dxpy 0.371.0__tar.gz → 0.373.0__tar.gz

{dxpy-0.371.0 → dxpy-0.373.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.371.0
+Version: 0.373.0
 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-0.371.0 → dxpy-0.373.0}/dxpy/api.py

@@ -961,6 +961,14 @@ def job_update(object_id, input_params={}, always_retry=True, **kwargs):
     """
     return DXHTTPRequest('/%s/update' % object_id, input_params, always_retry=always_retry, **kwargs)
 
+def job_get_identity_token(object_id, input_params={}, always_retry=True, **kwargs):
+    """
+    Invokes the /job-xxxx/getIdentityToken API method.
+
+    For more info, see: https://documentation.dnanexus.com/developer/api/running-analyses/applets-and-entry-points#api-method-job-xxxx-getIdentityToken
+    """
+    return DXHTTPRequest('/%s/getIdentityToken' % object_id, input_params, always_retry=always_retry, **kwargs)
+
 def job_new(input_params={}, always_retry=True, **kwargs):
     """
     Invokes the /job/new API method.

{dxpy-0.371.0 → dxpy-0.373.0}/dxpy/bindings/dxproject.py

@@ -284,7 +284,7 @@ class DXProject(DXContainer):
     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,
+            external_upload_restricted=None, default_symlink=None,
             **kwargs):
         """
         :param name: The name of the project
@@ -313,6 +313,8 @@ class DXProject(DXContainer):
         :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 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
 
         Creates a new project. Initially only the user performing this action
         will be in the permissions/member list, with ADMINISTER access.
@@ -321,6 +323,7 @@ class DXProject(DXContainer):
         method for more info.
 
         """
+
         input_hash = {}
         input_hash["name"] = name
         if summary is not None:
@@ -347,6 +350,8 @@ class DXProject(DXContainer):
             input_hash["tags"] = tags
         if properties is not None:
             input_hash["properties"] = properties
+        if default_symlink is not None:
+            input_hash["defaultSymlink"] = default_symlink
 
         self.set_id(dxpy.api.project_new(input_hash, **kwargs)["id"])
         self._desc = {}

dxpy-0.373.0/dxpy/nextflow/awscli_assets.json

@@ -0,0 +1,8 @@
+{
+  "aws:ap-southeast-2": "record-Ggjx0YQ5qP61v7Q7Qq4QQ2f7",
+  "aws:eu-central-1": "record-Ggjx2Jj4jbKyKxGXYfZgpJYy",
+  "aws:eu-west-2-g": "record-Ggjx4qBKYFQ35Gp87ybKV28Z",
+  "aws:us-east-1": "record-GgjvvP00GFJ5JjG1gX3Jbx6j",
+  "azure:westeurope": "record-Ggjx8Z8BxzQqXY9Fv4vXBqpj",
+  "azure:westus": "record-GgjxGf89ZB67Bz7f3815qk11"
+}

dxpy-0.373.0/dxpy/nextflow/awscli_assets.staging.json

@@ -0,0 +1,8 @@
+{
+  "aws:ap-southeast-2": "record-Ggjp4Fj50y9Vp27Fx8gB65fY",
+  "aws:eu-central-1": "record-Ggjp62Q4PFG1K0g562PKZgbV",
+  "aws:eu-west-2-g": "record-Ggjp7K2K60b11G4p2X4X8B98",
+  "aws:us-east-1": "record-Ggjp2p009010jB06F520vZQG",
+  "azure:westeurope": "record-GgjpB2QB7Vp4Kz8FV25Q68Jv",
+  "azure:westus": "record-GgjpJ509bvJ1p27Fx8gB65jg"
+}

dxpy-0.373.0/dxpy/nextflow/nextaur_assets.json

@@ -0,0 +1,8 @@
+{
+    "aws:ap-southeast-2": "record-GgZBbZ85p6jyZ1vyP78Yz8jq",
+    "aws:eu-central-1": "record-GgZBg8Q47BzfBB4FZVkYB3ZB",
+    "aws:eu-west-2-g": "record-GgZBjbXK55x4PBF5v265b2zZ",
+    "aws:us-east-1": "record-GgZBZ180yJVJQ0X3v70fGk5z",
+    "azure:westeurope": "record-GgZBq60BqQpZqzqP5K2g7zk0",
+    "azure:westus": "record-GgZByJ89K0f13FGj9Z5K7Q0q"
+}

dxpy-0.373.0/dxpy/nextflow/nextaur_assets.staging.json

@@ -0,0 +1,8 @@
+{
+    "aws:ap-southeast-2": "record-GgZB78850V715qfyb7QJ2j4k",
+    "aws:eu-central-1": "record-GgZB8jQ4q2vQkZ81YJyPB6P6",
+    "aws:eu-west-2-g": "record-GgZB9zBK8G200PKfy6ZPbkXP",
+    "aws:us-east-1": "record-GgZB0jQ0zJ8fPbKvfvqPk7J0",
+    "azure:westeurope": "record-GgZBJ40BYgvQkZ81YJyPB6PP",
+    "azure:westus": "record-GgZBVPQ92xJ9JFjFZgfyx7kV"
+}

{dxpy-0.371.0 → dxpy-0.373.0}/dxpy/nextflow/nextflow_utils.py

@@ -95,7 +95,7 @@ def write_dxapp(folder, content):
 
 
 def get_regional_options(region, resources_dir, profile, cache_docker, nextflow_pipeline_params):
-    nextaur_asset, nextflow_asset = get_nextflow_assets(region)
+    nextaur_asset, nextflow_asset, awscli_asset = get_nextflow_assets(region)
     regional_instance_type = get_instance_type(region)
     if cache_docker:
         image_refs = run_nextaur_collect(resources_dir, profile, nextflow_pipeline_params)
@@ -111,7 +111,8 @@ def get_regional_options(region, resources_dir, profile, cache_docker, nextflow_
             },
             "assetDepends": [
                 {"id": nextaur_asset},
-                {"id": nextflow_asset}
+                {"id": nextflow_asset},
+                {"id": awscli_asset}
             ],
             "bundledDepends": image_bundled
         }
@@ -138,15 +139,18 @@ def get_nextflow_assets(region):
     # The order of assets in the tuple is: nextaur, nextflow
     nextaur_assets = path.join(nextflow_basepath, "nextaur_assets.json")
     nextflow_assets = path.join(nextflow_basepath, "nextflow_assets.json")
+    awscli_assets = path.join(nextflow_basepath, "awscli_assets.json")
     try:
-        with open(nextaur_assets, 'r') as nextaur_f, open(nextflow_assets, 'r') as nextflow_f:
+        with open(nextaur_assets, 'r') as nextaur_f, open(nextflow_assets, 'r') as nextflow_f, open(awscli_assets, 'r') as awscli_f:
             nextaur = json.load(nextaur_f)[region]
             nextflow = json.load(nextflow_f)[region]
-        dxpy.describe(nextaur, fields={})
-        return nextaur, nextflow
+            awscli = json.load(awscli_f)[region]
+        dxpy.describe(nextaur, fields={})  # existence check
+        return nextaur, nextflow, awscli
     except ResourceNotFound:
         nextaur_assets = path.join(nextflow_basepath, "nextaur_assets.staging.json")
         nextflow_assets = path.join(nextflow_basepath, "nextflow_assets.staging.json")
+        awscli_assets = path.join(nextflow_basepath, "awscli_assets.staging.json")
 
-        with open(nextaur_assets, 'r') as nextaur_f, open(nextflow_assets, 'r') as nextflow_f:
-            return json.load(nextaur_f)[region], json.load(nextflow_f)[region]
+        with open(nextaur_assets, 'r') as nextaur_f, open(nextflow_assets, 'r') as nextflow_f, open(awscli_assets, 'r') as awscli_f:
+            return json.load(nextaur_f)[region], json.load(nextflow_f)[region], json.load(awscli_f)[region]

{dxpy-0.371.0 → dxpy-0.373.0}/dxpy/scripts/dx.py

@@ -1437,7 +1437,8 @@ def new_project(args):
         inputs["monthlyComputeLimit"] = args.monthly_compute_limit
     if args.monthly_egress_bytes_limit is not None:
         inputs["monthlyEgressBytesLimit"] = args.monthly_egress_bytes_limit
-
+    if args.default_symlink is not None:
+        inputs["defaultSymlink"] = json.loads(args.default_symlink)
     try:
         resp = dxpy.api.project_new(inputs)
         if args.brief:
@@ -5797,6 +5798,7 @@ parser_new_project.add_argument('--database-ui-view-only', help='Viewers on the
                                 action='store_true')
 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('--default-symlink', help='Default symlink for external store account')
 parser_new_project.set_defaults(func=new_project)
 register_parser(parser_new_project, subparsers_action=subparsers_new, categories='fs')
 

{dxpy-0.371.0 → dxpy-0.373.0}/dxpy/templating/templates/nextflow/dxapp.json

@@ -103,8 +103,7 @@
   "categories": [],
   "access": {
     "network": ["*"],
-    "project": "UPLOAD",
-    "allProjects": "VIEW"
+    "project": "UPLOAD"
   },
   "ignoreReuse": true
 }

dxpy-0.373.0/dxpy/toolkit_version.py

@@ -0,0 +1 @@
+version = '0.373.0'

{dxpy-0.371.0 → dxpy-0.373.0}/dxpy/utils/describe.py

@@ -414,7 +414,7 @@ def print_project_desc(desc, verbose=False):
         'appCaches', 'billTo', 'version', 'createdBy', 'totalSponsoredEgressBytes', 'consumedSponsoredEgressBytes',
         'containsPHI', 'databaseUIViewOnly', 'externalUploadRestricted', 'region', 'storageCost', 'pendingTransfer',
         'atSpendingLimit', 'currentMonthComputeAvailableBudget', 'currentMonthEgressBytesAvailableBudget',
-        'currentMonthComputeUsage', 'currentMonthEgressBytesUsage',
+        'currentMonthComputeUsage', 'currentMonthEgressBytesUsage', 'defaultSymlink'
         # Following are app container-specific
         'destroyAt', 'project', 'type', 'app', 'appName'
     ]
@@ -452,6 +452,8 @@ def print_project_desc(desc, verbose=False):
         print_json_field('Database UI View Only', desc['databaseUIViewOnly'])
     if 'externalUploadRestricted' in desc and desc['externalUploadRestricted']:
         print_json_field('External Upload Restricted', desc['externalUploadRestricted'])
+    if 'defaultSymlink' in desc and verbose:
+        print_json_field('Default Symlink', desc['defaultSymlink'])
 
     # Usage
     print_field("Created", render_timestamp(desc['created']))

{dxpy-0.371.0 → dxpy-0.373.0}/dxpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.371.0
+Version: 0.373.0
 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-0.371.0 → dxpy-0.373.0}/dxpy.egg-info/SOURCES.txt

@@ -88,6 +88,8 @@ dxpy/dx_extract_utils/somatic_filter_payload.py
 dxpy/nextflow/ImageRef.py
 dxpy/nextflow/ImageRefFactory.py
 dxpy/nextflow/__init__.py
+dxpy/nextflow/awscli_assets.json
+dxpy/nextflow/awscli_assets.staging.json
 dxpy/nextflow/collect_images.py
 dxpy/nextflow/nextaur_assets.json
 dxpy/nextflow/nextaur_assets.staging.json
@@ -149,6 +151,7 @@ scripts/dx-fetch-bundled-depends
 scripts/dx-generate-dxapp
 scripts/dx-jobutil-add-output
 scripts/dx-jobutil-dxlink
+scripts/dx-jobutil-get-identity-token
 scripts/dx-jobutil-new-job
 scripts/dx-jobutil-parse-link
 scripts/dx-jobutil-report-error

dxpy-0.373.0/scripts/dx-jobutil-get-identity-token

@@ -0,0 +1,69 @@
+#!/usr/bin/env python3
+#
+# Copyright (C) 2013-2024 DNAnexus, Inc.
+#
+# This file is part of dx-toolkit (DNAnexus platform client libraries).
+#
+#   Licensed under the Apache License, Version 2.0 (the "License"); you may not
+#   use this file except in compliance with the License. You may obtain a copy
+#   of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
+#   WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
+#   License for the specific language governing permissions and limitations
+#   under the License.
+
+import dxpy
+import os, argparse, sys
+
+
+def _parse_args():
+    """
+    Parse the input arguments.
+    """
+    parser = argparse.ArgumentParser(
+        description="calls job-xxxx/getIdentityToken and retrieves a JWT token based on aud and subject claims input"
+    )
+    parser.add_argument(
+        "--aud", help="Audience URI the JWT is intended for", required=True
+    )
+    parser.add_argument(
+        "--subject_claims",
+        action="append",
+        metavar="<subject_claims>",
+        help="Defines the subject claims to be validated by the cloud provider",
+    )
+
+    return parser.parse_args()
+
+
+def main(aud, subject_claims):
+    job_get_identity_token_input = {}
+
+    # Parse out audience and subject_claims from args
+    job_get_identity_token_input["audience"] = aud
+
+    if subject_claims is not None:
+        # Iterate over subject_claims and flatten them into a single list
+        subject_claims_input = []
+        for subject_claim in subject_claims:
+            subject_claims_input.extend(subject_claim.split(","))
+        job_get_identity_token_input["subject_claims"] = subject_claims_input
+
+    # Call job-xxxx/getIdentityToken
+    if "DX_JOB_ID" in os.environ:
+        response = dxpy.api.job_get_identity_token(
+            dxpy.JOB_ID, job_get_identity_token_input
+        )
+        sys.stdout.write(response["Token"])
+    else:
+        print("This script should be run from within a job environment.")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    args = _parse_args()
+    main(args.aud, args.subject_claims)