diff env/lib/python3.9/site-packages/bioblend/galaxy/objects/client.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/galaxy/objects/client.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,428 @@
+"""
+Clients for interacting with specific Galaxy entity types.
+
+Classes in this module should not be instantiated directly, but used
+via their handles in :class:`~.galaxy_instance.GalaxyInstance`.
+"""
+import abc
+import json
+from collections.abc import (
+    Mapping,
+    Sequence,
+)
+
+import bioblend
+from . import wrappers
+
+
+class ObjClient(metaclass=abc.ABCMeta):
+
+    @abc.abstractmethod
+    def __init__(self, obj_gi):
+        self.obj_gi = obj_gi
+        self.gi = self.obj_gi.gi
+        self.log = bioblend.log
+
+    @abc.abstractmethod
+    def get_previews(self, **kwargs):
+        """
+        Get a list of object previews.
+
+        Previews entity summaries provided by REST collection URIs, e.g.
+        ``http://host:port/api/libraries``.  Being the most lightweight objects
+        associated to the various entities, these are the ones that should be
+        used to retrieve their basic info.
+
+        :rtype: list
+        :return: a list of object previews
+        """
+        pass
+
+    @abc.abstractmethod
+    def list(self, **kwargs):
+        """
+        Get a list of objects.
+
+        This method first gets the entity summaries, then gets the complete
+        description for each entity with an additional GET call, so may be slow.
+
+        :rtype: list
+        :return: a list of objects
+        """
+        pass
+
+    def _select_ids(self, id_=None, name=None):
+        """
+        Return the id list that corresponds to the given id or name info.
+        """
+        if id_ is None and name is None:
+            self._error('neither id nor name provided', err_type=TypeError)
+        if id_ is not None and name is not None:
+            self._error('both id and name provided', err_type=TypeError)
+        if id_ is None:
+            return [_.id for _ in self.get_previews(name=name)]
+        else:
+            return [id_]
+
+    def _error(self, msg, err_type=RuntimeError):
+        self.log.error(msg)
+        raise err_type(msg)
+
+    def _get_dict(self, meth_name, reply):
+        if reply is None:
+            self._error('%s: no reply' % meth_name)
+        elif isinstance(reply, Mapping):
+            return reply
+        try:
+            return reply[0]
+        except (TypeError, IndexError):
+            self._error(f'{meth_name}: unexpected reply: {reply!r}')
+
+
+class ObjDatasetContainerClient(ObjClient):
+
+    def _get_container(self, id_, ctype):
+        show_fname = 'show_%s' % ctype.__name__.lower()
+        gi_client = getattr(self.gi, ctype.API_MODULE)
+        show_f = getattr(gi_client, show_fname)
+        res = show_f(id_)
+        cdict = self._get_dict(show_fname, res)
+        cdict['id'] = id_  # overwrite unencoded id
+        c_infos = show_f(id_, contents=True)
+        if not isinstance(c_infos, Sequence):
+            self._error(f'{show_fname}: unexpected reply: {c_infos!r}')
+        c_infos = [ctype.CONTENT_INFO_TYPE(_) for _ in c_infos]
+        return ctype(cdict, content_infos=c_infos, gi=self.obj_gi)
+
+
+class ObjLibraryClient(ObjDatasetContainerClient):
+    """
+    Interacts with Galaxy libraries.
+    """
+
+    def __init__(self, obj_gi):
+        super().__init__(obj_gi)
+
+    def create(self, name, description=None, synopsis=None):
+        """
+        Create a data library with the properties defined in the arguments.
+
+        :rtype: :class:`~.wrappers.Library`
+        :return: the library just created
+        """
+        res = self.gi.libraries.create_library(name, description, synopsis)
+        lib_info = self._get_dict('create_library', res)
+        return self.get(lib_info['id'])
+
+    def get(self, id_):
+        """
+        Retrieve the data library corresponding to the given id.
+
+        :rtype: :class:`~.wrappers.Library`
+        :return: the library corresponding to ``id_``
+        """
+        return self._get_container(id_, wrappers.Library)
+
+    def get_previews(self, name=None, deleted=False):
+        dicts = self.gi.libraries.get_libraries(name=name, deleted=deleted)
+        return [wrappers.LibraryPreview(_, gi=self.obj_gi) for _ in dicts]
+
+    def list(self, name=None, deleted=False):
+        """
+        Get libraries owned by the user of this Galaxy instance.
+
+        :type name: str
+        :param name: return only libraries with this name
+        :type deleted: bool
+        :param deleted: if ``True``, return libraries that have been deleted
+
+        :rtype: list of :class:`~.wrappers.Library`
+        """
+        dicts = self.gi.libraries.get_libraries(name=name, deleted=deleted)
+        if not deleted:
+            # return Library objects only for not-deleted libraries since Galaxy
+            # does not filter them out and Galaxy release_14.08 and earlier
+            # crashes when trying to get a deleted library
+            return [self.get(_['id']) for _ in dicts if not _['deleted']]
+        else:
+            return [self.get(_['id']) for _ in dicts]
+
+    def delete(self, id_=None, name=None):
+        """
+        Delete the library with the given id or name.
