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2020-06-12species dictionaryAndrea Guarracino
2020-06-12species are managed in another dictionary, try-catch added to avoid ↵Andrea Guarracino
unexpected stops
2020-06-07the script is more verbose; added other countriesAndreaGuarracino
2020-06-06fixed collection_location when it is not present in the dictionary termsAndreaGuarracino
2020-06-06fixed collection-date management using a parserAndreaGuarracino
2020-06-06fixed collection-date management; updated assembly info management for new IDsAndreaGuarracino
2020-05-31Added new speciesman sourcesAndrea Guarracino
2020-05-31Added new sequencing technologiesAndrea Guarracino
2020-05-31Added new countriesAndrea Guarracino
2020-05-31Added new species and specimen sourcesAndrea Guarracino
2020-05-31Updated the host_sex and host_age managementAndrea Guarracino
2020-05-31The NCBI Virus entries are updated automaticallyAndrea Guarracino
2020-05-20Virtuoso update in CRONPjotr Prins
2020-05-13Virtuoso uploader: always upload countries and labelsPjotr Prins
2020-05-13Virtuoso: split named graphsPjotr Prins
2020-05-12Virtuoso uploader: does not delete graph yetPjotr Prins
2020-05-12Update graph scriptPjotr Prins
2020-04-30fixed UO_0000036 for yearAndrea Guarracino
2020-04-30Merge pull request #41 from AndreaGuarracino/patch-14LLTommy
the date is now handled more formally (YYYY-MM-DD)
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>
2020-04-29the date is now handled more formallyAndrea Guarracino
all the date are saved as "YYYY-MM-DD"
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
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