Merge branch 'master' into DEVEX-2431

CHANGELOG.md

@@ -6,7 +6,27 @@ Categories for each release: Added, Changed, Deprecated, Removed, Fixed, Securit
 
 ## Unreleased
 
-## [385.0] - beta
+## [387.0] - beta
+
+### Added
+
+* `--name-mode` parameter for `dx find data`
+
+### Fixed
+
+* Nonce generation for python 3
+
+## [386.0] - 2024.12.2
+
+### Added
+
+* `--database-results-restricted` `--unset-database-results-restricted` for `dx new project`
+
+### Fixed
+
+* Remove pipes import for Python 3.13 compatibility
+
+## [385.0] - 2024.11.8
 
 ### Added
 

src/R/dxR/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dxR
 Type: Package
 Title: DNAnexus R Client Library
-Version: 0.385.0
+Version: 0.387.0
 Author: Katherine Lai
 Maintainer: Katherine Lai <klai@dnanexus.com>
 Description: dxR is an R extension containing API wrapper functions for

src/R/dxR/R/dxR-package.R

@@ -4,7 +4,7 @@
 ##' the new DNAnexus platform.
 ##' 
 ##' \tabular{ll}{ Package: \tab dxR\cr Type: \tab Package\cr Version: \tab
-##' 0.385.0\cr License: \tab Apache License (== 2.0)\cr
+##' 0.387.0\cr License: \tab Apache License (== 2.0)\cr
 ##' }
 ##' 
 ##' @name dxR-package

src/R/dxR/man/dxR-package.Rd

@@ -9,7 +9,7 @@
 }
 \details{
   \tabular{ll}{ Package: \tab dxR\cr Type: \tab Package\cr
-  Version: \tab 0.385.0\cr License: \tab Apache License (==
+  Version: \tab 0.387.0\cr License: \tab Apache License (==
   2.0)\cr }
 }
 \author{

src/python/dxpy/bindings/dxproject.py

@@ -285,6 +285,7 @@ def new(self, name, summary=None, description=None, region=None, protected=None,
             restricted=None, download_restricted=None, contains_phi=None,
             tags=None, properties=None, bill_to=None, database_ui_view_only=None,
             external_upload_restricted=None, default_symlink=None,
+            database_results_restricted=None,
             **kwargs):
         """
         :param name: The name of the project
@@ -313,6 +314,8 @@ def new(self, name, summary=None, description=None, region=None, protected=None,
         :type database_ui_view_only: boolean
         :param external_upload_restricted: If provided, whether project members can upload data to project from external sources, e.g. outside of job
         :type external_upload_restricted: boolean
+        :param database_results_restricted: If provided, minimum amount of data that project members with VIEW access can see from databases in the project
+        :type database_results_restricted: int
         :param default_symlink: If provided, the details needed to have writable symlinks in the project. Dict must include drive, container, and optional prefix.
         :type default_symlink: dict
 
@@ -346,6 +349,8 @@ def new(self, name, summary=None, description=None, region=None, protected=None,
             input_hash["databaseUIViewOnly"] = database_ui_view_only
         if external_upload_restricted is not None:
             input_hash["externalUploadRestricted"] = external_upload_restricted
+        if database_results_restricted is not None:
+            input_hash["databaseResultsRestricted"] = database_results_restricted
         if tags is not None:
             input_hash["tags"] = tags
         if properties is not None:
@@ -360,7 +365,9 @@ def new(self, name, summary=None, description=None, region=None, protected=None,
     def update(self, name=None, summary=None, description=None, protected=None,
                restricted=None, download_restricted=None, version=None,
                allowed_executables=None, unset_allowed_executables=None,
-               database_ui_view_only=None, external_upload_restricted=None, **kwargs):
+               database_ui_view_only=None, external_upload_restricted=None,
+               database_results_restricted=None, unset_database_results_restricted=None,
+               **kwargs):
         """
         :param name: If provided, the new project name
         :type name: string
@@ -376,10 +383,16 @@ def update(self, name=None, summary=None, description=None, protected=None,
         :type download_restricted: boolean
         :param allowed_executables: If provided, these are the only executable ID(s) allowed to run as root executions in this project
         :type allowed_executables: list
+        :param unset_allowed_executables: If provided, removes any restrictions set by allowed_executables
+        :type unset_allowed_executables: boolean
         :param database_ui_view_only: If provided, whether the viewers on the project can access the database data directly
         :type database_ui_view_only: boolean
         :param external_upload_restricted: If provided, whether project members can upload data to project from external sources, e.g. outside of job
         :type external_upload_restricted: boolean
+        :param database_results_restricted: If provided, minimum amount of data that project members with VIEW access can see from databases in the project
+        :type database_results_restricted: int
+        :param unset_database_results_restricted: If provided, removes any restrictions set by database_results_restricted
+        :type unset_database_results_restricted: boolean
         :param version: If provided, the update will only occur if the value matches the current project's version number
         :type version: int
 
@@ -413,6 +426,10 @@ def update(self, name=None, summary=None, description=None, protected=None,
             update_hash["databaseUIViewOnly"] = database_ui_view_only
         if external_upload_restricted is not None:
             update_hash["externalUploadRestricted"] = external_upload_restricted
+        if database_results_restricted is not None:
+            update_hash["databaseResultsRestricted"] = database_results_restricted
+        if unset_database_results_restricted is not None:
+            update_hash["databaseResultsRestricted"] = None
         dxpy.api.project_update(self._dxid, update_hash, **kwargs)
 
     def invite(self, invitee, level, send_email=True, **kwargs):

src/python/dxpy/cli/parsers.py

@@ -446,6 +446,10 @@ def get_update_project_args(args):
         input_params['allowedExecutables'] = args.allowed_executables
     if args.unset_allowed_executables:
         input_params['allowedExecutables'] = None
+    if args.database_results_restricted is not None:
+        input_params['databaseResultsRestricted'] = args.database_results_restricted
+    if args.unset_database_results_restricted:
+        input_params['databaseResultsRestricted'] = None
     if args.external_upload_restricted is not None:
         input_params['externalUploadRestricted'] = args.external_upload_restricted == 'true'
     return input_params

src/python/dxpy/scripts/dx.py

@@ -1432,6 +1432,8 @@ def new_project(args):
         inputs["containsPHI"] = True
     if args.database_ui_view_only:
         inputs["databaseUIViewOnly"] = True
+    if args.database_results_restricted is not None:
+        inputs["databaseResultsRestricted"] = args.database_results_restricted
     if args.monthly_compute_limit is not None:
         inputs["monthlyComputeLimit"] = args.monthly_compute_limit
     if args.monthly_egress_bytes_limit is not None:
@@ -2479,7 +2481,7 @@ 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,
@@ -5427,6 +5429,9 @@ def positive_number(value):
 allowed_executables_group = parser_update_project.add_mutually_exclusive_group()
 allowed_executables_group.add_argument('--allowed-executables', help='Executable ID(s) this project is allowed to run.  This operation overrides any existing list of executables.', type=str, nargs="+")
 allowed_executables_group.add_argument('--unset-allowed-executables', help='Removes any restriction to run executables as set by --allowed-executables', action='store_true')
+database_results_restricted_group = parser_update_project.add_mutually_exclusive_group()
+database_results_restricted_group.add_argument('--database-results-restricted', help='Viewers on the project can access only more than specified size of visual data from databases', type=positive_integer)
+database_results_restricted_group.add_argument('--unset-database-results-restricted', help='Removes any restriction to return data from databases as set by --database-results-restricted', action='store_true')
 
