bam-masterdata 0.3.0__tar.gz → 0.3.1__tar.gz

{bam_masterdata-0.3.0 → bam_masterdata-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bam-masterdata
-Version: 0.3.0
+Version: 0.3.1
 Summary: The BAM Data Store utility tools and masterdata models wrapped in a Python package with a front-end web interface.
 Author-email: BAM Data Store <datastore@bam.de>
 Maintainer-email: "Jose M. Pizarro" <jose.pizarro-blanco@bam.de>

{bam_masterdata-0.3.0 → bam_masterdata-0.3.1}/bam_masterdata/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.3.0'
-__version_tuple__ = version_tuple = (0, 3, 0)
+__version__ = version = '0.3.1'
+__version_tuple__ = version_tuple = (0, 3, 1)

bam_masterdata-0.3.1/bam_masterdata/checker/__init__.py

@@ -0,0 +1 @@
+from .checker import MasterdataChecker, no_validation_errors

{bam_masterdata-0.3.0 → bam_masterdata-0.3.1}/bam_masterdata/checker/checker.py

@@ -1,5 +1,3 @@
-import os
-
 from bam_masterdata.checker.masterdata_validator import MasterdataValidator
 from bam_masterdata.checker.source_loader import SourceLoader
 from bam_masterdata.logger import logger
@@ -47,6 +45,7 @@ class MasterdataChecker:
         - "validate" -> Validate both the current model and new entities.
         - "compare" -> Compare new entities against the current model.
         - "all" -> Run both validation types.
+        - "individual" -> Run individual repositories validations.
 
         Before running, ensure that required models are loaded based on the mode.
 
@@ -84,3 +83,19 @@ class MasterdataChecker:
             self.new_entities, self.current_model, self.validation_rules
         )
         return validator.validate(mode)
+
+
+def no_validation_errors(validation_results: dict) -> bool:
+    """
+    Check if there are no validation errors in the results.
+
+    Args:
+        validation_results (dict): The dictionary containing the specific validation results.
+
+    Returns:
+        bool: True if there are no validation errors, False otherwise.
+    """
+
+    if not isinstance(validation_results, dict):
+        return False
+    return all(no_validation_errors(v) for v in validation_results.values())

{bam_masterdata-0.3.0 → bam_masterdata-0.3.1}/bam_masterdata/checker/masterdata_validator.py

@@ -30,6 +30,7 @@ class MasterdataValidator:
         - "validate": Validate both current and incoming models but do not compare.
         - "compare": Validate new entities against the current model.
         - "all": Run both.
+        - "individual": Validate new entities and compare them with the current model.
 
          Returns:
             dict: Validation results.
@@ -568,10 +569,10 @@ class MasterdataValidator:
                             codes.add(property_item["code"])
                 # Recursively check for more nested structures
                 elif isinstance(value, (dict, list)):
-                    codes.extend(self.extract_property_codes(value))
+                    codes.update(self.extract_property_codes(value))
 
         elif isinstance(data, list):
             for item in data:
-                codes.extend(self.extract_property_codes(item))
+                codes.update(self.extract_property_codes(item))
 
         return codes

{bam_masterdata-0.3.0 → bam_masterdata-0.3.1}/bam_masterdata/cli/cli.py

@@ -9,13 +9,14 @@ from decouple import config as environ
 from openpyxl import Workbook
 from rdflib import Graph
 
-from bam_masterdata.checker import MasterdataChecker
+from bam_masterdata.checker import MasterdataChecker, no_validation_errors
 from bam_masterdata.cli.entities_to_excel import entities_to_excel
 from bam_masterdata.cli.entities_to_rdf import entities_to_rdf
 from bam_masterdata.cli.fill_masterdata import MasterdataCodeGenerator
 from bam_masterdata.logger import logger
 from bam_masterdata.metadata.entities_dict import EntitiesDict
 from bam_masterdata.utils import (
+    DATAMODEL_DIR,
     delete_and_create_dir,
     duplicated_property_types,
     import_module,
@@ -23,27 +24,6 @@ from bam_masterdata.utils import (
 )
 
 
-def find_datamodel_dir():
-    """Search for 'datamodel/' in possible locations and return its absolute path."""
-    possible_locations = [
-        # Case: Running from a project with `datamodel/`
-        Path.cwd() / "datamodel",
-        # Case: Running inside bam-masterdata
-        Path.cwd() / "bam_masterdata" / "datamodel",
-        # Case: Running inside installed package
-        Path(__file__).parent.parent / "datamodel",
-    ]
-
-    for path in possible_locations:
-        if path.exists():
-            return str(path.resolve())
-
-    raise FileNotFoundError("Could not find a valid 'datamodel/' directory.")
-
-
-DATAMODEL_DIR = find_datamodel_dir()
-
-
 @click.group(help="Entry point to run `bam_masterdata` CLI commands.")
 def cli():
     pass
@@ -389,7 +369,8 @@ def export_to_rdf(force_delete, python_path, export_dir):
     "--mode",
     "mode",  # alias
     type=click.Choice(
-        ["self", "incoming", "validate", "compare", "all"], case_sensitive=False
+        ["self", "incoming", "validate", "compare", "all", "individual"],
+        case_sensitive=False,
     ),
     default="all",
     help="""Specify the mode for the checker. Options are:
@@ -397,7 +378,8 @@ def export_to_rdf(force_delete, python_path, export_dir):
     "incoming" -> Validate only the new entity structure.
     "validate" -> Validate both the current model and new entities.
     "compare" -> Compare new entities against the current model.
-    "all" -> Run all validations and comparison. (Default)""",
+    "all" -> Run all validations and comparison. (Default).
+    "individual" -> Run individual repositories validations.""",
 )
 @click.option(
     "--datamodel-path",
@@ -420,27 +402,57 @@ def checker(file_path, mode, datamodel_path):
     validation_results = checker.check(mode=mode)
 
     # Check if there are problems with the current model
-    if mode in ["self", "all", "validate"] and validation_results.get("current_model"):
-        click.echo(
-            "There are problems in the current model that need to be solved"  #: {validation_results['current_model']}"
-        )
+    if mode in ["self", "all", "validate"] and validation_results.get(
+        "current_model", {}
+    ):
+        for entity, errors in validation_results.get("current_model", {}).items():
+            if errors:
+                click.echo(
+                    f"There are problems in the current model for entity {entity} that need to be solved"
+                )
+                click.echo(f"Errors: {errors}")
 
     # Check if there are problems with the incoming model
     if mode in ["incoming", "all", "validate"] and validation_results.get(
-        "incoming_model"
+        "incoming_model", {}
     ):
-        click.echo(
-            f"There are problems in the incoming model located in {file_path} that need to be solved"  #: {validation_results['incoming_model']}"
-        )
+        for entity, errors in validation_results.get("incoming_model", {}).items():
+            if errors:
+                click.echo(
+                    f"There are problems in the incoming model in {file_path} for entity {entity} that need to be solved"
+                )
+                click.echo(f"Errors: {errors}")
 
     # Check if there are comparison problems
-    if mode in ["compare", "all"] and validation_results.get("comparisons"):
-        click.echo(
-            f"There are problems when checking the incoming model located in {file_path} against the current data model that need to be solved"  #: {validation_results['comparisons']}"
-        )
+    if mode in ["compare", "all"] and validation_results.get("comparisons", {}):
+        for entity, errors in validation_results.get("comparisons", {}).items():
+            if errors:
+                click.echo(
+                    f"There are problems when checking the incoming model in {file_path} against the current model {datamodel_path} for entity {entity} that need to be solved"
+                )
+                click.echo(f"Errors: {errors}")
+
+    # Check if there are individual repository problems
+    if (
+        mode in ["individual"]
+        and validation_results.get("incoming_model", {})
+        and validation_results.get("comparisons", {})
+    ):
+        for entity, errors in validation_results.get("individual", {}).items():
+            if errors:
+                click.echo(
+                    f"There are problems in the individual repositories when validating them for entity {entity} that need to be solved"
+                )
+                click.echo(f"Errors: {errors}")
+        for entity, errors in validation_results.get("comparisons", {}).items():
+            if errors:
+                click.echo(
+                    f"There are problems in the individual repositories when comparing them with respect to bam-masterdata for entity {entity} that need to be solved"
+                )
+                click.echo(f"Errors: {errors}")
 
     # Check if no problems were found
-    if all(value == {} for value in validation_results.values()):
+    if no_validation_errors(validation_results):
         click.echo("No problems found in the datamodel and incoming model.")
 
 

{bam_masterdata-0.3.0 → bam_masterdata-0.3.1}/bam_masterdata/cli/entities_to_rdf.py

@@ -11,7 +11,7 @@ from rdflib.namespace import DC, OWL, RDF, RDFS
 
 from bam_masterdata.utils import import_module
 
-BAM = Namespace("https://bamresearch.github.io/bam-masterdata/")
+BAM = Namespace("https://bamresearch.github.io/bam-masterdata/#")
 PROV = Namespace("http://www.w3.org/ns/prov#")
 
 

