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AgeCommit message (Expand)Author
2020-08-22Relaxing the location attributePjotr Prins
2020-07-16Report similarity == 0•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-07-16Improve uploader reporting.•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-07-16Make license optional•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-07-16Make license optional for now•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-07-16Make license optional for nowPjotr Prins
2020-07-15License RDFPjotr Prins
2020-07-15Add RDF outputPjotr Prins
2020-07-15Web: add license to input formPjotr Prins
2020-07-13Add ontology and schema for license information. For review.Pjotr Prins
2020-07-08Try to fix lab_address wrong predicate, fix submitter shape on the way and ho...lltommy
2020-07-08Give uploader an option to trust local validation (for batch imports)•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> upload-download-statusPeter Amstutz
2020-07-08Uploader checks for duplicatesPeter Amstutz
2020-07-08Avoid redundant loading of schemaPeter Amstutz
2020-07-08Hack in a valid-uri check•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-07-07minimap2 returns nothing when there is no alignment.Peter Amstutz
2020-07-07Use minimap2 instead of clustalw for fasta QC•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-07-05Add bh20-seq-analyzer --print-status•••Get status from new property "status: validated/rejected" Also store QC fail error message. Peter Amstutz
2020-07-03Add --skip-qc for faster batch importPeter Amstutz
2020-07-03Adding --skip-qc•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-07-03Fix qc_fasta bug closing stream.Peter Amstutz
2020-07-03Fix single arg upload•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-06-22Better invalid sequence QC handlingPeter Amstutz
2020-06-22Handle upload & assembly of gzipped, paired-end fastqPeter Amstutz
2020-05-29Changed doc comment in schemaPjotr Prins
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
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