Source code for bioblend.toolshed.repositories

"""
Interaction with a Tool Shed instance
"""
from six.moves.urllib.parse import urljoin

from bioblend.galaxy.client import Client
from bioblend.util import attach_file


[docs]class ToolShedClient(Client): def __init__(self, toolshed_instance): self.module = 'repositories' super(ToolShedClient, self).__init__(toolshed_instance)
[docs] def get_repositories(self): """ Get a list of all the repositories in a Galaxy Tool Shed :rtype: list :return: Returns a list of dictionaries containing information about repositories present in the Tool Shed. For example:: [{u'times_downloaded': 0, u'user_id': u'5cefd48bc04af6d4', u'description': u'Order Contigs', u'deleted': False, u'deprecated': False, u'private': False, u'url': u'/api/repositories/287bd69f724b99ce', u'owner': u'billybob', u'id': u'287bd69f724b99ce', u'name': u'best_tool_ever'}] .. versionchanged:: 0.4.1 Changed method name from ``get_tools`` to ``get_repositories`` to better align with the Tool Shed concepts """ return Client._get(self)
[docs] def show_repository(self, toolShed_id): """ Display information of a repository from Tool Shed :type toolShed_id: string :param toolShed_id: Encoded toolShed ID :rtype: dictionary :return: Information about the tool For example:: {{u'times_downloaded': 0, u'user_id': u'5cefd48bc04af6d4', u'description': u'Order Contigs', u'deleted': False, u'deprecated': False, u'private': False, u'url': u'/api/repositories/287bd69f724b99ce', u'owner': u'billybob', u'id': u'287bd69f724b99ce', u'name': u'best_tool_ever'} .. versionchanged:: 0.4.1 Changed method name from ``show_tool`` to ``show_repository`` to better align with the Tool Shed concepts """ return Client._get(self, id=toolShed_id)
[docs] def get_ordered_installable_revisions(self, name, owner): """ Returns the ordered list of changeset revision hash strings that are associated with installable revisions. As in the changelog, the list is ordered oldest to newest. :type name: string :param name: the name of the repository :type owner: string :param owner: the owner of the repository :rtype: list :return: List of changeset revision hash string from oldest to newest """ url = self.url + '/get_ordered_installable_revisions' params = {} params['name'] = name params['owner'] = owner r = Client._get(self, url=url, params=params) return r
[docs] def get_repository_revision_install_info(self, name, owner, changeset_revision): """ Return a list of dictionaries of metadata about a certain changeset revision for a single tool. :type name: string :param name: the name of the repository :type owner: string :param owner: the owner of the repository :type changeset_revision: string :param changeset_revision: the changset_revision of the RepositoryMetadata object associated with the repository :rtype: List of dictionaries :return: Returns a list of the following dictionaries: - a dictionary defining the repository - a dictionary defining the repository revision (RepositoryMetadata) - a dictionary including the additional information required to install the repository For example:: [{u'times_downloaded': 269, u'user_id': u'1de29d50c3c44272', u'description': u'Galaxy Freebayes Bayesian genetic variant detector tool', u'deleted': False, u'deprecated': False, u'private': False, u'long_description': u'Galaxy Freebayes Bayesian genetic variant detector tool originally included in the Galaxy code distribution but migrated to the tool shed.', u'url': u'/api/repositories/491b7a3fddf9366f', u'owner': u'devteam', u'id': u'491b7a3fddf9366f', u'name': u'freebayes'}, {u'repository_id': u'491b7a3fddf9366f', u'has_repository_dependencies': False, u'includes_tools_for_display_in_tool_panel': True, u'url': u'/api/repository_revisions/504be8aaa652c154', u'malicious': False, u'includes_workflows': False, u'downloadable': True, u'includes_tools': True, u'changeset_revision': u'd291dc763c4c', u'id': u'504be8aaa652c154', u'includes_tool_dependencies': True, u'includes_datatypes': False}, {u'freebayes': [u'Galaxy Freebayes Bayesian genetic variant detector tool', u'http://takadonet@toolshed.g2.bx.psu.edu/repos/devteam/freebayes', u'd291dc763c4c', u'9', u'devteam', {}, {u'freebayes/0.9.6_9608597d12e127c847ae03aa03440ab63992fedf': {u'repository_name': u'freebayes', u'name': u'freebayes', u'readme': u'FreeBayes requires g++ and the standard C and C++ development libraries. Additionally, cmake is required for building the BamTools API.', u'version': u'0.9.6_9608597d12e127c847ae03aa03440ab63992fedf', u'repository_owner': u'devteam', u'changeset_revision': u'd291dc763c4c', u'type': u'package'}, u'samtools/0.1.18': {u'repository_name': u'freebayes', u'name': u'samtools', u'readme': u'Compiling SAMtools requires the ncurses and zlib development libraries.', u'version': u'0.1.18', u'repository_owner': u'devteam', u'changeset_revision': u'd291dc763c4c', u'type': u'package'}}]}] """ url = self.url + '/get_repository_revision_install_info' params = {} params['name'] = name params['owner'] = owner params['changeset_revision'] = changeset_revision return Client._get(self, url=url, params=params)
[docs] def repository_revisions( self, downloadable=None, malicious=None, tools_functionally_correct=None, missing_test_components=None, do_not_test=None, includes_tools=None, test_install_error=None, skip_tool_test=None): """ Returns a (possibly filtered) list of dictionaries that include information about all repository revisions. The following parameters can be used to filter the list. :type downloadable: Boolean :param downloadable: Can the tool be downloaded :type malicious: Boolean :param malicious: :type tools_functionally_correct: Boolean :param tools_functionally_correct: :type missing_test_components: Boolean :param missing_test_components: :type do_not_test: Boolean :param do_not_test: :type includes_tools: Boolean :param includes_tools: :type test_install_error: Boolean :param test_install_error: :type skip_tool_test: Boolean :param skip_tool_test: :rtype: List of dictionaries :return: Returns a (possibly filtered) list of dictionaries that include information about all repository revisions. For example:: [{u'repository_id': u'78f2604ff5e65707', u'has_repository_dependencies': False, u'includes_tools_for_display_in_tool_panel': True, u'url': u'/api/repository_revisions/92250afff777a169', u'malicious': False, u'includes_workflows': False, u'downloadable': True, u'includes_tools': True, u'changeset_revision': u'6e26c5a48e9a', u'id': u'92250afff777a169', u'includes_tool_dependencies': False, u'includes_datatypes': False}, {u'repository_id': u'f9662009da7bfce0', u'has_repository_dependencies': False, u'includes_tools_for_display_in_tool_panel': True, u'url': u'/api/repository_revisions/d3823c748ae2205d', u'malicious': False, u'includes_workflows': False, u'downloadable': True, u'includes_tools': True, u'changeset_revision': u'15a54fa11ad7', u'id': u'd3823c748ae2205d', u'includes_tool_dependencies': False, u'includes_datatypes': False}] """ # Not using '_make_url' or '_get' to create url since the module id used # to create url is not the same as needed for this method url = self.gi.url + '/repository_revisions' params = {} # nice and long... my god! if downloadable: params['downloadable'] = 'True' if malicious: params['malicious'] = 'True' if tools_functionally_correct: params['tools_functionally_correct'] = 'True' if missing_test_components: params['missing_test_components'] = 'True' if do_not_test: params['do_not_test'] = 'True' if includes_tools: params['includes_tools'] = 'True' if test_install_error: params['test_install_error'] = 'True' if skip_tool_test: params['skip_tool_test'] = 'True' return Client._get(self, url=url, params=params)
