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2020-04-21Updated shex and manditory fields and stufflltommy
2020-04-20Add readsMergeDedup.fasta to output•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-20Make sure there is a newline in relabeled fasta (but no blank lines)Peter Amstutz
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
2020-04-20Relabel sequences to match metadata subjects.•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-20Move workflows into main repo•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-20Add ShEx validation•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-20Merge pull request #29 from inutano/fix-mappings•••fix MinION to ONTLLTommy
2020-04-20Merge pull request #28 from AndreaGuarracino/patch-8•••fixed missing variable and managed comma in dictsLLTommy
2020-04-20fix MinION to ONTTazro Inutano Ohta
2020-04-20Making collection date and collection location MANDATORY fields, turning orci...lltommy
2020-04-20Fixing string -> URI in speciman, plus other thingslltommy
2020-04-19added 'np/op' control for specimen_sourceAndrea Guarracino
2020-04-19Further updates to our NCBI dictonaries to translate this s*** to our modellltommy
2020-04-19fixed missing variable and managed comma in dictsAndrea Guarracino
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 #25 from AndreaGuarracino/patch-5•••accession list 2020/04/18Pjotr Prins
2020-04-19Merge 984f74f7d7219c83d280b6eee46cba4aed4298bbPjotr Prins
2020-04-19Merge pull request #26 from AndreaGuarracino/patch-6•••new script releasePjotr Prins
2020-04-19Merge branch 'master' into patch-6Pjotr Prins
2020-04-19Merge pull request #27 from AndreaGuarracino/patch-7•••updated term-mapping dictionariesPjotr Prins
2020-04-19Merge pull request #24 from adamnovak/dropdowns•••Add dropdown support to web uploader metadata formPjotr Prins
2020-04-19Merge pull request #23 from AndreaGuarracino/patch-3•••accessions list CoV-2 from NCBI Virus 2020/04/15Pjotr Prins
2020-04-19Merge pull request #22 from AndreaGuarracino/patch-4•••added type id checkPjotr Prins
2020-04-18dictionaries for mappingAndrea Guarracino
2020-04-18ncbi_speciesman_source mappingAndrea Guarracino
2020-04-18Delete dict_ontology_standardizationAndrea Guarracino
2020-04-18ncbi_speciesman_source mappingAndrea Guarracino
2020-04-18new script release•••- now the script is more gentle with the server, requesting metadata in batches, reducing the ovrall execution time; - in the YAML files are created field for sample_sequencing_technology, sample_sequencing_technology2, sample_sequencing_technology3, specimen_source, and specimen_source2; - in sequencing_coverage stuff like 'x', 'X', etc... is stripped, and the ',' replaced by '.'; - the script exploits the dictionaries in the /scripts/dict_ontology_standardization. Now I have used ncbi_specesman_source.csv, ncbi_sequencing_technology.csv, and ncbi_countries.csv. - in ncbi_sequencing_technology.csv I've added 'Oxford Nanopore' and 'MinION Oxford Nanopore' - for specimen_source, when there is one of 'NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', or 'np/np swab', I put both of them.Andrea Guarracino
2020-04-18accession list 2020/04/18Andrea Guarracino
2020-04-18Extending yaml schema a bit and adding additional information for the UIlltommy
2020-04-17Make ? link show doc info and a different link to the ontology IRIAdam Novak
2020-04-17Tooltip the whole labelAdam Novak
2020-04-17Pull 'doc' from the schema through to the frontendAdam Novak
2020-04-17Copy NCIT IRIs back to schema docAdam Novak
2020-04-17Spruce up the options file and add missing valuesAdam Novak
2020-04-17Remove extraneous printsAdam Novak
2020-04-17Create option dropdowns from an options fileAdam Novak
2020-04-17Correct maximum file size messageAdam Novak
2020-04-17Call URLs IRIs because that's more generalAdam Novak
2020-04-17Don't use @id as a URL if no URL is foundAdam Novak
2020-04-17Read schema from package resourceAdam Novak
2020-04-15added type id check•••what is not genomic DNA is removedAndrea Guarracino
2020-04-15accessions list CoV-2 from NCBI Virus 2020/04/15Andrea Guarracino
2020-04-15Merge pull request #20 from stain/patch-1•••submitter_orchid -> submitter_orcidPjotr Prins
2020-04-15Merge pull request #19 from AndreaGuarracino/patch-2•••added name and affiliationPjotr Prins
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