def perform_batch_validation(filename):
validators = {
'FILENAME': [NotEmptyValidator()],
'SEQ': [SetValidator(valid_set=["*..*", "*.*"])],
'COMPOUND_NAME': [NotEmptyValidator()],
'MOLECULEMASS': [FloatValidator()],
'INSTRUMENT': [
SetValidator(valid_set=[
"qTof", "QQQ", "Ion Trap", "Hybrid FT", "Orbitrap", "ToF"
])
],
'IONSOURCE':
[SetValidator(valid_set=["LC-ESI", "DI-ESI", "EI", "APCI", "ESI"])],
'EXTRACTSCAN': [IntValidator()],
'SMILES': [],
'INCHI': [],
'INCHIAUX': [],
'CHARGE': [IntValidator()],
'IONMODE': [SetValidator(valid_set=["Positive", "Negative"])],
'PUBMED': [NotEmptyValidator()],
'ACQUISITION': [
SetValidator(valid_set=[
"Crude", "Lysate", "Commercial", "Isolated", "Other"
])
],
'EXACTMASS': [FloatValidator()],
'DATACOLLECTOR': [NotEmptyValidator()],
'ADDUCT': [NotEmptyValidator()],
'INTEREST': [],
'LIBQUALITY': [SetValidator(valid_set=["1", "2", "3"])],
'GENUS': [],
'SPECIES': [],
'STRAIN': [],
'CASNUMBER': [NotEmptyValidator()],
'PI': [NotEmptyValidator()]
}
my_validator = Vlad(source=LocalFile(filename),
delimiter="\t",
ignore_missing_validators=True,
validators=validators)
passes_validation = my_validator.validate()
errors_list = []
for column in my_validator.failures:
for line_number in my_validator.failures[column]:
error_dict = {}
error_dict["header"] = column
error_dict[
"line_number"] = line_number + 1 #0 Indexed with 0 being the header row
error_dict["error_string"] = str(
my_validator.failures[column][line_number])
errors_list.append(error_dict)
for missing_field in my_validator.missing_fields:
error_dict = {}
error_dict["header"] = "Missing Header"
error_dict["line_number"] = "N/A"
error_dict["error_string"] = "Missing column %s" % (missing_field)
errors_list.append(error_dict)
valid_rows = []
row_count = 0
#Read in the good rows
try:
no_validation_lines = [
int(error["line_number"]) for error in errors_list
]
row_count = 0
with open(filename) as csvfile:
reader = csv.DictReader(csvfile, delimiter="\t")
for row in reader:
row_count += 1
if row_count in no_validation_lines:
continue
valid_rows.append(row)
except:
#raise
print("error reading file")
return passes_validation, my_validator.failures, errors_list, valid_rows, row_count
badfiles = []
for sfn in os.listdir(args.indir + args.sub):
if sfn not in skip and sfn.endswith(".tsv"):
validators = {
'docId': [
UniqueValidator(unique_with=['annotSet', 'annotId']),
#UniqueValidator(unique_with=['annotSet', 'startOffset'])
],
'annotId': [RegexValidator(pattern=r'T?\d*-?\d+', full=True)],
'annotType': [
SetValidator([
'Quantity', 'Qualifier', 'MeasuredProperty',
'MeasuredEntity'
])
],
'annotSet': [IntValidator()],
'startOffset': [IntValidator()],
'endOffset': [IntValidator()],
'other': [JsonValidator(empty_ok=True)],
'text': [LengthValidator()]
}
#print(sfn)
truth = Vlad(source=LocalFile(args.indir + args.sub + sfn),
validators=validators,
delimiter="\t").validate()
if truth == False:
allgood = False
badfiles.append(sfn)
# If any tsv files fail validation, report list to user and exit program
if allgood == False:
def test_int_validator_works(field):
IntValidator().validate(field)
def test_int_validator_fails(field):
with pytest.raises(ValidationException):
IntValidator().validate(field)
def perform_validation(filename):
validators = {
'filename': [
NotEmptyValidator()
],
"MassiveID" : [
Ignore()
],
'SampleType' : [
SetValidator(valid_set=['animal','beverage','blank_analysis','blank_extraction','blank_QC','culture_bacterial','culture_fungal','inanimate_object','environmental','built_environment','food','plant','reference material','culture_mammalian','culture_multiplespecies'])
