From 5faabed662c7f355b3e9d435c20e9655b52797cc Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Tue, 28 Apr 2026 12:19:18 +0200 Subject: [PATCH] deploy alphafind on qa1 --- files/galaxy/tools/alphafind.xml | 220 +++++ files/galaxy/tools/alphafind_search.py | 899 ++++++++++++++++++ group_vars/galaxyservers.yml | 2 + .../vars.yml | 3 +- .../config/local_tool_conf.xml.j2 | 1 + templates/galaxy/config/tpv_rules_meta.yml.j2 | 4 +- 6 files changed, 1126 insertions(+), 3 deletions(-) create mode 100644 files/galaxy/tools/alphafind.xml create mode 100755 files/galaxy/tools/alphafind_search.py diff --git a/files/galaxy/tools/alphafind.xml b/files/galaxy/tools/alphafind.xml new file mode 100644 index 00000000..3d504b88 --- /dev/null +++ b/files/galaxy/tools/alphafind.xml @@ -0,0 +1,220 @@ + + Search AlphaFind API for structurally similar proteins + + python + requests + + /dev/null || echo "1.0.0" + ]]> + + + + + + + + + + + + + +
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+ + + + 0.5 indicates significant structural similarity +* TM-score > 0.8 indicates very high structural similarity + +----- + +**Examples** + +1. **Basic search**: Query protein P0A6F5 with default settings + +2. **Find similar proteins in specific organism**: + + - Query: Q8Y547 + - Organism: Mycobacterium tuberculosis + +3. **Domain-level search**: + + - Query: F8U1Q0 + - Index: domains + - CATH annotation: 1.10.8.10 + +4. **High-confidence results**: + + - Query: P9WGR1 + - Sort by: TM-Score + - Sort order: Descending + +----- + +**References** + +* AlphaFind API: https://alphafind.ics.muni.cz +* AlphaFold DB: https://alphafold.ebi.ac.uk +* TM-Score paper: Yang & Skolnick, 2004 + +----- + +**Troubleshooting** + +* **"Protein not found"**: The query ID may not exist in AlphaFold DB or lacks embedding vectors. Verify the UniProt ID. +* **Timeout exceeded**: Increase the timeout value in Search Options. +* **Empty results**: Your filters may be too restrictive, or no similar proteins exist with the specified criteria. +* **"Search failed"**: The API encountered an error. Try again or check the API status. + ]]> + + 10.1038/nature14539 + + diff --git a/files/galaxy/tools/alphafind_search.py b/files/galaxy/tools/alphafind_search.py new file mode 100755 index 00000000..487e24a6 --- /dev/null +++ b/files/galaxy/tools/alphafind_search.py @@ -0,0 +1,899 @@ +#!/usr/bin/env python3 +""" +AlphaFind API Client + +Search AlphaFold protein structures for structural similarity via the AlphaFind API. + +Usage: + python3 alphafind_search.py --query P0A6F5 --output results.csv + +Search Features: + - Query by UniProt protein ID + - Multiple index types: chains, chains_90, chains_80, chains_70, domains + - Filters: organism, taxonomy ID, gene name, CATH annotation (domains) + - Pagination and sorting support + - Asynchronous computation with progress tracking + +Output: + CSV file with structural similarity results including TM-scores and metadata + +API Limitations: + - Maximum 5,000 results per query (hard limit) + - Page size limited to 100 results by the API + - TM-score calculations can take time for large result sets + +Common Use Cases: + 1. Basic search for similar structures: --query P0A6F5 + 2. Filter by organism: --filters '{"organism": "Mycobacterium tuberculosis"}' + 3. Sort by TM-score: --sort-by tm_score --sort-order desc + 4. Get more results: --options '{"size": 5000}' (max API limit) + +For queries with >5000 results, split by organism or tax_id and combine. + +Version: 1.0.0 +""" + +__version__ = "1.0.0" + +import argparse +import csv +import json +import logging +import sys +import time +from dataclasses import dataclass +from typing import Any, Dict, List, Optional + +import requests + +# ============================================================================ +# Constants +# ============================================================================ + +# Exit codes +EXIT_SUCCESS = 0 +EXIT_SEARCH_FAILED = 1 +EXIT_TIMEOUT = 2 +EXIT_HTTP_ERROR = 3 +EXIT_INTERRUPTED = 4 +EXIT_UNEXPECTED_ERROR = 5 + +# API defaults +DEFAULT_BASE_URL = "https://alphafind.ics.muni.cz" +DEFAULT_PAGE_SIZE = 100 +DEFAULT_TIMEOUT = 600 +DEFAULT_POLL_INTERVAL = 5 + +# Pagination: API max is 100 per page +MAX_PAGE_SIZE = 100 + +# Result limits +MAX_RESULTS_PER_QUERY = 5000 + +# Sort options +DEFAULT_SORT_BY = 'knn' +DEFAULT_SORT_ORDER = 'desc' +VALID_SORT_BY = ['knn', 'tm_score'] +VALID_SORT_ORDER = ['asc', 'desc'] + +# Index types +VALID_INDEXES = ['chains', 'chains_90', 'chains_80', 'chains_70', 'domains'] + +# CSV output columns +CSV_COLUMNS = [ + 'query_id', 'index_type', 'page_number', + 'target_id', 'score', 'organism', 'tax_id', + 'gene_name', 'protein_name', 'avg_plddt', + 'tm_score_query', 'tm_score_target', 'rmsd', + 'sequential_identity', 'aligned_residues', + 'status', 'created_at', 'completed_at', + 'has_experimental_structure', 'pdb_ids', + 'chopping', 'tar_index' +] + +# Status constants +STATUS_PENDING = 'pending' +STATUS_SCORING = 'scoring' +STATUS_COMPLETED = 'completed' +STATUS_FAILED = 'failed' +STATUS_FINAL = (STATUS_COMPLETED, STATUS_FAILED) + + +# ============================================================================ +# Data Classes +# ============================================================================ + +@dataclass +class SearchConfig: + """Configuration for a search operation.""" + query: str + index: Optional[List[str]] # None = use server default + filters: Dict[str, Any] + options: Dict[str, Any] + output_file: str + base_url: str + poll_interval: int + timeout: int + page_size: int + sort_by: str = DEFAULT_SORT_BY + sort_order: str = DEFAULT_SORT_ORDER + verbose: bool = False + dry_run: bool = False + quiet: bool = False + + +# ============================================================================ +# API Client +# ============================================================================ + +class AlphaFindClient: + """Client for interacting with the AlphaFind API.""" + + def __init__(self, base_url: str, timeout: int = 30): + """Initialize the AlphaFind client. + + Args: + base_url: Base URL of the AlphaFind API + timeout: Request timeout in seconds + """ + self.base_url = base_url.rstrip('/') + self.timeout = timeout + self.session = requests.Session() + self.session.headers.update({'Content-Type': 'application/json'}) + + def health_check(self) -> bool: + """Check if the API is accessible. + + Returns: + True if API is healthy, False otherwise + """ + try: + response = self.session.get( + f"{self.base_url}/api/health", + timeout=self.timeout + ) + response.raise_for_status() + return True + except requests.RequestException as e: + logging.warning(f"Health check failed: {e}") + return False + + def submit_search( + self, + query: str, + index: Optional[List[str]], + filters: Dict[str, Any], + options: Dict[str, Any] + ) -> tuple[str, str, str]: + """Submit a search query to the API. + + Args: + query: Protein ID to search for + index: Index types to search (None for server default) + filters: Filter criteria + options: Search options + + Returns: + Tuple of (query_id, index_type, status) + + Raises: + requests.HTTPError: If the API request fails + """ + payload = { + "query": query, + "filters": filters, + "options": options + } + + # Only include index if specified + if index: + payload["index"] = index + + logging.info(f"Submitting search for query: {query}") + logging.info(f"API URL: {self.base_url}/api/search") + logging.info(f"API Payload: {json.dumps(payload)}") + + response = self.session.post( + f"{self.base_url}/api/search", + json=payload, + timeout=self.timeout + ) + response.raise_for_status() + + data = response.json() + query_id = data['id'] + index_type = data['index_type'][0] + status = data['status'] + + logging.info(f"Search submitted: query_id={query_id}, " + f"index_type={index_type}, status={status}") + logging.debug(f"Response: {json.dumps(data, indent=2)}") + + return query_id, index_type, status + + def get_results( + self, + query_id: str, + index_type: str, + page: int = 1, + page_size: int = DEFAULT_PAGE_SIZE, + sort_by: str = DEFAULT_SORT_BY, + sort_order: str = DEFAULT_SORT_ORDER + ) -> Dict[str, Any]: + """Retrieve paginated search results. + + Args: + query_id: Query ID from search submission + index_type: Index type + page: Page number (1-indexed) + page_size: Number of results per page (max 100) + sort_by: Sort field ('knn' or 'tm_score') + sort_order: Sort order ('desc' or 'asc') + + Returns: + Dictionary containing results and metadata + + Raises: + requests.HTTPError: If the API request fails + """ + params = { + "page": page, + "page_size": page_size, + "sort_by": sort_by, + "sort_order": sort_order + } + + logging.debug(f"Fetching results: page={page}, page_size={page_size}") + + response = self.session.get( + f"{self.base_url}/api/search/{query_id}/{index_type}/results", + params=params, + timeout=self.timeout + ) + + # Handle 404 responses that contain error messages + if response.status_code == 404: + try: + error_data = response.json() + if error_data.get('status') == STATUS_FAILED: + error_message = error_data.get('message', 'Search query not found') + sys.stderr.write(f"ERROR: {error_message}\n") + sys.stderr.flush() + raise RuntimeError(f"Search failed: {error_message}") + except (ValueError, KeyError): + # If response is not JSON or doesn't have expected structure + sys.stderr.write(f"ERROR: Search query not found for query_id: {query_id}, index_type: {index_type}\n") + sys.stderr.flush() + raise RuntimeError(f"Search query not found: query_id={query_id}, index_type={index_type}") + + response.raise_for_status() + + return response.json() + + def wait_for_completion( + self, + query_id: str, + index_type: str, + poll_interval: int = DEFAULT_POLL_INTERVAL, + timeout: int = DEFAULT_TIMEOUT, + show_progress: bool = True + ) -> str: + """Poll the API until the search is completed or failed. + + Args: + query_id: Query ID to monitor + index_type: Index type + poll_interval: Seconds between polls + timeout: Maximum time to wait in seconds + show_progress: Whether to show progress indicator + + Returns: + Final status ('completed' or 'failed') + + Raises: + TimeoutError: If timeout is exceeded + """ + start_time = time.time() + status = STATUS_PENDING + + logging.info(f"Waiting for completion (timeout={timeout}s, " + f"poll_interval={poll_interval}s)") + + while time.time() - start_time < timeout: + try: + response = self.get_results(query_id, index_type, page=1, page_size=1) + status = response.get('status', STATUS_PENDING) + total_results = response.get('total_results', 0) + + if show_progress: + sys.stdout.write(f"\r Status: {status} | " + f"Elapsed: {int(time.time() - start_time)}s | " + f"Results: {total_results}") + sys.stdout.flush() + + if status in STATUS_FINAL: + if show_progress: + sys.stdout.write('\n') + logging.info(f"Search finished with status: {status}") + return status + + time.sleep(poll_interval) + + except requests.RequestException as e: + logging.warning(f"Polling error (will retry): {e}") + time.sleep(poll_interval) + + if show_progress: + sys.stdout.write('\n') + raise TimeoutError( + f"Search did not complete within {timeout} seconds. " + f"Last status: {status}" + ) + + def get_all_results( + self, + query_id: str, + index_type: str, + page_size: int = DEFAULT_PAGE_SIZE, + sort_by: str = DEFAULT_SORT_BY, + sort_order: str = DEFAULT_SORT_ORDER, + show_progress: bool = True + ) -> List[Dict[str, Any]]: + """Fetch all paginated results. + + Args: + query_id: Query ID + index_type: Index type + page_size: Number of results per page + sort_by: Sort field + sort_order: Sort order + show_progress: Whether to show progress + + Returns: + List of all result dictionaries + """ + all_results: List[Dict[str, Any]] = [] + page = 1 + total_pages = 1 + + logging.info(f"Fetching all results with page_size={page_size}") + + while page <= total_pages: + try: + response = self.get_results( + query_id, index_type, + page=page, + page_size=page_size, + sort_by=sort_by, + sort_order=sort_order + ) + + results = response.get('results', []) + all_results.extend(results) + + if page == 1: + total_pages = response.get('total_pages', 1) + + if show_progress: + sys.stdout.write(f"\r Fetching page {page}/{total_pages}") + sys.stdout.flush() + + page += 1 + + except requests.RequestException as e: + logging.error(f"Error fetching page {page}: {e}") + break + + if show_progress: + sys.stdout.write('\n') + logging.info(f"Fetched {len(all_results)} results") + + return all_results + + +# ============================================================================ +# Data Processing +# ============================================================================ + +def flatten_result( + result: Dict[str, Any], + query_id: str, + index_type: str, + page: int +) -> Dict[str, Any]: + """Flatten nested result dictionary for CSV export. + + Args: + result: Raw result from API + query_id: Query ID for this search + index_type: Index type for this search + page: Page number this result came from + + Returns: + Flattened dictionary ready for CSV export + """ + flattened = { + 'query_id': query_id, + 'index_type': index_type, + 'page_number': page, + 'target_id': result.get('target_id'), + 'score': result.get('score'), + 'organism': result.get('organism'), + 'tax_id': result.get('tax_id'), + 'gene_name': result.get('gene_name'), + 'protein_name': result.get('protein_name'), + 'avg_plddt': result.get('avg_plddt'), + 'tm_score_query': result.get('tm_score_query'), + 'tm_score_target': result.get('tm_score_target'), + 'rmsd': result.get('rmsd'), + 'sequential_identity': result.get('sequential_identity'), + 'aligned_residues': result.get('aligned_residues'), + } + + # Flatten metadata + metadata = result.get('metadata', {}) + flattened['status'] = metadata.get('status') + flattened['created_at'] = metadata.get('created_at') + flattened['completed_at'] = metadata.get('completed_at') + + # Flatten experimental_structure (can be None) + exp_structure = result.get('experimental_structure') + if exp_structure: + flattened['has_experimental_structure'] = exp_structure.get('has_experimental_structure') + pdb_ids = exp_structure.get('pdb_ids') + flattened['pdb_ids'] = ';'.join(pdb_ids) if pdb_ids else '' + else: + flattened['has_experimental_structure'] = None + flattened['pdb_ids'] = '' + + # Handle optional fields + if 'tar_index' in result: + flattened['tar_index'] = str(result['tar_index']) + + flattened['chopping'] = result.get('chopping', '') + + return flattened + + +def results_to_csv( + results: List[Dict[str, Any]], + query_id: str, + index_type: str, + filename: str, + page_size: int +) -> int: + """Write flattened results to CSV file. + + Args: + results: List of raw result dictionaries + query_id: Query ID for this search + index_type: Index type for this search + filename: Output CSV filename + page_size: Page size used (for page number assignment) + + Returns: + Number of results written + """ + if not results: + logging.warning("No results to write to CSV") + return 0 + + # Calculate page numbers and flatten all results + flattened_results = [] + for i, result in enumerate(results): + page = (i // page_size) + 1 + flattened_results.append( + flatten_result(result, query_id, index_type, page) + ) + + # Write to CSV + try: + with open(filename, 'w', newline='', encoding='utf-8') as f: + writer = csv.DictWriter(f, fieldnames=CSV_COLUMNS, extrasaction='ignore') + writer.writeheader() + writer.writerows(flattened_results) + + logging.info(f"Wrote {len(flattened_results)} results to {filename}") + return len(flattened_results) + + except IOError as e: + logging.error(f"Error writing CSV file: {e}") + raise + + +# ============================================================================ +# Argument Parsing +# ============================================================================ + +def parse_json_args(arg_string: str) -> Dict[str, Any]: + """Parse JSON string argument. + + Args: + arg_string: JSON string to parse + + Returns: + Parsed dictionary + + Raises: + argparse.ArgumentTypeError: If JSON is invalid + """ + if not arg_string: + return {} + + try: + return json.loads(arg_string) + except json.JSONDecodeError as e: + raise argparse.ArgumentTypeError(f"Invalid JSON: {e}") + + +def parse_arguments() -> SearchConfig: + """Parse command-line arguments. + + Returns: + SearchConfig with all parameters + """ + parser = argparse.ArgumentParser( + description='AlphaFind API Client - Search for protein structures', + formatter_class=argparse.RawDescriptionHelpFormatter, + epilog=""" +Examples: + # Basic search + python3 alphafind_search.py --query P0A6F5 + + # Search with organism filter + python3 alphafind_search.py --query Q8Y547 --filters '{"organism": "Mycobacterium tuberculosis"}' + + # Search with sorting + python3 alphafind_search.py --query Q9SBL1 --sort-by tm_score --sort-order desc + + # Request maximum results (API limit is 5000 per query) + python3 alphafind_search.py --query P69905 --options '{"size": 5000}' --timeout 1800 + """ + ) + + # Required: query + parser.add_argument( + '--query', + help='UniProt protein ID to search (e.g., "P0A6F5")' + ) + + # Optional: index selection + parser.add_argument( + '--index', + nargs='+', + help=f'Index types to search (uses server default if not specified). ' + f'Valid: {", ".join(VALID_INDEXES)}' + ) + + # Optional: filters + parser.add_argument( + '--filters', + type=parse_json_args, + default={}, + help='Filter criteria as JSON string (e.g., \'{"organism": "Mycobacterium tuberculosis"}\')' + ) + + # Optional: search options + parser.add_argument( + '--options', + type=parse_json_args, + default={}, + help='Search options as JSON string (e.g., \'{"size": 5000}\')' + ) + + # Optional: individual filters (for Galaxy compatibility) + parser.add_argument( + '--filter-organism', + help='Filter by organism name (e.g., "Mycobacterium tuberculosis")' + ) + parser.add_argument( + '--filter-tax-id', + type=int, + help='Filter by NCBI Taxonomy ID (numeric)' + ) + parser.add_argument( + '--filter-gene-name', + help='Filter by gene name' + ) + parser.add_argument( + '--filter-cath-annotation', + help='Filter by CATH annotation (only for domains index)' + ) + + # Optional: individual options (for Galaxy compatibility) + parser.add_argument( + '--option-k', + type=int, + help='Number of similar proteins to return (k parameter)' + ) + + # Optional: output + parser.add_argument( + '--output', + default='results.csv', + help='Output CSV filename (default: results.csv)' + ) + + # Optional: API configuration + parser.add_argument( + '--base-url', + default=DEFAULT_BASE_URL, + help=f'AlphaFind API base URL (default: {DEFAULT_BASE_URL})' + ) + + # Optional: timeouts and polling + parser.add_argument( + '--poll-interval', + type=int, + default=DEFAULT_POLL_INTERVAL, + help=f'Polling interval in seconds (default: {DEFAULT_POLL_INTERVAL})' + ) + + parser.add_argument( + '--timeout', + type=int, + default=DEFAULT_TIMEOUT, + help=f'Maximum wait time in seconds (default: {DEFAULT_TIMEOUT})' + ) + + # Optional: pagination + parser.add_argument( + '--page-size', + type=int, + default=DEFAULT_PAGE_SIZE, + choices=range(1, MAX_PAGE_SIZE + 1), + metavar=f'[1-{MAX_PAGE_SIZE}]', + help=f'Results per page (default: {DEFAULT_PAGE_SIZE}, max: {MAX_PAGE_SIZE})' + ) + + # Optional: sorting + parser.add_argument( + '--sort-by', + choices=VALID_SORT_BY, + default=DEFAULT_SORT_BY, + help=f'Sort results by (default: {DEFAULT_SORT_BY})' + ) + + parser.add_argument( + '--sort-order', + choices=VALID_SORT_ORDER, + default=DEFAULT_SORT_ORDER, + help=f'Sort order (default: {DEFAULT_SORT_ORDER})' + ) + + # Mode flags + parser.add_argument('-v', '--verbose', action='store_true', + help='Enable verbose logging') + parser.add_argument('-q', '--quiet', action='store_true', + help='Suppress informational output (recommended for Galaxy automation)') + parser.add_argument('--dry-run', action='store_true', + help='Show