after merge fixes round 1

platforma-open · Sep 7, 2024 · 0691009 · 0691009
1 parent 5234d1c
commit 0691009
Show file tree

Hide file tree

Showing 10 changed files with 44 additions and 141 deletions.
diff --git a/workflow/index.d.ts b/workflow/index.d.ts
@@ -1,4 +1,4 @@
 declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
-declare type TplName = "calculate-pfconv-params" | "export-clones" | "get-preset-spec" | "get-preset" | "list-presets" | "mixcr-analyze" | "prerun" | "process" | "test.columns.test" | "main";
+declare type TplName = "calculate-pfconv-params" | "export-clones" | "get-preset" | "list-presets" | "mixcr-analyze" | "prerun" | "process" | "test.columns.test" | "main";
 declare const Templates: Record<TplName, TemplateFromFile>;
 export { Templates };
diff --git a/workflow/index.js b/workflow/index.js
@@ -1,8 +1,6 @@
 module.exports = { Templates: {
   'calculate-pfconv-params': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/calculate-pfconv-params.plj.gz') },
   'export-clones': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/export-clones.plj.gz') },
-  'get-preset-spec': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/get-preset-spec.plj.gz') },
-  'get-preset-for-back': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/get-preset-for-back.plj.gz') },
   'get-preset': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/get-preset.plj.gz') },
   'list-presets': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/list-presets.plj.gz') },
   'mixcr-analyze': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/mixcr-analyze.plj.gz') },

diff --git a/workflow/src/get-preset-for-back.tpl.tengo b/workflow/src/get-preset-for-back.tpl.tengo
diff --git a/workflow/src/get-preset-spec.tpl.tengo b/workflow/src/get-preset-spec.tpl.tengo
diff --git a/workflow/src/get-preset.tpl.tengo b/workflow/src/get-preset.tpl.tengo
@@ -16,13 +16,13 @@ self.validateInputs({
 
 mixcrSw := assets.importSoftware("@milaboratory/mixcr:main")
 
-self.defineOutputs("preset")
+self.defineOutputs("preset", "presetSpecForBack")
 
 self.body(func(inputs) {
 	presetName := inputs.request.presetName
 	species := inputs.request.species
 
-	mixcrCmdBuilder := exec.builder().
+	mixcrExportPresetCmdBuilder := exec.builder().
 						software(mixcrSw).
 						printErrStreamToStdout().
 						arg("exportPreset").
@@ -38,16 +38,30 @@ self.body(func(inputs) {
 						arg("-cHit")
 
 	if !is_undefined(species) {
-		mixcrCmdBuilder.arg("--species").arg(species)
+		mixcrExportPresetCmdBuilder.arg("--species").arg(species)
 	}
 
-	mixcrCmd := mixcrCmdBuilder.arg("preset.json").
+	mixcrExportPresetCmd := mixcrExportPresetCmdBuilder.arg("preset.json").
 						saveFileContent("preset.json").
+						saveFile("preset.json").
 						run()
 
-	presetContent := mixcrCmd.getFileContent("preset.json")
+	presetContent := mixcrExportPresetCmd.getFileContent("preset.json")
+
+	mixcrForBackCmd := exec.builder().
+						software(mixcrSw).
+						printErrStreamToStdout().
+						arg("presetSpecificationsForBack").
+						addFile("preset.yaml", mixcrExportPresetCmd.getFile("preset.json")).
+						arg("preset.yaml").
+						arg("presetForBack.json").
+						saveFileContent("presetForBack.json").
+						run()
+
+	presetSpecForBackContent := mixcrForBackCmd.getFileContent("presetForBack.json")
 
 	return {
-		preset: presetContent
+		preset: presetContent,
+		presetSpecForBack: presetSpecForBackContent
 	}
 })
diff --git a/workflow/src/main.tpl.tengo b/workflow/src/main.tpl.tengo
@@ -14,8 +14,6 @@ exec := import("@milaboratory/tengo-sdk:exec")
 json := import("json")
 
 getPresetTpl := assets.importTemplate(":get-preset")
-getPresetSpecTpl := assets.importTemplate(":get-preset-spec")
-getPresetTpl := assets.importTemplate(":get-preset-for-back")
 calculatePfconvParamsTpl := assets.importTemplate(":calculate-pfconv-params")
 processTpl := assets.importTemplate(":process")
 
@@ -36,12 +34,8 @@ wf.body(func(args) {
 		}
 	})
 