],
'SampleTypeSub1' : [
SetValidator(valid_set=['biofluid','food_source_animal','tissue','beverage_nonalcoholic','beverage_alcoholic','blank_analysis','blank_extraction','bacterial culture','blank_QC','culture_bacterial','culture_fungal','mobile phone','keys','computer','purse_or_wallet','clothing','dissolvedorganicmatter_soil','dissolvedorganicmatter_water_saline','house','marine_invertebrates_insitu','marine_cyanobacteria_insitu','food_source_plant','food_source_complex','food_source_fungi','food_source_NOS','plant_angiospermae','plant_NOS','reference material_personalcareproduct','reference material_animalfeedorsupplement','reference material_chemicalstandard','reference material_collectionmaterial_microtubes','reference material_collectionmaterial_wellplates','not specified','not applicable','culture_mammalian','culture_multiplespecies','office','research lab','commercial_building','hospital'])
],
'NCBITaxonomy' : [
SetValidator(valid_set=['1003843|Halcyon smyrnensis','100858|Threskiornis aethiopicus','10088|Mus','10114|Rattus','10157|Myocastor coypus','1027292|Sporosarcina newyorkensis','1032505|Fusobacterium sp. OBRC1','1046468|Euphorbia hyssopifolia','1046491|Euphorbia ophthalmica','1054213|Acetobacteraceae bacterium AT-5844','1073351|Bacteroides stercoris','1073372|Streptococcus parasanguinis','1073373|Streptococcus sanguinis','1073376|Ruminococcus lactaris','1078085|Paenisporosarcina sp. HGH0030','1078764|Corynebacterium sp. HFH0082','1087772|Euphorbia nicaeensis','1087776|Euphorbia pithyusa','1095733|Streptococcus parasanguinis','109689|Chaetodon ephippium','109695|Chaetodon melannotus','109712|Pomacanthus navarchus','1100072|Eudistoma vannamei','110196|Bitis atropos','1105031|Clostridium sp. MSTE9','110555|Myxine','1111133|Peptoniphilus sp. BV3AC2','1111134|Peptoniphilus sp. BV3C26','1111454|Megasphaera sp. BV3C16-1','1115805|Staphylococcus epidermidis','1125693|Proteus mirabilis','1125694|Proteus mirabilis','1125718|Actinomyces massiliensis','1125724|Rothia aeria','1125778|Lachnoanaerobaculum sp. OBRC5-5','1129970|Euphorbia ammak','1129973|Euphorbia balsamifera subsp. balsamifera','1129992|Euphorbia fiherenensis','1129997|Euphorbia gymnocalycioides','1134785|Enterococcus faecalis','1134804|Enterococcus faecium','1134811|Enterococcus faecium','1134817|Enterococcus faecium','1134820|Enterococcus faecium','1134822|Enterococcus faecium','1134827|Enterococcus faecium','1134842|Staphylococcus aureus','113544|Arapaima gigas','1138341|Euphorbia bubalina','1138348|Euphorbia lactea','1138350|Euphorbia mammillaris','1138355|Euphorbia ornithopus','115645|Ducula bicolor','1161409|Bifidobacterium sp. MSTE12','1161413|Streptococcus sp. ACC21','1161414|Streptococcus sp. BS21','1161415|Streptococcus sp. BS29a','1161416|Streptococcus sp. SR1','1190621|Olsenella uli','119419|Tauraco schalowi','1203540|Bifidobacterium breve','1203544|Klebsiella pneumoniae','1203545|Klebsiella pneumoniae','1203546|Klebsiella pneumoniae','1203549|Microbacterium sp. oral taxon 186','1203550|Prevotella oralis','1203578|Pseudomonas sp. HPB0071','121123|Alouatta sara','1226325|Clostridium sp. KLE 1755','1227262|Actinomyces johnsonii','1227272|Porphyromonas sp. oral taxon 278','1227275|Streptococcus sobrinus','1243780|Pelecanus occidentalis californicus','1261057|Gardnerella vaginalis','1261058|Gardnerella vaginalis','1261059|Gardnerella