@platforma-open/milaboratories.mixcr-shm-trees.workflow 2.3.2 → 2.3.4

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Files changed (12) hide show
  1. package/.turbo/turbo-build.log +19 -0
  2. package/CHANGELOG.md +12 -0
  3. package/dist/tengo/lib/export-settings.lib.tengo +1 -1
  4. package/dist/tengo/lib/prepare-donor-column.lib.tengo +3 -3
  5. package/dist/tengo/tpl/main.plj.gz +0 -0
  6. package/dist/tengo/tpl/process.plj.gz +0 -0
  7. package/dist/tengo/tpl/reconstruct-shm-trees.plj.gz +0 -0
  8. package/package.json +4 -4
  9. package/src/export-settings.lib.tengo +1 -1
  10. package/src/prepare-donor-column.lib.tengo +3 -3
  11. package/src/process.tpl.tengo +3 -1
  12. package/src/reconstruct-shm-trees.tpl.tengo +5 -3
package/.turbo/turbo-build.log ADDED
@@ -0,0 +1,19 @@
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+  WARN  Issue while reading "/home/runner/work/mixcr-shm-trees/mixcr-shm-trees/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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+
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+ > @platforma-open/milaboratories.mixcr-shm-trees.workflow@2.3.4 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
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+ > rm -rf dist && pl-tengo check && pl-tengo build
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+
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+ Processing "src/export-settings.lib.tengo"...
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+ Processing "src/main.tpl.tengo"...
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+ Processing "src/prepare-donor-column.lib.tengo"...
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+ Processing "src/process.tpl.tengo"...
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+ Processing "src/reconstruct-shm-trees.tpl.tengo"...
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+ No syntax errors found.
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+ info: Compiling 'dist'...
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+ info: - writing /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow/dist/tengo/lib/export-settings.lib.tengo
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+ info: - writing /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow/dist/tengo/lib/prepare-donor-column.lib.tengo
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+ info: - writing /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow/dist/tengo/tpl/reconstruct-shm-trees.plj.gz
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+ info: - writing /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow/dist/tengo/tpl/process.plj.gz
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+ info: - writing /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow/dist/tengo/tpl/main.plj.gz
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+ info:
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+ info: Template Pack build done.
package/CHANGELOG.md CHANGED
@@ -1,5 +1,17 @@
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  # @platforma-open/milaboratories.mixcr-shm-trees.workflow
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+ ## 2.3.4
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+
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+ ### Patch Changes
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+
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+ - ef7df65: SDK upgrade
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+
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+ ## 2.3.3
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+
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+ ### Patch Changes
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+
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+ - 96a150e: Random seed added to main analysis routine
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+
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  ## 2.3.2
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16
 
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  ### Patch Changes
package/dist/tengo/lib/export-settings.lib.tengo CHANGED
@@ -444,7 +444,7 @@ shmTreeNodesTableOptions := func(dataDescription) {
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  // export data that is unique for clones, but not unique for a node
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  // (different clones could be in the same topology node, for example, different time points)
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  shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
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- donorColumnSpec := donorColumn.get("spec").getDataAsJson()
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+ donorColumnSpec := donorColumn.spec
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  axes := []
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  columns := []
package/dist/tengo/lib/prepare-donor-column.lib.tengo CHANGED
@@ -20,7 +20,7 @@ groupDataByDonorId := func(donorColumn, datasets) {
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  // axes[0]: sampleId
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  // value: fileRef resource
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- donorColumnSpec := donorColumn.get("spec").getDataAsJson()
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+ donorColumnSpec := donorColumn.spec
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  sampleIdAxis := donorColumnSpec.axesSpec[0]
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@@ -53,7 +53,7 @@ groupDataByDonorId := func(donorColumn, datasets) {
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  sampleToDonor := {}
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  // columns with meta could be fetched as data direcctly
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- for k, v in donorColumn.get("data").getDataAsJson()["data"] {
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+ for k, v in donorColumn.data.getDataAsJson()["data"] {
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  sampleId := json.decode(k)[0]
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  sampleToDonor[sampleId] = v
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  }
@@ -63,7 +63,7 @@ groupDataByDonorId := func(donorColumn, datasets) {
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  // collect all the clns files that we have into pColumn
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  for clonotypingBlockId, dataset in datasets {
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- for sKey, fileRef in dataset.get("data").inputs() {
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+ for sKey, fileRef in dataset.data.inputs() {
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  sampleId := json.decode(sKey)[0]
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  donor := sampleToDonor[sampleId]
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  dataBuilder.createInputField(json.encode([donor, sampleId, clonotypingBlockId])).set(fileRef)
package/dist/tengo/tpl/main.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/process.plj.gz CHANGED
Binary file
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@platforma-open/milaboratories.mixcr-shm-trees.workflow",
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- "version": "2.3.2",
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+ "version": "2.3.4",
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  "type": "module",
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  "description": "Tengo-based template",
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  "//": {
@@ -8,11 +8,11 @@
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  },
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  "devDependencies": {
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  "@platforma-sdk/tengo-builder": "^1.17.3",
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- "@platforma-sdk/workflow-tengo": "^2.6.0",
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+ "@platforma-sdk/workflow-tengo": "^2.8.0",
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  "@milaboratories/software-pframes-conv": "^2.1.2",
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- "@platforma-open/milaboratories.software-small-binaries": "^1.14.6",
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+ "@platforma-open/milaboratories.software-small-binaries": "^1.15.0",
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  "@platforma-open/milaboratories.software-mixcr": "4.7.0-133-develop",
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- "@platforma-sdk/test": "^1.17.0",
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+ "@platforma-sdk/test": "^1.20.0",
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  "vitest": "^2.1.8",
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  "typescript": "~5.6.3"
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  },
package/src/export-settings.lib.tengo CHANGED
@@ -444,7 +444,7 @@ shmTreeNodesTableOptions := func(dataDescription) {
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  // export data that is unique for clones, but not unique for a node
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  // (different clones could be in the same topology node, for example, different time points)
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  shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
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- donorColumnSpec := donorColumn.get("spec").getDataAsJson()
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+ donorColumnSpec := donorColumn.spec
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  axes := []
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  columns := []
package/src/prepare-donor-column.lib.tengo CHANGED
@@ -20,7 +20,7 @@ groupDataByDonorId := func(donorColumn, datasets) {
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  // axes[0]: sampleId
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  // value: fileRef resource
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- donorColumnSpec := donorColumn.get("spec").getDataAsJson()
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+ donorColumnSpec := donorColumn.spec
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  sampleIdAxis := donorColumnSpec.axesSpec[0]
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@@ -53,7 +53,7 @@ groupDataByDonorId := func(donorColumn, datasets) {
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  sampleToDonor := {}
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  // columns with meta could be fetched as data direcctly
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- for k, v in donorColumn.get("data").getDataAsJson()["data"] {
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+ for k, v in donorColumn.data.getDataAsJson()["data"] {
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  sampleId := json.decode(k)[0]
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  sampleToDonor[sampleId] = v
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  }
@@ -63,7 +63,7 @@ groupDataByDonorId := func(donorColumn, datasets) {
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  // collect all the clns files that we have into pColumn
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  for clonotypingBlockId, dataset in datasets {
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- for sKey, fileRef in dataset.get("data").inputs() {
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+ for sKey, fileRef in dataset.data.inputs() {
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  sampleId := json.decode(sKey)[0]
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  donor := sampleToDonor[sampleId]
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  dataBuilder.createInputField(json.encode([donor, sampleId, clonotypingBlockId])).set(fileRef)
package/src/process.tpl.tengo CHANGED
@@ -35,7 +35,9 @@ self.body(func(inputs) {
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  assemblingFeature := ""
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  for clonotypingBlockId, dataset in inputs.datasets {
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- presetAnnotations := dataset.get("spec").getDataAsJson()["annotations"]
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+ presetAnnotations := dataset.spec.annotations
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+
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+ ll.assert(!is_undefined(presetAnnotations), "No annotations in dataset specs")
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  datasetTypes[clonotypingBlockId] = "bulk"
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package/src/reconstruct-shm-trees.tpl.tengo CHANGED
@@ -3,6 +3,7 @@ pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
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  ll := import("@platforma-sdk/workflow-tengo:ll")
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  assets := import("@platforma-sdk/workflow-tengo:assets")
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  exec := import("@platforma-sdk/workflow-tengo:exec")
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+ times := import("times")
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  json := import("json")
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@@ -32,11 +33,13 @@ self.body(func(inputs) {
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  ll.assert(!is_undefined(datasetTypes), "datasetTypes undefined")
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+ seed := times.time_string(times.now())
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+
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  allelesCmdBuilder := exec.builder().
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  printErrStreamToStdout().
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  secret("MI_LICENSE", "MI_LICENSE").
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  env("MI_PROGRESS_PREFIX", progressPrefix).
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- env("SEED", "1").
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+ env("SEED", seed).
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  software(mixcrSw).
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  arg("findAlleles").
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  arg("--report").arg("report.txt").
@@ -120,6 +123,7 @@ self.body(func(inputs) {
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  printErrStreamToStdout().
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  secret("MI_LICENSE", "MI_LICENSE").
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  env("MI_PROGRESS_PREFIX", progressPrefix).
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+ env("SEED", seed).
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  software(mixcrSw).
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  arg("findShmTrees").
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  arg("--report").arg("report.txt").
@@ -147,7 +151,6 @@ self.body(func(inputs) {
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  printErrStreamToStdout().
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  inLightQueue().
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  secret("MI_LICENSE", "MI_LICENSE").
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- env("MI_PROGRESS_PREFIX", progressPrefix).
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  software(mixcrSw).
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  arg("exportShmTrees")
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@@ -169,7 +172,6 @@ self.body(func(inputs) {
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  printErrStreamToStdout().
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  inLightQueue().
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  secret("MI_LICENSE", "MI_LICENSE").
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- env("MI_PROGRESS_PREFIX", progressPrefix).
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  software(mixcrSw).
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  arg("exportShmTreesWithNodes")
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