Release 0.17.0

Also: - Using the deprecated ``history_id`` parameter of the ``HistoryClient.get_histories()`` method now raises a ``ValueError`` exception. - Docs fixes.
galaxyproject · May 9, 2022 · d676872 · d676872
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diff --git a/ABOUT.rst b/ABOUT.rst
@@ -4,7 +4,7 @@ interacting with `Galaxy`_ and `CloudMan`_  APIs.
 BioBlend is supported and tested on:
 
 - Python 3.7, 3.8, 3.9 and 3.10
-- Galaxy release_17.09 and later.
+- Galaxy release 17.09 and later.
 
 BioBlend's goal is to make it easier to script and automate the running of
 Galaxy analyses, administering of a Galaxy server, and cloud infrastructure

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,14 +1,63 @@
-### BioBlend v - unreleased
+### BioBlend v0.17.0 - 2022-05-09
 
 * Dropped support for Python 3.6. Added support for Python 3.10. Added support
   for Galaxy release 21.09 and 22.01.
 
+* Removed deprecated ``run_workflow()`` method of ``WorkflowClient``.
+
+* Using the deprecated ``history_id`` parameter of the
+  ``HistoryClient.get_histories()`` method now raises a ``ValueError``
+  exception.
+
+* Made ``tool_inputs_update`` parameter of ``JobsClient.rerun_job()`` more
+  flexible.
+
+* Added ``whoami()`` method to ``ConfigClient`` (thanks to
+  [cat-bro](https://github.com/cat-bro)).
+
 * Added ``get_extra_files()`` method to ``HistoryClient``.
 
+* Added ``build()`` and ``reload()`` methods to ``ToolClient`` (thanks to
+  [Jayadev Joshi](https://github.com/jaidevjoshi83) and
+  [cat-bro](https://github.com/cat-bro) respectively).
+
+* Added ``get_repositories()`` method to ``ToolShedCategoryClient`` (thanks to
+  [cat-bro](https://github.com/cat-bro)).
+
+* Added ``update_repository_metadata()`` method to ``ToolShedRepositoryClient``.
+
+* Added ``order_by`` parameter to ``JobsClient.get_jobs()`` method.
+
+* BioBlend.objects: Removed deprecated ``run()`` method of ``Workflow``.
+
 * BioBlend.objects: Fail if multiple libraries/histories/workflows match when
   deleting by name, instead of deleting them all.
 
-* Improvements to type annotations, tests and documentation
+* BioBlend.objects: in ``HistoryDatasetAssociation.get_stream()``, wait for
+  the dataset to be ready.
+
+* BioBlend.objects: in ``Workflow.invoke()``, check that the workflow is mapped
+  and runnable before invoking, allow the ``inputs`` parameter to be an instance
+  of a ``Dataset`` subclass, and allow the ``history`` parameter to be the name
+  of a new history.
+
+* BioBlend.objects: Added new ``datasets`` and ``dataset_collections``
+  attributes to ``GalaxyInstance`` objects, which are instances of the new
+  ``ObjDatasetClient`` and ``ObjDatasetCollectionClient`` respectively.
+
+* BioBlend.objects: Added ``refresh()``, ``get_outputs()`` and
+  ``get_output_collections()`` methods to ``InvocationStep``.
+
+* Fixed [error](https://github.com/galaxyproject/bioblend/issues/398) when
+  instantiating ``GalaxyInstance`` with ``email`` and ``password`` (reported by
+  [Peter Briggs](https://github.com/pjbriggs)).
+
+* Fixed parameter validation errors for POST requests with attached files on
+  upcoming Galaxy 22.05.
+
+* Code cleanups (thanks to [Martmists](https://github.com/Martmists-GH)).
+
+* Improvements to type annotations, tests and documentation.
 
 ### BioBlend v0.16.0 - 2021-06-13
 
@@ -280,7 +329,7 @@
 * BioBlend.objects: added ``update()`` method to ``LibraryDataset`` (thanks to
   [Anthony Bretaudeau](https://github.com/abretaud)).
 
