3, 10):
+    from importlib_metadata import entry_points
+else:
+    from importlib.metadata import entry_points
+import inspect
+from logging import getLogger
+import os
+from typing import NoReturn
 
 from .exceptions import *
-from typing import NoReturn
 
 _LOGGER = getLogger(__name__)
 
@@ -21,7 +24,7 @@ def pep_conversion_plugins():
     :raise EidoFilterError: if any of the filters has an invalid signature.
     """
     plugins = {}
-    for ep in iter_entry_points("pep.filters"):
+    for ep in entry_points(group="pep.filters"):
         plugin_fun = ep.load()
         if len(list(inspect.signature(plugin_fun).parameters)) != 2:
             raise EidoFilterError(

eido/conversion_plugins.py

@@ -1,4 +1,5 @@
 """ built-in PEP filters """
+
 from typing import Dict
 from .output_formatters import MultilineOutputFormatter
 
@@ -73,10 +74,12 @@ def processed_pep_filter(p, **kwargs) -> Dict[str, str]:
 
     return {
         "project": str(prj_repr),
-        "samples": str(p.samples)
-        if samples_as_objects
-        else str(p.sample_table.to_csv()),
-        "subsamples": str(p.subsamples)
-        if subsamples_as_objects
-        else str(p.subsample_table.to_csv()),
+        "samples": (
+            str(p.samples) if samples_as_objects else str(p.sample_table.to_csv())
+        ),
+        "subsamples": (
+            str(p.subsamples)
+            if subsamples_as_objects
+            else str(p.subsample_table.to_csv())
+        ),
     }

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

@@ -7,12 +7,13 @@ from ubiquerg import size
 
 from .const import (
     ALL_INPUTS_KEY,
-    FILES_KEY,
     INPUT_FILE_SIZE_KEY,
     MISSING_KEY,
     PROP_KEY,
-    REQUIRED_FILES_KEY,
     REQUIRED_INPUTS_KEY,
+    SIZING_KEY,
+    TANGIBLE_KEY,
+    SAMPLES_KEY,
 )
 from .schema import read_schema
 from .validation import _validate_sample_object, _get_attr_values
@@ -67,17 +68,21 @@ def get_input_files_size(sample, schema):
     all_inputs = set()
     required_inputs = set()
     schema = schema[-1]  # use only first schema, in case there are imports
-    sample_schema_dict = schema["properties"]["_samples"]["items"]
-    if FILES_KEY in sample_schema_dict:
-        all_inputs.update(_get_attr_values(sample, sample_schema_dict[FILES_KEY]))
-    if REQUIRED_FILES_KEY in sample_schema_dict:
+    sample_schema_dict = schema[PROP_KEY][SAMPLES_KEY]["items"]
+    if SIZING_KEY in sample_schema_dict:
+        all_inputs.update(_get_attr_values(sample, sample_schema_dict[SIZING_KEY]))
+    if TANGIBLE_KEY in sample_schema_dict:
         required_inputs = set(
-            _get_attr_values(sample, sample_schema_dict[REQUIRED_FILES_KEY])
+            _get_attr_values(sample, sample_schema_dict[TANGIBLE_KEY])
         )
         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/schema.py

@@ -2,7 +2,7 @@ from logging import getLogger
 
 from peppy.utils import load_yaml
 
-from .const import *
+from .const import SAMPLES_KEY, PROP_KEY
 
 _LOGGER = getLogger(__name__)
 
@@ -21,23 +21,15 @@ def preprocess_schema(schema_dict):
     :return dict: preprocessed schema
     """
     _LOGGER.debug(f"schema ori: {schema_dict}")
-    if "config" in schema_dict[PROP_KEY]:
-        schema_dict[PROP_KEY]["_config"] = schema_dict[PROP_KEY]["config"]
-        del schema_dict[PROP_KEY]["config"]
-    else:
-        _LOGGER.debug("No config section found in schema")
-    if "samples" in schema_dict[PROP_KEY]:
-        schema_dict[PROP_KEY]["_samples"] = schema_dict[PROP_KEY]["samples"]
-        del schema_dict[PROP_KEY]["samples"]
-        if "required" in schema_dict:
-            schema_dict["required"][
-                schema_dict["required"].index("samples")
-            ] = "_samples"
+    if "project" not in schema_dict[PROP_KEY]:
+        _LOGGER.debug("No project section found in schema")
+
+    if SAMPLES_KEY in schema_dict[PROP_KEY]:
         if (
-            "items" in schema_dict[PROP_KEY]["_samples"]
-            and PROP_KEY in schema_dict[PROP_KEY]["_samples"]["items"]
+            "items" in schema_dict[PROP_KEY][SAMPLES_KEY]
+            and PROP_KEY in schema_dict[PROP_KEY][SAMPLES_KEY]["items"]
         ):
-            s_props = schema_dict[PROP_KEY]["_samples"]["items"][PROP_KEY]
+            s_props = schema_dict[PROP_KEY][SAMPLES_KEY]["items"][PROP_KEY]
             for prop, val in s_props.items():
                 if "type" in val and val["type"] in ["string", "number", "boolean"]:
                     s_props[prop] = {}

eido/validation.py

@@ -1,4 +1,5 @@
 import os
+from typing import NoReturn, Mapping, Union
 from copy import deepcopy as dpcpy
 from logging import getLogger
 
@@ -6,34 +7,31 @@ from warnings import warn
 
 from .exceptions import EidoValidationError
 
-
 from pandas.core.common import flatten
 from jsonschema import Draft7Validator
+import peppy
 
-from .const import (
-    FILES_KEY,
-    PROP_KEY,
-    REQUIRED_FILES_KEY,
-)
+from .const import PROP_KEY, SIZING_KEY, TANGIBLE_KEY, SAMPLES_KEY
 from .exceptions import PathAttrNotFoundError
 from .schema import preprocess_schema, read_schema
 
 _LOGGER = getLogger(__name__)
 
 
-def _validate_object(object, schema, sample_name_colname=False):
+def _validate_object(obj: Mapping, schema: Union[str, dict], 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
@@ -58,13 +56,16 @@ def _validate_object(object, schema, sample_name_colname=False):
         _LOGGER.debug("Validation was successful...")
 
 
-def validate_project(project, schema):
+def validate_project(project: peppy.Project, schema: Union[str, dict]) -> NoReturn:
     """
     Validate a project object against a schema
 
     :param peppy.Project project: a project 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
+
+    :return: NoReturn
+    :raises EidoValidationError: if validation is unsuccessful
     """
     sample_name_colname = project.sample_name_colname
     schema_dicts = read_schema(schema=schema)
@@ -76,7 +77,7 @@ def validate_project(project, schema):
         _LOGGER.debug("Project validation successful")
 
 
-def _validate_sample_object(sample, schemas):
+def _validate_sample_object(sample: peppy.Sample, schemas):
     """
     Internal function that allows to validate a peppy.Sample object without
     requiring a reference to peppy.Project.
@@ -86,20 +87,24 @@ def _validate_sample_object(sample, schemas):
     """
     for schema_dict in schemas:
         schema_dict = preprocess_schema(schema_dict)
-        sample_schema_dict = schema_dict[PROP_KEY]["_samples"]["items"]
+        sample_schema_dict = schema_dict[PROP_KEY][SAMPLES_KEY]["items"]
         _validate_object(sample.to_dict(), sample_schema_dict)
         _LOGGER.debug(
             f"{getattr(sample, 'sample_name', '')} sample validation successful"
         )
 
 
-def validate_sample(project, sample_name, schema):
+def validate_sample(
+    project: peppy.Project, sample_name: Union[str, int], schema: Union[str, dict]
+) -> NoReturn:
     """
     Validate the selected sample object against a schema
 
     :param peppy.Project project: a project object to validate
     :param str | int sample_name: name or index of the sample to validate
     :param str | dict schema: schema dict to validate against or a path to one
+
+    :raises EidoValidationError: if validation is unsuccessful
     """
     sample = (
         project.samples[sample_name]
@@ -112,7 +117,9 @@ def validate_sample(project, sample_name, schema):
     )
 
 
-def validate_config(project, schema):
+def validate_config(
+    project: Union[peppy.Project, dict], schema: Union[str, dict]
+) -> NoReturn:
     """
     Validate the config part of the Project object against a schema
 