what would be done without executing') + parser.add_argument('--version', action='store_true', + help='Show version and exit') + + args = parser.parse_args() + + # Handle version flag + if args.version: + print(__version__) + sys.exit(EXIT_SUCCESS) + + # Validate required arguments + if not args.query and not args.dry_run: + parser.error('--query is required') + + # Build filters from both JSON and individual params + filters = dict(args.filters) + if args.filter_organism: + filters['organism'] = args.filter_organism + if args.filter_tax_id: + filters['tax_id'] = args.filter_tax_id + if args.filter_gene_name: + filters['gene_name'] = args.filter_gene_name + if args.filter_cath_annotation: + filters['cath_annotation'] = args.filter_cath_annotation + + # Build options from both JSON and individual params + options = dict(args.options) + if args.option_k: + options['k'] = args.option_k + + return SearchConfig( + query=args.query, + index=args.index, + filters=filters, + options=options, + output_file=args.output, + base_url=args.base_url, + poll_interval=args.poll_interval, + timeout=args.timeout, + page_size=args.page_size, + sort_by=args.sort_by, + sort_order=args.sort_order, + verbose=args.verbose, + dry_run=args.dry_run, + quiet=args.quiet + ) + + +# ============================================================================ +# Logging +# ============================================================================ + +def setup_logging(verbose: bool, quiet: bool = False) -> None: + """Configure logging based on verbosity and quiet mode. + + Args: + verbose: Whether to enable verbose logging + quiet: Whether to suppress all informational logging (for Galaxy) + """ + if quiet: + logging.basicConfig( + level=logging.ERROR, + format='%(message)s', + stream=sys.stderr + ) + else: + level = logging.DEBUG if verbose else logging.INFO + logging.basicConfig( + level=level, + format='%(asctime)s - %(levelname)s - %(message)s', + datefmt='%Y-%m-%d %H:%M:%S' + ) + + +def error_exit(message: str, exit_code: int = 1) -> None: + """Print error to stderr and exit. + + Args: + message: Error message to display + exit_code: Exit code to return + """ + sys.stderr.write(f"ERROR: {message}\n") + sys.stderr.flush() + sys.exit(exit_code) + + +# ============================================================================ +# Main Application +# ============================================================================ + +def run_search(client: AlphaFindClient, config: SearchConfig) -> int: + """Execute the search workflow. + + Args: + client: AlphaFind API client + config: Search configuration + + Returns: + Exit code (0 for success, non-zero for failure) + """ + show_progress = not config.quiet + + # Submit search + query_id, index_type, status = client.submit_search( + query=config.query, + index=config.index, + filters=config.filters, + options=config.options + ) + + # Wait for completion if needed + if status != STATUS_COMPLETED: + if not config.quiet: + logging.info("Waiting for search to complete...") + status = client.wait_for_completion( + query_id=query_id, + index_type=index_type, + poll_interval=config.poll_interval, + timeout=config.timeout, + show_progress=show_progress + ) + + # Check final status + if status == STATUS_FAILED: + error_msg = "Search failed. No results to retrieve." + logging.error(error_msg) + if config.quiet: + error_exit(error_msg, EXIT_SEARCH_FAILED) + return EXIT_SEARCH_FAILED + + # Get all results + results = client.get_all_results( + query_id=query_id, + index_type=index_type, + page_size=config.page_size, + sort_by=config.sort_by, + sort_order=config.sort_order, + show_progress=show_progress + ) + + # Save to CSV + if not results: + if not config.quiet: + logging.warning("No results found") + return EXIT_SUCCESS + + count = results_to_csv( + results=results, + query_id=query_id, + index_type=index_type, + filename=config.output_file, + page_size=config.page_size + ) + + if not config.quiet: + logging.info(f"Successfully