@platforma-open/milaboratories.mixcr-shm-trees.workflow 2.0.0

package/dist/tengo/lib/prepare-donor-column.lib.tengo

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+ll := import("@platforma-sdk/workflow-tengo:ll")
+smart := import("@platforma-sdk/workflow-tengo:smart")
+
+json := import("json")
+
+_P_COLUMN_DATA_RESOURCE_MAP := { Name: "PColumnData/ResourceMap", Version: "1" }
+
+groupDataByDonorId := func(donorColumn, datasets) {
+    // we need to form a pColumn with two axes:
+	//    axes[0]: donorId
+	//    axes[1]: sampleId
+	//    axes[2]: mixcrBlockId
+	//      value: fileRef resource
+
+	// we have:
+	//    column of donorIds:
+	//        axes[0]: sampleId
+	//          value: donorId
+	//    several columns of clns:
+	//        axes[0]: sampleId
+	//          value: fileRef resource
+
+    donorColumnSpec := donorColumn.get("spec").getDataAsJson()
+    
+    resultSpec := {
+        // annotations and domain could differ between datasets
+        "axesSpec": [
+            {
+                "annotations": donorColumnSpec["annotations"],
+                "domain": donorColumnSpec["domain"],
+                "name": donorColumnSpec["name"],
+                "type": donorColumnSpec["valueType"]
+            },
+            donorColumnSpec["axesSpec"][0],
+            {
+                "annotations": {
+                    "pl7.app/label": "Clonotyping block id"
+                },
+                "name": "pl7.app/blockId",
+                "type": "String"
+            }
+        ],
+        "kind": "PColumn",
+        "name": "mixcr.com/clns",
+        "valueType": "File"
+    }
+    
+
+    sampleToDonor := {}
+
+    // columns with meta could be fetched as data direcctly
+	for k, v in donorColumn.get("data").getDataAsJson()["data"] {
+        sampleId := json.decode(k)[0]
+        sampleToDonor[sampleId] = v
+	}
+
+    // build pColumn by hand
+    dataBuilder := smart.structBuilder(_P_COLUMN_DATA_RESOURCE_MAP, json.encode({ keyLength: 3 }))
+
+    // collect all the clns files that we have into pColumn
+	for blockId, dataset in datasets {
+		for sKey, fileRef in dataset.get("data").inputs() {
+            sampleId := json.decode(sKey)[0]
+            donor := sampleToDonor[sampleId]
+            dataBuilder.createInputField(json.encode([donor, sampleId, blockId])).set(fileRef)
+		}
+    }
+
+    return {
+        spec: resultSpec,
+        data: dataBuilder.lockAndBuild()
+    }
+}
+
+// to use the file as a library, we should explicitly export functions
+export ll.toStrict({
+	groupDataByDonorId: groupDataByDonorId
+})

package/format.el

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+;; This program formats all files inside src directory. Usage: emacs --script ./format.el
+
+(defun install-go-mode ()
+  "Installs go-mode"
+  (require 'package)
+  (add-to-list 'package-archives
+               '("melpa-stable" . "https://stable.melpa.org/packages/"))
+  (package-initialize)
+  (unless package-archive-contents
+    (package-refresh-contents))
+
+  (package-install 'go-mode t)
+  (require 'go-mode))
+
+;; spaces -> tabs only at the beginning of lines
+(setq tabify-regexp "^\t* [ \t]+")
+
+(defun format-file (file)
+  "Formats a file according to slightly changed Go rules"
+  (message "Format %s" file)
+  (save-excursion
+    (find-file file)
+    (delete-trailing-whitespace)            ;; deletes whitespaces
+    (go-mode)                               ;; sets golang rules for indentation
+    (tabify (point-min) (point-max))        ;; spaces -> tabs in the whole file
+    (indent-region (point-min) (point-max)) ;; indentation in the whole file
+    (save-buffer)))                         ;; save file
+
+(install-go-mode)
+
+;; change syntax of a standard go-mode a bit
+(advice-add
+ 'go--in-composite-literal-p
+ :filter-return
+ (lambda (&rest r) t))
+
+;; find all files in src
+(setq files (directory-files-recursively "src" "\\.tengo\\'"))
+
+;; call format on every file.
+(dolist (file files)
+  (format-file file))
+

package/index.d.ts

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+declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
+declare type TplName = "reconstruct-shm-trees" | "process" | "main";
+declare const Templates: Record<TplName, TemplateFromFile>;
+export { Templates };

package/index.js

@@ -0,0 +1,5 @@
+module.exports = { Templates: {
+  'reconstruct-shm-trees': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/reconstruct-shm-trees.plj.gz') },
+  'process': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/process.plj.gz') },
+  'main': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/main.plj.gz') }
+}}

package/package.json

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+{
+  "name": "@platforma-open/milaboratories.mixcr-shm-trees.workflow",
+  "version": "2.0.0",
+  "type": "module",
+  "description": "Tengo-based template",
+  "//": {
+    "build": "node ./scripts/build-static.mjs src/pfconv_params.json src/pfconv_params.lib.tengo && rm -rf dist && pl-tengo check && pl-tengo build && ./create_tags.sh"
+  },
+  "devDependencies": {
+    "@platforma-sdk/tengo-builder": "^1.15.0",
+    "@platforma-sdk/workflow-tengo": "^1.6.3",
+    "@milaboratories/software-pframes-conv": "^1.6.3",
+    "@platforma-open/milaboratories.software-small-binaries": "^1.14.4",
+    "@platforma-open/milaboratories.software-mixcr": "4.7.0-113-develop",
+    "@platforma-sdk/test": "^1.7.16",
+    "vitest": "^2.1.3",
+    "typescript": "~5.5.4"
+  },
+  "scripts": {
+    "build": "rm -rf dist && pl-tengo check && pl-tengo build",
+    "format": "/usr/bin/env emacs --script ./format.el"
+  }
+}