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2020-04-23Merge pull request #33 from AndreaGuarracino/patch-9•••script updatingLLTommy
2020-04-22code 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 fileAndrea Guarracino
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 typo•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-21Working on NCBI import•••Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com> Peter Amstutz
2020-04-21Updated shex and manditory fields and stufflltommy
2020-04-20Merge pull request #29 from inutano/fix-mappings•••fix MinION to ONTLLTommy
2020-04-20Merge pull request #28 from AndreaGuarracino/patch-8•••fixed missing variable and managed comma in dictsLLTommy
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-7•••updated term-mapping dictionariesPjotr Prins
2020-04-19Merge pull request #23 from AndreaGuarracino/patch-3•••accessions list CoV-2 from NCBI Virus 2020/04/15Pjotr Prins
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 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
2020-04-15added type id check•••what is not genomic DNA is removedAndrea Guarracino
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 scripts/from_genbank_to_fa...Andrea Guarracino
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