+
+        Note that the same name can map to multiple libraries.
+
+        .. warning::
+          Deleting a data library is irreversible - all of the data from
+          the library will be permanently deleted.
+        """
+        for id_ in self._select_ids(id_=id_, name=name):
+            res = self.gi.libraries.delete_library(id_)
+            if not isinstance(res, Mapping):
+                self._error(f'delete_library: unexpected reply: {res!r}')
+
+
+class ObjHistoryClient(ObjDatasetContainerClient):
+    """
+    Interacts with Galaxy histories.
+    """
+
+    def __init__(self, obj_gi):
+        super().__init__(obj_gi)
+
+    def create(self, name=None):
+        """
+        Create a new Galaxy history, optionally setting its name.
+
+        :rtype: :class:`~.wrappers.History`
+        :return: the history just created
+        """
+        res = self.gi.histories.create_history(name=name)
+        hist_info = self._get_dict('create_history', res)
+        return self.get(hist_info['id'])
+
+    def get(self, id_):
+        """
+        Retrieve the history corresponding to the given id.
+
+        :rtype: :class:`~.wrappers.History`
+        :return: the history corresponding to ``id_``
+        """
+        return self._get_container(id_, wrappers.History)
+
+    def get_previews(self, name=None, deleted=False):
+        dicts = self.gi.histories.get_histories(name=name, deleted=deleted)
+        return [wrappers.HistoryPreview(_, gi=self.obj_gi) for _ in dicts]
+
+    def list(self, name=None, deleted=False):
+        """
+        Get histories owned by the user of this Galaxy instance.
+
+        :type name: str
+        :param name: return only histories with this name
+        :type deleted: bool
+        :param deleted: if ``True``, return histories that have been deleted
+
+        :rtype: list of :class:`~.wrappers.History`
+        """
+        dicts = self.gi.histories.get_histories(name=name, deleted=deleted)
+        return [self.get(_['id']) for _ in dicts]
+
+    def delete(self, id_=None, name=None, purge=False):
+        """
+        Delete the history with the given id or name.
+
+        Note that the same name can map to multiple histories.
+
+        :type purge: bool
+        :param purge: if ``True``, also purge (permanently delete) the history
+
+        .. note::
+          For the purge option to work, the Galaxy instance must have the
+          ``allow_user_dataset_purge`` option set to ``true`` in the
+          ``config/galaxy.yml`` configuration file.
+        """
+        for id_ in self._select_ids(id_=id_, name=name):
+            res = self.gi.histories.delete_history(id_, purge=purge)
+            if not isinstance(res, Mapping):
+                self._error(f'delete_history: unexpected reply: {res!r}')
+
+
+class ObjWorkflowClient(ObjClient):
+    """
+    Interacts with Galaxy workflows.
+    """
+
+    def __init__(self, obj_gi):
+        super().__init__(obj_gi)
+
+    def import_new(self, src, publish=False):
+        """
+        Imports a new workflow into Galaxy.
+
+        :type src: dict or str
+        :param src: deserialized (dictionary) or serialized (str) JSON
+          dump of the workflow (this is normally obtained by exporting
+          a workflow from Galaxy).
+
+        :type publish: bool
+        :param publish:  if ``True`` the uploaded workflow will be published;
+                         otherwise it will be visible only by the user which uploads it (default).
+
+        :rtype: :class:`~.wrappers.Workflow`
+        :return: the workflow just imported
+        """
+        if isinstance(src, Mapping):
+            wf_dict = src
+        else:
+            try:
+                wf_dict = json.loads(src)
+            except (TypeError, ValueError):
+                self._error(f'src not supported: {src!r}')
+        wf_info = self.gi.workflows.import_workflow_dict(wf_dict, publish)
+        return self.get(wf_info['id'])
+
+    def import_shared(self, id_):
+        """
+        Imports a shared workflow to the user's space.
+
+        :type id_: str
+        :param id_: workflow id
+
+        :rtype: :class:`~.wrappers.Workflow`
+        :return: the workflow just imported
+        """
+        wf_info = self.gi.workflows.import_shared_workflow(id_)
+        return self.get(wf_info['id'])
+
+    def get(self, id_):
+        """
+        Retrieve the workflow corresponding to the given id.
