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github-merge-queue[bot] pushed a commit to branch release/v1.2
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The following commit(s) were added to refs/heads/release/v1.2 by this push:
new 7a5037c7f8 fix(dendrogram, v1.2): pass the color threshold to scipy as
a number (#7306)
7a5037c7f8 is described below
commit 7a5037c7f87fb5697e27358968a1166ad23116bb
Author: Kary Zheng <[email protected]>
AuthorDate: Tue Aug 4 14:28:13 2026 -0700
fix(dendrogram, v1.2): pass the color threshold to scipy as a number (#7306)
### What changes were proposed in this PR?
Backport of #7234 to `release/v1.2`. The automated backport, #7291,
landed with cherry-pick conflict markers on a branch in this repository
that I cannot push to, so this PR carries the resolved commit from my
fork instead.
The conflict was in `createDendrogram()`: `release/v1.2` still has the
older body, and the cherry-picked commit rewrites the same lines. The
resolution takes the cherry-picked side. It is line-for-line identical
to what landed on `main`, plus the three assert messages that already
exist on `main` and that the accompanying spec asserts on.
### Any related issues, documentation, discussions?
Backport of #7234, which closed #7232. Supersedes #7291.
### How was this PR tested?
`DendrogramOpDescSpec` on this branch: 9 tests, all passing.
`scalafmtCheckAll` and `scalafixAll --check` are both clean.
### Was this PR authored or co-authored using generative AI tooling?
Generated-by: Claude Code (claude-opus-5[1m])
---
.../dendrogram/DendrogramOpDesc.scala | 22 ++--
.../dendrogram/DendrogramOpDescSpec.scala | 125 +++++++++++++++++++++
2 files changed, 137 insertions(+), 10 deletions(-)
diff --git
a/common/workflow-operator/src/main/scala/org/apache/texera/amber/operator/visualization/dendrogram/DendrogramOpDesc.scala
b/common/workflow-operator/src/main/scala/org/apache/texera/amber/operator/visualization/dendrogram/DendrogramOpDesc.scala
index e92281369b..859826fb73 100644
---
a/common/workflow-operator/src/main/scala/org/apache/texera/amber/operator/visualization/dendrogram/DendrogramOpDesc.scala
+++
b/common/workflow-operator/src/main/scala/org/apache/texera/amber/operator/visualization/dendrogram/DendrogramOpDesc.scala
@@ -20,10 +20,11 @@
package org.apache.texera.amber.operator.visualization.dendrogram
import com.fasterxml.jackson.annotation.{JsonProperty, JsonPropertyDescription}
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize
import com.kjetland.jackson.jsonSchema.annotations.JsonSchemaTitle
import org.apache.texera.amber.core.tuple.{AttributeType, Schema}
import
org.apache.texera.amber.pybuilder.PythonTemplateBuilder.PythonTemplateBuilderStringContext
-import org.apache.texera.amber.pybuilder.PyStringTypes.EncodableString
+import org.apache.texera.amber.pybuilder.PyStringTypes.{EncodableString,
PythonLiteral}
import org.apache.texera.amber.core.workflow.PortIdentity
import org.apache.texera.amber.operator.PythonOperatorDescriptor
import
org.apache.texera.amber.operator.metadata.annotations.AutofillAttributeName
@@ -49,10 +50,13 @@ class DendrogramOpDesc extends PythonOperatorDescriptor {
@AutofillAttributeName
var labels: EncodableString = ""
+ // Numeric: scipy compares it against the linkage distances. contentAs names
the
+ // boxed class — Option erases its element type, and a blank must not read
as 0.
@JsonProperty(defaultValue = "", required = false)
@JsonSchemaTitle("Color Threshold")
@JsonPropertyDescription("Value at which separation of clusters will be
made")
- var threshold: EncodableString = ""
+ @JsonDeserialize(contentAs = classOf[java.lang.Double])
+ var threshold: Option[Double] = None
override def getOutputSchemas(
inputSchemas: Map[PortIdentity, Schema]
@@ -70,20 +74,18 @@ class DendrogramOpDesc extends PythonOperatorDescriptor {
)
private def createDendrogram(): PythonTemplateBuilder = {
- assert(xVal.nonEmpty)
- assert(yVal.nonEmpty)
- assert(labels.nonEmpty)
- val strippedThreshold: EncodableString = threshold.trim
- val isThreshold =
- if (strippedThreshold.nonEmpty) pyb"color_threshold=$strippedThreshold"
- else "color_threshold=None"
+ assert(xVal.nonEmpty, "Value X Column cannot be empty")
+ assert(yVal.nonEmpty, "Value Y Column cannot be empty")
+ assert(labels.nonEmpty, "Labels cannot be empty")
+ // Unset means None, which is scipy's own 0.7 * max distance.
