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Source code for galaxy.tool_util.deps.mulled.mulled_search

#!/usr/bin/env python

import argparse
import json
import logging
import sys
import tempfile
from datetime import (

import requests

from .mulled_list import get_singularity_containers
from .util import (

    from conda.cli.python_api import run_command
except ImportError:
    run_command = None

    from whoosh.fields import Schema
    from whoosh.fields import TEXT
    from whoosh.fields import STORED
    from whoosh.index import create_in
    from whoosh.qparser import QueryParser
except ImportError:
    Schema = TEXT = STORED = create_in = QueryParser = None

QUAY_API_URL = 'https://quay.io/api/v1/repository'

[docs]class QuaySearch(): """ Tool to search within a quay organization for a given software name. """
[docs] def __init__(self, organization): self.index = None self.organization = organization
[docs] def build_index(self): """ Create an index to quickly examine the repositories of a given quay.io organization. """ # download all information about the repositories from the # given organization in self.organization parameters = {'public': 'true', 'namespace': self.organization} r = requests.get(QUAY_API_URL, headers={ 'Accept-encoding': 'gzip'}, params=parameters, timeout=MULLED_SOCKET_TIMEOUT) tmp_dir = tempfile.mkdtemp() schema = Schema(title=TEXT(stored=True), content=STORED) self.index = create_in(tmp_dir, schema) json_decoder = json.JSONDecoder() decoded_request = json_decoder.decode(r.text) writer = self.index.writer() for repository in decoded_request['repositories']: writer.add_document( title=repository['name'], content=repository['description']) writer.commit()
[docs] def search_repository(self, search_string, non_strict): """ Search Docker containers on quay.io. Results are displayed with all available versions, including the complete image name. """ # with statement closes searcher after usage. with self.index.searcher() as searcher: query = QueryParser( "title", self.index.schema).parse(search_string) results = searcher.search(query) if non_strict: # look for spelling errors and use suggestions as a search term too corrector = searcher.corrector("title") suggestions = corrector.suggest(search_string, limit=2) # get all repositories with suggested keywords for suggestion in suggestions: search_string = f"*{suggestion}*" query = QueryParser( "title", self.index.schema).parse(search_string) results_tmp = searcher.search(query) results.extend(results_tmp) out = list() for result in results: title = result['title'] for version in self.get_additional_repository_information(title): out.append({'package': title, 'version': version, }) return out
[docs] def get_additional_repository_information(self, repository_string): """ Function downloads additional information from quay.io to get the tag-field which includes the version number. """ url = f"{QUAY_API_URL}/{self.organization}/{repository_string}" r = requests.get(url, headers={'Accept-encoding': 'gzip'}, timeout=MULLED_SOCKET_TIMEOUT) json_decoder = json.JSONDecoder() decoded_request = json_decoder.decode(r.text) return decoded_request['tags']
[docs]class CondaSearch(): """ Tool to search the bioconda channel """
[docs] def __init__(self, channel): self.channel = channel
[docs] def get_json(self, search_string): """ Function takes search_string variable and returns results from the bioconda channel in JSON format """ if run_command is None: raise Exception(f"Invalid search destination. {deps_error_message('conda')}") raw_out, err, exit_code = run_command( 'search', '-c', self.channel, search_string, use_exception_handler=True) if exit_code != 0: logging.info(f'Search failed with: {err}') return [] return [{'package': n.split()[0], 'version': n.split()[1], 'build': n.split()[2]} for n in raw_out.split('\n')[2:-1]]
[docs]class GitHubSearch(): """ Tool to search the GitHub bioconda-recipes repo """ @staticmethod def _check_response_rate_limit(response): if response.status_code == 403 and "API rate limit exceeded" in response.json()["message"]: # It can take tens of minutes before the rate limit window resets message = "GitHub API rate limit exceeded." rate_limit_reset_UTC_timestamp = response.headers.get("X-RateLimit-Reset") if rate_limit_reset_UTC_timestamp: rate_limit_reset_datetime = datetime.fromtimestamp(int(rate_limit_reset_UTC_timestamp), tz=timezone.utc) message += f" The rate limit window will reset at {rate_limit_reset_datetime.isoformat()}." raise Exception(message)
