Normalize compact YYYYMMDD dates in read-lab-metadata

CHANGELOG.md

@@ -21,6 +21,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Updated add-extra-config and included Initial configuration description in README.md [#861]https://github.com/BU-ISCIII/relecov-tools/pull/861
 - Updated test workflows to load initial_config-relecov.yaml first [#861]https://github.com/BU-ISCIII/relecov-tools/pull/861
 - Included three initial_config.yaml files for three projects: relecov, mepram & EQA2026 [#861]https://github.com/BU-ISCIII/relecov-tools/pull/861
+- Normalize compact YYYYMMDD dates in read-lab-metadata [#867]https://github.com/BU-ISCIII/relecov-tools/pull/867
 
 #### Fixes
 
@@ -38,6 +39,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Changed `assets/schema_utils/metadatalab_template.py`: Now supports iterative recursion to flatten nested schemas [#849](https://github.com/BU-ISCIII/relecov-tools/pull/849)
 - Updated how project name is extracted from config in read-lab-metadata [#861]https://github.com/BU-ISCIII/relecov-tools/pull/861
 - Include extra_config=True in all modules that did not have it [#863](https://github.com/BU-ISCIII/relecov-tools/pull/863)
+- Update relecov_schema.json title and add space removal check [#867]https://github.com/BU-ISCIII/relecov-tools/pull/867
 
 #### Removed
 

relecov_tools/build_schema.py

@@ -745,8 +745,12 @@ def build_new_schema(
             # Fill schema header
             # FIXME: it gets 'relecov-tools' instead of RELECOV
             project_name = relecov_tools.utils.get_package_name()
+            if isinstance(project_name, str):
+                project_name = project_name.strip()
+            if " " in project_name:
+                project_name = re.sub(r"\s+", "-", project_name)
             new_schema["$id"] = relecov_tools.utils.get_schema_url()
-            new_schema["title"] = f"{project_name} Schema."
+            new_schema["title"] = f"{project_name}-schema"
             new_schema["description"] = (
                 f"Json Schema that specifies the structure, content, and validation rules for {project_name}"
             )

relecov_tools/read_lab_metadata.py

@@ -932,13 +932,24 @@ def read_metadata_file(self):
                 )
                 if isinstance(key_for_checks, str) and "date" in key_for_checks.lower():
                     pattern = r"^\d{4}[-/.]\d{2}[-/.]\d{2}"
+                    compact_pattern = r"^\d{8}$"
                     if isinstance(raw_value, dtime):
                         value = str(raw_value.date())
                     elif re.match(pattern, str(raw_value)):
                         value = re.match(
                             pattern,
                             str(raw_value).replace("/", "-").replace(".", "-"),
                         ).group(0)
+                    elif re.match(compact_pattern, str(raw_value)):
+                        try:
+                            value = dtime.strptime(str(raw_value), "%Y%m%d").strftime(
+                                "%Y-%m-%d"
+                            )
+                        except ValueError:
+                            log_text = f"Invalid date format in {raw_key}: {raw_value}"
+                            self.logsum.add_error(sample=sample_id, entry=log_text)
+                            stderr.print(f"[red]{log_text} for sample {sample_id}")
+                            continue
                     else:
                         try:
                             value = str(int(float(str(raw_value))))