HfCacheManager Tutorial: Intelligent Cache Management for HuggingFace Datasets¶

The HfCacheManager class provides sophisticated cache management capabilities for HuggingFace genomics datasets. It extends DataCard functionality with intelligent caching strategies and automated cache cleanup tools.

This tutorial covers:

• Setting up HfCacheManager for cache management
• Understanding the 3-case metadata caching strategy
• Automated cache cleanup by age, size, and revision
• Cache monitoring and diagnostics
• Best practices for efficient cache management
• Integration with data loading workflows

Prerequisites: Basic familiarity with DataCard (see datacard_tutorial.ipynb) and HuggingFace datasets.

1. Setting Up HfCacheManager¶

The HfCacheManager extends DataCard with cache management capabilities. Unlike DataCard which focuses on dataset exploration, HfCacheManager adds intelligent caching and cleanup features.

In [ ]:

import duckdb
import logging
from tfbpapi.HfCacheManager import HfCacheManager
from huggingface_hub import scan_cache_dir

# Set up logging to see cache management activities
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)

# Create DuckDB connection for metadata caching
conn = duckdb.connect(':memory:')

# Initialize HfCacheManager
cache_manager = HfCacheManager(
    repo_id='BrentLab/mahendrawada_2025',
    duckdb_conn=conn,
    logger=logger
)

print(f"HfCacheManager initialized for: {cache_manager.repo_id}")
print(f"DuckDB connection: {'Active' if conn else 'None'}")
print(f"Logger configured: {'Yes' if logger else 'No'}")

# Show current cache status -- NOTE: this is from huggingface_hub,
# not from HfCacheManager
cache_info = scan_cache_dir()
print(f"Current HF cache size: {cache_info.size_on_disk_str}")
print(f"Cached repositories: {len(cache_info.repos)}")

import duckdb import logging from tfbpapi.HfCacheManager import HfCacheManager from huggingface_hub import scan_cache_dir # Set up logging to see cache management activities logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__name__) # Create DuckDB connection for metadata caching conn = duckdb.connect(':memory:') # Initialize HfCacheManager cache_manager = HfCacheManager( repo_id='BrentLab/mahendrawada_2025', duckdb_conn=conn, logger=logger ) print(f"HfCacheManager initialized for: {cache_manager.repo_id}") print(f"DuckDB connection: {'Active' if conn else 'None'}") print(f"Logger configured: {'Yes' if logger else 'No'}") # Show current cache status -- NOTE: this is from huggingface_hub, # not from HfCacheManager cache_info = scan_cache_dir() print(f"Current HF cache size: {cache_info.size_on_disk_str}") print(f"Cached repositories: {len(cache_info.repos)}")

HfCacheManager initialized for: BrentLab/hackett_2020
DuckDB connection: Active
Logger configured: Yes
Current HF cache size: 4.6G
Cached repositories: 9

In [76]:

cache_info

cache_info

Out[76]:

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2. Understanding the 3-Case Metadata Caching Strategy¶

HfCacheManager implements an intelligent 3-case strategy for metadata access that minimizes downloads and maximizes performance:

1. DuckDB Check: First check if metadata already exists in the DuckDB database
2. Cache Load: If not in DuckDB, try to load from local HuggingFace cache
3. Download: If not cached, download from HuggingFace Hub

This strategy is implemented in the internal _get_metadata_for_config() method and automatically used when loading data with HfQueryAPI.

Demonstrating the 3-Case Strategy¶

Let's see how the caching strategy works by examining what metadata tables would be created and checking the DuckDB state.

In [77]:

# Check current DuckDB state (Case 1 check)
tables = conn.execute(
    "SELECT table_name FROM information_schema.tables WHERE table_name LIKE 'metadata_%'"
).fetchall()

print("DuckDB Metadata Tables (Case 1):")
print("=" * 35)
if tables:
    for table in tables:
        count = conn.execute(f"SELECT COUNT(*) FROM {table[0]}").fetchone()[0]
        print(f"  • {table[0]}: {count} rows")
else:
    print("  No metadata tables found in DuckDB")
    print("  → Would proceed to Case 2 (check HF cache) or Case 3 (download)")

print(f"\nThe 3-case strategy ensures:")
print("• Fast access: DuckDB queries are nearly instantaneous")
print("• Minimal downloads: Reuse locally cached files when possible")  
print("• Automatic fallback: Download only when necessary")
print("• Transparent operation: Works automatically with HfQueryAPI")

# Check current DuckDB state (Case 1 check) tables = conn.execute( "SELECT table_name FROM information_schema.tables WHERE table_name LIKE 'metadata_%'" ).fetchall() print("DuckDB Metadata Tables (Case 1):") print("=" * 35) if tables: for table in tables: count = conn.execute(f"SELECT COUNT(*) FROM {table[0]}").fetchone()[0] print(f" • {table[0]}: {count} rows") else: print(" No metadata tables found in DuckDB") print(" → Would proceed to Case 2 (check HF cache) or Case 3 (download)") print(f"\nThe 3-case strategy ensures:") print("• Fast access: DuckDB queries are nearly instantaneous") print("• Minimal downloads: Reuse locally cached files when possible") print("• Automatic fallback: Download only when necessary") print("• Transparent operation: Works automatically with HfQueryAPI")

DuckDB Metadata Tables (Case 1):
===================================
  No metadata tables found in DuckDB
  → Would proceed to Case 2 (check HF cache) or Case 3 (download)

The 3-case strategy ensures:
• Fast access: DuckDB queries are nearly instantaneous
• Minimal downloads: Reuse locally cached files when possible
• Automatic fallback: Download only when necessary
• Transparent operation: Works automatically with HfQueryAPI

Checking HuggingFace Cache Status (Case 2)¶

The second case checks if files are already cached locally by HuggingFace. Let's examine the cache state for our target repository.

In [78]:

# Check if target repository is in HuggingFace cache
cache_info = scan_cache_dir()
target_repo = None

for repo in cache_info.repos:
    if repo.repo_id == cache_manager.repo_id:
        target_repo = repo
        break

print("HuggingFace Cache Status (Case 2):")
print("=" * 40)

if target_repo:
    print(f"✓ Repository {cache_manager.repo_id} found in cache")
    print(f"  Size: {target_repo.size_on_disk_str}")
    print(f"  Revisions: {len(target_repo.revisions)}")
    print(f"  Files: {target_repo.nb_files}")
    
    # Show latest revision info
    if target_repo.revisions:
        latest_rev = max(target_repo.revisions, key=lambda r: r.last_modified)
        print(f"  Latest revision: {latest_rev.commit_hash[:8]}")
        print(f"  Last accessed: {latest_rev.last_modified}")
        
    print("\n  → Case 2 would succeed: Load from local cache")
else:
    print(f"✗ Repository {cache_manager.repo_id} not found in cache")
    print("  → Would proceed to Case 3: Download from HuggingFace Hub")

print(f"\nCache efficiency: Using local files avoids re-downloading {target_repo.size_on_disk_str if target_repo else 'unknown size'}")

