dxpy 0.381.0__tar.gz → 0.382.0__tar.gz

{dxpy-0.381.0 → dxpy-0.382.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.381.0
+Version: 0.382.0
 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-0.381.0 → dxpy-0.382.0}/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-0.382.0}/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-0.382.0/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-0.382.0/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-0.382.0}/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-0.382.0/dxpy/toolkit_version.py

@@ -0,0 +1 @@
+version = '0.382.0'

{dxpy-0.381.0 → dxpy-0.382.0}/dxpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.381.0
+Version: 0.382.0
 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-0.381.0/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'