dxpy 0.386.0__tar.gz → 0.388.0__tar.gz

{dxpy-0.386.0 → dxpy-0.388.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.386.0
+Version: 0.388.0
 Summary: DNAnexus Platform API bindings for Python
 Home-page: https://github.com/dnanexus/dx-toolkit
 Author: Aleksandra Zalcman, Andrey Kislyuk, Anurag Biyani, Geet Duggal, Katherine Lai, Kurt Jensen, Marek Hrvol, Ohad Rodeh, Phil Sung

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/asset_builder.py

@@ -35,7 +35,15 @@ ASSET_BUILDER_TRUSTY = "app-create_asset_trusty"
 ASSET_BUILDER_XENIAL = "app-create_asset_xenial"
 ASSET_BUILDER_XENIAL_V1 = "app-create_asset_xenial_v1"
 ASSET_BUILDER_FOCAL = "app-create_asset_focal"
-
+ASSET_BUILDER_NOBLE = "app-create_asset_noble"
+ASSET_BUILDERS = {
+    '12.04': ASSET_BUILDER_PRECISE,
+    '14.04': ASSET_BUILDER_TRUSTY,
+    '16.04': ASSET_BUILDER_XENIAL,
+    '16.04_v1': ASSET_BUILDER_XENIAL_V1,
+    '20.04': ASSET_BUILDER_FOCAL,
+    '24.04': ASSET_BUILDER_NOBLE,
+}
 
 
 class AssetBuilderException(Exception):
@@ -85,8 +93,8 @@ def validate_conf(asset_conf):
         raise AssetBuilderException('The asset configuration does not contain the required field "name".')
 
     # Validate runSpec
-    if 'release' not in asset_conf or asset_conf['release'] not in ["20.04", "16.04", "14.04", "12.04"]:
-        raise AssetBuilderException('The "release" field value should be either "20.04", "16.04", "14.04" (DEPRECATED), or "12.04" (DEPRECATED)')
+    if 'release' not in asset_conf or asset_conf['release'] not in ["24.04", "20.04", "16.04", "14.04", "12.04"]:
+        raise AssetBuilderException('The "release" field value should be either "24.04", "20.04", "16.04" (DEPRECATED), "14.04" (DEPRECATED), or "12.04" (DEPRECATED)')
     if 'runSpecVersion' in asset_conf:
         if asset_conf['runSpecVersion'] not in ["0", "1"]:
             raise AssetBuilderException('The "runSpecVersion" field should be either "0", or "1"')
@@ -228,16 +236,11 @@ def build_asset(args):
             builder_run_options["systemRequirements"] = {"*": {"instanceType": asset_conf["instanceType"]}}
         if dest_folder_name:
             builder_run_options["folder"] = dest_folder_name
-        if asset_conf['release'] == "12.04":
-            app_run_result = dxpy.api.app_run(ASSET_BUILDER_PRECISE, input_params=builder_run_options)
-        elif asset_conf['release'] == "14.04":
-            app_run_result = dxpy.api.app_run(ASSET_BUILDER_TRUSTY, input_params=builder_run_options)
-        elif asset_conf['release'] == "16.04" and asset_conf['runSpecVersion'] == '1':
-            app_run_result = dxpy.api.app_run(ASSET_BUILDER_XENIAL_V1, input_params=builder_run_options)
-        elif asset_conf['release'] == "16.04":
-            app_run_result = dxpy.api.app_run(ASSET_BUILDER_XENIAL, input_params=builder_run_options)
-        elif asset_conf['release'] == "20.04":
-            app_run_result = dxpy.api.app_run(ASSET_BUILDER_FOCAL, input_params=builder_run_options)
+
+        release = asset_conf['release']
+        if asset_conf['runSpecVersion'] == '1':
+            release += '_v1'
+        app_run_result = dxpy.api.app_run(ASSET_BUILDERS[release], input_params=builder_run_options)
 
         job_id = app_run_result["id"]
 