# Check if target repository is in HuggingFace cache cache_info = scan_cache_dir() target_repo = None for repo in cache_info.repos: if repo.repo_id == cache_manager.repo_id: target_repo = repo break print("HuggingFace Cache Status (Case 2):") print("=" * 40) if target_repo: print(f"✓ Repository {cache_manager.repo_id} found in cache") print(f" Size: {target_repo.size_on_disk_str}") print(f" Revisions: {len(target_repo.revisions)}") print(f" Files: {target_repo.nb_files}") # Show latest revision info if target_repo.revisions: latest_rev = max(target_repo.revisions, key=lambda r: r.last_modified) print(f" Latest revision: {latest_rev.commit_hash[:8]}") print(f" Last accessed: {latest_rev.last_modified}") print("\n → Case 2 would succeed: Load from local cache") else: print(f"✗ Repository {cache_manager.repo_id} not found in cache") print(" → Would proceed to Case 3: Download from HuggingFace Hub") print(f"\nCache efficiency: Using local files avoids re-downloading {target_repo.size_on_disk_str if target_repo else 'unknown size'}")

HuggingFace Cache Status (Case 2):
========================================
✓ Repository BrentLab/hackett_2020 found in cache
  Size: 407.3M
  Revisions: 5
  Files: 17
  Latest revision: 60b3ecf6
  Last accessed: 1758155372.1328666

  → Case 2 would succeed: Load from local cache

Cache efficiency: Using local files avoids re-downloading 407.3M

3. Cache Management and Cleanup¶

HfCacheManager's primary value is in providing sophisticated cache management. Let's explore the different cleanup strategies available.

Cache Overview and Current Status¶

Before cleaning, let's understand what we're working with.

In [79]:

# Get comprehensive cache overview
cache_info = scan_cache_dir()

print("Current HuggingFace Cache Overview:")
print("=" * 40)
print(f"Total cache size: {cache_info.size_on_disk_str}")
print(f"Number of repositories: {len(cache_info.repos)}")

# Analyze cache by repository size
repo_sizes = []
for repo in cache_info.repos:
    repo_sizes.append((repo.repo_id, repo.size_on_disk, repo.size_on_disk_str, len(repo.revisions)))

# Sort by size (largest first)
repo_sizes.sort(key=lambda x: x[1], reverse=True)

print(f"\nLargest repositories (top 5):")
for repo_id, size_bytes, size_str, revisions in repo_sizes[:5]:
    print(f"  • {repo_id}: {size_str} ({revisions} revisions)")

if len(repo_sizes) > 5:
    print(f"  ... and {len(repo_sizes) - 5} more repositories")

# Calculate total revisions
total_revisions = sum(len(repo.revisions) for repo in cache_info.repos)
print(f"\nTotal revisions across all repos: {total_revisions}")

# Show age distribution
from datetime import datetime
now = datetime.now().timestamp()
old_revisions = 0
for repo in cache_info.repos:
    for rev in repo.revisions:
        age_days = (now - rev.last_modified) / (24 * 3600)
        if age_days > 30:
            old_revisions += 1

print(f"Revisions older than 30 days: {old_revisions}")
print(f"Recent revisions (≤30 days): {total_revisions - old_revisions}")

# Get comprehensive cache overview cache_info = scan_cache_dir() print("Current HuggingFace Cache Overview:") print("=" * 40) print(f"Total cache size: {cache_info.size_on_disk_str}") print(f"Number of repositories: {len(cache_info.repos)}") # Analyze cache by repository size repo_sizes = [] for repo in cache_info.repos: repo_sizes.append((repo.repo_id, repo.size_on_disk, repo.size_on_disk_str, len(repo.revisions))) # Sort by size (largest first) repo_sizes.sort(key=lambda x: x[1], reverse=True) print(f"\nLargest repositories (top 5):") for repo_id, size_bytes, size_str, revisions in repo_sizes[:5]: print(f" • {repo_id}: {size_str} ({revisions} revisions)") if len(repo_sizes) > 5: print(f" ... and {len(repo_sizes) - 5} more repositories") # Calculate total revisions total_revisions = sum(len(repo.revisions) for repo in cache_info.repos) print(f"\nTotal revisions across all repos: {total_revisions}") # Show age distribution from datetime import datetime now = datetime.now().timestamp() old_revisions = 0 for repo in cache_info.repos: for rev in repo.revisions: age_days = (now - rev.last_modified) / (24 * 3600) if age_days > 30: old_revisions += 1 print(f"Revisions older than 30 days: {old_revisions}") print(f"Recent revisions (≤30 days): {total_revisions - old_revisions}")

Current HuggingFace Cache Overview:
========================================
Total cache size: 4.6G
Number of repositories: 9

Largest repositories (top 5):
  • BrentLab/barkai_compendium: 3.6G (1 revisions)
  • BrentLab/hackett_2020: 407.3M (5 revisions)
  • BrentLab/kemmeren_2014: 319.2M (1 revisions)
  • BrentLab/rossi_2021: 213.7M (7 revisions)
  • BrentLab/hu_2007_reimand_2010: 42.7M (1 revisions)
  ... and 4 more repositories

Total revisions across all repos: 29
Revisions older than 30 days: 0
Recent revisions (≤30 days): 29

Querying Loaded Metadata¶

Once metadata is loaded into DuckDB, we can query it using SQL.

Internal Cache Management Methods¶

HfCacheManager provides several internal methods that work behind the scenes. Let's explore what these methods do and how they integrate with the caching strategy.

4. Working with Specific Metadata Configurations¶

You can also retrieve metadata for specific configurations rather than all at once.

In [80]:

# Demonstrate understanding of internal cache methods
print("HfCacheManager Internal Methods:")
print("=" * 35)

print("\n1. _get_metadata_for_config(config)")
print("   → Implements the 3-case strategy for a specific configuration")
print("   → Returns detailed result with strategy used and success status")

print("\n2. _check_metadata_exists_in_duckdb(table_name)")
print("   → Case 1: Checks if metadata table already exists in DuckDB")
print("   → Fast check using information_schema.tables")

print("\n3. _load_metadata_from_cache(config, table_name)")
print("   → Case 2: Attempts to load from local HuggingFace cache")
print("   → Uses try_to_load_from_cache() to find cached files")

print("\n4. _download_and_load_metadata(config, table_name)")
print("   → Case 3: Downloads from HuggingFace Hub if not cached")
print("   → Uses snapshot_download() for efficient file retrieval")

print("\n5. _create_duckdb_table_from_files(file_paths, table_name)")
print("   → Creates DuckDB views from parquet files")
print("   → Handles both single files and multiple files efficiently")

print("\n6. _extract_embedded_metadata_field(data_table, field, metadata_table)")
print("   → Extracts metadata fields from data tables")
print("   → Creates separate queryable metadata views")

print("\nThese methods work together to provide:")
print("• Transparent caching that 'just works'")
print("• Minimal network usage through intelligent fallbacks")
print("• Fast metadata access via DuckDB views")
print("• Automatic handling of different file structures")

