225 solve checker bugs

bam_masterdata/checker/masterdata_validator.py

@@ -120,7 +120,10 @@ def _validate_model(self, model: dict) -> dict:
                 # Collect ordered sections for each entity
                 entity_sections = []
                 # Validate 'properties' (except for vocabulary_types, which uses 'terms')
-                if entity_type != "vocabulary_types" and "properties" in entity_data:
+                if (
+                    entity_type != "vocabulary_types"
+                    and entity_type != "vocabulary_type"
+                ) and "properties" in entity_data:
                     for prop in entity_data["properties"]:
                         row_location = prop.get("row_location", "Unknown")
 
@@ -178,8 +181,8 @@ def _validate_model(self, model: dict) -> dict:
 
                 # Check if required properties exist in specific sections
                 required_properties = {
-                    "Additional Information": "NOTES",
-                    "Comments": "$XMLCOMMENTS",
+                    "Additional Information": ["notes"],
+                    "Comments": ["comments", "xmlcomments", "$xmlcomments"],
                 }
 
                 # Track found properties
@@ -190,11 +193,11 @@ def _validate_model(self, model: dict) -> dict:
                     property_code = entry["code"]
                     row_location = entry["row_location"]
 
-                    if (
-                        section in required_properties
-                        and property_code == required_properties[section]
-                    ):
-                        found_properties[section] = True
+                    # Check if this section is one we need to validate
+                    if section in required_properties:
+                        # Perform a case-insensitive check against the list of allowed property codes
+                        if property_code.lower() in required_properties[section]:
+                            found_properties[section] = True
 
                 # Log errors for missing required properties
                 for section, prop in required_properties.items():
@@ -208,7 +211,10 @@ def _validate_model(self, model: dict) -> dict:
                         )
 
                 # Validate 'terms' (only for vocabulary_types)
-                if entity_type == "vocabulary_types" and "terms" in entity_data:
+                if (
+                    entity_type == "vocabulary_types"
+                    or entity_type == "vocabulary_type"
+                ) and "terms" in entity_data:
                     for term in entity_data["terms"]:
                         row_location = term.get("row_location", "Unknown")
                         self._validate_fields(
@@ -363,7 +369,7 @@ def _compare_with_current_model(self, mode) -> dict:
                             )
 
                     # Special case for `property_types`
-                    if entity_type == "property_types":
+                    if entity_type in ("property_types", "property_type"):
                         incoming_row_location = incoming_entity.get(
                             "row_location", "Unknown"
                         )

bam_masterdata/checker/source_loader.py

@@ -64,7 +64,7 @@ def entities_to_json(self) -> dict:
             transformed_data[entity_type] = {}
 
             for entity_name, entity_data in entities.items():
-                if entity_type == "vocabulary_types":
+                if entity_type in ("vocabulary_type", "vocabulary_types"):
                     transformed_entity = {
                         "terms": [],  # Now placed before "defs"
                         "defs": {  # Metadata moved to the end
@@ -87,14 +87,17 @@ def entities_to_json(self) -> dict:
                                 entity_name
                             ),  # PascalCase for entity ID
                             "row_location": entity_data.get("row_location"),
-                            "validation_script": entity_data.get("validationPlugin")
-                            or None,  # Convert "" to None
+                            "validation_script": entity_data.get(
+                                "validationPlugin"
+                            ).strip()
+                            if isinstance(entity_data.get("validationPlugin"), str)
+                            else None,
                             "iri": entity_data.get("iri") or None,  # Convert "" to None
                         },
                     }
 
                 # Handle additional fields specific to dataset_types
-                if entity_type == "dataset_types":
+                if entity_type in ("dataset_types", "dataset_type"):
                     transformed_entity["defs"]["main_dataset_pattern"] = (
                         entity_data.get("main_dataset_pattern")
                     )
@@ -103,7 +106,7 @@ def entities_to_json(self) -> dict:
                     )
 
                 # Handle additional fields specific to object_types
-                if entity_type == "object_types":
+                if entity_type in ("object_types", "object_type"):
                     transformed_entity["defs"]["generated_code_prefix"] = (
                         entity_data.get("generatedCodePrefix")
                     )
@@ -140,7 +143,10 @@ def entities_to_json(self) -> dict:
                         transformed_entity["properties"].append(transformed_property)
 
                 if "terms" in entity_data:
-                    for term_name, term_data in entity_data["terms"].items():
+                    transformed_entity.setdefault("terms", [])
+                    for term_name, term_data in (
+                        entity_data.get("terms") or {}
+                    ).items():
                         transformed_term = {
                             "code": term_data.get("code"),
                             "description": term_data.get("description", ""),

