This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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

#!/usr/bin/env python

import argparse
import json
import sys
import tempfile

    import requests
except ImportError:
    requests = 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=12) 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: search_string = "*%s*" % search_string 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 = "*%s*" % suggestion query = QueryParser("title", self.index.schema).parse(search_string) results_tmp = searcher.search(query) results.extend(results_tmp) sys.stdout.write("The query \033[1m %s \033[0m resulted in %s result(s).\n" % (search_string, len(results))) if non_strict: sys.stdout.write('The search was relaxed and the following search terms were searched: ') sys.stdout.write('\033[1m %s \033[0m\n' % ', '.join(suggestions)) out = list() for result in results: title = result['title'] for version in self.get_additional_repository_information(title): row = [title] row.append(version) out.append(row) if out: col_width = max(len(word) for row in out for word in row) + 2 # padding for row in out: name = row[0] version = row[1] sys.stdout.write("".join(word.ljust(col_width) for word in row) + "docker pull quay.io/%s/%s:%s\n" % (self.organization, name, version)) else: sys.stdout.write("No results found for %s in quay.io/%s.\n" % (search_string, self.organization))
[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 = "%s/%s/%s" % (QUAY_API_URL, self.organization, repository_string) r = requests.get(url, headers={'Accept-encoding': 'gzip'}, timeout=12) json_decoder = json.JSONDecoder() decoded_request = json_decoder.decode(r.text) return decoded_request['tags']
[docs]def main(argv=None): parser = argparse.ArgumentParser(description='Searches in a given quay organization for a repository') parser.add_argument('-o', '--organization', dest='organization_string', default="biocontainers", help='Change organization. Default is biocontainers.') 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('-s', '--search', required=True, help='The name of the tool you want to search for.') args = parser.parse_args() quay = QuaySearch(args.organization_string) quay.build_index() quay.search_repository(args.search, args.non_strict)
if __name__ == "__main__": main()