annotate env/lib/python3.9/site-packages/bioblend/toolshed/repositories/__init__.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

"""
Interaction with a Tool Shed instance repositories
"""
from bioblend.galaxy.client import Client
from bioblend.util import attach_file


class ToolShedRepositoryClient(Client):

    def __init__(self, toolshed_instance):
        self.module = 'repositories'
        super().__init__(toolshed_instance)

    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::

            [{'category_ids': ['c1df3132f6334b0e', 'f6d7b0037d901d9b'],
              'deleted': False,
              'deprecated': False,
              'description': 'Order Contigs',
              'homepage_url': '',
              'id': '287bd69f724b99ce',
              'name': 'best_tool_ever',
              'owner': 'billybob',
              'private': False,
              'remote_repository_url': '',
              'times_downloaded': 0,
              'type': 'unrestricted',
              'url': '/api/repositories/287bd69f724b99ce',
              'user_id': '5cefd48bc04af6d4'}]

        .. versionchanged:: 0.4.1
          Changed method name from ``get_tools`` to ``get_repositories`` to
          better align with the Tool Shed concepts.
        """
        return self._get()

    def search_repositories(self, q, page=1, page_size=10):
        """
        Search for repositories in a Galaxy Tool Shed.

        :type  q: str
        :param q: query string for searching purposes

        :type  page: int
        :param page: page requested

        :type  page_size: int
        :param page_size: page size requested

        :rtype:  dict
        :return: dictionary containing search hits as well as metadata for the
          search.
          For example::

            {'hits': [{'matched_terms': [],
                       'repository': {'approved': 'no',
                                      'description': 'Convert export file to fastq',
                                      'full_last_updated': '2015-01-18 09:48 AM',
                                      'homepage_url': '',
                                      'id': 'bdfa208f0cf6504e',
                                      'last_updated': 'less than a year',
                                      'long_description': 'This is a simple too to convert Solexas Export files to FASTQ files.',
                                      'name': 'export_to_fastq',
                                      'remote_repository_url': '',
                                      'repo_owner_username': 'louise',
                                      'times_downloaded': 164},
                       'score': 4.92},
                      {'matched_terms': [],
                       'repository': {'approved': 'no',
                                      'description': 'Convert BAM file to fastq',
                                      'full_last_updated': '2015-04-07 11:57 AM',
                                      'homepage_url': '',
                                      'id': '175812cd7caaf439',
                                      'last_updated': 'less than a month',
                                      'long_description': 'Use Picards SamToFastq to convert a BAM file to fastq. Useful for storing reads as BAM in Galaxy and converting to fastq when needed for analysis.',
                                      'name': 'bam_to_fastq',
                                      'remote_repository_url': '',
                                      'repo_owner_username': 'brad-chapman',
                                      'times_downloaded': 138},
                       'score': 4.14}],
             'hostname': 'https://testtoolshed.g2.bx.psu.edu/',
             'page': '1',
             'page_size': '2',
             'total_results': '64'}
        """
        params = dict(q=q, page=page, page_size=page_size)
        return self._get(params=params)

    def show_repository(self, toolShed_id):
        """
        Display information of a repository from Tool Shed

        :type toolShed_id: str
        :param toolShed_id: Encoded Tool Shed ID

        :rtype: dict
        :return: Information about the tool.
          For example::

            {'category_ids': ['c1df3132f6334b0e', 'f6d7b0037d901d9b'],
             'deleted': False,
             'deprecated': False,
             'description': 'Order Contigs',
             'homepage_url': '',
             'id': '287bd69f724b99ce',
             'long_description': '',
             'name': 'best_tool_ever',
             'owner': 'billybob',
             'private': False,
             'remote_repository_url': '',
             'times_downloaded': 0,
             'type': 'unrestricted',
             'url': '/api/repositories/287bd69f724b99ce',
             'user_id': '5cefd48bc04af6d4'}

        .. versionchanged:: 0.4.1
          Changed method name from ``show_tool`` to ``show_repository`` to
          better align with the Tool Shed concepts.
        """
        return self._get(id=toolShed_id)

    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: str
        :param name: the name of the repository

        :type owner: str
        :param owner: the owner of the repository

        :rtype: list
        :return: List of changeset revision hash strings from oldest to newest
        """
        url = self._make_url() + '/get_ordered_installable_revisions'
        params = {
            'name': name,
            'owner': owner
        }
        r = self._get(url=url, params=params)

        return r

    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: str
        :param name: the name of the repository

        :type owner: str
        :param owner: the owner of the repository

        :type changeset_revision: str
        :param changeset_revision: the changeset_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::

