From ce17f9dfc4a13bb22824f525847061314144d85b Mon Sep 17 00:00:00 2001 From: Vadim Piven Date: Thu, 14 Nov 2024 20:52:29 +0400 Subject: [PATCH 1/3] Migration to new pfconv version --- .gitignore | 1 + pnpm-lock.yaml | 1631 +++++++++-------- pnpm-workspace.yaml | 28 +- test/test_config.json | 5 + ui/src/SettingsPanel.vue | 2 +- .../src/calculate-pfconv-params.tpl.tengo | 1 - workflow/src/export-clones-bulk.tpl.tengo | 4 +- workflow/src/mixcr-analyze.tpl.tengo | 3 +- workflow/src/pfconv_params.lib.tengo | 52 +- workflow/src/process.tpl.tengo | 2 +- 10 files changed, 902 insertions(+), 827 deletions(-) create mode 100644 test/test_config.json diff --git a/.gitignore b/.gitignore index 0c2ee11..97cbc1d 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ log/ .test_auth.json .turbo vite.config.*.timestamp-* +.DS_Store diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 8f2569c..9de15b3 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -7,17 +7,17 @@ settings: catalogs: default: '@ag-grid-community/client-side-row-model': - specifier: ^32.3.2 - version: 32.3.2 + specifier: ^32.3.3 + version: 32.3.3 '@ag-grid-community/core': - specifier: ^32.3.2 - version: 32.3.2 + specifier: ^32.3.3 + version: 32.3.3 '@ag-grid-community/styles': - specifier: ^32.3.2 - version: 32.3.2 + specifier: ^32.3.3 + version: 32.3.3 '@ag-grid-community/vue3': - specifier: ^32.3.2 - version: 32.3.2 + specifier: ^32.3.3 + version: 32.3.3 '@changesets/cli': specifier: ^2.27.9 version: 2.27.9 @@ -25,41 +25,41 @@ catalogs: specifier: ^1.6.6 version: 1.6.6 '@milaboratories/software-pframes-conv': - specifier: 1.6.8 - version: 1.6.8 + specifier: 2.0.1 + version: 2.0.1 '@platforma-open/milaboratories.samples-and-data': - specifier: ^1.6.3 - version: 1.6.3 + specifier: ^1.6.5 + version: 1.6.5 '@platforma-open/milaboratories.samples-and-data.model': - specifier: ^1.6.0 - version: 1.6.0 + specifier: ^1.6.1 + version: 1.6.1 '@platforma-open/milaboratories.software-mixcr': - specifier: 4.7.0-113-develop - version: 4.7.0-113-develop + specifier: 4.7.0-133-develop + version: 4.7.0-133-develop '@platforma-open/milaboratories.software-small-binaries': - specifier: ^1.14.5 - version: 1.14.5 + specifier: ^1.14.6 + version: 1.14.6 '@platforma-sdk/block-tools': - specifier: ^2.3.21 - version: 2.3.21 + specifier: ^2.3.24 + version: 2.3.24 '@platforma-sdk/model': - specifier: ^1.7.20 - version: 1.7.20 + specifier: ^1.8.0 + version: 1.8.0 '@platforma-sdk/tengo-builder': specifier: ^1.16.1 version: 1.16.1 '@platforma-sdk/test': - specifier: ^1.7.52 - version: 1.7.52 + specifier: ^1.8.13 + version: 1.8.13 '@platforma-sdk/ui-vue': - specifier: ^1.7.51 - version: 1.7.51 + specifier: ^1.8.11 + version: 1.8.11 '@platforma-sdk/workflow-tengo': - specifier: ^1.7.5 - version: 1.7.5 + specifier: ^2.0.1 + version: 2.0.1 '@vitejs/plugin-vue': - specifier: ^5.1.4 - version: 5.1.4 + specifier: ^5.2.0 + version: 5.2.0 '@vueuse/core': specifier: ^11.2.0 version: 11.2.0 @@ -76,11 +76,11 @@ catalogs: specifier: ^3.11.0 version: 3.11.0 vite: - specifier: ^5.4.10 - version: 5.4.10 + specifier: ^5.4.11 + version: 5.4.11 vitest: - specifier: ^2.1.4 - version: 2.1.4 + specifier: ^2.1.5 + version: 2.1.5 vue: specifier: ^3.5.12 version: 3.5.12 @@ -106,14 +106,14 @@ importers: version: link:workflow '@platforma-sdk/model': specifier: 'catalog:' - version: 1.7.20 + version: 1.8.0 devDependencies: '@changesets/cli': specifier: 'catalog:' version: 2.27.9 '@platforma-sdk/block-tools': specifier: 'catalog:' - version: 2.3.21 + version: 2.3.24 turbo: specifier: 'catalog:' version: 2.2.3 @@ -122,14 +122,14 @@ importers: dependencies: '@platforma-sdk/model': specifier: 'catalog:' - version: 1.7.20 + version: 1.8.0 zod: specifier: 'catalog:' version: 3.23.8 devDependencies: '@platforma-sdk/block-tools': specifier: 'catalog:' - version: 2.3.21 + version: 2.3.24 tsup: specifier: 'catalog:' version: 8.1.2(postcss@8.4.47)(typescript@5.5.4)(yaml@2.6.0) @@ -138,47 +138,47 @@ importers: version: 5.5.4 vite: specifier: 'catalog:' - version: 5.4.10(@types/node@22.7.5) + version: 5.4.11(@types/node@22.7.5) vitest: specifier: 'catalog:' - version: 2.1.4(@types/node@22.7.5) + version: 2.1.5(@types/node@22.7.5) test: dependencies: '@platforma-open/milaboratories.samples-and-data': specifier: 'catalog:' - version: 1.6.3 + version: 1.6.5 '@platforma-open/milaboratories.samples-and-data.model': specifier: 'catalog:' - version: 1.6.0 + version: 1.6.1 this-block: specifier: workspace:@platforma-open/milaboratories.mixcr-clonotyping@* version: link:.. devDependencies: '@platforma-sdk/test': specifier: 'catalog:' - version: 1.7.52(@types/node@22.7.5) + version: 1.8.13(@types/node@22.7.5) typescript: specifier: 'catalog:' version: 5.5.4 vitest: specifier: 'catalog:' - version: 2.1.4(@types/node@22.7.5) + version: 2.1.5(@types/node@22.7.5) ui: dependencies: '@ag-grid-community/client-side-row-model': specifier: 'catalog:' - version: 32.3.2 + version: 32.3.3 '@ag-grid-community/core': specifier: 'catalog:' - version: 32.3.2 + version: 32.3.3 '@ag-grid-community/styles': specifier: 'catalog:' - version: 32.3.2 + version: 32.3.3 '@ag-grid-community/vue3': specifier: 'catalog:' - version: 32.3.2(typescript@5.5.4) + version: 32.3.3(typescript@5.5.4) '@milaboratories/helpers': specifier: 'catalog:' version: 1.6.6 @@ -187,10 +187,10 @@ importers: version: link:../model '@platforma-sdk/model': specifier: 'catalog:' - version: 1.7.20 + version: 1.8.0 '@platforma-sdk/ui-vue': specifier: 'catalog:' - version: 1.7.51(typescript@5.5.4) + version: 1.8.11(typescript@5.5.4) '@vueuse/core': specifier: 'catalog:' version: 11.2.0(vue@3.5.12(typescript@5.5.4)) @@ -206,16 +206,16 @@ importers: devDependencies: '@vitejs/plugin-vue': specifier: 'catalog:' - version: 5.1.4(vite@5.4.10(@types/node@22.7.5))(vue@3.5.12(typescript@5.5.4)) + version: 5.2.0(vite@5.4.11(@types/node@22.7.5))(vue@3.5.12(typescript@5.5.4)) typescript: specifier: 'catalog:' version: 5.5.4 vite: specifier: 'catalog:' - version: 5.4.10(@types/node@22.7.5) + version: 5.4.11(@types/node@22.7.5) vitest: specifier: 'catalog:' - version: 