isatab errors

isatab deque error

2017-04-24 09:22:56 ERROR    data_set_manager.tasks:513 parse_isatab() - None
2017-04-24 09:47:36 INFO     data_set_manager.isa_tab_parser:1110 get_dataset_name() - Supplied path "/data/media/file_store/temp/johnDD_archive.zip" is not a directory. Assuming ISArchive file.
2017-04-24 09:47:39 INFO     data_set_manager.isa_tab_parser:1139 get_dataset_name() - ISArchive extracted to "/tmp/tmp2sJZho".
2017-04-24 09:47:39 INFO     data_set_manager.isa_tab_parser:1156 get_dataset_name() - Investigation file path: /tmp/tmp2sJZho/i_Investigation.txt
2017-04-24 09:47:39 INFO     data_set_manager.isa_tab_parser:945 run() - Supplied path "/data/media/file_store/temp/johnDD_archive.zip" is not a directory. Assuming ISArchive file.
2017-04-24 09:47:43 INFO     data_set_manager.isa_tab_parser:974 run() - ISArchive extracted to "/tmp/tmpPiu5UD".
2017-04-24 09:47:43 INFO     data_set_manager.isa_tab_parser:703 _create_investigation_file_section_model() - Column 1 in section ONTOLOGY SOURCE REFERENCE has no non-empty cells and was ignored.
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Comment[Created With Configuration] found in column 1 when parsing "INVESTIGATION" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Comment[Last Opened With Configuration] found in column 1 when parsing "INVESTIGATION" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 INFO     data_set_manager.isa_tab_parser:703 _create_investigation_file_section_model() - Column 0 in section INVESTIGATION PUBLICATIONS has no non-empty cells and was ignored.
2017-04-24 09:47:43 INFO     data_set_manager.isa_tab_parser:703 _create_investigation_file_section_model() - Column 0 in section INVESTIGATION CONTACTS has no non-empty cells and was ignored.
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Comment[Study Grant Number] found in column 1 when parsing "STUDY" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Comment[Study Funding Agency] found in column 1 when parsing "STUDY" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 INFO     data_set_manager.models:86 normalize_date() - Converting date 2017-04-07 ...
2017-04-24 09:47:43 INFO     data_set_manager.models:102 normalize_date() - Failed to convert date 2017-04-07
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Study Protocol Parameters Name found in column 1 when parsing "STUDY PROTOCOLS" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Study Protocol Parameters Name Term Accession Number found in column 1 when parsing "STUDY PROTOCOLS" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Study Protocol Parameters Name Term Source REF found in column 1 when parsing "STUDY PROTOCOLS" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Study Protocol Components Name found in column 1 when parsing "STUDY PROTOCOLS" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Study Protocol Components Type found in column 1 when parsing "STUDY PROTOCOLS" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Study Protocol Components Type Term Accession Number found in column 1 when parsing "STUDY PROTOCOLS" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Study Protocol Components Type Term Source REF found in column 1 when parsing "STUDY PROTOCOLS" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 WARNING  data_set_manager.isa_tab_parser:836 _parse_investigation_file_section() - Undefined field Comment[Study Person REF] found in column 1 when parsing "STUDY CONTACTS" from /tmp/tmpPiu5UD/i_Investigation.txt.
2017-04-24 09:47:43 INFO     data_set_manager.tasks:139 fix_last_col() - trying to fix the last column if necessary
2017-04-24 09:47:43 ERROR    data_set_manager.isa_tab_parser:391 _parse_node() - Unexpected element Term Source REF when parsing node in line 2, column 1.
2017-04-24 09:47:43 ERROR    data_set_manager.isa_tab_parser:391 _parse_node() - Unexpected element Term Accession Number when parsing node in line 2, column 2.
2017-04-24 09:47:44 INFO     data_set_manager.isa_tab_parser:347 _parse_node() - New node Sample Name: Table1_1 (0 parents, 0 children | species: None, genome build: None) created.
2017-04-24 09:47:44 INFO     data_set_manager.isa_tab_parser:347 _parse_node() - New node Source Name: a (0 parents, 0 children | species: None, genome build: None) created.
2017-04-24 09:47:44 ERROR    data_set_manager.tasks:504 parse_isatab() - *** print_tb:
[2017-04-24 09:47:44,128: WARNING/Worker-1] File "/srv/refinery-platform/refinery/data_set_manager/tasks.py", line 500, in parse_isatab
[2017-04-24 09:47:44,129: WARNING/Worker-1] preisa_archive=pre_isa_archive)
[2017-04-24 09:47:44,129: WARNING/Worker-1] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 999, in run
[2017-04-24 09:47:44,129: WARNING/Worker-1] self._parse_study_file(study, study_file_name)
[2017-04-24 09:47:44,129: WARNING/Worker-1] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 663, in _parse_study_file
[2017-04-24 09:47:44,130: WARNING/Worker-1] self._parse_node(headers, row)
[2017-04-24 09:47:44,131: WARNING/Worker-1] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 383, in _parse_node
[2017-04-24 09:47:44,131: WARNING/Worker-1] self._parse_attribute(headers, row)
[2017-04-24 09:47:44,131: WARNING/Worker-1] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 424, in _parse_attribute
[2017-04-24 09:47:44,131: WARNING/Worker-1] value=row[0],
2017-04-24 09:47:44 ERROR    data_set_manager.tasks:506 parse_isatab() - None
2017-04-24 09:47:44 ERROR    data_set_manager.tasks:507 parse_isatab() - *** print_exception:
[2017-04-24 09:47:44,132: WARNING/Worker-1] Traceback (most recent call last):
[2017-04-24 09:47:44,132: WARNING/Worker-1] File "/srv/refinery-platform/refinery/data_set_manager/tasks.py", line 500, in parse_isatab
[2017-04-24 09:47:44,132: WARNING/Worker-1] preisa_archive=pre_isa_archive)
[2017-04-24 09:47:44,133: WARNING/Worker-1] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 999, in run
[2017-04-24 09:47:44,133: WARNING/Worker-1] self._parse_study_file(study, study_file_name)
[2017-04-24 09:47:44,133: WARNING/Worker-1] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 663, in _parse_study_file
[2017-04-24 09:47:44,133: WARNING/Worker-1] self._parse_node(headers, row)
[2017-04-24 09:47:44,133: WARNING/Worker-1] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 383, in _parse_node
[2017-04-24 09:47:44,134: WARNING/Worker-1] self._parse_attribute(headers, row)
[2017-04-24 09:47:44,134: WARNING/Worker-1] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 424, in _parse_attribute
[2017-04-24 09:47:44,134: WARNING/Worker-1] value=row[0],
[2017-04-24 09:47:44,134: WARNING/Worker-1] IndexError: deque index out of range