Merge pull request #529 from anuprulez/main

Adds a method to extract tool's helptext

Author: nsoranzo

CHANGELOG.md

@@ -2,9 +2,17 @@
 
 * Dropped support for Python 3.9. Added support for Galaxy release 26.0.
 
+* Added ``copy_history()`` method to ``HistoryClient`` (thanks to
+  [Peter van Heusden ](https://github.com/pvanheus)).
+
+* Added ``get_tool_source()`` method to ``ToolClient`` (thanks to
+  [Anup Kumar](https://github.com/anuprulez)).
+
 * Added ``preferred_object_store_id`` parameter to
   ``HistoryClient.update_history()``.
 
+* Improvements to documentation and tests.
+
 ## BioBlend v1.7.0 - 2025-11-07
 
 * Deprecation: this is the last release to support end-of-life Python 3.9.

bioblend/_tests/TestGalaxyTools.py

@@ -175,3 +175,10 @@ def test_get_tool_tests(self):
         assert first_test["tool_id"] == "random_lines1", first_test
         assert "inputs" in first_test
         assert "outputs" in first_test
+
+    @test_util.skip_unless_galaxy("release_22.01")
+    @test_util.skip_unless_tool("random_lines1")
+    def test_get_tool_source(self):
+        tool_source = self.gi.tools.get_tool_source("random_lines1")
+        assert tool_source.startswith("<tool")
+        assert tool_source.endswith("</tool>")

bioblend/galaxy/tools/__init__.py

@@ -182,6 +182,26 @@ def uninstall_dependencies(self, tool_id: str) -> dict:
         url = self._make_url(tool_id) + "/dependencies"
         return self._delete(url=url)
 
+    def get_tool_source(self, tool_id: str) -> str:
+        """
+        Get the raw tool XML source for a given tool ID.
+
+        :type tool_id: str
+        :param tool_id: id of the requested tool
+
+        :rtype: str
+        :return: Tool XML source as a string
+
+        .. note::
+          This method works only on Galaxy 22.01 or later and if the user is a
+          Galaxy admin or the Galaxy instance has the
+          ``enable_tool_source_display`` option set to ``true`` in the
+          ``config/galaxy.yml`` configuration file.
+        """
+        raw_source_url = self._make_url(tool_id) + "/raw_tool_source"
+        ht_response = self._get(url=raw_source_url, json=False)
+        return ht_response.text
+
     def show_tool(self, tool_id: str, io_details: bool = False, link_details: bool = False) -> dict[str, Any]:
         """
         Get details of a given tool.
@@ -216,7 +236,8 @@ def get_tool_tests(self, tool_id: str, tool_version: str | None = None) -> list[
           the tests for all available tool versions.
 
         :rtype: list
-        :return: List of test case definitions, e.g.::
+        :return: List of test case definitions.
+          For example::
 
             [
                 {
@@ -551,10 +572,10 @@ def post_to_fetch(self, path: str, history_id: str, session_id: str, **kwargs: A
         :type session_id: str
         :param session_id: Session ID returned by the tus service
 
-        See :meth:`upload_file` for additional parameters.
-
         :rtype: dict
         :return: Information about the created upload job
+
+        See :meth:`upload_file` for additional parameters.
         """
         payload = self._fetch_payload(path, history_id, session_id, **kwargs)
         url = "/".join((self.gi.url, "tools/fetch"))
@@ -571,10 +592,10 @@ def upload_from_ftp(self, path: str, history_id: str, **kwargs: Any) -> dict[str
         :type history_id: str
         :param history_id: id of the history where to upload the file
 
-        See :meth:`upload_file` for the optional parameters.
-
         :rtype: dict
         :return: Information about the created upload job
+
+        See :meth:`upload_file` for the optional parameters.
         """
         payload = self._upload_payload(history_id, **kwargs)
         payload["files_0|ftp_files"] = path

bioblend/galaxy/workflows/__init__.py

@@ -422,17 +422,17 @@ def invoke_workflow(
 
         :type preferred_object_store_id: str
         :param preferred_object_store_id: The object store id where you want all
-        outputs of this workflow run be stored.
+          outputs of this workflow run be stored.
 
         :type preferred_intermediate_object_store_id: str
         :param preferred_intermediate_object_store_id: The object store id where
-        you want the intermediate outputs of this workflow run to be stored.
-        Cannot be set if ``preferred_object_store_id`` is set.
+          you want the intermediate outputs of this workflow run to be stored.
+          Cannot be set if ``preferred_object_store_id`` is set.
 
         :type preferred_outputs_object_store_id: str
         :param preferred_outputs_object_store_id: The object store id where
-        you want the priamry outputs of this workflow run to be stored.
-        Cannot be set if ``preferred_object_store_id`` is set.
+          you want the priamry outputs of this workflow run to be stored.
+          Cannot be set if ``preferred_object_store_id`` is set.
 
         :rtype: dict
         :return: A dict containing the workflow invocation describing the