From 4f5a153ffe45ad6616399b36a4f65179ee8b6142 Mon Sep 17 00:00:00 2001 From: Jonas Kellerer Date: Tue, 28 May 2024 14:29:50 +0200 Subject: [PATCH] chore(root): remove lapis v1 - move lapis2 to lapis - move lapis2-docs to lapis-docs - move siloLapisTests to lapis-e2e --- .commitlintrc.js | 6 +- .github/dependabot.yml | 12 +- .github/workflows/docs_docker.yaml | 38 - .../{lapis2-docs.yml => lapis-docs.yml} | 12 +- .github/workflows/{lapis2.yml => lapis.yml} | 38 +- .../{release-lapis2.yml => release-lapis.yml} | 10 +- .github/workflows/server_docker.yml | 38 - .github/workflows/swagger_docker.yaml | 38 - .github/workflows/test.yml | 36 - .gitignore | 2 - .../{lapis2_docs.xml => lapis_docs.xml} | 8 +- .../{LapisV2Open.xml => lapis_open.xml} | 4 +- ...pisV2Protected.xml => lapis_protected.xml} | 4 +- README.md | 40 +- {lapis2-docs => lapis-docs}/.dockerignore | 0 lapis-docs/.env.example | 4 + {lapis2-docs => lapis-docs}/.gitignore | 0 {lapis2-docs => lapis-docs}/.prettierignore | 0 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.../source/ng/NextstrainDownloadService.java | 36 - .../ng/NextstrainFileToDatabaseService.java | 689 ----- .../source/ng/NextstrainGenbankHashes.java | 45 - .../ng/NextstrainGenbankMetadataEntry.java | 43 - .../NextstrainGenbankMetadataFileReader.java | 100 - .../ng/NextstrainGenbankMutationAAWorker.java | 216 -- .../ng/NextstrainGenbankNextcladeEntry.java | 517 ---- .../NextstrainGenbankNextcladeFileReader.java | 155 - .../source/ng/NextstrainGenbankService.java | 39 - .../ch/ethz/lapis/source/ng/package-info.java | 4 - .../ch/ethz/lapis/source/package-info.java | 4 - .../s3c/S3CAdditionalMetadataEntry.java | 96 - .../lapis/source/s3c/S3CVineyardService.java | 96 - .../ethz/lapis/source/s3c/package-info.java | 4 - .../CompressionTrainingAndBenchmark.java | 294 -- .../SequenceRowToColumnTransformer.java | 169 -- .../lapis/transform/TransformService.java | 679 ----- .../ch/ethz/lapis/transform/package-info.java | 5 - .../ethz/lapis/util/DeflateSeqCompressor.java | 84 - .../java/ch/ethz/lapis/util/FastaEntry.java | 19 - .../ch/ethz/lapis/util/FastaFileReader.java | 99 - .../ch/ethz/lapis/util/PangoLineageAlias.java | 4 - .../lapis/util/PangoLineageAliasResolver.java | 87 - .../util/PangoLineageQueryConverter.java | 79 - .../java/ch/ethz/lapis/util/ParsedDate.java | 112 - .../ethz/lapis/util/ReferenceGenomeData.java | 99 - .../ch/ethz/lapis/util/SeqCompressor.java | 9 - .../java/ch/ethz/lapis/util/StopWatch.java | 73 - .../java/ch/ethz/lapis/util/TimeFactory.java | 10 - .../main/java/ch/ethz/lapis/util/Utils.java | 197 -- .../ch/ethz/lapis/util/ZstdSeqCompressor.java | 71 - .../java/org/jooq/lapis/DefaultCatalog.java | 44 - .../java/org/jooq/lapis/DefaultSchema.java | 143 - .../src/main/java/org/jooq/lapis/Indexes.java | 75 - server/src/main/java/org/jooq/lapis/Keys.java | 67 - .../src/main/java/org/jooq/lapis/Tables.java | 98 - .../jooq/lapis/tables/YMainAaSequence.java | 146 - .../lapis/tables/YMainAaSequenceColumnar.java | 146 - .../YMainAaSequenceColumnarStaging.java | 146 - .../lapis/tables/YMainAaSequenceStaging.java | 146 - .../org/jooq/lapis/tables/YMainMetadata.java | 406 --- .../lapis/tables/YMainMetadataStaging.java | 404 --- .../org/jooq/lapis/tables/YMainSequence.java | 181 -- .../lapis/tables/YMainSequenceColumnar.java | 141 - .../tables/YMainSequenceColumnarStaging.java | 141 - .../lapis/tables/YMainSequenceStaging.java | 181 -- .../jooq/lapis/tables/YNextstrainGenbank.java | 552 ---- .../lapis/tables/YPangolinAssignment.java | 141 - .../main/java/org/jooq/lapis/tables/YS3c.java | 161 - .../java/org/jooq/lapis/tables/YTree.java | 141 - .../YMainAaSequenceColumnarRecord.java | 180 -- .../YMainAaSequenceColumnarStagingRecord.java | 180 -- .../tables/records/YMainAaSequenceRecord.java | 180 -- .../records/YMainAaSequenceStagingRecord.java | 180 -- .../tables/records/YMainMetadataRecord.java | 883 ------ .../records/YMainMetadataStagingRecord.java | 874 ------ .../records/YMainSequenceColumnarRecord.java | 143 - .../YMainSequenceColumnarStagingRecord.java | 143 - .../tables/records/YMainSequenceRecord.java | 439 --- .../records/YMainSequenceStagingRecord.java | 439 --- .../records/YNextstrainGenbankRecord.java | 1339 --------- .../records/YPangolinAssignmentRecord.java | 143 - .../jooq/lapis/tables/records/YS3cRecord.java | 318 -- .../lapis/tables/records/YTreeRecord.java | 143 - .../src/main/resources/aa-seq-dictionary.txt | 1 - server/src/main/resources/genemap.gff | 17 - server/src/main/resources/logback-spring.xml | 51 - .../main/resources/reference-dictionary.txt | 1 - .../src/main/resources/reference-genome.json | 53 - .../resources/simple-AAcodons-dictionary.txt | 1 - .../resources/simple-ATCGNdel-dictionary.txt | 1 - .../ethz/lapis/VariableArgumentsProvider.java | 49 - .../java/ch/ethz/lapis/VariableSource.java | 19 - .../v1/GisaidSampleControllerTest.java | 98 - .../controller/v1/HelloControllerTest.java | 46 - .../v1/OpenSampleControllerTest.java | 295 -- .../lapis/api/controller/v1/TestConfig.java | 26 - .../lapis/api/entity/DetailsFieldTest.java | 41 - .../ethz/lapis/api/entry/AAInsertionTest.java | 27 - .../ethz/lapis/api/entry/AAMutationTest.java | 48 - .../lapis/api/entry/NucInsertionTest.java | 28 - .../ethz/lapis/api/entry/NucMutationTest.java | 53 - .../log/RequestContextLoggerFilterTest.java | 133 - .../lapis/api/query/MutationStoreTest.java | 73 - .../ch/ethz/lapis/api/sql/SqlClientTest.java | 68 - .../lapis/core/ConfigurationManagerTest.java | 41 - .../ethz/lapis/source/MutationFinderTest.java | 61 - .../ethz/lapis/source/TestDataGenerator.java | 159 - .../SequenceRowToColumnTransformerTest.java | 57 - .../util/PangoLineageAliasResolverTest.java | 51 - .../util/PangoLineageQueryConverterTest.java | 43 - .../ch/ethz/lapis/util/SeqCompressorTest.java | 29 - server/src/test/resources/config.test.yml | 11 - server/startServer.sh | 4 - 587 files changed, 276 insertions(+), 31182 deletions(-) delete mode 100644 .github/workflows/docs_docker.yaml rename .github/workflows/{lapis2-docs.yml => lapis-docs.yml} (90%) rename .github/workflows/{lapis2.yml => lapis.yml} (82%) rename .github/workflows/{release-lapis2.yml => release-lapis.yml} (91%) delete mode 100644 .github/workflows/server_docker.yml delete mode 100644 .github/workflows/swagger_docker.yaml delete mode 100644 .github/workflows/test.yml rename .idea/runConfigurations/{lapis2_docs.xml => lapis_docs.xml} (55%) rename .idea/runConfigurations/{LapisV2Open.xml => lapis_open.xml} (69%) rename .idea/runConfigurations/{LapisV2Protected.xml => lapis_protected.xml} (62%) rename {lapis2-docs => lapis-docs}/.dockerignore (100%) create mode 100644 lapis-docs/.env.example rename {lapis2-docs => lapis-docs}/.gitignore (100%) rename {lapis2-docs => lapis-docs}/.prettierignore (100%) rename {lapis2-docs => lapis-docs}/.prettierrc (100%) rename {lapis2-docs => lapis-docs}/Dockerfile (100%) rename {lapis2-docs => lapis-docs}/README.md (88%) rename {lapis2-docs => lapis-docs}/astro.config.mjs (99%) rename {lapis2-docs => lapis-docs}/package-lock.json (99%) rename {lapis2-docs => lapis-docs}/package.json (90%) rename {lapis2-docs => lapis-docs}/playwright.config.ts (100%) rename {lapis2-docs => lapis-docs}/public/favicon.svg (100%) rename {lapis2-docs => lapis-docs}/src/components/BaseAwareLink.astro (100%) rename {lapis2-docs => lapis-docs}/src/components/CacheSizeEndpointLink.astro (100%) rename {lapis2-docs => lapis-docs}/src/components/CodeBlock.