vaginalis','1261061|Gardnerella vaginalis','1261062|Gardnerella vaginalis','1261063|Gardnerella vaginalis','1261064|Gardnerella vaginalis','1261065|Gardnerella vaginalis','1261066|Gardnerella vaginalis','1261067|Gardnerella vaginalis','1261068|Gardnerella vaginalis','1261071|Gardnerella vaginalis','1261072|Bifidobacterium breve','1280|Staphylococcus aureus','1297064|Trichechus manatus manatus','130080|Oculina patagonica','1321778|Clostridiales bacterium oral taxon 876','1334443|Chamaesyce','13442|Coffea','13489|Dicentrarchus labrax','1382|Atopobium parvulum','1386|Bacillus','1390567|Ptilinopus cinctus','1423|Bacillus subtilis','147464|Dinornis giganteus','1502|Clostridium perfringens','1543402|Geocapromys brownii','154990|Euphorbia helioscopia','168694|Salinispora','1696|Brevibacterium','170820|Hemiscyllium ocellatum','1715253|Trichoderma sp.','175825|Aceros corrugatus','184245|Tomistoma schlegelii','187114|Ducula aenea','1883|Streptomyces','190893|Vibrio coralliilyticus','194526|Gegeneophis ramaswamii','195635|Pleuronichthys verticalis','2013|Nocardiopsis','202946|Apteryx australis mantelli','209321|Euphorbia cylindrifolia','209333|Euphorbia alluaudii','209356|Euphorbia stenoclada','212836|Euphorbia prostrata','212842|Euphorbia abdelkuri','212844|Euphorbia acanthothamnos','212900|Euphorbia graminea','212925|Euphorbia lathyris','212941|Euphorbia myrsinites','212944|Euphorbia obesa','212960|Euphorbia platyclada','212981|Euphorbia sipolisii','213002|Euphorbia weberbaueri','213047|Euphorbia globosa','216475|Euphorbia dentata','216478|Euphorbia ingens','216816|Bifidobacterium longum','216998|Euphorbia jansenvillensis','216999|Euphorbia horrida','227231|Himantopus mexicanus','241562|Amazona leucocephala','2711|Citrus sinensis','28125|Prevotella bivia','28713|Lanius ludovicianus','30406|Tragopan blythii','30461|Bubo bubo','311359|Cochoa','318061|Euphorbia thymifolia','318062|Euphorbia hirta','334663|Euphorbia aeruginosa','334676|Euphorbia grandicornis','334689|Euphorbia neriifolia','33589|Leptoptilos crumeniferus','34433|Leucoagaricus','34720|Trachymyrmex septentrionalis','357276|Bacteroides dorei','3635|Gossypium hirsutum','3702|Arabidopsis thaliana','37083|Eudyptula minor','3750|Malus domestica','37578|Morus bassanus','377254|Megophrys nasuta','381107|Cinnyricinclus leucogaster','38626|Phascolarctos cinereus','38843|Euphorbia amygdaloides','38844|Euphorbia cyparissias','38845|Euphorbia dendroides','38846|Euphorbia peplus','38847|Euphorbia segetalis','403904|Onychostoma angustistomata','40833|Bucephala islandica','411481|Bifidobacterium adolescentis','411486|Clostridium sp. M62/1','41691|Cygnus melancoryphus','43311|Fratercula cirrhata','43490|Gyps africanus','435830|Actinomyces graevenitzii','435832|Neisseria mucosa','435838|Staphylococcus caprae','435842|Streptococcus sp. C150','441894|Struthio camelus australis','4441|Camellia','444138|Ducula rufigaster','44489|Carettochelys insculpta','450749|Veillonella sp. 6_1_27','457243|Euphorbia cotinifolia','457387|Bacteroides sp. 1_1_30','457393|Bacteroides sp. 4_1_36','457395|Bacteroides sp. 9_1_42FAA','457396|Clostridium sp. 7_2_43FAA','457402|Eubacterium sp. 3_1_31','457416|Veillonella sp. 3_1_44','457424|Bacteroides fragilis','469586|Bacteroides sp. 1_1_6','469587|Bacteroides sp. 2_1_16','469588|Bacteroides sp. 2_1_22','469592|Bacteroides sp. 3_1_19','469594|Bifidobacterium sp. 12_1_47BFAA','469595|Citrobacter sp. 30_2','469597|Coprobacillus sp. 8_2_54BFAA','469598|Escherichia sp. 