dxpy 0.395.0__tar.gz → 0.397.0__tar.gz

{dxpy-0.395.0 → dxpy-0.397.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.395.0
+Version: 0.397.0
 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-0.395.0 → dxpy-0.397.0}/dxpy/__init__.py

@@ -524,6 +524,9 @@ def DXHTTPRequest(resource, data, method='POST', headers=None, auth=True,
        through to :func:`DXHTTPRequest`.
 
     '''
+    # option wasn't named correctly, so to not break existing clients rename it locally for clarity
+    safe_to_retry = always_retry
+
     if headers is None:
         headers = {}
 
@@ -729,7 +732,7 @@ def DXHTTPRequest(resource, data, method='POST', headers=None, auth=True,
                 # up to (max_retries) subsequent retries.
                 total_allowed_tries = max_retries + 1
                 ok_to_retry = False
-                is_retryable = always_retry or (method == 'GET') or _is_retryable_exception(e)
+                is_retryable = safe_to_retry or (method == 'GET') or _is_retryable_exception(e)
                 # Because try_index is not incremented until we escape
                 # this iteration of the loop, try_index is equal to the
                 # number of tries that have failed so far, minus one.
@@ -810,7 +813,7 @@ def DXHTTPRequest(resource, data, method='POST', headers=None, auth=True,
                              want_full_response=want_full_response,
                              decode_response_body=decode_response_body, prepend_srv=prepend_srv,
                              session_handler=session_handler,
-                             max_retries=max_retries, always_retry=always_retry, **kwargs)
+                             max_retries=max_retries, always_retry=safe_to_retry, **kwargs)
     raise AssertionError('Should never reach this line: should never break out of loop')
 
 

{dxpy-0.395.0 → dxpy-0.397.0}/dxpy/bindings/dxproject.py

@@ -367,7 +367,7 @@ class DXProject(DXContainer):
                allowed_executables=None, unset_allowed_executables=None,
                database_ui_view_only=None, external_upload_restricted=None,
                database_results_restricted=None, unset_database_results_restricted=None,
-               **kwargs):
+               https_app_isolated_browsing=None, **kwargs):
         """
         :param name: If provided, the new project name
         :type name: string
@@ -395,6 +395,9 @@ class DXProject(DXContainer):
         :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
+        :param https_app_isolated_browsing: Whether all https access to jobs in this project should be wrapped in Isolated Browsing.
+                                            If true, httpsApp-enabled executables must have httpsApp.shared_access set to 'NONE' to run in this project.
+        :type https_app_isolated_browsing: boolean
 
         Updates the project with the new fields. All fields are
         optional. Fields that are not provided are not changed.
@@ -430,6 +433,8 @@ class DXProject(DXContainer):
             update_hash["databaseResultsRestricted"] = database_results_restricted
         if unset_database_results_restricted is not None:
             update_hash["databaseResultsRestricted"] = None
+        if https_app_isolated_browsing is not None:
+            update_hash["httpsAppIsolatedBrowsing"] = https_app_isolated_browsing
         dxpy.api.project_update(self._dxid, update_hash, **kwargs)
 
     def invite(self, invitee, level, send_email=True, **kwargs):

{dxpy-0.395.0 → dxpy-0.397.0}/dxpy/cli/parsers.py

@@ -452,6 +452,8 @@ def get_update_project_args(args):
         input_params['databaseResultsRestricted'] = None
     if args.external_upload_restricted is not None:
         input_params['externalUploadRestricted'] = args.external_upload_restricted == 'true'
+    if args.https_app_isolated_browsing is not None:
+        input_params['httpsAppIsolatedBrowsing'] = args.https_app_isolated_browsing == 'true'
     return input_params
 
 def process_phi_param(args):

dxpy-0.397.0/dxpy/nextflow/app_asset_projects_ids_prod.json

@@ -0,0 +1,9 @@
+{
+    "aws:ap-southeast-2": "project-F4gVXbj5qkxXq3v038V7qjxq",
+    "aws:eu-central-1": "project-F3zqG304yvb1GVkZ6987jP9F",
+    "aws:eu-west-2-g": "project-G4B9FBpKKgK6g9v13q423FXk",
+    "aws:me-south-1": "project-GvGXBYV3pK4v9X7F2jv9zz94",
+    "aws:us-east-1": "project-B6JG897KGbkGb6Z7pQ9Q02jG",
+    "azure:westeurope": "project-FGZZFkjBPJqBXq1X84pq4VJf",
+    "azure:westus": "project-F3vk1q09FX8Jxxp20pq6z8P9"
+}