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/cli/cp.py

@@ -151,7 +151,8 @@ def cp(args):
                                     {"objects": src_objects,
                                      "folders": src_folders,
                                      "project": dest_proj,
-                                     "destination": dest_path})['exists']
+                                     "destination": dest_path,
+                                     "targetFileRelocation": args.target_file_relocation})['exists']
         if len(exists) > 0:
             print(fill('The following objects already existed in the destination container ' +
                        'and were left alone:') + '\n ' + '\n '.join(exists))

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/nextflow/awscli_assets.json

@@ -2,6 +2,7 @@
   "aws:ap-southeast-2": "record-Ggjx0YQ5qP61v7Q7Qq4QQ2f7",
   "aws:eu-central-1": "record-Ggjx2Jj4jbKyKxGXYfZgpJYy",
   "aws:eu-west-2-g": "record-Ggjx4qBKYFQ35Gp87ybKV28Z",
+  "aws:me-south-1": "record-GxFKpy135qFZjpBqPyPV0Z4F",
   "aws:us-east-1": "record-GgjvvP00GFJ5JjG1gX3Jbx6j",
   "azure:westeurope": "record-Ggjx8Z8BxzQqXY9Fv4vXBqpj",
   "azure:westus": "record-GgjxGf89ZB67Bz7f3815qk11"

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/nextflow/awscli_assets.staging.json

@@ -2,7 +2,8 @@
   "aws:ap-southeast-2": "record-Ggjp4Fj50y9Vp27Fx8gB65fY",
   "aws:eu-central-1": "record-Ggjp62Q4PFG1K0g562PKZgbV",
   "aws:eu-west-2-g": "record-Ggjp7K2K60b11G4p2X4X8B98",
+  "aws:me-south-1": "record-GxFJy0V3kVvxjKfZF7p3JbGV",
   "aws:us-east-1": "record-Ggjp2p009010jB06F520vZQG",
   "azure:westeurope": "record-GgjpB2QB7Vp4Kz8FV25Q68Jv",
   "azure:westus": "record-GgjpJ509bvJ1p27Fx8gB65jg"
-}
+}

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/nextflow/nextaur_assets.json

@@ -2,6 +2,7 @@
     "aws:ap-southeast-2": "record-GpzQzk852Z6F46605Q45G2fk",
     "aws:eu-central-1": "record-GpzV15j4Gp5b5GpyJ67GX24x",
     "aws:eu-west-2-g": "record-GpzV2xXKqzvbxk4z6884j8jQ",
+    "aws:me-south-1": "record-GxFKf693XYGq0ZbVf1FjpjkP",
     "aws:us-east-1": "record-GpzQxg00Zb6YVFZ1bBJ0QFQY",
     "azure:westeurope": "record-GpzV6kQBGXPfFK2jBq1P5fqK",
     "azure:westus": "record-GpzVFv894pgvz7qyjKY3GJbG"

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/nextflow/nextaur_assets.staging.json

@@ -2,6 +2,7 @@
   "aws:ap-southeast-2": "record-GpyvF1Q5Ky99FPzYYgZKK1VP",
   "aws:eu-central-1": "record-GpyvGVj4gv75gPB1F7jP18kx",
   "aws:eu-west-2-g": "record-GpyvJbBKVkbzYxqfQ409202F",
+  "aws:me-south-1": "record-GxFJbvk3jfbfyPj9VjK660qp",
   "aws:us-east-1": "record-Gpyv8jj023vP2x068G1bZ7Zz",
   "azure:westeurope": "record-GpyvQvQB69bFPJZFgY0J3807",
   "azure:westus": "record-GpyvZ3Q9vf40pyGqgb5G7Kvp"

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/nextflow/nextflow_assets.json

@@ -2,6 +2,7 @@
     "aws:ap-southeast-2": "record-GbqXZx85YkJYkXbJGx2712B0",
     "aws:eu-central-1": "record-GbqXbKQ4f06Fb6yFVJ2jf91z",
     "aws:eu-west-2-g": "record-GbqXffpKbPkPGyqxBKj4bkGP",
+    "aws:me-south-1": "record-GxFKjXV3v1BFj0jJ8Bz53k5Q",
     "aws:us-east-1": "record-GbqX3YQ0zF96QY6XkKgGj6zJ",
     "azure:westeurope": "record-GbqXq50By9ZZF5JpzzvZVX3F",
     "azure:westus": "record-GbqXy9Q91ggZQg52Z4Ffk84q"