3_2_53FAA','469599|Fusobacterium sp. 2_1_31','469608|Klebsiella sp. 1_1_55','491074|Enterococcus faecalis','491075|Enterococcus faecalis','491076|Lactobacillus crispatus','493209|Atta texana','507972|Ptilopsis granti','51861|Corallus caninus','525278|Enterococcus faecalis','525279|Enterococcus faecium','525329|Lactobacillus jensenii','525341|Lactobacillus reuteri','525361|Lactobacillus rhamnosus','525376|Staphylococcus epidermidis','525377|Staphylococcus lugdunensis','526192|Euphorbia characias subsp. wulfenii','537972|Helicobacter pullorum','545774|Streptococcus gallolyticus','54672|Euphorbia lagascae','553199|Propionibacterium acnes','553209|Enterococcus faecalis','553212|Staphylococcus capitis','556259|Bacteroides sp. D2','556266|Escherichia coli','559301|Lactobacillus gasseri','56072|Ardea herodias','56117|Tapirus bairdii','562971|Achromobacter xylosoxidans','562973|Actinomyces viscosus','562981|Gemella haemolysans','562983|Gemella sanguinis','563032|Rothia dentocariosa','563191|Acidaminococcus sp. D21','563193|Parabacteroides sp. D13','56549|Lycodon semicarinatus','5693|Trypanosoma cruzi','571338|Macrochelys temminckii','575593|Lachnospiraceae bacterium oral taxon 500','575595|Lactobacillus crispatus','575596|Lactobacillus crispatus','575597|Lactobacillus crispatus','575603|Lactobacillus gasseri','575604|Lactobacillus gasseri','575605|Lactobacillus jensenii','575607|Lactobacillus jensenii','575609|Peptoniphilus sp. oral taxon 386','575611|Prevotella buccae','575612|Prevotella melaninogenica','575615|Prevotella sp. oral taxon 317','57571|Salamandra salamandra','585466|Burhinus grallarius','585501|Oribacterium sinus','585538|Helicobacter pylori','585543|Bacteroides sp. D20','596309|Rhodococcus erythropolis','596312|Micrococcus luteus','596317|Staphylococcus epidermidis','596318|Acinetobacter radioresistens','596320|Neisseria flavescens','596322|Streptococcus salivarius','596325|Lactobacillus jensenii','596327|Porphyromonas uenonis','596330|Peptoniphilus lacrimalis','61316|Hypentelium nigricans','619693|Prevotella sp. oral taxon 472','62165|Chlorophanes spiza','629742|Staphylococcus hominis','641149|Neisseria sp. oral taxon 014','649742|Actinomyces odontolyticus','649743|Actinomyces sp. oral taxon 848','649760|Prevotella oris','649761|Prevotella veroralis','651656|Incilius','65559|Euphorbia milii','658080|Ralstonia sp. 5_2_56FAA','658082|Lachnospiraceae bacterium 2_1_58FAA','658085|Lachnospiraceae bacterium 5_1_57FAA','658087|Lachnospiraceae bacterium 7_1_58FAA','658663|Porphyromonas sp. 31_2','661087|Olsenella sp. oral taxon 809','665937|Anaerostipes sp. 3_2_56FAA','665944|Klebsiella sp. 4_1_44FAA','665945|Lactobacillus sp. 7_1_47FAA','665948|Pseudomonas sp. 2_1_26','665952|Bacillus smithii','665953|Bacteroides eggerthii','665954|Bacteroides ovatus','679189|Prevotella timonensis','679191|Prevotella amnii','679193|Propionibacterium acnes','679196|Lactobacillus gasseri','679198|Aggregatibacter aphrophilus','679202|Escherichia coli','679204|Escherichia coli','679205|Escherichia coli','679206|Escherichia coli','681183|Astrapia mayeri','689|Vibrio mediterranei','693991|Fusobacterium nucleatum','699185|Enterococcus faecalis','699186|Enterococcus faecalis','702437|Selenomonas noxia','702439|Prevotella nigrescens','704175|Phoenicoparrus minor','706437|Streptococcus anginosus','7102|Helicoverpa virescens','71240|eudicotyledons','740693|Cephaloscyllium ventriosum','742722|Collinsella sp. 4_8_47FAA','742730|Citrobacter freundii','742732|[Clostridium] bolteae','742735|Clostridium clostridioforme','742736|Clostridium clostridioforme','742737|Clostridium hathewayi','742738|Clostridium orbiscindens','742740|Clostridium symbiosum','742741|Clostridium symbiosum','749491|Enterococcus faecalis','749523|Enterococcus faecium','749527|Escherichia coli','749529|Escherichia coli','749531|Escherichia coli','749535|Klebsiella sp. MS 92-3','749536|Escherichia coli','749537|Escherichia coli','749542|Escherichia coli','749548|Escherichia coli','749549|Escherichia coli','749550|Escherichia coli','75024|Holacanthus ciliaris','754025|Staphylococcus aureus','754026|Staphylococcus aureus','75988|Pachymedusa dacnicolor','762963|Actinomyces sp. oral taxon 170','762965|Haemophilus sp. oral taxon 851','765065|Propionibacterium acnes','765066|Propionibacterium acnes','765067|Propionibacterium acnes','765068|Propionibacterium acnes','765069|Propionibacterium acnes','765070|Propionibacterium acnes','765071|Propionibacterium acnes','765072|Propionibacterium acnes','765073|Propionibacterium acnes','765074|Propionibacterium acnes','765077|Propionibacterium acnes','765079|Propionibacterium acnes','765080|Propionibacterium acnes','765084|Propionibacterium acnes','765085|Propionibacterium acnes','765089|Propionibacterium acnes','765090|Propionibacterium acnes','765091|Propionibacterium acnes','765092|Propionibacterium acnes','765093|Propionibacterium acnes','765095|Propionibacterium acnes','765096|Propionibacterium acnes','765097|Propionibacterium acnes','765098|Propionibacterium acnes','765099|Propionibacterium acnes','765100|Propionibacterium acnes','765101|Propionibacterium acnes','765102|Propionibacterium acnes','765103|Propionibacterium acnes','765104|Propionibacterium acnes','765105|Propionibacterium acnes','765106|Propionibacterium acnes','765107|Propionibacterium acnes','765108|Propionibacterium acnes','765109|Propionibacterium acnes','765110|Propionibacterium acnes','765111|Propionibacterium acnes','765112|Propionibacterium acnes','765113|Propionibacterium acnes','765114|Propionibacterium acnes','765115|Propionibacterium acnes','765116|Propionibacterium acnes','765117|Propionibacterium acnes','765118|Propionibacterium acnes','765119|Propionibacterium acnes','765121|Propionibacterium acnes','765122|Propionibacterium acnes','765123|Propionibacterium acnes','767100|Parvimonas sp. oral taxon 110','768724|Peptoniphilus sp. oral taxon 836','78394|Eptatretus cirrhatus','7897|Latimeria chalumnae','797473|Cardiobacterium valvarum','797515|Lactobacillus parafarraginis','797516|Lactobacillus kisonensis','81903|Fulica americana','83391|Coryphaenoides cinereus','8450|Hypogeophis rostratus','8467|Caretta caretta','8503|Crocodylus novaeguineae','85101|Urocolius macrourus','8557|Varanus exanthematicus','857291|Prevotella histicola','86377|Taeniura lymma','864566|Campylobacter coli','8682|Hydrophis schistosus','873517|Capnocytophaga ochracea','8790|Dromaius novaehollandiae','879296|Lactobacillus iners','879301|Lactobacillus iners','879302|Lactobacillus iners','879304|Lactobacillus iners','879307|Gardnerella vaginalis','879309|Veillonella sp. oral taxon 158','8797|Rhea americana','8801|Struthio camelus','883109|Eubacterium infirmum','883116|Klebsiella oxytoca','883117|Klebsiella oxytoca','883118|Klebsiella oxytoca','883119|Klebsiella oxytoca','883120|Klebsiella oxytoca','883121|Klebsiella oxytoca','883123|Klebsiella oxytoca','883124|Klebsiella oxytoca','883125|Klebsiella oxytoca','883167|Streptococcus intermedius','8863|Coscoroba coscoroba','888050|Actinomyces cardiffensis','888051|Actinomyces sp. oral taxon 178','8884|Oxyura jamaicensis','888825|Streptococcus sanguinis','888826|Campylobacter upsaliensis','888827|Arcobacter butzleri','8924|Vultur gryphus','8961|Aquila audax','904293|Streptococcus downei','904306|Streptococcus vestibularis','908340|Clostridium sp. HGF2','91789|Capito niger','9258|Ornithorhynchus anatinus','92683|Spheniscus demersus','928327|Lactobacillus iners','9316|Macropus fuliginosus','936556|Peptostreptococcaceae bacterium AS15','936562|Fusobacterium sp. CM21','936563|Fusobacterium sp. CM22','936565|Klebsiella sp. OBRC7','936575|Streptococcus sp. AC15','936576|Streptococcus sp. ACS2','936578|Streptococcus sp. AS20','936580|Streptococcus sp. CM6','936581|Streptococcus sp. CM7','936587|Streptococcus sp. OBRC6','936588|Veillonella sp. ACP1','936589|Veillonella sp. AS16','936594|Lachnoanaerobaculum sp. ICM7','944562|Lactobacillus oris','944564|Veillonella sp. oral taxon 780','9600|Pongo pygmaeus','9606|H**o sapiens','9636|Melursus ursinus','9755|Physeter catodon','979202|Staphylococcus epidermidis','979203|Staphylococcus epidermidis','979211|Staphylococcus epidermidis','979213|Staphylococcus epidermidis','979214|Staphylococcus epidermidis','979215|Staphylococcus epidermidis','979216|Staphylococcus epidermidis','979217|Staphylococcus epidermidis','979218|Staphylococcus epidermidis','979219|Staphylococcus epidermidis','979221|Staphylococcus epidermidis','979222|Staphylococcus epidermidis','9913|Bos taurus','997346|Desmospora sp. 8437','997873|Bacteroides caccae','997874|Bacteroides cellulosilyticus','997875|Bacteroides dorei','997876|Bacteroides dorei','997879|Bacteroides fragilis','997882|Bacteroides fragilis','997883|Bacteroides fragilis','997887|Bacteroides salyersiae','997888|Bacteroides finegoldii','997891|Bacteroides vulgatus','999414|Fusobacterium nucleatum','999419|Parabacteroides johnsonii','999420|Parabacteroides merdae','999421|Parabacteroides merdae','999427|Treponema denticola','999440|Treponema denticola','none specified|Euherdmania','not applicable','not collected','not specified','not specified|Euphorbia pithyusa ssp. cupanii'])
],
'YearOfAnalysis' : [
IntValidator(),
RangeValidator(low=2000, high=2030)
],
'SampleCollectionMethod' : [
SetValidator(valid_set=['blood draw, capillary','blood draw, venous','blood NOS','liquid','not applicable','solid material, dried','solid material, fresh','solid material, frozen','swabs, dry','swabs, moist (50% EtOH)','urine, 24-hour','urine, NOS','urine, spot','extract, solid phase extraction (C18)','liquid, solid phase extraction (C18)','solid, solid phase extraction (C18)','solid material, NOS','not specified','liquid, solid phase extraction (PPL)'])
],
"SampleExtractionMethod" : [
SetValidator(valid_set=['ethanol-water (9:1)','methanol-water (1:1)','dichloromethane-methanol (2:1)','ethanol-water (19:1)','water (94_deg_C)','water (95_deg_C)','water (100%) (deg_C_NOS)','chloroform-methanol-water (1:3:1)','methanol (100%)','ethanol (100%)','ethanol-water (1:1)','water-acetonitrile (250:1)','methanol-acetonitrile (3:7)','methanol-water (4:1)','methanol-water (9:1)','not collected','ethyl acetate (100%)','methanol-water (7:3)','water-acetonitrile (149:1)','not specified','methanol-water (3:2)','acetonitrile (100%)','acetonitrile-water (7:3)','acetonitrile-methanol (1:1)','acetonitrile-isopropanol-water (3:3:2)','dichloromethane-methanol (3:1)'])
],
'InternalStandardsUsed' : [
