Add get_containers (#59)

* create get_containers method and add to container wrapper
* Update CHANGE.txt
* Bump version to 2.5.0
* Format with black

Author: jryurkanin

CHANGE.txt

@@ -2,11 +2,15 @@
 LabKey Python Client API News
 +++++++++++
 
-What's New in the LabKey 2.4.2 package
+What's New in the LabKey 2.5.0 package
 ==============================
 
-*Release date: TBD*
-- Container API - add ability to rename containers
+*Release date: 07/06/2023*
+- Container API
+    - add rename
+    - add get_containers
+- Add transform_helper to labkey.utils
+    - See docs in docs/transform_helper.md for more information
 
 What's New in the LabKey 2.4.1 package
 ==============================

labkey/__init__.py

@@ -14,6 +14,6 @@
 # limitations under the License.
 #
 __title__ = "labkey"
-__version__ = "2.4.1"
+__version__ = "2.5.0"
 __author__ = "LabKey"
 __license__ = "Apache License 2.0"

labkey/container.py

@@ -70,9 +70,43 @@ def rename(
     return server_context.make_request(url, json=payload)
 
 
+def get_containers(
+    server_context: ServerContext,
+    container_path: str = None,
+    include_effective_permissions: bool = True,
+    include_subfolders: bool = False,
+    depth: int = 50,
+    include_standard_properties: bool = True,
+):
+    """
+    Gets the containers for a given container_path
+    :param server_context: a ServerContext object
+    :param container_path: The container path to query against, defaults to the container path of the ServerContext
+    :param include_effective_permissions: If set to false, the effective permissions for this container resource will
+    not be included (defaults to True)
+    :param include_subfolders: If set to true, the entire branch of containers will be returned. If false, only the
+    immediate children of the starting container will be returned (defaults to False).
+    :param depth: May be used to control the depth of recursion if includeSubfolders is set to true
+    :param include_standard_properties: Includes the standard properties for containers, if f False returns a limited
+    subset of properties: ['path', 'children', 'name', 'id'] (defaults to True)
+    :return:
+    """
+    url = server_context.build_url("project", "getContainers.view", container_path=container_path)
+    payload = {
+        "includeSubfolders": include_subfolders,
+        "includeEffectivePermissions": include_effective_permissions,
+        "includeStandardProperties": include_standard_properties,
+    }
+
+    if include_subfolders:
+        payload["depth"] = depth
+
+    return server_context.make_request(url, json=payload)
+
+
 class ContainerWrapper:
     """
-    Wrapper for all of the API methods exposed in the container module. Used by the APIWrapper class.
+    Wrapper for all the API methods exposed in the container module. Used by the APIWrapper class.
     """
 
     def __init__(self, server_context: ServerContext):
@@ -95,6 +129,27 @@ def delete(self, container_path: str = None):
         return delete(self.server_context, container_path)
 
     def rename(
-        self, name: str = None, title: str = None, add_alias: bool = True, container_path: str = None
+        self,
+        name: str = None,
+        title: str = None,
+        add_alias: bool = True,
+        container_path: str = None,
     ):
         return rename(self.server_context, name, title, add_alias, container_path)
+
+    def get_containers(
+        self,
+        container_path: str = None,
+        include_effective_permissions: bool = True,
+        include_subfolders: bool = True,
+        depth: int = 50,
+        include_standard_properties: bool = True,
+    ):
+        return get_containers(
+            self.server_context,
+            container_path,
+            include_effective_permissions,
+            include_subfolders,
+            depth,
+            include_standard_properties,
+        )

labkey/utils.py

@@ -34,39 +34,40 @@ def json_dumps(*args, **kwargs):
 
 
 def transform_helper(user_transform_func, file_path_run_properties):
-    #file_path_run_properties must be explicitly defined as ${runInfo} within the user's transform script
-    #parse run properties to for results data in and out filepaths
-    file_path_in = ''
-    file_path_out = ''
+    # file_path_run_properties must be explicitly defined as ${runInfo} within the user's transform script
+    # parse run properties to for results data in and out filepaths
+    file_path_in = ""
+    file_path_out = ""
     with open(file_path_run_properties) as file_run_properties:
         for l in file_run_properties:
-            row = l.strip().split('\t')
-            if row[0] == 'runDataFile':
+            row = l.strip().split("\t")
+            if row[0] == "runDataFile":
                 file_path_out = row[3]
-            if row[0] == 'runDataUploadedFile':
+            if row[0] == "runDataUploadedFile":
                 file_path_in = row[1]
-    
-    #parse results data into array, confirming supported file type is used
+
+    # parse results data into array, confirming supported file type is used
     with open(file_path_in) as file_in:
         data_grid = []
 
         for l in file_in:
-            if '\t' in l:
-                row = l.replace('\n', '').split('\t')
-            elif ',' in l:
-                row = l.replace('\n', '').split(',')
+            if "\t" in l:
+                row = l.replace("\n", "").split("\t")
+            elif "," in l:
+                row = l.replace("\n", "").split(",")
             else:
-                raise ValueError('Unsupported file type or delimiter used. Header used: \n' + str(l))
-            data_grid.append(row)    
-    
-    #run user transform on parsed results data array
+                raise ValueError(
+                    "Unsupported file type or delimiter used. Header used: \n" + str(l)
+                )
+            data_grid.append(row)
+
+    # run user transform on parsed results data array
     transformed_grid = user_transform_func(data_grid)
-    
-    #write transformed results data array to LabKey assay results data grid
-    #transformed array must be a python list object, not a numpy array or pandas dataframe
-    with open(file_path_out, mode='w') as file_out:
+
+    # write transformed results data array to LabKey assay results data grid
+    # transformed array must be a python list object, not a numpy array or pandas dataframe
+    with open(file_path_out, mode="w") as file_out:
         for row in transformed_grid:
             row = [str(el).strip() for el in row]
-            row = '\t'.join(row)        
-            file_out.write(row + '\n')
-    
+            row = "\t".join(row)
+            file_out.write(row + "\n")