{bam_masterdata-0.3.0 → bam_masterdata-0.3.1}/bam_masterdata/utils/__init__.py

@@ -1,3 +1,4 @@
+from .paths import DATAMODEL_DIR, VALIDATION_RULES_DIR, find_dir
 from .utils import (
     code_to_class_name,
     convert_enums,

bam_masterdata-0.3.1/bam_masterdata/utils/paths.py

@@ -0,0 +1,43 @@
+from pathlib import Path
+
+
+def find_dir(possible_locations: list[Path]) -> str:
+    """
+    Search for a valid directory in a list of possible locations.
+
+    Args:
+        possible_locations (list[Path]): A list of possible locations to search for a directory.
+
+    Raises:
+        FileNotFoundError: If no valid directory is found.
+
+    Returns:
+        str: The path of the valid directory.
+    """
+    for path in possible_locations:
+        if path.exists():
+            return str(path.resolve())
+
+    raise FileNotFoundError("Could not find a valid directory.")
+
+
+DIRECTORIES = {
+    "datamodel": [
+        # Case: Running from a project with `datamodel/`
+        Path.cwd() / "datamodel",
+        # Case: Running inside bam-masterdata
+        Path.cwd() / "bam_masterdata" / "datamodel",
+        # Case: Running inside installed package
+        Path(__file__).parent.parent / "datamodel",
+    ],
+    "validation_rules_checker": [
+        Path.cwd() / "bam_masterdata" / "checker" / "validation_rules",
+        Path(__file__).parent.parent / "checker" / "validation_rules",
+    ],
+}
+
+
+DATAMODEL_DIR = find_dir(possible_locations=DIRECTORIES["datamodel"])
+VALIDATION_RULES_DIR = find_dir(
+    possible_locations=DIRECTORIES["validation_rules_checker"]
+)

{bam_masterdata-0.3.0 → bam_masterdata-0.3.1}/bam_masterdata/utils/utils.py

@@ -10,6 +10,7 @@ from itertools import chain
 from typing import TYPE_CHECKING, Any, Optional
 
 from bam_masterdata.logger import logger
+from bam_masterdata.utils import VALIDATION_RULES_DIR
 
 if TYPE_CHECKING:
     from structlog._config import BoundLoggerLazyProxy
@@ -142,7 +143,7 @@ def code_to_class_name(
 
 def load_validation_rules(
     logger: "BoundLoggerLazyProxy",
-    file_path: str = "./bam_masterdata/checker/validation_rules/validation_rules.json",
+    file_path: str = os.path.join(VALIDATION_RULES_DIR, "validation_rules.json"),
 ):
     if not os.path.exists(file_path):
         logger.error(f"Validation rules file not found: {file_path}")

{bam_masterdata-0.3.0 → bam_masterdata-0.3.1}/bam_masterdata.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bam-masterdata
-Version: 0.3.0
+Version: 0.3.1
 Summary: The BAM Data Store utility tools and masterdata models wrapped in a Python package with a front-end web interface.
 Author-email: BAM Data Store <datastore@bam.de>
 Maintainer-email: "Jose M. Pizarro" <jose.pizarro-blanco@bam.de>

{bam_masterdata-0.3.0 → bam_masterdata-0.3.1}/bam_masterdata.egg-info/SOURCES.txt

@@ -46,6 +46,7 @@ bam_masterdata/openbis/__init__.py
 bam_masterdata/openbis/get_entities.py
 bam_masterdata/openbis/login.py
 bam_masterdata/utils/__init__.py
+bam_masterdata/utils/paths.py
 bam_masterdata/utils/utils.py
 bam_masterdata/validation_rules/excel_validation_rules.json
 bam_masterdata/validation_rules/validation_rules.json
@@ -120,4 +121,5 @@ tests/excel/test_excel_to_entities.py
 tests/metadata/test_definitions.py
 tests/metadata/test_entities.py
 tests/metadata/test_entities_dict.py
+tests/utils/test_paths.py
 tests/utils/test_utils.py

bam_masterdata-0.3.1/tests/utils/test_paths.py

@@ -0,0 +1,14 @@
+from pathlib import Path
+
+from bam_masterdata.utils import DATAMODEL_DIR, VALIDATION_RULES_DIR, find_dir
+
+
+def test_find_dir():
+    assert find_dir(possible_locations=[Path.cwd()]) == str(Path.cwd())
+
+
+def test_default_dirs():
+    assert DATAMODEL_DIR == str(Path.cwd() / "bam_masterdata" / "datamodel")
+    assert VALIDATION_RULES_DIR == str(
+        Path.cwd() / "bam_masterdata" / "checker" / "validation_rules"
+    )

{bam_masterdata-0.3.0 → bam_masterdata-0.3.1}/tests/utils/test_utils.py

@@ -74,6 +74,7 @@ def test_delete_and_create_dir(
         (
             "./tests/utils",
             [
+                "./tests/utils/test_paths.py",
                 "./tests/utils/test_utils.py",
             ],
             None,

bam_masterdata-0.3.0/bam_masterdata/checker/__init__.py

@@ -1 +0,0 @@
-from .checker import MasterdataChecker