Fix column order validation #182
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
sdrf_pipelines/sdrf/sdrf_schema.py (1)
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295-302: Improve Variable Naming for Clarity.The variables
tempanderrorare generic and could be renamed to more descriptive names to enhance code clarity.For example:
- Rename
temptofactor_columns.- Rename
errortomisplaced_columns.Apply this diff to update the variable names:
if factor_tag: - temp = [] - error = [] + factor_columns = [] + misplaced_columns = [] for column in cnames[factor_index:]: - if "comment" in column or "characteristics" in column: - error.extend(temp) - temp = [] + if "comment" in column or "characteristics" in column: + misplaced_columns.extend(factor_columns) + factor_columns = [] elif "factor value" in column: - temp.append(column) + factor_columns.append(column) if len(error): - error_message = "The following factor column should be last: {}".format(", ".join(error)) + error_message = "The following factor columns should be last: {}".format(", ".join(misplaced_columns)) error_columns_order.append(LogicError(error_message, error_type=logging.ERROR))
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🔇 Additional comments (4)
sdrf_pipelines/sdrf/sdrf_schema.py (4)
283-283: Variable Renaming Enhances Clarity: Change Approved.Renaming
indextoassay_indeximproves code readability by explicitly indicating that this index corresponds to the "assay name" column.
285-285: Use ofenumerateImproves Code Efficiency and Readability.Switching to
enumeratefor iterating over column names simplifies index tracking and enhances code readability.
286-287: Validation Logic Correctly Enforces "comment" Columns Position.The condition properly checks that "comment" columns do not appear before the "assay name" column, ensuring the column order is validated as per the schema.
291-292: Inclusion of "technology type" in Order Validation Strengthens Schema Enforcement.Adding "technology type" to the validation logic ensures that this column is not positioned after the "assay name," aligning with the intended column order.
sdrf_pipelines/sdrf/sdrf_schema.py
Outdated
| or "technology type" in column) and idx > assay_index: | ||
| error_message = "The column " + column + " cannot be after the assay name" |
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🛠️ Refactor suggestion
Refactor Conditional Statement for Improved Readability.
The complex conditional can be refactored for better readability by restructuring the conditions.
Consider reorganizing the condition:
if idx > assay_index and (
"characteristics" in column
or ("material type" in column and "factor value" not in column)
or "technology type" in column
):This places the index check upfront and groups the column-related conditions together, making the logic clearer.
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
sdrf_pipelines/sdrf/sdrf_schema.py (1)
289-289: Use f-strings for constructing error messagesFor improved readability and consistency, consider using f-strings when constructing error messages throughout the validation logic.
Apply these diffs:
# Line 289 - error_message = "The column " + column + " cannot be before the assay name" + error_message = f"The column {column} cannot be before the assay name" # Line 292 (after applying previous suggestion) - error_message = f"The column {column} cannot be before the assay name" + error_message = f"The column {column} cannot be before the assay name" # Line 302 - error_message = "The column " + column + " cannot be after the assay name" + error_message = f"The column {column} cannot be after the assay name" # Line 305 - error_message = "The column " + column + " must be immediately after the assay name" + error_message = f"The column {column} must be immediately after the assay name"Also applies to: 292-292, 302-302, 305-305
User description
Fixes #177.
list.indexcalls withenumerateRaise error when "technology type" is after "assay name" and not beforeImplement the new decision (Major PR to update some inconsistencies in the specification. proteomics-sample-metadata#726) wheretechnology typeshould be immediately afterassay namebut it is only a warning if it is immediately before.PR Type
Bug fix
Description
list.indexcalls withenumerateto improve performance in column order validation.Changes walkthrough 📝
sdrf_schema.py
Improve column order validation logic and error messagessdrf_pipelines/sdrf/sdrf_schema.py
list.indexcalls withenumeratefor efficiency.name".
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Summary by CodeRabbit
New Features
Bug Fixes