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/ConfigGenerator/AdditionalInformationWizard.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/ConfigGenerator/BasicInformationWizard.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/ConfigGenerator/ConfigGenerator.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/ConfigGenerator/ConfigWizard.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/ConfigGenerator/Icons.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/ConfigGenerator/MetadataWizard.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/ConfigGenerator/Results.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/ConfigGenerator/UploadConfig.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/ConfigGenerator/configContext.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/ConfigGenerator/pathoplexusConfig.ts (100%) rename {lapis2-docs => lapis-docs}/src/components/ConfigGenerator/siloConfig.ts (100%) rename {lapis2-docs => lapis-docs}/src/components/Configuration/MetadataTypesList.astro (100%) rename {lapis2-docs => lapis-docs}/src/components/DatabaseConfig.astro (100%) rename {lapis2-docs => lapis-docs}/src/components/FieldsTable.astro (100%) rename {lapis2-docs => lapis-docs}/src/components/FiltersTable/FiltersTable.astro (100%) rename {lapis2-docs => lapis-docs}/src/components/FiltersTable/getFilters.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/MutationFilters/AminoAcidMutationExample.astro (100%) rename {lapis2-docs => lapis-docs}/src/components/MutationFilters/GeneNames.astro (100%) rename {lapis2-docs => lapis-docs}/src/components/MutationFilters/MaybeAminoAcidMutationExample.astro (100%) rename {lapis2-docs => lapis-docs}/src/components/MutationFilters/NucleotideMutations.astro (100%) rename {lapis2-docs => lapis-docs}/src/components/MutationFilters/SegmentNames.astro (100%) rename {lapis2-docs => lapis-docs}/src/components/OnlyIf.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/QueryGenerator/FiltersSelection.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/QueryGenerator/LabelledInput.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/QueryGenerator/OrderLimitOffsetSelection.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/QueryGenerator/OutputFormatSelection.tsx 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lapis-docs}/src/components/TabsBox/react/TabsBox.tsx (100%) rename {lapis2-docs => lapis-docs}/src/components/TsvExample.astro (100%) rename {lapis2-docs => lapis-docs}/src/config.ts (100%) rename {lapis2-docs => lapis-docs}/src/content/config.ts (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/architecture-and-dev-docs/01-introduction.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/architecture-and-dev-docs/02-architecture-and-constraints.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/architecture-and-dev-docs/03-system-scope-and-context.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/architecture-and-dev-docs/04-solution-strategy.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/architecture-and-dev-docs/05-building-block-view.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/architecture-and-dev-docs/06-runtime-view.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/architecture-and-dev-docs/99-glossary.