Merge pull request #484 from cat-bro/bioblend_galaxy_histories_keys

Add view, keys, limit and offset to get_histories

bioblend/_tests/TestGalaxyHistories.py

@@ -85,6 +85,14 @@ def test_get_histories(self):
         )
         assert len(old_histories) == 0
 
+        # Test detailed view: check for presence of "size" field
+        histories_detailed = self.gi.histories.get_histories(view="detailed")
+        assert "size" in histories_detailed[0]
+
+        # Test keys: check that fields requested are returned
+        histories_with_keys = self.gi.histories.get_histories(keys=["id", "user_id", "size"])
+        assert {key for key in histories_with_keys[0]} >= {"id", "user_id", "size"}
+
         # TODO: check whether deleted history is returned correctly
         # At the moment, get_histories() returns only not-deleted histories
         # and get_histories(deleted=True) returns only deleted histories,

bioblend/galaxy/histories/__init__.py

@@ -94,6 +94,10 @@ def _get_histories(
         update_time_min: Optional[str] = None,
         update_time_max: Optional[str] = None,
         all: Optional[bool] = False,
+        view: Optional[Literal["summary", "detailed"]] = None,
+        keys: Optional[List[str]] = None,
+        limit: Optional[int] = None,
+        offset: Optional[int] = None,
     ) -> List[Dict[str, Any]]:
         """
         Hidden method to be used by both get_histories() and get_published_histories()
@@ -124,6 +128,14 @@ def _get_histories(
             params.setdefault("qv", []).append(update_time_max)
         if all:
             params["all"] = True
+        if view:
+            params["view"] = view
+        if keys:
+            params["keys"] = ",".join(keys)
+        if limit:
+            params["limit"] = limit
+        if offset:
+            params["offset"] = offset
 
         url = "/".join((self._make_url(), "published")) if get_all_published else None
         histories = self._get(url=url, params=params)
@@ -144,6 +156,10 @@ def get_histories(
         update_time_min: Optional[str] = None,
         update_time_max: Optional[str] = None,
         all: Optional[bool] = False,
+        view: Optional[Literal["summary", "detailed"]] = None,
+        keys: Optional[List[str]] = None,
+        limit: Optional[int] = None,
+        offset: Optional[int] = None,
     ) -> List[Dict[str, Any]]:
         """
         Get all histories, or select a subset by specifying optional arguments
@@ -187,6 +203,20 @@ def get_histories(
           parameter works only on Galaxy 20.01 or later and can be specified
           only if the user is a Galaxy admin.
 
+        :type view: str
+        :param view: Options are 'summary' or 'detailed'. This defaults to 'summary'.
+          Setting view to 'detailed' results in a larger number of fields returned.
+
+        :type keys: List[str]
+        :param keys: List of fields to return
+
+        :type limit: int
+        :param limit: How many items to return (upper bound).
+
+        :type offset: int
+        :param offset: skip the first ( offset - 1 ) items and begin returning
+          at the Nth item.
+
         :rtype: list
         :return: List of history dicts.
 
@@ -205,6 +235,10 @@ def get_histories(
             get_all_published=False,
             slug=slug,
             all=all,
+            view=view,
+            keys=keys,
+            limit=limit,
+            offset=offset,
             create_time_min=create_time_min,
             create_time_max=create_time_max,
             update_time_min=update_time_min,
@@ -282,6 +316,7 @@ def show_history(
         visible: Optional[bool] = None,
         details: Optional[str] = None,
         types: Optional[List[str]] = None,
+        keys: Optional[List[str]] = None,
     ) -> List[Dict[str, Any]]: ...
 
     # Fallback in case the caller provides a regular bool as contents
@@ -294,6 +329,7 @@ def show_history(
         visible: Optional[bool] = None,
         details: Optional[str] = None,
         types: Optional[List[str]] = None,
+        keys: Optional[List[str]] = None,
     ) -> Union[Dict[str, Any], List[Dict[str, Any]]]:
         pass
 
@@ -305,6 +341,7 @@ def show_history(
         visible: Optional[bool] = None,
         details: Optional[str] = None,
         types: Optional[List[str]] = None,
+        keys: Optional[List[str]] = None,
     ) -> Union[Dict[str, Any], List[Dict[str, Any]]]:
         """
         Get details of a given history. By default, just get the history meta
@@ -340,6 +377,9 @@ def show_history(
           ``['dataset_collection']``,  return only dataset collections. If not
           set, no filtering is applied.
 
+        :type keys: List[str]
+        :param keys: List of fields to return
+
         :rtype: dict or list of dicts
         :return: details of the given history or list of dataset info
 
@@ -359,6 +399,8 @@ def show_history(
                 params["visible"] = visible
             if types is not None:
                 params["types"] = types
+        if keys:
+            params["keys"] = ",".join(keys)
         return self._get(id=history_id, contents=contents, params=params)
 
     def delete_dataset(self, history_id: str, dataset_id: str, purge: bool = False) -> None: