upload dnanexus example for url making

dnanexus-make-url-example/dxapp.json

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+{
+  "name": "generate_external_download_urls",
+  "title": "Generate External Download URLs",
+  "summary": "Generates External Download URLs",
+  "dxapi": "1.0.0",
+  "version": "0.0.1",
+  "inputSpec": [
+    {
+      "name": "input_files",
+      "label": "Input Files",
+      "class": "array:file",
+      "optional": false
+    },
+    {
+      "name": "token_file",
+      "label": "Token File",
+      "class": "file",
+      "optional": false
+    }
+  ],
+  "outputSpec": [
+    {
+      "name": "download_urls",
+      "label": "Download URLs",
+      "class": "array:string"
+    }
+  ],
+  "runSpec": {
+    "timeoutPolicy": {
+      "*": {
+        "hours": 48
+      }
+    },
+    "interpreter": "python3",
+    "file": "src/generate_external_download_urls.py",
+    "distribution": "Ubuntu",
+    "release": "20.04",
+    "version": "0"
+  },
+    "access": {
+    "network": [
+      "*"
+    ]
+  },
+  "regionalOptions": {
+    "aws:us-east-1": {
+      "systemRequirements": {
+        "*": {
+          "instanceType": "mem1_ssd1_v2_x4"
+        }
+      }
+    }
+  }
+}

dnanexus-make-url-example/src/generate_external_download_urls.py

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+#!/usr/bin/env python
+
+import os
+import dxpy
+
+@dxpy.entry_point('main')
+def main(input_files, token_file):
+
+    # Parse token_hash from token file input
+    token_file = dxpy.DXFile(token_file)
+    dxpy.download_dxfile(token_file.get_id(), "token_file")
+
+    with open('token_file', 'r') as f:
+        token_hash = f.readline().strip()
+    f.close()
+
+    # Create the environment.json file and get pre-set values for parent_project and job ids
+    job_id = os.environ.get('DX_JOB_ID')
+    parent_project = os.environ.get('DX_PROJECT_CONTEXT_ID')
+    dxpy.config.write("DX_PROJECT_CONTEXT_ID", parent_project)
+    dxpy.config.write("DX_CLI_WD", "/")
+    dxpy.config.save()
+
+    # Unset and clear the environment variables and the values in the environment.json file
+    del os.environ['DX_WORKSPACE_ID']
+    del os.environ['DX_APISERVER_HOST']
+    del os.environ['DX_PROJECT_CONTEXT_ID']
+    del os.environ['DX_JOB_ID']
+    del os.environ['DX_APISERVER_PORT']
+    del os.environ['DX_APISERVER_PROTOCOL']
+    del os.environ['DX_SECURITY_CONTEXT']
+    dxpy.config.clear(reset=True)
+
+    # set config variables and save them to environment.json file
+    dxpy.config.write("DX_JOB_ID", job_id)
+    dxpy.config.write("DX_PROJECT_CONTEXT_ID", parent_project)
+    dxpy.config.write("DX_CLI_WD", "/")
+    sec_context = '{"auth_token":"' + token_hash + '","auth_token_type":"Bearer"}'
+    os.environ['DX_SECURITY_CONTEXT'] = sec_context
+    dxpy.set_security_context(json.loads(sec_context))
+    dxpy.config.write("DX_SECURITY_CONTEXT", sec_context)
+    dxpy.config.write("DX_USERNAME", dxpy.whoami())
+    dxpy.config.save()
+
+    # Get URLs for the input files
+    all_urls = []
+
+    for item in input_files:
+
+        dxfile = dxpy.DXFile(item, project=parent_project)
+
+        download_url, headers = dxfile.get_download_url(preauthenticated=True, duration=86400, filename=dxfile.name, project=parent_project)
+
+        all_urls.append(download_url)
+    else:
+        print("All files processed successfully...")
+
+    output = {}
+    output["download_urls"] = all_urls
+
+    return output
+
+dxpy.run()