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/concepts/ambiguous-symbols.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/concepts/data-versions.md (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/concepts/mutation-filters.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/concepts/pango-lineage-query.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/concepts/request-id.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/concepts/request-methods.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/concepts/response-format.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/concepts/variant-query.mdx (91%) rename {lapis2-docs => lapis-docs}/src/content/docs/getting-started/generate-your-request.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/getting-started/introduction.mdx (100%) rename {lapis2-docs => 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{lapis2-docs => lapis-docs}/src/content/docs/references/fields.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/references/filters.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/references/introduction.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/references/nucleotide-and-amino-acid-symbols.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/references/open-api-definition.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/references/reference-genomes.mdx (100%) rename {lapis2-docs => lapis-docs}/src/content/docs/tutorials/plot-global-distribution-of-sequences-in-r.mdx (100%) rename {lapis2-docs => lapis-docs}/src/env.d.ts (100%) rename {lapis2-docs => lapis-docs}/src/images/concepts/example_nucleotide_mutation_response_200.png (100%) rename {lapis2-docs => lapis-docs}/src/images/concepts/example_nucleotide_mutation_schema.png (100%) rename {lapis2-docs => lapis-docs}/src/images/references/media_type.png (100%) rename {lapis2-docs => lapis-docs}/src/lapisUrl.ts (100%) rename {lapis2-docs => lapis-docs}/src/plantuml/.gitignore (100%) rename {lapis2-docs => lapis-docs}/src/plantuml/README.md (100%) rename {lapis2-docs => lapis-docs}/src/plantuml/building-block-view.puml (100%) rename {lapis2-docs => lapis-docs}/src/plantuml/building-block-view.svg (100%) rename {lapis2-docs => lapis-docs}/src/plantuml/runtime-view.puml (100%) rename {lapis2-docs => lapis-docs}/src/plantuml/runtime-view.svg (100%) rename {lapis2-docs => lapis-docs}/src/reference_genomes.ts (100%) rename {lapis2-docs => lapis-docs}/src/styles/custom.css (100%) rename {lapis2-docs => lapis-docs}/src/utils/code-generators/python/generator.ts (100%) rename {lapis2-docs => lapis-docs}/src/utils/code-generators/types.ts (100%) rename {lapis2-docs => lapis-docs}/tailwind.config.cjs (100%) rename {lapis2-docs => lapis-docs}/test-docker-compose.yml (50%) rename {lapis2-docs => lapis-docs}/tests/configGenerator.page.ts (100%) rename {lapis2-docs => lapis-docs}/tests/configGenerator.spec.ts (100%) rename {lapis2-docs => lapis-docs}/tests/docs.spec.ts (100%) rename {lapis2-docs => lapis-docs}/tests/queryGenerator.page.ts (100%) rename {lapis2-docs => lapis-docs}/tests/queryGenerator.spec.ts (100%) rename {lapis2-docs => lapis-docs}/tsconfig.json (100%) rename {siloLapisTests => lapis-e2e}/.gitignore (100%) rename {siloLapisTests => lapis-e2e}/.mocharc.json (100%) rename {siloLapisTests => lapis-e2e}/.prettierignore (100%) rename {siloLapisTests => lapis-e2e}/.prettierrc.json (100%) create mode 100644 lapis-e2e/README.md rename {siloLapisTests => lapis-e2e}/openapitools.json (100%) rename {siloLapisTests => lapis-e2e}/package-lock.json (99%) rename {siloLapisTests => lapis-e2e}/package.json (60%) rename {siloLapisTests => lapis-e2e}/test/aggregated.spec.ts (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/aggregrationFields.