@@ -123,17 +130,21 @@ def validate_config(project, schema):
     for schema_dict in schema_dicts:
         schema_cpy = preprocess_schema(dpcpy(schema_dict))
         try:
-            del schema_cpy[PROP_KEY]["_samples"]
+            del schema_cpy[PROP_KEY][SAMPLES_KEY]
         except KeyError:
             pass
         if "required" in schema_cpy:
             try:
-                schema_cpy["required"].remove("_samples")
+                schema_cpy["required"].remove(SAMPLES_KEY)
             except ValueError:
                 pass
-        project_dict = project.to_dict()
-        _validate_object(project_dict, schema_cpy)
-        _LOGGER.debug("Config validation successful")
+        if isinstance(project, dict):
+            _validate_object({"project": project}, schema_cpy)
+
+        else:
+            project_dict = project.to_dict()
+            _validate_object(project_dict, schema_cpy)
+            _LOGGER.debug("Config validation successful")
 
 
 def _get_attr_values(obj, attrlist):
@@ -157,7 +168,11 @@ def _get_attr_values(obj, attrlist):
     return list(flatten([getattr(obj, attr, "") for attr in attrlist]))
 
 
-def validate_input_files(project, schemas, sample_name=None):
+def validate_input_files(
+    project: peppy.Project,
+    schemas: Union[str, dict],
+    sample_name: Union[str, int] = None,
+):
     """
     Determine which of the required and optional files are missing.
 
@@ -197,12 +212,12 @@ def validate_input_files(project, schemas, sample_name=None):
         all_inputs = set()
         required_inputs = set()
         schema = schemas[-1]  # use only first schema, in case there are imports
-        sample_schema_dict = schema["properties"]["_samples"]["items"]
-        if FILES_KEY in sample_schema_dict:
-            all_inputs.update(_get_attr_values(sample, sample_schema_dict[FILES_KEY]))
-        if REQUIRED_FILES_KEY in sample_schema_dict:
+        sample_schema_dict = schema[PROP_KEY][SAMPLES_KEY]["items"]
+        if SIZING_KEY in sample_schema_dict:
+            all_inputs.update(_get_attr_values(sample, sample_schema_dict[SIZING_KEY]))
+        if TANGIBLE_KEY in sample_schema_dict:
             required_inputs = set(
-                _get_attr_values(sample, sample_schema_dict[REQUIRED_FILES_KEY])
+                _get_attr_values(sample, sample_schema_dict[TANGIBLE_KEY])
             )
             all_inputs.update(required_inputs)
 

{eido-0.2.1.dist-info → eido-0.2.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: eido
-Version: 0.2.1
+Version: 0.2.3
 Summary: A project metadata validator
 Home-page: https://github.com/pepkit/eido/
 Author: Michal Stolarczyk, Nathan Sheffield
@@ -15,11 +15,12 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: jsonschema (>=3.0.1)
-Requires-Dist: logmuse (>=0.2.5)
+Requires-Dist: jsonschema>=3.0.1
+Requires-Dist: logmuse>=0.2.5
 Requires-Dist: pandas
-Requires-Dist: peppy (>=0.35.5)
-Requires-Dist: ubiquerg (>=0.5.2)
+Requires-Dist: peppy>=0.40.6
+Requires-Dist: ubiquerg>=0.5.2
+Requires-Dist: importlib-metadata; python_version < "3.10"
 
 # <img src="docs/img/eido.svg" alt="eido logo" height="70">
 
@@ -28,4 +29,4 @@ Requires-Dist: ubiquerg (>=0.5.2)
 [![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-[PEP](http://pepkit.github.io) validation tool based on [jsonschema](https://github.com/Julian/jsonschema). See [documentation](http://eido.databio.org) for usage.
+[PEP](https://pep.databio.org) validation tool based on [jsonschema](https://github.com/Julian/jsonschema). See [documentation](http://pep.databio.org/eido) for usage.