-	getSpecs := render.create(getPresetSpecTpl, {
-		preset: args.preset
-	})
-
 	presetContent := getPreset.output("preset", 24 * 60 * 60 * 1000)
-	specsContent := getSpecs.output("specs", 24 * 60 * 60 * 1000)
+	specsContent := getPreset.output("presetSpecForBack", 24 * 60 * 60 * 1000)
 
 	calculatePfconvParams := render.create(calculatePfconvParamsTpl, {
 		preset: presetContent,

diff --git a/workflow/src/pfconv_params.lib.tengo b/workflow/src/pfconv_params.lib.tengo
@@ -177,7 +177,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "FR1 Nt"
+          "pl7.app/label": "FR1 nt"
         }
       }
     }, {
@@ -207,7 +207,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "FR2 Nt"
+          "pl7.app/label": "FR2 nt"
         }
       }
     }, {
@@ -236,7 +236,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "FR3 Nt"
+          "pl7.app/label": "FR3 nt"
         }
       }
     }, {
@@ -265,7 +265,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "FR4 Nt"
+          "pl7.app/label": "FR4 nt"
         }
       }
     }, {
@@ -294,7 +294,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "CDR1 Nt"
+          "pl7.app/label": "CDR1 nt"
         }
       }
     }, {
@@ -323,7 +323,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "CDR2 Nt"
+          "pl7.app/label": "CDR2 nt"
         }
       }
     }, {
@@ -352,7 +352,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "CDR3 Nt"
+          "pl7.app/label": "CDR3 nt"
         }
       }
     }, {
@@ -381,7 +381,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "FR1 AA"
+          "pl7.app/label": "FR1 aa"
         }
       }
     }, {
@@ -396,7 +396,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "FR2 AA"
+          "pl7.app/label": "FR2 aa"
         }
       }
     }, {
@@ -411,7 +411,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "FR3 AA"
+          "pl7.app/label": "FR3 aa"
         }
       }
     }, {
@@ -426,7 +426,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "FR4 AA"
+          "pl7.app/label": "FR4 aa"
         }
       }
     }, {
@@ -441,7 +441,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "CDR1 AA"
+          "pl7.app/label": "CDR1 aa"
         }
       }
     }, {
@@ -456,7 +456,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "CDR2 AA"
+          "pl7.app/label": "CDR2 aa"
         }
       }
     }, {
@@ -471,7 +471,7 @@ export {
         },
         "annotations": {
           "type": "sequence",
-          "pl7.app/label": "CDR3 AA"
+          "pl7.app/label": "CDR3 aa"
         }
       }
     }, {

diff --git a/workflow/src/prerun.tpl.tengo b/workflow/src/prerun.tpl.tengo
@@ -6,7 +6,7 @@ ll := import("@milaboratory/tengo-sdk:ll")
 assets := import("@milaboratory/tengo-sdk:assets")
 
 listPresetsTpl := assets.importTemplate(":list-presets")
-getPresetTpl := assets.importTemplate(":get-preset-for-back")
+getPresetTpl := assets.importTemplate(":get-preset")
 
 wf.body(func(args) {
 
@@ -22,7 +22,7 @@ wf.body(func(args) {
 				species: args.species
 			}
 		})
-		outputs.preset = getPreset.output("preset", 24 * 60 * 60 * 1000)
+		outputs.preset = getPreset.output("presetSpecForBack", 24 * 60 * 60 * 1000)
 	}
 
 	return {

diff --git a/workflow/src/test/columns.test.tpl.tengo b/workflow/src/test/columns.test.tpl.tengo
@@ -5,25 +5,20 @@ assets := import("@milaboratory/tengo-sdk:assets")
 render := import("@milaboratory/tengo-sdk:render")
 
 getPresetTpl := assets.importTemplate(":get-preset")
-getPresetSpecTpl := assets.importTemplate(":get-preset-spec")
 calculateColumnsParamsTpl := assets.importTemplate(":calculate-pfconv-params")
 
 self.defineOutputs("conf")
 
 self.body(func(inputs) {
 	request := inputs.request
 
-	preset := render.create(getPresetTpl, {
+	getPreset := render.create(getPresetTpl, {
 		request: request
-	}).output("preset")
-
-	specs := render.create(getPresetSpecTpl, {
-		preset: presetName
-	}).output("specs")
+	})
 
 	pfconvConfig := render.create(calculateColumnsParamsTpl, {
-		preset: preset,
-		specs: specs
+		preset: getPreset.output("preset"),
+		specs: getPreset.output("presetSpecForBack")
 	}).output("params")
 
 	return {

diff --git a/workflow/src/test/columns.test.ts b/workflow/src/test/columns.test.ts
@@ -25,6 +25,7 @@ const testCases: TestCase[] = [
   },
   {
     presetName: '10x-sc-xcr-vdj',
+    species: 'human',
     check: (expect, config) => {
       console.dir(config, { depth: 5 });
       expect(config.axes).to.have.lengthOf(2);
@@ -89,6 +90,7 @@ const testCases: TestCase[] = [
   },
   {
     presetName: 'rna-seq',
+    species: 'human',
     check: (expect, config) => {
       console.dir(config, { depth: 5 });
       expect(config.axes).to.have.lengthOf(1);