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2020-04-21Tweak handling of "coverage" also fix typoPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Working on NCBI importPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Updated shex and manditory fields and stufflltommy
2020-04-20Reconsidered these should be noLinkCheckPeter Amstutz
2020-04-20Add identity:true to collection_locationPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Schema changes from @LLTommyPeter Amstutz
2020-04-20Better handling of duplicate sequencesPeter Amstutz
Also save original fasta label in metadata
2020-04-20Make doc not contradict option listAdam Novak
2020-04-20Put back Intersex with the closest PATO equivalentAdam Novak
These options still disagree with the doc string in the schema.
2020-04-20Add ShEx validationPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-20Making collection date and collection location MANDATORY fields, turning ↵lltommy
orcid into IRI
2020-04-20Fixing string -> URI in speciman, plus other thingslltommy
2020-04-19small updates to the yaml schema, updating the example fileslltommy
2020-04-19Updating NCBI dictonaries, adding UI options, small yaml schema changeslltommy
2020-04-19Merge pull request #24 from adamnovak/dropdownsPjotr Prins
Add dropdown support to web uploader metadata form
2020-04-18Extending yaml schema a bit and adding additional information for the UIlltommy
2020-04-17Copy NCIT IRIs back to schema docAdam Novak
2020-04-17Spruce up the options file and add missing valuesAdam Novak
2020-04-17Create option dropdowns from an options fileAdam Novak
2020-04-15Typo: submitter_orchid -> submitter_orcidStian Soiland-Reyes
2020-04-15Changing vaccination URIlltommy
2020-04-15Fixing small typolltommy
2020-04-15relaxing regEx cause orichids can look like whatever it seems, not only numberslltommy
2020-04-14Updated yaml schema and examples - plus ShEX shape to go along with it. ↵lltommy
Still work in progress but getting better and better I guess
2020-04-13Inject path to find module bh20sequploaderPjotr Prins
2020-04-13Add __init__.py and fix importsPeter Amstutz
2020-04-13Closes #5Pjotr Prins
2020-04-13Starting to turn values into IRIs ...lltommy
2020-04-11Adding noLinkCheck to rootlltommy
2020-04-11Adding descriptions to the yml schema, slight changes to the yml schemalltommy
2020-04-10Propagating metadata to output works now.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-10Fix swapped fasta/fastqPeter Amstutz
Replace example sequence with COV19 reference instead of HIV. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-10Add qc_fastaPeter Amstutz
2020-04-10Fix up fasta/fastq validationPeter Amstutz
2020-04-10Validate & propagate metadataPeter Amstutz
2020-04-10Merge pull request #6 from uniqueg/fa_fq_validationPjotr Prins
validate seq format with magic file
2020-04-10Fixed TypeError: 'module' object is not callablePjotr Prins
2020-04-10validate seq format with magic fileAlex Kanitz
2020-04-10Updating schema and examples, including URIslltommy
2020-04-09Moved Guix documentation into separate file (as it confused people ;)Pjotr Prins
2020-04-09Add "sequencefile" for the metadata subject.Peter Amstutz
2020-04-09Adding functionality of turning keys into ontology terms (URI). This is work ↵lltommy
in progress - of course!
2020-04-09Updating schema and examples. This is still work in progress but we get therelltommy
2020-04-08Fastq now runs through fastq2fasta pipelinePeter Amstutz
then gets added to pangenome analysis.
2020-04-07Add metadata validation with schema-saladPeter Amstutz
2020-04-07Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-04-07adding dummy metadata qc to the projectlltommy
2020-04-07Now moves collections into 'validated sequences' projectPeter Amstutz
Improve logging for seq service Fix uploader bug Runs workflow with all validated sequences.
2020-04-06- Added some output and run main() by defaultPjotr Prins
- Disabled ssl checking which does not work if you lack a certificate
2020-04-06Remove backup filePjotr Prins
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