YDA-5496: added touch microservice and support for overwriting data o…

…bjects and collections

Co-authored-by: Lazlo Westerhof <l.r.westerhof@uu.nl>

research.py

@@ -91,12 +91,13 @@ def api_research_folder_add(ctx, coll, new_folder_name):
 
 
 @api.make()
-def api_research_folder_copy(ctx, folder_path, new_folder_path):
+def api_research_folder_copy(ctx, folder_path, new_folder_path, overwrite=False):
     """Copy a folder in a research folder.
 
     :param ctx:             Combined type of a callback and rei struct
     :param folder_path:     Path to the folder to copy
     :param new_folder_path: Path to the new copy of the folder
+    :param overwrite:       Overwrite folder if it already exists
 
     :returns: Dict with API status result
     """
@@ -139,25 +140,26 @@ def api_research_folder_copy(ctx, folder_path, new_folder_path):
         return api.Error('invalid_source', 'The original folder ' + folder_path + ' can not be found')
 
     # Collection exists in destination?
-    if collection.exists(ctx, new_folder_path):
+    if not overwrite and collection.exists(ctx, new_folder_path):
         return api.Error('invalid_destination', 'Folder with this name already exists in destination. Please choose another destination')
 
     # All requirements OK
     try:
-        collection.copy(ctx, folder_path, new_folder_path)
+        collection.copy(ctx, folder_path, new_folder_path, force=overwrite)
     except msi.Error:
         return api.Error('internal', 'Something went wrong. Please try again')
 
     return api.Result.ok()
 
 
 @api.make()
-def api_research_folder_move(ctx, folder_path, new_folder_path):
+def api_research_folder_move(ctx, folder_path, new_folder_path, overwrite=False):
     """Move a folder in a research folder.
 
     :param ctx:             Combined type of a callback and rei struct
     :param folder_path:     Path to the folder to move
     :param new_folder_path: Path to the new folder
+    :param overwrite:       Overwrite folder if it already exists
 
     :returns: Dict with API status result
     """
@@ -200,12 +202,12 @@ def api_research_folder_move(ctx, folder_path, new_folder_path):
         return api.Error('invalid_source', 'The original folder ' + folder_path + ' can not be found')
 
     # Collection exists in destination?
-    if collection.exists(ctx, new_folder_path):
+    if not overwrite and collection.exists(ctx, new_folder_path):
         return api.Error('invalid_destination', 'Folder with this name already exists in destination. Please choose another destination')
 
     # All requirements OK
     try:
-        collection.move(ctx, folder_path, new_folder_path)
+        collection.move(ctx, folder_path, new_folder_path, force=overwrite)
     except msi.Error:
         return api.Error('internal', 'Something went wrong. Please try again')
 
@@ -360,12 +362,13 @@ def api_research_list_temporary_files(ctx, coll):
 
 
 @api.make()
-def api_research_file_copy(ctx, filepath, new_filepath):
+def api_research_file_copy(ctx, filepath, new_filepath, overwrite=False):
     """Copy a file in a research folder.
 
     :param ctx:          Combined type of a callback and rei struct
     :param filepath:     Path to the file to copy
     :param new_filepath: Path to the new copy of the file
+    :param overwrite:    Overwrite file if it already exists
 
     :returns: Dict with API status result
     """
@@ -410,12 +413,12 @@ def api_research_file_copy(ctx, filepath, new_filepath):
         return api.Error('invalid_source', 'The original file ' + data_name + ' can not be found')
 
     # new filename already exists?
-    if data_object.exists(ctx, new_filepath):
+    if not overwrite and data_object.exists(ctx, new_filepath):
         return api.Error('invalid_destination', 'The file ' + data_name + ' already exists')
 
     # All requirements OK
     try:
-        data_object.copy(ctx, filepath, new_filepath)
+        data_object.copy(ctx, filepath, new_filepath, force=overwrite)
     except msi.Error:
         return api.Error('internal', 'Something went wrong. Please try again')
 
@@ -493,12 +496,13 @@ def api_research_file_rename(ctx, new_file_name, coll, org_file_name):
 
 
 @api.make()
-def api_research_file_move(ctx, filepath, new_filepath):
+def api_research_file_move(ctx, filepath, new_filepath, overwrite=False):
     """Move a file in a research folder.
 
