| Age | Commit message (Expand) | Author |
|---|
| 2020-04-30 | fixed UO_0000036 for year | Andrea Guarracino |
| 2020-04-30 | Merge pull request #41 from AndreaGuarracino/patch-14•••the date is now handled more formally (YYYY-MM-DD) | LLTommy |
| 2020-04-30 | Wrap import script to run as a workflow•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
| Peter Amstutz |
| 2020-04-29 | the date is now handled more formally•••all the date are saved as "YYYY-MM-DD" | Andrea Guarracino |
| 2020-04-28 | updated to manage list fields and added new control on nasopharyngeal/throat ... | Andrea Guarracino |
| 2020-04-28 | Changes to the structure - we use lists now instead of strings where it makes... | lltommy |
| 2020-04-23 | code cleaning, refactoring, submitter name and address•••- additional_submitter_information for information not equal to name or address
- added another check for coverage | Andrea Guarracino |
| 2020-04-22 | code cleaning, checking and writing missing term on file•••- the script checks for country and specimen_source
- now the missing terms are written on a tsv file | Andrea Guarracino |
| 2020-04-22 | Small changes all around, trying to make the importer/metadata better | lltommy |
| 2020-04-21 | Tweak handling of "coverage" also fix typo•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
| Peter Amstutz |
| 2020-04-21 | Working on NCBI import•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
| Peter Amstutz |
| 2020-04-21 | Updated shex and manditory fields and stuff | lltommy |
| 2020-04-19 | added 'np/op' control for specimen_source | Andrea Guarracino |
| 2020-04-19 | fixed missing variable and managed comma in dicts | Andrea Guarracino |
| 2020-04-18 | new 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 |
| 2020-04-14 | Rename script/from_genbank_to_fasta_and_yaml.py to scripts/from_genbank_to_fa... | Andrea Guarracino |