[docs] def get_json(self, search_string): """ Takes search_string variable and return results from the bioconda-recipes github repository in JSON format DEPRECATED: this method is currently unreliable because the API query sometimes succeeds but returns no items. """ response = requests.get( f"https://api.github.com/search/code?q={search_string}+in:path+repo:bioconda/bioconda-recipes+path:recipes", timeout=MULLED_SOCKET_TIMEOUT, ) self._check_response_rate_limit(response) response.raise_for_status() return response.json()
[docs] def process_json(self, json_response, search_string): """ Take JSON input and process it, returning the required data """ top_10_items = json_response['items'][0:10] # get top ten results return [{'name': result['name'], 'path': result['path']} for result in top_10_items]
[docs] def recipe_present(self, search_string): """ Check if a recipe exists in bioconda-recipes which matches search_string exactly """ response = requests.get( f"https://api.github.com/repos/bioconda/bioconda-recipes/contents/recipes/{search_string}", timeout=MULLED_SOCKET_TIMEOUT, ) self._check_response_rate_limit(response) return response.status_code == 200
[docs]def get_package_hash(packages, versions): """ Take packages and versions (if the latter are given) and returns a hash for each. Also checks github to see if the container is already present. """ hash_results = {} targets = [] if versions: for p in packages: targets.append(build_target(p, version=versions[p])) else: # if versions are not given only calculate the package hash for p in packages: targets.append(build_target(p)) # make the hash from the processed targets package_hash = v2_image_name(targets) hash_results['package_hash'] = package_hash.split(':')[0] if versions: hash_results['version_hash'] = package_hash.split(':')[1] r = requests.get(f"https://quay.io/api/v1/repository/biocontainers/{hash_results['package_hash']}", timeout=MULLED_SOCKET_TIMEOUT) if r.status_code == 200: hash_results['container_present'] = True if versions: # now test if the version hash is listed in the repository tags # remove -0, -1, etc from end of the tag tags = [n[:-2] for n in r.json()['tags']] if hash_results['version_hash'] in tags: hash_results['container_present_with_version'] = True else: hash_results['container_present_with_version'] = False else: hash_results['container_present'] = False return hash_results
[docs]def readable_output(json, organization='biocontainers', channel='bioconda'): # if json is empty: if sum(len(json[destination][results]) for destination in json for results in json[destination]) == 0: sys.stdout.write('No results found for that query.\n') return # return results for quay, conda and singularity together if sum(len(json[destination][results]) for destination in ['quay', 'conda', 'singularity', ] for results in json.get(destination, [])) > 0: sys.stdout.write("The query returned the following result(s).\n") # put quay, conda etc results as lists in lines lines = [['LOCATION', 'NAME', 'VERSION', 'COMMAND\n']] for results in json.get('quay', {}).values(): for result in results: lines.append(['quay', result['package'], result['version'], 'docker pull quay.io/%s/%s:%s\n' % (organization, result['package'], result['version'])]) # NOT a real solution for results in json.get('conda', {}).values(): for result in results: lines.append(['conda', result['package'], f"{result['version']}--{result['build']}", f"conda install -c {channel} {result['package']}={result['version']}={result['build']}\n"]) for results in json.get('singularity', {}).values(): for result in results: lines.append(['singularity', result['package'], result['version'], f"wget https://depot.galaxyproject.org/singularity/{result['package']}:{result['version']}\n"]) col_width0, col_width1, col_width2 = (max(len( line[n]) for line in lines) + 2 for n in (0, 1, 2)) # def max col widths for the output # create table for line in lines: sys.stdout.write("".join((line[0].ljust(col_width0), line[1].ljust( col_width1), line[2].ljust(col_width2), line[3]))) # output if json.get('github_recipe_present', False): sys.stdout.write('\n' if 'lines' in locals() else '') sys.stdout.write( 'The following recipes were found in the bioconda-recipes repository which exactly matched one of the search terms:\n') lines = [['QUERY', 'LOCATION\n']] for recipe in json['github_recipe_present']['recipes']: lines.append( [recipe, f"https://api.github.com/repos/bioconda/bioconda-recipes/contents/recipes/{recipe}\n"]) col_width0 = max(len(line[0]) for line in lines) + 2 for line in lines: sys.stdout.write( "".join((line[0].ljust(col_width0), line[1]))) # output if sum(len(json['github'][results]) for results in json.get('github', [])) > 0: sys.stdout.write('\n' if 'lines' in locals() else '') sys.stdout.write( "Other result(s) on the bioconda-recipes GitHub repository:\n") lines = [['QUERY', 'FILE', 'URL\n']] for search_string, results in json.get('github', {}).items(): for result in results: lines.append([search_string, result['name'], f"https://github.com/bioconda/bioconda-recipes/tree/master/{result['path']}\n"]) # def max col widths for the output col_width0, col_width1 = ( max(len(line[n]) for line in lines) + 2 for n in (0, 1)) for line in lines: sys.stdout.write("".join( (line[0].ljust(col_width0), line[1].ljust(col_width1), line[2]))) # output
[docs]def deps_error_message(package): return f"Required dependency [{package}] is not installed. Run 'pip install galaxy-tool-util[mulled]'."
[docs]def main(argv=None): if Schema is None: sys.stdout.write(deps_error_message("Whoosh")) return destination_defaults = ['quay', 'singularity', 'github'] if run_command is not None: destination_defaults.append('conda') parser = argparse.ArgumentParser( description='Searches in a given quay organization for a repository') parser.add_argument('-d', '--destination', dest='search_dest', nargs='+', default=destination_defaults, help="Choose where to search. Options are 'conda', 'quay', 'singularity' and 'github'. If no option are given, all will be searched.") parser.add_argument('-o', '--organization', dest='organization_string', default="biocontainers", help='Change quay organization to search; default is biocontainers.') parser.add_argument('-c', '--channel', dest='channel_string', default="bioconda", help='Change conda channel to search; default is bioconda.') parser.add_argument('--non-strict', dest='non_strict', action="store_true", help='Autocorrection of typos activated. Lists more results but can be confusing.\ For too many queries quay.io blocks the request and the results can be incomplete.') parser.add_argument('-j', '--json', dest='json', action="store_true", help='Returns results as JSON.') parser.add_argument('-s', '--search', required=True, nargs='+', help='The name of the tool(s) to search for.') args = parser.parse_args() json_results = {dest: {} for dest in args.search_dest} versions = {} if len(args.search) > 1: # get hash if multiple packages are searched args.search.append(get_package_hash( args.search, versions)['package_hash']) if 'conda' in args.search_dest: conda_results = {} conda = CondaSearch(args.channel_string) for item in args.search: conda_results[item] = conda.get_json(item) json_results['conda'] = conda_results if 'github' in args.search_dest: github_results = {} github_recipe_present = [] github = GitHubSearch() for item in args.search: if github.recipe_present(item): github_recipe_present.append(item) else: github_json = github.get_json(item) github_results[item] = github.process_json(github_json, item) json_results['github'] = github_results json_results['github_recipe_present'] = { 'recipes': github_recipe_present} if 'quay' in args.search_dest: quay_results = {} quay = QuaySearch(args.organization_string) quay.build_index() for item in args.search: quay_results[item] = quay.search_repository(item, args.non_strict) json_results['quay'] = quay_results if 'singularity' in args.search_dest: singularity_results = {} for item in args.search: singularity_results[item] = singularity_search(item) json_results['singularity'] = singularity_results if args.json: print(json_results) else: readable_output(json_results, args.organization_string, args.channel_string)
if __name__ == "__main__": main()