dthoward96
commented
5 months ago Changed schema validation to per database. This added a lot more schemas but allows for more functionality.
- Seqsender
- Pipeline schema
- Upload log schema
- Genbank
- Main schema
- Source file schema
- comment file schema
- SRA schema
- GISAID
- COV schema
- FLU schema
- POX schema
- ARBO schema
- BioSample (Schema is created from biosample package xml)
- Generic.1.0 schema
- SARS-CoV-2.cl.1.0 schema
- SARS-CoV-2.wwsurv.1.0 schema
- Pathogen.cl.1.0 schema
- Pathogen.env.1.0 schema
- OneHealthEnteric.1.0 schema
- Microbe.1.0 schema
- Model.organism.animal.1.0 schema
- Metagenome.environmental.1.0 schema
- Invertebrate.1.0 schema
- Human.1.0 schema
- Plant.1.0 schema
- Virus.1.0 schema
- Beta-lactamase.1.0 schema
- MIGS.ba.6.0 schema
- MIGS.ba.agriculture.6.0 schema
- MIGS.ba.air.6.0 schema
- MIGS.ba.built.6.0 schema
- MIGS.ba.food-animal.6.0 schema
- MIGS.ba.food-farm_env.6.0 schema
- MIGS.ba.food-prod_facility.6.0 schema
- MIGS.ba.food-human_foods.6.0 schema
- MIGS.ba.host-associated.6.0 schema
- MIGS.ba.human-associated.6.0 schema
- MIGS.ba.human-gut.6.0 schema
- MIGS.ba.human-oral.6.0 schema
- MIGS.ba.human-skin.6.0 schema
- MIGS.ba.human-vaginal.6.0 schema
- MIGS.ba.hydrocarbon-cores.6.0 schema
- MIGS.ba.hydrocarbon-fluids_swabs.6.0 schema
- MIGS.ba.microbial.6.0 schema
- MIGS.ba.miscellaneous.6.0 schema
- MIGS.ba.plant-associated.6.0 schema
- MIGS.ba.sediment.6.0 schema
- MIGS.ba.soil.6.0 schema
- MIGS.ba.symbiont-associated.6.0 schema
- MIGS.ba.wastewater.6.0 schema
- MIGS.ba.water.6.0 schema
- MIGS.eu.6.0 schema
- MIGS.eu.agriculture.6.0 schema
- MIGS.eu.air.6.0 schema
- MIGS.eu.built.6.0 schema
- MIGS.eu.food-animal.6.0 schema
- MIGS.eu.food-farm_env.6.0 schema
- MIGS.eu.food-prod_facility.6.0 schema
- MIGS.eu.food-human_foods.6.0 schema
- MIGS.eu.host-associated.6.0 schema
- MIGS.eu.human-associated.6.0 schema
- MIGS.eu.human-gut.6.0 schema
- MIGS.eu.human-oral.6.0 schema
- MIGS.eu.human-skin.6.0 schema
- MIGS.eu.human-vaginal.6.0 schema
- MIGS.eu.hydrocarbon-cores.6.0 schema
- MIGS.eu.hydrocarbon-fluids_swabs.6.0 schema
- MIGS.eu.microbial.6.0 schema
- MIGS.eu.miscellaneous.6.0 schema
- MIGS.eu.plant-associated.6.0 schema
- MIGS.eu.sediment.6.0 schema
- MIGS.eu.soil.6.0 schema
- MIGS.eu.symbiont-associated.6.0 schema
- MIGS.eu.wastewater.6.0 schema
- MIGS.eu.water.6.0 schema
- MIGS.vi.6.0 schema
- MIGS.vi.agriculture.6.0 schema
- MIGS.vi.air.6.0 schema
- MIGS.vi.built.6.0 schema
- MIGS.vi.food-animal.6.0 schema
- MIGS.vi.food-farm_env.6.0 schema
- MIGS.vi.food-prod_facility.6.0 schema
- MIGS.vi.food-human_foods.6.0 schema
- MIGS.vi.host-associated.6.0 schema
- MIGS.vi.human-associated.6.0 schema
- MIGS.vi.human-gut.6.0 schema
- MIGS.vi.human-oral.6.0 schema
- MIGS.vi.human-skin.6.0 schema
- MIGS.vi.human-vaginal.6.0 schema
- MIGS.vi.hydrocarbon-cores.6.0 schema
- MIGS.vi.hydrocarbon-fluids_swabs.6.0 schema
