Python transformer.Transform类代码示例

    def create_folder(cls, name, parent=None, project=None,
                      api=None):
        """Create a new folder
        :param name: Folder name
        :param parent: Parent folder
        :param project: Project to create folder in
        :param api: Api instance
        :return: New folder
        """
        api = api or cls._API

        data = {
            'name': name,
            'type': cls.FOLDER_TYPE
        }

        if not parent and not project:
            raise SbgError('Parent or project must be provided')

        if parent and project:
            raise SbgError(
                'Providing both "parent" and "project" is not allowed'
            )

        if parent:
            data['parent'] = Transform.to_file(file_=parent)

        if project:
            data['project'] = Transform.to_project(project=project)

        response = api.post(url=cls._URL['create_folder'], data=data).json()
        return cls(api=api, **response)

    def upload(cls, path, project=None, parent=None, file_name=None,
               overwrite=False, retry=5, timeout=10,
               part_size=PartSize.UPLOAD_MINIMUM_PART_SIZE, wait=True,
               api=None):
        """
        Uploads a file using multipart upload and returns an upload handle
        if the wait parameter is set to False. If wait is set to True it
        will block until the upload is completed.

        :param path: File path on local disc.
        :param project: Project identifier
        :param parent: Parent folder identifier
        :param file_name: Optional file name.
        :param overwrite: If true will overwrite the file on the server.
        :param retry:  Number of retries if error occurs during upload.
        :param timeout:  Timeout for http requests.
        :param part_size:  Part size in bytes.
        :param wait:  If true will wait for upload to complete.
        :param api: Api instance.
        """

        api = api or cls._API
        extra = {'resource': cls.__name__, 'query': {
            'path': path,
            'project': project,
            'file_name': file_name,
            'overwrite': overwrite,
            'retry': retry,
            'timeout': timeout,
            'part_size': part_size,
            'wait': wait,
        }}
        logger.info('Uploading file', extra=extra)

        if not project and not parent:
            raise SbgError('A project or parent identifier is required.')

        if project and parent:
            raise SbgError(
                'Project and parent identifiers are mutually exclusive.'
            )

        if project:
            project = Transform.to_project(project)

        if parent:
            parent = Transform.to_file(parent)

        upload = Upload(
            file_path=path, project=project, parent=parent,
            file_name=file_name, overwrite=overwrite, retry_count=retry,
            timeout=timeout, part_size=part_size, api=api
        )
        if wait:
            upload.start()
            upload.wait()
            return upload
        else:
            return upload

    def submit_export(cls, file, volume, location, properties=None,
                      overwrite=False, copy_only=False, api=None):

        """
        Submit new export job.
        :param file: File to be exported.
        :param volume: Volume identifier.
        :param location: Volume location.
        :param properties: Properties dictionary.
        :param overwrite: If true it will overwrite file if exists
        :param copy_only: If true files are kept on SevenBridges bucket.
        :param api: Api Instance.
        :return: Export object.
        """
        data = {}
        params = {}

        volume = Transform.to_volume(volume)
        file = Transform.to_file(file)
        destination = {
            'volume': volume,
            'location': location
        }
        source = {
            'file': file
        }
        if properties:
            data['properties'] = properties

        data['source'] = source
        data['destination'] = destination
        data['overwrite'] = overwrite

        extra = {
            'resource': cls.__name__,
            'query': data
        }
        logger.info('Submitting export', extra=extra)

        api = api if api else cls._API
        if copy_only:
            params['copy_only'] = True
            _export = api.post(
                cls._URL['query'], data=data, params=params).json()
        else:
            _export = api.post(
                cls._URL['query'], data=data).json()

        return Export(api=api, **_export)

    def create(cls, name, billing_group, description=None, tags=None,
               api=None):
        """
        Create a project.
        :param name:  Project name.
        :param billing_group: Project billing group.
        :param description:  Project description.
        :param tags: Project tags.
        :param api: Api instance.
        :return:
        """
        api = api if api else cls._API

        billing_group = Transform.to_billing_group(billing_group)
        if name is None:
            raise SbgError('Project name is required!')

        data = {
            'name': name,
            'billing_group': billing_group,
        }
        if description:
            data['description'] = description
        if tags:
            data['tags'] = tags

        project_data = api.post(url=cls._URL['query'],
                                data=data).json()
        return Project(api=api, **project_data)

 def query(cls, division, offset=None, limit=None, api=None):
     division = Transform.to_division(division)
     api = api if api else cls._API
     return super(Team, cls)._query(
         url=cls._URL['query'], division=division, offset=offset,
         limit=limit, fields='_all', api=api
     )

    def add_member(self, user, permissions):
        """
        Add a member to the project.
        :param user:  Member username
        :param permissions: Permissions dictionary.
        :return: Member object.
        """
        user = Transform.to_user(user)
        data = {'username': user, 'type': 'USER'}
        if isinstance(permissions, dict):
            data.update({
                'permissions': permissions
            })

        extra = {
            'resource': self.__class__.__name__,
            'query': {
                'id': self.id,
                'data': data,
            }
        }
        logger.info('Adding member using username', extra=extra)
        response = self._api.post(
            url=self._URL['members_query'].format(id=self.id), data=data)
        member_data = response.json()
        return Member(api=self._api, **member_data)

