From 9a99a0dbac719fb06eb3db93e023d01424506d40 Mon Sep 17 00:00:00 2001 From: Dmitry Bolotin Date: Tue, 22 Oct 2024 13:07:08 +0200 Subject: [PATCH] multiple fixes --- .changeset/cuddly-feet-trade.md | 9 + .changeset/popular-bugs-grow.md | 5 + .changeset/purple-kings-report.md | 5 + .changeset/tiny-beans-decide.md | 5 + model/src/index.ts | 2 +- model/src/preset.ts | 3 + pnpm-lock.yaml | 1003 +++++++++++++++---------- pnpm-workspace.yaml | 22 +- test/assets/expected_results/mixcr.sh | 8 +- test/src/wf.test.ts | 1 + ui/src/SettingsPanel.vue | 16 +- workflow/src/process.tpl.tengo | 16 +- 12 files changed, 690 insertions(+), 405 deletions(-) create mode 100644 .changeset/cuddly-feet-trade.md create mode 100644 .changeset/popular-bugs-grow.md create mode 100644 .changeset/purple-kings-report.md create mode 100644 .changeset/tiny-beans-decide.md diff --git a/.changeset/cuddly-feet-trade.md b/.changeset/cuddly-feet-trade.md new file mode 100644 index 0000000..c5f330d --- /dev/null +++ b/.changeset/cuddly-feet-trade.md @@ -0,0 +1,9 @@ +--- +'@platforma-open/milaboratories.mixcr-clonotyping.workflow': patch +'@platforma-open/milaboratories.mixcr-clonotyping.model': patch +'@platforma-open/milaboratories.mixcr-clonotyping.test': patch +'@platforma-open/milaboratories.mixcr-clonotyping.ui': patch +'@platforma-open/milaboratories.mixcr-clonotyping': patch +--- + +SDK upgrade diff --git a/.changeset/popular-bugs-grow.md b/.changeset/popular-bugs-grow.md new file mode 100644 index 0000000..a78dae0 --- /dev/null +++ b/.changeset/popular-bugs-grow.md @@ -0,0 +1,5 @@ +--- +'@platforma-open/milaboratories.mixcr-clonotyping.workflow': patch +--- + +fixes error when using presets with floating assembling features diff --git a/.changeset/purple-kings-report.md b/.changeset/purple-kings-report.md new file mode 100644 index 0000000..87d356d --- /dev/null +++ b/.changeset/purple-kings-report.md @@ -0,0 +1,5 @@ +--- +'@platforma-open/milaboratories.mixcr-clonotyping.ui': patch +--- + +fixes quick args multi-set problem diff --git a/.changeset/tiny-beans-decide.md b/.changeset/tiny-beans-decide.md new file mode 100644 index 0000000..efe354b --- /dev/null +++ b/.changeset/tiny-beans-decide.md @@ -0,0 +1,5 @@ +--- +'@platforma-open/milaboratories.mixcr-clonotyping.model': patch +--- + +fixes absence of mitool-based presets diff --git a/model/src/index.ts b/model/src/index.ts index b0d42c2..7c89fcf 100644 --- a/model/src/index.ts +++ b/model/src/index.ts @@ -153,7 +153,7 @@ export const platforma = BlockModel.create('Heavy') return [{ type: 'link', href: '/', label: 'Main' }]; }) - .inputsValid((ctx) => BlockArgsValid.safeParse(ctx.args).success) + .argsValid((ctx) => BlockArgsValid.safeParse(ctx.args).success) .done(); diff --git a/model/src/preset.ts b/model/src/preset.ts index c730678..7ec49aa 100644 --- a/model/src/preset.ts +++ b/model/src/preset.ts @@ -1,6 +1,9 @@ import { z } from 'zod'; const MiXCRStage = z.union([ + z.literal('mitool-parse'), + z.literal('mitool-refine-tags'), + z.literal('mitool-consensus'), z.literal('parse'), z.literal('refineTags'), z.literal('consensus'), diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 78746ba..3ffc263 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -25,35 +25,35 @@ catalogs: specifier: ^1.6.5 version: 1.6.5 '@milaboratories/software-pframes-conv': - specifier: ^1.5.10 - version: 1.5.10 + specifier: ^1.6.1 + version: 1.6.1 '@milaboratories/software-small-binaries': specifier: ^1.11.0 version: 1.12.0 '@platforma-open/milaboratories.samples-and-data': - specifier: ^1.4.0 - version: 1.4.0 + specifier: ^1.5.2 + version: 1.5.2 '@platforma-open/milaboratories.samples-and-data.model': - specifier: ^1.4.0 - version: 1.4.0 + specifier: ^1.4.2 + version: 1.4.2 '@platforma-open/milaboratories.software-mixcr': specifier: 4.7.0-112-develop version: 4.7.0-112-develop '@platforma-sdk/block-tools': - specifier: ^2.3.14 - version: 2.3.14 + specifier: ^2.3.17 + version: 2.3.17 '@platforma-sdk/model': - specifier: ^1.7.0 - version: 1.7.0 + specifier: ^1.7.9 + version: 1.7.9 '@platforma-sdk/tengo-builder': specifier: ^1.14.13 version: 1.14.13 '@platforma-sdk/test': - specifier: ^1.5.37 - version: 1.5.51 + specifier: ^1.7.9 + version: 1.7.9 '@platforma-sdk/ui-vue': - specifier: ^1.7.1 - version: 1.7.1 + specifier: ^1.7.9 + version: 1.7.9 '@platforma-sdk/workflow-tengo': specifier: ^1.5.0 version: 1.5.0 @@ -67,8 +67,8 @@ catalogs: specifier: ~8.1.2 version: 8.1.2 turbo: - specifier: ^2.1.3 - version: 2.1.3 + specifier: ^2.2.3 + version: 2.2.3 typescript: specifier: ~5.5.4 version: 5.5.4 @@ -76,14 +76,14 @@ catalogs: specifier: ^3.11.0 version: 3.11.0 vite: - specifier: ^5.4.8 - version: 5.4.8 + specifier: ^5.4.9 + version: 5.4.9 vitest: - specifier: ^2.1.2 - version: 2.1.2 + specifier: ^2.1.3 + version: 2.1.3 vue: - specifier: ^3.5.11 - version: 3.5.11 + specifier: ^3.5.12 + version: 3.5.12 vue-tsc: specifier: ^2.1.6 version: 2.1.6 @@ -106,30 +106,30 @@ 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'@platforma-open/milaboratories.samples-and-data': specifier: 'catalog:' - version: 1.4.0(typescript@5.5.4) + version: 1.5.2 '@platforma-open/milaboratories.samples-and-data.model': specifier: 'catalog:' - version: 1.4.0 + version: 1.4.2 this-block: specifier: workspace:@platforma-open/milaboratories.mixcr-clonotyping@* version: link:.. devDependencies: '@platforma-sdk/test': specifier: 'catalog:' - version: 1.5.51(@types/node@22.7.5) + version: 1.7.9(@types/node@22.7.5) typescript: specifier: 'catalog:' version: 5.5.4 vitest: specifier: 'catalog:' - version: 2.1.2(@types/node@22.7.5) + version: 2.1.3(@types/node@22.7.5) ui: dependencies: @@ -187,35 +187,35 @@ importers: version: link:../model '@platforma-sdk/model': specifier: 'catalog:' - version: 1.7.0 + version: 1.7.9 '@platforma-sdk/ui-vue': specifier: 'catalog:' - version: 1.7.1(typescript@5.5.4) + version: 1.7.9(typescript@5.5.4) '@vueuse/core': specifier: 'catalog:' - version: 11.1.0(vue@3.5.11(typescript@5.5.4)) + version: 11.1.0(vue@3.5.12(typescript@5.5.4)) utility-types: specifier: 'catalog:' version: 3.11.0 vue: specifier: 'catalog:' - version: 3.5.11(typescript@5.5.4) + version: 3.5.12(typescript@5.5.4) zod: specifier: 'catalog:' version: 3.23.8 devDependencies: '@vitejs/plugin-vue': specifier: 'catalog:' - version: 5.1.4(vite@5.4.8(@types/node@22.7.5))(vue@3.5.11(typescript@5.5.4)) + version: 5.1.4(vite@5.4.9(@types/node@22.7.5))(vue@3.5.12(typescript@5.5.4)) typescript: specifier: 'catalog:' version: 5.5.4 vite: specifier: 'catalog:' - version: 5.4.8(@types/node@22.7.5) + version: 5.4.9(@types/node@22.7.5) vitest: specifier: 'catalog:' - version: 2.1.2(@types/node@22.7.5) + version: 2.1.3(@types/node@22.7.5) vue-tsc: specifier: 'catalog:' version: 2.1.6(typescript@5.5.4) @@ -224,7 +224,7 @@ importers: devDependencies: '@milaboratories/software-pframes-conv': specifier: 'catalog:' - version: 1.5.10 + version: 1.6.1 '@milaboratories/software-small-binaries': specifier: 'catalog:' version: 1.12.0 @@ 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'@platforma-sdk/test@1.5.51(@types/node@22.7.5)': + '@platforma-sdk/test@1.7.9(@types/node@22.7.5)': dependencies: - '@milaboratories/computable': 2.1.12 - '@milaboratories/pl-client': 2.5.0 - '@milaboratories/pl-middle-layer': 1.11.5 - '@milaboratories/pl-tree': 1.4.1 - '@milaboratories/ts-helpers': 1.0.30 - '@platforma-sdk/model': 1.7.0 - vitest: 2.1.2(@types/node@22.7.5) + '@milaboratories/computable': 2.2.0 + '@milaboratories/pl-client': 2.5.4 + '@milaboratories/pl-middle-layer': 1.13.6 + '@milaboratories/pl-tree': 1.4.5 + '@milaboratories/ts-helpers': 1.1.0 + '@platforma-sdk/model': 1.7.9 + vitest: 2.1.3(@types/node@22.7.5) transitivePeerDependencies: - '@edge-runtime/vm' - '@types/node' @@ -4144,30 +4222,28 @@ snapshots: - supports-color - terser - '@platforma-sdk/ui-vue@1.6.0(typescript@5.5.4)': + '@platforma-sdk/ui-vue@1.7.9(typescript@5.5.4)': dependencies: - '@milaboratories/uikit': 1.2.20(typescript@5.5.4) - '@platforma-sdk/model': 1.7.0 - canonicalize: 2.0.0 - lru-cache: 11.0.1 - vue: 3.5.11(typescript@5.5.4) - transitivePeerDependencies: - - typescript - - '@platforma-sdk/ui-vue@1.7.1(typescript@5.5.4)': - dependencies: - '@milaboratories/uikit': 1.2.20(typescript@5.5.4) - '@platforma-sdk/model': 1.7.0 + '@ag-grid-community/client-side-row-model': 32.2.2 + '@ag-grid-community/core': 32.2.2 + '@ag-grid-community/csv-export': 32.2.2 + '@ag-grid-community/infinite-row-model': 32.2.2 + '@ag-grid-community/styles': 32.2.2 + '@ag-grid-community/vue3': 32.2.2(typescript@5.5.4) + '@ag-grid-enterprise/clipboard': 32.2.2 + '@ag-grid-enterprise/core': 32.2.2 + '@ag-grid-enterprise/excel-export': 32.2.2 + '@ag-grid-enterprise/menu': 32.2.2 + '@ag-grid-enterprise/range-selection': 32.2.2 + '@ag-grid-enterprise/rich-select': 32.2.2 + '@milaboratories/uikit': 1.2.25(typescript@5.5.4) + '@platforma-sdk/model': 1.7.9 canonicalize: 2.0.0 lru-cache: 11.0.1 - vue: 3.5.11(typescript@5.5.4) + vue: 3.5.12(typescript@5.5.4) transitivePeerDependencies: - typescript - '@platforma-sdk/workflow-tengo@1.4.2': - dependencies: - '@milaboratories/software-pframes-conv': 1.6.1 - '@platforma-sdk/workflow-tengo@1.5.0': dependencies: '@milaboratories/software-pframes-conv': 1.6.1 @@ -4618,48 +4694,48 @@ snapshots: '@types/web-bluetooth@0.0.20': {} - '@vitejs/plugin-vue@5.1.4(vite@5.4.8(@types/node@22.7.5))(vue@3.5.11(typescript@5.5.4))': + '@vitejs/plugin-vue@5.1.4(vite@5.4.9(@types/node@22.7.5))(vue@3.5.12(typescript@5.5.4))': dependencies: - vite: 5.4.8(@types/node@22.7.5) - vue: 3.5.11(typescript@5.5.4) + vite: 5.4.9(@types/node@22.7.5) + vue: 3.5.12(typescript@5.5.4) - '@vitest/expect@2.1.2': + '@vitest/expect@2.1.3': dependencies: - '@vitest/spy': 2.1.2 - '@vitest/utils': 2.1.2 + '@vitest/spy': 2.1.3 + '@vitest/utils': 2.1.3 chai: 5.1.1 tinyrainbow: 1.2.0 - '@vitest/mocker@2.1.2(@vitest/spy@2.1.2)(vite@5.4.8(@types/node@22.7.5))': + '@vitest/mocker@2.1.3(@vitest/spy@2.1.3)(vite@5.4.9(@types/node@22.7.5))': dependencies: - '@vitest/spy': 2.1.2 + '@vitest/spy': 2.1.3 estree-walker: 3.0.3 magic-string: 0.30.11 optionalDependencies: - vite: 5.4.8(@types/node@22.7.5) + vite: 5.4.9(@types/node@22.7.5) - '@vitest/pretty-format@2.1.2': + '@vitest/pretty-format@2.1.3': dependencies: tinyrainbow: 1.2.0 - '@vitest/runner@2.1.2': + '@vitest/runner@2.1.3': dependencies: - '@vitest/utils': 2.1.2 + '@vitest/utils': 2.1.3 pathe: 1.1.2 - '@vitest/snapshot@2.1.2': + '@vitest/snapshot@2.1.3': dependencies: - '@vitest/pretty-format': 2.1.2 + '@vitest/pretty-format': 2.1.3 magic-string: 0.30.11 pathe: 1.1.2 - '@vitest/spy@2.1.2': + '@vitest/spy@2.1.3': dependencies: tinyspy: 3.0.2 - '@vitest/utils@2.1.2': + '@vitest/utils@2.1.3': dependencies: - '@vitest/pretty-format': 2.1.2 + '@vitest/pretty-format': 2.1.3 loupe: 3.1.2 tinyrainbow: 1.2.0 @@ -4683,27 +4759,40 @@ snapshots: estree-walker: 2.0.2 source-map-js: 1.2.1 + '@vue/compiler-core@3.5.12': + dependencies: + '@babel/parser': 7.25.8 + '@vue/shared': 3.5.12 + entities: 4.5.0 + estree-walker: 2.0.2 + source-map-js: 1.2.1 + '@vue/compiler-dom@3.5.11': dependencies: '@vue/compiler-core': 3.5.11 '@vue/shared': 3.5.11 - '@vue/compiler-sfc@3.5.11': + '@vue/compiler-dom@3.5.12': + dependencies: + '@vue/compiler-core': 3.5.12 + '@vue/shared': 3.5.12 + + '@vue/compiler-sfc@3.5.12': dependencies: '@babel/parser': 7.25.8 - '@vue/compiler-core': 3.5.11 - '@vue/compiler-dom': 3.5.11 - '@vue/compiler-ssr': 3.5.11 - '@vue/shared': 3.5.11 + '@vue/compiler-core': 3.5.12 + '@vue/compiler-dom': 3.5.12 + '@vue/compiler-ssr': 3.5.12 + '@vue/shared': 3.5.12 estree-walker: 2.0.2 magic-string: 0.30.11 postcss: 8.4.47 source-map-js: 1.2.1 - '@vue/compiler-ssr@3.5.11': + '@vue/compiler-ssr@3.5.12': dependencies: - '@vue/compiler-dom': 3.5.11 - '@vue/shared': 3.5.11 + '@vue/compiler-dom': 3.5.12 + '@vue/shared': 3.5.12 '@vue/compiler-vue2@2.7.16': dependencies: @@ -4723,45 +4812,47 @@ snapshots: optionalDependencies: typescript: 5.5.4 - '@vue/reactivity@3.5.11': + '@vue/reactivity@3.5.12': dependencies: - '@vue/shared': 3.5.11 + '@vue/shared': 3.5.12 - '@vue/runtime-core@3.5.11': + '@vue/runtime-core@3.5.12': dependencies: - '@vue/reactivity': 3.5.11 - '@vue/shared': 3.5.11 + '@vue/reactivity': 3.5.12 + '@vue/shared': 3.5.12 - '@vue/runtime-dom@3.5.11': + '@vue/runtime-dom@3.5.12': dependencies: - '@vue/reactivity': 3.5.11 - '@vue/runtime-core': 3.5.11 - '@vue/shared': 3.5.11 + '@vue/reactivity': 3.5.12 + '@vue/runtime-core': 3.5.12 + '@vue/shared': 3.5.12 csstype: 3.1.3 - '@vue/server-renderer@3.5.11(vue@3.5.11(typescript@5.5.4))': + '@vue/server-renderer@3.5.12(vue@3.5.12(typescript@5.5.4))': dependencies: - '@vue/compiler-ssr': 3.5.11 - '@vue/shared': 3.5.11 - vue: 3.5.11(typescript@5.5.4) + '@vue/compiler-ssr': 3.5.12 + '@vue/shared': 3.5.12 + vue: 3.5.12(typescript@5.5.4) '@vue/shared@3.5.11': {} - '@vueuse/core@11.1.0(vue@3.5.11(typescript@5.5.4))': + '@vue/shared@3.5.12': {} + + '@vueuse/core@11.1.0(vue@3.5.12(typescript@5.5.4))': dependencies: '@types/web-bluetooth': 0.0.20 '@vueuse/metadata': 11.1.0 - '@vueuse/shared': 11.1.0(vue@3.5.11(typescript@5.5.4)) - vue-demi: 0.14.10(vue@3.5.11(typescript@5.5.4)) + '@vueuse/shared': 11.1.0(vue@3.5.12(typescript@5.5.4)) + vue-demi: 0.14.10(vue@3.5.12(typescript@5.5.4)) transitivePeerDependencies: - '@vue/composition-api' - vue '@vueuse/metadata@11.1.0': {} - '@vueuse/shared@11.1.0(vue@3.5.11(typescript@5.5.4))': + '@vueuse/shared@11.1.0(vue@3.5.12(typescript@5.5.4))': dependencies: - vue-demi: 0.14.10(vue@3.5.11(typescript@5.5.4)) + vue-demi: 0.14.10(vue@3.5.12(typescript@5.5.4)) transitivePeerDependencies: - '@vue/composition-api' - vue @@ -4864,6 +4955,11 @@ snapshots: binary-extensions@2.3.0: {} + bl@1.2.3: + dependencies: + readable-stream: 2.3.8 + safe-buffer: 5.2.1 + bowser@2.11.0: {} brace-expansion@1.1.11: @@ -4879,6 +4975,22 @@ snapshots: dependencies: fill-range: 7.1.1 + buffer-alloc-unsafe@1.1.0: {} + + buffer-alloc@1.2.0: + dependencies: + buffer-alloc-unsafe: 1.1.0 + buffer-fill: 1.0.0 + + buffer-crc32@0.2.13: {} + + buffer-fill@1.0.0: {} + + buffer@5.7.1: + dependencies: + base64-js: 1.5.1 + ieee754: 1.2.1 + buffer@6.0.3: dependencies: base64-js: 1.5.1 @@ -4971,6 +5083,8 @@ snapshots: color: 3.2.1 text-hex: 1.0.0 + commander@2.20.3: {} + commander@4.1.1: {} computeds@0.0.1: {} @@ -4981,6 +5095,8 @@ snapshots: console-control-strings@1.1.0: {} + core-util-is@1.0.3: {} + cross-spawn@5.1.0: dependencies: lru-cache: 4.1.5 @@ -5003,6 +5119,44 @@ snapshots: optionalDependencies: supports-color: 8.1.1 + decompress-tar@4.1.1: + dependencies: + file-type: 5.2.0 + is-stream: 1.1.0 + tar-stream: 1.6.2 + + decompress-tarbz2@4.1.1: + dependencies: + decompress-tar: 4.1.1 + file-type: 6.2.0 + is-stream: 1.1.0 + seek-bzip: 1.0.6 + unbzip2-stream: 1.4.3 + + decompress-targz@4.1.1: + dependencies: + decompress-tar: 4.1.1 + file-type: 5.2.0 + is-stream: 1.1.0 + + decompress-unzip@4.0.1: + dependencies: + file-type: 3.9.0 + get-stream: 2.3.1 + pify: 2.3.0 + yauzl: 2.10.0 + + decompress@4.2.1: + dependencies: + decompress-tar: 4.1.1 + decompress-tarbz2: 4.1.1 + decompress-targz: 4.1.1 + decompress-unzip: 4.0.1 + graceful-fs: 4.2.11 + make-dir: 1.3.0 + pify: 2.3.0 + strip-dirs: 2.1.0 + deep-eql@5.0.2: {} delegates@1.0.0: {} @@ -5147,8 +5301,18 @@ snapshots: dependencies: reusify: 1.0.4 + fd-slicer@1.1.0: + dependencies: + pend: 1.2.0 + fecha@4.2.3: {} + file-type@3.9.0: {} + + file-type@5.2.0: {} + + file-type@6.2.0: {} + filelist@1.0.4: dependencies: minimatch: 5.1.6 @@ -5169,6 +5333,8 @@ snapshots: cross-spawn: 7.0.3 signal-exit: 4.1.0 + fs-constants@1.0.0: {} + fs-extra@7.0.1: dependencies: graceful-fs: 4.2.11 @@ -5206,6 +5372,11 @@ snapshots: get-package-type@0.1.0: {} + get-stream@2.3.1: + dependencies: + object-assign: 4.1.1 + pinkie-promise: 2.0.1 + get-stream@6.0.1: {} glob-parent@5.1.2: @@ -5302,8 +5473,12 @@ snapshots: dependencies: is-docker: 3.0.0 + is-natural-number@4.0.1: {} + is-number@7.0.0: {} + is-stream@1.1.0: {} + is-stream@2.0.1: {} is-subdir@1.2.0: @@ -5316,6 +5491,8 @@ snapshots: dependencies: is-inside-container: 1.0.0 + isarray@1.0.0: {} + isexe@2.0.0: {} jackspeak@3.4.3: @@ -5386,6 +5563,10 @@ snapshots: dependencies: '@jridgewell/sourcemap-codec': 1.5.0 + make-dir@1.3.0: + dependencies: + pify: 3.0.0 + make-dir@3.1.0: dependencies: semver: 6.3.1 @@ -5533,12 +5714,24 @@ snapshots: pathval@2.0.0: {} + pend@1.2.0: {} + picocolors@1.1.0: {} picomatch@2.3.1: {} + pify@2.3.0: {} + + pify@3.0.0: {} + pify@4.0.1: {} + pinkie-promise@2.0.1: + dependencies: + pinkie: 2.0.4 + + pinkie@2.0.4: {} + pirates@4.0.6: {} postcss-load-config@6.0.1(postcss@8.4.47)(yaml@2.5.1): @@ -5556,6 +5749,8 @@ snapshots: prettier@2.8.8: {} + process-nextick-args@2.0.1: {} + process@0.11.10: {} protobufjs@7.4.0: @@ -5605,6 +5800,16 @@ snapshots: pify: 4.0.1 strip-bom: 3.0.0 + readable-stream@2.3.8: + dependencies: + core-util-is: 1.0.3 + inherits: 2.0.4 + isarray: 1.0.0 + process-nextick-args: 2.0.1 + safe-buffer: 5.1.2 + string_decoder: 1.1.1 + util-deprecate: 1.0.2 + readable-stream@3.6.2: dependencies: inherits: 2.0.4 @@ -5665,12 +5870,18 @@ snapshots: dependencies: queue-microtask: 1.2.3 + safe-buffer@5.1.2: {} + safe-buffer@5.2.1: {} safe-stable-stringify@2.5.0: {} safer-buffer@2.1.2: {} + seek-bzip@1.0.6: + dependencies: + commander: 2.20.3 + semver@6.3.1: {} semver@7.6.3: {} @@ -5740,6 +5951,10 @@ snapshots: emoji-regex: 9.2.2 strip-ansi: 7.1.0 + string_decoder@1.1.1: + dependencies: + safe-buffer: 5.1.2 + string_decoder@1.3.0: dependencies: safe-buffer: 5.2.1 @@ -5754,6 +5969,10 @@ snapshots: strip-bom@3.0.0: {} + strip-dirs@2.1.0: + dependencies: + is-natural-number: 4.0.1 + strip-final-newline@2.0.0: {} strnum@1.0.5: {} @@ -5784,6 +6003,16 @@ snapshots: bare-fs: 2.3.5 bare-path: 2.1.3 + tar-stream@1.6.2: + dependencies: + bl: 1.2.3 + buffer-alloc: 1.2.0 + end-of-stream: 1.4.4 + fs-constants: 1.0.0 + readable-stream: 2.3.8 + to-buffer: 1.1.1 + xtend: 4.0.2 + tar-stream@3.1.7: dependencies: b4a: 1.6.7 @@ -5824,6 +6053,8 @@ snapshots: dependencies: any-promise: 1.3.0 + through@2.3.8: {} + tinybench@2.9.0: {} tinyexec@0.3.0: {} @@ -5838,6 +6069,8 @@ snapshots: dependencies: os-tmpdir: 1.0.2 + to-buffer@1.1.1: {} + to-fast-properties@2.0.0: {} to-regex-range@5.0.1: @@ -5884,32 +6117,32 @@ snapshots: - tsx - yaml - turbo-darwin-64@2.1.3: + turbo-darwin-64@2.2.3: optional: true - turbo-darwin-arm64@2.1.3: + turbo-darwin-arm64@2.2.3: optional: true - turbo-linux-64@2.1.3: + turbo-linux-64@2.2.3: optional: true - turbo-linux-arm64@2.1.3: + turbo-linux-arm64@2.2.3: optional: true - turbo-windows-64@2.1.3: + turbo-windows-64@2.2.3: optional: true - turbo-windows-arm64@2.1.3: + turbo-windows-arm64@2.2.3: optional: true - turbo@2.1.3: + turbo@2.2.3: optionalDependencies: - turbo-darwin-64: 2.1.3 - turbo-darwin-arm64: 2.1.3 - turbo-linux-64: 2.1.3 - turbo-linux-arm64: 2.1.3 - turbo-windows-64: 2.1.3 - turbo-windows-arm64: 2.1.3 + turbo-darwin-64: 2.2.3 + turbo-darwin-arm64: 2.2.3 + turbo-linux-64: 2.2.3 + turbo-linux-arm64: 2.2.3 + turbo-windows-64: 2.2.3 + turbo-windows-arm64: 2.2.3 type-fest@0.21.3: {} @@ -5917,6 +6150,11 @@ snapshots: typescript@5.5.4: {} + unbzip2-stream@1.4.3: + dependencies: + buffer: 5.7.1 + through: 2.3.8 + undici-types@6.19.8: {} undici@6.20.0: {} @@ -5929,12 +6167,12 @@ snapshots: uuid@9.0.1: {} - vite-node@2.1.2(@types/node@22.7.5): + vite-node@2.1.3(@types/node@22.7.5): dependencies: cac: 6.7.14 debug: 4.3.7(supports-color@8.1.1) pathe: 1.1.2 - vite: 5.4.8(@types/node@22.7.5) + vite: 5.4.9(@types/node@22.7.5) transitivePeerDependencies: - '@types/node' - less @@ -5946,7 +6184,7 @@ snapshots: - supports-color - terser - vite@5.4.8(@types/node@22.7.5): + vite@5.4.9(@types/node@22.7.5): dependencies: esbuild: 0.21.5 postcss: 8.4.47 @@ -5955,15 +6193,15 @@ snapshots: '@types/node': 22.7.5 fsevents: 2.3.3 - vitest@2.1.2(@types/node@22.7.5): + vitest@2.1.3(@types/node@22.7.5): dependencies: - '@vitest/expect': 2.1.2 - '@vitest/mocker': 2.1.2(@vitest/spy@2.1.2)(vite@5.4.8(@types/node@22.7.5)) - '@vitest/pretty-format': 2.1.2 - '@vitest/runner': 2.1.2 - '@vitest/snapshot': 2.1.2 - '@vitest/spy': 2.1.2 - '@vitest/utils': 2.1.2 + '@vitest/expect': 2.1.3 + '@vitest/mocker': 2.1.3(@vitest/spy@2.1.3)(vite@5.4.9(@types/node@22.7.5)) + '@vitest/pretty-format': 2.1.3 + '@vitest/runner': 2.1.3 + '@vitest/snapshot': 2.1.3 + '@vitest/spy': 2.1.3 + '@vitest/utils': 2.1.3 chai: 5.1.1 debug: 4.3.7(supports-color@8.1.1) magic-string: 0.30.11 @@ -5973,8 +6211,8 @@ snapshots: tinyexec: 0.3.0 tinypool: 1.0.1 tinyrainbow: 1.2.0 - vite: 5.4.8(@types/node@22.7.5) - vite-node: 2.1.2(@types/node@22.7.5) + vite: 5.4.9(@types/node@22.7.5) + vite-node: 2.1.3(@types/node@22.7.5) why-is-node-running: 2.3.0 optionalDependencies: '@types/node': 22.7.5 @@ -5991,9 +6229,9 @@ snapshots: vscode-uri@3.0.8: {} - vue-demi@0.14.10(vue@3.5.11(typescript@5.5.4)): + vue-demi@0.14.10(vue@3.5.12(typescript@5.5.4)): dependencies: - vue: 3.5.11(typescript@5.5.4) + vue: 3.5.12(typescript@5.5.4) vue-tsc@2.1.6(typescript@5.5.4): dependencies: @@ -6002,13 +6240,13 @@ snapshots: semver: 7.6.3 typescript: 5.5.4 - vue@3.5.11(typescript@5.5.4): + vue@3.5.12(typescript@5.5.4): dependencies: - '@vue/compiler-dom': 3.5.11 - '@vue/compiler-sfc': 3.5.11 - '@vue/runtime-dom': 3.5.11 - '@vue/server-renderer': 3.5.11(vue@3.5.11(typescript@5.5.4)) - '@vue/shared': 3.5.11 + '@vue/compiler-dom': 3.5.12 + '@vue/compiler-sfc': 3.5.12 + '@vue/runtime-dom': 3.5.12 + '@vue/server-renderer': 3.5.12(vue@3.5.12(typescript@5.5.4)) + '@vue/shared': 3.5.12 optionalDependencies: typescript: 5.5.4 @@ -6084,6 +6322,8 @@ snapshots: wrappy@1.0.2: {} + xtend@4.0.2: {} + y18n@5.0.8: {} yallist@2.1.2: {} @@ -6106,4 +6346,9 @@ snapshots: y18n: 5.0.8 yargs-parser: 21.1.1 + yauzl@2.10.0: + dependencies: + buffer-crc32: 0.2.13 + fd-slicer: 1.1.0 + zod@3.23.8: {} diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml index e4ba8f6..bba591c 100644 --- a/pnpm-workspace.yaml +++ b/pnpm-workspace.yaml @@ -7,19 +7,19 @@ packages: catalog: '@platforma-sdk/workflow-tengo': ^1.5.0 - '@platforma-sdk/model': ^1.7.0 - '@platforma-sdk/ui-vue': ^1.7.1 + '@platforma-sdk/model': ^1.7.9 + '@platforma-sdk/ui-vue': ^1.7.9 '@platforma-sdk/tengo-builder': ^1.14.13 - '@platforma-sdk/block-tools': ^2.3.14 + '@platforma-sdk/block-tools': ^2.3.17 - '@platforma-sdk/test': ^1.5.37 + '@platforma-sdk/test': ^1.7.9 '@milaboratories/helpers': ^1.6.5 - '@milaboratories/software-pframes-conv': ^1.5.10 + '@milaboratories/software-pframes-conv': ^1.6.1 '@milaboratories/software-small-binaries': ^1.11.0 '@platforma-open/milaboratories.software-mixcr': 4.7.0-112-develop - 'vue': ^3.5.11 + 'vue': ^3.5.12 'vue-tsc': ^2.1.6 'zod': ^3.23.8 @@ -27,10 +27,10 @@ catalog: 'typescript': ~5.5.4 'tsup': ~8.1.2 - 'turbo': ^2.1.3 + 'turbo': ^2.2.3 - 'vite': ^5.4.8 - 'vitest': ^2.1.2 + 'vite': ^5.4.9 + 'vitest': ^2.1.3 '@vitejs/plugin-vue': ^5.1.4 '@vueuse/core': ^11.1.0 @@ -44,5 +44,5 @@ catalog: # other blocks used in tests - '@platforma-open/milaboratories.samples-and-data': ^1.4.0 - '@platforma-open/milaboratories.samples-and-data.model': ^1.4.0 + '@platforma-open/milaboratories.samples-and-data': ^1.5.2 + '@platforma-open/milaboratories.samples-and-data.model': ^1.4.2 diff --git a/test/assets/expected_results/mixcr.sh b/test/assets/expected_results/mixcr.sh index c233169..0c5b303 100755 --- a/test/assets/expected_results/mixcr.sh +++ b/test/assets/expected_results/mixcr.sh @@ -2,7 +2,13 @@ set -e -mixcr exportPreset --preset-name milab-human-dna-xcr-7genes-multiplex -f preset.json +mixcr listPresetSpecificationsForUI presets.json + +mixcr exportPreset --preset-name milab-human-dna-xcr-7genes-multiplex -f preset-7genes.json +mixcr presetSpecificationsForBack preset-7genes.json preset-7genes-ui.json + +mixcr exportPreset --preset-name 10x-sc-5gex --species hsa -f preset-10x.json +mixcr presetSpecificationsForBack preset-10x.json preset-10x-ui.json # --add-step assembleContigs mixcr analyze milab-human-dna-xcr-7genes-multiplex -f ../small_data_R1.fastq.gz ../small_data_R2.fastq.gz result > log.txt diff --git a/test/src/wf.test.ts b/test/src/wf.test.ts index 61e6dbf..57d00ab 100644 --- a/test/src/wf.test.ts +++ b/test/src/wf.test.ts @@ -22,6 +22,7 @@ blockTest('empty imputs', { timeout: 30000 }, async ({ rawPrj: project, ml, help expect(stableState.outputs).toMatchObject({ inputOptions: { ok: true, value: [] } }); const presets = wrapOutputs(stableState.outputs).presets; expect(presets).length.gt(10); + expect(presets?.map((p) => p.presetName)).toContain('10x-sc-xcr-vdj'); }); blockTest( diff --git a/ui/src/SettingsPanel.vue b/ui/src/SettingsPanel.vue index 671354e..9b80481 100644 --- a/ui/src/SettingsPanel.vue +++ b/ui/src/SettingsPanel.vue @@ -8,8 +8,6 @@ const app = useApp(); const inputOptions = computed(() => app.outputValues.inputOptions ?? []); -const args = app.createArgsModel(); - const presets = retentive(computed(() => app.outputValues.presets)) const presetOptions = computed(() => { @@ -21,12 +19,12 @@ const needSpecies = computed(() => preset.value === undefined ? undefined : (pre watch(needSpecies, ns => { if (ns === false && // everething is loaded and we know that species is not specified as flag - args.model.species !== undefined) - args.model.species = undefined; + app.model.args.species !== undefined) + app.model.args.species = undefined; if (ns === true && // the opposite of the above - args.model.species === undefined) - args.model.species = "hsa"; + app.model.args.species === undefined) + app.model.args.species = "hsa"; }) const speciesOptions = [ @@ -40,7 +38,7 @@ const speciesOptions = [ diff --git a/workflow/src/process.tpl.tengo b/workflow/src/process.tpl.tengo index f6560bf..48af67f 100644 --- a/workflow/src/process.tpl.tengo +++ b/workflow/src/process.tpl.tengo @@ -127,6 +127,14 @@ self.body(func(inputs) { } clones = clones.build() + joinOrUndefined := func(arr) { + if is_undefined(arr) { + return undefined + } else { + return text.join(arr, ",") + } + } + return { "qc.spec": { kind: "PColumn", @@ -191,10 +199,10 @@ self.body(func(inputs) { "pl7.app/blockId": blockId }, annotations: { - "mixcr.com/assemblingFeature": text.join(presetContent.assemblingFeature, ","), - "mixcr.com/cellTags": text.join(presetContent.cellTags, ","), - "mixcr.com/coveredFeaturesOnExport": text.join(presetContent.coveredFeaturesOnExport, ","), - "mixcr.com/umiTags": text.join(presetContent.umiTags, ","), + "mixcr.com/assemblingFeature": joinOrUndefined(presetContent.assemblingFeature), + "mixcr.com/cellTags": joinOrUndefined(presetContent.cellTags), + "mixcr.com/coveredFeaturesOnExport": joinOrUndefined(presetContent.coveredFeaturesOnExport), + "mixcr.com/umiTags": joinOrUndefined(presetContent.umiTags), "pl7.app/label": datasetLabel + " / MiXCR Clonotypes" }, valueType: "File",