diff --git a/README.md b/README.md index e4a65c3..3a667e0 100644 --- a/README.md +++ b/README.md @@ -17,14 +17,21 @@ To get ReDU up and running on your local system, it should be as easy as server-compose-interactive ``` +## Unit Testing + +We have unit tests to test the validators. There are several naming conventions: + +1. ```valid_*``` - These are valid files implying passing validation and finding the same number of files in MassIVE +1. ```invalid_*``` - These are invalid files that fail validation +1. ```invaliddata_*``` - These are valid files that pass validation but fail to match with data in MassIVE + ## Updating ReDU Data Procedure One of the key steps in ReDU is the updating of the database to include the latest identifications for files within ReDU. These are the following steps: 1. Download batch template for GNPS at ```/metabatchdump``` 1. Run Batch Workflow for Spectral Library Search -1. Get the set of tasks as tsv and save to [here](https://github.com/mwang87/ReDU-MS2-GNPS/blob/refactor-read-me-for-developers/database/global_tasks.tsv). -1. Remove database [here](https://github.com/mwang87/ReDU-MS2-GNPS/tree/refactor-read-me-for-developers/database) -1. Run XXX command to drop identifications table +1. Get the set of tasks as tsv and save to [here](https://github.com/mwang87/ReDU-MS2-GNPS/blob/master/database/global_tasks.tsv). +1. Remove database [here](https://github.com/mwang87/ReDU-MS2-GNPS/tree/master/database) 1. Start ReDU back up and it will autopopulate diff --git a/code/Makefile b/code/Makefile index 3f9c971..992995e 100644 --- a/code/Makefile +++ b/code/Makefile @@ -37,6 +37,10 @@ server-compose-interactive: docker-compose build docker-compose --log-level DEBUG up +server-compose-background: + docker-compose build + docker-compose up -d + server-compose-production: docker-compose build docker-compose -f docker-compose.yml -f docker-compose-production.yml up -d diff --git a/code/metadata_validator.py b/code/metadata_validator.py index 4beeddb..0dbbaf3 100644 --- a/code/metadata_validator.py +++ b/code/metadata_validator.py @@ -26,6 +26,7 @@ def get_dataset_files(dataset_accession, collection_name): massive_host = ftputil.FTPHost("massive.ucsd.edu", "anonymous", "") dataset_files = ming_proteosafe_library.get_all_files_in_dataset_folder_ftp(dataset_accession, collection_name, massive_host=massive_host) + return dataset_files def perform_validation_against_massive(filename): @@ -43,8 +44,8 @@ def perform_validation_against_massive(filename): all_resolved_filenames = [] for query_filename in metadata["filename"]: - print(query_filename) dataset_filename = resolve_metadata_filename_to_all_files(query_filename, dataset_files) + print(query_filename, dataset_filename) if dataset_filename == None: continue @@ -54,14 +55,20 @@ def perform_validation_against_massive(filename): return True, "Success", len(all_resolved_filenames) def resolve_metadata_filename_to_all_files(filename, dataset_files): - stripped_extension = ming_fileio_library.get_filename_without_extension(filename) + stripped_extension = ming_fileio_library.get_filename_without_extension(filename) + "." + + print(stripped_extension) + + acceptable_filenames = ["f." + dataset_filename for dataset_filename in dataset_files if stripped_extension in dataset_filename] - acceptable_filenames = ["f." + dataset_filename for dataset_filename in dataset_files if dataset_filename.find(stripped_extension) != -1] + print("ACCEPTED", acceptable_filenames) - if len(acceptable_filenames) != 1: - return None + # NOTE: We are revising to not allow ambiguity anymore + if len(acceptable_filenames) == 1: + return acceptable_filenames[0] + return None - return acceptable_filenames[0] + def rewrite_metadata(metadata_filename): @@ -101,7 +108,7 @@ def perform_validation(filename): SetValidator(valid_set=['beverage_alcoholic','beverage_nonalcoholic','biofluid','blank_analysis','blank_culturemedia','blank_extraction','blank_QC','clothing','commercial_building','computer','culture_bacterial','culture_fungal','culture_mammalian','culture_multiplespecies','dissolvedorganicmatter_soil','dissolvedorganicmatter_water_saline','food_source_animal','food_source_complex','food_source_fungi','food_source_NOS','food_source_plant','hospital','house','keys','marine_cyanobacteria_insitu','marine_invertebrates_insitu','mobile phone','not applicable','not specified','office','plant_angiospermae','plant_NOS','purse_or_wallet','reference material_animalfeedorsupplement','reference material_chemicalstandard','reference material_collectionmaterial_microtubes','reference material_collectionmaterial_wellplates','reference material_personalcareproduct','research lab','tissue','frog']) ], '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|Homo 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','73337|Ceratotherium simum simum','70919|Sarcophyton glaucum','205097|Sarcophyton trocheliophorum','358796|Sarcophyton cinereum','1073351|Bacteroides stercoris CC31F','1073356|Clostridium cadaveris CC44_001G','1073357|Clostridium cadaveris CC88A','1073364|Parabacteroides goldsteinii CC87F','1261072|Bifidobacterium breve JCP7499','1321778|Clostridiales sp. F0540','1357382|Bifidobacterium angulatum F16_22','1357384|Catabacter hongkongensis AB8_9','585501|Oribacterium sinus F0268','879307|Gardnerella vaginalis UPII 315-A','457408|Phascolarctobacterium sp. 3_1_syn4','552395|Clostridiales bacterium 4_1_37FAA','457424|Bacteroides fragilis 3_1_12','665953|Bacteroides eggerthii 1_2_48FAA','665954|Bacteroides ovatus 3_8_47FAA','562973|Actinomyces viscosus C505','556260|Bacteroides dorei 5_1_36/D4','216816|Bifidobacterium sp. 12_1_47BFAA','742738|Clostridium orbiscindens 1_3_50AFAA','742731|Clostridium aldenense WAL-18727','742741|Clostridium symbiosum WAL-14673','858694|Bifidobacterium breve EX336960VC18','858695|Bifidobacterium breve EX336960VC19','796942|Stomatobaculum longum ACC2','457404|Fusobacterium ulcerans, 12_1B','999427|Treponema denticola ASLM','999426|Treponema denticola AL-2','411481|Bifidobacterium adolescentis L2-32','997882|Bacteroides fragilis CL07T00C01','997883|Bacteroides fragilis CL07T12C05','997880|Bacteroides fragilis CL05T00C42','997879|Bacteroides fragilis CL03T12C07','997875|Bacteroides dorei CL02T00C15','997877|Bacteroides dorei CL03T12C01','997876|Bacteroides dorei CL02T12C06','997891|Bacteroides vulgatus CL09T03C04','997887|Bacteroides salyersiae CL02T12C01','997874|Bacteroides cellulosilyticus CL02T12C19','997888|Bacteroides finegoldii CL09T03C10','997873|Bacteroides caccae CL03T12C61','999421|Parabacteroides merdae CL09T00C40','999420|Parabacteroides merdae CL03T12C32','999419|Parabacteroides johnsonii CL02T12C29','936595|Clostridiales sp. OBRC5-5','187327|Acidaminococcus sp. D21','1161743|Bifidobacterium longum subsp. longum 44B','1161744|Bifidobacterium longum subsp. longum 1-6B','1161904|Bifidobacterium longum subsp. longum 35B','1161745|Bifidobacterium longum subsp. longum 2-2B','100884|Coprobacillus sp. D6 (29_1)','1203540|Bifidobacterium breve HPH0326','1125704|Lachnospiraceae sp. CC70A','1073358|Clostridium orbiscindens CC43_001K','1073374|Parvimonas micra CC57A','1261057|Gardnerella vaginalis JCP7275','1261058|Gardnerella vaginalis JCP7276','1261059|Gardnerella vaginalis JCP7659','1261060|Gardnerella vaginalis JCP7672','1261061|Gardnerella vaginalis JCP7719','1261062|Gardnerella vaginalis JCP8017A','1261063|Gardnerella vaginalis JCP8017B','1261064|Gardnerella vaginalis JCP8066','1261066|Gardnerella vaginalis JCP8108','1261066|Gardnerella vaginalis JCP8108','1261067|Gardnerella vaginalis JCP8151A','1261068|Gardnerella vaginalis JCP8151B','1261070|Gardnerella vaginalis JCP8481B','1261071|Gardnerella vaginalis JCP8522','1401070|Peptoniphilus lacrimalis DNF00528','596328|Mobiluncus mulieris UPII 28-I','658082|Lachnospiraceae sp. 2_1_58FAA','not specified|Parabacteroides sp. 31_2','661087|Olsenella sp. F0356','767100|Parvimonas sp. 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ICM7','1134785|Enterococcus faecalis ERV103','1134804|Enterococcus faecium 503','1134811|Enterococcus faecium 513','1134817|Enterococcus faecium E417','1134820|Enterococcus faecium ERV102','1134822|Enterococcus faecium ERV165','1134827|Enterococcus faecium ERV99','1204474|Fusobacterium nucleatum CTI-01','1204476|Fusobacterium nucleatum CTI-03','1316587|Fusobacterium nucleatum CTI-06','1073365|Peptostreptococcus sp. CC14N','1073366|Prevotella nigrescens CC14M','1227272|Porphyromonas sp. W7784','1287476|Prevotella bivia DNF00188','1401067|Veillonella montpellierensis DNF00314','1401072|Prevotella bivia DNF00650','1401075|Prevotella disiens DNF00882','1401077|Prevotella denticola DNF00960','553199|Propionibacterium acnes SK137','679189|Prevotella timonensis CRIS 5C-B1','679191|Prevotella amnii CRIS 21A-A','619693|Prevotella sp. 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AS15','997829|Porphyromonas sp. KLE1280','553198|Propionibacterium acidifaciens F0233','575612|Prevotella melaninogenica D18','1203550|Prevotella oralis HGA0225','1203554|Sutterella wadsworthensis HGA0223','649761|Prevotella veroralis F0319','649760|Prevotella oris F0302','1163663|Plagiodontia aedium','41691|Oxyura jamaicensis','54359|Psophia crepitans','187124|Goura victoria','1244804|Penelopides manillae manillae','8839|Anas platyrhynchos','187121|Gallicolumba luzonica','56291|Coracias','177143|Columba pulchricollis','8930|Columbidae','8832|Aix galericulata','175844|Bycanistes bucinator','57387|Momotidae','30415|Grus japonensis','30385|Aythya americana','119412|Musophaga rossae','54359|Psophia crepitans','119417|Tauraco livingstonii','47245|Zenaida macroura','135635|Streptopelia senegalensis','121526|Criniferoides leucogaster','33576|Plegadis ridgwayi','57412|Colius striatus','1496258|Halcyon pileata','57426|Momotus momota','103954|Corythaeola cristata','175830|Buceros bicornis','175832|Ceratogymna 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thula','8889|Tadorna radjah','658917|Lophonetta specularioides specularioides','1706834|Anastomus','2231447|Halcyon albiventris','54132|Pygathrix','75843|Anas erythrorhyncha','67940|Nanger dama','66444|Oreotragus oreotragus','344753|Oryx beisa','9495|Callimico goeldii','335483|Eudocimus ruber','52779|Leptoptilos javanicus','63824|Ozotoceros bezoarticus','561742|Naemorhedus griseus','9333|Pseudocheirus