    def add_member_division(self, division, permissions):
        """
        Add a member (team) to a project.
        :param division: Division object or division identifier.
        :param permissions: Permissions dictionary.
        :return: Member object.
        """
        division = Transform.to_division(division)
        data = {'id': division, 'type': 'DIVISION'}
        if isinstance(permissions, dict):
            data.update({
                'permissions': permissions
            })

        extra = {
            'resource': self.__class__.__name__,
            'query': {
                'id': self.id,
                'data': data,
            }
        }
        logger.info('Adding team member using division id', extra=extra)
        response = self._api.post(
            url=self._URL['members_query'].format(id=self.id), data=data)
        member_data = response.json()
        return Member(api=self._api, **member_data)

    def add_member_team(self, team, permissions):
        """
        Add a member (team) to a volume.
        :param team: Team object or team identifier.
        :param permissions: Permissions dictionary.
        :return: Member object.
        """
        team = Transform.to_team(team)
        data = {'id': team, 'type': 'TEAM'}

        if 'execute' in permissions:
            permissions.pop('execute')

        if isinstance(permissions, dict):
            data.update({
                'permissions': permissions
            })

        extra = {
            'resource': self.__class__.__name__,
            'query': {
                'id': self.id,
                'data': data,
            }
        }
        logger.info('Adding volume team member using team id', extra=extra)
        response = self._api.post(
            url=self._URL['members_query'].format(id=self.id), data=data)
        member_data = response.json()
        return Member(api=self._api, **member_data)

    def create(cls, file, name, position, chromosome, private=True, api=None):
        """
        Create a marker on a file.
        :param file: File object or identifier.
        :param name: Marker name.
        :param position: Marker position object.
        :param chromosome: Chromosome number.
        :param private: Whether the marker is private or public.
        :param api: Api instance.
        :return: Marker object.
        """
        api = api if api else cls._API

        file = Transform.to_file(file)
        data = {
            'file': file,
            'name': name,
            'position': position,
            'chromosome': chromosome,
            'private': private
        }

        extra = {
            'resource': cls.__name__,
            'query': data
        }
        logger.info('Creating marker', extra=extra)
        marker_data = api.post(url=cls._URL['query'], data=data).json()
        return Marker(api=api, **marker_data)

 def remove_member(self, user):
     """
     Remove member from the project.
     :param user: User to be removed.
     """
     member = Transform.to_user(user)
     self._api.delete(url=self._URL['members_get'].format(
         id=self.id,
         member=member))

    def bulk_submit(cls, exports, copy_only=False, api=None):
        """
        Create exports in bulk.
        :param exports: Exports to be submitted in bulk.
        :param copy_only: If true files are kept on SevenBridges bucket.
        :param api: Api instance.
        :return: list of ExportBulkRecord objects.
        """
        if not exports:
            raise SbgError('Exports are required')

        api = api or cls._API

        items = []
        for export in exports:
            file_ = Transform.to_file(export.get('file'))
            volume = Transform.to_volume(export.get('volume'))
            location = Transform.to_location(export.get('location'))
            properties = export.get('properties', {})
            overwrite = export.get('overwrite', False)

            item = {
                'source': {
                    'file': file_
                },
                'destination': {
                    'volume': volume,
                    'location': location
                },
                'properties': properties,
                'overwrite': overwrite
            }

            items.append(item)

        data = {'items': items}
        params = {'copy_only': copy_only}

        response = api.post(
            url=cls._URL['bulk_create'], params=params, data=data
        )
        return ExportBulkRecord.parse_records(response=response, api=api)

    def get_file_delete_job(cls, id, api=None):
        """
        :param id: Async job identifier
        :param api: Api instance
        :return:
        """
        id = Transform.to_async_job(id)

        api = api if api else cls._API
        async_job = api.get(
            url=cls._URL['get_file_delete_job'].format(id=id)
        ).json()
        return AsyncJob(api=api, **async_job)

    def bulk_get(cls, exports, api=None):
        """
        Retrieve exports in bulk.
        :param exports: Exports to be retrieved.
        :param api: Api instance.
        :return: list of ExportBulkRecord objects.
        """
        api = api or cls._API
        export_ids = [Transform.to_export(export) for export in exports]
        data = {'export_ids': export_ids}

        response = api.post(url=cls._URL['bulk_get'], data=data)
        return ExportBulkRecord.parse_records(response=response, api=api)

    def bulk_delete(cls, files, api=None):
        """
        Delete files with specified ids in bulk
        :param files: Files to be deleted.
        :param api: Api instance.
        :return: List of FileBulkRecord objects.
        """
        api = api or cls._API
        file_ids = [Transform.to_file(file_) for file_ in files]
        data = {'file_ids': file_ids}

        logger.info('Deleting files in bulk.')
        response = api.post(url=cls._URL['bulk_delete'], data=data)
        return FileBulkRecord.parse_records(response=response, api=api)

    def remove_member(self, member, api=None):
        """Remove member from a dataset
        :param member: Member username
        :param api: Api instance
        :return: None
        """
        api = api or self._API
        username = Transform.to_member(member)

        api.delete(
            url=self._URL['member'].format(
                id=self.id,
                username=username
            )
        )