Mercurial > repos > greg > validate_affy_metadata
changeset 18:38166b76f47a draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 22 Jan 2019 11:05:08 -0500 |
| parents | 17db886fbfad |
| children | 26bb15827aa7 |
| files | test-data/affy_metadata.tabular validate_affy_metadata.py validate_affy_metadata.xml |
| diffstat | 3 files changed, 130 insertions(+), 132 deletions(-) [+] |
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--- a/test-data/affy_metadata.tabular Tue Dec 04 13:51:21 2018 -0500 +++ b/test-data/affy_metadata.tabular Tue Jan 22 11:05:08 2019 -0500 @@ -1,97 +1,97 @@ -#date_entered_db user_specimen_id field_call bcoral_genet_id bsym_genet_id reef region latitude longitude geographic_origin sample_location latitude_outplant longitude_outplant depth dist_shore disease_resist bleach_resist mortality tle spawning collector_last_name collector_first_name org collection_date contact_email seq_facility array_version public public_after_date -2018-11-08 test_002 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 5 yes Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_003 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 6 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_005 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 7 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_006 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_007 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 2 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_008 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 1 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_010 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 10 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_011 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 12 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_012 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 24 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_013 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 6 yes Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_014 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 15 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_015 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_016 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 13 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_017 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 10 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_018 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 6 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_019 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 15 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_020 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_021 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 13 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_022 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 13 yes Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_023 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 5 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_024 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 6 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_025 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 7 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_026 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_027 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 2 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_028 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 1 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_029 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 2 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_030 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 6 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_031 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 6 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_032 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 6 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_033 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 6 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_034 palmata Curlew Belize 16.7909389 -88.0830056 Reef 17 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_035 palmata Curlew Belize 16.7909389 -88.0830056 Reef 17 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_036 palmata Curlew Belize 16.7909389 -88.0830056 Reef 23 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_037 palmata Curlew Belize 16.7909389 -88.0830056 Reef 7 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_038 palmata Curlew Belize 16.7909389 -88.0830056 Reef 9 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_039 palmata Curlew Belize 16.7909389 -88.0830056 Reef 6 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_040 palmata Curlew Belize 16.7909389 -88.0830056 Reef 3 yes Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_041 palmata Curlew Belize 16.7909389 -88.0830056 Reef 11 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_042 palmata Curlew Belize 16.7909389 -88.0830056 Reef 10 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_043 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_044 palmata Curlew Belize 16.7909389 -88.0830056 Reef 17 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_045 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_046 palmata Curlew Belize 16.7909389 -88.0830056 Reef 7 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_047 palmata Curlew Belize 16.7909389 -88.0830056 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_048 palmata Curlew Belize 16.7909389 -88.0830056 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_049 palmata Curlew Belize 16.7909389 -88.0830056 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_050 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_051 palmata Curlew Belize 16.7909389 -88.0830056 Reef 6 yes Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_052 palmata Curlew Belize 16.7909389 -88.0830056 Reef 5 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_053 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_054 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_055 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_056 palmata Curlew Belize 16.7909389 -88.0830056 Reef 1 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_057 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes Yes -2018-11-08 test_058 palmata Curlew Belize 16.7909389 -88.0830056 Reef 1 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_059 palmata Curlew Belize 16.7909389 -88.0830056 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_060 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_061 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 4 yes Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_062 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 2 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_063 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 5 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_064 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_065 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 27 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_066 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 25 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_067 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 13 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_068 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_069 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 9 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_070 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 6 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_072 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 16 yes Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_073 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_074 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 11 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_075 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_076 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 5 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_077 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 6 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_078 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 16 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_079 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_080 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 11 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_081 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_083 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 5 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_084 prolifera SeaAquarium2 Curacao 12.0842 -68.8966 Reef 2 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_085 prolifera SeaAquarium2 Curacao 12.0842 -68.8966 Reef 1 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_086 prolifera SeaAquarium2 Curacao 12.0842 -68.8966 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_087 prolifera SeaAquarium2 Curacao 12.0842 -68.8966 Reef 5 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_088 palmata Margara PuertoRico 17.949552 -66.727433 Reef 6 yes Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_089 palmata Margara PuertoRico 17.949552 -66.727433 Reef 7 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_090 palmata Margara PuertoRico 17.949552 -66.727433 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_091 palmata Margara PuertoRico 17.949552 -66.727433 Reef 4 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_092 palmata Margara PuertoRico 17.949552 -66.727433 Reef 2 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_093 palmata Margara PuertoRico 17.949552 -66.727433 Reef 1 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_094 palmata Margara PuertoRico 17.949552 -66.727433 Reef 2 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_095 cervicornis Margara PuertoRico 17.949552 -66.727433 Reef 10 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_096 cervicornis Margara PuertoRico 17.949552 -66.727433 Reef 8 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_001 cervicornis Margara PuertoRico 17.949552 -66.727433 Reef 7 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_004 cervicornis Margara PuertoRico 17.949552 -66.727433 Reef 6 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_009 cervicornis Margara PuertoRico 17.949552 -66.727433 Reef 10 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_071 cervicornis Margara PuertoRico 17.949552 -66.727433 Reef 3 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No -2018-11-08 test_082 cervicornis Margara PuertoRico 17.949552 -66.727433 Reef 5 No Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 Yes No +user_specimen_id,field_call,bcoral_genet_id,bsym_genet_id,reef,region,latitude,longitude,geographic_origin,sample_location,latitude_outplant,longitude_outplant,depth,dist_shore,disease_resist,bleach_resist,mortality,tle,spawning,collector_last_name,collector_first_name,org,collection_date,contact_email,seq_facility,array_version,public,public_after_date +test_002 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 5 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_003 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_005 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 7 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_006 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_007 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 2 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_008 prolifera JohnsonsReef Bahamas 18.361733 -64.7743 Reef 1 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_010 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 10 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_011 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 12 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_012 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 24 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_013 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_014 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 15 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_015 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_016 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 13 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_017 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 10 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_018 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_019 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 15 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_020 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_021 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 13 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_022 cervicornis LittleGrecian Florida 25.11844009 -80.3171895 Reef 13 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_023 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 5 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_024 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_025 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 7 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_026 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_027 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 2 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_028 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 1 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_029 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 2 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_030 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_031 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_032 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_033 prolifera Curlew Belize 16.7909389 -88.0830056 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_034 palmata Curlew Belize 16.7909389 -88.0830056 Reef 17 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_035 palmata Curlew Belize 16.7909389 -88.0830056 Reef 17 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_036 palmata Curlew Belize 16.7909389 -88.0830056 Reef 23 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_037 palmata Curlew Belize 16.7909389 -88.0830056 Reef 7 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_038 palmata Curlew Belize 16.7909389 -88.0830056 Reef 9 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_039 palmata Curlew Belize 16.7909389 -88.0830056 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_040 palmata Curlew Belize 16.7909389 -88.0830056 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_041 palmata Curlew Belize 16.7909389 -88.0830056 Reef 11 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_042 palmata Curlew Belize 16.7909389 -88.0830056 Reef 10 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_043 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_044 palmata Curlew Belize 16.7909389 -88.0830056 Reef 17 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_045 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_046 palmata Curlew Belize 16.7909389 -88.0830056 Reef 7 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_047 palmata Curlew Belize 16.7909389 -88.0830056 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_048 palmata Curlew Belize 16.7909389 -88.0830056 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_049 palmata Curlew Belize 16.7909389 -88.0830056 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_050 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_051 palmata Curlew Belize 16.7909389 -88.0830056 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_052 palmata Curlew Belize 16.7909389 -88.0830056 Reef 5 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_053 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_054 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_055 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_056 palmata Curlew Belize 16.7909389 -88.0830056 Reef 1 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_057 palmata Curlew Belize 16.7909389 -88.0830056 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_058 palmata Curlew Belize 16.7909389 -88.0830056 Reef 1 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_059 palmata Curlew Belize 16.7909389 -88.0830056 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_060 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_061 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_062 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 2 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_063 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 5 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_064 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_065 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 27 