dxpy-0.397.0/dxpy/nextflow/app_asset_projects_ids_staging.json

@@ -0,0 +1,9 @@
+{
+    "aws:ap-southeast-2": "project-G0zG49j5K4gjfv5V4FfqFK9X",
+    "aws:eu-central-1": "project-G0zG4F04KqpFYVz84FQkvF1P",
+    "aws:eu-west-2-g": "project-G4gyXkXK8BX9B0jp1V6029vJ",
+    "aws:me-south-1": "project-Gv8PVXk32gZ83kfp0pZ1v3V2",
+    "aws:us-east-1": "project-G0zG4B808VFFYVz84FQkvF1K",
+    "azure:westeurope": "project-G0zG4BQBq1XQby2F4FqQpPXv",
+    "azure:westus": "project-G0zG4B09ZJ5gx1Vz4Fb8Q9XX"
+}

dxpy-0.397.0/dxpy/nextflow/nextaur_assets.json

@@ -0,0 +1,9 @@
+{
+    "aws:ap-southeast-2": "record-GzyP89850x72260z2yYyZQfJ",
+    "aws:eu-central-1": "record-GzyP7584vB9Yp0j7qfv5F134",
+    "aws:eu-west-2-g": "record-GzyP80XKPQ6K81G8XV89fyvZ",
+    "aws:me-south-1": "record-GzyP85V306B9xkQ4Pv1yf7Kz",
+    "aws:us-east-1": "record-GzyP6580KGjqV4gp6QXFGBzX",
+    "azure:westeurope": "record-GzyP9z0BzJx8zjf6bpvY6Yqv",
+    "azure:westus": "record-GzyP9vQ9zggPyfkj5GKKYVG5"
+}

dxpy-0.397.0/dxpy/nextflow/nextaur_assets.staging.json

@@ -0,0 +1,9 @@
+{
+    "aws:ap-southeast-2": "record-GzyJ2F0506kK1651KKg3K1Xq",
+    "aws:eu-central-1": "record-GzyJ2Yj4f2xpzzypx8G484FB",
+    "aws:eu-west-2-g": "record-GzyJ28XKKGJ7758Yj62X97bV",
+    "aws:me-south-1": "record-GzyJ2GV311jBJYzx2XpgZXQ0",
+    "aws:us-east-1": "record-GzyJ08002j9B36YfkbQQxpkf",
+    "azure:westeurope": "record-GzyJ4B8B095jZ8F4BF5p2Ggz",
+    "azure:westus": "record-GzyJ3q89X1QBpvfvgx9bZzgP"
+}

dxpy-0.397.0/dxpy/nextflow/nextflow_assets.json

@@ -0,0 +1,9 @@
+{
+    "aws:ap-southeast-2": "record-GzyP8B05q2Y748ZfZXQ4139j",
+    "aws:eu-central-1": "record-GzyP7FQ4p6pX7q2Qbx06zX9v",
+    "aws:eu-west-2-g": "record-GzyP8FXKkjkqfjBjjZzFv68F",
+    "aws:me-south-1": "record-GzyP8593PgfZjYXPJP9FFqV4",
+    "aws:us-east-1": "record-GzyP6X00F3gq8p88gP7PQFkx",
+    "azure:westeurope": "record-GzyPB98BB2b867v2KK1BXx8p",
+    "azure:westus": "record-GzyPB6j9b5Yy81G8XV89jkZX"
+}

dxpy-0.397.0/dxpy/nextflow/nextflow_assets.staging.json

@@ -0,0 +1,9 @@
+{
+    "aws:ap-southeast-2": "record-GzyJ2Y05x444p61z5XKFP54Q",
+    "aws:eu-central-1": "record-GzyJ2xQ4Pffppvfvgx9bZzg6",
+    "aws:eu-west-2-g": "record-GzyJ2Z2KppXG1ZXvQ2kp08YQ",
+    "aws:me-south-1": "record-GzyJ2Y93z3b2Q4202Jpx1j78",
+    "aws:us-east-1": "record-GzyJ19j08Ffppvfvgx9bZzfz",
+    "azure:westeurope": "record-GzyJ4QjByJz29GJg3K3Gv2yB",
+    "azure:westus": "record-GzyJ45Q9xQPB36YfkbQQxpp8"
+}

{dxpy-0.395.0 → dxpy-0.397.0}/dxpy/nextflow/nextflow_utils.py

@@ -5,6 +5,7 @@ import errno
 import dxpy
 import json
 import shutil
+import logging
 from dxpy.exceptions import ResourceNotFound
 from dxpy.nextflow.collect_images import run_nextaur_collect, bundle_docker_images
 
@@ -37,6 +38,22 @@ def get_template_dir():
     return path.join(path.dirname(dxpy.__file__), 'templating', 'templates', 'nextflow')
 
 
+def get_project_with_assets(region):
+    nextflow_basepath = path.join(path.dirname(dxpy.__file__), 'nextflow')
+    projects_path = path.join(nextflow_basepath, "app_asset_projects_ids_prod.json")
+
+    try:
+        with open(projects_path, 'r') as projects_f:
+            project = json.load(projects_f)[region]
+            dxpy.describe(project, fields={})  # existence check
+    except ResourceNotFound:
+        projects_path = path.join(nextflow_basepath, "app_asset_projects_ids_staging.json")
+        with open(projects_path, 'r') as projects_f:
+            project = json.load(projects_f)[region]
+
+    return project
+
+
 def is_importer_job():
     try:
         with open("/home/dnanexus/dnanexus-job.json", "r") as f:
@@ -102,6 +119,8 @@ def get_regional_options(region, resources_dir, profile, cache_docker, nextflow_
         image_bundled = bundle_docker_images(image_refs)
     else:
         image_bundled = {}
+
+    project_with_assets = get_project_with_assets(region)
     regional_options = {
         region: {
             "systemRequirements": {
@@ -110,9 +129,18 @@ def get_regional_options(region, resources_dir, profile, cache_docker, nextflow_
                 }
             },
             "assetDepends": [
-                {"id": nextaur_asset},
-                {"id": nextflow_asset},
-                {"id": awscli_asset}
+                {"id": {"$dnanexus_link": {
+                    "id": nextaur_asset,
+                    "project": project_with_assets
+                }}},
+                {"id": {"$dnanexus_link": {
+                    "id": nextflow_asset,
+                    "project": project_with_assets
+                }}},
+                {"id": {"$dnanexus_link": {
+                    "id": awscli_asset,
+                    "project": project_with_assets
+                }}}
             ],
             "bundledDepends": image_bundled
         }

{dxpy-0.395.0 → dxpy-0.397.0}/dxpy/scripts/dx.py

@@ -5412,6 +5412,10 @@ parser_update_project.add_argument('--external-upload-restricted', choices=["tru
 parser_update_project.add_argument('--database-ui-view-only', choices=["true", "false"],
                                    help="Whether the viewers on the project can access the database data directly")
 parser_update_project.add_argument('--bill-to', help="Update the user or org ID of the billing account", type=str)
+parser_update_project.add_argument('--https-app-isolated-browsing',
+                                   help="Whether all https access to jobs in this project should be wrapped in Isolated Browsing."
+                                        " If true, httpsApp-enabled executables must have httpsApp.shared_access set to 'NONE' to run in this project.",
+                                   choices=["true", "false"])
 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')

dxpy-0.397.0/dxpy/toolkit_version.py

@@ -0,0 +1 @@
+version = '0.397.0'

{dxpy-0.395.0 → dxpy-0.397.0}/dxpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.395.0
+Version: 0.397.0
 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-0.395.0 → dxpy-0.397.0}/dxpy.egg-info/SOURCES.txt

@@ -90,6 +90,8 @@ dxpy/dx_extract_utils/somatic_filter_payload.py
 dxpy/nextflow/ImageRef.py
 dxpy/nextflow/ImageRefFactory.py
 dxpy/nextflow/__init__.py
+dxpy/nextflow/app_asset_projects_ids_prod.json
+dxpy/nextflow/app_asset_projects_ids_staging.json
 dxpy/nextflow/awscli_assets.json
 dxpy/nextflow/awscli_assets.staging.json
 dxpy/nextflow/collect_images.py

{dxpy-0.395.0 → dxpy-0.397.0}/test/test_dxclient.py

@@ -6848,7 +6848,8 @@ class TestDXClientNewUser(DXTestCase):
             "cloudIntegrationManagement": False,
             "appAccess": True,
             "projectAccess": "CONTRIBUTE",
-            "id": user_id
+            "id": user_id,
+            "treManagement": False
         }
         res = dxpy.api.org_find_members(self.org_id, {"id": [user_id]})["results"][0]
         self.assertEqual(res, exp)
@@ -6867,7 +6868,8 @@ class TestDXClientNewUser(DXTestCase):
             "cloudIntegrationManagement": False,
             "appAccess": True,
             "projectAccess": "CONTRIBUTE",
-            "id": user_id
+            "id": user_id,
+            "treManagement": False
         }
         res = dxpy.api.org_find_members(self.org_id, {"id": [user_id]})["results"][0]
         self.assertEqual(res, exp)
@@ -6884,7 +6886,8 @@ class TestDXClientNewUser(DXTestCase):
             "cloudIntegrationManagement": False,
             "appAccess": False,
             "projectAccess": "VIEW",
-            "id": user_id
+            "id": user_id,
+            "treManagement": False
         }
         res = dxpy.api.org_find_members(self.org_id, {"id": [user_id]})["results"][0]
         self.assertEqual(res, exp)
@@ -6902,7 +6905,8 @@ class TestDXClientNewUser(DXTestCase):
             "cloudIntegrationManagement": False,
             "appAccess": True,
             "projectAccess": "ADMINISTER",
-            "id": user_id
+            "id": user_id,
+            "treManagement": False
         }
         res = dxpy.api.org_find_members(self.org_id, {"id": [user_id]})["results"][0]
         self.assertEqual(res, exp)
@@ -7016,7 +7020,8 @@ class TestDXClientMembership(DXTestCase):
                           "allowBillableActivities": True,
                           "cloudIntegrationManagement": False,
                           "appAccess": True,
-                          "projectAccess": "ADMINISTER"}
+                          "projectAccess": "ADMINISTER",
+                          "treManagement": False}
         membership = self._org_find_members(self.user_id)
         self.assertEqual(membership, exp_membership)
 
@@ -7028,7 +7033,8 @@ class TestDXClientMembership(DXTestCase):
                           "allowBillableActivities": False,
                           "cloudIntegrationManagement": False,
                           "appAccess": True,
-                          "projectAccess": "CONTRIBUTE"}
+                          "projectAccess": "CONTRIBUTE",
+                          "treManagement": False}
         membership = self._org_find_members(self.user_id)
         self.assertEqual(membership, exp_membership)
 
@@ -7089,7 +7095,8 @@ class TestDXClientMembership(DXTestCase):
                           "allowBillableActivities": True,
                           "cloudIntegrationManagement": False,
                           "appAccess": True,
-                          "projectAccess": "ADMINISTER"}
+                          "projectAccess": "ADMINISTER",
+                          "treManagement": False}
         membership = self._org_find_members(self.user_id)
         self.assertEqual(membership, exp_membership)
 
@@ -7216,7 +7223,8 @@ class TestDXClientMembership(DXTestCase):
                           "allowBillableActivities": True,
                           "cloudIntegrationManagement": False,
                           "appAccess": True,
-                          "projectAccess": "ADMINISTER"}
+                          "projectAccess": "ADMINISTER",
+                          "treManagement": False}
         membership = self._org_find_members(self.user_id)
         self.assertEqual(membership, exp_membership)
 