-* Run tests with pytest instead of nose
+* Run tests with pytest instead of nose.
 
 ### BioBlend v0.11.0 - 2018-04-18
 
@@ -413,7 +462,7 @@
 
 * Added ``install_resolver_dependencies`` parameter to
   ``ToolShedClient.install_repository_revision()``, applicable for Galaxy
-  release_16.07 and later (thanks to
+  release 16.07 and later (thanks to
   [Marius van den Beek](https://github.com/mvdbeek)).
 
 * Improve ``DatasetClient.download_dataset()`` by downloading the dataset in
@@ -529,7 +578,7 @@
 * Project source moved to new URL - https://github.com/galaxyproject/bioblend
 
 * Huge improvements to automated testing, tests now run against Galaxy
-  release_14.02 and all later versions to ensure backward compatibility
+  release 14.02 and all later versions to ensure backward compatibility
   (see `.travis.yml` for details).
 
 * Many documentation improvements (thanks to
@@ -553,7 +602,7 @@
   deployments.
 
 * Made ``LibraryClient._get_root_folder_id()`` method safer and faster for
-  Galaxy release_13.06 and later.
+  Galaxy release 13.06 and later.
 
 * Deprecate and ignore invalid ``deleted`` parameter to
   ``WorkflowClient.get_workflows()``.

diff --git a/README.rst b/README.rst
@@ -17,7 +17,7 @@ APIs.
 BioBlend is supported and tested on:
 
 - Python 3.7, 3.8, 3.9 and 3.10
-- Galaxy release_17.09 and later.
+- Galaxy release 17.09 and later.
 
 Full docs are available at https://bioblend.readthedocs.io/ with a quick library
 overview also available in `ABOUT.rst <./ABOUT.rst>`_.

diff --git a/bioblend/__init__.py b/bioblend/__init__.py
@@ -8,7 +8,7 @@
 )
 
 # Current version of the library
-__version__ = '0.16.0'
+__version__ = '0.17.0'
 
 # default chunk size (in bytes) for reading remote data
 try:

diff --git a/bioblend/galaxy/config/__init__.py b/bioblend/galaxy/config/__init__.py
@@ -56,6 +56,7 @@ def whoami(self):
         :rtype: dict
         :return: Information about current authenticated user
           For example::
+
             {'active': True,
              'deleted': False,
              'email': '[email protected]',

diff --git a/bioblend/galaxy/dataset_collections/__init__.py b/bioblend/galaxy/dataset_collections/__init__.py
@@ -128,7 +128,7 @@ def download_dataset_collection(self, dataset_collection_id: str, file_path: str
         .. note::
           This method downloads a ``zip`` archive for Galaxy 21.01 and later.
           For earlier versions of Galaxy this method downloads a ``tgz`` archive.
-          This method is only supported by Galaxy 18.01 or later.
+          This method works only on Galaxy 18.01 or later.
         """
         url = self._make_url(module_id=dataset_collection_id) + '/download'
         r = self.gi.make_get_request(url, stream=True)

diff --git a/bioblend/galaxy/datasets/__init__.py b/bioblend/galaxy/datasets/__init__.py
@@ -320,7 +320,7 @@ def publish_dataset(self, dataset_id: str, published: bool = False):
         :return: Current roles for all available permission types.
 
         .. note::
-          This method can only be used with Galaxy ``release_19.05`` or later.
+          This method works only on Galaxy 19.05 or later.
         """
         payload: Dict[str, Any] = {
             'action': 'remove_restrictions' if published else 'make_private'
@@ -349,7 +349,7 @@ def update_permissions(self, dataset_id: str, access_ids: Optional[list] = None,
         :return: Current roles for all available permission types.
 
         .. note::
-          This method can only be used with Galaxy ``release_19.05`` or later.
+          This method works only on Galaxy 19.05 or later.
         """
         payload: Dict[str, Any] = {
             'action': 'set_permissions'

diff --git a/bioblend/galaxy/histories/__init__.py b/bioblend/galaxy/histories/__init__.py
@@ -5,7 +5,6 @@
 import re
 import sys
 import time
-import warnings
 import webbrowser
 from typing import List
 from urllib.parse import urljoin
@@ -56,12 +55,10 @@ def import_history(self, file_path=None, url=None):
 
         return self._post(payload=payload, files_attached=file_path is not None)
 
-    def _get_histories(self, history_id=None, name=None, deleted=False, filter_user_published=None, get_all_published=False, slug=None):
+    def _get_histories(self, name=None, deleted=False, filter_user_published=None, get_all_published=False, slug=None):
         """
         Hidden method to be used by both get_histories() and get_published_histories()
         """
-        if history_id is not None and name is not None:
-            raise ValueError('Provide only one argument between name or history_id, but not both')
         assert not (filter_user_published is not None and get_all_published)
 
         params = {}
@@ -78,10 +75,7 @@ def _get_histories(self, history_id=None, name=None, deleted=False, filter_user_
         url = '/'.join((self._make_url(), 'published')) if get_all_published else None
         histories = self._get(url=url, params=params)
 
-        if history_id is not None:
-            history = next((_ for _ in histories if _['id'] == history_id), None)
-            histories = [history] if history is not None else []
-        elif name is not None:
+        if name is not None:
             histories = [_ for _ in histories if _['name'] == name]
         return histories
 
@@ -90,13 +84,6 @@ def get_histories(self, history_id=None, name=None, deleted=False, published=Non
         Get all histories, or select a subset by specifying optional arguments
         for filtering (e.g. a history name).
 
-        :type history_id: str
-        :param history_id: Encoded history ID to filter on
-
-          .. deprecated:: 0.15.0
-             To get details of a history for which you know the ID, use the much
-             more efficient :meth:`show_history` instead.
-
         :type name: str
         :param name: History name to filter on.
 
@@ -116,13 +103,16 @@ def get_histories(self, history_id=None, name=None, deleted=False, published=Non
 
         :rtype: list
         :return: List of history dicts.
+
+        .. versionchanged:: 0.17.0
+            Using the deprecated ``history_id`` parameter now raises a
+            ``ValueError`` exception.
         """
         if history_id is not None:
-            warnings.warn(
-                'The history_id parameter is deprecated, use the show_history() method to view details of a history for which you know the ID.',
-                category=FutureWarning
+            raise ValueError(
+                'The history_id parameter has been removed, use the show_history() method to view details of a history for which you know the ID.',
             )
-        return self._get_histories(history_id=history_id, name=name, deleted=deleted, filter_user_published=published, get_all_published=False, slug=slug)
+        return self._get_histories(name=name, deleted=deleted, filter_user_published=published, get_all_published=False, slug=slug)
 
     def get_published_histories(self, name=None, deleted=False, slug=None):
         """
@@ -217,9 +207,9 @@ def delete_dataset(self, history_id, dataset_id, purge=False):
         :return: None
 
         .. 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.
+          The ``purge`` option works only if the Galaxy instance has the
+          ``allow_user_dataset_purge`` option set to ``true`` in the
+          ``config/galaxy.yml`` configuration file.
         """
         url = '/'.join((self._make_url(history_id, contents=True), dataset_id))
         payload = {}
@@ -542,7 +532,7 @@ def delete_history(self, history_id, purge=False):
                  purged).
 
         .. note::
-          For the purge option to work, the Galaxy instance must have the
+          The ``purge`` option works only if the Galaxy instance has the
           ``allow_user_dataset_purge`` option set to ``true`` in the
           ``config/galaxy.yml`` configuration file.
         """
@@ -773,7 +763,7 @@ def get_extra_files(self, history_id: str, dataset_id: str) -> List[dict]:
         :return: List of extra files
 
         .. note::
-          This method is only supported by Galaxy 19.01 or later.
+          This method works only on Galaxy 19.01 or later.
         """
         url = '/'.join((self._make_url(history_id, contents=True), dataset_id, 'extra_files'))
         return self._get(url=url)
diff --git a/bioblend/galaxy/invocations/__init__.py b/bioblend/galaxy/invocations/__init__.py
@@ -194,7 +194,7 @@ def rerun_invocation(self, invocation_id: str, inputs_update: Optional[dict] = N
         :return: A dict describing the new workflow invocation.
 
         .. note::
-          This method can only be used with Galaxy ``release_21.01`` or later.
+          This method works only on Galaxy 21.01 or later.
         """
         invocation_details = self.show_invocation(invocation_id)
         workflow_id = invocation_details['workflow_id']

diff --git a/bioblend/galaxy/jobs/__init__.py b/bioblend/galaxy/jobs/__init__.py
@@ -97,8 +97,8 @@ def get_jobs(self, state=None, history_id=None, invocation_id=None, tool_id=None
               'update_time': '2014-03-01T16:05:39.558458'}]
 
         .. note::
-          The following filtering options can only be used with Galaxy ``release_21.05`` or later:
-            user_id, limit, offset, workflow_id, invocation_id
+          The following options work only on Galaxy 21.05 or later: ``user_id``,
+          ``limit``, ``offset``, ``workflow_id``, ``invocation_id``.
         """
         params = {
             'limit': limit,
@@ -204,7 +204,7 @@ def rerun_job(self, job_id, remap=False, tool_inputs_update=None, history_id=Non
         :return: Information about outputs and the rerun job
 
         .. note::
-          This method can only be used with Galaxy ``release_21.01`` or later.
+          This method works only on Galaxy 21.01 or later.
         """
         job_rerun_params = self._build_for_rerun(job_id)
         job_inputs = job_rerun_params['state_inputs']
@@ -277,7 +277,7 @@ def search_jobs(self, tool_id: str, inputs: dict, state: Optional[str] = None) -
           ``inputs`` and ``state``.
 
         .. note::
-          This method is only supported by Galaxy 18.01 or later.
+          This method works only on Galaxy 18.01 or later.
         """
         job_info = {
             'tool_id': tool_id,
@@ -342,7 +342,7 @@ def report_error(self, job_id: str, dataset_id: str, message: str, email: str =
         :return: dict containing job error reply
 
         .. note::
-          This method is only supported by Galaxy 20.01 or later.
+          This method works only on Galaxy 20.01 or later.
         """
         payload = {
             "message": message,
@@ -366,7 +366,7 @@ def get_common_problems(self, job_id: str) -> dict:
         :return: dict containing potential problems
 
         .. note::
-          This method is only supported by Galaxy 19.05 or later.
+          This method works only on Galaxy 19.05 or later.
         """
         url = self._make_url(module_id=job_id) + '/common_problems'
         return self._get(url=url)
@@ -408,7 +408,7 @@ def resume_job(self, job_id: str) -> dict:
         :return: dict containing output dataset associations
 
         .. note::
-          This method is only supported by Galaxy 18.09 or later.
+          This method works only on Galaxy 18.09 or later.
         """
         url = self._make_url(module_id=job_id) + '/resume'
         return self._put(url=url)
@@ -425,8 +425,8 @@ def get_destination_params(self, job_id: str) -> dict:
         :return: Destination parameters for the given job
 
         .. note::
-          This method is only supported by Galaxy 20.05 or later and requires
-          the user to be an admin.
+          This method works only on Galaxy 20.05 or later and if the user is a
+          Galaxy admin.
         """
         url = self._make_url(module_id=job_id) + '/destination_params'
         return self._get(url=url)
@@ -440,8 +440,8 @@ def show_job_lock(self) -> bool:
         :return: Status of the job lock
 
         .. note::
-          This method is only supported by Galaxy 20.05 or later and requires
-          the user to be an admin.
+          This method works only on Galaxy 20.05 or later and if the user is a
+          Galaxy admin.
         """
         url = self.gi.url + '/job_lock'
         response = self._get(url=url)
@@ -457,8 +457,8 @@ def update_job_lock(self, active=False) -> bool:
         :return: Updated status of the job lock
 
         .. note::
-          This method is only supported by Galaxy 20.05 or later and requires
-          the user to be an admin.
+          This method works only on Galaxy 20.05 or later and if the user is a
+          Galaxy admin.
         """
         payload = {
             'active': active,