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_066 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 25 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_067 cervicornis SeaAquarium2 Curacao 12.0842 -68.8966 Reef 13 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_068 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_069 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 9 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_070 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_072 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 16 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_073 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_074 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 11 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_075 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_076 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 5 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_077 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_078 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 16 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_079 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_080 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 11 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_081 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_083 palmata SeaAquarium2 Curacao 12.0842 -68.8966 Reef 5 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_084 prolifera SeaAquarium2 Curacao 12.0842 -68.8966 Reef 2 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_085 prolifera SeaAquarium2 Curacao 12.0842 -68.8966 Reef 1 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_086 prolifera SeaAquarium2 Curacao 12.0842 -68.8966 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_087 prolifera SeaAquarium2 Curacao 12.0842 -68.8966 Reef 5 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_088 palmata Margara Puerto Rico 17.949552 -66.727433 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_089 palmata Margara Puerto Rico 17.949552 -66.727433 Reef 7 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_090 palmata Margara Puerto Rico 17.949552 -66.727433 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_091 palmata Margara Puerto Rico 17.949552 -66.727433 Reef 4 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_092 palmata Margara Puerto Rico 17.949552 -66.727433 Reef 2 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_093 palmata Margara Puerto Rico 17.949552 -66.727433 Reef 1 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_094 palmata Margara Puerto Rico 17.949552 -66.727433 Reef 2 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_095 cervicornis Margara Puerto Rico 17.949552 -66.727433 Reef 10 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_096 cervicornis Margara Puerto Rico 17.949552 -66.727433 Reef 8 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_001 cervicornis Margara Puerto Rico 17.949552 -66.727433 Reef 7 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_004 cervicornis Margara Puerto Rico 17.949552 -66.727433 Reef 6 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_009 cervicornis Margara Puerto Rico 17.949552 -66.727433 Reef 10 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_071 cervicornis Margara Puerto Rico 17.949552 -66.727433 Reef 3 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True +test_082 cervicornis Margara Puerto Rico 17.949552 -66.727433 Reef 5 False Kitchen Sheila Penn State 2018-11-08 sak89@psu.edu Affymetrix 1 True
--- a/validate_affy_metadata.py Tue Dec 04 13:51:21 2018 -0500 +++ b/validate_affy_metadata.py Tue Jan 22 11:05:08 2019 -0500 @@ -76,86 +76,84 @@ accumulated_msgs = add_error_msg(accumulated_msgs, "The input file contains more than 97 lines (must be 1 header line and no more than 96 data lines).") stop_error(accumulated_msgs) items = line.split("\t") - if len(items) != 29: - accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 29)." % (i, len(items))) + if len(items) != 28: + accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 28)." % (i, len(items))) stop_error(accumulated_msgs) # Required and validated. - date_entered_db = items[0] - accumulated_msgs = validate_date_string(i, date_entered_db, accumulated_msgs) # Required. - user_specimen_id = items[1] + user_specimen_id = items[0] if len(user_specimen_id) == 0: accumulated_msgs = empty_value(i, "user_specimen_id", accumulated_msgs) # Optional. - field_call = items[2] + field_call = items[1] # Optional. - bcoral_genet_id = items[3] + bcoral_genet_id = items[2] # Optional. - bsym_genet_id = items[4] + bsym_genet_id = items[3] # Required. - reef = items[5] + reef = items[4] if len(reef) == 0: accumulated_msgs = empty_value(i, "reef", accumulated_msgs) # Required. - region = items[6] + region = items[5] if len(region) == 0: accumulated_msgs = empty_value(i, "region", accumulated_msgs) # Required and validated. - latitude = items[7] + latitude = items[6] accumulated_msgs = validate_decimal(i, latitude, accumulated_msgs) # Required and validated. - longitude = items[8] + longitude = items[7] accumulated_msgs = validate_decimal(i, longitude, accumulated_msgs) # Optional. - geographic_origin = items[9] + geographic_origin = items[8] # Optional. - sample_location = items[10] + sample_location = items[9] # Optional. - latitude_outplant = items[11] + latitude_outplant = items[10] # Optional. - longitude_outplant = items[12] + longitude_outplant = items[11] # Optional. - depth = items[13] + depth = items[12] # Optional. - dist_shore = items[14] + dist_shore = items[13] # Optional. - disease_resist = items[15] + disease_resist = items[14] # Optional. - bleach_resist = items[16] + bleach_resist = items[15] # Optional. - mortality = items[17] + mortality = items[16] # Optional. - tle = items[18] + tle = items[17] # Optional. - spawning = string_as_boolean_string(items[19]) + spawning = string_as_boolean_string(items[18]) # Required. - collector_last_name = items[20] + collector_last_name = items[19] if len(collector_last_name) == 0: accumulated_msgs = empty_value(i, "collector_last_name", accumulated_msgs) # Required. - collector_first_name = items[21] + collector_first_name = items[20] if len(collector_first_name) == 0: accumulated_msgs = empty_value(i, "collector_first_name", accumulated_msgs) # Required. - org = items[22] + org = items[21] if len(org) == 0: accumulated_msgs = empty_value(i, "org", accumulated_msgs) # Required and validated. - collection_date = items[23] - accumulated_msgs = validate_date_string(i, date_entered_db, accumulated_msgs) + collection_date = items[22] + accumulated_msgs = validate_date_string(i, collection_date, accumulated_msgs) # Required and validated. - contact_email = items[24] + contact_email = items[23] accumulated_msgs = validate_email(i, contact_email, accumulated_msgs) # Required. - seq_facility = items[25] + seq_facility = items[24] if len(seq_facility) == 0: accumulated_msgs = empty_value(i, "seq_facility", accumulated_msgs) # Optional. - array_version = items[26] + array_version = items[25] # Optional. - public = string_as_boolean_string(items[27]) + public = string_as_boolean_string(items[26]) # Optional. - public_after_date = items[28] + public_after_date = items[27] accumulated_msga = validate_date_string(i, public_after_date, accumulated_msgs) if len(accumulated_msgs) > 0:
--- a/validate_affy_metadata.xml Tue Dec 04 13:51:21 2018 -0500 +++ b/validate_affy_metadata.xml Tue Jan 22 11:05:08 2019 -0500 @@ -6,7 +6,7 @@ --output '$output']]></command> <inputs> <param name="input" type="data" format="tabular" label="Affymetrix 96 well plate metadata file"> - <validator type="expression" message="96 well plate data must have 29 columns and no more than 96 lines of data"><![CDATA[value is not None and value.metadata.columns==29 and value.metadata.data_lines<=96]]></validator> + <validator type="expression" message="96 well plate data must have 28 columns and no more than 96 lines of data"><![CDATA[value is not None and value.metadata.columns==28 and value.metadata.data_lines<=96]]></validator> </param> </inputs> <outputs> @@ -21,7 +21,7 @@ <help> **What it does** -Validates an Affymetrix metadata file for 96 well plate data. These files consist of 29 columns and no more than 96 data lines. +Validates an Affymetrix metadata file for 96 well plate data. These files consist of 28 columns and no more than 96 data lines. The tool will output the input file if it is valid. -----