@platforma-open/milaboratories.sequence-properties.workflow 1.1.1 → 1.1.2

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/sequence-properties/sequence-properties/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.sequence-properties.workflow@1.1.1 build /home/runner/work/sequence-properties/sequence-properties/workflow
+> @platforma-open/milaboratories.sequence-properties.workflow@1.1.2 build /home/runner/work/sequence-properties/sequence-properties/workflow
 > shx rm -rf dist && pl-tengo check && pl-tengo build
 
   info: Skipping unknown file type: wf.test.ts

package/CHANGELOG.md

@@ -1,5 +1,20 @@
 # @platforma-open/MiLaboratories.sequence-properties.workflow
 
+## 1.1.2
+
+### Patch Changes
+
+- 9d628d9: **Workflow (SD-008):** Derive receptor from `pl7.app/vdj/chain` when `pl7.app/vdj/receptor` is absent. Bulk MiXCR axes carry the chain key (`IGHeavy`, `IGLight`, `TCRAlpha`, `TCRBeta`, `TCRGamma`, `TCRDelta`) without the receptor key, which previously fired R13b's "Receptor type not detected" warning on every bulk run. Detection precedence now: axis receptor → axis chain → per-column receptor → per-column chain → IG default + warning. Inputs that carry receptor explicitly are unaffected.
+
+  **Model:** Default-visible single upstream amino-acid sequence column matching the analysed coverage tier — peptide (`pl7.app/sequence`, feature=peptide) for peptide mode; full-chain VDJRegion (`pl7.app/vdj/sequence`, feature=VDJRegion or VDJRegionInFrame, chain A) for `full_chain` tier; CDR3 (`pl7.app/vdj/sequence`, feature=CDR3, chain A) for `cdr3_only` and `partial` tiers. Chain B (light / beta / delta) and secondary alleles stay available via the column picker.
+
+  **UI:** Move the "Input dataset" picker into a Settings slide-out drawer (matches the convention used by clonotype-clustering and other sibling blocks). Drawer auto-opens on first load when no input is selected, auto-closes when the workflow starts running.
+
+  **Software:** Switch the Python runenv from `runenv-python-3:3.12.10` to `runenv-python-3:3.12.10-scientific-slim`. The scientific-slim image now ships biopython, so the per-block dependency install is faster and matches the convention used by sibling python blocks (e.g. `titeseq-analysis`).
+
+- Updated dependencies [9d628d9]
+  - @platforma-open/milaboratories.sequence-properties.software@1.1.1
+
 ## 1.1.1
 
 ### Patch Changes

package/package.json

@@ -1,11 +1,11 @@
 {
   "name": "@platforma-open/milaboratories.sequence-properties.workflow",
-  "version": "1.1.1",
+  "version": "1.1.2",
   "description": "Block Workflow",
   "type": "module",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "5.16.0",
-    "@platforma-open/milaboratories.sequence-properties.software": "1.1.0"
+    "@platforma-open/milaboratories.sequence-properties.software": "1.1.1"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "2.5.17",

package/src/main.tpl.tengo

@@ -58,6 +58,44 @@ contains := func(arr, x) {
 	return false
 }
 
+// Spec deviation SD-008 — see docs/spec-deviations.md.
+// Bulk MiXCR axes carry `pl7.app/vdj/chain` without the spec-required
+// `pl7.app/vdj/receptor`. The chain enum maps unambiguously to a receptor —
+// derive it when receptor is absent. Returns "" for unrecognised input;
+// caller falls through to the IG default + R13b warning, which still fires
+// for genuinely unknown datasets.
+CHAIN_TO_RECEPTOR := {
+	IGHeavy: "IG",
+	IGLight: "IG",
+	IGKappa: "IG",
+	IGLambda: "IG",
+	TCRAlpha: "TCRAB",
+	TCRBeta: "TCRAB",
+	TCRGamma: "TCRGD",
+	TCRDelta: "TCRGD"
+}
+
+chainToReceptor := func(chain) {
+	if chain == undefined { return "" }
+	r := CHAIN_TO_RECEPTOR[chain]
+	if r == undefined { return "" }
+	return r
+}
+
+// Resolve receptor from a (receptor, chain) domain pair. Explicit receptor
+// wins; chain-derived receptor is the fallback. Returns { value, seen };
+// `seen` false when neither key resolves.
+resolveReceptor := func(receptorVal, chainVal) {
+	if receptorVal == "IG" || receptorVal == "TCRAB" || receptorVal == "TCRGD" {
+		return { value: receptorVal, seen: true }
+	}
+	derived := chainToReceptor(chainVal)
+	if derived != "" {
+		return { value: derived, seen: true }
+	}
+	return { value: "", seen: false }
+}
+
 wf.prepare(func(args) {
 	bb := wf.createPBundleBuilder()
 	bb.ignoreMissingDomains()
@@ -132,10 +170,17 @@ wf.body(func(args) {
 	// anchor's secondary axis), not on per-region sequence column domains. Read
 	// from the axis first; the per-column check inside the loop stays as a
 	// fallback for non-MiXCR producers.
+	//
+	// Spec deviation SD-008 — bulk MiXCR axes lack `pl7.app/vdj/receptor` but
+	// carry `pl7.app/vdj/chain`; derive receptor from chain when receptor is
+	// absent. See docs/spec-deviations.md.
 	if keyAxisSpec.domain != undefined {
-		axisR := keyAxisSpec.domain["pl7.app/vdj/receptor"]
-		if axisR == "IG" || axisR == "TCRAB" || axisR == "TCRGD" {
-			receptor = axisR
+		r := resolveReceptor(
+			keyAxisSpec.domain["pl7.app/vdj/receptor"],
+			keyAxisSpec.domain["pl7.app/vdj/chain"]
+		)
+		if r.seen {
+			receptor = r.value
 			receptorSeen = true
 		}
 	}
@@ -192,9 +237,10 @@ wf.body(func(args) {
 			}
 
 			// Same receptor value is expected on every input column; last seen wins.
-			r := d["pl7.app/vdj/receptor"]
-			if r == "IG" || r == "TCRAB" || r == "TCRGD" {
-				receptor = r
+			// SD-008: derive from chain when explicit receptor key is absent.
+			rec := resolveReceptor(d["pl7.app/vdj/receptor"], d["pl7.app/vdj/chain"])
+			if rec.seen {
+				receptor = rec.value
 				receptorSeen = true
 			}