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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.
2020-04-18Extending yaml schema a bit and adding additional information for the UIlltommy
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
2020-04-13Inject path to find module bh20sequploaderPjotr Prins
2020-04-13Merge branch 'master' of github.com:arvados/bh20-seq-resourcePjotr Prins
2020-04-13Add modulePjotr Prins
2020-04-13Add __init__.py and fix importsPeter Amstutz
2020-04-13More testing and outputPjotr Prins
2020-04-13Closes #5Pjotr Prins
2020-04-13Format stack dump in outputPjotr Prins
2020-04-13Image credits & enable buttonPjotr Prins
2020-04-13Logo heightPjotr Prins
2020-04-13Merge branch 'master' of github.com:arvados/bh20-seq-resourcePjotr Prins
2020-04-13Web layout and logosPjotr Prins
2020-04-13Merge branch 'master' of https://github.com/arvados/bh20-seq-resourcelltommy
2020-04-13Starting to turn values into IRIs ...lltommy
2020-04-12Web: added Arvados logo - need to change CSSPjotr Prins
2020-04-12Add pop-up to give upload advicePjotr Prins
2020-04-12Paper: add BonfacePjotr Prins
2020-04-12ImagePjotr Prins
2020-04-12Web pagePjotr Prins
2020-04-12Website: working on layoutPjotr Prins
2020-04-12Merge pull request #7 from BonfaceKilz/masterPjotr Prins
Add custom css styling
2020-04-12Merge pull request #8 from adamnovak/ui-improvementsPjotr Prins
Clarify support for FASTQ
2020-04-12Paper: reorderPjotr Prins
2020-04-12Merge pull request #1 from mr-c/patch-1Pjotr Prins
update my affiliation & ORCID
2020-04-12Merge branch 'master' into patch-1Pjotr Prins
2020-04-12Merge pull request #2 from heuermh/patch-1Pjotr Prins
Add author and affiliation
2020-04-12Merge branch 'master' into patch-1Pjotr Prins
2020-04-12Merge branch 'master' of github.com:pjotrp/bh20-seq-resourcePjotr Prins
2020-04-12Merge branch 'master' of github.com:arvados/bh20-seq-resourcePjotr Prins
2020-04-11Merge pull request #3 from adamnovak/patch-2Pjotr Prins
Paper Edits
2020-04-11Adding noLinkCheck to rootlltommy
2020-04-11Adding descriptions to the yml schema, slight changes to the yml schemalltommy
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