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/complexVariantQuery.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/countryIsSwitzerland.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/date.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/dateBetween.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/dateFrom.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/dateTo.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/filterByBoolean.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/filterByMultipleValuesForTheSameField.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/filterByNullValue.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/floatBetween.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/floatEquals.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/groupByBoolean.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/intBetween.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/intEquals.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/maybeAminoAcidMutation.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/maybeNucleotideMutation.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/mutationC23270A.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/mutationWithoutExplicitFromNucleotide23270A.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/noMutationAt230.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/pangoLineageIsB_1_1_7.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/pangoLineageIsB_1_1_7endingWithDotIncludingSublineages.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/pangoLineageIsB_1_1_7includingSublineages.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/regionIsEurope.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/twoAminoAcidMutations.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/twoMutationsC23270A_A23062T.json (100%) rename {siloLapisTests => lapis-e2e}/test/aggregatedQueries/variantQuery.json (100%) rename {siloLapisTests => lapis-e2e}/test/alignedNucleotideSequence.spec.ts (100%) rename {siloLapisTests => lapis-e2e}/test/aminoAcidInsertions.spec.ts (100%) rename {siloLapisTests => lapis-e2e}/test/aminoAcidMutations.spec.ts (100%) rename {siloLapisTests => lapis-e2e}/test/aminoAcidSequence.spec.ts (100%) rename {siloLapisTests => lapis-e2e}/test/badRequest.spec.ts (100%) rename {siloLapisTests => lapis-e2e}/test/common.spec.ts (100%) rename {siloLapisTests => lapis-e2e}/test/common.ts (100%) rename {siloLapisTests => 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20b6ab8b6..d8f830d2d 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -7,7 +7,7 @@ updates: commit-message: prefix: "chore(github-actions)" - package-ecosystem: gradle - directory: lapis2/ + directory: lapis/ schedule: interval: weekly groups: @@ -16,9 +16,9 @@ updates: - "minor" - "patch" commit-message: - prefix: "chore(lapis2)" + prefix: "chore(lapis)" - package-ecosystem: npm - directory: siloLapisTests/ + directory: lapis-e2e/ schedule: interval: weekly groups: @@ -27,9 +27,9 @@ updates: - "minor" - "patch" commit-message: - prefix: "chore(siloLapisTests)" + prefix: "chore(lapis-e2e)" - package-ecosystem: npm - directory: lapis2-docs/ + directory: lapis-docs/ schedule: interval: weekly groups: @@ -38,7 +38,7 @@ updates: - "minor" - "patch" commit-message: - prefix: "chore(lapis2-docs)" + prefix: "chore(lapis-docs)" - package-ecosystem: npm directory: / schedule: diff --git a/.github/workflows/docs_docker.yaml b/.github/workflows/docs_docker.yaml deleted file mode 100644 index 32b1463d2..000000000 --- a/.github/workflows/docs_docker.yaml +++ /dev/null @@ -1,38 +0,0 @@ -name: Docker (docs) - -on: - push: - branches: - schedule: - - cron: '0 7 */2 * *' - -env: - IMAGE_NAME: ghcr.io/genspectrum/lapis-docs - -jobs: - docker: - runs-on: ubuntu-latest - permissions: - packages: write - defaults: - run: - working-directory: ./docs/slate - steps: - - uses: actions/checkout@v4 - - name: Set environment variable "BRANCH" - run: | - echo "BRANCH=$(eval 'echo $GITHUB_REF | sed s/refs\\/heads\\/// | sed s/\\//__/g ')" >> $GITHUB_ENV - - name: Build image - run: docker build -t new_image . - - name: Login to Github Container Registry - run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin - - name: Add tags and push - if: ${{ !contains(env.BRANCH, 'dependabot') }} - run: | - docker tag new_image ${{ env.IMAGE_NAME }}:br-${{ env.BRANCH }} - docker push ${{ env.IMAGE_NAME }}:br-${{ env.BRANCH }} - - name: Add "public" tag and push - if: env.BRANCH == 'public' - run: | - docker tag new_image ${{ env.IMAGE_NAME }}:public - docker push ${{ env.IMAGE_NAME }}:public diff --git a/.github/workflows/lapis2-docs.yml b/.github/workflows/lapis-docs.yml similarity index 90% rename from .github/workflows/lapis2-docs.yml rename to .github/workflows/lapis-docs.yml index d5666640f..7867c3b6f 100644 --- a/.github/workflows/lapis2-docs.yml +++ b/.github/workflows/lapis-docs.yml @@ -1,13 +1,13 @@ -name: LAPIS v2 Docs +name: LAPIS Docs on: [push] env: - DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-v2-docs + DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-docs defaults: run: - working-directory: ./lapis2-docs + working-directory: ./lapis-docs jobs: checks: @@ -21,7 +21,7 @@ jobs: - uses: actions/cache@v4 with: path: ~/.npm - key: ${{ runner.os }}-node-${{ hashFiles('lapis2-docs/**/package-lock.json') }} + key: ${{ runner.os }}-node-${{ hashFiles('lapis-docs/**/package-lock.json') }} - run: npm ci - run: npm run check-format - run: npm run check-types @@ -56,7 +56,7 @@ jobs: - name: Build and push image uses: docker/build-push-action@v5 with: - context: ./lapis2-docs + context: ./lapis-docs push: true tags: ${{ steps.dockerMetadata.outputs.tags }} @@ -95,5 +95,5 @@ jobs: if: ${{ failure() }} with: name: playwright-report - path: lapis2-docs/playwright-report/ + path: lapis-docs/playwright-report/ retention-days: 7 diff --git a/.github/workflows/lapis2.yml b/.github/workflows/lapis.yml similarity index 82% rename from .github/workflows/lapis2.yml rename to .github/workflows/lapis.yml index 8eb18396b..c7f193c38 100644 --- a/.github/workflows/lapis2.yml +++ b/.github/workflows/lapis.yml @@ -1,9 +1,9 @@ -name: LAPIS v2 +name: LAPIS on: [ push ] env: - DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-v2 + DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis jobs: Tests: @@ -19,12 +19,12 @@ jobs: uses: gradle/actions/setup-gradle@v3 with: arguments: test - build-root-directory: lapis2 + build-root-directory: lapis - name: Check Format And Lint uses: gradle/actions/setup-gradle@v3 with: arguments: ktlintCheck - build-root-directory: lapis2 + build-root-directory: lapis dockerImage: name: Build Docker Image @@ -56,10 +56,10 @@ jobs: - name: Build and push image uses: docker/build-push-action@v5 with: - context: ./lapis2 + context: ./lapis tags: ${{ steps.dockerMetadata.outputs.tags }} - cache-from: type=gha,scope=lapis2-${{ github.ref }} - cache-to: type=gha,mode=max,scope=lapis2-${{ github.ref }} + cache-from: type=gha,scope=lapis-${{ github.ref }} + cache-to: type=gha,mode=max,scope=lapis-${{ github.ref }} platforms: ${{ github.ref == 'refs/heads/main' && 'linux/amd64,linux/arm64' || 'linux/amd64' }} push: true @@ -83,35 +83,35 @@ jobs: uses: gradle/actions/setup-gradle@v3 with: arguments: generateOpenApiDocs - build-root-directory: lapis2 + build-root-directory: lapis - name: Build OpenAPI Spec Protected uses: gradle/actions/setup-gradle@v3 with: arguments: generateOpenApiDocs -PopennessLevel=protected - build-root-directory: lapis2 + build-root-directory: lapis - name: Cache .npm uses: actions/cache@v4 with: path: ~/.npm - key: ${{ runner.os }}-node-${{ hashFiles('siloLapisTests/**/package-lock.json') }} + key: ${{ runner.os }}-node-${{ hashFiles('lapis-e2e/**/package-lock.json') }} - name: Prepare Tests run: npm ci - working-directory: siloLapisTests + working-directory: lapis-e2e - name: Generate Lapis Client run: npm run generateLapisClient - working-directory: siloLapisTests + working-directory: lapis-e2e - name: Generate Lapis Client Protected run: npm run generateLapisClientProtected - working-directory: siloLapisTests + working-directory: lapis-e2e - name: Check Format run: npm run check-format - working-directory: siloLapisTests + working-directory: lapis-e2e - name: Docker metadata id: dockerMetadata @@ -137,9 +137,9 @@ jobs: - name: Start SILO and LAPIS and Run Tests run: | - docker compose -f lapis2/docker-compose.yml pull - docker compose -f lapis2/docker-compose.yml up -d --wait - cd siloLapisTests && npm run test + docker compose -f lapis/docker-compose.yml pull + docker compose -f lapis/docker-compose.yml up -d --wait + cd lapis-e2e && npm run test env: SILO_TAG: latest LAPIS_TAG: ${{ steps.lapisBranchTag.outputs.lapisTag }} @@ -147,7 +147,7 @@ jobs: - name: Store Logs if: ${{ always() }} run: | - cd lapis2 + cd lapis mkdir p e2e-logs docker compose logs silo > e2e-logs/silo.log docker compose logs lapisOpen > e2e-logs/lapisOpen.log @@ -161,4 +161,4 @@ jobs: uses: actions/upload-artifact@v4 with: name: logs - path: lapis2/e2e-logs + path: lapis/e2e-logs diff --git a/.github/workflows/release-lapis2.yml b/.github/workflows/release-lapis.yml similarity index 91% rename from .github/workflows/release-lapis2.yml rename to .github/workflows/release-lapis.yml index d172e6c3e..8109966f9 100644 --- a/.github/workflows/release-lapis2.yml +++ b/.github/workflows/release-lapis.yml @@ -1,14 +1,14 @@ -name: Release LAPIS 2 +name: Release LAPIS on: workflow_run: - workflows: [LAPIS v2] + workflows: [LAPIS] types: [completed] branches: [main] env: - LAPIS_DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-v2 - DOCS_DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-v2-docs + LAPIS_DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis + DOCS_DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-docs jobs: release-please: @@ -50,7 +50,7 @@ jobs: username: ${{ github.actor }} password: ${{ secrets.GITHUB_TOKEN }} - - name: Wait for Lapis 2 Docs Docker Image + - name: Wait for Lapis Docs Docker Image if: ${{ steps.release.outputs.release_created }} uses: lewagon/wait-on-check-action@v1.3.4 with: diff --git a/.github/workflows/server_docker.yml b/.github/workflows/server_docker.yml deleted file mode 100644 index ca43743ed..000000000 --- a/.github/workflows/server_docker.yml +++ /dev/null @@ -1,38 +0,0 @@ -name: Docker (server) - -on: - push: - branches: - schedule: - - cron: '0 7 */2 * *' - -env: - IMAGE_NAME: ghcr.io/genspectrum/lapis-server - -jobs: - docker: - runs-on: ubuntu-latest - permissions: - packages: write - defaults: - run: - working-directory: ./server - steps: - - uses: actions/checkout@v4 - - name: Set environment variable "BRANCH" - run: | - echo "BRANCH=$(eval 'echo $GITHUB_REF | sed s/refs\\/heads\\/// | sed s/\\//__/g ')" >> $GITHUB_ENV - - name: Build image - run: docker build -t new_image . - - name: Login to Github Container Registry - run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin - - name: Add tags and push - if: ${{ !contains(env.BRANCH, 'dependabot') }} - run: | - docker tag new_image ${{ env.IMAGE_NAME }}:br-${{ env.BRANCH }} - docker push ${{ env.IMAGE_NAME }}:br-${{ env.BRANCH }} - - name: Add "public" tag and push - if: env.BRANCH == 'public' - run: | - docker tag new_image ${{ env.IMAGE_NAME }}:public - docker push ${{ env.IMAGE_NAME }}:public diff --git a/.github/workflows/swagger_docker.yaml b/.github/workflows/swagger_docker.yaml deleted file mode 100644 index 3c89c4b05..000000000 --- a/.github/workflows/swagger_docker.yaml +++ /dev/null @@ -1,38 +0,0 @@ -name: Docker (swagger) - -on: - push: - branches: - schedule: - - cron: '0 7 */2 * *' - -env: - IMAGE_NAME: ghcr.io/genspectrum/lapis-swagger - -jobs: - docker: - runs-on: ubuntu-latest - permissions: - packages: write - defaults: - run: - working-directory: ./docs/openapi_spec - steps: - - uses: actions/checkout@v4 - - name: Set environment variable "BRANCH" - run: | - echo "BRANCH=$(eval 'echo $GITHUB_REF | sed s/refs\\/heads\\/// | sed s/\\//__/g ')" >> $GITHUB_ENV - - name: Build image - run: docker build -t new_image . - - name: Login to Github Container Registry - run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin - - name: Add tags and push - if: ${{ !contains(env.BRANCH, 'dependabot') }} - run: | - docker tag new_image ${{ env.IMAGE_NAME }}:br-${{ env.BRANCH }} - docker push ${{ env.IMAGE_NAME }}:br-${{ env.BRANCH }} - - name: Add "public" tag and push - if: env.BRANCH == 'public' - run: | - docker tag new_image ${{ env.IMAGE_NAME }}:public - docker push ${{ env.IMAGE_NAME }}:public diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml deleted file mode 100644 index 61f27ff8f..000000000 --- a/.github/workflows/test.yml +++ /dev/null @@ -1,36 +0,0 @@ -name: Tests & Co - -on: [push] - -jobs: - lint: - runs-on: ubuntu-latest - defaults: - run: - working-directory: ./server - steps: - - uses: actions/checkout@v4 - - name: Set up JDK 17 - uses: actions/setup-java@v4 - with: - java-version: '17' - distribution: 'adopt' - - name: Validate Gradle wrapper - uses: gradle/wrapper-validation-action@216d1ad2b3710bf005dc39237337b9673fd8fcd5 - - name: Build with Gradle - run: ./gradlew editorconfigCheck - - test: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - name: Set up JDK 17 - uses: actions/setup-java@v4 - with: - java-version: '17' - distribution: 'adopt' - - name: Execute tests - uses: gradle/actions/setup-gradle@v3 - with: - arguments: test - build-root-directory: server diff --git a/.gitignore b/.gitignore index d54bd1a1c..f3d08d4be 100644 --- a/.gitignore +++ b/.gitignore @@ -6,8 +6,6 @@ # Personal preference playground/ -docker-compose.override.yml - log/ logs/ diff --git a/.idea/runConfigurations/lapis2_docs.xml b/.idea/runConfigurations/lapis_docs.xml similarity index 55% rename from .idea/runConfigurations/lapis2_docs.xml rename to .idea/runConfigurations/lapis_docs.xml index 76ccc9647..73c04cdb8 100644 --- a/.idea/runConfigurations/lapis2_docs.xml +++ b/.idea/runConfigurations/lapis_docs.xml @@ -1,6 +1,6 @@ - - + +