dxpy 0.381.0__tar.gz → 0.383.1__tar.gz

{dxpy-0.381.0 → dxpy-0.383.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.381.0
+Version: 0.383.1
 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-0.381.0 → dxpy-0.383.1}/dxpy/bindings/__init__.py

@@ -661,6 +661,8 @@ class DXDataObject(DXObject):
         elapsed = 0
         i = 0
         describe_input = {"fields": {"parts": True, "state": True}}
+        if self._proj is not None:
+            describe_input["project"] = self._proj
         while True:
             describe = self._describe(self._dxid, describe_input, **kwargs)
             state, parts = describe["state"], describe["parts"]

{dxpy-0.381.0 → dxpy-0.383.1}/dxpy/nextflow/collect_images.py

@@ -18,6 +18,7 @@
 #   under the License.
 
 import json
+import os.path
 import subprocess
 from dxpy.nextflow.ImageRefFactory import ImageRefFactory, ImageRefFactoryError
 
@@ -66,7 +67,9 @@ def run_nextaur_collect(resources_dir, profile, nextflow_pipeline_params):
     pipeline_params_arg = "pipelineParams={}".format(nextflow_pipeline_params) if nextflow_pipeline_params else ""
     profile_arg = "profile={}".format(profile) if profile else ""
     nextaur_cmd = " ".join([base_cmd, pipeline_params_arg, profile_arg])
-    _ = subprocess.check_output(nextaur_cmd, shell=True)
+    process = subprocess.run(nextaur_cmd, shell=True, capture_output=True, text=True)
+    if not os.path.exists(CONTAINERS_JSON):
+        raise ImageRefFactoryError(process.stdout)
     with open(CONTAINERS_JSON, "r") as json_file:
         image_refs = json.load(json_file).get("processes", None)
         if not image_refs:

dxpy-0.383.1/dxpy/nextflow/nextaur_assets.json

@@ -0,0 +1,8 @@
+{
+    "aws:ap-southeast-2": "record-GpzQzk852Z6F46605Q45G2fk",
+    "aws:eu-central-1": "record-GpzV15j4Gp5b5GpyJ67GX24x",
+    "aws:eu-west-2-g": "record-GpzV2xXKqzvbxk4z6884j8jQ",
+    "aws:us-east-1": "record-GpzQxg00Zb6YVFZ1bBJ0QFQY",
+    "azure:westeurope": "record-GpzV6kQBGXPfFK2jBq1P5fqK",
+    "azure:westus": "record-GpzVFv894pgvz7qyjKY3GJbG"
+}

dxpy-0.383.1/dxpy/nextflow/nextaur_assets.staging.json

@@ -0,0 +1,8 @@
+{
+  "aws:ap-southeast-2": "record-GpyvF1Q5Ky99FPzYYgZKK1VP",
+  "aws:eu-central-1": "record-GpyvGVj4gv75gPB1F7jP18kx",
+  "aws:eu-west-2-g": "record-GpyvJbBKVkbzYxqfQ409202F",
+  "aws:us-east-1": "record-Gpyv8jj023vP2x068G1bZ7Zz",
+  "azure:westeurope": "record-GpyvQvQB69bFPJZFgY0J3807",
+  "azure:westus": "record-GpyvZ3Q9vf40pyGqgb5G7Kvp"
+}

{dxpy-0.381.0 → dxpy-0.383.1}/dxpy/scripts/dx.py

@@ -1185,12 +1185,11 @@ def describe(args):
         # Always retrieve details too (just maybe don't render them)
         json_input["details"] = True
         if is_data_obj_id(args.path):
-            # Should prefer the current project's version if possible
+            # Prefer the current project's version if possible
             if dxpy.WORKSPACE_ID is not None:
                 try:
-                    # But only put it in the JSON if you still have
-                    # access.
-                    dxpy.api.project_list_folder(dxpy.WORKSPACE_ID)
+                    # But only put it in the JSON if you still have access
+                    dxpy.api.project_describe(dxpy.WORKSPACE_ID, input_params={"fields": {"id": True}})
                     json_input['project'] = dxpy.WORKSPACE_ID
                 except dxpy.DXAPIError as e:
                     if not isinstance(e, ResourceNotFound):

{dxpy-0.381.0 → dxpy-0.383.1}/dxpy/templating/templates/nextflow/src/nextflow.sh

@@ -45,10 +45,6 @@ main() {
   validate_run_opts
 
   # set default NXF env constants
-
-  # Disable use of newer flag --cpus when running Docker
-  # Can be enabled when Docker version on DNAnexus workers supports it
-  export NXF_DOCKER_LEGACY=true
   export NXF_HOME=/opt/nextflow
   export NXF_ANSI_LOG=false
   export NXF_PLUGINS_DEFAULT=nextaur@$NXF_PLUGINS_VERSION

dxpy-0.383.1/dxpy/toolkit_version.py

@@ -0,0 +1 @@
+version = '0.383.1'

{dxpy-0.381.0 → dxpy-0.383.1}/dxpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.381.0
+Version: 0.383.1
 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-0.381.0 → dxpy-0.383.1}/test/test_dxclient.py

@@ -6799,6 +6799,7 @@ class TestDXClientNewUser(DXTestCase):
         exp = {
             "level": "MEMBER",
             "allowBillableActivities": False,
+            "cloudIntegrationManagement": False,
             "appAccess": True,
             "projectAccess": "CONTRIBUTE",
             "id": user_id
@@ -6817,6 +6818,7 @@ class TestDXClientNewUser(DXTestCase):
         exp = {
             "level": "MEMBER",
             "allowBillableActivities": False,
+            "cloudIntegrationManagement": False,
             "appAccess": True,
             "projectAccess": "CONTRIBUTE",
             "id": user_id
@@ -6833,6 +6835,7 @@ class TestDXClientNewUser(DXTestCase):
         exp = {
             "level": "MEMBER",
             "allowBillableActivities": True,
+            "cloudIntegrationManagement": False,
             "appAccess": False,
             "projectAccess": "VIEW",
             "id": user_id
@@ -6850,6 +6853,7 @@ class TestDXClientNewUser(DXTestCase):
         exp = {
             "level": "ADMIN",
             "allowBillableActivities": True,
+            "cloudIntegrationManagement": False,
             "appAccess": True,
             "projectAccess": "ADMINISTER",
             "id": user_id
@@ -6871,6 +6875,7 @@ class TestDXClientNewUser(DXTestCase):
         exp = {
             "level": "MEMBER",
             "allowBillableActivities": True,
+            "cloudIntegrationManagement": False,
             "appAccess": True,
             "projectAccess": "VIEW",
             "id": user_id
@@ -6887,6 +6892,7 @@ class TestDXClientNewUser(DXTestCase):
         exp = {
             "level": "ADMIN",
             "allowBillableActivities": True,
+            "cloudIntegrationManagement": False,
             "appAccess": True,
             "projectAccess": "ADMINISTER",
             "id": user_id
@@ -6962,6 +6968,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "ADMIN",
                           "allowBillableActivities": True,
+                          "cloudIntegrationManagement": False,
                           "appAccess": True,
                           "projectAccess": "ADMINISTER"}
         membership = self._org_find_members(self.user_id)
@@ -6973,6 +6980,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "MEMBER",
                           "allowBillableActivities": False,
+                          "cloudIntegrationManagement": False,
                           "appAccess": True,
                           "projectAccess": "CONTRIBUTE"}
         membership = self._org_find_members(self.user_id)
@@ -6986,6 +6994,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "ADMIN",
                           "allowBillableActivities": True,
+                          "cloudIntegrationManagement": False,
                           "appAccess": True,
                           "projectAccess": "ADMINISTER"}
         membership = self._org_find_members(self.user_id)
@@ -6998,6 +7007,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "MEMBER",
                           "allowBillableActivities": True,
+                          "cloudIntegrationManagement": False,
                           "appAccess": False,
                           "projectAccess": "NONE"}
         membership = self._org_find_members(self.user_id)
@@ -7031,6 +7041,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "ADMIN",
                           "allowBillableActivities": True,
+                          "cloudIntegrationManagement": False,
                           "appAccess": True,
                           "projectAccess": "ADMINISTER"}
         membership = self._org_find_members(self.user_id)
@@ -7046,6 +7057,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "ADMIN",
                           "allowBillableActivities": True,
+                          "cloudIntegrationManagement": False,
                           "appAccess": True,
                           "projectAccess": "ADMINISTER"}
         membership = self._org_find_members(self.user_id)
@@ -7093,6 +7105,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "ADMIN",
                           "allowBillableActivities": True,
+                          "cloudIntegrationManagement": False,
                           "appAccess": True,
                           "projectAccess": "ADMINISTER"}
         membership = self._org_find_members(self.user_id)
@@ -7155,6 +7168,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "ADMIN",
                           "allowBillableActivities": True,
+                          "cloudIntegrationManagement": False,
                           "appAccess": True,
                           "projectAccess": "ADMINISTER"}
         membership = self._org_find_members(self.user_id)
@@ -7165,6 +7179,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "MEMBER",
                           "allowBillableActivities": False,
+                          "cloudIntegrationManagement": False,
                           "projectAccess": "VIEW",
                           "appAccess": True}
         membership = self._org_find_members(self.user_id)
@@ -7175,6 +7190,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "MEMBER",
                           "allowBillableActivities": True,
+                          "cloudIntegrationManagement": False,
                           "projectAccess": "VIEW",
                           "appAccess": False}
 
