Migration to new pfconv version

platforma-open · Nov 14, 2024 · fea8af4 · fea8af4
1 parent b20615d
commit fea8af4
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Showing 11 changed files with 901 additions and 827 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml
@@ -6,18 +6,18 @@ packages:
   - .
 
 catalog:
-  '@platforma-sdk/workflow-tengo': ^1.7.5
-  '@platforma-sdk/model': ^1.7.20
-  '@platforma-sdk/ui-vue': ^1.7.51
+  '@platforma-sdk/workflow-tengo': ^2.0.1
+  '@platforma-sdk/model': ^1.8.0
+  '@platforma-sdk/ui-vue': ^1.8.11
   '@platforma-sdk/tengo-builder': ^1.16.1
-  '@platforma-sdk/block-tools': ^2.3.21
+  '@platforma-sdk/block-tools': ^2.3.24
 
-  '@platforma-sdk/test': ^1.7.52
+  '@platforma-sdk/test': ^1.8.13
   '@milaboratories/helpers': ^1.6.6
 
-  '@milaboratories/software-pframes-conv': 1.6.8
-  '@platforma-open/milaboratories.software-small-binaries': ^1.14.5
-  '@platforma-open/milaboratories.software-mixcr': 4.7.0-113-develop
+  '@milaboratories/software-pframes-conv': 2.0.1
+  '@platforma-open/milaboratories.software-small-binaries': ^1.14.6
+  '@platforma-open/milaboratories.software-mixcr': 4.7.0-133-develop
 
   'vue': ^3.5.12
   'vue-tsc': ^2.1.10
@@ -29,13 +29,13 @@ catalog:
   'tsup': ~8.1.2
   'turbo': ^2.2.3
 
-  'vite': ^5.4.10
-  'vitest': ^2.1.4
-  '@vitejs/plugin-vue': ^5.1.4
+  'vite': ^5.4.11
+  'vitest': ^2.1.5
+  '@vitejs/plugin-vue': ^5.2.0
 
   '@vueuse/core': ^11.2.0
 
-  '@ag-grid-community/core': &ag-grid ^32.3.2
+  '@ag-grid-community/core': &ag-grid ^32.3.3
   '@ag-grid-community/client-side-row-model': *ag-grid
   '@ag-grid-community/vue3': *ag-grid
   '@ag-grid-community/styles': *ag-grid
@@ -44,5 +44,5 @@ catalog:
 
   # other blocks used in tests
 
-  '@platforma-open/milaboratories.samples-and-data': ^1.6.3
-  '@platforma-open/milaboratories.samples-and-data.model': ^1.6.0
+  '@platforma-open/milaboratories.samples-and-data': ^1.6.5
+  '@platforma-open/milaboratories.samples-and-data.model': ^1.6.1
diff --git a/test/.DS_Store b/test/.DS_Store
diff --git a/test/test_config.json b/test/test_config.json
@@ -0,0 +1,5 @@
+{
+  "address": "http://127.0.0.1:6345?tx-delay=5&force-sync=true",
+  "test_user": "test_user",
+  "test_password": "test_password"
+}
diff --git a/ui/src/SettingsPanel.vue b/ui/src/SettingsPanel.vue
@@ -94,7 +94,7 @@ function setLimitInput() {
 
   <PlDropdown v-if="needSpecies" :options="speciesOptions" v-model="app.model.args.species" label="Select species" />
 
-  <PlTextField :model-value="app.model.args.limitInput !== undefined ? String(app.model.args.limitInput) : undefined"
+  <PlTextField :model-value="app.model.args.limitInput !== undefined ? String(app.model.args.limitInput) : ''"
     @update:model-value="v => app.model.args.limitInput = v && !isNaN(parseInt(v)) ? parseInt(v) : undefined"
     label="Take only this number of reads into analysis" :rules="[v => !isNaN(parseInt(v))]" />
 </template>
diff --git a/workflow/src/calculate-pfconv-params.tpl.tengo b/workflow/src/calculate-pfconv-params.tpl.tengo
@@ -97,7 +97,6 @@ self.body(func(inputs) {
 		params: {
 			"axes": axes,
 			"columns": columns,
-			"naStr": "region_not_covered",
 			"storageFormat": "Binary",
 			"partitionKeyLength": 0
 		}

diff --git a/workflow/src/export-clones-bulk.tpl.tengo b/workflow/src/export-clones-bulk.tpl.tengo
@@ -3,7 +3,7 @@
 ll := import("@platforma-sdk/workflow-tengo:ll")
 xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
 self := import("@platforma-sdk/workflow-tengo:tpl")
-pframes := import("@platforma-sdk/workflow-tengo:pframes")
+pcolumn := import("@platforma-sdk/workflow-tengo:pframes.pcolumn")
 pConstants := import("@platforma-sdk/workflow-tengo:pframes.constants")
 
 text := import("text")
@@ -20,7 +20,7 @@ self.body(func(inputs) {
 	pfconvParams := inputs.pfconvParams
 	data := self.rawInputs().data.getValue()
 
-	csvMap := pframes.pColumnResourceMapDataBuilder(/* key length */ 1)
+	csvMap := pcolumn.resourceMapBuilder(/* key length */ 1)
 
 	for fileName, file in data.inputs() {
 		if !text.has_prefix(fileName, FILE_NAME_PREFIX) || !text.has_suffix(fileName, FILE_NAME_SUFFIX) {

diff --git a/workflow/src/mixcr-analyze.tpl.tengo b/workflow/src/mixcr-analyze.tpl.tengo
@@ -8,6 +8,7 @@ exec := import("@platforma-sdk/workflow-tengo:exec")
 assets := import("@platforma-sdk/workflow-tengo:assets")
 render := import("@platforma-sdk/workflow-tengo:render")
 pframes := import("@platforma-sdk/workflow-tengo:pframes")
+pcolumn := import("@platforma-sdk/workflow-tengo:pframes.pcolumn")
 xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
 mixcr := import(":mixcr")
 
@@ -142,7 +143,7 @@ self.body(func(inputs) {
 
 	// collecting results
 
-	reportsMap := pframes.pColumnResourceMapDataBuilder( /* keyLength */ 2 )
+	reportsMap := pcolumn.resourceMapBuilder( /* keyLength */ 2 )
 	for report in reports {
 		reportsMap.add([report.id, "json"], mixcrCmd.getFile(report.fileJson))
 		reportsMap.add([report.id, "txt"], mixcrCmd.getFile(report.fileTxt))