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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-5Pjotr Prins
accession list 2020/04/18
2020-04-19Merge 984f74f7d7219c83d280b6eee46cba4aed4298bbPjotr Prins
2020-04-19Merge pull request #26 from AndreaGuarracino/patch-6Pjotr Prins
new script release
2020-04-19Merge branch 'master' into patch-6Pjotr Prins
2020-04-19Merge pull request #27 from AndreaGuarracino/patch-7Pjotr Prins
updated term-mapping dictionaries
2020-04-19Merge pull request #24 from adamnovak/dropdownsPjotr Prins
Add dropdown support to web uploader metadata form
2020-04-19Merge pull request #23 from AndreaGuarracino/patch-3Pjotr Prins
accessions list CoV-2 from NCBI Virus 2020/04/15
2020-04-19Merge pull request #22 from AndreaGuarracino/patch-4Pjotr Prins
added type id check
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 releaseAndrea Guarracino
- 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.
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 checkAndrea Guarracino
what is not genomic DNA is removed
2020-04-15accessions list CoV-2 from NCBI Virus 2020/04/15Andrea Guarracino
2020-04-15Merge pull request #20 from stain/patch-1Pjotr Prins
submitter_orchid -> submitter_orcid
2020-04-15Merge pull request #19 from AndreaGuarracino/patch-2Pjotr Prins
added name and affiliation
2020-04-15Typo: submitter_orchid -> submitter_orcidStian Soiland-Reyes
2020-04-15submitter_orchid -> submitter_orcidStian Soiland-Reyes
"orchid" is the flower :) also use an actual ORCID example <https://orcid.org/0000-0002-1825-0097> which is fictitious person (with a real record!) - dedicated for example use.
2020-04-15Changing vaccination URIlltommy
2020-04-15Fixing small typolltommy
2020-04-15Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-04-15relaxing regEx cause orichids can look like whatever it seems, not only numberslltommy
2020-04-15added name and affiliationAndrea Guarracino
2020-04-14Merge pull request #18 from AndreaGuarracino/patch-1Pjotr Prins
added script from genbank to fasta and yaml
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
2020-04-14accessions list CoV-2 from NCBI Virus 2020/04/14Andrea Guarracino
2020-04-14Rename script/from_genbank_to_fasta_and_yaml.py to ↵Andrea Guarracino
scripts/from_genbank_to_fasta_and_yaml.py
2020-04-14script from genbank to fasta and yamlAndrea Guarracino
2020-04-13Merge pull request #17 from BonfaceKilz/masterPjotr Prins
[Fix] Correctly render form element inside chromium (closes #9)
2020-04-13Fix wrong rendering of form elements inside chromium (closes #9)BonfaceKilz
https://css-tricks.com/almanac/properties/b/break-inside/
2020-04-13Added link to REDCapPjotr Prins
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