Merge pull request #47 from EATRIS/46-other-issue-add-resourceid-vali…

…dation

added resourceID validation

src/motbxtools/motbxschema.py

@@ -11,6 +11,7 @@
 import validators
 import yaml
 from contextlib import contextmanager
+from pathlib import Path
 
 
 class MotbxSchema():
@@ -75,6 +76,7 @@ def validate(self, motbx_schema):
         :raises Exception: Validation of URL fails
         """
         assert isinstance(motbx_schema, MotbxSchema)
+        # schema validation
         try:
             # validate against JSON schema
             # this includes checking URL for pattern https://* or *.pdf
@@ -83,6 +85,13 @@ def validate(self, motbx_schema):
                 format_checker=jsonschema.FormatChecker())
         except jsonschema.exceptions.ValidationError:
             raise
+        # ID validation
+        p = Path(self._yaml_path)
+        try:
+            assert self.resource["resourceID"] == p.stem
+        except AssertionError:
+            assert self.resource["resourceID"] == f'{p.parent.name}:{p.stem}'
+        # URL validation
         url = self.resource["resourceUrl"]
         try:
             # validate URL

tests/resources_fail/testfailID.yaml

@@ -0,0 +1,23 @@
+resourceCategory: Quality Control and Assessment
+resourceDescription: ISO Guide 80:2014 guidance for the in-house preparation of quality
+  control materials (QCMs). ISO Guide 80 outlines the characteristics and preparation
+  processes of reference materials for quality control. It applies to stable materials
+  used locally and those transported without significant property changes. Laboratory
+  staff preparing in-house quality control materials should follow ISO Guides 34 and
+  35 for transportation-based supply chains. The preparation of quality control materials
+  requires assessments for homogeneity, stability, and limited characterization. It
+  aims to demonstrate statistical control in a measurement system but does not provide
+  usage guidance. The guide offers general information on preparation and includes
+  case studies for different sectors. Users should have material knowledge and be
+  aware of matrix effects and contamination risks.
+resourceID: 'testfailIDdiffersFromFilename'
+resourceSubcategory: Guidelines and best practices
+resourceTags:
+- ISO standard
+- guidelines
+- quality control material
+- in-house
+- genomics
+resourceTitle: 'ISO Guide 80:2014: Guidance for in-house preparation of quality control
+  materials'
+resourceUrl: https://www.iso.org/standard/44313.html

tests/resources_fail/testfailSubcategory.yaml

@@ -10,7 +10,7 @@ resourceDescription: ISO Guide 80:2014 guidance for the in-house preparation of
   usage guidance. The guide offers general information on preparation and includes
   case studies for different sectors. Users should have material knowledge and be
   aware of matrix effects and contamination risks.
-resourceID: '1'
+resourceID: 'testfailSubcategory'
 resourceSubcategory: Protocols
 resourceTags:
 - ISO standard

tests/resources_fail/testfailUrl1.yaml

@@ -21,4 +21,4 @@ resourceTags:
 resourceTitle: 'ISO Guide 80:2014: Guidance for in-house preparation of quality
   control materials'
 resourceUrl: https://wwwiso.org/standard/44313.html
-resourceID: 'testfailurl1'
+resourceID: 'testfailUrl1'

tests/resources_fail/testfailUrl2.yaml

@@ -21,4 +21,4 @@ resourceTags:
 resourceTitle: 'ISO Guide 80:2014: Guidance for in-house preparation of quality
   control materials'
 resourceUrl: https://www.iso.org/standard/4431333.html
-resourceID: 'testfailurl2'
+resourceID: 'testfailUrl2'

tests/resources_fail/testfailUrl3.yaml

@@ -21,4 +21,4 @@ resourceTags:
 resourceTitle: 'ISO Guide 80:2014: Guidance for in-house preparation of quality
   control materials'
 resourceUrl: http://www.iso.org/standard/44313.html
-resourceID: 'testfailurl3'
+resourceID: 'testfailUrl3'

tests/resources_pass/test1.yaml

@@ -10,7 +10,7 @@ resourceDescription: ISO Guide 80:2014 guidance for the in-house preparation of
   usage guidance. The guide offers general information on preparation and includes
   case studies for different sectors. Users should have material knowledge and be
   aware of matrix effects and contamination risks.
-resourceID: '1'
+resourceID: 'test1'
 resourceSubcategory: Guidelines and best practices
 resourceTags:
 - ISO standard

tests/resources_pass/testID.yaml

@@ -0,0 +1,23 @@
+resourceCategory: Quality Control and Assessment
+resourceDescription: ISO Guide 80:2014 guidance for the in-house preparation of quality
+  control materials (QCMs). ISO Guide 80 outlines the characteristics and preparation
+  processes of reference materials for quality control. It applies to stable materials
+  used locally and those transported without significant property changes. Laboratory
+  staff preparing in-house quality control materials should follow ISO Guides 34 and
+  35 for transportation-based supply chains. The preparation of quality control materials
+  requires assessments for homogeneity, stability, and limited characterization. It
+  aims to demonstrate statistical control in a measurement system but does not provide
+  usage guidance. The guide offers general information on preparation and includes
+  case studies for different sectors. Users should have material knowledge and be
+  aware of matrix effects and contamination risks.
+resourceID: 'resources_pass:testID'
+resourceSubcategory: Guidelines and best practices
+resourceTags:
+- ISO standard
+- guidelines
+- quality control material
+- in-house
+- genomics
+resourceTitle: 'ISO Guide 80:2014: Guidance for in-house preparation of quality control
+  materials'
+resourceUrl: https://www.iso.org/standard/44313.html

tests/test_motbxtools/test_motbxschema.py

@@ -80,6 +80,12 @@ def test_validate_failUrl3(self):
                 os.path.join(self.resources_fail, "testfailUrl3.yaml"))
             resource.validate(self.schema)
 
+    def test_validate_failID(self):
+        with self.assertRaises(AssertionError):
+            resource = motbxschema.MotbxResource(
+                os.path.join(self.resources_fail, "testfailID.yaml"))
+            resource.validate(self.schema)
+
 
 if __name__ == '__main__':
     unittest.main()