oc_pruner

A tool for removing rows from an OpenCitations metadata or citations table based on the table's validation report, with support for running complete validation and pruning pipelines.

Features

• Selective filtering: Filter by error type (error/warning) and/or specific error labels
• Flexible configuration: Configure via CLI arguments or configuration files
• Row-level deletion: Removes entire rows containing issues
• Verbose output: Detailed information about processing when needed
• Complete pipeline: Run validation + pruning pipeline with multiple rounds for thorough cleaning
• Configurable pipeline: Customise validation and pruning options when running the pipeline via CLI flags or config files

Quick Start

Run the Complete Pipeline

Run a full validation and pruning pipeline for metadata and citations files:

oc_pruner pipeline --meta metadata.csv --cits citations.csv --out-dir output_dir

This will:

1. Validate both files
2. Remove invalid rows
3. Re-validate the cleaned files
4. Repeat the process to catch any newly exposed issues
5. Perform a final validation check

You can customise the pipeline behaviour (which errors to ignore, whether to verify ID existence, etc.) via CLI flags or a configuration file:

# Using CLI flags
oc_pruner pipeline -m metadata.csv -c citations.csv -o output_dir --ignore-labels br_id_syntax --verify-id-existence

# Using a config file
oc_pruner pipeline -m metadata.csv -c citations.csv -o output_dir --config pipeline_config.yaml

See the Configuration section for details on the available options.

Prune a Single Table Based On Its Existing Validation Report

Remove all issues (errors and warnings) from a CSV file:

oc_pruner --csv input.csv --report report.json --output output.csv

Or use the explicit prune subcommand:

oc_pruner prune --csv input.csv --report report.json --output output.csv

With Verbose Output

See detailed information about what's being processed:

oc_pruner prune --csv input.csv --report report.json --output output.csv --verbose

Configuration

CLI Arguments for pipeline mode (pipeline subcommand)

Argument	Abbreviation	Required	Description
--meta PATH	-m	Yes	Path to the input metadata CSV file
--cits PATH	-c	Yes	Path to the input citations CSV file
--out-dir PATH	-o	Yes	Path to the output directory where to write the output (pruned) files
--config PATH	—	No	Path to a YAML/JSON configuration file for pipeline options
--error-type	-e	No	Filter issues by error type: all or error
--ignore-labels LABELS	-i	No	Comma-separated list of error labels to ignore
--verify-id-existence	—	No	Verify that bibliographic IDs exist via API lookup
--use-meta-endpoint	—	No	Use the OC Meta endpoint for ID existence checks
--strict-sequentiality	—	No	Skip closure check when individual validations report errors
--help	-h	No	Show help message

CLI Arguments for single document mode (prune subcommand)

Argument	Abbreviation	Required	Description
--csv PATH	-t	Yes	Path to the input CSV file
--report PATH	-r	Yes	Path to the validation report JSON file
--output PATH	-o	Yes	Path for the output CSV file
--config PATH	-c	No	Path to configuration file (YAML or JSON)
--error-type	-e	No	Filter by error type: all or error
--ignore-labels	-i	No	Comma-separated error labels to ignore
--verbose	-v	No	Show detailed processing information
--init-config	—	No	Generate a configuration file template
--list-labels	—	No	List all valid error labels
--help	-h	No	Show help message

Configuration File

Create a configuration file for default settings. The tool looks for:

1. Explicitly specified file (via --config)
2. oc_pruner_config.yaml or oc_pruner_config.json in current directory
3. ~/.oc_pruner_config.yaml in home directory

Generate a template:

oc_pruner --init-config

Example oc_pruner_config.yaml:

# oc_pruner Configuration File

# ============================================================
# Pruning options (used by both 'prune' and 'pipeline')
# ============================================================

# Filter by error type: "all" (errors and warnings) or "error" (errors only)
error_type_filter: "all"

# List of error labels to ignore (rows with these issues will be kept, unless interested by other issues)
ignore_error_labels:
- "extra_space"
- "br_id_format"

# ============================================================
# Validation options (used by 'pipeline')
# ============================================================

# Whether to verify that bibliographic IDs exist via API lookup
verify_id_existence: false

# Whether to use the OC Meta endpoint for ID existence checks
use_meta_endpoint: false

# Whether to skip closure check when individual validations report errors
strict_sequentiality: false

# Whether to use LMDB for caching (recommended for large files)
use_lmdb: false

# Maximum size in bytes for LMDB environments (default: 1 GB)
# map_size: 1073741824

# Base directory for LMDB caches
# cache_dir: null

Configuration Priority

Settings are applied in this order (later override earlier):

1. Default values from the code
2. Configuration file if found
3. CLI arguments (highest priority)

Usage Examples

Run the Complete Validation + Pruning Pipeline from CLI

For thorough cleaning of OpenCitations metadata and citations files, use the pipeline command:

oc_pruner pipeline -m metadata.csv -c citations.csv -o output_dir

Pipeline Arguments:

Argument	Abbreviation	Required	Description
--meta PATH	-m	Yes	Path to original metadata CSV
--cits PATH	-c	Yes	Path to original citations CSV
--out-dir	-o	Yes	Base output directory for results
--config PATH	—	No	Path to a YAML/JSON config file for pipeline options
--error-type	-e	No	Filter issues by error type: all or error
--ignore-labels	-i	No	Comma-separated error labels to ignore
--verify-id-existence	—	No	Verify bibliographic IDs via API lookup
--use-meta-endpoint	—	No	Use OC Meta endpoint for ID checks
--strict-sequentiality	—	No	Skip closure check on validation errors

What the pipeline does:

1. First validation: Validates both metadata and citations files
2. First pruning: Removes rows with validation errors
3. Second validation: Re-validates the cleaned files to catch new issues
4. Second pruning: Removes any newly exposed errors
5. Third validation: Re-validates again (removing citations may expose further metadata issues)
6. Third pruning: Final cleanup of any remaining errors
7. Final validation: Performs a sanity check on the final cleaned files

You can customise the pipeline via CLI flags or a config file. CLI flags override the config file:

# Using CLI flags
oc_pruner pipeline -m metadata.csv -c citations.csv -o output_dir --ignore-labels br_id_syntax --verify-id-existence

# Using a config file
oc_pruner pipeline -m metadata.csv -c citations.csv -o output_dir --config pipeline_config.yaml

The pipeline creates the following structure in the output directory:

output_dir/
├── cleaned/
│   ├── metadata.csv       # Final cleaned metadata
│   └── citations.csv      # Final cleaned citations
└── validation_reports/
    ├── first_round/
    │   ├── metadata/
    │   └── citations/
    ├── second_round/
    │   ├── metadata/
    │   └── citations/
    ├── third_round/
    │   ├── metadata/
    │   └── citations/
    └── final_round/
        ├── metadata/
        └── citations/

All operations are logged to logs/pipeline_YYYYMMDD_HHMMSS.log.

Remove Only Errors (Single Document)

Ignore warnings and only remove rows with errors:

oc_pruner --csv data.csv --report report.json --output clean.csv --error-type error

Ignore Specific Error Labels (Single Document)

Keep rows that have specific issues:

oc_pruner --csv data.csv --report report.json --output clean.csv \
 --ignore-labels extra_space,br_id_format

Use Configuration File (Single Document)

Create a config file and use it:

oc_pruner --init-config
# Edit oc_pruner_config.yaml
oc_pruner --csv data.csv --report report.json --output clean.csv

Combine Filters (Single Document)

Remove only errors except for specific labels:

oc_pruner --csv data.csv --report report.json --output clean.csv \
  --error-type error \
  --ignore-labels extra_space,type_format

List Available Error Labels

See all valid error labels:

oc_pruner --list-labels

Validation Report Model

The validation report is a JSON file following the validation report schema. It consists of a list of issue objects, where each object represents a validation issue tied to specific locations in the CSV table.

Issue Object Structure

{
  "validation_level": "csv_wellformedness",
  "error_type": "error",
  "error_label": "extra_space",
  "message": "The value in this field is not expressed in compliance with the syntax...",
  "valid": false,
  "position": {
    "located_in": "item",
    "table": {
      "0": {
        "id": [1]
      }
    }
  }
}

Error Labels Reference

The supported issue labels are listed in the validation report schema and the associated issues are explained in this summary table.

How It Works

1. Load Files: Reads the CSV file and validation report
2. Filter Issues: Based on configuration, determines which issues to consider
   • --error-type error: Only considers "error" type issues
   • --ignore-labels: Ignores issues with specified labels
3. Extract Affected Rows: For each relevant issue, extracts row numbers from the position data
4. Remove Rows: Removes entire rows that contain any non-ignored issue
5. Write Output: Saves the cleaned CSV file

Important: If a row has both an ignorable issue and a non-ignorable issue, the entire row is removed (the non-ignorable issue takes precedence).

API Usage

You can also use oc_pruner as a Python library:

Prune a Single Document

from oc_pruner import prune
from oc_pruner.config import PrunerConfig

# Create configuration
config = PrunerConfig(
    error_type_filter="all",
    ignore_error_labels=["extra_space"]
)

# Prune the CSV file
prune(
    csv_path="input.csv",
    report_path="report.json",
    output_path="output.csv",
    config=config,
    verbose=True
)

Run the Pipeline

from oc_pruner.pipeline import run_pruning_pipeline
from oc_pruner.config import PipelineConfig

# Create pipeline configuration
config = PipelineConfig(
    error_type_filter="all",
    ignore_error_labels=["extra_space"],
    verify_id_existence=False,
    use_meta_endpoint=False,
    strict_sequentiality=False,
)

# Run the pipeline
run_pruning_pipeline(
    original_fp_meta="metadata.csv",
    original_fp_cits="citations.csv",
    base_out_dir="output",
    pipeline_config=config,
)