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2020-11-11Documenting and QC of YAML. Some conflicts discovered that need reviewlltommy
2020-11-11Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-11-11restricting specimen_source to obo:NCIT which would have prevented the ncbi ↵lltommy
taxon bug
2020-11-07RDF: use URIsPjotr Prins
2020-11-07Fixed the License error (https!!)Pjotr Prins
2020-11-06Uploader script improvementsPjotr Prins
2020-11-04fixed sequence_assembly_method field descriptionAndreaGuarracino
2020-10-27Commented in uploader main.pyPjotr Prins
2020-10-01sequence divergence to 5% for minimap2 in the FASTA quality controlAndreaGuarracino
2020-10-01show more information in the error messagesAndreaGuarracino
2020-09-04fixed bugs in in index management and type conversionAndreaGuarracino
2020-08-28local QC is optionalAndreaGuarracino
2020-08-28added control (locally and in the validation) that sample_id has to be the ↵AndreaGuarracino
same in the metadata and in the FASTA header #103
2020-08-28qc_fasta returns also the seq_type; verified that only one FASTA is sent at ↵AndreaGuarracino
a time; code cleaning
2020-08-28fixed local QC, modifying the regex for FASTA/FASTQ to be more generalAndreaGuarracino
2020-08-26updated parameter nameAndreaGuarracino
2020-08-26typos in the code; little code refactoringAndreaGuarracino
2020-08-24reverted the relaxation on the location attributeAndreaGuarracino
2020-08-22Relaxing the location attributePjotr Prins
2020-07-16Report similarity == 0Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-16Improve uploader reporting.Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-16Make license optionalPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-16Make license optional for nowPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
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 ↵lltommy
hopefully brought it in synch with the yaml
2020-07-08Give uploader an option to trust local validation (for batch imports)upload-download-statusPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-08Uploader checks for duplicatesPeter Amstutz
2020-07-08Avoid redundant loading of schemaPeter Amstutz
2020-07-08Hack in a valid-uri checkPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-07minimap2 returns nothing when there is no alignment.Peter Amstutz
2020-07-07Use minimap2 instead of clustalw for fasta QCPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-05Add bh20-seq-analyzer --print-statusPeter Amstutz
Get status from new property "status: validated/rejected" Also store QC fail error message.
2020-07-03Add --skip-qc for faster batch importPeter Amstutz
2020-07-03Adding --skip-qcPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-03Fix qc_fasta bug closing stream.Peter Amstutz
2020-07-03Fix single arg uploadPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
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 usernamePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-30Last addition/edits to the meta data schemalltommy
2020-04-29Use subprocess invocation is backwards compatible with Python 3.5Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
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