peregrinus','9904|Bos gaurus','9301|Sminthopsis crassicaudata','439328|Giraffa tippelskirchi','28735|Macroscelididae','54601|Macaca silenus','9261|Tachyglossus aculeatus','36241|Ciconia nigra','9592|Gorilla','54600|Macaca nigra','561742|Naemorhedus griseus','56640|Bubalus quarlesi','1343485|Coracias benghalensis','38605|Didelphimorphia','72540|Capra caucasica','30531|Axis axis','52780|Mycteria cinerea','38605|Didelphimorphia','219518|Megalaima virens','9330|Wallabia bicolor','75569|Cercocebus chrysogaster','69308|Eudorcas thomsonii','9825|Sus scrofa domesticus','30602|Eulemur macaco','37737|Perameles gunnii','30591|Aotus azarai','509052|Ovis orientalis gmelini','69298|Tragelaphus spekii','9917|Boselaphus tragocamelus','1088130|Rusa timorensis','47180|Mirza coquereli','659500|Bos javanicus javanicus','59523|Antidorcas marsupialis','38605|Didelphimorphia','52785|Ephippiorhynchus senegalensis','13557|Hapalemur griseus','34825|Propithecus verreauxi','8833|Aix sponsa','59515|Addax nasomaculatus','1143719|Cervus nippon mantchuricus','9832|Hippopotamus','65612|Isoodon obesulus','36224|Cercopithecus diana','37179|Hemitragus jemlahicus','186613|Toxicodryas pulverulenta','509052|Ovis orientalis gmelini','662561|Rusa unicolor','59523|Antidorcas marsupialis','9848|Tragulus napu','9888|Muntiacus muntjak','52231|Callithrix geoffroyi','9597|Pan paniscus','75877|Pteronetta hartlaubii','9917|Boselaphus tragocamelus','59544|Raphicerus campestris','344753|Oryx beisa','9521|Saimiri sciureus','1579530|Cercopithecus sclateri','37174|Ovis canadensis','47178|Eulemur fulvus collaris','9849|Tragulus javanicus','43332|Elaphurus davidianus','9460|Cheirogaleus medius','30611|Otolemur garnettii','509052|Ovis orientalis gmelini','9462|Galago','9599|Pongo','30588|Leontopithecus rosalia','9556|Papio cynocephalus','57737|Axis porcinus','1874132|Bison bonasus caucasicus','9822|Sus','9544|Macaca mulatta','72542|Capra ibex','9940|Ovis aries','59534|Oryx dammah','68415|Moschus moschiferus','9447|Lemur catta','69298|Tragelaphus spekii','9947|Tragelaphus imberbis','72540|Capra caucasica','509052|Ovis orientalis gmelini','415978|Sus scrofa scrofa','9597|Pan paniscus','164931|Cervus hanglu bactrianus','9897|Aepyceros melampus','9945|Tragelaphus oryx','9598|Pan troglodytes','9548|Macaca radiata','34875|Saiga tatarica','144737|Cervus elaphus barbarus','1088058|Przewalskium albirostris','59542|Pseudois nayaur','59527|Beatragus hunteri','9470|Nycticebus coucang','9511|Ateles sp.','9499|Alouatta','34873|Oreamnos americanus','34875|Saiga tatarica','43777|Pithecia 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specularis','75875|Marmaronetta angustirostris','8882|Neochen jubata','75844|Mareca falcata','8887|Sarkidiornis melanotos','45640|Nettapus','1965262|Ducula forsteni','56278|Sibirionetta formosa','28680|Anas acuta ','91879|Kobus leche kafuensis','72544|Capra sibirica','8872|Dendrocygna arcuata','658921|Netta erythrophthalma','1390996|Ptilinopus ornatus','757429|Platalea flavipes','30388|Chauna torquata','9689|Panthera leo','60182|Dendrocygna javanica','9247|Turnix','118783|Actophilornis africanus','54506|Irediparra gallinacea','33581|Scopus umbretta','30387|Netta rufina','187139|Ptilinopus superbus','1391001|Ptilinopus porphyreus','117000|Phoenicopterus chilensis','30389|Ardea','1158920|Ardeola grayii','189533|Aythya affinis','75865|Tadorna tadorna','110620|Ardea alba','796400|Ptilinopus magnificus','279934|Bucephala albeola','2316026|Vanellus albiceps','187116|Ducula zoeae','1390574|Ptilinopus iozonus','1390575|Ptilinopus jambu','110682|Egretta caerulea','1390577|Ptilinopus 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grisegena','472786|Campylopterus hemileucurus','239374|Cymbirhynchus macrorhynchos','9943|Ovis dalli','1200961|Dendrocitta vagabunda','261969|Dicrurus macrocercus','9807|Ceratotherium simum','285011|Pteroglossus viridis','240722|Pogoniulus chrysoconus','9234|Aptenodytes patagonicus','94188|Cryptoprocta ferox','40181|Alectoris philbyi','39958|Lophorina superba','254645|Prionops plumatus','175936|Euphonia hirundinacea','722595|Sporophila corvina','175135|Psarisomus dalhousiae','237439|Stelgidopteryx serripennis','397309|Pitta moluccensis','39638|Agelaius phoeniceus','205797|Platylophus galericulatus','110227|Eristicophis macmahoni','142467|Baeolophus inornatus','1948888|Kittacincla malabarica','247516|Lagonosticta virata','266349|Entomyzon cyanotis','1216351|Bitis parviocula','414897|Erythrura hyperythra','9126|Passeriformes','201348|Minla ignotincta','190696|Myiarchus cinerascens','8697|Cerastes cerastes','1892170|Crithagra mozambica','9162|Pitta','125280|Laniarius 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muricata','1561750|Banisteriopsis stellaris','1816322|Banisteriopsis variabilis','1561751|Banisteriopsis vernoniifolia','151797|Blepharandra heteropetala','1027080|Blepharandra hypoleuca','1561753|Bronwenia megaptera','1561762|Bunchosia montana','1561763|Bunchosia pallescens','1027102|Byrsonima coccolobifolia','4270|Byrsonima crassifolia','1801580|Byrsonima intermedia','1472305|Byrsonima ligustrifolia','1801593|Byrsonima sericea','883765|Byrsonima spicata','1801599|Byrsonima