SetValidator(valid_set=['sulfamethizole;sulfachloropyridazine','sulfamethazine','sulfamethazine;sulfadimethoxine','sulfadimethoxine','sulfamethizole;sulfachloropyridazine;sulfadimethoxine;sulfamethazine;coumarin-314;amitryptiline','amitryptiline','none','fluconazole','amitryptiline;fluconazole','sulfadimethoxine;sulfachloropyridazine','cholic_acid-d4;lithocholic_acid-d4','cocaine;cocaine-d3','cocaine-d3','sulfamethizole','not specified'])
],
'MassSpectrometer' : [
SetValidator(valid_set=['impact|MS:1002077','impact HD|MS:1002667','Q Exactive|MS:1001911','Q Exactive Plus|MS:1002634','micrOTOF-Q II|MS:1000704','not specified','6540 Q-TOF LC/MS|MS:1002789','LTQ Orbitrap XL|MS:1000556','maXis II|MS:1003004'])
],
'IonizationSourceAndPolarity' : [
SetValidator(valid_set=['electrospray ionization (positive)','electrospray ionization (negative)','atmospheric pressure chemical ionization (positive)','atmospheric pressure chemical ionization (negative)','atmospheric pressure photoionization (positive)','atmospheric pressure photoionization (negative)','electrospray ionization (alternating)','not specified'])
],
'ChromatographyAndPhase' : [
SetValidator(valid_set=['reverse phase (C18)','reverse phase (C8)','reverse phase (Phenyl-Hexyl)','normal phase (HILIC)','mixed mode (Scherzo SM-C18)','not specified'])
],
'BiologicalSex': [
SetValidator(valid_set=['female','male','asexual','not collected','not applicable','not specified'])
],
'Country': [
SetValidator(valid_set=['not applicable','not collected','not specified','Afghanistan','Albania','Algeria','Andorra','Angola','Antigua and Barbuda','Argentina','Armenia','Australia','Austria','Azerbaijan','Bahamas','Bahrain','Bangladesh','Barbados','Belarus','Belgium','Belize','Benin','Bhutan','Bolivia','Bosnia and Herzegovina','Botswana','Brazil','Brunei','Bulgaria','Burkina Faso','Burundi','Cabo Verde','Cambodia','Cameroon','Canada','Central African Republic (CAR)','Chad','Chile','China','Colombia','Comoros','Congo, Democratic Republic of the','Congo, Republic of the','Costa Rica','Cote dIvoire','Croatia','Cuba','Cyprus','Czechia','Denmark','Djibouti','Dominica','Dominican Republic','Ecuador','Egypt','El Salvador','Equatorial Guinea','Eritrea','Estonia','Eswatini (formerly Swaziland)','Ethiopia','Fiji','Finland','France','Gabon','Gambia','Georgia','Germany','Ghana','Greece','Grenada','Guatemala','Guinea','Guinea-Bissau','Guyana','Haiti','Honduras','Hungary','Iceland','India','Indonesia','Iran','Iraq','Ireland','Israel','Italy','Jamaica','Japan','Jordan','Kazakhstan','Kenya','Kiribati','Kosovo','Kuwait','Kyrgyzstan','Laos','Latvia','Lebanon','Lesotho','Liberia','Libya','Liechtenstein','Lithuania','Luxembourg','Madagascar','Malawi','Malaysia','Maldives','Mali','Malta','Marshall Islands','Mauritania','Mauritius','Mexico','Micronesia','Moldova','Monaco','Mongolia','Montenegro','Morocco','Mozambique','Myanmar (formerly Burma)','Namibia','Nauru','Nepal','Netherlands','New Zealand','Nicaragua','Niger','Nigeria','North Korea','North Macedonia (formerly Macedonia)','Norway','Oman','Pakistan','Palau','Palestine','Panama','Papua New Guinea','Paraguay','Peru','Philippines','Poland','Portugal','Qatar','Romania','Russia','Rwanda','Saint Kitts and Nevis','Saint Lucia','Saint Vincent and the Grenadines','Samoa','San Marino','Sao Tome and Principe','Saudi Arabia','Senegal','Serbia','Seychelles','Sierra Leone','Singapore','Slovakia','Slovenia','Solomon Islands','Somalia','South Africa','South Korea','South Sudan','Spain','Sri Lanka','Sudan','Suriname','Sweden','Switzerland','Syria','Taiwan','Tajikistan','Tanzania','Thailand','Timor-Leste','Togo','Tonga','Trinidad and Tobago','Tunisia','Turkey','Turkmenistan','Tuvalu','Uganda','Ukraine','United Arab Emirates','United Kingdom','United States of America','Uruguay','Uzbekistan','Vanuatu','Vatican City (Holy See)','Venezuela','Vietnam','Yemen','Zambia','Zimbabwe','Isle of Man','Jersey','Czech Republic','not specified','not applicble'])
],
'HumanPopulationDensity' : [
SetValidator(valid_set=['Urban','Rural','not collected','not applicable','not specified'])
],
'LifeStage' : [
SetValidator(valid_set=['not applicable','not collected','Infancy (<2 yrs)','Early Childhood (2 yrs < x <=8 yrs)','Adolescence (8 yrs < x <= 18 yrs)','Early Adulthood (18 yrs < x <= 45 yrs)','Middle Adulthood (45 yrs < x <= 65 yrs)','Later Adulthood (>65 yrs)','not specified'])
],
'UBERONOntologyIndex' : [
SetValidator(valid_set=['UBERON:0001353','UBERON:0002427','UBERON:0015474','UBERON:0001970','UBERON:0000178','UBERON:0001969','UBERON:0001977','UBERON:0001153','UBERON:0001091','UBERON:0004148','UBERON:0001621','UBERON:0001555','UBERON:0001988','UBERON:0002110','UBERON:0012180','UBERON:0004907','UBERON:0002048','UBERON:0001045','UBERON:0001913','UBERON:0001707','not applicable','UBERON:0000167','UBERON:0002012','UBERON:0002016','UBERON:0001836','UBERON:0001511','UBERON:0001519','UBERON:0001513','UBERON:0001085','UBERON:0007311','UBERON:0004908','UBERON:0001088','UBERON:0000996','UBERON:0000955','UBERON:0002097','UBERON:0002387','UBERON:0001690','UBERON:0002106','UBERON:0002107','UBERON:0001264','UBERON:0000945','UBERON:0002114','UBERON:0002115','UBERON:0002116','UBERON:0001155','UBERON:0018707','UBERON:0002113','UBERON:0002369','UBERON:0000992','UBERON:0000995','UBERON:0000002','UBERON:0000948','UBERON:0003126','UBERON:0001043','UBERON:0002370','not applicable','UBERON:0002097'])
],
'DOIDOntologyIndex' : [
SetValidator(valid_set=['DOID:1485','DOID:9351','disease NOS','DOID:10763','DOID:0050589','no disease reported','not applicable','DOID:8893','no DOID avaliable','no DOID avaliable','DOID:12140','DOID:9970','DOID:12155','DOID:8778','DOID:13378','DOID:0050338','no DOID avaliable','no DOID avaliable','no DOID avaliable','not applicable','DOID:8577','DOID:216'])
]
}
my_validator = Vlad(source=LocalFile(filename),delimiter="\t",ignore_missing_validators=True,validators=validators)
passes_validation = my_validator.validate()
errors_list = []
for column in my_validator.failures:
for line_number in my_validator.failures[column]:
error_dict = {}
error_dict["header"] = column
error_dict["line_number"] = line_number + 1 #0 Indexed with 0 being the header row
error_dict["error_string"] = str(my_validator.failures[column][line_number])
errors_list.append(error_dict)
for missing_field in my_validator.missing_fields:
error_dict = {}
error_dict["header"] = "Missing Header"
error_dict["line_number"] = "N/A"
error_dict["error_string"] = "Missing column %s" % (missing_field)
errors_list.append(error_dict)
valid_rows = []
row_count = 0
#Read in the good rows
try:
no_validation_lines = [int(error["line_number"]) for error in errors_list]
row_count = 0
with open(filename) as csvfile:
reader = csv.DictReader(csvfile, delimiter="\t")
for row in reader:
row_count += 1
if row_count in no_validation_lines:
continue
valid_rows.append(row)
except:
#raise
print("error reading file")
return passes_validation, my_validator.failures, errors_list, valid_rows, row_count