2.1.4(@types/node@22.7.5) + version: 2.1.5(@types/node@22.7.5) vue-tsc: specifier: 'catalog:' version: 2.1.10(typescript@5.5.4) @@ -224,51 +224,54 @@ importers: devDependencies: '@milaboratories/software-pframes-conv': specifier: 'catalog:' - version: 1.6.8 + version: 2.0.1 '@platforma-open/milaboratories.software-mixcr': specifier: 'catalog:' - version: 4.7.0-113-develop + version: 4.7.0-133-develop '@platforma-open/milaboratories.software-small-binaries': specifier: 'catalog:' - version: 1.14.5 + version: 1.14.6 '@platforma-sdk/tengo-builder': specifier: 'catalog:' version: 1.16.1 '@platforma-sdk/test': specifier: 'catalog:' - version: 1.7.52(@types/node@22.7.5) + version: 1.8.13(@types/node@22.7.5) '@platforma-sdk/workflow-tengo': specifier: 'catalog:' - version: 1.7.5 + version: 2.0.1 typescript: specifier: 'catalog:' version: 5.5.4 vitest: specifier: 'catalog:' - 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'@aws-sdk/types': 3.679.0 - '@smithy/types': 3.5.0 + '@aws-sdk/types': 3.686.0 + '@smithy/types': 3.6.0 bowser: 2.11.0 tslib: 2.7.0 - '@aws-sdk/util-user-agent-node@3.682.0': + '@aws-sdk/util-user-agent-node@3.691.0': dependencies: - '@aws-sdk/middleware-user-agent': 3.682.0 - '@aws-sdk/types': 3.679.0 - '@smithy/node-config-provider': 3.1.8 - '@smithy/types': 3.5.0 + '@aws-sdk/middleware-user-agent': 3.691.0 + '@aws-sdk/types': 3.686.0 + '@smithy/node-config-provider': 3.1.9 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@aws-sdk/xml-builder@3.679.0': + '@aws-sdk/xml-builder@3.686.0': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 tslib: 2.7.0 '@babel/helper-string-parser@7.25.7': {} @@ -3981,11 +3997,11 @@ snapshots: '@milaboratories/helpers@1.6.6': {} - '@milaboratories/pframes-node@1.6.8(@milaboratories/pl-model-common@1.5.2)': + '@milaboratories/pframes-node@2.0.1(@milaboratories/pl-model-common@1.6.1)': dependencies: '@mapbox/node-pre-gyp': 1.0.11 - 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'@milaboratories/pframes-node': 2.0.1(@milaboratories/pl-model-common@1.6.1) '@milaboratories/pl-client': 2.5.9 '@milaboratories/pl-config': 1.3.1 - '@milaboratories/pl-drivers': 1.3.13 + '@milaboratories/pl-drivers': 1.3.15 '@milaboratories/pl-local': 1.5.2 - '@milaboratories/pl-model-common': 1.5.2 - '@milaboratories/pl-model-middle-layer': 1.5.5 + '@milaboratories/pl-model-common': 1.6.1 + '@milaboratories/pl-model-middle-layer': 1.5.8 '@milaboratories/pl-tree': 1.4.10 '@milaboratories/resolve-helper': 1.0.1 '@milaboratories/ts-helpers': 1.1.1 - '@platforma-sdk/block-tools': 2.3.21 - '@platforma-sdk/model': 1.7.20 - '@platforma-sdk/workflow-tengo': 1.7.5 + '@platforma-sdk/block-tools': 2.3.24 + '@platforma-sdk/model': 1.8.0 + '@platforma-sdk/workflow-tengo': 2.0.1 canonicalize: 2.0.0 denque: 2.1.0 lru-cache: 11.0.2 @@ -4073,13 +4089,13 @@ snapshots: - encoding - supports-color - '@milaboratories/pl-model-common@1.5.2': + '@milaboratories/pl-model-common@1.6.1': dependencies: zod: 3.23.8 - '@milaboratories/pl-model-middle-layer@1.5.5': + '@milaboratories/pl-model-middle-layer@1.5.8': dependencies: - '@milaboratories/pl-model-common': 1.5.2 + '@milaboratories/pl-model-common': 1.6.1 utility-types: 3.11.0 zod: 3.23.8 @@ -4096,7 +4112,7 @@ snapshots: '@milaboratories/resolve-helper@1.0.1': {} - '@milaboratories/software-pframes-conv@1.6.8': {} + '@milaboratories/software-pframes-conv@2.0.1': {} '@milaboratories/tengo-tester@1.4.5': {} @@ -4109,7 +4125,7 @@ snapshots: dependencies: denque: 2.1.0 - '@milaboratories/uikit@2.0.11(typescript@5.5.4)': + '@milaboratories/uikit@2.1.2(typescript@5.5.4)': dependencies: vue: 3.5.12(typescript@5.5.4) transitivePeerDependencies: @@ -4151,30 +4167,30 @@ snapshots: '@pkgjs/parseargs@0.11.0': optional: true - '@platforma-open/milaboratories.samples-and-data.model@1.6.0': + '@platforma-open/milaboratories.samples-and-data.model@1.6.1': dependencies: - '@platforma-sdk/model': 1.7.20 + '@platforma-sdk/model': 1.8.0 zod: 3.23.8 - '@platforma-open/milaboratories.samples-and-data.ui@1.11.2': {} + '@platforma-open/milaboratories.samples-and-data.ui@1.11.3': {} - '@platforma-open/milaboratories.samples-and-data.workflow@1.7.5': {} + '@platforma-open/milaboratories.samples-and-data.workflow@1.7.7': {} - '@platforma-open/milaboratories.samples-and-data@1.6.3': + '@platforma-open/milaboratories.samples-and-data@1.6.5': dependencies: - '@platforma-open/milaboratories.samples-and-data.model': 1.6.0 - '@platforma-open/milaboratories.samples-and-data.ui': 1.11.2 - '@platforma-open/milaboratories.samples-and-data.workflow': 1.7.5 - '@platforma-sdk/model': 1.7.20 + '@platforma-open/milaboratories.samples-and-data.model': 1.6.1 + '@platforma-open/milaboratories.samples-and-data.ui': 1.11.3 + '@platforma-open/milaboratories.samples-and-data.workflow': 1.7.7 + '@platforma-sdk/model': 1.8.0 - '@platforma-open/milaboratories.software-mixcr@4.7.0-113-develop': {} + '@platforma-open/milaboratories.software-mixcr@4.7.0-133-develop': {} - '@platforma-open/milaboratories.software-small-binaries@1.14.5': {} + '@platforma-open/milaboratories.software-small-binaries@1.14.6': {} - '@platforma-sdk/block-tools@2.3.21': + '@platforma-sdk/block-tools@2.3.24': dependencies: - '@aws-sdk/client-s3': 3.685.0 - '@milaboratories/pl-model-middle-layer': 1.5.5 + '@aws-sdk/client-s3': 3.691.0 + '@milaboratories/pl-model-middle-layer': 1.5.8 '@milaboratories/resolve-helper': 1.0.1 '@milaboratories/ts-helpers': 1.1.1 '@milaboratories/ts-helpers-oclif': 1.1.10 @@ -4189,9 +4205,9 @@ snapshots: transitivePeerDependencies: - aws-crt - '@platforma-sdk/model@1.7.20': + '@platforma-sdk/model@1.8.0': dependencies: - '@milaboratories/pl-model-common': 1.5.2 + '@milaboratories/pl-model-common': 1.6.1 utility-types: 3.11.0 zod: 3.23.8 @@ -4202,15 +4218,15 @@ snapshots: canonicalize: 2.0.0 winston: 3.15.0 - '@platforma-sdk/test@1.7.52(@types/node@22.7.5)': + '@platforma-sdk/test@1.8.13(@types/node@22.7.5)': dependencies: '@milaboratories/computable': 2.2.1 '@milaboratories/pl-client': 2.5.9 - '@milaboratories/pl-middle-layer': 1.14.18 + '@milaboratories/pl-middle-layer': 1.14.28 '@milaboratories/pl-tree': 1.4.10 '@milaboratories/ts-helpers': 1.1.1 - '@platforma-sdk/model': 1.7.20 - vitest: 2.1.4(@types/node@22.7.5) + '@platforma-sdk/model': 1.8.0 + vitest: 2.1.5(@types/node@22.7.5) transitivePeerDependencies: - '@edge-runtime/vm' - '@types/node' @@ -4230,15 +4246,15 @@ snapshots: - supports-color - terser - '@platforma-sdk/ui-vue@1.7.51(typescript@5.5.4)': + '@platforma-sdk/ui-vue@1.8.11(typescript@5.5.4)': dependencies: - '@ag-grid-community/client-side-row-model': 32.3.2 - '@ag-grid-community/core': 32.3.2 + '@ag-grid-community/client-side-row-model': 32.3.3 + '@ag-grid-community/core': 32.3.3 '@ag-grid-community/csv-export': 32.3.2 '@ag-grid-community/infinite-row-model': 32.3.2 - '@ag-grid-community/styles': 32.3.2 + '@ag-grid-community/styles': 32.3.3 '@ag-grid-community/theming': 32.3.2 - '@ag-grid-community/vue3': 32.3.2(typescript@5.5.4) + '@ag-grid-community/vue3': 32.3.3(typescript@5.5.4) '@ag-grid-enterprise/clipboard': 32.3.2 '@ag-grid-enterprise/core': 32.3.2 '@ag-grid-enterprise/excel-export': 32.3.2 @@ -4246,18 +4262,18 @@ snapshots: '@ag-grid-enterprise/range-selection': 32.3.2 '@ag-grid-enterprise/rich-select': 32.3.2 '@ag-grid-enterprise/server-side-row-model': 32.3.2 - '@milaboratories/uikit': 2.0.11(typescript@5.5.4) - '@platforma-sdk/model': 1.7.20 + '@milaboratories/uikit': 2.1.2(typescript@5.5.4) + '@platforma-sdk/model': 1.8.0 canonicalize: 2.0.0 lru-cache: 11.0.2 vue: 3.5.12(typescript@5.5.4) transitivePeerDependencies: - typescript - '@platforma-sdk/workflow-tengo@1.7.5': + '@platforma-sdk/workflow-tengo@2.0.1': dependencies: - '@milaboratories/software-pframes-conv': 1.6.8 - '@platforma-open/milaboratories.software-small-binaries': 1.14.5 + '@milaboratories/software-pframes-conv': 2.0.1 + '@platforma-open/milaboratories.software-small-binaries': 1.14.6 '@protobuf-ts/grpc-transport@2.9.4(@grpc/grpc-js@1.12.2)': dependencies: @@ -4357,110 +4373,108 @@ snapshots: '@rollup/rollup-win32-x64-msvc@4.24.0': optional: true - '@smithy/abort-controller@3.1.5': + '@smithy/abort-controller@3.1.6': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/chunked-blob-reader-native@3.0.0': + '@smithy/chunked-blob-reader-native@3.0.1': dependencies: '@smithy/util-base64': 3.0.0 tslib: 2.7.0 - '@smithy/chunked-blob-reader@3.0.0': + '@smithy/chunked-blob-reader@4.0.0': dependencies: tslib: 2.7.0 - '@smithy/config-resolver@3.0.9': + '@smithy/config-resolver@3.0.10': dependencies: - '@smithy/node-config-provider': 3.1.8 - '@smithy/types': 3.5.0 + '@smithy/node-config-provider': 3.1.9 + '@smithy/types': 3.6.0 '@smithy/util-config-provider': 3.0.0 - '@smithy/util-middleware': 3.0.7 + '@smithy/util-middleware': 3.0.8 tslib: 2.7.0 - '@smithy/core@2.4.8': + '@smithy/core@2.5.1': dependencies: - '@smithy/middleware-endpoint': 3.1.4 - '@smithy/middleware-retry': 3.0.23 - '@smithy/middleware-serde': 3.0.7 - '@smithy/protocol-http': 4.1.4 - '@smithy/smithy-client': 3.4.0 - '@smithy/types': 3.5.0 + '@smithy/middleware-serde': 3.0.8 + '@smithy/protocol-http': 4.1.5 + '@smithy/types': 3.6.0 '@smithy/util-body-length-browser': 3.0.0 - '@smithy/util-middleware': 3.0.7 + '@smithy/util-middleware': 3.0.8 + '@smithy/util-stream': 3.2.1 '@smithy/util-utf8': 3.0.0 tslib: 2.7.0 - '@smithy/credential-provider-imds@3.2.4': + '@smithy/credential-provider-imds@3.2.5': dependencies: - '@smithy/node-config-provider': 3.1.8 - '@smithy/property-provider': 3.1.7 - '@smithy/types': 3.5.0 - '@smithy/url-parser': 3.0.7 + '@smithy/node-config-provider': 3.1.9 + '@smithy/property-provider': 3.1.8 + '@smithy/types': 3.6.0 + '@smithy/url-parser': 3.0.8 tslib: 2.7.0 - '@smithy/eventstream-codec@3.1.6': + '@smithy/eventstream-codec@3.1.7': dependencies: '@aws-crypto/crc32': 5.2.0 - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 '@smithy/util-hex-encoding': 3.0.0 tslib: 2.7.0 - '@smithy/eventstream-serde-browser@3.0.10': + '@smithy/eventstream-serde-browser@3.0.11': dependencies: - '@smithy/eventstream-serde-universal': 3.0.9 - '@smithy/types': 3.5.0 + '@smithy/eventstream-serde-universal': 3.0.10 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/eventstream-serde-config-resolver@3.0.7': + '@smithy/eventstream-serde-config-resolver@3.0.8': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/eventstream-serde-node@3.0.9': + '@smithy/eventstream-serde-node@3.0.10': dependencies: - '@smithy/eventstream-serde-universal': 3.0.9 - '@smithy/types': 3.5.0 + '@smithy/eventstream-serde-universal': 3.0.10 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/eventstream-serde-universal@3.0.9': + '@smithy/eventstream-serde-universal@3.0.10': dependencies: - '@smithy/eventstream-codec': 3.1.6 - '@smithy/types': 3.5.0 + '@smithy/eventstream-codec': 3.1.7 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/fetch-http-handler@3.2.9': + '@smithy/fetch-http-handler@4.0.0': dependencies: - '@smithy/protocol-http': 4.1.4 - '@smithy/querystring-builder': 3.0.7 - '@smithy/types': 3.5.0 + '@smithy/protocol-http': 4.1.5 + '@smithy/querystring-builder': 3.0.8 + '@smithy/types': 3.6.0 '@smithy/util-base64': 3.0.0 tslib: 2.7.0 - '@smithy/hash-blob-browser@3.1.6': + '@smithy/hash-blob-browser@3.1.7': dependencies: - '@smithy/chunked-blob-reader': 3.0.0 - '@smithy/chunked-blob-reader-native': 3.0.0 - '@smithy/types': 3.5.0 + '@smithy/chunked-blob-reader': 4.0.0 + '@smithy/chunked-blob-reader-native': 3.0.1 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/hash-node@3.0.7': + '@smithy/hash-node@3.0.8': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 '@smithy/util-buffer-from': 3.0.0 '@smithy/util-utf8': 3.0.0 tslib: 2.7.0 - '@smithy/hash-stream-node@3.1.6': + '@smithy/hash-stream-node@3.1.7': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 '@smithy/util-utf8': 3.0.0 tslib: 2.7.0 - '@smithy/invalid-dependency@3.0.7': + '@smithy/invalid-dependency@3.0.8': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 tslib: 2.7.0 '@smithy/is-array-buffer@2.2.0': @@ -4471,123 +4485,125 @@ snapshots: dependencies: tslib: 2.7.0 - '@smithy/md5-js@3.0.7': + '@smithy/md5-js@3.0.8': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 '@smithy/util-utf8': 3.0.0 tslib: 2.7.0 - '@smithy/middleware-content-length@3.0.9': + '@smithy/middleware-content-length@3.0.10': dependencies: - '@smithy/protocol-http': 4.1.4 - '@smithy/types': 3.5.0 + '@smithy/protocol-http': 4.1.5 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/middleware-endpoint@3.1.4': + '@smithy/middleware-endpoint@3.2.1': dependencies: - '@smithy/middleware-serde': 3.0.7 - '@smithy/node-config-provider': 3.1.8 - '@smithy/shared-ini-file-loader': 3.1.8 - '@smithy/types': 3.5.0 - '@smithy/url-parser': 3.0.7 - '@smithy/util-middleware': 3.0.7 + '@smithy/core': 2.5.1 + '@smithy/middleware-serde': 3.0.8 + '@smithy/node-config-provider': 3.1.9 + '@smithy/shared-ini-file-loader': 3.1.9 + '@smithy/types': 3.6.0 + '@smithy/url-parser': 3.0.8 + '@smithy/util-middleware': 3.0.8 tslib: 2.7.0 - '@smithy/middleware-retry@3.0.23': + '@smithy/middleware-retry@3.0.25': dependencies: - '@smithy/node-config-provider': 3.1.8 - '@smithy/protocol-http': 4.1.4 - '@smithy/service-error-classification': 3.0.7 - '@smithy/smithy-client': 3.4.0 - '@smithy/types': 3.5.0 - '@smithy/util-middleware': 3.0.7 - '@smithy/util-retry': 3.0.7 + '@smithy/node-config-provider': 3.1.9 + '@smithy/protocol-http': 4.1.5 + '@smithy/service-error-classification': 3.0.8 + '@smithy/smithy-client': 3.4.2 + '@smithy/types': 3.6.0 + '@smithy/util-middleware': 3.0.8 + '@smithy/util-retry': 3.0.8 tslib: 2.7.0 uuid: 9.0.1 - '@smithy/middleware-serde@3.0.7': + '@smithy/middleware-serde@3.0.8': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/middleware-stack@3.0.7': + '@smithy/middleware-stack@3.0.8': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/node-config-provider@3.1.8': + '@smithy/node-config-provider@3.1.9': dependencies: - '@smithy/property-provider': 3.1.7 - '@smithy/shared-ini-file-loader': 3.1.8 - '@smithy/types': 3.5.0 + '@smithy/property-provider': 3.1.8 + '@smithy/shared-ini-file-loader': 3.1.9 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/node-http-handler@3.2.4': + '@smithy/node-http-handler@3.2.5': dependencies: - '@smithy/abort-controller': 3.1.5 - '@smithy/protocol-http': 4.1.4 - '@smithy/querystring-builder': 3.0.7 - '@smithy/types': 3.5.0 + '@smithy/abort-controller': 3.1.6 + '@smithy/protocol-http': 4.1.5 + '@smithy/querystring-builder': 3.0.8 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/property-provider@3.1.7': + '@smithy/property-provider@3.1.8': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/protocol-http@4.1.4': + '@smithy/protocol-http@4.1.5': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/querystring-builder@3.0.7': + '@smithy/querystring-builder@3.0.8': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 '@smithy/util-uri-escape': 3.0.0 tslib: 2.7.0 - '@smithy/querystring-parser@3.0.7': + '@smithy/querystring-parser@3.0.8': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/service-error-classification@3.0.7': + '@smithy/service-error-classification@3.0.8': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 - '@smithy/shared-ini-file-loader@3.1.8': + '@smithy/shared-ini-file-loader@3.1.9': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/signature-v4@4.2.0': + '@smithy/signature-v4@4.2.1': dependencies: '@smithy/is-array-buffer': 3.0.0 - '@smithy/protocol-http': 4.1.4 - '@smithy/types': 3.5.0 + '@smithy/protocol-http': 4.1.5 + '@smithy/types': 3.6.0 '@smithy/util-hex-encoding': 3.0.0 - '@smithy/util-middleware': 3.0.7 + '@smithy/util-middleware': 3.0.8 '@smithy/util-uri-escape': 3.0.0 '@smithy/util-utf8': 3.0.0 tslib: 2.7.0 - '@smithy/smithy-client@3.4.0': + '@smithy/smithy-client@3.4.2': dependencies: - '@smithy/middleware-endpoint': 3.1.4 - '@smithy/middleware-stack': 3.0.7 - '@smithy/protocol-http': 4.1.4 - '@smithy/types': 3.5.0 - '@smithy/util-stream': 3.1.9 + '@smithy/core': 2.5.1 + '@smithy/middleware-endpoint': 3.2.1 + '@smithy/middleware-stack': 3.0.8 + '@smithy/protocol-http': 4.1.5 + '@smithy/types': 3.6.0 + '@smithy/util-stream': 3.2.1 tslib: 2.7.0 - '@smithy/types@3.5.0': + '@smithy/types@3.6.0': dependencies: tslib: 2.7.0 - '@smithy/url-parser@3.0.7': + '@smithy/url-parser@3.0.8': dependencies: - '@smithy/querystring-parser': 3.0.7 - '@smithy/types': 3.5.0 + '@smithy/querystring-parser': 3.0.8 + '@smithy/types': 3.6.0 tslib: 2.7.0 '@smithy/util-base64@3.0.0': @@ -4618,50 +4634,50 @@ snapshots: dependencies: tslib: 2.7.0 - '@smithy/util-defaults-mode-browser@3.0.23': + '@smithy/util-defaults-mode-browser@3.0.25': dependencies: - '@smithy/property-provider': 3.1.7 - '@smithy/smithy-client': 3.4.0 - '@smithy/types': 3.5.0 + '@smithy/property-provider': 3.1.8 + '@smithy/smithy-client': 3.4.2 + '@smithy/types': 3.6.0 bowser: 2.11.0 tslib: 2.7.0 - '@smithy/util-defaults-mode-node@3.0.23': + '@smithy/util-defaults-mode-node@3.0.25': dependencies: - '@smithy/config-resolver': 3.0.9 - '@smithy/credential-provider-imds': 3.2.4 - '@smithy/node-config-provider': 3.1.8 - '@smithy/property-provider': 3.1.7 - '@smithy/smithy-client': 3.4.0 - '@smithy/types': 3.5.0 + '@smithy/config-resolver': 3.0.10 + '@smithy/credential-provider-imds': 3.2.5 + '@smithy/node-config-provider': 3.1.9 + '@smithy/property-provider': 3.1.8 + '@smithy/smithy-client': 3.4.2 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/util-endpoints@2.1.3': + '@smithy/util-endpoints@2.1.4': dependencies: - '@smithy/node-config-provider': 3.1.8 - '@smithy/types': 3.5.0 + '@smithy/node-config-provider': 3.1.9 + '@smithy/types': 3.6.0 tslib: 2.7.0 '@smithy/util-hex-encoding@3.0.0': dependencies: tslib: 2.7.0 - '@smithy/util-middleware@3.0.7': + '@smithy/util-middleware@3.0.8': dependencies: - '@smithy/types': 3.5.0 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/util-retry@3.0.7': + '@smithy/util-retry@3.0.8': dependencies: - '@smithy/service-error-classification': 3.0.7 - '@smithy/types': 3.5.0 + '@smithy/service-error-classification': 3.0.8 + '@smithy/types': 3.6.0 tslib: 2.7.0 - '@smithy/util-stream@3.1.9': + '@smithy/util-stream@3.2.1': dependencies: - '@smithy/fetch-http-handler': 3.2.9 - '@smithy/node-http-handler': 3.2.4 - '@smithy/types': 3.5.0 + '@smithy/fetch-http-handler': 4.0.0 + '@smithy/node-http-handler': 3.2.5 + '@smithy/types': 3.6.0 '@smithy/util-base64': 3.0.0 '@smithy/util-buffer-from': 3.0.0 '@smithy/util-hex-encoding': 3.0.0 @@ -4682,10 +4698,10 @@ snapshots: '@smithy/util-buffer-from': 3.0.0 tslib: 2.7.0 - '@smithy/util-waiter@3.1.6': + '@smithy/util-waiter@3.1.7': dependencies: - '@smithy/abort-controller': 3.1.5 - '@smithy/types': 3.5.0 + '@smithy/abort-controller': 3.1.6 + '@smithy/types': 3.6.0 tslib: 2.7.0 '@types/estree@1.0.6': {} @@ -4704,48 +4720,48 @@ snapshots: '@types/web-bluetooth@0.0.20': {} - '@vitejs/plugin-vue@5.1.4(vite@5.4.10(@types/node@22.7.5))(vue@3.5.12(typescript@5.5.4))': + '@vitejs/plugin-vue@5.2.0(vite@5.4.11(@types/node@22.7.5))(vue@3.5.12(typescript@5.5.4))': dependencies: - vite: 5.4.10(@types/node@22.7.5) + vite: 5.4.11(@types/node@22.7.5) vue: 3.5.12(typescript@5.5.4) - '@vitest/expect@2.1.4': + '@vitest/expect@2.1.5': dependencies: - '@vitest/spy': 2.1.4 - '@vitest/utils': 2.1.4 + '@vitest/spy': 2.1.5 + '@vitest/utils': 2.1.5 chai: 5.1.2 tinyrainbow: 1.2.0 - '@vitest/mocker@2.1.4(vite@5.4.10(@types/node@22.7.5))': + '@vitest/mocker@2.1.5(vite@5.4.11(@types/node@22.7.5))': dependencies: - '@vitest/spy': 2.1.4 + '@vitest/spy': 2.1.5 estree-walker: 3.0.3 magic-string: 0.30.12 optionalDependencies: - vite: 5.4.10(@types/node@22.7.5) + vite: 5.4.11(@types/node@22.7.5) - '@vitest/pretty-format@2.1.4': + '@vitest/pretty-format@2.1.5': dependencies: tinyrainbow: 1.2.0 - '@vitest/runner@2.1.4': + '@vitest/runner@2.1.5': dependencies: - '@vitest/utils': 2.1.4 + '@vitest/utils': 2.1.5 pathe: 1.1.2 - '@vitest/snapshot@2.1.4': + '@vitest/snapshot@2.1.5': dependencies: - '@vitest/pretty-format': 2.1.4 + '@vitest/pretty-format': 2.1.5 magic-string: 0.30.12 pathe: 1.1.2 - '@vitest/spy@2.1.4': + '@vitest/spy@2.1.5': dependencies: tinyspy: 3.0.2 - '@vitest/utils@2.1.4': + '@vitest/utils@2.1.5': dependencies: - '@vitest/pretty-format': 2.1.4 + '@vitest/pretty-format': 2.1.5 loupe: 3.1.2 tinyrainbow: 1.2.0 @@ -4860,6 +4876,8 @@ snapshots: ag-charts-types@10.3.1: {} + ag-charts-types@10.3.3: {} + agent-base@6.0.2: dependencies: debug: 4.3.7(supports-color@8.1.1) @@ -5189,6 +5207,8 @@ snapshots: entities@4.5.0: {} + es-module-lexer@1.5.4: {} + esbuild@0.21.5: optionalDependencies: '@esbuild/aix-ppc64': 0.21.5 @@ -5926,7 +5946,7 @@ snapshots: stackback@0.0.2: {} - std-env@3.7.0: {} + std-env@3.8.0: {} streamx@2.20.1: dependencies: @@ -6164,12 +6184,13 @@ snapshots: uuid@9.0.1: {} - vite-node@2.1.4(@types/node@22.7.5): + vite-node@2.1.5(@types/node@22.7.5): dependencies: cac: 6.7.14 debug: 4.3.7(supports-color@8.1.1) + es-module-lexer: 1.5.4 pathe: 1.1.2 - vite: 5.4.10(@types/node@22.7.5) + vite: 5.4.11(@types/node@22.7.5) transitivePeerDependencies: - '@types/node' - less @@ -6181,7 +6202,7 @@ snapshots: - supports-color - terser - vite@5.4.10(@types/node@22.7.5): + vite@5.4.11(@types/node@22.7.5): dependencies: esbuild: 0.21.5 postcss: 8.4.47 @@ -6190,27 +6211,27 @@ snapshots: '@types/node': 22.7.5 fsevents: 2.3.3 - vitest@2.1.4(@types/node@22.7.5): + vitest@2.1.5(@types/node@22.7.5): dependencies: - '@vitest/expect': 2.1.4 - '@vitest/mocker': 2.1.4(vite@5.4.10(@types/node@22.7.5)) - '@vitest/pretty-format': 2.1.4 - '@vitest/runner': 2.1.4 - '@vitest/snapshot': 2.1.4 - '@vitest/spy': 2.1.4 - '@vitest/utils': 2.1.4 + '@vitest/expect': 2.1.5 + '@vitest/mocker': 2.1.5(vite@5.4.11(@types/node@22.7.5)) + '@vitest/pretty-format': 2.1.5 + '@vitest/runner': 2.1.5 + '@vitest/snapshot': 2.1.5 + '@vitest/spy': 2.1.5 + '@vitest/utils': 2.1.5 chai: 5.1.2 debug: 4.3.7(supports-color@8.1.1) expect-type: 1.1.0 magic-string: 0.30.12 pathe: 1.1.2 - std-env: 3.7.0 + std-env: 3.8.0 tinybench: 2.9.0 tinyexec: 0.3.1 tinypool: 1.0.1 tinyrainbow: 1.2.0 - vite: 5.4.10(@types/node@22.7.5) - vite-node: 2.1.4(@types/node@22.7.5) + vite: 5.4.11(@types/node@22.7.5) + vite-node: 2.1.5(@types/node@22.7.5) why-is-node-running: 2.3.0 optionalDependencies: '@types/node': 22.7.5 diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml index 052f099..00c35a8 100644 --- a/pnpm-workspace.yaml +++ b/pnpm-workspace.yaml @@ -6,18 +6,18 @@ packages: - . catalog: - '@platforma-sdk/workflow-tengo': ^1.7.5 - '@platforma-sdk/model': ^1.7.20 - '@platforma-sdk/ui-vue': ^1.7.51 + '@platforma-sdk/workflow-tengo': ^2.0.1 + '@platforma-sdk/model': ^1.8.0 + '@platforma-sdk/ui-vue': ^1.8.11 '@platforma-sdk/tengo-builder': ^1.16.1 - '@platforma-sdk/block-tools': ^2.3.21 + '@platforma-sdk/block-tools': ^2.3.24 - '@platforma-sdk/test': ^1.7.52 + '@platforma-sdk/test': ^1.8.13 '@milaboratories/helpers': ^1.6.6 - '@milaboratories/software-pframes-conv': 1.6.8 - '@platforma-open/milaboratories.software-small-binaries': ^1.14.5 - '@platforma-open/milaboratories.software-mixcr': 4.7.0-113-develop + '@milaboratories/software-pframes-conv': 2.0.1 + '@platforma-open/milaboratories.software-small-binaries': ^1.14.6 + '@platforma-open/milaboratories.software-mixcr': 4.7.0-133-develop 'vue': ^3.5.12 'vue-tsc': ^2.1.10 @@ -29,13 +29,13 @@ catalog: 'tsup': ~8.1.2 'turbo': ^2.2.3 - 'vite': ^5.4.10 - 'vitest': ^2.1.4 - '@vitejs/plugin-vue': ^5.1.4 + 'vite': ^5.4.11 + 'vitest': ^2.1.5 + '@vitejs/plugin-vue': ^5.2.0 '@vueuse/core': ^11.2.0 - '@ag-grid-community/core': &ag-grid ^32.3.2 + '@ag-grid-community/core': &ag-grid ^32.3.3 '@ag-grid-community/client-side-row-model': *ag-grid '@ag-grid-community/vue3': *ag-grid '@ag-grid-community/styles': *ag-grid @@ -44,5 +44,5 @@ catalog: # other blocks used in tests - '@platforma-open/milaboratories.samples-and-data': ^1.6.3 - '@platforma-open/milaboratories.samples-and-data.model': ^1.6.0 + '@platforma-open/milaboratories.samples-and-data': ^1.6.5 + '@platforma-open/milaboratories.samples-and-data.model': ^1.6.1 diff --git a/test/test_config.json b/test/test_config.json new file mode 100644 index 0000000..297c77f --- /dev/null +++ b/test/test_config.json @@ -0,0 +1,5 @@ +{ + "address": "http://127.0.0.1:6345?tx-delay=5&force-sync=true", + "test_user": "test_user", + "test_password": "test_password" +} diff --git a/ui/src/SettingsPanel.vue b/ui/src/SettingsPanel.vue index 9d0a75c..8137196 100644 --- a/ui/src/SettingsPanel.vue +++ b/ui/src/SettingsPanel.vue @@ -94,7 +94,7 @@ function setLimitInput() { - diff --git a/workflow/src/calculate-pfconv-params.tpl.tengo b/workflow/src/calculate-pfconv-params.tpl.tengo index 433b456..d7ab572 100644 --- a/workflow/src/calculate-pfconv-params.tpl.tengo +++ b/workflow/src/calculate-pfconv-params.tpl.tengo @@ -97,7 +97,6 @@ self.body(func(inputs) { params: { "axes": axes, "columns": columns, - "naStr": "region_not_covered", "storageFormat": "Binary", "partitionKeyLength": 0 } diff --git a/workflow/src/export-clones-bulk.tpl.tengo b/workflow/src/export-clones-bulk.tpl.tengo index 2a65521..190afb3 100644 --- a/workflow/src/export-clones-bulk.tpl.tengo +++ b/workflow/src/export-clones-bulk.tpl.tengo @@ -3,7 +3,7 @@ ll := import("@platforma-sdk/workflow-tengo:ll") xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv") self := import("@platforma-sdk/workflow-tengo:tpl") -pframes := import("@platforma-sdk/workflow-tengo:pframes") +pcolumn := import("@platforma-sdk/workflow-tengo:pframes.pcolumn") pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants") text := import("text") @@ -20,7 +20,7 @@ self.body(func(inputs) { pfconvParams := inputs.pfconvParams data := self.rawInputs().data.getValue() - csvMap := pframes.pColumnResourceMapDataBuilder(/* key length */ 1) + csvMap := pcolumn.resourceMapBuilder(/* key length */ 1) for fileName, file in data.inputs() { if !text.has_prefix(fileName, FILE_NAME_PREFIX) || !text.has_suffix(fileName, FILE_NAME_SUFFIX) { diff --git a/workflow/src/mixcr-analyze.tpl.tengo b/workflow/src/mixcr-analyze.tpl.tengo index eeca5f2..f1b4767 100644 --- a/workflow/src/mixcr-analyze.tpl.tengo +++ b/workflow/src/mixcr-analyze.tpl.tengo @@ -8,6 +8,7 @@ exec := import("@platforma-sdk/workflow-tengo:exec") assets := import("@platforma-sdk/workflow-tengo:assets") render := import("@platforma-sdk/workflow-tengo:render") pframes := import("@platforma-sdk/workflow-tengo:pframes") +pcolumn := import("@platforma-sdk/workflow-tengo:pframes.pcolumn") xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv") mixcr := import(":mixcr") @@ -142,7 +143,7 @@ self.body(func(inputs) { // collecting results - reportsMap := pframes.pColumnResourceMapDataBuilder( /* keyLength */ 2 ) + reportsMap := pcolumn.resourceMapBuilder( /* keyLength */ 2 ) for report in reports { reportsMap.add([report.id, "json"], mixcrCmd.getFile(report.fileJson)) reportsMap.add([report.id, "txt"], mixcrCmd.getFile(report.fileTxt)) diff --git a/workflow/src/pfconv_params.lib.tengo b/workflow/src/pfconv_params.lib.tengo index 5468ccc..a76f62d 100644 --- a/workflow/src/pfconv_params.lib.tengo +++ b/workflow/src/pfconv_params.lib.tengo @@ -5,6 +5,7 @@ getColumns := func(blockId) { "axes": [ { "column": "cloneId", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/cloneId", "type": "Long", @@ -18,6 +19,7 @@ getColumns := func(blockId) { } }, { "column": "tagValueCELL", + "naRegex": "", "spec": { "name": "pl7.app/vdj/tagValueCELL", "type": "String", @@ -33,6 +35,7 @@ getColumns := func(blockId) { { "column": "cellGroup", "id": "cell-group", + "naRegex": "region_not_covered", "allowNA": false, "spec": { "name": "pl7.app/vdj/cellGroup", @@ -46,6 +49,7 @@ getColumns := func(blockId) { }, { "column": "readCount", "id": "read-count", + "naRegex": "region_not_covered", "allowNA": false, "spec": { "name": "pl7.app/vdj/readCount", @@ -59,6 +63,7 @@ getColumns := func(blockId) { }, { "column": "readFraction", "id": "read-fraction", + "naRegex": "region_not_covered", "allowNA": false, "spec": { "name": "pl7.app/vdj/readFraction", @@ -72,6 +77,7 @@ getColumns := func(blockId) { }, { "column": "uniqueMoleculeCount", "id": "umi-count", + "naRegex": "region_not_covered", "allowNA": false, "spec": { "name": "pl7.app/vdj/uniqueMoleculeCount", @@ -85,6 +91,7 @@ getColumns := func(blockId) { }, { "column": "uniqueMoleculeFraction", "id": "umi-fraction", + "naRegex": "region_not_covered", "allowNA": false, "spec": { "name": "pl7.app/vdj/uniqueMoleculeFraction", @@ -98,6 +105,7 @@ getColumns := func(blockId) { }, { "column": "targetSequences", "id": "n-seq-clonal-sequences", + "naRegex": "", "allowNA": false, "spec": { "name": "pl7.app/vdj/sequence", @@ -116,6 +124,7 @@ getColumns := func(blockId) { }, { "column": "targetQualities", "id": "clonal-qualities", + "naRegex": "", "allowNA": false, "spec": { "name": "pl7.app/vdj/sequenceQuality", @@ -132,6 +141,7 @@ getColumns := func(blockId) { }, { "column": "bestVHit", "id": "best-v-hit", + "naRegex": "", "allowNA": false, "spec": { "name": "pl7.app/vdj/geneHit", @@ -144,12 +154,12 @@ getColumns := func(blockId) { "pl7.app/label": "Best V hit", "pl7.app/table/visibility": "default", "pl7.app/table/orderPriority": "1104" - } } }, { "column": "bestDHit", "id": "best-d-hit", + "naRegex": "", "spec": { "name": "pl7.app/vdj/geneHit", "valueType": "String", @@ -166,6 +176,7 @@ getColumns := func(blockId) { }, { "column": "bestJHit", "id": "best-j-hit", + "naRegex": "", "allowNA": false, "spec": { "name": "pl7.app/vdj/geneHit", @@ -183,6 +194,7 @@ getColumns := func(blockId) { }, { "column": "bestCHit", "id": "best-c-hit", + "naRegex": "", "spec": { "name": "pl7.app/vdj/geneHit", "valueType": "String", @@ -199,6 +211,7 @@ getColumns := func(blockId) { }, { "column": "nSeqFR1", "id": "n-seq-fr1", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -215,6 +228,7 @@ getColumns := func(blockId) { }, { "column": "minQualFR1", "id": "min-qual-fr1", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequenceQuality", "valueType": "Int", @@ -230,10 +244,10 @@ getColumns := func(blockId) { }, { "column": "nSeqFR2", "id": "n-seq-fr2", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", - "domain": { "pl7.app/vdj/feature": "FR2", "pl7.app/alphabet": "nucleotide" @@ -247,6 +261,7 @@ getColumns := func(blockId) { }, { "column": "minQualFR2", "id": "min-qual-fr2", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequenceQuality", "valueType": "Int", @@ -262,6 +277,7 @@ getColumns := func(blockId) { }, { "column": "nSeqFR3", "id": "n-seq-fr3", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -278,6 +294,7 @@ getColumns := func(blockId) { }, { "column": "minQualFR3", "id": "min-qual-fr3", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequenceQuality", "valueType": "Int", @@ -293,6 +310,7 @@ getColumns := func(blockId) { }, { "column": "nSeqFR4", "id": "n-seq-fr4", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -309,6 +327,7 @@ getColumns := func(blockId) { }, { "column": "minQualFR4", "id": "min-qual-fr4", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequenceQuality", "valueType": "Int", @@ -324,6 +343,7 @@ getColumns := func(blockId) { }, { "column": "nSeqCDR1", "id": "n-seq-cdr1", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -340,6 +360,7 @@ getColumns := func(blockId) { }, { "column": "minQualCDR1", "id": "min-qual-cdr1", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/minQualCDR1", "valueType": "Int", @@ -355,6 +376,7 @@ getColumns := func(blockId) { }, { "column": "nSeqCDR2", "id": "n-seq-cdr2", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -371,6 +393,7 @@ getColumns := func(blockId) { }, { "column": "minQualCDR2", "id": "min-qual-cdr2", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequenceQuality", "valueType": "Int", @@ -386,6 +409,7 @@ getColumns := func(blockId) { }, { "column": "nSeqCDR3", "id": "n-seq-cdr3", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -402,6 +426,7 @@ getColumns := func(blockId) { }, { "column": "minQualCDR3", "id": "min-qual-cdr3", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequenceQuality", "valueType": "Int", @@ -417,6 +442,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqFR1", "id": "aa-seq-fr1", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -433,6 +459,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqFR2", "id": "aa-seq-fr2", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -449,6 +476,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqFR3", "id": "aa-seq-fr3", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -465,6 +493,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqFR4", "id": "aa-seq-fr4", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -481,6 +510,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqCDR1", "id": "aa-seq-cdr1", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -497,6 +527,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqCDR2", "id": "aa-seq-cdr2", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -513,6 +544,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqCDR3", "id": "aa-seq-cdr3", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -529,6 +561,7 @@ getColumns := func(blockId) { }, { "column": "nSeqImputedFR1", "id": "n-seq-imputed-fr1", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -545,6 +578,7 @@ getColumns := func(blockId) { }, { "column": "nSeqImputedFR2", "id": "n-seq-imputed-fr2", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -561,6 +595,7 @@ getColumns := func(blockId) { }, { "column": "nSeqImputedFR3", "id": "n-seq-imputed-fr3", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -577,6 +612,7 @@ getColumns := func(blockId) { }, { "column": "nSeqImputedFR4", "id": "n-seq-imputed-fr4", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -593,6 +629,7 @@ getColumns := func(blockId) { }, { "column": "nSeqImputedCDR1", "id": "n-seq-imputed-cdr1", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -609,6 +646,7 @@ getColumns := func(blockId) { }, { "column": "nSeqImputedCDR2", "id": "n-seq-imputed-cdr2", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -625,6 +663,7 @@ getColumns := func(blockId) { }, { "column": "nSeqImputedCDR3", "id": "n-seq-imputed-CDR3", + "naRegex": "", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -641,6 +680,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqImputedFR1", "id": "aa-seq-imputed-fr1", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -657,6 +697,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqImputedFR2", "id": "aa-seq-imputed-fr2", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -673,6 +714,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqImputedFR3", "id": "aa-seq-imputed-fr3", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -689,6 +731,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqImputedFR4", "id": "aa-seq-imputed-fr4", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -705,6 +748,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqImputedCDR1", "id": "aa-seq-imputed-cdr1", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -721,6 +765,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqImputedCDR2", "id": "aa-seq-imputed-cdr2", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -737,6 +782,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqImputedCDR3", "id": "aa-seq-imputed-CDR3", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -753,6 +799,7 @@ getColumns := func(blockId) { }, { "column": "isotype", "id": "isotype", + "naRegex": "", "spec": { "valueType": "String", "name": "pl7.app/vdj/isotype", @@ -765,6 +812,7 @@ getColumns := func(blockId) { }, { "column": "topChains", "id": "top-chains", + "naRegex": "", "allowNA": false, "spec": { "valueType": "String", diff --git a/workflow/src/process.tpl.tengo b/workflow/src/process.tpl.tengo index 600cfaa..4355ccb 100644 --- a/workflow/src/process.tpl.tengo +++ b/workflow/src/process.tpl.tengo @@ -81,7 +81,7 @@ self.body(func(inputs) { }) } - decomposition := pUtil.decomposePfconvCfg(pfconvParams, { + decomposition := pUtil.decomposePfconvImportCfg(pfconvParams, { additionalAxesSpec: cColumnsAdditionalAxesSpec }) purifiedPfconvCfg := decomposition.purifiedCfg From 4e97b9050f9e5ce5c6752a62661e43fcfb59463a Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 14 Nov 2024 23:32:31 +0100 Subject: [PATCH 2/3] Fix pfconv params & add MiXCR cache --- workflow/src/mixcr-analyze.tpl.tengo | 2 ++ workflow/src/pfconv_params.lib.tengo | 52 ++++++++++++++-------------- 2 files changed, 28 insertions(+), 26 deletions(-) diff --git a/workflow/src/mixcr-analyze.tpl.tengo b/workflow/src/mixcr-analyze.tpl.tengo index f1b4767..abdb618 100644 --- a/workflow/src/mixcr-analyze.tpl.tengo +++ b/workflow/src/mixcr-analyze.tpl.tengo @@ -11,6 +11,7 @@ pframes := import("@platforma-sdk/workflow-tengo:pframes") pcolumn := import("@platforma-sdk/workflow-tengo:pframes.pcolumn") xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv") mixcr := import(":mixcr") +times := import("times") json := import("json") @@ -139,6 +140,7 @@ self.body(func(inputs) { mixcrCmdBuilder.saveFileSet("clones", "^result\\.clones_[A-Z0-9]+\\.tsv$") } + mixcrCmdBuilder = mixcrCmdBuilder.cache(48 * times.hour) mixcrCmd := mixcrCmdBuilder.run() // collecting results diff --git a/workflow/src/pfconv_params.lib.tengo b/workflow/src/pfconv_params.lib.tengo index a76f62d..6bd1073 100644 --- a/workflow/src/pfconv_params.lib.tengo +++ b/workflow/src/pfconv_params.lib.tengo @@ -1,11 +1,10 @@ ll := import("@platforma-sdk/workflow-tengo:ll") getColumns := func(blockId) { - return { + cols := { "axes": [ { "column": "cloneId", - "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/cloneId", "type": "Long", @@ -35,8 +34,8 @@ getColumns := func(blockId) { { "column": "cellGroup", "id": "cell-group", - "naRegex": "region_not_covered", - "allowNA": false, + "naRegex": "undefined", + "allowNA": true, "spec": { "name": "pl7.app/vdj/cellGroup", "valueType": "Long", @@ -49,7 +48,6 @@ getColumns := func(blockId) { }, { "column": "readCount", "id": "read-count", - "naRegex": "region_not_covered", "allowNA": false, "spec": { "name": "pl7.app/vdj/readCount", @@ -63,7 +61,6 @@ getColumns := func(blockId) { }, { "column": "readFraction", "id": "read-fraction", - "naRegex": "region_not_covered", "allowNA": false, "spec": { "name": "pl7.app/vdj/readFraction", @@ -77,7 +74,6 @@ getColumns := func(blockId) { }, { "column": "uniqueMoleculeCount", "id": "umi-count", - "naRegex": "region_not_covered", "allowNA": false, "spec": { "name": "pl7.app/vdj/uniqueMoleculeCount", @@ -91,7 +87,6 @@ getColumns := func(blockId) { }, { "column": "uniqueMoleculeFraction", "id": "umi-fraction", - "naRegex": "region_not_covered", "allowNA": false, "spec": { "name": "pl7.app/vdj/uniqueMoleculeFraction", @@ -159,7 +154,7 @@ getColumns := func(blockId) { }, { "column": "bestDHit", "id": "best-d-hit", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/geneHit", "valueType": "String", @@ -176,7 +171,7 @@ getColumns := func(blockId) { }, { "column": "bestJHit", "id": "best-j-hit", - "naRegex": "", + "naRegex": "region_not_covered", "allowNA": false, "spec": { "name": "pl7.app/vdj/geneHit", @@ -194,7 +189,7 @@ getColumns := func(blockId) { }, { "column": "bestCHit", "id": "best-c-hit", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/geneHit", "valueType": "String", @@ -211,7 +206,7 @@ getColumns := func(blockId) { }, { "column": "nSeqFR1", "id": "n-seq-fr1", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -228,7 +223,7 @@ getColumns := func(blockId) { }, { "column": "minQualFR1", "id": "min-qual-fr1", - "naRegex": "region_not_covered", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequenceQuality", "valueType": "Int", @@ -244,7 +239,7 @@ getColumns := func(blockId) { }, { "column": "nSeqFR2", "id": "n-seq-fr2", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -277,7 +272,7 @@ getColumns := func(blockId) { }, { "column": "nSeqFR3", "id": "n-seq-fr3", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -310,7 +305,7 @@ getColumns := func(blockId) { }, { "column": "nSeqFR4", "id": "n-seq-fr4", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -343,7 +338,7 @@ getColumns := func(blockId) { }, { "column": "nSeqCDR1", "id": "n-seq-cdr1", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -376,7 +371,7 @@ getColumns := func(blockId) { }, { "column": "nSeqCDR2", "id": "n-seq-cdr2", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "name": "pl7.app/vdj/sequence", "valueType": "String", @@ -409,7 +404,7 @@ getColumns := func(blockId) { }, { "column": "nSeqCDR3", "id": "n-seq-cdr3", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -442,7 +437,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqFR1", "id": "aa-seq-fr1", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -459,7 +454,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqFR2", "id": "aa-seq-fr2", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -476,7 +471,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqFR3", "id": "aa-seq-fr3", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -493,7 +488,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqFR4", "id": "aa-seq-fr4", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -510,7 +505,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqCDR1", "id": "aa-seq-cdr1", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -527,7 +522,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqCDR2", "id": "aa-seq-cdr2", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -544,7 +539,7 @@ getColumns := func(blockId) { }, { "column": "aaSeqCDR3", "id": "aa-seq-cdr3", - "naRegex": "", + "naRegex": "region_not_covered", "spec": { "valueType": "String", "name": "pl7.app/vdj/sequence", @@ -828,6 +823,11 @@ getColumns := func(blockId) { "storageFormat": "Binary", "partitionKeyLength": 0 } + + for col in cols.columns { + col["allowNA"] = true + } + return cols } export ll.toStrict({ From fddc283744c05956a74c7ddb8d4c4cda204cb543 Mon Sep 17 00:00:00 2001 From: Stanislav Poslavsky Date: Thu, 14 Nov 2024 23:34:06 +0100 Subject: [PATCH 3/3] changeset --- .changeset/ninety-foxes-reply.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 .changeset/ninety-foxes-reply.md diff --git a/.changeset/ninety-foxes-reply.md b/.changeset/ninety-foxes-reply.md new file mode 100644 index 0000000..e723ab5 --- /dev/null +++ b/.changeset/ninety-foxes-reply.md @@ -0,0 +1,9 @@ +--- +'@platforma-open/milaboratories.mixcr-clonotyping.workflow': minor +'@platforma-open/milaboratories.mixcr-clonotyping.test': minor +'@platforma-open/milaboratories.mixcr-clonotyping.ui': minor +'@platforma-open/milaboratories.mixcr-clonotyping': minor +--- + +- Cache MiXCR results for 48h +- Migrate to new pfconv params & fix columns