Import into EMX-2
Opened this issue · 1 comments
aubinthomas commented
Hello,
I'm trying to upload fair genome into Molgenis EMX2 (v10.20 through Java command line) . I zipped the content of generated/molgenis-emx2 folder.
The general template has been loaded but no ontologies have been taken in account. At import I have this output:
Progress of current upload:
Import csv file in 2974ms
Import metadata in 2896ms
Loaded tables and columns from 'molgenis' sheet
Members loading skipped: 'molgenis_members' sheet not included in the file
Loading settings skipped: 'molgenis_settings' sheet not included in the file
Import from store in 4ms
Sheet with name 'molgenis-emx2/allowrecontacting' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/analysesperformed' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/anatomicalsource' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/ancestry' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/biospecimentype' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/clinicaldiagnosis' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/collectedby' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/consentformcreator' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/countryofbirth' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/countryofresidence' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/dataformatsstored' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/datausemodifiers' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/datausepermissions' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/familymembersaffected' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/familymemberssequenced' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/genderatbirth' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/genderidentity' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/genotypicsex' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/inclusioncriteria' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/inclusionstatus' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/librarypreparationkit' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/medicalhistory' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/medication' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/moleculardiagnosisgene' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/molgenis' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/pathologicalstate' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/phenotype' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/phenotypicdataavailable' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/primaryaffiliatedinstitute' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/referencegenomeused' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/representedby' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/resourcesinotherinstitutes' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/SEMANTICS' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/sequencinginstrumentmodel' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/sequencingmethod' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/sequencingplatform' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/storageconditions' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/targetenrichmentkit' was skipped: no table with that name found
Sheet with name 'molgenis-emx2/unobservedphenotype' was skipped: no table with that name found
Import data skipped: No data sheet included
Committing in 33ms
As result I have no ontology at all available.
How can I upload the ontologies next?
Thank you in advance
aubinthomas commented
I think I found the error, the files inside the directory are all in lower case.
If I put the letters in upper case exactly as inside molgenis.csv it works