     :param ctx:          Combined type of a callback and rei struct
     :param filepath:     Path to the file to move
     :param new_filepath: Path to the new location of the file
+    :param overwrite:    Overwrite file if it already exists
 
     :returns: Dict with API status result
     """
@@ -543,12 +547,16 @@ def api_research_file_move(ctx, filepath, new_filepath):
         return api.Error('invalid_source', 'The original file ' + data_name + ' can not be found')
 
     # new filename already exists?
-    if data_object.exists(ctx, new_filepath):
+    if not overwrite and data_object.exists(ctx, new_filepath):
         return api.Error('invalid_destination', 'The file ' + data_name + ' already exists')
 
     # All requirements OK
     try:
-        data_object.rename(ctx, filepath, new_filepath)
+        if overwrite:
+            data_object.copy(ctx, filepath, new_filepath, force=overwrite)
+            data_object.remove(ctx, filepath)
+        else:
+            data_object.rename(ctx, filepath, new_filepath)
     except msi.Error:
         return api.Error('internal', 'Something went wrong. Please try again')
 

util/collection.py

@@ -5,6 +5,7 @@
 __license__   = 'GPLv3, see LICENSE'
 
 import itertools
+import json
 import sys
 if sys.version_info > (2, 7):
     from functools import reduce
@@ -164,45 +165,55 @@ def create(ctx, path, entire_tree=''):
                     irods_types.BytesBuf())
 
 
-def copy(ctx, path_org, path_copy):
+def copy(ctx, path_org, path_copy, force=True):
     """Copy a collection.
 
     :param ctx:       Combined type of a callback and rei struct
     :param path_org:  Collection original path
     :param path_copy: Collection copy path
+    :param force:     Applies "forceFlag"
 
     This may raise a error.UUError if the collection does not exist, or when
     the user does not have write permission.
     """
-    create(ctx, path_copy)
+    if not force:
+        create(ctx, path_copy)
+
     for row in genquery.row_iterator("DATA_NAME",
                                      "COLL_NAME = '{}'".format(path_org),
                                      genquery.AS_LIST,
                                      ctx):
         data_obj = row[0]
         data_object.copy(ctx,
                          path_org + "/" + data_obj,
-                         path_copy + "/" + data_obj)
+                         path_copy + "/" + data_obj,
+                         force)
 
     for row in genquery.row_iterator("COLL_NAME",
                                      "COLL_PARENT_NAME = '{}'".format(path_org),
                                      genquery.AS_LIST,
                                      ctx):
         coll = row[0]
-        copy(ctx, coll, path_copy + coll[len(path_org):])
+        copy(ctx, coll, path_copy + coll[len(path_org):], force)
+
+    # Update modified date for collection if overwrite
+    if force:
+        json_inp = {"logical_path": path_copy}
+        msi.touch(ctx, json.dumps(json_inp))
 
 
-def move(ctx, path_org, path_move):
+def move(ctx, path_org, path_move, force=True):
     """Move a collection.
 
     :param ctx:       Combined type of a callback and rei struct
     :param path_org:  Collection original path
     :param path_move: Collection move path
+    :param force:     Applies "forceFlag"
 
     This may raise a error.UUError if the collection does not exist, or when
     the user does not have write permission.
     """
-    copy(ctx, path_org, path_move)
+    copy(ctx, path_org, path_move, force)
     msi.rm_coll(ctx,
                 path_org,
                 '',

util/msi.py

@@ -137,6 +137,8 @@ def _make_exception(name, message):
 
 sudo_obj_acl_set, SudoObjAclSetError = make('SudoObjAclSet', 'Could not set ACLs as admin')
 
+touch, TouchError = make('_touch', 'Could not update the data object or collection')
+
 
 def kvpair(ctx, k, v):
     """Create a keyvalpair object, needed by certain msis."""