Mercurial > repos > greg > validate_affy_metadata
changeset 17:17db886fbfad draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 04 Dec 2018 13:51:21 -0500 |
| parents | b5bbc8f1f225 |
| children | 38166b76f47a |
| files | test-data/affy_metadata.csv test-data/affy_metadata.tabular validate_affy_metadata.py validate_affy_metadata.xml |
| diffstat | 4 files changed, 103 insertions(+), 102 deletions(-) [+] |
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line diff
--- a/test-data/affy_metadata.csv Mon Nov 19 13:43:29 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,97 +0,0 @@ -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,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,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, -2018-11-08,test_088,palmata,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,6,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_089,palmata,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,7,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_090,palmata,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,3,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_091,palmata,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,4,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_092,palmata,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,2,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_093,palmata,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,1,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_094,palmata,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,2,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_095,cervicornis,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,10,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_096,cervicornis,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,8,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_001,cervicornis,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,7,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_004,cervicornis,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,6,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_009,cervicornis,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,10,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_071,cervicornis,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,3,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True, -2018-11-08,test_082,cervicornis,,,Margara,PuertoRico,17.949552,-66.727433,Reef,,,,5,,,,,,False,Kitchen,Sheila,Penn State,2018-11-08,sak89@psu.edu,Affymetrix,1,True,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/affy_metadata.tabular Tue Dec 04 13:51:21 2018 -0500 @@ -0,0 +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
--- a/validate_affy_metadata.py Mon Nov 19 13:43:29 2018 -0500 +++ b/validate_affy_metadata.py Tue Dec 04 13:51:21 2018 -0500 @@ -75,7 +75,7 @@ if i > 97: 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(",") + 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))) stop_error(accumulated_msgs)
--- a/validate_affy_metadata.xml Mon Nov 19 13:43:29 2018 -0500 +++ b/validate_affy_metadata.xml Tue Dec 04 13:51:21 2018 -0500 @@ -5,17 +5,17 @@ --input '$input' --output '$output']]></command> <inputs> - <param name="input" type="data" format="csv" label="Affymetrix 96 well plate metadata file"> + <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> </param> </inputs> <outputs> - <data name="output" format="csv"/> + <data name="output" format="tabular"/> </outputs> <tests> <test> - <param name="input" value="affy_metadata.csv" ftype="csv"/> - <output name="output" file="affy_metadata.csv" ftype="csv"/> + <param name="input" value="affy_metadata.tabular" ftype="tabular"/> + <output name="output" file="affy_metadata.tabular" ftype="tabular"/> </test> </tests> <help> @@ -61,3 +61,4 @@ <citations> </citations> </tool> +