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/nextflow/nextflow_assets.staging.json

@@ -2,6 +2,7 @@
     "aws:ap-southeast-2": "record-GbqVfV85P3j22G98Qk3Pbp54",
     "aws:eu-central-1": "record-GbqVj684y262YXY4gkXP12YK",
     "aws:eu-west-2-g": "record-GbqVkkpKqzF471k20pKZkpZJ",
+    "aws:me-south-1": "record-GxFJpgk3gX2Kf655z3KP1x80",
     "aws:us-east-1": "record-GbqVBJ80g9g6vzxj51xYzYj6",
     "azure:westeurope": "record-GbqVv98B1PXF5g7GGYVqfFjx",
     "azure:westus": "record-GbqVz1Q9K7yp85ZVKQVbVgz7"

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/nextflow/nextflow_utils.py

@@ -125,6 +125,7 @@ def get_instance_type(region):
         "aws:ap-southeast-2": "mem2_ssd1_v2_x4",
         "aws:eu-central-1": "mem2_ssd1_v2_x4",
         "aws:us-east-1": "mem2_ssd1_v2_x4",
+        "aws:me-south-1": "mem2_ssd1_v2_x4",
         "azure:westeurope": "azure:mem2_ssd1_x4",
         "azure:westus": "azure:mem2_ssd1_x4",
         "aws:eu-west-2-g": "mem2_ssd1_v2_x4"

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/scripts/dx.py

@@ -1037,7 +1037,8 @@ def mv(args):
                 if src_results[0]['describe']['folder'] != dest_folder:
                     dxpy.api.project_move(src_proj,
                                           {"objects": [result['id'] for result in src_results],
-                                           "destination": dest_folder})
+                                           "destination": dest_folder,
+                                           "targetFileRelocation": args.target_file_relocation})
                 for result in src_results:
                     dxpy.DXHTTPRequest('/' + result['id'] + '/rename',
                                        {"project": src_proj,
@@ -1065,7 +1066,8 @@ def mv(args):
         dxpy.api.project_move(src_proj,
                               {"objects": src_objects,
                                "folders": src_folders,
-                               "destination": dest_path})
+                               "destination": dest_path,
+                               "targetFileRelocation": args.target_file_relocation})
     except:
         err_exit()
 
@@ -2481,7 +2483,7 @@ def find_data(args):
                                          visibility=args.visibility,
                                          properties=args.properties,
                                          name=args.name,
-                                         name_mode='glob',
+                                         name_mode=args.name_mode,
                                          typename=args.type,
                                          tags=args.tag, link=args.link,
                                          project=args.project,
@@ -4803,6 +4805,7 @@ cp_sources_action = parser_cp.add_argument('sources', help='Objects and/or folde
                                            nargs='+')
 cp_sources_action.completer = DXPathCompleter()
 parser_cp.add_argument('destination', help=fill('Folder into which to copy the sources or new pathname (if only one source is provided).  Must be in a different project/container than all source paths.', width_adjustment=-15))
+parser_cp.add_argument('--target-file-relocation', help='Allow symlink target file relocation in external storage while cloning a symlink.', action='store_true', default=False)
 parser_cp.set_defaults(func=cp)
 register_parser(parser_cp, categories='fs')
 
@@ -4818,6 +4821,7 @@ mv_sources_action = parser_mv.add_argument('sources', help='Objects and/or folde
                                            nargs='+')
 mv_sources_action.completer = DXPathCompleter()
 parser_mv.add_argument('destination', help=fill('Folder into which to move the sources or new pathname (if only one source is provided).  Must be in the same project/container as all source paths.', width_adjustment=-15))
+parser_mv.add_argument('--target-file-relocation', help='Allow symlink target file relocation in external storage while moving a symlink.', action='store_true', default=False)
 parser_mv.set_defaults(func=mv)
 register_parser(parser_mv, categories='fs')
 