+ val thresholdExpr: PythonLiteral =
threshold.map(_.toString).getOrElse("None")
pyb"""
| x = np.array(table[$xVal])
| y = np.array(table[$yVal])
| data = np.column_stack((x, y))
| labels = table[$labels].tolist()
|
- | fig = ff.create_dendrogram(data, labels=labels, $isThreshold)
+ | fig = ff.create_dendrogram(data, labels=labels,
color_threshold=$thresholdExpr)
| fig.update_layout(yaxis_title="Linkage Distance",
margin=dict(l=0, r=0, b=0, t=0))
|"""
}
diff --git
a/common/workflow-operator/src/test/scala/org/apache/texera/amber/operator/visualization/dendrogram/DendrogramOpDescSpec.scala
b/common/workflow-operator/src/test/scala/org/apache/texera/amber/operator/visualization/dendrogram/DendrogramOpDescSpec.scala
new file mode 100644
index 0000000000..b56ffae273
--- /dev/null
+++
b/common/workflow-operator/src/test/scala/org/apache/texera/amber/operator/visualization/dendrogram/DendrogramOpDescSpec.scala
@@ -0,0 +1,125 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+package org.apache.texera.amber.operator.visualization.dendrogram
+
+import org.apache.texera.amber.operator.LogicalOp
+import org.apache.texera.amber.util.JSONUtils.objectMapper
+import org.scalatest.BeforeAndAfter
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+import java.nio.charset.StandardCharsets
+import java.util.Base64
+
+class DendrogramOpDescSpec extends AnyFlatSpec with BeforeAndAfter with
Matchers {
+
+ var opDesc: DendrogramOpDesc = _
+
+ before {
+ opDesc = new DendrogramOpDesc()
+ }
+
+ private def b64(s: String): String =
+ Base64.getEncoder.encodeToString(s.getBytes(StandardCharsets.UTF_8))
+
+ private def carries(output: String, name: String): Boolean =
+ output.contains(name) || output.contains(b64(name))
+
+ private def fieldPart(msg: String): String =
+ msg.toLowerCase.replace("cannot be empty", "")
+
+ // createDendrogram() is private; generatePythonCode() is the public
+ // entry point that reaches its asserts.
+ it should "throw AssertionError naming the X column when all fields are
empty" in {
+ val ex = intercept[AssertionError](opDesc.generatePythonCode())
+ ex.getMessage should not be null
+ ex.getMessage should include("cannot be empty")
+ fieldPart(ex.getMessage) should include("x")
+ }
+
+ it should "throw AssertionError naming the Y column when only xVal and
labels are set" in {
+ opDesc.xVal = "coord_a"
+ opDesc.labels = "label_col"
+ val ex = intercept[AssertionError](opDesc.generatePythonCode())
+ ex.getMessage should not be null
+ ex.getMessage should include("cannot be empty")
+ fieldPart(ex.getMessage) should include("y")
+ }
+
+ it should "throw AssertionError naming the Labels column when only xVal and
yVal are set" in {
+ opDesc.xVal = "coord_a"
+ opDesc.yVal = "coord_b"
+ val ex = intercept[AssertionError](opDesc.generatePythonCode())
+ ex.getMessage should not be null
+ ex.getMessage should include("cannot be empty")
+ fieldPart(ex.getMessage) should include("label")
+ }
+
+ it should "generate python code carrying all three configured columns" in {
+ opDesc.xVal = "coord_a"
+ opDesc.yVal = "coord_b"
+ opDesc.labels = "label_col"
+ val code = opDesc.generatePythonCode()
+ assert(carries(code, "coord_a"))
+ assert(carries(code, "coord_b"))
+ assert(carries(code, "label_col"))
+ code should include("create_dendrogram")
+ // empty threshold falls back to color_threshold=None
+ code should include("color_threshold=None")
+ }
+
+ it should "generate python code passing a configured threshold as a number"
in {
+ opDesc.xVal = "coord_a"
+ opDesc.yVal = "coord_b"
+ opDesc.labels = "label_col"
+ opDesc.threshold = Some(42.5)
+ val code = opDesc.generatePythonCode()
+ // A number, not a decoded string: a string raises inside scipy.
+ code should include("color_threshold=42.5")
+ code should not include "color_threshold=None"
+ }
+
+ /** Reads the shapes a stored workflow can hold. Without `contentAs` a JSON
string
+ * stays unconverted inside the Option and the first use throws.
+ */
+ private def readThreshold(json: String): Option[Double] =
+ objectMapper
+ .readValue(s"""{"operatorType":"Dendrogram"$json}""", classOf[LogicalOp])
+ .asInstanceOf[DendrogramOpDesc]
+ .threshold
+
+ "DendrogramOpDesc.threshold" should "deserialize a JSON number" in {
+ readThreshold(""","threshold":42.5""") shouldBe Some(42.5)
+ }
+
+ it should "deserialize the numeric string a workflow saved before the field
was numeric" in {
+ readThreshold(""","threshold":"42.5"""") shouldBe Some(42.5)
+ }
+
+ it should "read an absent, null or blank value as unset rather than as zero"
in {
+ readThreshold("") shouldBe None
+ readThreshold(""","threshold":null""") shouldBe None
+ readThreshold(""","threshold":""""") shouldBe None
+ }
+
+ it should "hold a Double, not the raw JSON value" in {
+ readThreshold(""","threshold":"42.5"""").map(_ * 2) shouldBe Some(85.0)
+ }
+}