[docs] def show_repository_revision(self, metadata_id): ''' Returns a dictionary that includes information about a specified repository revision. :type metadata_id: string :param metadata_id: Encoded repository metadata ID :rtype: dictionary :return: Returns a dictionary that includes information about a specified repository revision. For example:: {u'repository_id': u'491b7a3fddf9366f', u'has_repository_dependencies': False, u'includes_tools_for_display_in_tool_panel': True, u'test_install_error': False, u'url': u'/api/repository_revisions/504be8aaa652c154', u'malicious': False, u'includes_workflows': False, u'id': u'504be8aaa652c154', u'do_not_test': False, u'downloadable': True, u'includes_tools': True, u'tool_test_results': {u'missing_test_components': [],, u'includes_datatypes': False} ''' # Not using '_make_url' or '_get' to create url since the module id used # to create url is not the same as needed for this method # since metadata_id has to be defined, easy to create the url here url = self.gi.url + '/repository_revisions/' + metadata_id return Client._get(self, url=url)
[docs] def get_categories(self): """ Returns a list of dictionaries that contain descriptions of the repository categories found on the given Tool Shed instance. :rtype: list :return: A list of dictionaries containing information about repository categories present in the Tool Shed. For example:: [{u'deleted': False, u'description': u'Tools for manipulating data', u'id': u'175812cd7caaf439', u'model_class': u'Category', u'name': u'Text Manipulation', u'url': u'/api/categories/175812cd7caaf439'},] .. versionadded:: 0.5.2 """ url = urljoin(self.url, 'categories') return Client._get(self, url=url)
[docs] def update_repository(self, id, tar_ball_path, commit_message=None): """ Update the contents of a tool shed repository with specified tar ball. :type id: string :param id: Encoded repository ID :type tar_ball_path: string :param tar_ball_path: Path to file containing tar ball to upload. :type commit_message: string :param commit_message: Commit message used for underlying mercurial repository backing tool shed repository. :rtype: dict :return: Returns a dictionary that includes repository content warnings. Most valid uploads will result in no such warning and an exception will be raised generally if there are problems. For example a successful upload will look like:: {u'content_alert': u'', u'message': u''} .. versionadded:: 0.5.2 """ url = self.gi._make_url(self, id) + '/changeset_revision' payload = {} if commit_message is not None: payload['commit_message'] = commit_message payload["file"] = attach_file(tar_ball_path) try: return Client._post(self, id=id, payload=payload, files_attached=True, url=url) finally: payload["file"].close()
[docs] def create_repository(self, name, synopsis, description=None, type="unrestricted", remote_repository_url=None, homepage_url=None, category_ids=None): """ Create a new repository in a Tool Shed :type name: str :param name: Name of the repository :type synopsis: str :param synopsis: Synopsis of the repository :type description: str :param description: Optional description of the repository :type type: str :param type: type of the repository. One of "unrestricted", "repository_suite_definition", or "tool_dependency_definition" :type remote_repository_url: str :param remote_repository_url: Remote URL (e.g. github/bitbucket repository) :type homepage_url: str :param homepage_url: Upstream's homepage for the project. :type category_ids: list :param category_ids: List of encoded category IDs :rtype: dict :return: a dictionary containing information about the new repository. For example:: { "deleted": false, "deprecated": false, "description": "new_synopsis", "homepage_url": "https://github.com/galaxyproject/", "id": "8cf91205f2f737f4", "long_description": "this is some repository", "model_class": "Repository", "name": "new_repo_17", "owner": "qqqqqq", "private": false, "remote_repository_url": "https://github.com/galaxyproject/tools-devteam", "times_downloaded": 0, "type": "unrestricted", "user_id": "adb5f5c93f827949" } """ payload = { 'name': name, 'synopsis': synopsis, } if description is not None: payload['description'] = description if description is not None: payload['description'] = description if type is not None: payload['type'] = type if remote_repository_url is not None: payload['remote_repository_url'] = remote_repository_url if homepage_url is not None: payload['homepage_url'] = homepage_url if category_ids is not None: payload['category_ids[]'] = category_ids return Client._post(self, payload)