verbascifolia','1027110|Callaeum antifebrile','1027114|Callaeum psilophyllum','151851|Carolus chasei','1027120|Christianella multiglandulosa','1801601|Diacidia aracaensis','1027122|Dicella bracteosa','1027124|Dicella macroptera','1027129|Diplopterys pubipetala','151817|Ectopopterys soejartoi','1027132|Galphimia brasiliensis','151825|Gaudichaudia albida','151830|Heladena multiflora','259657|Heteropterys bicolor','1027142|Heteropterys brachiata','259658|Heteropterys byrsonimifolia','259661|Heteropterys chrysophylla','176641|Heteropterys leona','1027148|Heteropterys leschenaultiana','259665|Heteropterys pauciflora','151834|Hiptage benghalensis','1125931|Hiraea reclinata','1027163|Janusia janusioides','151842|Janusia mediterranea','1561795|Janusia schwannioides','1027172|Malpighia mexicana','151854|Mascagnia sepium','151857|Mcvaughia bahiana','1027193|Niedenzuella acutifolia','1816324|Niedenzuella multiglandulosa','1816325|Niedenzuella poeppigiana','1027194|Niedenzuella sericea','151855|Niedenzuella stannea','1027196|Peixotoa cordistipula','151863|Peixotoa glabra','1561815|Peixotoa hispidula','1027199|Peixotoa reticulata','1561816|Peixotoa tomentosa','151869|Ptilochaeta bahiensis','1027204|Sphedamnocarpus angolensis','1804184|Stigmaphyllon acuminatum','1804185|Stigmaphyllon alternifolium','1804186|Stigmaphyllon angustilobum','1804188|Stigmaphyllon auriculatum','1804190|Stigmaphyllon blanchetii','1804191|Stigmaphyllon bonariense','1804192|Stigmaphyllon caatingicola','1804193|Stigmaphyllon cavernulosum','1027211|Stigmaphyllon ciliatum','1804194|Stigmaphyllon convolvulifolium','1804195|Stigmaphyllon gayanum','1804196|Stigmaphyllon harleyi','1804197|Stigmaphyllon hatschbachii','1804199|Stigmaphyllon lalandianum','1804200|Stigmaphyllon macropodum','2662167|Stigmaphyllon palmatum','151877|Stigmaphyllon paralias','1804201|Stigmaphyllon puberulum','1804202|Stigmaphyllon salzmannii','1804203|Stigmaphyllon saxicola','1804204|Stigmaphyllon sinuatum','1804205|Stigmaphyllon tomentosum','1804206|Stigmaphyllon urenifolium']) + 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. 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ICM7','944562|Lactobacillus oris','944564|Veillonella sp. oral taxon 780','9600|Pongo pygmaeus','9606|Homo 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','73337|Ceratotherium simum simum','70919|Sarcophyton glaucum','205097|Sarcophyton trocheliophorum','358796|Sarcophyton cinereum','1073351|Bacteroides stercoris CC31F','1073356|Clostridium cadaveris CC44_001G','1073357|Clostridium cadaveris CC88A','1073364|Parabacteroides goldsteinii CC87F','1261072|Bifidobacterium breve JCP7499','1321778|Clostridiales sp. F0540','1357382|Bifidobacterium angulatum F16_22','1357384|Catabacter hongkongensis AB8_9','585501|Oribacterium sinus F0268','879307|Gardnerella vaginalis UPII 315-A','457408|Phascolarctobacterium sp. 3_1_syn4','552395|Clostridiales bacterium 4_1_37FAA','457424|Bacteroides fragilis 3_1_12','665953|Bacteroides eggerthii 1_2_48FAA','665954|Bacteroides ovatus 3_8_47FAA','562973|Actinomyces viscosus C505','556260|Bacteroides dorei 5_1_36/D4','216816|Bifidobacterium sp. 12_1_47BFAA','742738|Clostridium orbiscindens 1_3_50AFAA','742731|Clostridium aldenense WAL-18727','742741|Clostridium symbiosum WAL-14673','858694|Bifidobacterium breve EX336960VC18','858695|Bifidobacterium breve EX336960VC19','796942|Stomatobaculum longum ACC2','457404|Fusobacterium ulcerans, 12_1B','999427|Treponema denticola ASLM','999426|Treponema denticola AL-2','411481|Bifidobacterium adolescentis L2-32','997882|Bacteroides fragilis CL07T00C01','997883|Bacteroides fragilis CL07T12C05','997880|Bacteroides fragilis CL05T00C42','997879|Bacteroides fragilis CL03T12C07','997875|Bacteroides dorei CL02T00C15','997877|Bacteroides dorei CL03T12C01','997876|Bacteroides dorei CL02T12C06','997891|Bacteroides vulgatus CL09T03C04','997887|Bacteroides salyersiae CL02T12C01','997874|Bacteroides cellulosilyticus CL02T12C19','997888|Bacteroides finegoldii CL09T03C10','997873|Bacteroides caccae CL03T12C61','999421|Parabacteroides merdae CL09T00C40','999420|Parabacteroides merdae CL03T12C32','999419|Parabacteroides johnsonii CL02T12C29','936595|Clostridiales sp. OBRC5-5','187327|Acidaminococcus sp. D21','1161743|Bifidobacterium longum subsp. longum 44B','1161744|Bifidobacterium longum subsp. longum 1-6B','1161904|Bifidobacterium longum subsp. longum 35B','1161745|Bifidobacterium longum subsp. longum 2-2B','100884|Coprobacillus sp. D6 (29_1)','1203540|Bifidobacterium breve HPH0326','1125704|Lachnospiraceae sp. CC70A','1073358|Clostridium orbiscindens CC43_001K','1073374|Parvimonas micra CC57A','1261057|Gardnerella vaginalis JCP7275','1261058|Gardnerella vaginalis JCP7276','1261059|Gardnerella vaginalis JCP7659','1261060|Gardnerella vaginalis JCP7672','1261061|Gardnerella vaginalis JCP7719','1261062|Gardnerella vaginalis JCP8017A','1261063|Gardnerella vaginalis JCP8017B','1261064|Gardnerella vaginalis JCP8066','1261066|Gardnerella vaginalis JCP8108','1261066|Gardnerella vaginalis JCP8108','1261067|Gardnerella vaginalis JCP8151A','1261068|Gardnerella vaginalis JCP8151B','1261070|Gardnerella vaginalis JCP8481B','1261071|Gardnerella vaginalis JCP8522','1401070|Peptoniphilus lacrimalis DNF00528','596328|Mobiluncus mulieris UPII 28-I','658082|Lachnospiraceae sp. 2_1_58FAA','not specified|Parabacteroides sp. 31_2','661087|Olsenella sp. F0356','767100|Parvimonas sp. F0139','693991|Fusobacterium nucleatum subsp. polymorphum F0401','866779|Finegoldia magna SY01','858663|Lactobacillus jensenii EX849587VC03','858665|Lactobacillus jensenii EX849587VC06','858666|Lactobacillus gasseri EX336960VC01','858668|Lactobacillus gasseri EX336960VC03','858674|Lactobacillus vaginalis EX336960VC05','858669|Lactobacillus gasseri EX336960VC06','858670|Lactobacillus gasseri EX336960VC07','858675|Lactobacillus vaginalis EX336960VC11','858676|Lactobacillus vaginalis EX336960VC12','858672|Lactobacillus gasseri EX336960VC13','858673|Lactobacillus gasseri EX336960VC15','620833|Fusobacterium periodonticum 1_A_54/D10','not specified|Lactobacillus gasseri EX336960VC16','749523|Enterococcus faecium TX0133a04','575609|Peptoniphilus sp. F0131','575593|Lachnospiraceae sp. F0167','999414|Fusobacterium nucleatum subsp. animalis F0419','936594|Lachnospiraceae sp. ICM7','1134785|Enterococcus faecalis ERV103','1134804|Enterococcus faecium 503','1134811|Enterococcus faecium 513','1134817|Enterococcus faecium E417','1134820|Enterococcus faecium ERV102','1134822|Enterococcus faecium ERV165','1134827|Enterococcus faecium ERV99','1204474|Fusobacterium nucleatum CTI-01','1204476|Fusobacterium nucleatum CTI-03','1316587|Fusobacterium nucleatum CTI-06','1073365|Peptostreptococcus sp. CC14N','1073366|Prevotella nigrescens CC14M','1227272|Porphyromonas sp. W7784','1287476|Prevotella bivia DNF00188','1401067|Veillonella montpellierensis DNF00314','1401072|Prevotella bivia DNF00650','1401075|Prevotella disiens DNF00882','1401077|Prevotella denticola DNF00960','553199|Propionibacterium acnes SK137','679189|Prevotella timonensis CRIS 5C-B1','679191|Prevotella amnii CRIS 21A-A','619693|Prevotella sp. 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AS15','997829|Porphyromonas sp. KLE1280','553198|Propionibacterium acidifaciens F0233','575612|Prevotella melaninogenica D18','1203550|Prevotella oralis HGA0225','1203554|Sutterella wadsworthensis HGA0223','649761|Prevotella veroralis F0319','649760|Prevotella oris F0302','1163663|Plagiodontia aedium','41691|Oxyura jamaicensis','54359|Psophia crepitans','187124|Goura victoria','1244804|Penelopides manillae manillae','8839|Anas platyrhynchos','187121|Gallicolumba luzonica','56291|Coracias','177143|Columba pulchricollis','8930|Columbidae','8832|Aix galericulata','175844|Bycanistes bucinator','57387|Momotidae','30415|Grus japonensis','30385|Aythya americana','119412|Musophaga rossae','54359|Psophia crepitans','119417|Tauraco livingstonii','47245|Zenaida macroura','135635|Streptopelia senegalensis','121526|Criniferoides leucogaster','33576|Plegadis ridgwayi','57412|Colius striatus','1496258|Halcyon pileata','57426|Momotus momota','103954|Corythaeola cristata','175830|Buceros bicornis','175832|Ceratogymna 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specularis','75875|Marmaronetta angustirostris','8882|Neochen jubata','75844|Mareca falcata','8887|Sarkidiornis melanotos','45640|Nettapus','1965262|Ducula forsteni','56278|Sibirionetta formosa','28680|Anas acuta ','91879|Kobus leche kafuensis','72544|Capra sibirica','8872|Dendrocygna arcuata','658921|Netta erythrophthalma','1390996|Ptilinopus ornatus','757429|Platalea flavipes','30388|Chauna torquata','9689|Panthera leo','60182|Dendrocygna javanica','9247|Turnix','118783|Actophilornis africanus','54506|Irediparra gallinacea','33581|Scopus umbretta','30387|Netta rufina','187139|Ptilinopus superbus','1391001|Ptilinopus porphyreus','117000|Phoenicopterus chilensis','30389|Ardea','1158920|Ardeola grayii','189533|Aythya affinis','75865|Tadorna tadorna','110620|Ardea alba','796400|Ptilinopus magnificus','279934|Bucephala albeola','2316026|Vanellus albiceps','187116|Ducula zoeae','1390574|Ptilinopus iozonus','1390575|Ptilinopus jambu','110682|Egretta caerulea','1390577|Ptilinopus marchei','371913|Eudocimus albus','317792|Anhinga rufa','8930|Columbidae','8901|Nycticorax nycticorax','1965264|Ducula mullerii','425371|Threskiornis melanocephalus','110687|Syrigma sibilatrix','52777|Ciconia maguari','187115|Ducula pinon','444147|Ptilinopus pulchellus','115625|Ducula','115625|Ducula','1390998|Ptilinopus perlatus','9620|Cerdocyon thous','9708|Odobenus rosmarus divergens','240203|Chionis albus','55040|Urocyon cinereoargenteus','30399|Necrosyrtes monachus','9692|Panthera pardus orientalis','9702|Otariidae','9711|Halichoerus grypus','9718|Pusa hispida','9720|Phoca vitulina','68725|Canis mesomelas','8849|Anser caerulescens','371860|Branta hutchinsii','435638|Phoenicopterus roseus','118793|Rostratula benghalensis','425648|Onychoprion fuscatus','50365|Anser albifrons','425641|Hydroprogne caspia','471862|Sternula antillarum','9690|Panthera onca','35669|Larus argentatus','9612|Canis lupus','223475|Buteo lineatus','13746|Uria aalge','50403|Vanellus','8962|Aquila 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stellio','1240242|Lampropeltis californiae','94880|Lampropeltis zonata pulchra','384065|Crotalus mitchellii','8718|Agkistrodon bilineatus','8770|Tropidolaemus wagleri','8167|Perca flavescens','125877|Crotalus lepidus klauberi','1458430|Dendrelaphis punctulatus','243556|Trimeresurus mcgregori','74366|Elaphe moellendorffi','118651|Anolis trinitatis','8406|Pelophylax ridibundus','39602|Leptopelis vermiculatus','8355|Xenopus laevis','384065|Crotalus mitchellii','94880|Lampropeltis zonata pulchra','8238|Thunnus orientalis','92519|Boiga irregularis','8735|Crotalus ruber','8746|Crotalus cerastes','88087|Protobothrops flavoviridis','864585|Trachylepis affinis','8355|Xenopus laevis','236742|Uromastyx benti','61263|Cerorhinca monocerata','8724|Bothrops jararaca','184449|Stereolepis gigas','8022|Oncorhynchus mykiss','201439|Zamenis longissimus','184544|Crotalus durissus unicolor','64174|Bothrops alternatus','81389|Regalecus glesne','96731|Corucia zebrata','8554|Heloderma 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amblycephala','44492|Chelodina oblonga','1344800|Cacatua tenuirostris','1240242|Lampropeltis californiae','84847|Psarocolius decumanus','338144|Arborophila javanica','230833|Plecturocebus donacophilus','238859|Garrulax poecilorhynchus','48437|Phalaenoptilus nuttallii','1540822|Centrochelys sulcata','256448|Tangara larvata','62198|Euphonia','62087|Tangara gyrola','62166|Chlorophonia','256439|Tangara dowii','1608482|Puma yagouaroundi','451408|Lamprotornis regius','1265749|Forpus xanthops','36263|Cicinnurus regius','1243782|Pelecanus rufescens','338144|Arborophila javanica','371924|Selasphorus sasin','274070|Psittaculirostris desmarestii','9490|Saguinus oedipus','95723|Ramphastos toco','322582|Ramphastos sulfuratus','285011|Pteroglossus viridis','36267|Paradisaea rudolphi','503985|Cyclopsitta diophthalma','91770|Pogonornis bidentatus','31138|Trachemys scripta elegans','335392|Glyptemys insculpta','85066|Corvus brachyrhynchos','44495|Chelus fimbriata','34933|Chlamydera cerviniventris','441677|Euplectes macroura','27787|Eretmochelys imbricata','37040|Gavia stellata','689266|Oreotrochilus melanogaster','240735|Pogonornis melanopterus','98117|Lanius collaris','549727|Litoria splendida × Litoria caerulea','38772|Gopherus agassizii','228316|Cossypha niveicapilla','427697|Niltava davidi','114303|Gymnoderus foetidus','1105364|Euphonia violacea','8475|Chelydra serpentina','9126|Passeriformes','88031|Ptychadena mascareniensis','697287|Euphonia anneae','201335|Leiothrix argentauris','9000|Bonasa umbellus','205797|Platylophus galericulatus','9101|Meleagris ocellata','111975|Setophaga coronata','56790|Pyrrhocorax pyrrhocorax','127930|Myadestes ralloides','36301|Pelecanus onocrotalus','240720|Stactolaema leucotis','681201|Parotia carolae','107205|Dicrurus paradiseus','196027|Chiroxiphia caudata','114367|Pipreola chlorolepidota','240716|Megalaima haemacephala','60713|Mimus polyglottos','317791|Pelecanus conspicillatus','146612|Urile penicillatus','80367|Podiceps grisegena','472786|Campylopterus hemileucurus','239374|Cymbirhynchus macrorhynchos','9943|Ovis dalli','1200961|Dendrocitta vagabunda','261969|Dicrurus macrocercus','9807|Ceratotherium simum','285011|Pteroglossus viridis','240722|Pogoniulus chrysoconus','9234|Aptenodytes patagonicus','94188|Cryptoprocta ferox','40181|Alectoris philbyi','39958|Lophorina superba','254645|Prionops plumatus','175936|Euphonia hirundinacea','722595|Sporophila corvina','175135|Psarisomus dalhousiae','237439|Stelgidopteryx serripennis','397309|Pitta moluccensis','39638|Agelaius phoeniceus','205797|Platylophus galericulatus','110227|Eristicophis macmahoni','142467|Baeolophus inornatus','1948888|Kittacincla malabarica','247516|Lagonosticta virata','266349|Entomyzon cyanotis','1216351|Bitis parviocula','414897|Erythrura hyperythra','9126|Passeriformes','201348|Minla ignotincta','190696|Myiarchus cinerascens','8697|Cerastes cerastes','1892170|Crithagra mozambica','9162|Pitta','125280|Laniarius ferrugineus','8704|Vipera ammodytes','8905|Podargus strigoides','40353|Echis carinatus','164630|Passerina ciris','75862|Anas undulata','254652|Promerops cafer','187426|Estrilda','8694|Bitis gabonica','8940|Cuculiformes','187433|Hypargos niveoguttatus','414892|Lonchura punctulata','114336|Perissocephalus tricolor','241768|Pycnonotus melanicterus dispar','768612|Icterus croconotus','84785|Sturnella neglecta','201299|Lioparus chrysotis','36293|Ficedula narcissina','634342|Phyllanthus atripennis','66707|Polioptila caerulea','1931066|Melipotes gymnops','48399|Crocodylus acutus','239378|Eurylaimus ochromalus','38654|Alligator sinensis','592668|Tiaris olivaceus','184242|Osteolaemus tetraspis','118183|Chordeiles acutipennis','1055197|Ailuroedus buccoides','30457|Pygoscelis papua','194944|Erythrura prasina','184238|Crocodylus palustris','56069|Nannopterum auritus','114294|Cotinga cayana','98156|Yuhina gularis','183532|Sayornis saya','8501|Crocodylus niloticus','43161|Melidectes belfordi','8499|Caiman crocodilus','266327|Philemon buceroides','54380|Cariama cristata','84834|Molothrus ater','9233|Aptenodytes forsteri','98156|Yuhina gularis','33618|Pelecanus erythrorhynchos','244446|Fregata ariel','37087|Sula nebouxii','181635|Yuhina