- MIGS.vi.microbial.6.0 schema
- MIGS.vi.miscellaneous.6.0 schema
- MIGS.vi.plant-associated.6.0 schema
- MIGS.vi.sediment.6.0 schema
- MIGS.vi.soil.6.0 schema
- MIGS.vi.symbiont-associated.6.0 schema
- MIGS.vi.wastewater.6.0 schema
- MIGS.vi.water.6.0 schema
- MIMAG.6.0 schema
- MIMAG.agriculture.6.0 schema
- MIMAG.air.6.0 schema
- MIMAG.built.6.0 schema
- MIMAG.food-animal.6.0 schema
- MIMAG.food-farm_env.6.0 schema
- MIMAG.food-prod_facility.6.0 schema
- MIMAG.food-human_foods.6.0 schema
- MIMAG.host-associated.6.0 schema
- MIMAG.human-associated.6.0 schema
- MIMAG.human-gut.6.0 schema
- MIMAG.human-oral.6.0 schema
- MIMAG.human-skin.6.0 schema
- MIMAG.human-vaginal.6.0 schema
- MIMAG.hydrocarbon-cores.6.0 schema
- MIMAG.hydrocarbon-fluids_swabs.6.0 schema
- MIMAG.microbial.6.0 schema
- MIMAG.miscellaneous.6.0 schema
- MIMAG.plant-associated.6.0 schema
- MIMAG.sediment.6.0 schema
- MIMAG.soil.6.0 schema
- MIMAG.symbiont-associated.6.0 schema
- MIMAG.wastewater.6.0 schema
- MIMAG.water.6.0 schema
- MIMARKS.specimen.6.0 schema
- MIMARKS.specimen.agriculture.6.0 schema
- MIMARKS.specimen.air.6.0 schema
- MIMARKS.specimen.built.6.0 schema
- MIMARKS.specimen.food-animal.6.0 schema
- MIMARKS.specimen.food-farm_env.6.0 schema
- MIMARKS.specimen.food-prod_facility.6.0 schema
- MIMARKS.specimen.food-human_foods.6.0 schema
- MIMARKS.specimen.host-associated.6.0 schema
- MIMARKS.specimen.human-associated.6.0 schema
- MIMARKS.specimen.human-gut.6.0 schema
- MIMARKS.specimen.human-oral.6.0 schema
- MIMARKS.specimen.human-skin.6.0 schema
- MIMARKS.specimen.human-vaginal.6.0 schema
- MIMARKS.specimen.hydrocarbon-cores.6.0 schema
- MIMARKS.specimen.hydrocarbon-fluids_swabs.6.0 schema
- MIMARKS.specimen.microbial.6.0 schema
- MIMARKS.specimen.miscellaneous.6.0 schema
- MIMARKS.specimen.plant-associated.6.0 schema
- MIMARKS.specimen.sediment.6.0 schema
- MIMARKS.specimen.soil.6.0 schema
- MIMARKS.specimen.symbiont-associated.6.0 schema
- MIMARKS.specimen.wastewater.6.0 schema
- MIMARKS.specimen.water.6.0 schema
- MIMARKS.survey.agriculture.6.0 schema
- MIMARKS.survey.air.6.0 schema
- MIMARKS.survey.built.6.0 schema
- MIMARKS.survey.food-animal.6.0 schema
- MIMARKS.survey.food-farm_env.6.0 schema
- MIMARKS.survey.food-prod_facility.6.0 schema
- MIMARKS.survey.food-human_foods.6.0 schema
- MIMARKS.survey.host-associated.6.0 schema
- MIMARKS.survey.human-associated.6.0 schema
- MIMARKS.survey.human-gut.6.0 schema
- MIMARKS.survey.human-oral.6.0 schema
- MIMARKS.survey.human-skin.6.0 schema
- MIMARKS.survey.human-vaginal.6.0 schema
- MIMARKS.survey.hydrocarbon-cores.6.0 schema
- MIMARKS.survey.hydrocarbon-fluids_swabs.6.0 schema
- MIMARKS.survey.microbial.6.0 schema
- MIMARKS.survey.miscellaneous.6.0 schema
- MIMARKS.survey.plant-associated.6.0 schema
- MIMARKS.survey.sediment.6.0 schema
- MIMARKS.survey.soil.6.0 schema
- MIMARKS.survey.symbiont-associated.6.0 schema
