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feature: provide data for SILO in e2e tests
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Due to GenSpectrum/LAPIS-SILO#124
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@fengelniederhammer
fengelniederhammer committed Jun 30, 2023
1 parent 6f58b5c commit 4f74c62
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1 change: 0 additions & 1 deletion .github/workflows/lapis2.yml
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Expand Up @@ -145,4 +145,3 @@ jobs:
env:
SILO_TAG: latest
LAPIS_TAG: ${{ steps.lapisBranchTag.outputs.lapisTag }}
DATABASE_CONFIG: ../siloLapisTests/testDatabaseConfig.yaml
2 changes: 1 addition & 1 deletion lapis2/build.gradle
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Expand Up @@ -79,7 +79,7 @@ openApi {
customBootRun {
args.set([
"--silo.url=does.not.matter.here",
"--lapis.databaseConfig.path=../siloLapisTests/testDatabaseConfig.yaml"
"--lapis.databaseConfig.path=../siloLapisTests/testData/testDatabaseConfig.yaml"
])
}
}
10 changes: 9 additions & 1 deletion lapis2/docker-compose.yml
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Expand Up @@ -7,10 +7,18 @@ services:
command: --silo.url=http://silo:8081 --lapis.databaseConfig.path=databaseConfig.yaml
volumes:
- type: bind
source: ${DATABASE_CONFIG}
source: ../siloLapisTests/testData/testDatabaseConfig.yaml
target: /workspace/databaseConfig.yaml
read_only: true
silo:
image: ghcr.io/genspectrum/lapis-silo:${SILO_TAG}
ports:
- ":8081"
command:
- "--api"
- "--preprocessingConfig=/data/preprocessingConfig.yaml"
- "--databaseConfig=/data/testDatabaseConfig.yaml"
volumes:
- type: bind
source: ../siloLapisTests/testData
target: /data
121 changes: 121 additions & 0 deletions siloLapisTests/testData/pango_alias.txt
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C B.1.1.1
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6 changes: 6 additions & 0 deletions siloLapisTests/testData/preprocessingConfig.yaml
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inputDirectory: ./
outputDirectory: ./output/
metadataFilename: small_metadata_set.tsv
sequenceFilename: small_sequence_set.fasta
pangoLineageDefinitionFilename: pango_alias.txt
referenceGenomeFilename: reference_genome.txt
1 change: 1 addition & 0 deletions siloLapisTests/testData/reference_genome.txt
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101 changes: 101 additions & 0 deletions siloLapisTests/testData/small_metadata_set.tsv
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gisaid_epi_isl pango_lineage date region country division unsorted_date age
EPI_ISL_1408408 B.1.1.7 2021-03-18 Europe Switzerland Basel-Land 2021-01-15 4
EPI_ISL_1749899 B.1.1.7 2021-04-13 Europe Switzerland Bern 2020-03-08 5
EPI_ISL_2016901 B.1.1.7 2021-04-25 Europe Switzerland Aargau 2021-01-29 6
EPI_ISL_1749892 B.1.1.7 2021-04-13 Europe Switzerland Bern 2020-12-24 4
EPI_ISL_1597932 B.1.1.7 2021-03-19 Europe Switzerland Solothurn 2021-02-10 54
EPI_ISL_1407962 B.1.1.7 2021-03-15 Europe Switzerland Solothurn 2021-01-16 55
EPI_ISL_1750503 B.1.258.17 2020-12-24 Europe Switzerland Zürich 2021-02-14 56
EPI_ISL_1360935 B.1.1.7 2021-03-08 Europe Switzerland Jura 2021-01-03 57
EPI_ISL_2019235 B.1.1.7 2021-04-28 Europe Switzerland Basel-Stadt 2021-01-22 58
EPI_ISL_1749960 B.1.1.7 2021-04-15 Europe Switzerland Basel-Land 2021-02-03 59
EPI_ISL_1361468 B.1.1.7 2021-03-06 Europe Switzerland Zürich 2021-01-20 50
EPI_ISL_1408062 B.1.1.7 2021-03-03 Europe Switzerland Valais 2020-11-24 50
EPI_ISL_1597890 B.1.1.7 2021-03-21 Europe Switzerland Vaud 2021-01-25 51
EPI_ISL_1682849 B.1.236 2020-12-17 Europe Switzerland Thurgau 2021-01-21 52
EPI_ISL_1408805 B.1.221 2020-11-24 Europe Switzerland Schwyz 2020-12-09 53
EPI_ISL_1750868 B.1.1.189 2020-12-15 Europe Switzerland Solothurn 2021-01-20 54
EPI_ISL_2019350 B.1.1.7 2021-04-27 Europe Switzerland Valais 2020-12-21 55
EPI_ISL_2017036 B.1.1.7 2021-04-23 Europe Switzerland Solothurn 2021-03-09 56
EPI_ISL_1599113 B.1.1.39 2020-12-08 Europe Switzerland Zürich 2021-03-05 57
EPI_ISL_2214128 B.1.1.7 2021-05-10 Europe Switzerland Geneva 2020-11-13 58
EPI_ISL_2408472 B.1.1.7 2021-05-25 Europe Switzerland Obwalden 2021-03-02 59
EPI_ISL_830864 B.1.177 2020-10-08 Europe Switzerland Basel-Stadt 2021-03-03 50
EPI_ISL_581968 B.1.160 2020-08-17 Europe Switzerland Basel-Stadt 2021-03-25 50
EPI_ISL_2213804 Q.7 2021-05-08 Europe Switzerland Geneva 2021-04-12 51
EPI_ISL_2405276 B.1.1.7 2021-05-24 Europe Switzerland Vaud 2021-04-28 52
EPI_ISL_2213934 B.1.1.7 2021-05-13 Europe Switzerland Geneva 2021-04-23 53
EPI_ISL_2213984 B.1.1.7 2021-05-08 Europe Switzerland Geneva 2021-05-09 54
EPI_ISL_2574088 B.1.1.7 2021-06-10 Europe Switzerland Sankt Gallen 2021-05-05 55
EPI_ISL_2544226 B.1.1.7 2021-06-05 Europe Switzerland Ticino 2021-05-12 56
EPI_ISL_2360326 Q.7 2021-05-23 Europe Switzerland Ticino 2021-03-10 57
EPI_ISL_2379651 B.1.1.7 2021-05-11 Europe Switzerland Valais 2021-06-01 58
EPI_ISL_1036103 B.1.258 2020-12-09 Europe Switzerland Aargau 2021-06-03 59
EPI_ISL_931279 B.1.1 2020-10-28 Europe Switzerland Basel-Stadt 2021-05-11 50
EPI_ISL_931031 B.1.177 2020-10-22 Europe Switzerland Basel-Stadt 2021-05-10 50
EPI_ISL_1273458 B.1.1.7 2021-01-26 Europe Switzerland Basel-Land 2021-05-18 51
EPI_ISL_1273715 B.1.160 2021-01-20 Europe Switzerland Basel-Stadt 2021-05-08 52
EPI_ISL_737604 B.1.1 2020-12-14 Europe Switzerland Bern 2021-05-14 53
EPI_ISL_1129663 B.1.1.7 2020-12-29 Europe Switzerland Bern 2021-05-07 54
EPI_ISL_1003629 B.1.1.39 2021-01-25 Europe Switzerland Aargau 2021-05-18 55
EPI_ISL_737715 B.1.177 2020-12-13 Europe Switzerland Bern 2021-05-16 56
EPI_ISL_1003036 B.1.177 2021-01-16 Europe Switzerland Aargau 2021-07-14 57
EPI_ISL_899762 B.1.177 2020-12-25 Europe Switzerland Schwyz 2021-07-19 58
EPI_ISL_899725 B.1.177 2021-01-12 Europe Switzerland Solothurn 2021-07-14 59
EPI_ISL_1195052 B.1.1.7 2021-02-23 Europe Switzerland Solothurn 2021-07-04 50
EPI_ISL_1003519 B.1.160.16 2021-01-22 Europe Switzerland Solothurn 2021-07-29 50
EPI_ISL_1003010 B.1.36.35 2021-01-15 Europe Switzerland Solothurn 2021-07-19 51
EPI_ISL_1119584 B.1.1 2020-11-04 Europe Switzerland Solothurn 2021-07-05 52
EPI_ISL_1002052 B.1 2021-01-15 Europe Switzerland Solothurn 2021-07-15 53
EPI_ISL_466942 B.1 2020-03-08 Europe Switzerland Basel-Stadt 2021-05-12 54
EPI_ISL_1003849 B.1.160 2021-01-29 Europe Switzerland Neuchâtel 2021-08-05 55
EPI_ISL_768148 B.1.160 2020-12-24 Europe Switzerland Sankt Gallen 2020-03-16 56
EPI_ISL_1080536 B.1.1.7 2021-02-10 Europe Switzerland Basel-Land 2021-08-04 57
EPI_ISL_1002156 B.1.221 2021-01-16 Europe Switzerland Basel-Land 2021-02-03 58
EPI_ISL_1119315 B.1.1.7 2021-02-14 Europe Switzerland Graubünden 2021-03-18 59
EPI_ISL_1004495 B.1.177.44 2021-01-03 Europe Switzerland Bern 2021-04-13 50
EPI_ISL_1001920 B.1.177 2021-01-22 Europe Switzerland Bern 2021-04-25 50
EPI_ISL_1131102 B.1.160 2021-02-03 Europe Switzerland Zürich 2021-04-13 51
EPI_ISL_1003373 B.1.177 2021-01-20 Europe Switzerland Zürich 2021-03-19 52
EPI_ISL_721941 B.1.1.70 2020-11-24 Europe Switzerland Zürich 2021-03-15 53
EPI_ISL_1130868 B.1.525 2021-01-25 Europe Switzerland Zürich 2020-12-24 54
EPI_ISL_1003425 B.1.177 2021-01-21 Europe Switzerland Uri 2021-03-08 55
EPI_ISL_737860 B.1.160 2020-12-09 Europe Switzerland Valais 2021-04-28 56
EPI_ISL_1001493 B.1.177.44 2021-01-20 Europe Switzerland Vaud 2021-04-15 57
EPI_ISL_1260480 B.1.160 2020-12-21 Europe Switzerland Zürich 2021-03-06 58
EPI_ISL_1747885 B.1.1.7 2021-03-09 Europe Switzerland Solothurn 2021-03-03 59
EPI_ISL_1747752 B.1.1.7 2021-03-05 Europe Switzerland Basel-Land 2021-03-21 50
EPI_ISL_1005148 B.1.221 2020-11-13 Europe Switzerland Solothurn 2020-12-17 50
EPI_ISL_1748243 B.1.1.7 2021-03-02 Europe Switzerland Solothurn 2020-11-24 51
EPI_ISL_1748215 B.1.1.7 2021-03-03 Europe Switzerland Solothurn 2020-12-15 52
EPI_ISL_1748395 B.1.1.7 2021-03-25 Europe Switzerland Basel-Stadt 2021-04-27 53
EPI_ISL_1760534 B.1.1.7 2021-04-12 Europe Switzerland Ticino 2021-04-23 54
EPI_ISL_2086867 C.36.3 2021-04-28 Europe Switzerland Zürich 2020-12-08 55
EPI_ISL_1840634 Q.7 2021-04-23 Europe Switzerland Ticino 2021-05-10 56
EPI_ISL_2180995 B.1.1.7 2021-05-09 Europe Switzerland Basel-Stadt 2021-05-25 57
EPI_ISL_2181005 B.1.1.7 2021-05-05 Europe Switzerland Basel-Stadt 2020-10-08 58
EPI_ISL_2180023 B.1.1.7 2021-05-12 Europe Switzerland Ticino 2020-08-17 59
EPI_ISL_2270139 B.1.1.7 2021-03-10 Europe Switzerland Basel-Stadt 2021-05-08 50
EPI_ISL_2544452 B.1.1.7 2021-06-01 Europe Switzerland Schwyz 2021-05-24 50
EPI_ISL_2544332 B.1.1.7 2021-06-03 Europe Switzerland Bern 2021-05-13 51
EPI_ISL_2307766 B.1.1.7 2021-05-11 Europe Switzerland Bern 2021-05-08 52
EPI_ISL_2375490 B.1.1.7 2021-05-10 Europe Switzerland Valais 2021-06-10 53
EPI_ISL_2374969 B.1.1.7 2021-05-18 Europe Switzerland Aargau 2021-06-05 54
EPI_ISL_2307888 B.1.1.7 2021-05-08 Europe Switzerland Solothurn 2021-05-23 55
EPI_ISL_2375247 B.1.1.7 2021-05-14 Europe Switzerland Sankt Gallen 2021-05-11 56
EPI_ISL_2308054 B.1.1.7 2021-05-07 Europe Switzerland Zürich 2020-12-09 57
EPI_ISL_2375165 B.1.1.7 2021-05-18 Europe Switzerland Basel-Land 2020-10-28 58
EPI_ISL_2375097 B.1.1.7 2021-05-16 Europe Switzerland Basel-Land 2020-10-22 59
EPI_ISL_3128737 AY.9.2 2021-07-14 Europe Switzerland Zürich 2021-01-26 50
EPI_ISL_3128811 B.1.617.2 2021-07-19 Europe Switzerland Aargau 2021-01-20 50
EPI_ISL_3086369 AY.122 2021-07-14 Europe Switzerland Ticino 2020-12-14 51
EPI_ISL_3259931 AY.43 2021-07-04 Europe Switzerland Vaud 2020-12-29 52
EPI_ISL_3267832 AY.43 2021-07-29 Europe Switzerland Bern 2021-01-25 53
EPI_ISL_3128796 B.1.617.2 2021-07-19 Europe Switzerland Zürich 2020-12-13 54
EPI_ISL_3016465 B.1.1.7 2021-07-05 Europe Switzerland Valais 2021-01-16 55
EPI_ISL_3247294 AY.42 2021-07-15 Europe Switzerland Basel-Stadt 2020-12-25 56
EPI_ISL_3578231 P.1 2021-05-12 Europe Switzerland Zürich 2021-01-12 57
EPI_ISL_3465732 AY.43 2021-08-05 Europe Switzerland Vaud 2021-02-23 58
EPI_ISL_2367431 B.1 2020-03-16 Europe Switzerland Vaud 2021-01-22 59
EPI_ISL_3465556 AY.43 2021-08-04 Europe Switzerland Solothurn 2021-01-15 50
EPI_ISL_2359636 B.1.1.189 2021-02-03 Europe Switzerland Vaud 2020-11-04 57
200 changes: 200 additions & 0 deletions siloLapisTests/testData/small_sequence_set.fasta
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0 siloLapisTests/testDatabaseConfig.yaml → ...pisTests/testData/testDatabaseConfig.yaml
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