brunneiceps','79643|Pygoscelis antarcticus','36300|Pelecanus crispus','240722|Pogoniulus chrysoconus','9101|Meleagris ocellata','57236|Aechmophorus occidentalis','9050|Pavo muticus','9244|Calypte anna','30403|Polyplectron napoleonis','57241|Fregata minor','9238|Pygoscelis adeliae','9076|Afropavo congensis','79626|Eudyptes chrysocome','472919|Rhodopis vesper','9240|Spheniscus humboldti','9071|Tragopan temminckii','142659|Polyplectron inopinatum','79627|Eudyptes chrysolophus','9031|Gallus gallus','8707|Daboia russelii','84986|Crax daubentoni','85099|Podiceps nigricollis','1171711|Anthropoides paradiseus','140443|Lophura erythrophthalma','9040|Lophophorus impejanus','441706|Ploceus castaneiceps','36268|Paradisaea raggiana','125070|Pauxi pauxi','84985|Crax alector','54383|Eurypyga helias','9103|Meleagris gallopavo','85099|Podiceps nigricollis','9115|Grus vipio','54570|Aramides cajanea','89385|Eupodotis senegalensis','925459|Balearica regulorum','79631|Hydrobates furcatus','8787|Casuarius casuarius','36304|Strix','292133|Turnix suscitator','9125|Gallirallus australis','9081|Argusianus argus','111820|Pulsatrix perspicillata','198471|Crypturellus parvirostris','9096|Crossoptilon auritum','73107|Otis tarda','9072|Phasianinae','30466|Rhynchotus rufescens','925459|Balearica regulorum','9063|Syrmaticus ellioti','8992|Acryllium vulturinum','51906|Guaruba guarouba','228248|Lophophorus lhuysii','9043|Lophura edwardsi','84984|Crax alberti','9049|Pavo cristatus','111818|Phodilus badius','54386|Rhynochetos jubatus','9042|Lophura bulweri','7902|Acipenser gueldenstaedtii','325340|Merops bulocki','56268|Bubo virginianus','371907|Bubo scandiacus','183607|Nerodia cyclopion','8407|Rana temporaria','302047|Seriola lalandi','1213717|Torpedo torpedo','109044|Tetraogallus himalayensis','56313|Tyto alba','9917|Boselaphus tragocamelus','56554|Coregonus zenithicus','9858|Capreolus capreolus','57441|Micrathene whitneyi','272787|Pomacanthus asfur','89386|Ardeotis kori','9069|Tragopan','9089|Chrysolophus pictus','7892|Neoceratodus forsteri','1567149|Rallus crepitans','30407|Tragopan caboti','9034|Gallus varius','37057|Macronectes giganteus','316435|Escherichia coli Nissle 1917','92733|Allobates femoralis','111123|Allobates trilineatus','92737|Ameerega trivittata','1091406|Ranitomeya toraro','4577|Zea mays L.','3656|Cucumis melo','535026|Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051','267747|Cutibacterium acnes KPA171202','not specified|Staphylococcus aureus JE3','1789648|Microcosmus exasperatus','569429|Phallusia nigra','7733|Herdmania momus','587753|Pseudomonas chlororaphis','104087|Pseudomonas frederiksbergensis','1163398|Pseudomonas donghuensis HYS','1390|Bacillus amyloliquefaciens','321661|Pseudomonas vranovensis','294|Pseudomonas fluorescens','1563158|Erwinia endophytica','34038|Rahnella aquatilis','1478|Bacillus simplex','303|Pseudomonas putida','674054|Pseudomonas baetica','76759|Pseudomonas monteilii','70775|Pseudomonas plecoglossicida','158877|Yokenella regensburgei','82992|Buttiauxella noackiae','1561394|Alicia anisopetala','151794|Banisteriopsis membranifolia','151794|Banisteriopsis parvglandula','151794|Banisteriopsis quadriglandula','124937|Barnebya harleyi','1027090|Bunchosia glandulifera','151798|Burdachia duckei','4269|Byrsonima incarnata','1561775|Camarea affinis','259653|Camarea ericoides','151831|Heteropterys aenea','151831|Heteropterys brunnea','151831|Heteropterys campestris','151831|Heteropterys coleoptera','151831|Heteropterys eglandulosa','151831|Heteropterys hatschbachii','151831|Heteropterys intermedia','151831|Heteropterys oberdanii','151831|Heteropterys tomentosa','151831|Heteropterys umbellata','151835|Hiraea cuiabensis','151835|Hiraea hatschbachii','151835|Hiraea restingae','151838|Janusia occhionii','151848|Mascagnia','1027192|Niedenzuella lucida','151862|Peixotoa spinensis','151868|Ptilochaeta densiflora','151876|Stigmaphyllon hispidum','151876|Stigmaphyllon occidentale','151880|Tetrapterys ramiflora','151880|Tetrapterys xylosteifolia','151891|Verrucularina glaucophylla','151890|Verrucularia piresii','151786|Acmanthera latifolia','217129|Acridocarpus smeathmannii','212253|Aenigmatanthera lasiandra','1816314|Amorimia andersonii','1816319|Amorimia concinna','1816315|Amorimia coriacea','1816320|Amorimia pubiflora','1561735|Amorimia septentrionalis','1027057|Aspicarpa harleyi','1027063|Banisteriopsis adenopoda','1027065|Banisteriopsis argyrophylla','1561738|Banisteriopsis anisandra','1561740|Banisteriopsis campestris','1027069|Banisteriopsis harleyi','1027070|Banisteriopsis laevifolia','1561743|Banisteriopsis malifolia','1561744|Banisteriopsis megaphylla','1027072|Banisteriopsis muricata','1561750|Banisteriopsis stellaris','1816322|Banisteriopsis variabilis','1561751|Banisteriopsis vernoniifolia','151797|Blepharandra heteropetala','1027080|Blepharandra hypoleuca','1561753|Bronwenia megaptera','1561762|Bunchosia montana','1561763|Bunchosia pallescens','1027102|Byrsonima coccolobifolia','4270|Byrsonima crassifolia','1801580|Byrsonima intermedia','1472305|Byrsonima ligustrifolia','1801593|Byrsonima sericea','883765|Byrsonima spicata','1801599|Byrsonima