completed. {count} results saved to {config.output_file}") + + return EXIT_SUCCESS + + +def main() -> int: + """Main entry point. + + Returns: + Exit code (0 for success, non-zero for failure) + """ + config = parse_arguments() + setup_logging(config.verbose, config.quiet) + + # Log configuration if not in quiet mode + if not config.quiet: + logging.info("=" * 60) + logging.info("AlphaFind API Client") + logging.info("=" * 60) + logging.info(f"Query: {config.query}") + logging.info(f"Index: {config.index or 'Server default'}") + logging.info(f"Filters: {config.filters}") + logging.info(f"Options: {config.options}") + logging.info(f"Output: {config.output_file}") + logging.info(f"Base URL: {config.base_url}") + logging.info(f"Timeout: {config.timeout}s, Poll interval: {config.poll_interval}s") + logging.info(f"Page size: {config.page_size}, Sort by: {config.sort_by} {config.sort_order}") + logging.info("=" * 60) + + if config.dry_run: + logging.info("DRY RUN - No API calls will be made") + logging.info(f"Query: {config.query}") + logging.info(f"Results would be saved to: {config.output_file}") + return EXIT_SUCCESS + + try: + client = AlphaFindClient(config.base_url) + + # Health check (optional, just warns if fails) + if not client.health_check() and not config.quiet: + logging.warning("Health check failed. Continuing anyway...") + + return run_search(client, config) + + except TimeoutError as e: + error_msg = str(e) + logging.error(error_msg) + if config.quiet: + error_exit(error_msg, EXIT_TIMEOUT) + return EXIT_TIMEOUT + + except requests.HTTPError as e: + response_text = e.response.text if e.response else 'No response' + error_msg = f"HTTP error: {e}\nResponse: {response_text}" + logging.error(error_msg) + if config.quiet: + error_exit(error_msg, EXIT_HTTP_ERROR) + return EXIT_HTTP_ERROR + + except KeyboardInterrupt: + if not config.quiet: + logging.info("\nInterrupted by user") + return EXIT_INTERRUPTED + + except Exception as e: + error_msg = f"Unexpected error: {e}" + logging.error(error_msg, exc_info=config.verbose) + if config.quiet: + error_exit(error_msg, EXIT_UNEXPECTED_ERROR) + return EXIT_UNEXPECTED_ERROR + + +if __name__ == '__main__': + sys.exit(main()) diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml index a8f3ff20..ae5c7fea 100644 --- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -295,6 +295,8 @@ galaxy_local_tools: - testing.xml - testing_pbs.xml - testing_html.xml + - alphafind.xml + - alphafind_search.py galaxy_extra_dirs: - "{{ galaxy_mutable_data_dir }}" diff --git a/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml b/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml index 2e842eb6..cf3cac32 100644 --- a/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml +++ b/host_vars/galaxy-qa1.galaxy.cloud.e-infra.cz/vars.yml @@ -1,9 +1,8 @@ -galaxy_commit_id: release_25.1 galaxy_build_client: false galaxy_client_make_target: client-production galaxy_repo: https://github.com/CESNET/galaxy.git -galaxy_commit_id: cesnet_invenio +galaxy_commit_id: cesnet_invenio_26.0 csnt_brand: "QA1-TEST-{{ galaxy_commit_id }}" csnt_log_level: DEBUG diff --git a/templates/galaxy-qa1.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 b/templates/galaxy-qa1.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 index 7f54acdd..d248419c 100644 --- a/templates/galaxy-qa1.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 +++ b/templates/galaxy-qa1.galaxy.cloud.e-infra.cz/config/local_tool_conf.xml.j2 @@ -3,4 +3,5 @@ + diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2 index 326a40ab..565bf241 100644 --- a/templates/galaxy/config/tpv_rules_meta.yml.j2 +++ b/templates/galaxy/config/tpv_rules_meta.yml.j2 @@ -253,11 +253,13 @@ tools: scheduling: require: - alphafold + alphafind_search*: + inherits: local_running_tools toolshed.g2.bx.psu.edu/repos/bgruening/llm_hub/llm_hub/.*: inherits: local_running_tools env: LITELLM_CONFIG_FILE: "{{ galaxy_config_dir }}/llm_hub_config.yaml" - + roles: training.*: