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

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/bioblend/toolshed/repositories/__init__.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,467 @@
+"""
+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)