            [{'deleted': False,
              'deprecated': False,
              'description': 'Galaxy Freebayes Bayesian genetic variant detector tool',
              'homepage_url': '',
              'id': '491b7a3fddf9366f',
              'long_description': 'Galaxy Freebayes Bayesian genetic variant detector tool originally included in the Galaxy code distribution but migrated to the tool shed.',
              'name': 'freebayes',
              'owner': 'devteam',
              'private': False,
              'remote_repository_url': '',
              'times_downloaded': 269,
              'type': 'unrestricted',
              'url': '/api/repositories/491b7a3fddf9366f',
              'user_id': '1de29d50c3c44272'},
             {'changeset_revision': 'd291dc763c4c',
              'do_not_test': False,
              'downloadable': True,
              'has_repository_dependencies': False,
              'id': '504be8aaa652c154',
              'includes_datatypes': False,
              'includes_tool_dependencies': True,
              'includes_tools': True,
              'includes_tools_for_display_in_tool_panel': True,
              'includes_workflows': False,
              'malicious': False,
              'repository_id': '491b7a3fddf9366f',
              'url': '/api/repository_revisions/504be8aaa652c154'},
             {'freebayes': ['Galaxy Freebayes Bayesian genetic variant detector tool',
                            'http://testtoolshed.g2.bx.psu.edu/repos/devteam/freebayes',
                            'd291dc763c4c',
                            '9',
                            'devteam',
                            {},
                            {'freebayes/0.9.6_9608597d12e127c847ae03aa03440ab63992fedf': {'changeset_revision': 'd291dc763c4c',
                                                                                          'name': 'freebayes',
                                                                                          'repository_name': 'freebayes',
                                                                                          'repository_owner': 'devteam',
                                                                                          'type': 'package',
                                                                                          'version': '0.9.6_9608597d12e127c847ae03aa03440ab63992fedf'},
                             'samtools/0.1.18': {'changeset_revision': 'd291dc763c4c',
                                                 'name': 'samtools',
                                                 'repository_name': 'freebayes',
                                                 'repository_owner': 'devteam',
                                                 'type': 'package',
                                                 'version': '0.1.18'}}]}]
        """
        url = self._make_url() + '/get_repository_revision_install_info'
        params = {
            'name': name,
            'owner': owner,
            'changeset_revision': changeset_revision
        }
        return self._get(url=url, params=params)

    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: bool
        :param downloadable: Can the tool be downloaded

        :type malicious: bool
        :param malicious:

        :type tools_functionally_correct: bool
        :param tools_functionally_correct:

        :type missing_test_components: bool
        :param missing_test_components:

        :type do_not_test: bool
        :param do_not_test:

        :type includes_tools: bool
        :param includes_tools:

        :type test_install_error: bool
        :param test_install_error:

        :type skip_tool_test: bool
        :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::

            [{'changeset_revision': '6e26c5a48e9a',
              'do_not_test': False,
              'downloadable': True,
              'has_repository_dependencies': False,
              'id': '92250afff777a169',
              'includes_datatypes': False,
              'includes_tool_dependencies': False,
              'includes_tools': True,
              'includes_tools_for_display_in_tool_panel': True,
              'includes_workflows': False,
              'malicious': False,
              'missing_test_components': False,
              'repository_id': '78f2604ff5e65707',
              'test_install_error': False,
              'time_last_tested': None,
              'tools_functionally_correct': False,
              'url': '/api/repository_revisions/92250afff777a169'},
             {'changeset_revision': '15a54fa11ad7',
              'do_not_test': False,
              'downloadable': True,
              'has_repository_dependencies': False,
              'id': 'd3823c748ae2205d',
              'includes_datatypes': False,
              'includes_tool_dependencies': False,
              'includes_tools': True,
              'includes_tools_for_display_in_tool_panel': True,
              'includes_workflows': False,
              'malicious': False,
              'missing_test_components': False,
              'repository_id': 'f9662009da7bfce0',
              'test_install_error': False,
              'time_last_tested': None,
              'tools_functionally_correct': False,
              'url': '/api/repository_revisions/d3823c748ae2205d'}]
        """
        # 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 = {}
        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 self._get(url=url, params=params)

    def show_repository_revision(self, metadata_id):
        '''
        Returns a dictionary that includes information about a specified
        repository revision.

        :type metadata_id: str
        :param metadata_id: Encoded repository metadata ID

        :rtype: dict
        :return: Returns a dictionary that includes information about a
          specified repository revision.
          For example::

            {'changeset_revision': '7602de1e7f32',
             'do_not_test': False,
             'downloadable': True,
             'has_repository_dependencies': False,
             'id': '504be8aaa652c154',
             'includes_datatypes': False,
             'includes_tool_dependencies': False,
             'includes_tools': True,
             'includes_tools_for_display_in_tool_panel': True,
             'includes_workflows': False,
             'malicious': False,
             'missing_test_components': True,
             'repository_id': '491b7a3fddf9366f',
             'test_install_error': False,
             'time_last_tested': None,
             'tool_test_results': {'missing_test_components': []},
             'tools_functionally_correct': False,
             'url': '/api/repository_revisions/504be8aaa652c154'}
        '''
        # 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 = '/'.join((self.gi.url, 'repository_revisions', metadata_id))
        return self._get(url=url)

    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: str
        :param id: Encoded repository ID

        :type tar_ball_path: str
        :param tar_ball_path: Path to file containing tar ball to upload.

        :type commit_message: str
        :param commit_message: Commit message used for the 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::

            {'content_alert': '',
             'message': ''}

        .. versionadded:: 0.5.2
        """
        url = self._make_url(id) + '/changeset_revision'
        payload = {
            'file': attach_file(tar_ball_path)
        }
        if commit_message is not None:
            payload['commit_message'] = commit_message
        try:
            return self._post(payload=payload, files_attached=True, url=url)
        finally:
            payload['file'].close()

    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 self._post(payload)