verbascifolia','1027110|Callaeum antifebrile','1027114|Callaeum psilophyllum','151851|Carolus chasei','1027120|Christianella multiglandulosa','1801601|Diacidia aracaensis','1027122|Dicella bracteosa','1027124|Dicella macroptera','1027129|Diplopterys pubipetala','151817|Ectopopterys soejartoi','1027132|Galphimia brasiliensis','151825|Gaudichaudia albida','151830|Heladena multiflora','259657|Heteropterys bicolor','1027142|Heteropterys brachiata','259658|Heteropterys byrsonimifolia','259661|Heteropterys chrysophylla','176641|Heteropterys leona','1027148|Heteropterys leschenaultiana','259665|Heteropterys pauciflora','151834|Hiptage benghalensis','1125931|Hiraea reclinata','1027163|Janusia janusioides','151842|Janusia mediterranea','1561795|Janusia schwannioides','1027172|Malpighia mexicana','151854|Mascagnia sepium','151857|Mcvaughia bahiana','1027193|Niedenzuella acutifolia','1816324|Niedenzuella multiglandulosa','1816325|Niedenzuella poeppigiana','1027194|Niedenzuella sericea','151855|Niedenzuella stannea','1027196|Peixotoa cordistipula','151863|Peixotoa glabra','1561815|Peixotoa hispidula','1027199|Peixotoa reticulata','1561816|Peixotoa tomentosa','151869|Ptilochaeta bahiensis','1027204|Sphedamnocarpus angolensis','1804184|Stigmaphyllon acuminatum','1804185|Stigmaphyllon alternifolium','1804186|Stigmaphyllon angustilobum','1804188|Stigmaphyllon auriculatum','1804190|Stigmaphyllon blanchetii','1804191|Stigmaphyllon bonariense','1804192|Stigmaphyllon caatingicola','1804193|Stigmaphyllon cavernulosum','1027211|Stigmaphyllon ciliatum','1804194|Stigmaphyllon convolvulifolium','1804195|Stigmaphyllon gayanum','1804196|Stigmaphyllon harleyi','1804197|Stigmaphyllon hatschbachii','1804199|Stigmaphyllon lalandianum','1804200|Stigmaphyllon macropodum','2662167|Stigmaphyllon palmatum','151877|Stigmaphyllon paralias','1804201|Stigmaphyllon puberulum','1804202|Stigmaphyllon salzmannii','1804203|Stigmaphyllon saxicola','1804204|Stigmaphyllon sinuatum','1804205|Stigmaphyllon tomentosum','1804206|Stigmaphyllon urenifolium','1804207|Stigmaphyllon vitifolium','1027214|Tetrapterys ambigua','1561826|Tetrapterys cardiophylla','151881|Tetrapterys microphylla','1561831|Tetrapterys mucronata','1027218|Tetrapterys phlomoides','1027220|Tetrapterys schiedeana','151883|Thryallis latifolia','not specified|Mascagnia conformis']) ], 'YearOfAnalysis' : [ IntValidator(), @@ -111,7 +118,7 @@ def perform_validation(filename): SetValidator(valid_set=['blood draw, capillary','blood draw, venous','blood NOS','extract, solid phase extraction (C18)','liquid','liquid, solid phase extraction (C18)','liquid, solid phase extraction (PPL)','not applicable','not specified','solid material, dried','solid material, fresh','solid material, frozen','solid material, NOS','solid, solid phase extraction (C18)','swabs, dry','swabs, moist (50% EtOH)','urine, 24-hour','urine, NOS','urine, spot','liquid, solid phase extraction (ABN)','swabs, solution (95% EtOH)','swabs, solution (100% EtOH)']) ], "SampleExtractionMethod" : [ - SetValidator(valid_set=['acetonitrile (100%)','acetonitrile-isopropanol-water (3:3:2)','acetonitrile-methanol (1:1)','acetonitrile-water (7:3)','chloroform-methanol-water (1:3:1)','dichloromethane-methanol (1:1)','dichloromethane-methanol (2:1)','dichloromethane-methanol (3:1)','ethanol (100%)','ethanol-water (1:1)','ethanol-water (19:1)','ethanol-water (9:1)','ethyl acetate (100%)','methanol (100%)','methanol-acetonitrile (3:7)','methanol-water (1:1)','methanol-water (3:2)','methanol-water (4:1)','methanol-water (7:3)','methanol-water (9:1)','not collected','not specified','water (100%) (deg_C_NOS)','water (94_deg_C)','water (95_deg_C)','water-acetonitrile (149:1)','water-acetonitrile (250:1)']) + SetValidator(valid_set=['acetonitrile (100%)','acetonitrile-isopropanol-water (3:3:2)','acetonitrile-methanol (1:1)','acetonitrile-water (7:3)','chloroform-methanol-water (1:3:1)','dichloromethane-methanol (1:1)','dichloromethane-methanol (2:1)','dichloromethane-methanol (3:1)','ethanol (100%)','ethanol-water (1:1)','ethanol-water (19:1)','ethanol-water (9:1)','ethyl acetate (100%)','methanol (100%)','methanol-acetonitrile (3:7)','methanol-water (1:1)','methanol-water (3:2)','methanol-water (4:1)','methanol-water (7:3)','methanol-water (9:1)','not collected','not specified','water (100%) (deg_C_NOS)','water (94_deg_C)','water (95_deg_C)','water-acetonitrile (149:1)','water-acetonitrile (250:1)','ethanol-water (4:1)']) ], 'InternalStandardsUsed' : [ SetValidator(valid_set=['amitryptiline','amitryptiline;fluconazole','cholic_acid-d4;lithocholic_acid-d4','cocaine-d3','cocaine;cocaine-d3','fluconazole','none','not specified','sulfadimethoxine','sulfadimethoxine;sulfachloropyridazine','sulfamethazine','sulfamethazine;sulfadimethoxine','sulfamethizole','sulfamethizole;sulfachloropyridazine','sulfamethizole;sulfachloropyridazine;sulfadimethoxine;sulfamethazine;coumarin-314;amitryptiline','decahydroquinoline','sulfachloropyridazine','coumarin-314']) diff --git a/code/templates/layout.html b/code/templates/layout.html index a5a45b8..0831602 100644 --- a/code/templates/layout.html +++ b/code/templates/layout.html @@ -79,6 +79,10 @@ +
+