 parser_update_project.set_defaults(func=update_project)
 register_parser(parser_update_project, subparsers_action=subparsers_update, categories="metadata")
@@ -5813,6 +5818,7 @@ def __call__(self, parser, namespace, values, option_string=None):
                                 action='store_true')
 parser_new_project.add_argument('--database-ui-view-only', help='Viewers on the project cannot access database data directly', default=False,
                                 action='store_true')
+parser_new_project.add_argument('--database-results-restricted', help='Viewers on the project can access only more than specified size of visual data from databases', type=positive_integer)
 parser_new_project.add_argument('--monthly-compute-limit', type=positive_integer, help='Monthly project spending limit for compute')
 parser_new_project.add_argument('--monthly-egress-bytes-limit', type=positive_integer, help='Monthly project spending limit for egress (in Bytes)')
 parser_new_project.add_argument('--monthly-storage-limit', type=positive_number, help='Monthly project spending limit for storage')
@@ -6137,7 +6143,8 @@ def __call__(self, parser, namespace, values, option_string=None):
 )
 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')

src/python/dxpy/toolkit_version.py

@@ -1 +1 @@
-version = '0.385.0'
+version = '0.387.0'

src/python/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

src/python/dxpy/utils/describe.py

@@ -415,7 +415,7 @@ def print_project_desc(desc, verbose=False):
         'containsPHI', 'databaseUIViewOnly', 'externalUploadRestricted', 'region', 'storageCost', 'pendingTransfer',
         'atSpendingLimit', 'currentMonthComputeAvailableBudget', 'currentMonthEgressBytesAvailableBudget',
         'currentMonthStorageAvailableBudget', 'currentMonthComputeUsage', 'currentMonthEgressBytesUsage', 
-        'currentMonthExpectedStorageUsage', 'defaultSymlink'
+        'currentMonthExpectedStorageUsage', 'defaultSymlink', 'databaseResultsRestricted',
         # Following are app container-specific
         'destroyAt', 'project', 'type', 'app', 'appName'
     ]
@@ -455,6 +455,8 @@ def print_project_desc(desc, verbose=False):
         print_json_field('External Upload Restricted', desc['externalUploadRestricted'])
     if 'defaultSymlink' in desc and verbose:
         print_json_field('Default Symlink', desc['defaultSymlink'])
+    if 'databaseResultsRestricted' in desc and desc['databaseResultsRestricted']:
+        print_json_field('Database Results Restricted', desc['databaseResultsRestricted'])
 
     # Usage
     print_field("Created", render_timestamp(desc['created']))

src/python/test/test_dxpy.py

@@ -139,6 +139,7 @@ def test_new(self):
             self.assertEqual(desc["databaseUIViewOnly"], False)
             self.assertEqual(desc["externalUploadRestricted"], False)
             self.assertEqual(desc["tags"], [])
+            self.assertEqual(desc["databaseResultsRestricted"], None)
             prop = dxpy.api.project_describe(dxproject.get_id(),
                                              {'fields': {'properties': True}})
             self.assertEqual(prop['properties'], {})
@@ -192,6 +193,7 @@ def test_update_describe(self):
                          download_restricted=True,
                          external_upload_restricted=False,
                          allowed_executables=["applet-abcdefghijklmnopqrstuzwx"],
+                         database_results_restricted=10,
                          description="new description")
         desc = dxproject.describe()
         self.assertEqual(desc["id"], self.proj_id)
@@ -203,13 +205,15 @@ def test_update_describe(self):
         self.assertEqual(desc["externalUploadRestricted"], False)
         self.assertEqual(desc["description"], "new description")
         self.assertEqual(desc["allowedExecutables"][0], "applet-abcdefghijklmnopqrstuzwx")
+        self.assertEqual(desc["databaseResultsRestricted"], 10)
         self.assertTrue("created" in desc)
 
-        dxproject.update(restricted=False, download_restricted=False, unset_allowed_executables=True)
+        dxproject.update(restricted=False, download_restricted=False, unset_allowed_executables=True, unset_database_results_restricted=True)
         desc = dxproject.describe()
         self.assertEqual(desc["restricted"], False)
         self.assertEqual(desc["downloadRestricted"], False)
-        self.assertTrue("allowedExecutables" not in desc)
+        self.assertEqual(desc["allowedExecutables"], None)
+        self.assertEqual(desc["databaseResultsRestricted"], None)
 
     def test_new_list_remove_folders(self):
         dxproject = dxpy.DXProject()