- MIMARKS.survey.wastewater.6.0 schema
- MIMARKS.survey.water.6.0 schema
- MIMS.me.agriculture.6.0 schema
- MIMS.me.air.6.0 schema
- MIMS.me.built.6.0 schema
- MIMS.me.food-animal.6.0 schema
- MIMS.me.food-farm_env.6.0 schema
- MIMS.me.food-prod_facility.6.0 schema
- MIMS.me.food-human_foods.6.0 schema
- MIMS.me.host-associated.6.0 schema
- MIMS.me.human-associated.6.0 schema
- MIMS.me.human-gut.6.0 schema
- MIMS.me.human-oral.6.0 schema
- MIMS.me.human-skin.6.0 schema
- MIMS.me.human-vaginal.6.0 schema
- MIMS.me.hydrocarbon-cores.6.0 schema
- MIMS.me.hydrocarbon-fluids_swabs.6.0 schema
- MIMS.me.microbial.6.0 schema
- MIMS.me.miscellaneous.6.0 schema
- MIMS.me.plant-associated.6.0 schema
- MIMS.me.sediment.6.0 schema
- MIMS.me.soil.6.0 schema
- MIMS.me.symbiont-associated.6.0 schema
- MIMS.me.wastewater.6.0 schema
- MIMS.me.water.6.0 schema
- MISAG.6.0 schema
- MISAG.agriculture.6.0 schema
- MISAG.air.6.0 schema
- MISAG.built.6.0 schema
- MISAG.food-animal.6.0 schema
- MISAG.food-farm_env.6.0 schema
- MISAG.food-prod_facility.6.0 schema
- MISAG.food-human_foods.6.0 schema
- MISAG.host-associated.6.0 schema
- MISAG.human-associated.6.0 schema
- MISAG.human-gut.6.0 schema
- MISAG.human-oral.6.0 schema
- MISAG.human-skin.6.0 schema
- MISAG.human-vaginal.6.0 schema
- MISAG.hydrocarbon-cores.6.0 schema
- MISAG.hydrocarbon-fluids_swabs.6.0 schema
- MISAG.microbial.6.0 schema
- MISAG.miscellaneous.6.0 schema
- MISAG.plant-associated.6.0 schema
- MISAG.sediment.6.0 schema
- MISAG.soil.6.0 schema
- MISAG.symbiont-associated.6.0 schema
- MISAG.wastewater.6.0 schema
- MISAG.water.6.0 schema
- MIUVIG.6.0 schema
- MIUVIG.agriculture.6.0 schema
- MIUVIG.air.6.0 schema
- MIUVIG.built.6.0 schema
- MIUVIG.food-animal.6.0 schema
- MIUVIG.food-farm_env.6.0 schema
- MIUVIG.food-prod_facility.6.0 schema
- MIUVIG.food-human_foods.6.0 schema
- MIUVIG.host-associated.6.0 schema
- MIUVIG.human-associated.6.0 schema
- MIUVIG.human-gut.6.0 schema
- MIUVIG.human-oral.6.0 schema
- MIUVIG.human-skin.6.0 schema
- MIUVIG.human-vaginal.6.0 schema
- MIUVIG.hydrocarbon-cores.6.0 schema
- MIUVIG.hydrocarbon-fluids_swabs.6.0 schema
- MIUVIG.microbial.6.0 schema
- MIUVIG.miscellaneous.6.0 schema
- MIUVIG.plant-associated.6.0 schema
- MIUVIG.sediment.6.0 schema
- MIUVIG.soil.6.0 schema
- MIUVIG.symbiont-associated.6.0 schema
- MIUVIG.wastewater.6.0 schema
- MIUVIG.water.6.0 schema
User metadata can be validated using pandera validation. This will allow for metadata field requirements based on a schema file. This will allow seqsender to automatically detect issues with user metadata. Pandera is a better alternative than hardcoding metadata field validation into seqsender because a schema can be created for each virus with multiple valid options for each field. This can then be easily expanded to include restrictions for other viruses or to roll back restrictions.
Pandera metadata schema files: