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AgeCommit message (Expand)Author
2020-05-29Improved error output for the web uploaderPjotr Prins
2020-05-28Web: debugging metadata submissionPjotr Prins
2020-05-28Uploader: validate metadata first (it is faster)Pjotr Prins
2020-05-06Adding additional frontend option (PATO_0001340) to QClltommy
2020-04-30Handle running in a container with no username•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-30Last addition/edits to the meta data schemalltommy
2020-04-29Use subprocess invocation is backwards compatible with Python 3.5•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-29Add reference•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-28Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-04-28Decision to settle for float instead of integers for the coveragelltommy
2020-04-28Call clustalw to compare sequence to reference•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-28Changes to the structure - we use lists now instead of strings where it makes...lltommy
2020-04-23adding a submitter comment fieldlltommy
2020-04-23Adding a third sequence technology optionlltommy
2020-04-23Merge branch 'master' into patch-3LLTommy
2020-04-22Fixing ShEx expression, one ? too muchlltommy
2020-04-22Forgot to add _idlltommy
2020-04-22Including restrictions to the host statuslltommy
2020-04-22Small changes all around, trying to make the importer/metadata betterlltommy
2020-04-21Work around CWL content size limit by chunking•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-21add noLinkCheck to specimen_source2Peter Amstutz
2020-04-21Tweak handling of "coverage" also fix typo•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-21Working on NCBI import•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-21Updated shex and manditory fields and stufflltommy
2020-04-20Reconsidered these should be noLinkCheckPeter Amstutz
2020-04-20Add identity:true to collection_location•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-20Schema changes from @LLTommyPeter Amstutz
2020-04-20Better handling of duplicate sequences•••Also save original fasta label in metadata Peter Amstutz
2020-04-20Make doc not contradict option listAdam Novak
2020-04-20Put back Intersex with the closest PATO equivalent•••These options still disagree with the doc string in the schema.Adam Novak
2020-04-20Add ShEx validation•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-20Making collection date and collection location MANDATORY fields, turning orci...lltommy
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/dropdowns•••Add dropdown support to web uploader metadata formPjotr Prins
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. Still...lltommy
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
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