@@ -7189,6 +7205,7 @@ class TestDXClientMembership(DXTestCase):
         exp = {"id": self.user_id,
                "level": "ADMIN",
                "allowBillableActivities": True,
+               "cloudIntegrationManagement": False,
                "projectAccess": "ADMINISTER",
                "appAccess": True}
         membership_response = self._org_find_members(self.user_id)
@@ -7199,6 +7216,7 @@ class TestDXClientMembership(DXTestCase):
                "level": "MEMBER",
                "allowBillableActivities": False,
                "projectAccess": "CONTRIBUTE",
+               "cloudIntegrationManagement": False,
                "appAccess": True}
         membership_response = self._org_find_members(self.user_id)
         self.assertEqual(membership_response, exp)
@@ -7208,6 +7226,7 @@ class TestDXClientMembership(DXTestCase):
         exp = {"id": self.user_id,
                "level": "MEMBER",
                "allowBillableActivities": True,
+               "cloudIntegrationManagement": False,
                "projectAccess": "CONTRIBUTE",
                "appAccess": True}
         membership_response = self._org_find_members(self.user_id)
@@ -7257,6 +7276,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "MEMBER",
                           "allowBillableActivities": False,
+                          "cloudIntegrationManagement": False,
                           "appAccess": True,
                           "projectAccess": "UPLOAD"}
         membership = self._org_find_members(self.user_id)
@@ -7273,6 +7293,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "ADMIN",
                           "allowBillableActivities": True,
+                          "cloudIntegrationManagement": False,
                           "appAccess": True,
                           "projectAccess": "ADMINISTER"}
         membership = self._org_find_members(self.user_id)
@@ -7299,6 +7320,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "MEMBER",
                           "allowBillableActivities": False,
+                          "cloudIntegrationManagement": False,
                           "appAccess": True,
                           "projectAccess": "UPLOAD"}
         membership = self._org_find_members(self.user_id)
@@ -7315,6 +7337,7 @@ class TestDXClientMembership(DXTestCase):
         exp_membership = {"id": self.user_id,
                           "level": "ADMIN",
                           "allowBillableActivities": True,
+                          "cloudIntegrationManagement": False,
                           "appAccess": True,
                           "projectAccess": "ADMINISTER"}
         membership = self._org_find_members(self.user_id)

dxpy-0.381.0/dxpy/nextflow/nextaur_assets.json

@@ -1,8 +0,0 @@
-{
-    "aws:ap-southeast-2": "record-GkBJ6405j8p425gQBZ7k8bQ2",
-    "aws:eu-central-1": "record-GkBJ7xj4Kx3fkX2ZYXZff26K",
-    "aws:eu-west-2-g": "record-GkBJB42K37yxbZz9xg2XFzq9",
-    "aws:us-east-1": "record-GkBJ3380P8VyqFk5Zy7B6j6Z",
-    "azure:westeurope": "record-GkBJJFQBPGZFPxgpG6X19y2V",
-    "azure:westus": "record-GkBJV489GKBFK2fvJBp30QbP"
-}

dxpy-0.381.0/dxpy/nextflow/nextaur_assets.staging.json

@@ -1,8 +0,0 @@
-{
-    "aws:ap-southeast-2": "record-GkBJ06Q5KKF2j13Z10P326PZ",
-    "aws:eu-central-1": "record-GkBJ1jj4KXKxZ6KZkbqBv4k1",
-    "aws:eu-west-2-g": "record-GkBJ33XK7pkkY6JZ29zFZ9pV",
-    "aws:us-east-1": "record-GkB8gQj0J43977ZQ6z8gP7kq",
-    "azure:westeurope": "record-GkBJ688BkjvGx6q414zKjzzx",
-    "azure:westus": "record-GkBJ9X09pP8J8ZjzVGbPQBK0"
-}

dxpy-0.381.0/dxpy/toolkit_version.py

@@ -1 +0,0 @@
-version = '0.381.0'