{"action":"created","comment":{"url":"https://api.github.com/repos/AstraZeneca-NGS/DNAnexus/pulls/comments/130449772","pull_request_review_id":53327244,"id":130449772,"diff_hunk":"@@ -110,29 +146,29 @@ def main(**job_inputs):\n     print(\"bcbio yaml: \" + bcbio_yaml)\n     with open(bcbio_yaml) as f:\n         conf_d = load_yaml(f)\n-    assert \"upload\" in conf_d, \"upload not in bcbio_yaml \" + bcbio_yaml\n+    assert \"upload\" in conf_d, \"upload not in bcbio_yaml: \" + bcbio_yaml\n     final_dir = conf_d[\"upload\"][\"dir\"]\n-    if not final_dir.startswith('/'): \n+    if not final_dir.startswith('/'):\n         print(\"final_dir \" + final_dir + ' is not absolute')\n         final_dir = '/dream_chr21/final'  # test data\n     sample_section = conf_d[\"details\"][0][\"algorithm\"]\n-    bed_files = [v for k, v in sample_section.items() if k in ['variant_regions', 'sv_regions', 'coverage']]\n+    bed_files = [v for k, v in sample_section.iteritems() if k in ['variant_regions', 'sv_regions', 'coverage']]\n     for bed_file in bed_files:\n-        print(\"Uploading BED file \" + bed_file)        \n-        if not bed_file.startswith('/'): \n+        print(\"Uploading BED file \" + bed_file)\n+        if not bed_file.startswith('/'):\n             bed_file = os.path.abspath(os.path.join(final_dir, bed_file))\n             print(\"  path of the BED file is not absolute, changing to \" + bed_file)\n-        copy_folder_to_proj(\n-            src_proj=os.environ['DX_PROJECT_CONTEXT_ID'], \n-            src_proj_fld=os.path.dirname(bed_file), \n-            target_fld_prefix='',\n+        copy_platform_folder_to_local(\n+            src_proj=os.environ['DX_PROJECT_CONTEXT_ID'],\n+            src_proj_fld=os.path.dirname(bed_file),\n+            dest_fld_prefix='/',","path":"ngs_reporting/src/code.py","position":136,"original_position":115,"commit_id":"6b7c21af389f62517cdf9d2c3a6b856147f8fe90","original_commit_id":"2230375f80d878f5d589c3e97bfe34731370ad41","user":{"login":"vladsaveliev","id":1575412,"avatar_url":"https://avatars0.githubusercontent.com/u/1575412?v=4","gravatar_id":"","url":"https://api.github.com/users/vladsaveliev","html_url":"https://github.com/vladsaveliev","followers_url":"https://api.github.com/users/vladsaveliev/followers","following_url":"https://api.github.com/users/vladsaveliev/following{/other_user}","gists_url":"https://api.github.com/users/vladsaveliev/gists{/gist_id}","starred_url":"https://api.github.com/users/vladsaveliev/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vladsaveliev/subscriptions","organizations_url":"https://api.github.com/users/vladsaveliev/orgs","repos_url":"https://api.github.com/users/vladsaveliev/repos","events_url":"https://api.github.com/users/vladsaveliev/events{/privacy}","received_events_url":"https://api.github.com/users/vladsaveliev/received_events","type":"User","site_admin":false},"body":"Ok, got it!","created_at":"2017-07-31T20:15:14Z","updated_at":"2017-07-31T20:15:14Z","html_url":"https://github.com/AstraZeneca-NGS/DNAnexus/pull/2#discussion_r130449772","pull_request_url":"https://api.github.com/repos/AstraZeneca-NGS/DNAnexus/pulls/2","_links":{"self":{"href":"https://api.github.com/repos/AstraZeneca-NGS/DNAnexus/pulls/comments/130449772"},"html":{"href":"https://github.com/AstraZeneca-NGS/DNAnexus/pull/2#discussion_r130449772"},"pull_request":{"href":"https://api.github.com/repos/AstraZeneca-NGS/DNAnexus/pulls/2"}}},"pull_request":{"url":"https://api.github.com/repos/AstraZeneca-NGS/DNAnexus/pulls/2","id":133176321,"html_url":"https://github.com/AstraZeneca-NGS/DNAnexus/pull/2","diff_url":"https://github.com/AstraZeneca-NGS/DNAnexus/pull/2.diff","patch_url":"https://github.com/AstraZeneca-NGS/DNAnexus/pull/2.patch","issue_url":"https://api.github.com/repos/AstraZeneca-NGS/DNAnexus/issues/2","number":2,"state":"open","locked":false,"title":"App to Applet 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applet\r\n* lowered permissions on applet to minimum required\r\n  * Removed network access `*`\r\n  * Removed CONTRIBUTE access to parent project, defaults to VIEW on parent project\r\n  * Removed VIEW access to all running user projects\r\n* Removed multiregion fields added by App transition (in dxapp.json) \r\n* Added test run in asset creation applet\r\n\r\n**Considerations**\r\n* Maintain repo travis CI test\r\n  * Old continuous integration process with Travis allowed for a rather fast turn around time on development changes. 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