eido-0.2.3.dist-info/RECORD

@@ -0,0 +1,19 @@
+eido/__init__.py,sha256=D3CD9BefyY5Yckz-LswPca_VH_RIcZpr53_siXkbi14,612
+eido/__main__.py,sha256=L1wnnEreqYv27ZaaCwwImCIHZK0Mz5IxS80ZsNcS1zg,189
+eido/_version.py,sha256=PNiDER4qM19h9zdsdfgKt2_dT4WgYK7EguJ8RU2qA_g,22
+eido/argparser.py,sha256=vx59eO8CClaQpXehcW052y4HW5mttGTqM96PoJJwWkE,4806
+eido/cli.py,sha256=dXPaqF6uUYnGMlW2H9Mc628CfhCl3pEinxWYnQ94SVc,5814
+eido/const.py,sha256=Tb-fDKvneyZX3qLgLYVWtGGs4Hw4tRogB3OXIlwtpdY,1109
+eido/conversion.py,sha256=MKuJWvLB10opq_noTiOSviiiJgMLY7n8B2stfCjEELE,4002
+eido/conversion_plugins.py,sha256=zqjJbUo1p3l50NddGcO2KccnK5fXvQPe-GFyABr5Pg4,2529
+eido/exceptions.py,sha256=C9gc_XnxYXT8uH7xXoh1NN7KUFXbRvLp4VN7H1DqF9w,1213
+eido/inspection.py,sha256=rfuXnAawGBWQFz_hbJA2VYP_sFvpYxztxOiXL6t610o,3223
+eido/output_formatters.py,sha256=bKqaashXRh-Vp6WbQzq8lQXbNHtvOR9IdXkn31rCmL8,4481
+eido/schema.py,sha256=I75jlUlUdswkne6Xq2XLD8zm-f8p7VITQIj7J_x7aH8,2664
+eido/validation.py,sha256=vmujhaDmNp2SFLhjBrh1SVGhM_NDf3ARVt91ZHaqrUA,8527
+eido-0.2.3.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
+eido-0.2.3.dist-info/METADATA,sha256=kku0Ni4ZW43It53F7_xXQVVyKl7r9HIiBdRecT3USFM,1519
+eido-0.2.3.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
+eido-0.2.3.dist-info/entry_points.txt,sha256=pu2Iw-IUjVa_bKRgt0xUtPT9iwfR0y2nfRYyaRlkLZU,263
+eido-0.2.3.dist-info/top_level.txt,sha256=oltuMelApqcnJZ09Rrg3lF7kmTkmU5bcA6oRvXhNu6A,5
+eido-0.2.3.dist-info/RECORD,,

{eido-0.2.1.dist-info → eido-0.2.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.40.0)
+Generator: setuptools (74.1.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

eido-0.2.1.dist-info/RECORD

@@ -1,19 +0,0 @@
-eido/__init__.py,sha256=D3CD9BefyY5Yckz-LswPca_VH_RIcZpr53_siXkbi14,612
-eido/__main__.py,sha256=L1wnnEreqYv27ZaaCwwImCIHZK0Mz5IxS80ZsNcS1zg,189
-eido/_version.py,sha256=HfjVOrpTnmZ-xVFCYSVmX50EXaBQeJteUHG-PD6iQs8,22
-eido/argparser.py,sha256=xsMMxmZ_9zU5JI_xAApUtO4oRtcpWgbfoQ1ABCt7FIE,5137
-eido/cli.py,sha256=H_YCYNpFzPhaIgv4u4t8eLq36dm7l3k95z2cPxTdGBg,5871
-eido/const.py,sha256=_t-T7erHpBJYDALTkQR8noItmgKe4hTGHt5ifzc6kO4,1096
-eido/conversion.py,sha256=gNGH7uBQcgR6Ngn_ZfnEysB9eBs1OQzAa5hd9v9LYl0,3912
-eido/conversion_plugins.py,sha256=Kcj3C6jHgM3NVwDcT2ZiyV2lwdMwuoNUe-pZ3DQLvSI,2488
-eido/exceptions.py,sha256=21RZCdScSo6uiHGWrh_yxi4ejGbtshK_IqYEqnZ10pk,1080
-eido/inspection.py,sha256=CiI1YEmUtPmXGaq_QohHWbtg_55LEcQB-TKxitlyjPY,3148
-eido/output_formatters.py,sha256=bKqaashXRh-Vp6WbQzq8lQXbNHtvOR9IdXkn31rCmL8,4481
-eido/schema.py,sha256=NXDUtwKtrWfCTGUqT72CNB1yAWPIfBSYQUNO2gszFvA,3042
-eido/validation.py,sha256=PIQut96FM3RLZtbWzFikQJXjUyQfgOCR68zD9O1Wt8E,7941
-eido-0.2.1.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
-eido-0.2.1.dist-info/METADATA,sha256=ADJo6e_labpQmevfqk3MM0U2T9h0Fpp6BFtYJxxl8kk,1468
-eido-0.2.1.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-eido-0.2.1.dist-info/entry_points.txt,sha256=pu2Iw-IUjVa_bKRgt0xUtPT9iwfR0y2nfRYyaRlkLZU,263
-eido-0.2.1.dist-info/top_level.txt,sha256=oltuMelApqcnJZ09Rrg3lF7kmTkmU5bcA6oRvXhNu6A,5
-eido-0.2.1.dist-info/RECORD,,