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Fremmedartsbase SwissKnife

Tool for batchtasks, import, export and similar stuff. See all functions below

No secrets - all input via command line.

dotnet run:

Toolkit for Alien species db

Usage: SwissKnife [command] [options]

Options:
  -?|-h|--help  Show help information.

Commands:
  createjson    Run tasks for creating static json data files
	Commands:
		nin2 - bruker kode-api og lager lokal json fil med naturtyper
		trueteogsjeldnenaturtyper - csv fil til json format

  maintenance   Run tasks for maintaining database
	Commands:
		importfiles                update ekspansjonsdata on assessments
		importgenerationtime       update generaiontime on assessments
		
		importhsdata               Import and create assessments from names with data from horisontscanning
		importnames                Import and create assessments from names
		
		nighttasks                 nightly maintenance, basic night tasks check changed references, dowload missing artskart data ....
		
		patchhs                    Patch horizon scanned assessments based on - used for fixing assessments after production went live
		patchmigration             Patch migrated assessments from original json dump - used for fixing assessments after production went live - lots of issues fixed
		
		taxonomywash               Check and update taxonomy on assessments - create comments to reflect result
		taxonomywashdirect         Check and update taxonomy on assessments direct with history - do taxonomic wash - also splits - without creating comments
		
		transferacrossassessments  Transfer information from-to assessment - replicate most info from one assessment to spesific other and create link between
		transferfromhs             transfer current result from horizontscan - all HS assessment with specific result move to full assessment
		
  newDb         Interact with new sql database instance
	Commands:
		import - importerer til sql server og nytt format fra outputfiler generert av olddb
		
  oldDb         Interact with old 2018 RavenDb instance
	Commands:
		dump    dump content from db to json files
		info    show some statistics from db

Run 'SwissKnife [command] -?|-h|--help' for more information about a command.

Info / statistics from old db



dotnet run -- olddb info --url http://localhost:8080 --db fab3 --fs fab3fs
Livsmedium:
Found 1 item of Livsmedium
Koder:
Found 1 item of Koder
KodeGrupper:
Found 1 item of KodeGrupper
MigrationPathwayCode:
Found 1 item of MigrationPathwayCode
RedlistedNaturetypeGroup:
Found 1 item of RedlistedNaturetypeGroup
Fab2018:
Found 3204 item of Fab2018
Fab2018Files:
Found 2537 item of Fab2018Files

Dump content from 2018 Database into folder for data exchange in json format:

dotnet run -- olddb dump --url http://localhost:8080 --db fab3 --fs fab3fs --outputfolder ./Dump
Dumping content of old db to folder:C:\Users\sah\Source\Repos\Artsdatabanken\Fremmedartsbase2023\SwissKnife\Dump
Dumped 1 items to file Codes.json
Dumped 1 items to file Livsmedium.json
Dumped 1 items to file KodeGrupper.json
Dumped 1 items to file MigrationPathwayCode.json
Dumped 1 items to file RedlistedNaturetypeGroups.json
Dumped 3204 items to file Fa3.json
done...

Import content from 2018 Dump into new database:

dotnet run -- newdb import --connectionstring "Server=localhost;Database=FAB20233;Integrated Security=true;MultipleActiveResultSets=true" --inputfolder ./Dump

Do taxonomy wash

dotnet run -- maintenance taxonomywash --connectionstring "Server=localhost;Database=FAB2023;Integrated Security=true;MultipleActiveResultSets=true"

Fill empty database and import two new files:

dotnet run -- newdb import --connectionstring "Server=localhost;Database=FAB2023;Integrated Security=true;MultipleActiveResultSets=true" --inputfolder ./Dump

dotnet run -- maintenance importnames --connectionstring "Server=localhost;Database=FAB2023;Integrated Security=true;MultipleActiveResultSets=true" --speciesgroup "Alger" --csvfile ./Importfiler/Alger.txt
dotnet run -- maintenance importnames --connectionstring "Server=localhost;Database=FAB2023;Integrated Security=true;MultipleActiveResultSets=true" --speciesgroup "Terrestriske invertebrater" --csvfile ./Importfiler/TerrestriskeInvertebrater.txt

Maintenance

dotnet run -- maintenance --help

Run tasks for maintaining database

Usage: SwissKnife maintenance [command] [options]

Options:
  --help          Show help information.

Commands:
  importnames     Import and create assessments from names
  patchmigration  Patch migrated assessments from original json dump
  taxonomywash    Check and update taxonomy on assessments


dotnet run -- maintenance patchmigration --connectionstring "Server=localhost;Database=fab4;Integrated Security=true;MultipleActiveResultSets=true" --inputfolder ./Dump

dotnet run -- maintenance nighttasks --connectionstring "Server=localhost;Database=fab4;Integrated Security=true;MultipleActiveResultSets=true"

import av horisontscannende karplanter

dotnet run -- maintenance importhsdata --connectionstring "Server=localhost;Database=fab4;Integrated Security=true;MultipleActiveResultSets=true" --csvfile ./Importfiler/Karplanter_til_Horisontskanning_20220107_til_FAB.csv
dotnet run -- maintenance taxonomywashdirect --connectionstring "Server=localhost;Database=fab4;Integrated Security=true;MultipleActiveResultSets=true" --speciesgroup "Fugler"

Overføre vurderinger fra horisontscanning til full vurdering

dotnet run -- maintenance transferfromhs --connectionstring "Server=localhost;Database=fab4;Integrated Security=true;MultipleActiveResultSets=true"