# Demonstrate understanding of internal cache methods print("HfCacheManager Internal Methods:") print("=" * 35) print("\n1. _get_metadata_for_config(config)") print(" → Implements the 3-case strategy for a specific configuration") print(" → Returns detailed result with strategy used and success status") print("\n2. _check_metadata_exists_in_duckdb(table_name)") print(" → Case 1: Checks if metadata table already exists in DuckDB") print(" → Fast check using information_schema.tables") print("\n3. _load_metadata_from_cache(config, table_name)") print(" → Case 2: Attempts to load from local HuggingFace cache") print(" → Uses try_to_load_from_cache() to find cached files") print("\n4. _download_and_load_metadata(config, table_name)") print(" → Case 3: Downloads from HuggingFace Hub if not cached") print(" → Uses snapshot_download() for efficient file retrieval") print("\n5. _create_duckdb_table_from_files(file_paths, table_name)") print(" → Creates DuckDB views from parquet files") print(" → Handles both single files and multiple files efficiently") print("\n6. _extract_embedded_metadata_field(data_table, field, metadata_table)") print(" → Extracts metadata fields from data tables") print(" → Creates separate queryable metadata views") print("\nThese methods work together to provide:") print("• Transparent caching that 'just works'") print("• Minimal network usage through intelligent fallbacks") print("• Fast metadata access via DuckDB views") print("• Automatic handling of different file structures")

HfCacheManager Internal Methods:
===================================

1. _get_metadata_for_config(config)
   → Implements the 3-case strategy for a specific configuration
   → Returns detailed result with strategy used and success status

2. _check_metadata_exists_in_duckdb(table_name)
   → Case 1: Checks if metadata table already exists in DuckDB
   → Fast check using information_schema.tables

3. _load_metadata_from_cache(config, table_name)
   → Case 2: Attempts to load from local HuggingFace cache
   → Uses try_to_load_from_cache() to find cached files

4. _download_and_load_metadata(config, table_name)
   → Case 3: Downloads from HuggingFace Hub if not cached
   → Uses snapshot_download() for efficient file retrieval

5. _create_duckdb_table_from_files(file_paths, table_name)
   → Creates DuckDB views from parquet files
   → Handles both single files and multiple files efficiently

6. _extract_embedded_metadata_field(data_table, field, metadata_table)
   → Extracts metadata fields from data tables
   → Creates separate queryable metadata views

These methods work together to provide:
• Transparent caching that 'just works'
• Minimal network usage through intelligent fallbacks
• Fast metadata access via DuckDB views
• Automatic handling of different file structures

5. Extracting Embedded Metadata¶

Some datasets have metadata embedded within their data files. The HfCacheManager can extract this embedded metadata into separate, queryable tables.

4. Embedded Metadata Extraction¶

One unique feature of HfCacheManager is the ability to extract embedded metadata fields from data tables into separate, queryable metadata tables.

Demonstrate embedded metadata extraction concept¶

print("Embedded Metadata Extraction:") print("=" * 35)

print("\nScenario: You have a data table with embedded metadata fields") print("Example: genomics data with 'experimental_condition' field")

Create sample data to demonstrate the concept¶

conn.execute(""" CREATE TABLE sample_genomics_data AS SELECT 'gene_' || (row_number() OVER()) as gene_id, random() * 1000 as expression_value, CASE WHEN (row_number() OVER()) % 4 = 0 THEN 'control' WHEN (row_number() OVER()) % 4 = 1 THEN 'treatment_A' WHEN (row_number() OVER()) % 4 = 2 THEN 'treatment_B' ELSE 'stress_condition' END as experimental_condition, CASE WHEN (row_number() OVER()) % 3 = 0 THEN 'timepoint_0h' WHEN (row_number() OVER()) % 3 = 1 THEN 'timepoint_6h' ELSE 'timepoint_24h' END as timepoint FROM range(100) """)

print("✓ Created sample genomics data with embedded metadata fields")

Show the data structure¶

sample_data = conn.execute( "SELECT * FROM sample_genomics_data LIMIT 5" ).fetchall()

print(f"\nSample data structure:") print("gene_id | expression_value | experimental_condition | timepoint") print("-" * 65) for row in sample_data: print(f"{row[0]:8} | {row[1]:15.1f} | {row[2]:20} | {row[3]}")

print(f"\nEmbedded metadata fields identified:") print("• experimental_condition: Contains treatment/control information") print("• timepoint: Contains temporal sampling information")

Use HfCacheManager to extract embedded metadata¶

print("Using HfCacheManager for Metadata Extraction:") print("=" * 50)

Extract experimental_condition metadata¶

success1 = cache_manager._extract_embedded_metadata_field( 'sample_genomics_data', 'experimental_condition', 'metadata_experimental_conditions' )

Extract timepoint metadata¶

success2 = cache_manager._extract_embedded_metadata_field( 'sample_genomics_data', 'timepoint', 'metadata_timepoints' )

print(f"Experimental condition extraction: {'✓ Success' if success1 else '✗ Failed'}") print(f"Timepoint extraction: {'✓ Success' if success2 else '✗ Failed'}")

Show extracted metadata tables¶

if success1: print(f"\nExtracted experimental conditions:") conditions = conn.execute( "SELECT value, count FROM metadata_experimental_conditions ORDER BY count DESC" ).fetchall()

for condition, count in conditions:
    print(f"  • {condition}: {count} samples")

if success2: print(f"\nExtracted timepoints:") timepoints = conn.execute( "SELECT value, count FROM metadata_timepoints ORDER BY count DESC" ).fetchall()

for timepoint, count in timepoints:
    print(f"  • {timepoint}: {count} samples")

print(f"\nBenefits of extraction:") print("• Separate queryable metadata tables") print("• Fast metadata-based filtering and analysis") print("• Clear separation of data and metadata concerns") print("• Reusable metadata across different analyses")

In [81]:

from huggingface_hub import scan_cache_dir

# Get current cache information  
cache_info = scan_cache_dir()

print("Current HuggingFace Cache Status:")
print("=" * 35)
print(f"Total size: {cache_info.size_on_disk_str}")
print(f"Number of repositories: {len(cache_info.repos)}")

print("\nRepository breakdown:")
for repo in list(cache_info.repos)[:5]:  # Show first 5 repos
    print(f"  • {repo.repo_id}: {repo.size_on_disk_str} ({len(repo.revisions)} revisions)")

if len(cache_info.repos) > 5:
    print(f"  ... and {len(cache_info.repos) - 5} more repositories")

# Show target repository if it exists in cache
target_repo = None
for repo in cache_info.repos:
    if repo.repo_id == cache_manager.repo_id:
        target_repo = repo
        break

if target_repo:
    print(f"\nTarget repository ({cache_manager.repo_id}) cache info:")
    print(f"  Size: {target_repo.size_on_disk_str}")
    print(f"  Revisions: {len(target_repo.revisions)}")
    if target_repo.revisions:
        latest_rev = max(target_repo.revisions, key=lambda r: r.last_modified)
        print(f"  Latest revision: {latest_rev.commit_hash[:8]}")
        print(f"  Last modified: {latest_rev.last_modified}")
else:
    print(f"\nTarget repository ({cache_manager.repo_id}) not found in cache.")
    print("It may need to be downloaded first.")

from huggingface_hub import scan_cache_dir # Get current cache information cache_info = scan_cache_dir() print("Current HuggingFace Cache Status:") print("=" * 35) print(f"Total size: {cache_info.size_on_disk_str}") print(f"Number of repositories: {len(cache_info.repos)}") print("\nRepository breakdown:") for repo in list(cache_info.repos)[:5]: # Show first 5 repos print(f" • {repo.repo_id}: {repo.size_on_disk_str} ({len(repo.revisions)} revisions)") if len(cache_info.repos) > 5: print(f" ... and {len(cache_info.repos) - 5} more repositories") # Show target repository if it exists in cache target_repo = None for repo in cache_info.repos: if repo.repo_id == cache_manager.repo_id: target_repo = repo break if target_repo: print(f"\nTarget repository ({cache_manager.repo_id}) cache info:") print(f" Size: {target_repo.size_on_disk_str}") print(f" Revisions: {len(target_repo.revisions)}") if target_repo.revisions: latest_rev = max(target_repo.revisions, key=lambda r: r.last_modified) print(f" Latest revision: {latest_rev.commit_hash[:8]}") print(f" Last modified: {latest_rev.last_modified}") else: print(f"\nTarget repository ({cache_manager.repo_id}) not found in cache.") print("It may need to be downloaded first.")

Current HuggingFace Cache Status:
===================================
Total size: 4.6G
Number of repositories: 9

Repository breakdown:
  • BrentLab/mahendrawada_2025: 2.0M (3 revisions)
  • BrentLab/yeast_genome_resources: 114.5K (7 revisions)
  • BrentLab/barkai_compendium: 3.6G (1 revisions)
  • BrentLab/rossi_2021: 213.7M (7 revisions)
  • BrentLab/harbison_2004: 12.3K (2 revisions)
  ... and 4 more repositories

Target repository (BrentLab/hackett_2020) cache info:
  Size: 407.3M
  Revisions: 5
  Latest revision: 60b3ecf6
  Last modified: 1758155372.1328666

Cache Cleanup by Age¶

In [82]:

# Clean cache entries older than 30 days (dry run)
print("Cleaning cache by age (30+ days old):")
print("=" * 40)

age_cleanup = cache_manager.clean_cache_by_age(
    max_age_days=30,
    dry_run=True  # Set to False to actually execute
)

print(f"\nCleanup strategy created:")
print(f"Expected space freed: {age_cleanup.expected_freed_size_str}")

# Count total items to delete across all categories
total_items = len(age_cleanup.blobs) + len(age_cleanup.refs) + len(age_cleanup.repos) + len(age_cleanup.snapshots)
print(f"Items to delete: {total_items}")

# Show breakdown of what would be deleted
if total_items > 0:
    print(f"\nBreakdown of items to delete:")
    print(f"  • Blob files: {len(age_cleanup.blobs)}")
    print(f"  • Reference files: {len(age_cleanup.refs)}")
    print(f"  • Repository directories: {len(age_cleanup.repos)}")
    print(f"  • Snapshot directories: {len(age_cleanup.snapshots)}")
    
    # Show some example items
    if age_cleanup.blobs:
        print(f"\nSample blob files to delete:")
        for item in list(age_cleanup.blobs)[:3]:
            print(f"  • {item}")
        if len(age_cleanup.blobs) > 3:
            print(f"  ... and {len(age_cleanup.blobs) - 3} more blob files")
else:
    print("No old files found for cleanup.")

# Clean cache entries older than 30 days (dry run) print("Cleaning cache by age (30+ days old):") print("=" * 40) age_cleanup = cache_manager.clean_cache_by_age( max_age_days=30, dry_run=True # Set to False to actually execute ) print(f"\nCleanup strategy created:") print(f"Expected space freed: {age_cleanup.expected_freed_size_str}") # Count total items to delete across all categories total_items = len(age_cleanup.blobs) + len(age_cleanup.refs) + len(age_cleanup.repos) + len(age_cleanup.snapshots) print(f"Items to delete: {total_items}") # Show breakdown of what would be deleted if total_items > 0: print(f"\nBreakdown of items to delete:") print(f" • Blob files: {len(age_cleanup.blobs)}") print(f" • Reference files: {len(age_cleanup.refs)}") print(f" • Repository directories: {len(age_cleanup.repos)}") print(f" • Snapshot directories: {len(age_cleanup.snapshots)}") # Show some example items if age_cleanup.blobs: print(f"\nSample blob files to delete:") for item in list(age_cleanup.blobs)[:3]: print(f" • {item}") if len(age_cleanup.blobs) > 3: print(f" ... and {len(age_cleanup.blobs) - 3} more blob files") else: print("No old files found for cleanup.")

Cleaning cache by age (30+ days old):
========================================

INFO:__main__:No old revisions found to delete
INFO:__main__:Found 0 old revisions. Will free 0.0
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion

Cleanup strategy created:
Expected space freed: 0.0
Items to delete: 0
No old files found for cleanup.

Cache Cleanup by Size¶

In [83]:

# Clean cache to target size (dry run)
target_size = "1GB"
print(f"Cleaning cache to target size: {target_size}")
print("=" * 40)

size_cleanup = cache_manager.clean_cache_by_size(
    target_size=target_size,
    strategy="oldest_first",  # Can be: oldest_first, largest_first, least_used
    dry_run=True
)

print(f"\nSize-based cleanup strategy:")
print(f"Expected space freed: {size_cleanup.expected_freed_size_str}")

# Count total items to delete across all categories
total_items = len(size_cleanup.blobs) + len(size_cleanup.refs) + len(size_cleanup.repos) + len(size_cleanup.snapshots)
print(f"Items to delete: {total_items}")

# Compare different strategies
strategies = ["oldest_first", "largest_first", "least_used"]
print(f"\nComparing cleanup strategies for {target_size}:")

for strategy in strategies:
    try:
        strategy_result = cache_manager.clean_cache_by_size(
            target_size=target_size,
            strategy=strategy,
            dry_run=True
        )
        strategy_total = (len(strategy_result.blobs) + len(strategy_result.refs) + 
                         len(strategy_result.repos) + len(strategy_result.snapshots))
        print(f"  • {strategy:15}: {strategy_result.expected_freed_size_str:>8} "
              f"({strategy_total} items)")
    except Exception as e:
        print(f"  • {strategy:15}: Error - {e}")

# Clean cache to target size (dry run) target_size = "1GB" print(f"Cleaning cache to target size: {target_size}") print("=" * 40) size_cleanup = cache_manager.clean_cache_by_size( target_size=target_size, strategy="oldest_first", # Can be: oldest_first, largest_first, least_used dry_run=True ) print(f"\nSize-based cleanup strategy:") print(f"Expected space freed: {size_cleanup.expected_freed_size_str}") # Count total items to delete across all categories total_items = len(size_cleanup.blobs) + len(size_cleanup.refs) + len(size_cleanup.repos) + len(size_cleanup.snapshots) print(f"Items to delete: {total_items}") # Compare different strategies strategies = ["oldest_first", "largest_first", "least_used"] print(f"\nComparing cleanup strategies for {target_size}:") for strategy in strategies: try: strategy_result = cache_manager.clean_cache_by_size( target_size=target_size, strategy=strategy, dry_run=True ) strategy_total = (len(strategy_result.blobs) + len(strategy_result.refs) + len(strategy_result.repos) + len(strategy_result.snapshots)) print(f" • {strategy:15}: {strategy_result.expected_freed_size_str:>8} " f"({strategy_total} items)") except Exception as e: print(f" • {strategy:15}: Error - {e}")

Cleaning cache to target size: 1GB
========================================

INFO:__main__:Selected 14 revisions for deletion. Will free 4.0G
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion

Size-based cleanup strategy:
Expected space freed: 4.0G
Items to delete: 30

Comparing cleanup strategies for 1GB:

INFO:__main__:Selected 14 revisions for deletion. Will free 4.0G
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion

  • oldest_first   :     4.0G (30 items)

INFO:__main__:Selected 1 revisions for deletion. Will free 3.6G
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion

  • largest_first  :     3.6G (1 items)

INFO:__main__:Selected 14 revisions for deletion. Will free 4.0G
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion

  • least_used     :     4.0G (30 items)

Cleaning Unused Revisions¶

In [84]:

# Clean unused revisions, keeping only the latest 2 per repository
print("Cleaning unused revisions (keep latest 2 per repo):")
print("=" * 50)

revision_cleanup = cache_manager.clean_unused_revisions(
    keep_latest=2,
    dry_run=True
)

print(f"\nRevision cleanup strategy:")
print(f"Expected space freed: {revision_cleanup.expected_freed_size_str}")

# Count total items to delete across all categories
total_items = len(revision_cleanup.blobs) + len(revision_cleanup.refs) + len(revision_cleanup.repos) + len(revision_cleanup.snapshots)
print(f"Items to delete: {total_items}")

# Show breakdown
if total_items > 0:
    print(f"\nBreakdown of cleanup:")
    print(f"  • Blob files: {len(revision_cleanup.blobs)}")
    print(f"  • Reference files: {len(revision_cleanup.refs)}")  
    print(f"  • Repository directories: {len(revision_cleanup.repos)}")
    print(f"  • Snapshot directories: {len(revision_cleanup.snapshots)}")

# Show repository-specific breakdown
cache_info = scan_cache_dir()
if cache_info.repos:
    print("\nPer-repository revision analysis:")
    for repo in list(cache_info.repos)[:3]:
        print(f"\n  • {repo.repo_id}:")
        print(f"    Total revisions: {len(repo.revisions)}")
        print(f"    Would keep: {min(2, len(repo.revisions))}")
        print(f"    Would delete: {max(0, len(repo.revisions) - 2)}")
        
        # Show revision details
        sorted_revisions = sorted(repo.revisions, key=lambda r: r.last_modified, reverse=True)
        for i, rev in enumerate(sorted_revisions[:2]):
            print(f"    Keep: {rev.commit_hash[:8]} (modified: {rev.last_modified})")
        
        for rev in sorted_revisions[2:3]:  # Show one that would be deleted
            print(f"    Delete: {rev.commit_hash[:8]} (modified: {rev.last_modified})")

# Clean unused revisions, keeping only the latest 2 per repository print("Cleaning unused revisions (keep latest 2 per repo):") print("=" * 50) revision_cleanup = cache_manager.clean_unused_revisions( keep_latest=2, dry_run=True ) print(f"\nRevision cleanup strategy:") print(f"Expected space freed: {revision_cleanup.expected_freed_size_str}") # Count total items to delete across all categories total_items = len(revision_cleanup.blobs) + len(revision_cleanup.refs) + len(revision_cleanup.repos) + len(revision_cleanup.snapshots) print(f"Items to delete: {total_items}") # Show breakdown if total_items > 0: print(f"\nBreakdown of cleanup:") print(f" • Blob files: {len(revision_cleanup.blobs)}") print(f" • Reference files: {len(revision_cleanup.refs)}") print(f" • Repository directories: {len(revision_cleanup.repos)}") print(f" • Snapshot directories: {len(revision_cleanup.snapshots)}") # Show repository-specific breakdown cache_info = scan_cache_dir() if cache_info.repos: print("\nPer-repository revision analysis:") for repo in list(cache_info.repos)[:3]: print(f"\n • {repo.repo_id}:") print(f" Total revisions: {len(repo.revisions)}") print(f" Would keep: {min(2, len(repo.revisions))}") print(f" Would delete: {max(0, len(repo.revisions) - 2)}") # Show revision details sorted_revisions = sorted(repo.revisions, key=lambda r: r.last_modified, reverse=True) for i, rev in enumerate(sorted_revisions[:2]): print(f" Keep: {rev.commit_hash[:8]} (modified: {rev.last_modified})") for rev in sorted_revisions[2:3]: # Show one that would be deleted print(f" Delete: {rev.commit_hash[:8]} (modified: {rev.last_modified})")

Cleaning unused revisions (keep latest 2 per repo):
==================================================

INFO:__main__:Found 14 unused revisions. Will free 216.4M
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion

Revision cleanup strategy:
Expected space freed: 216.4M
Items to delete: 75

Breakdown of cleanup:
  • Blob files: 61
  • Reference files: 0
  • Repository directories: 0
  • Snapshot directories: 14

Per-repository revision analysis:

  • BrentLab/mahendrawada_2025:
    Total revisions: 3
    Would keep: 2
    Would delete: 1
    Keep: 8bea431b (modified: 1758155849.9076133)
    Keep: d602c165 (modified: 1757439229.7949307)
    Delete: 66e0cf1f (modified: 1756858618.1383443)

  • BrentLab/yeast_genome_resources:
    Total revisions: 7
    Would keep: 2
    Would delete: 5
    Keep: 42beb284 (modified: 1758155946.5549896)
    Keep: 15fdb72f (modified: 1755819093.2306638)
    Delete: 7441b9a8 (modified: 1755816785.6988702)

  • BrentLab/barkai_compendium:
    Total revisions: 1
    Would keep: 1
    Would delete: 0
    Keep: a987ef37 (modified: 1756926783.3167186)

Automated Cache Management¶

In [85]:

# Automated cache cleanup with multiple strategies
print("Automated cache cleanup (comprehensive):")
print("=" * 40)

auto_cleanup = cache_manager.auto_clean_cache(
    max_age_days=30,           # Remove anything older than 30 days
    max_total_size="5GB",      # Target maximum cache size
    keep_latest_per_repo=2,    # Keep 2 latest revisions per repo
    dry_run=True               # Dry run for safety
)

print(f"\nAutomated cleanup executed {len(auto_cleanup)} strategies:")

total_freed = 0
for i, strategy in enumerate(auto_cleanup, 1):
    print(f"  {i}. Strategy freed: {strategy.expected_freed_size_str}")
    total_freed += strategy.expected_freed_size

print(f"\nTotal space that would be freed: {cache_manager._format_bytes(total_freed)}")

# Calculate final cache size
current_cache = scan_cache_dir()
final_size = current_cache.size_on_disk - total_freed
print(f"Cache size after cleanup: {cache_manager._format_bytes(max(0, final_size))}")

# Automated cache cleanup with multiple strategies print("Automated cache cleanup (comprehensive):") print("=" * 40) auto_cleanup = cache_manager.auto_clean_cache( max_age_days=30, # Remove anything older than 30 days max_total_size="5GB", # Target maximum cache size keep_latest_per_repo=2, # Keep 2 latest revisions per repo dry_run=True # Dry run for safety ) print(f"\nAutomated cleanup executed {len(auto_cleanup)} strategies:") total_freed = 0 for i, strategy in enumerate(auto_cleanup, 1): print(f" {i}. Strategy freed: {strategy.expected_freed_size_str}") total_freed += strategy.expected_freed_size print(f"\nTotal space that would be freed: {cache_manager._format_bytes(total_freed)}") # Calculate final cache size current_cache = scan_cache_dir() final_size = current_cache.size_on_disk - total_freed print(f"Cache size after cleanup: {cache_manager._format_bytes(max(0, final_size))}")

INFO:__main__:Starting automated cache cleanup...

Automated cache cleanup (comprehensive):
========================================

INFO:__main__:No old revisions found to delete
INFO:__main__:Found 0 old revisions. Will free 0.0
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion
INFO:__main__:Found 14 unused revisions. Will free 216.4M
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion
INFO:__main__:Automated cleanup complete. Total freed: 206.4MB

Automated cleanup executed 2 strategies:
  1. Strategy freed: 0.0
  2. Strategy freed: 216.4M

Total space that would be freed: 206.4MB
Cache size after cleanup: 4.1GB

7. Best Practices and Performance Tips¶

Here are some best practices for using HfCacheManager effectively:

Performance Best Practices¶

In [86]:

import time

print("Performance Demonstration: Cache Management Benefits")
print("=" * 55)

print("\nDemonstrating cache cleanup performance...")

# Show performance of cache scanning and cleanup strategy creation
print("\n1. Cache scanning performance:")
start_time = time.time()
cache_info = scan_cache_dir()
scan_time = time.time() - start_time
print(f"   Time to scan cache: {scan_time:.3f} seconds")
print(f"   Repositories found: {len(cache_info.repos)}")
print(f"   Total cache size: {cache_info.size_on_disk_str}")

# Show performance of cleanup strategy creation
print("\n2. Cleanup strategy creation performance:")

start_time = time.time()
age_strategy = cache_manager.clean_cache_by_age(max_age_days=30, dry_run=True)
age_time = time.time() - start_time
print(f"   Age cleanup strategy: {age_time:.3f} seconds")

start_time = time.time()
size_strategy = cache_manager.clean_cache_by_size(target_size="1GB", dry_run=True)
size_time = time.time() - start_time
print(f"   Size cleanup strategy: {size_time:.3f} seconds")

start_time = time.time()
revision_strategy = cache_manager.clean_unused_revisions(keep_latest=2, dry_run=True)
revision_time = time.time() - start_time
print(f"   Revision cleanup strategy: {revision_time:.3f} seconds")

print(f"\nPerformance insights:")
print(f"• Cache scanning is fast: {scan_time:.3f}s for {len(cache_info.repos)} repos")
print(f"• Cleanup strategy creation is efficient")
print(f"• Dry runs allow safe preview of cleanup operations")
print(f"• Multiple strategies can be compared quickly")

import time print("Performance Demonstration: Cache Management Benefits") print("=" * 55) print("\nDemonstrating cache cleanup performance...") # Show performance of cache scanning and cleanup strategy creation print("\n1. Cache scanning performance:") start_time = time.time() cache_info = scan_cache_dir() scan_time = time.time() - start_time print(f" Time to scan cache: {scan_time:.3f} seconds") print(f" Repositories found: {len(cache_info.repos)}") print(f" Total cache size: {cache_info.size_on_disk_str}") # Show performance of cleanup strategy creation print("\n2. Cleanup strategy creation performance:") start_time = time.time() age_strategy = cache_manager.clean_cache_by_age(max_age_days=30, dry_run=True) age_time = time.time() - start_time print(f" Age cleanup strategy: {age_time:.3f} seconds") start_time = time.time() size_strategy = cache_manager.clean_cache_by_size(target_size="1GB", dry_run=True) size_time = time.time() - start_time print(f" Size cleanup strategy: {size_time:.3f} seconds") start_time = time.time() revision_strategy = cache_manager.clean_unused_revisions(keep_latest=2, dry_run=True) revision_time = time.time() - start_time print(f" Revision cleanup strategy: {revision_time:.3f} seconds") print(f"\nPerformance insights:") print(f"• Cache scanning is fast: {scan_time:.3f}s for {len(cache_info.repos)} repos") print(f"• Cleanup strategy creation is efficient") print(f"• Dry runs allow safe preview of cleanup operations") print(f"• Multiple strategies can be compared quickly")

Performance Demonstration: Cache Management Benefits
=======================================================

Demonstrating cache cleanup performance...

1. Cache scanning performance:
   Time to scan cache: 0.111 seconds
   Repositories found: 9
   Total cache size: 4.6G

2. Cleanup strategy creation performance:

INFO:__main__:No old revisions found to delete
INFO:__main__:Found 0 old revisions. Will free 0.0
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion

   Age cleanup strategy: 0.109 seconds

INFO:__main__:Selected 14 revisions for deletion. Will free 4.0G
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion

   Size cleanup strategy: 0.105 seconds

INFO:__main__:Found 14 unused revisions. Will free 216.4M
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion

   Revision cleanup strategy: 0.111 seconds

Performance insights:
• Cache scanning is fast: 0.111s for 9 repos
• Cleanup strategy creation is efficient
• Dry runs allow safe preview of cleanup operations
• Multiple strategies can be compared quickly

Memory and Storage Optimization¶

In [87]:

print("Memory and Storage Optimization Tips:")
print("=" * 40)

print("\n1. DuckDB Views vs Tables:")
print("   • HfCacheManager creates VIEWS by default (not tables)")
print("   • Views reference original parquet files without duplication")
print("   • This saves storage space while enabling fast SQL queries")

print("\n2. Metadata-First Workflow:")
print("   • Load metadata first to understand data structure")
print("   • Use metadata to filter and select specific data subsets")
print("   • Avoid loading entire datasets when only portions are needed")

print("\n3. Cache Management Strategy:")
print("   • Run automated cleanup regularly")
print("   • Keep cache size reasonable for your system")
print("   • Prioritize keeping recent and frequently-used datasets")

# Demonstrate DuckDB view benefits
tables_info = conn.execute(
    "SELECT table_name, table_type FROM information_schema.tables WHERE table_name LIKE 'metadata_%'"
).fetchall()

if tables_info:
    print(f"\nCurrent DuckDB objects ({len(tables_info)} total):")
    for table_name, table_type in tables_info:
        print(f"   • {table_name}: {table_type}")
    
    view_count = sum(1 for _, table_type in tables_info if table_type == 'VIEW')
    print(f"\n   {view_count} views created (space-efficient!)")

print("Memory and Storage Optimization Tips:") print("=" * 40) print("\n1. DuckDB Views vs Tables:") print(" • HfCacheManager creates VIEWS by default (not tables)") print(" • Views reference original parquet files without duplication") print(" • This saves storage space while enabling fast SQL queries") print("\n2. Metadata-First Workflow:") print(" • Load metadata first to understand data structure") print(" • Use metadata to filter and select specific data subsets") print(" • Avoid loading entire datasets when only portions are needed") print("\n3. Cache Management Strategy:") print(" • Run automated cleanup regularly") print(" • Keep cache size reasonable for your system") print(" • Prioritize keeping recent and frequently-used datasets") # Demonstrate DuckDB view benefits tables_info = conn.execute( "SELECT table_name, table_type FROM information_schema.tables WHERE table_name LIKE 'metadata_%'" ).fetchall() if tables_info: print(f"\nCurrent DuckDB objects ({len(tables_info)} total):") for table_name, table_type in tables_info: print(f" • {table_name}: {table_type}") view_count = sum(1 for _, table_type in tables_info if table_type == 'VIEW') print(f"\n {view_count} views created (space-efficient!)")

Memory and Storage Optimization Tips:
========================================

1. DuckDB Views vs Tables:
   • HfCacheManager creates VIEWS by default (not tables)
   • Views reference original parquet files without duplication
   • This saves storage space while enabling fast SQL queries

2. Metadata-First Workflow:
   • Load metadata first to understand data structure
   • Use metadata to filter and select specific data subsets
   • Avoid loading entire datasets when only portions are needed

3. Cache Management Strategy:
   • Run automated cleanup regularly
   • Keep cache size reasonable for your system
   • Prioritize keeping recent and frequently-used datasets

8. Integration with Other Components¶

The HfCacheManager works seamlessly with other components in the tfbpapi ecosystem.

In [88]:

print("HfCacheManager Integration Workflow:")
print("=" * 40)

print("\n1. Cache Management Setup:")
print("   from tfbpapi.HfCacheManager import HfCacheManager")
print("   cache_mgr = HfCacheManager(repo_id, duckdb_conn)")
print("   # Inherits all DataCard functionality + cache management")

print("\n2. Proactive Cache Cleanup:")
print("   # Clean before large operations")
print("   cache_mgr.auto_clean_cache(max_total_size='5GB', dry_run=False)")
print("   # Or use specific strategies")
print("   cache_mgr.clean_cache_by_age(max_age_days=30)")

print("\n3. Data Loading with Cache Awareness:")
print("   # The 3-case strategy works automatically with HfQueryAPI")
print("   from tfbpapi import HfQueryAPI")
print("   query_api = HfQueryAPI(repo_id, duckdb_conn)")
print("   # Metadata loading uses cache manager's strategy")
print("   data_df = query_api.get_pandas('config_name')")

print("\n4. Embedded Metadata Extraction:")
print("   # Extract metadata fields after data loading")
print("   cache_mgr._extract_embedded_metadata_field(")
print("       'data_table_name', 'metadata_field', 'metadata_table_name')")

print("\n5. Regular Cache Maintenance:")
print("   # Schedule regular cleanup")
print("   cache_mgr.clean_unused_revisions(keep_latest=2)")
print("   cache_mgr.clean_cache_by_size('10GB', strategy='oldest_first')")

# Show current state
print(f"\nCurrent Session State:")
print(f"Repository: {cache_manager.repo_id}")
print(f"DuckDB tables: {len(conn.execute('SELECT table_name FROM information_schema.tables').fetchall())}")

cache_info = scan_cache_dir()
print(f"HF cache size: {cache_info.size_on_disk_str}")
print(f"Cache repositories: {len(cache_info.repos)}")

print("HfCacheManager Integration Workflow:") print("=" * 40) print("\n1. Cache Management Setup:") print(" from tfbpapi.HfCacheManager import HfCacheManager") print(" cache_mgr = HfCacheManager(repo_id, duckdb_conn)") print(" # Inherits all DataCard functionality + cache management") print("\n2. Proactive Cache Cleanup:") print(" # Clean before large operations") print(" cache_mgr.auto_clean_cache(max_total_size='5GB', dry_run=False)") print(" # Or use specific strategies") print(" cache_mgr.clean_cache_by_age(max_age_days=30)") print("\n3. Data Loading with Cache Awareness:") print(" # The 3-case strategy works automatically with HfQueryAPI") print(" from tfbpapi import HfQueryAPI") print(" query_api = HfQueryAPI(repo_id, duckdb_conn)") print(" # Metadata loading uses cache manager's strategy") print(" data_df = query_api.get_pandas('config_name')") print("\n4. Embedded Metadata Extraction:") print(" # Extract metadata fields after data loading") print(" cache_mgr._extract_embedded_metadata_field(") print(" 'data_table_name', 'metadata_field', 'metadata_table_name')") print("\n5. Regular Cache Maintenance:") print(" # Schedule regular cleanup") print(" cache_mgr.clean_unused_revisions(keep_latest=2)") print(" cache_mgr.clean_cache_by_size('10GB', strategy='oldest_first')") # Show current state print(f"\nCurrent Session State:") print(f"Repository: {cache_manager.repo_id}") print(f"DuckDB tables: {len(conn.execute('SELECT table_name FROM information_schema.tables').fetchall())}") cache_info = scan_cache_dir() print(f"HF cache size: {cache_info.size_on_disk_str}") print(f"Cache repositories: {len(cache_info.repos)}")

HfCacheManager Integration Workflow:
========================================

1. Cache Management Setup:
   from tfbpapi.HfCacheManager import HfCacheManager
   cache_mgr = HfCacheManager(repo_id, duckdb_conn)
   # Inherits all DataCard functionality + cache management

2. Proactive Cache Cleanup:
   # Clean before large operations
   cache_mgr.auto_clean_cache(max_total_size='5GB', dry_run=False)
   # Or use specific strategies
   cache_mgr.clean_cache_by_age(max_age_days=30)

3. Data Loading with Cache Awareness:
   # The 3-case strategy works automatically with HfQueryAPI
   from tfbpapi import HfQueryAPI
   query_api = HfQueryAPI(repo_id, duckdb_conn)
   # Metadata loading uses cache manager's strategy
   data_df = query_api.get_pandas('config_name')

4. Embedded Metadata Extraction:
   # Extract metadata fields after data loading
   cache_mgr._extract_embedded_metadata_field(
       'data_table_name', 'metadata_field', 'metadata_table_name')

5. Regular Cache Maintenance:
   # Schedule regular cleanup
   cache_mgr.clean_unused_revisions(keep_latest=2)
   cache_mgr.clean_cache_by_size('10GB', strategy='oldest_first')

Current Session State:
Repository: BrentLab/hackett_2020
DuckDB tables: 0
HF cache size: 4.6G
Cache repositories: 9

9. Troubleshooting and Error Handling¶

The HfCacheManager includes comprehensive error handling and diagnostic capabilities.

In [89]:

print("Cache Management Troubleshooting:")
print("=" * 35)

print("\n1. Import and Setup Issues:")
print("   • Ensure correct import: from tfbpapi.HfCacheManager import HfCacheManager")
print("   • Verify DuckDB connection: conn = duckdb.connect(':memory:')")
print("   • Check repository access permissions")

print("\n2. Cache Space and Performance Issues:")
try:
    cache_info = scan_cache_dir()
    print(f"   Current cache size: {cache_info.size_on_disk_str}")
    print("   • Use auto_clean_cache() for automated management")
    print("   • Monitor cache growth with scan_cache_dir()")
    print("   • Set appropriate size limits for your system")
    
    # Show if cache is getting large
    total_gb = cache_info.size_on_disk / (1024**3)
    if total_gb > 10:
        print(f"   ⚠️  Large cache detected ({total_gb:.1f}GB) - consider cleanup")
    
except Exception as e:
    print(f"   Cache scan error: {e}")

print("\n3. Cache Cleanup Issues:")
print("   • Use dry_run=True first to preview changes")
print("   • Check disk permissions for cache directory")
print("   • Verify no active processes are using cached files")

print("\n4. DuckDB Integration Issues:")
print("   • Ensure DuckDB connection is active")
print("   • Check memory limits for in-memory databases")
print("   • Verify table names don't conflict")

# Perform health checks
print(f"\nCache Health Check:")

# Test DuckDB
try:
    test_result = conn.execute("SELECT 'DuckDB OK' as status").fetchone()
    print(f"✓ DuckDB connection: {test_result[0]}")
except Exception as e:
    print(f"✗ DuckDB connection: {e}")

# Test cache access
try:
    cache_info = scan_cache_dir()
    print(f"✓ Cache access: {len(cache_info.repos)} repositories found")
except Exception as e:
    print(f"✗ Cache access: {e}")

# Test cache manager methods
try:
    test_cleanup = cache_manager.clean_cache_by_age(max_age_days=999, dry_run=True)
    print(f"✓ Cache cleanup methods: Working")
except Exception as e:
    print(f"✗ Cache cleanup methods: {e}")

print(f"\nCurrent Status:")
print(f"Repository: {cache_manager.repo_id}")
print(f"Logger configured: {cache_manager.logger is not None}")
print(f"Cache management ready: ✓")

print("Cache Management Troubleshooting:") print("=" * 35) print("\n1. Import and Setup Issues:") print(" • Ensure correct import: from tfbpapi.HfCacheManager import HfCacheManager") print(" • Verify DuckDB connection: conn = duckdb.connect(':memory:')") print(" • Check repository access permissions") print("\n2. Cache Space and Performance Issues:") try: cache_info = scan_cache_dir() print(f" Current cache size: {cache_info.size_on_disk_str}") print(" • Use auto_clean_cache() for automated management") print(" • Monitor cache growth with scan_cache_dir()") print(" • Set appropriate size limits for your system") # Show if cache is getting large total_gb = cache_info.size_on_disk / (1024**3) if total_gb > 10: print(f" ⚠️ Large cache detected ({total_gb:.1f}GB) - consider cleanup") except Exception as e: print(f" Cache scan error: {e}") print("\n3. Cache Cleanup Issues:") print(" • Use dry_run=True first to preview changes") print(" • Check disk permissions for cache directory") print(" • Verify no active processes are using cached files") print("\n4. DuckDB Integration Issues:") print(" • Ensure DuckDB connection is active") print(" • Check memory limits for in-memory databases") print(" • Verify table names don't conflict") # Perform health checks print(f"\nCache Health Check:") # Test DuckDB try: test_result = conn.execute("SELECT 'DuckDB OK' as status").fetchone() print(f"✓ DuckDB connection: {test_result[0]}") except Exception as e: print(f"✗ DuckDB connection: {e}") # Test cache access try: cache_info = scan_cache_dir() print(f"✓ Cache access: {len(cache_info.repos)} repositories found") except Exception as e: print(f"✗ Cache access: {e}") # Test cache manager methods try: test_cleanup = cache_manager.clean_cache_by_age(max_age_days=999, dry_run=True) print(f"✓ Cache cleanup methods: Working") except Exception as e: print(f"✗ Cache cleanup methods: {e}") print(f"\nCurrent Status:") print(f"Repository: {cache_manager.repo_id}") print(f"Logger configured: {cache_manager.logger is not None}") print(f"Cache management ready: ✓")

Cache Management Troubleshooting:
===================================

1. Import and Setup Issues:
   • Ensure correct import: from tfbpapi.HfCacheManager import HfCacheManager
   • Verify DuckDB connection: conn = duckdb.connect(':memory:')
   • Check repository access permissions

2. Cache Space and Performance Issues:
   Current cache size: 4.6G
   • Use auto_clean_cache() for automated management
   • Monitor cache growth with scan_cache_dir()
   • Set appropriate size limits for your system

3. Cache Cleanup Issues:
   • Use dry_run=True first to preview changes
   • Check disk permissions for cache directory
   • Verify no active processes are using cached files

4. DuckDB Integration Issues:
   • Ensure DuckDB connection is active
   • Check memory limits for in-memory databases
   • Verify table names don't conflict

Cache Health Check:
✓ DuckDB connection: DuckDB OK
✓ Cache access: 9 repositories found

INFO:__main__:No old revisions found to delete
INFO:__main__:Found 0 old revisions. Will free 0.0
INFO:__main__:Dry run completed. Use dry_run=False to execute deletion

✓ Cache cleanup methods: Working

Current Status:
Repository: BrentLab/hackett_2020
Logger configured: True
Cache management ready: ✓

10. Summary and Best Practices¶

The HfCacheManager provides a sophisticated and efficient way to manage metadata and cache for HuggingFace genomics datasets.

Key HfCacheManager Features:¶

1. 3-Case Metadata Strategy: Intelligent caching that checks DuckDB → HF cache → download
2. Automated Cache Cleanup: Multiple strategies (age, size, revision-based) for cache management
3. Cache Monitoring: Real-time cache analysis and diagnostics
4. DuckDB Integration: Efficient metadata storage and querying without data duplication
5. Embedded Metadata Extraction: Extract metadata fields from data tables into queryable views

Cache Management Best Practices:¶

1. Monitor Cache Size: Regular scan_cache_dir() checks prevent disk space issues
2. Proactive Cleanup: Use auto_clean_cache() before large data operations
3. Strategic Retention: Keep recent revisions, clean old ones with clean_unused_revisions()
4. Size Management: Set cache size limits appropriate for your system resources
5. Integration with DataCard: Use DataCard for exploration, HfCacheManager for cache management

Recommended Cache Management Workflow:¶

# 1. Initialize cache manager
from tfbpapi.HfCacheManager import HfCacheManager
import duckdb

conn = duckdb.connect(':memory:')
cache_mgr = HfCacheManager(repo_id, conn)

# 2. Check current cache status
from huggingface_hub import scan_cache_dir
cache_info = scan_cache_dir()
print(f"Current cache: {cache_info.size_on_disk_str}")

# 3. Automated cleanup before heavy operations
cache_mgr.auto_clean_cache(
    max_total_size="10GB",
    max_age_days=30,
    keep_latest_per_repo=2,
    dry_run=False
)

# 4. Load data (uses 3-case strategy automatically)
from tfbpapi import HfQueryAPI
query_api = HfQueryAPI(repo_id, conn)
data = query_api.get_pandas('config_name')

# 5. Extract embedded metadata if needed
cache_mgr._extract_embedded_metadata_field(
    'data_table', 'metadata_field', 'metadata_table'
)

# 6. Regular maintenance
cache_mgr.clean_cache_by_age(max_age_days=30, dry_run=False)

This approach ensures optimal cache performance while maintaining efficient access to genomics datasets.