@@ -6143,7 +6147,8 @@ parser_find_data.add_argument('--class', dest='classname', choices=['record', 'f
 )
 parser_find_data.add_argument('--state', choices=['open', 'closing', 'closed', 'any'], help='State of the object')
 parser_find_data.add_argument('--visibility', choices=['hidden', 'visible', 'either'], default='visible', help='Whether the object is hidden or not')
-parser_find_data.add_argument('--name', help='Name of the object')
+parser_find_data.add_argument('--name', help='Search criteria for the object name, interpreted according to the --name-mode')
+parser_find_data.add_argument('--name-mode', default='glob', help='Name mode to use for searching', choices=['glob', 'exact', 'regexp'])
 parser_find_data.add_argument('--type', help='Type of the data object')
 parser_find_data.add_argument('--link', help='Object ID that the data object links to')
 parser_find_data.add_argument('--all-projects', '--allprojects', help='Extend search to all projects (excluding public projects)', action='store_true')

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/scripts/dx_build_app.py

@@ -516,7 +516,7 @@ def _build_app_remote(mode, src_dir, publish=False, destination_override=None,
 
     app_spec = _parse_app_spec(src_dir)
     builder_versions = {"12.04": "", "14.04": "_trusty", "16.04": "_xenial",
-                        "20.04": "_focal"}
+                        "20.04": "_focal", "24.04": "_noble"}
     release = app_spec['runSpec'].get('release')
     # Remote builder app/applet for 16.04 version 1
     if release == "16.04" and app_spec['runSpec'].get('version', '0') == '1':

dxpy-0.388.0/dxpy/toolkit_version.py

@@ -0,0 +1 @@
+version = '0.388.0'

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy/utils/__init__.py

@@ -292,10 +292,10 @@ class Nonce:
     '''
     def __init__(self):
         try:
-            self.nonce = "%s%f" % (str(binascii.hexlify(os.urandom(32))), time.time())
+            self.nonce = "%s%f" % (binascii.hexlify(os.urandom(32)).decode('utf-8'), time.time())
         except:
             random.seed(time.time())
-            self.nonce = "%s%f" % (str(random.getrandbits(8*26)), time.time())
+            self.nonce = "%s%f" % (random.getrandbits(8*26), time.time())
 
     def __str__(self):
         return self.nonce

{dxpy-0.386.0 → dxpy-0.388.0}/dxpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.386.0
+Version: 0.388.0
 Summary: DNAnexus Platform API bindings for Python
 Home-page: https://github.com/dnanexus/dx-toolkit
 Author: Aleksandra Zalcman, Andrey Kislyuk, Anurag Biyani, Geet Duggal, Katherine Lai, Kurt Jensen, Marek Hrvol, Ohad Rodeh, Phil Sung

{dxpy-0.386.0 → dxpy-0.388.0}/test/test_dxpy.py

@@ -139,7 +139,7 @@ class TestDXProject(unittest.TestCase):
             self.assertEqual(desc["databaseUIViewOnly"], False)
             self.assertEqual(desc["externalUploadRestricted"], False)
             self.assertEqual(desc["tags"], [])
-            self.assertTrue("databaseResultsRestricted" not in desc)
+            self.assertEqual(desc["databaseResultsRestricted"], None)
             prop = dxpy.api.project_describe(dxproject.get_id(),
                                              {'fields': {'properties': True}})
             self.assertEqual(prop['properties'], {})
@@ -212,8 +212,8 @@ class TestDXProject(unittest.TestCase):
         desc = dxproject.describe()
         self.assertEqual(desc["restricted"], False)
         self.assertEqual(desc["downloadRestricted"], False)
-        self.assertTrue("allowedExecutables" not in desc)
-        self.assertTrue("databaseResultsRestricted" not in desc)
+        self.assertEqual(desc["allowedExecutables"], None)
+        self.assertEqual(desc["databaseResultsRestricted"], None)
 
     def test_new_list_remove_folders(self):
         dxproject = dxpy.DXProject()

dxpy-0.386.0/dxpy/toolkit_version.py

@@ -1 +0,0 @@
-version = '0.386.0'