+
+        :rtype: :class:`~.wrappers.Workflow`
+        :return: the workflow corresponding to ``id_``
+        """
+        res = self.gi.workflows.show_workflow(id_)
+        wf_dict = self._get_dict('show_workflow', res)
+        return wrappers.Workflow(wf_dict, gi=self.obj_gi)
+
+    # the 'deleted' option is not available for workflows
+    def get_previews(self, name=None, published=False):
+        dicts = self.gi.workflows.get_workflows(name=name, published=published)
+        return [wrappers.WorkflowPreview(_, gi=self.obj_gi) for _ in dicts]
+
+    # the 'deleted' option is not available for workflows
+    def list(self, name=None, published=False):
+        """
+        Get workflows owned by the user of this Galaxy instance.
+
+        :type name: str
+        :param name: return only workflows with this name
+        :type published: bool
+        :param published: if ``True``, return also published workflows
+
+        :rtype: list of :class:`~.wrappers.Workflow`
+        """
+        dicts = self.gi.workflows.get_workflows(name=name, published=published)
+        return [self.get(_['id']) for _ in dicts]
+
+    def delete(self, id_=None, name=None):
+        """
+        Delete the workflow with the given id or name.
+
+        Note that the same name can map to multiple workflows.
+
+        .. warning::
+          Deleting a workflow is irreversible - all of the data from
+          the workflow will be permanently deleted.
+        """
+        for id_ in self._select_ids(id_=id_, name=name):
+            res = self.gi.workflows.delete_workflow(id_)
+            if not isinstance(res, str):
+                self._error('delete_workflow: unexpected reply: %r' % res)
+
+
+class ObjToolClient(ObjClient):
+    """
+    Interacts with Galaxy tools.
+    """
+
+    def __init__(self, obj_gi):
+        super().__init__(obj_gi)
+
+    def get(self, id_, io_details=False, link_details=False):
+        """
+        Retrieve the tool corresponding to the given id.
+
+        :type io_details: bool
+        :param io_details: if True, get also input and output details
+
+        :type link_details: bool
+        :param link_details: if True, get also link details
+
+        :rtype: :class:`~.wrappers.Tool`
+        :return: the tool corresponding to ``id_``
+        """
+        res = self.gi.tools.show_tool(id_, io_details=io_details,
+                                      link_details=link_details)
+        tool_dict = self._get_dict('show_tool', res)
+        return wrappers.Tool(tool_dict, gi=self.obj_gi)
+
+    def get_previews(self, name=None, trackster=None):
+        """
+        Get the list of tools installed on the Galaxy instance.
+
+        :type name: str
+        :param name: return only tools with this name
+
+        :type trackster: bool
+        :param trackster: if True, only tools that are compatible with
+          Trackster are returned
+
+        :rtype: list of :class:`~.wrappers.Tool`
+        """
+        dicts = self.gi.tools.get_tools(name=name, trackster=trackster)
+        return [wrappers.Tool(_, gi=self.obj_gi) for _ in dicts]
+
+    # the 'deleted' option is not available for tools
+    def list(self, name=None, trackster=None):
+        """
+        Get the list of tools installed on the Galaxy instance.
+
+        :type name: str
+        :param name: return only tools with this name
+
+        :type trackster: bool
+        :param trackster: if True, only tools that are compatible with
+          Trackster are returned
+
+        :rtype: list of :class:`~.wrappers.Tool`
+        """
+        # dicts = self.gi.tools.get_tools(name=name, trackster=trackster)
+        # return [self.get(_['id']) for _ in dicts]
+        # As of 2015/04/15, GET /api/tools returns also data manager tools for
+        # non-admin users, see
+        # https://trello.com/c/jyl0cvFP/2633-api-tool-list-filtering-doesn-t-filter-data-managers-for-non-admins
+        # Trying to get() a data manager tool would then return a 404 Not Found
+        # error.
+        # Moreover, the dicts returned by gi.tools.get_tools() are richer than
+        # those returned by get(), so make this an alias for get_previews().
+        return self.get_previews(name, trackster)
+
+
+class ObjJobClient(ObjClient):
+    """
+    Interacts with Galaxy jobs.
+    """
+
+    def __init__(self, obj_gi):
+        super().__init__(obj_gi)
+
+    def get(self, id_, full_details=False):
+        """
+        Retrieve the job corresponding to the given id.
+
+        :type full_details: bool
+        :param full_details: if ``True``, return the complete list of details
+          for the given job.
+
+        :rtype: :class:`~.wrappers.Job`
+        :return: the job corresponding to ``id_``
+        """
+        res = self.gi.jobs.show_job(id_, full_details)
+        job_dict = self._get_dict('job_tool', res)
+        return wrappers.Job(job_dict, gi=self.obj_gi)
+
+    def get_previews(self):
+        dicts = self.gi.jobs.get_jobs()
+        return [wrappers.JobPreview(_, gi=self.obj_gi) for _ in dicts]
+
+    def list(self):
+        """
+        Get the list of jobs of the current user.
+
+        :rtype: list of :class:`~.wrappers.Job`
+        """
+        dicts = self.gi.jobs.get_jobs()
+        return [self.get(_['id']) for _ in dicts]