{"action":"created","issue":{"url":"https://api.github.com/repos/WorkflowConversion/CTDConverter/issues/35","repository_url":"https://api.github.com/repos/WorkflowConversion/CTDConverter","labels_url":"https://api.github.com/repos/WorkflowConversion/CTDConverter/issues/35/labels{/name}","comments_url":"https://api.github.com/repos/WorkflowConversion/CTDConverter/issues/35/comments","events_url":"https://api.github.com/repos/WorkflowConversion/CTDConverter/issues/35/events","html_url":"https://github.com/WorkflowConversion/CTDConverter/issues/35","id":296118632,"number":35,"title":"Unable to parse CTD from Seqan 2.4.0","user":{"login":"mr-c","id":1330696,"avatar_url":"https://avatars3.githubusercontent.com/u/1330696?v=4","gravatar_id":"","url":"https://api.github.com/users/mr-c","html_url":"https://github.com/mr-c","followers_url":"https://api.github.com/users/mr-c/followers","following_url":"https://api.github.com/users/mr-c/following{/other_user}","gists_url":"https://api.github.com/users/mr-c/gists{/gist_id}","starred_url":"https://api.github.com/users/mr-c/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mr-c/subscriptions","organizations_url":"https://api.github.com/users/mr-c/orgs","repos_url":"https://api.github.com/users/mr-c/repos","events_url":"https://api.github.com/users/mr-c/events{/privacy}","received_events_url":"https://api.github.com/users/mr-c/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-02-10T17:42:29Z","updated_at":"2018-02-12T10:22:50Z","closed_at":null,"author_association":"NONE","body":"Even when the missing `ctdVersion` is added, CTDOpts gets grumpy with empty `values` like this snippet from `flexbar --write-ctd` using Seqan 2.4.0\r\n\r\n```\r\n<ITEM name=\"barcode-tail-length\" value=\"\" type=\"int\" description=\"Region size in tail trim-end modes. Default: barcode length.\" required=\"false\" advanced=\"true\" />\r\n```\r\n\r\n```\r\n(ctd-converter) mcrusoe@mrcdev:~$ python ~/src/CTDConverter/convert.py cwl  -i ~/debian/flexbar/flexbar.ctd -o f.c\r\nINFO: Using cwl converter\r\nWARNING: Validation against a schema has not been enabled.\r\nINFO: Parsing /home/mcrusoe/debian/flexbar/flexbar.ctd\r\nTraceback (most recent call last):\r\n  File \"/home/mcrusoe/src/CTDConverter/convert.py\", line 215, in main\r\n    converter.get_preferred_file_extension())\r\n  File \"/home/mcrusoe/src/CTDConverter/common/utils.py\", line 118, in parse_input_ctds\r\n    parsed_ctds.append(ParsedCTD(CTDModel(from_file=input_ctd), input_ctd, output_file))\r\n  File \"/home/mcrusoe/miniconda2/envs/ctd-converter/lib/python2.7/site-packages/CTDopts/CTDopts.py\", line 643, in __init__\r\n    self._load_from_file(from_file)\r\n  File \"/home/mcrusoe/miniconda2/envs/ctd-converter/lib/python2.7/site-packages/CTDopts/CTDopts.py\", line 688, in _load_from_file\r\n    self.parameters = self._build_param_model(params_container_node, base=None)\r\n  File \"/home/mcrusoe/miniconda2/envs/ctd-converter/lib/python2.7/site-packages/CTDopts/CTDopts.py\", line 708, in _build_param_model\r\n    self._build_param_model(child, current_group)\r\n  File \"/home/mcrusoe/miniconda2/envs/ctd-converter/lib/python2.7/site-packages/CTDopts/CTDopts.py\", line 713, in _build_param_model\r\n    base.add(**setup)  # register parameter in model\r\n  File \"/home/mcrusoe/miniconda2/envs/ctd-converter/lib/python2.7/site-packages/CTDopts/CTDopts.py\", line 564, in add\r\n    self.parameters[name] = Parameter(name, self, **kwargs)\r\n  File \"/home/mcrusoe/miniconda2/envs/ctd-converter/lib/python2.7/site-packages/CTDopts/CTDopts.py\", line 376, in __init__\r\n    self._validate_numerical_defaults(default)\r\n  File \"/home/mcrusoe/miniconda2/envs/ctd-converter/lib/python2.7/site-packages/CTDopts/CTDopts.py\", line 456, in _validate_numerical_defaults\r\n    \"default\": ', '.join(map(str, errors_so_far))})\r\nModelParsingError: An error occurred while parsing the CTD file: Invalid default value(s) provided for parameter barcode-min-overlap of type <type 'int'>: ''\r\nERROR: There seems to be a problem with one of your input CTDs.\r\nTraceback (most recent call last):\r\n  File \"/home/mcrusoe/src/CTDConverter/convert.py\", line 272, in <module>\r\n    sys.exit(main())\r\n  File \"/home/mcrusoe/src/CTDConverter/convert.py\", line 234, in main\r\n    utils.error(\"Reason: \" + e.msg, 0)\r\nAttributeError: 'ModelParsingError' object has no attribute 'msg'\r\n```\r\n\r\nTagging in @h-2"},"comment":{"url":"https://api.github.com/repos/WorkflowConversion/CTDConverter/issues/comments/364881548","html_url":"https://github.com/WorkflowConversion/CTDConverter/issues/35#issuecomment-364881548","issue_url":"https://api.github.com/repos/WorkflowConversion/CTDConverter/issues/35","id":364881548,"user":{"login":"chahuistle","id":1537189,"avatar_url":"https://avatars3.githubusercontent.com/u/1537189?v=4","gravatar_id":"","url":"https://api.github.com/users/chahuistle","html_url":"https://github.com/chahuistle","followers_url":"https://api.github.com/users/chahuistle/followers","following_url":"https://api.github.com/users/chahuistle/following{/other_user}","gists_url":"https://api.github.com/users/chahuistle/gists{/gist_id}","starred_url":"https://api.github.com/users/chahuistle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chahuistle/subscriptions","organizations_url":"https://api.github.com/users/chahuistle/orgs","repos_url":"https://api.github.com/users/chahuistle/repos","events_url":"https://api.github.com/users/chahuistle/events{/privacy}","received_events_url":"https://api.github.com/users/chahuistle/received_events","type":"User","site_admin":false},"created_at":"2018-02-12T10:22:49Z","updated_at":"2018-02-12T10:22:49Z","author_association":"CONTRIBUTOR","body":"Could you attach a sample input CTD and a command line that replicates this issue?"}}
{"actor":{"display_login":"chahuistle"}}