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2020-04-30Import script fixesPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-30Wrap import script to run as a workflowPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-29Reverting country list back, something went wrong therelltommy
2020-04-28updated to manage list fields and added new control on nasopharyngeal/throat ↵Andrea Guarracino
swab
2020-04-28Updated with new termsAndrea Guarracino
2020-04-28Updated with new termsAndrea Guarracino
2020-04-28Updated - 1731 IDs - 2020/04/28Andrea Guarracino
2020-04-28Changes to the structure - we use lists now instead of strings where it ↵lltommy
makes sense. This allows us to have multiple values where in makes sense
2020-04-26Updating dicslltommy
2020-04-24Add script that updates Virtuoso - run as a CRON jobPjotr Prins
2020-04-23Merge pull request #1 from AndreaGuarracino/patch-11Andrea Guarracino
Patch 11
2020-04-23code cleaning, refactoring, submitter name and addressAndrea Guarracino
- additional_submitter_information for information not equal to name or address - added another check for coverage
2020-04-23added nasal swab for several new IDsAndrea Guarracino
2020-04-23updated IDs list - 2020/04/23 - 1436 IDsAndrea Guarracino
2020-04-23Adding a third sequence technology optionlltommy
2020-04-23Merge pull request #33 from AndreaGuarracino/patch-9LLTommy
script updating
2020-04-22code cleaning, checking and writing missing term on fileAndrea Guarracino
- the script checks for country and specimen_source - now the missing terms are written on a tsv file
2020-04-22created dict for host health statusAndrea Guarracino
2020-04-22added some rows in the speciesman dictAndrea Guarracino
2020-04-22added some rows in the ncbi_countries dictAndrea Guarracino
2020-04-22updated IDs list - 2020/04/22Andrea Guarracino
2020-04-22Small changes all around, trying to make the importer/metadata betterlltommy
2020-04-21Tweak handling of "coverage" also fix typoPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Working on NCBI importPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-21Updated shex and manditory fields and stufflltommy
2020-04-20Merge pull request #29 from inutano/fix-mappingsLLTommy
fix MinION to ONT
2020-04-20Merge pull request #28 from AndreaGuarracino/patch-8LLTommy
fixed missing variable and managed comma in dicts
2020-04-20fix MinION to ONTTazro Inutano Ohta
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
2020-04-19Updating NCBI dictonaries, adding UI options, small yaml schema changeslltommy
2020-04-19Merge 984f74f7d7219c83d280b6eee46cba4aed4298bbPjotr Prins
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 #23 from AndreaGuarracino/patch-3Pjotr Prins
accessions list CoV-2 from NCBI Virus 2020/04/15
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.
2020-04-15added type id checkAndrea Guarracino
what is not genomic DNA is removed
2020-04-15accessions list CoV-2 from NCBI Virus 2020/04/15Andrea Guarracino
2020-04-14accessions 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
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