Created
April 24, 2017 13:04
-
-
Save drj11/a3231e8fd10414e342b9887b6e10647d to your computer and use it in GitHub Desktop.
isa tab parsing fails
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 2017-04-24 08:50:10 INFO data_set_manager.isa_tab_parser:1110 get_dataset_name() - Supplied path "/data/media/file_store/temp/test_johnDD.zip" is not a directory. Assuming ISArchive file. | |
| 2017-04-24 08:50:10 INFO data_set_manager.isa_tab_parser:1139 get_dataset_name() - ISArchive extracted to "/tmp/tmpmrZshL/test_johnDD/". | |
| 2017-04-24 08:50:10 INFO data_set_manager.isa_tab_parser:1156 get_dataset_name() - Investigation file path: /tmp/tmpmrZshL/test_johnDD/i_11111.txt | |
| 2017-04-24 08:50:10 INFO data_set_manager.isa_tab_parser:945 run() - Supplied path "/data/media/file_store/temp/test_johnDD.zip" is not a directory. Assuming ISArchive file. | |
| 2017-04-24 08:50:10 INFO data_set_manager.isa_tab_parser:974 run() - ISArchive extracted to "/tmp/tmpkLygx1/test_johnDD/". | |
| 2017-04-24 08:50:10 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 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 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 08:50:10 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 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 INFO data_set_manager.models:86 normalize_date() - Converting date 2017-04-07 ... | |
| 2017-04-24 08:50:10 INFO data_set_manager.models:102 normalize_date() - Failed to convert date 2017-04-07 | |
| 2017-04-24 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 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/tmpkLygx1/test_johnDD/i_11111.txt. | |
| 2017-04-24 08:50:10 INFO data_set_manager.tasks:139 fix_last_col() - trying to fix the last column if necessary | |
| 2017-04-24 08:50:10 ERROR data_set_manager.tasks:504 parse_isatab() - *** print_tb: | |
| [2017-04-24 08:50:10,633: WARNING/Worker-3] File "/srv/refinery-platform/refinery/data_set_manager/tasks.py", line 500, in parse_isatab | |
| [2017-04-24 08:50:10,634: WARNING/Worker-3] preisa_archive=pre_isa_archive) | |
| [2017-04-24 08:50:10,634: WARNING/Worker-3] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 998, in run | |
| [2017-04-24 08:50:10,634: WARNING/Worker-3] if data_set_manager.tasks.fix_last_col(study_file_name): | |
| [2017-04-24 08:50:10,635: WARNING/Worker-3] File "/srv/refinery-platform/refinery/data_set_manager/tasks.py", line 141, in fix_last_col | |
| [2017-04-24 08:50:10,635: WARNING/Worker-3] reader = csv.reader(open(file, 'rU'), dialect='excel-tab') | |
| 2017-04-24 08:50:10 ERROR data_set_manager.tasks:506 parse_isatab() - None | |
| 2017-04-24 08:50:10 ERROR data_set_manager.tasks:507 parse_isatab() - *** print_exception: | |
| [2017-04-24 08:50:10,635: WARNING/Worker-3] Traceback (most recent call last): | |
| [2017-04-24 08:50:10,636: WARNING/Worker-3] File "/srv/refinery-platform/refinery/data_set_manager/tasks.py", line 500, in parse_isatab | |
| [2017-04-24 08:50:10,636: WARNING/Worker-3] preisa_archive=pre_isa_archive) | |
| [2017-04-24 08:50:10,636: WARNING/Worker-3] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 998, in run | |
| [2017-04-24 08:50:10,636: WARNING/Worker-3] if data_set_manager.tasks.fix_last_col(study_file_name): | |
| [2017-04-24 08:50:10,636: WARNING/Worker-3] File "/srv/refinery-platform/refinery/data_set_manager/tasks.py", line 141, in fix_last_col | |
| [2017-04-24 08:50:10,637: WARNING/Worker-3] reader = csv.reader(open(file, 'rU'), dialect='excel-tab') | |
| [2017-04-24 08:50:10,637: WARNING/Worker-3] IOError: [Errno 2] No such file or directory: u'/tmp/tmpkLygx1/test_johnDD/s_Pathology and prognosis in ALS in microglia.txt' | |
| 2017-04-24 08:50:10 ERROR data_set_manager.tasks:513 parse_isatab() - None | |
| 2017-04-24 08:52:10 INFO data_set_manager.isa_tab_parser:1110 get_dataset_name() - Supplied path "/data/media/file_store/temp/test_johnDD.zip" is not a directory. Assuming ISArchive file. | |
| 2017-04-24 08:52:10 INFO data_set_manager.isa_tab_parser:1139 get_dataset_name() - ISArchive extracted to "/tmp/tmpV_Nf1U". | |
| 2017-04-24 08:52:10 INFO data_set_manager.isa_tab_parser:1156 get_dataset_name() - Investigation file path: /tmp/tmpV_Nf1U/i_11111.txt | |
| 2017-04-24 08:52:10 INFO data_set_manager.isa_tab_parser:945 run() - Supplied path "/data/media/file_store/temp/test_johnDD.zip" is not a directory. Assuming ISArchive file. | |
| 2017-04-24 08:52:10 INFO data_set_manager.isa_tab_parser:974 run() - ISArchive extracted to "/tmp/tmpEnmTiK". | |
| 2017-04-24 08:52:10 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 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 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 08:52:10 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 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 INFO data_set_manager.models:86 normalize_date() - Converting date 2017-04-07 ... | |
| 2017-04-24 08:52:10 INFO data_set_manager.models:102 normalize_date() - Failed to convert date 2017-04-07 | |
| 2017-04-24 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 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/tmpEnmTiK/i_11111.txt. | |
| 2017-04-24 08:52:10 INFO data_set_manager.tasks:139 fix_last_col() - trying to fix the last column if necessary | |
| 2017-04-24 08:52:10 ERROR data_set_manager.tasks:504 parse_isatab() - *** print_tb: | |
| [2017-04-24 08:52:10,662: WARNING/Worker-2] File "/srv/refinery-platform/refinery/data_set_manager/tasks.py", line 500, in parse_isatab | |
| [2017-04-24 08:52:10,662: WARNING/Worker-2] preisa_archive=pre_isa_archive) | |
| [2017-04-24 08:52:10,663: WARNING/Worker-2] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 998, in run | |
| [2017-04-24 08:52:10,663: WARNING/Worker-2] if data_set_manager.tasks.fix_last_col(study_file_name): | |
| [2017-04-24 08:52:10,663: WARNING/Worker-2] File "/srv/refinery-platform/refinery/data_set_manager/tasks.py", line 141, in fix_last_col | |
| [2017-04-24 08:52:10,664: WARNING/Worker-2] reader = csv.reader(open(file, 'rU'), dialect='excel-tab') | |
| 2017-04-24 08:52:10 ERROR data_set_manager.tasks:506 parse_isatab() - None | |
| 2017-04-24 08:52:10 ERROR data_set_manager.tasks:507 parse_isatab() - *** print_exception: | |
| [2017-04-24 08:52:10,664: WARNING/Worker-2] Traceback (most recent call last): | |
| [2017-04-24 08:52:10,664: WARNING/Worker-2] File "/srv/refinery-platform/refinery/data_set_manager/tasks.py", line 500, in parse_isatab | |
| [2017-04-24 08:52:10,665: WARNING/Worker-2] preisa_archive=pre_isa_archive) | |
| [2017-04-24 08:52:10,665: WARNING/Worker-2] File "/srv/refinery-platform/refinery/data_set_manager/isa_tab_parser.py", line 998, in run | |
| [2017-04-24 08:52:10,665: WARNING/Worker-2] if data_set_manager.tasks.fix_last_col(study_file_name): | |
| [2017-04-24 08:52:10,665: WARNING/Worker-2] File "/srv/refinery-platform/refinery/data_set_manager/tasks.py", line 141, in fix_last_col | |
| [2017-04-24 08:52:10,665: WARNING/Worker-2] reader = csv.reader(open(file, 'rU'), dialect='excel-tab') | |
| [2017-04-24 08:52:10,666: WARNING/Worker-2] IOError: [Errno 2] No such file or directory: u'/tmp/tmpEnmTiK/s_Pathology and prognosis in ALS in microglia.txt' | |
| 2017-04-24 08:52:10 ERROR data_set_manager.tasks:513 parse_isatab() - None |
There are two failed uploads here.
Note that the "cause of death" for the first upload is: IOError: [Errno 2] No such file or directory: u'/tmp/tmpkLygx1/test_johnDD/s_Pathology and prognosis in ALS in microglia.txt';
suggesting that the filenames referenced in the metadata should in fact match the filenames found in the ISA archive.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
These logs are found in
/srv/refinery-platform/refinery/log/celeryd-w1.log