@@ -7227,7 +7235,8 @@ class TestDXClientMembership(DXTestCase):
                           "allowBillableActivities": False,
                           "cloudIntegrationManagement": False,
                           "projectAccess": "VIEW",
-                          "appAccess": True}
+                          "appAccess": True,
+                          "treManagement": False}
         membership = self._org_find_members(self.user_id)
         self.assertEqual(membership, exp_membership)
 
@@ -7238,7 +7247,8 @@ class TestDXClientMembership(DXTestCase):
                           "allowBillableActivities": True,
                           "cloudIntegrationManagement": False,
                           "projectAccess": "VIEW",
-                          "appAccess": False}
+                          "appAccess": False,
+                          "treManagement": False}
 
         membership = self._org_find_members(self.user_id)
         self.assertEqual(membership, exp_membership)

dxpy-0.395.0/dxpy/nextflow/nextaur_assets.json

@@ -1,9 +0,0 @@
-{
-    "aws:ap-southeast-2": "record-GzKXzG85y5b99vKK95b4vpKy",
-    "aws:eu-central-1": "record-GzKY0y04V0179X5Bz9K355k3",
-    "aws:eu-west-2-g": "record-GzKY3jBKXjZ413XPP0yv4fgy",
-    "aws:me-south-1": "record-GzKY5G132j8qz8yk710gjKJk",
-    "aws:us-east-1": "record-GzKXx300FZzQ73Q0ykjvQ1GV",
-    "azure:westeurope": "record-GzKY8zjB5PzvxVg2Gy3g77QK",
-    "azure:westus": "record-GzKYJf099Z602KYFxJzvJQj1"
-}

dxpy-0.395.0/dxpy/nextflow/nextaur_assets.staging.json

@@ -1,9 +0,0 @@
-{
-    "aws:ap-southeast-2": "record-GzKXFyj51PXF1f67BYjP54Px",
-    "aws:eu-central-1": "record-GzKXJgj4bPkjfBg634qfx8pF",
-    "aws:eu-west-2-g": "record-GzKXPJ2K5b2xPyZbyx3pZg7Y",
-    "aws:me-south-1": "record-GzKXQv93j7qB0fVgGXVf71Z9",
-    "aws:us-east-1": "record-GzKX8p00kP5q1f67BYjP54PZ",
-    "azure:westeurope": "record-GzKXZGjB6fJ6vb04b7VBV2Kx",
-    "azure:westus": "record-GzKXgVj9YqqxPyZbyx3pZg8G"
-}

dxpy-0.395.0/dxpy/nextflow/nextflow_assets.json

@@ -1,9 +0,0 @@
-{
-    "aws:ap-southeast-2": "record-Gyv7f7858VGjqZ1jjJjyjJpv",
-    "aws:eu-central-1": "record-Gyv7g28474vK3JPK4g5BP1PB",
-    "aws:eu-west-2-g": "record-Gyv810BKZkKyyxkJGzbK2yV4",
-    "aws:me-south-1": "record-Gyv82vk306Q8b9VbyqJpjbpj",
-    "aws:us-east-1": "record-Gyv6XQ00zzv5bfPgGqqPJ6Gq",
-    "azure:westeurope": "record-Gyv86X8B9bQ8160VF0Gfp8QX",
-    "azure:westus": "record-Gyv8B3j94xjy8K0PK914Pvfp"
-}

dxpy-0.395.0/dxpy/nextflow/nextflow_assets.staging.json

@@ -1,9 +0,0 @@
-{
-    "aws:ap-southeast-2": "record-Gyqpv0Q5yv814Pf0P8x5Xq79",
-    "aws:eu-central-1": "record-Gyqpxv842Yx54X2y8zVkQzb5",
-    "aws:eu-west-2-g": "record-Gyqpz9pKP7qXqyjjGP2Vx4Bp",
-    "aws:me-south-1": "record-Gyqq12k3q795K9pb8Pfqvzf2",
-    "aws:us-east-1": "record-GyqkJ5j0z0fqyxpy40ygBGpK",
-    "azure:westeurope": "record-Gyqq478BqQQGgPBPYK78qJ1J",
-    "azure:westus": "record-Gyqq7zQ9JP62qyjjGP2Vx4F3"
-}

dxpy-0.395.0/dxpy/toolkit_version.py

@@ -1 +0,0 @@
-version = '0.395.0'