bam_masterdata/checker/validation_rules/excel_validation_rules.json

@@ -4,7 +4,7 @@
     "Description": {"key": "description", "pattern": ".*", "is_description": true},
     "Validation script": {
       "key": "validationPlugin",
-      "pattern": "^[A-Za-z0-9_]+\\.py$",
+      "pattern": "^[A-Za-z0-9_\\.]+\\.py$",
       "allow_empty": true
     },
     "Generated code prefix": {
@@ -19,7 +19,7 @@
     "Description": {"key": "description", "pattern": ".*", "is_description": true},
     "Validation script": {
       "key": "validationPlugin",
-      "pattern": "^[A-Za-z0-9_]+\\.py$",
+      "pattern": "^[A-Za-z0-9_\\.]+\\.py$",
       "allow_empty": true
     },
     "Generated code prefix": {
@@ -34,7 +34,7 @@
     "Description": {"key": "description", "pattern": ".*", "is_description": true},
     "Validation script": {
       "key": "validationPlugin",
-      "pattern": "^[A-Za-z0-9_\\.]+$",
+      "pattern": "^[A-Za-z0-9_\\.]+\\.py$",
       "allow_empty": true
     }
   },
@@ -43,7 +43,7 @@
     "Description": {"key": "description", "pattern": ".*", "is_description": true},
     "Validation script": {
       "key": "validationPlugin",
-      "pattern": "^[A-Za-z0-9_]+\\.py$",
+      "pattern": "^[A-Za-z0-9_\\.]+\\.py$",
       "allow_empty": true
     },
     "Main dataset pattern": {"key": "main_dataset_pattern", "pattern": ".*", "allow_empty": true},
@@ -58,7 +58,7 @@
     "Metadata": {"key": "metadata", "pattern": ".*"},
     "Dynamic script": {
       "key": "plugin",
-      "pattern": "^[A-Za-z0-9_]+\\.py$",
+      "pattern": "^[A-Za-z0-9_\\.]+\\.py$",
       "allow_empty": true
     }
   },

bam_masterdata/checker/validation_rules/validation_rules.json

@@ -71,7 +71,7 @@
       "is_bool": true
     },
     "section": {
-      "pattern": "^([A-Z][a-z]*|[A-Z]+)( ([A-Z][a-z]*|[A-Z]+))*$",
+      "pattern": "^([A-Z][a-z]*|[A-Z]+)( (([A-Z][a-z]*|[A-Z]+)|\\(([A-Z][a-z]*|[A-Z]+)( ([A-Z][a-z]*|[A-Z]+))*\\)))*$",
       "is_section": true,
       "allow_empty": true
     },

bam_masterdata/excel/excel_to_entities.py

@@ -1,5 +1,6 @@
 import os
 import re
+import sys
 from typing import TYPE_CHECKING, Any
 
 from bam_masterdata.utils import is_reduced_version, load_validation_rules
@@ -577,21 +578,30 @@ def process_term_cell(term, cell_value, coordinate, sheet_title):
                     process_term_cell(term, cell.value, cell.coordinate, sheet.title)
                 )
 
-        # Combine extracted values into a dictionary
+        if not extracted_columns.get("Code"):
+            self.logger.error(
+                f"The required 'Code' column for terms was not found in sheet {sheet.title}."
+            )
+            return {}
+
+        # Combine extracted values into a dictionary safely
         for i in range(len(extracted_columns["Code"])):
-            terms_dict[extracted_columns["Code"][i]] = {
-                "permId": extracted_columns["Code"][i],
-                "code": extracted_columns["Code"][i],
+            code = extracted_columns["Code"][i]
+            terms_dict[code] = {
+                "permId": code,
+                "code": code,
             }
+            # Also correct a typo here: "descriptions" -> "description"
             for key, pybis_val in {
                 "Description": "descriptions",
                 "Url template": "url_template",
                 "Label": "label",
                 "Official": "official",
             }.items():
-                if extracted_columns.get(key):
+                # THE CRITICAL FIX: Only try to access a value if the column exists and has an entry for this row.
+                if extracted_columns.get(key) and i < len(extracted_columns[key]):
                     value = extracted_columns[key][i]
-                    terms_dict[extracted_columns["Code"][i]][pybis_val] = value
+                    terms_dict[code][pybis_val] = value
 
         return terms_dict
 

bam_masterdata/openbis/login.py

@@ -14,5 +14,7 @@ def ologin(url: str = "") -> Openbis:
         Openbis: Openbis object for the specific openBIS instance defined in `URL`.
     """
     o = Openbis(url)
-    o.login(environ("OPENBIS_USERNAME"), environ("OPENBIS_PASSWORD"), save_token=True)
+    o.login(
+        environ("OPENBIS_USERNAME"), environ("OPENBIS_NEW_PASSWORD"), save_token=True
+    )
     return o