Age | Commit message (Collapse) | Author | |
---|---|---|---|
2020-04-20 | Better handling of duplicate sequences | Peter Amstutz | |
Also save original fasta label in metadata | |||
2020-04-20 | Relabel sequences to match metadata subjects. | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-04-20 | Move workflows into main repo | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-04-20 | Add ShEx validation | Peter Amstutz | |
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> | |||
2020-04-20 | Merge pull request #29 from inutano/fix-mappings | LLTommy | |
fix MinION to ONT | |||
2020-04-20 | Merge pull request #28 from AndreaGuarracino/patch-8 | LLTommy | |
fixed missing variable and managed comma in dicts | |||
2020-04-20 | fix MinION to ONT | Tazro Inutano Ohta | |
2020-04-20 | Making collection date and collection location MANDATORY fields, turning ↵ | lltommy | |
orcid into IRI | |||
2020-04-20 | Fixing string -> URI in speciman, plus other things | lltommy | |
2020-04-19 | added 'np/op' control for specimen_source | Andrea Guarracino | |
2020-04-19 | Further updates to our NCBI dictonaries to translate this s*** to our model | lltommy | |
2020-04-19 | fixed missing variable and managed comma in dicts | Andrea Guarracino | |
2020-04-19 | small updates to the yaml schema, updating the example files | lltommy | |
2020-04-19 | Updating NCBI dictonaries, adding UI options, small yaml schema changes | lltommy | |
2020-04-19 | Merge pull request #25 from AndreaGuarracino/patch-5 | Pjotr Prins | |
accession list 2020/04/18 | |||
2020-04-19 | Merge 984f74f7d7219c83d280b6eee46cba4aed4298bb | Pjotr Prins | |
2020-04-19 | Merge pull request #26 from AndreaGuarracino/patch-6 | Pjotr Prins | |
new script release | |||
2020-04-19 | Merge branch 'master' into patch-6 | Pjotr Prins | |
2020-04-19 | Merge pull request #27 from AndreaGuarracino/patch-7 | Pjotr Prins | |
updated term-mapping dictionaries | |||
2020-04-19 | Merge pull request #24 from adamnovak/dropdowns | Pjotr Prins | |
Add dropdown support to web uploader metadata form | |||
2020-04-19 | Merge pull request #23 from AndreaGuarracino/patch-3 | Pjotr Prins | |
accessions list CoV-2 from NCBI Virus 2020/04/15 | |||
2020-04-19 | Merge pull request #22 from AndreaGuarracino/patch-4 | Pjotr Prins | |
added type id check | |||
2020-04-18 | dictionaries for mapping | Andrea Guarracino | |
2020-04-18 | ncbi_speciesman_source mapping | Andrea Guarracino | |
2020-04-18 | Delete dict_ontology_standardization | Andrea Guarracino | |
2020-04-18 | ncbi_speciesman_source mapping | Andrea Guarracino | |
2020-04-18 | new script release | Andrea 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. | |||
2020-04-18 | accession list 2020/04/18 | Andrea Guarracino | |
2020-04-18 | Extending yaml schema a bit and adding additional information for the UI | lltommy | |
2020-04-17 | Make ? link show doc info and a different link to the ontology IRI | Adam Novak | |
2020-04-17 | Tooltip the whole label | Adam Novak | |
2020-04-17 | Pull 'doc' from the schema through to the frontend | Adam Novak | |
2020-04-17 | Copy NCIT IRIs back to schema doc | Adam Novak | |
2020-04-17 | Spruce up the options file and add missing values | Adam Novak | |
2020-04-17 | Remove extraneous prints | Adam Novak | |
2020-04-17 | Create option dropdowns from an options file | Adam Novak | |
2020-04-17 | Correct maximum file size message | Adam Novak | |
2020-04-17 | Call URLs IRIs because that's more general | Adam Novak | |
2020-04-17 | Don't use @id as a URL if no URL is found | Adam Novak | |
2020-04-17 | Read schema from package resource | Adam Novak | |
2020-04-15 | added type id check | Andrea Guarracino | |
what is not genomic DNA is removed | |||
2020-04-15 | accessions list CoV-2 from NCBI Virus 2020/04/15 | Andrea Guarracino | |
2020-04-15 | Merge pull request #20 from stain/patch-1 | Pjotr Prins | |
submitter_orchid -> submitter_orcid | |||
2020-04-15 | Merge pull request #19 from AndreaGuarracino/patch-2 | Pjotr Prins | |
added name and affiliation | |||
2020-04-15 | Typo: submitter_orchid -> submitter_orcid | Stian Soiland-Reyes | |
2020-04-15 | submitter_orchid -> submitter_orcid | Stian 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. | |||
2020-04-15 | Changing vaccination URI | lltommy | |
2020-04-15 | Fixing small typo | lltommy | |
2020-04-15 | Merge branch 'master' of https://github.com/arvados/bh20-seq-resource | lltommy | |
2020-04-15 | relaxing regEx cause orichids can look like whatever it seems, not only numbers | lltommy | |