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royjacobsonroyjacobson
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Improve testing, add Decimal class as possible object
1 parent 080492c commit 396bdd0

3 files changed

Lines changed: 125 additions & 10 deletions

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‎plugins/nf-python/src/main/nextflow/python/PythonExtension.groovy‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -85,10 +85,12 @@ class PythonExtension extends PluginExtensionPoint {
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if (obj instanceof String) return ["String", obj]
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if (obj instanceof Integer) return ["Integer", obj]
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if (obj instanceof Long) return ["Integer", obj]
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if (obj instanceof BigDecimal) return ["Decimal", obj]
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if (obj instanceof Double || obj instanceof Float) return ["Float", obj]
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if (obj instanceof Boolean) return ["Boolean", obj]
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if (obj instanceof java.nio.file.Path) return ["Path", obj.toString()]
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if (obj instanceof Duration) return ["Duration", obj.toMillis()]
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if (obj instanceof java.time.Duration) return ["Duration", obj.toMillis()]
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if (obj instanceof MemoryUnit) return ["MemoryUnit", obj.toBytes()]
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if (obj instanceof VersionNumber) return ["VersionNumber", [obj.getMajor(), obj.getMinor(), obj.getPatch()]]
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// Add more as needed
@@ -118,6 +120,7 @@ class PythonExtension extends PluginExtensionPoint {
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}
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case 'String': return data
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case 'Integer': return data
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case 'Decimal': return data instanceof String ? new BigDecimal(data as String) : null
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case 'Float': return data
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case 'Boolean': return data
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case 'Null': return null

‎py/nf_python/nextflow.py‎

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Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
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import sys
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import pathlib
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import datetime
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import decimal
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class MemoryUnit:
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UNITS = ["B", "KB", "MB", "GB", "TB", "PB", "EB", "ZB"]
@@ -59,6 +60,8 @@ def parse_nf(serialized_object):
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return data
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elif nf_type == "Integer":
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return int(data)
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elif nf_type == "Decimal":
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return decimal.Decimal(data)
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elif nf_type == "Float":
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return data
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elif nf_type == "Boolean":
@@ -82,6 +85,8 @@ def pack_python(python_object):
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return ["String", python_object]
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elif isinstance(python_object, int):
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return ["Integer", python_object]
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elif isinstance(python_object, decimal.Decimal):
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return ["Decimal", str(python_object)]
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elif isinstance(python_object, float):
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return ["Float", python_object]
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elif isinstance(python_object, bool):

‎test/test_flow.nf‎

Lines changed: 117 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -15,18 +15,125 @@ process PyProcess {
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}
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workflow {
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// Test pyFunction in a process: should return correct sum and difference
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PyProcess(10, 3)
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.view()
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.view { result ->
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assert result == [x: 10, y: 3]
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println "[TEST] PyProcess returned: $result"
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}
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Channel.of([x: 10, y: 3], [x: 1, y: 5])
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.pyOperator(script: 'echo_kwargs.py') |
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view()
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// Test pyOperator with a map input
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Channel.of([x: 10, y: 3])
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.pyOperator(script: 'echo_kwargs.py')
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.view { result ->
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assert result == [x: 10, y: 3]
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println "[TEST] pyOperator map input returned: $result"
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}
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// Test all supported types and roundtrip
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Channel.of(1, 2, 3)
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.pyOperator(script: 'echo_kwargs.py', foo: 'bar', bar: 123, baz: [1,2,3], qux: [a: 1, b: 2], path: '/tmp/example.txt', duration: 90)
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.view()
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// Test pyOperator with primitive input and options
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Channel.of(1)
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.pyOperator(script: 'echo_kwargs.py', foo: 'bar', bar: 123)
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.view { result ->
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assert result == [value: 1, foo: 'bar', bar: 123]
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println "[TEST] pyOperator primitive+opts returned: $result"
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}
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30-
// Example: Launch a Python script as a standalone function (no channel input)
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pyFunction(script: 'echo_kwargs.py', foo: 'standalone', bar: 42)
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// Test pyFunction as a standalone function
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def standalone = pyFunction(script: 'echo_kwargs.py', foo: 'standalone', bar: 42)
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assert standalone == [foo: 'standalone', bar: 42]
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println "[TEST] pyFunction standalone returned: $standalone"
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// Test all supported types and roundtrip, one script call at a time
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Channel.of(42)
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.pyOperator(script: 'echo_kwargs.py')
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.view { result ->
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assert result.value == 42
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println "[TEST] int roundtrip: $result"
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}
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Channel.of(3.14)
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.pyOperator(script: 'echo_kwargs.py')
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.view { result ->
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assert Math.abs(result.value - 3.14) < 1e-6
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println "[TEST] float roundtrip: $result"
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}
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61+
Channel.of('hello')
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.pyOperator(script: 'echo_kwargs.py')
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.view { result ->
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assert result.value == 'hello'
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println "[TEST] str roundtrip: $result"
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}
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Channel.of(true)
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.pyOperator(script: 'echo_kwargs.py')
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.view { result ->
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assert result.value == true
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println "[TEST] bool roundtrip: $result"
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}
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Channel.of(null)
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.pyOperator(script: 'echo_kwargs.py')
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.view { result ->
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assert result.value == null
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println "[TEST] null roundtrip: $result"
80+
}
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82+
Channel.of([1, 2, 3])
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.pyOperator(script: 'echo_kwargs.py')
84+
.view { result ->
85+
assert result.value == [1, 2, 3]
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println "[TEST] list roundtrip: $result"
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}
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Channel.of([4, 5, 6] as Set)
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.pyOperator(script: 'echo_kwargs.py')
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.view { result ->
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assert (result.value as Set) == [4, 5, 6] as Set
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println "[TEST] set roundtrip: $result"
94+
}
95+
96+
Channel.of([a: 1, b: 2])
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.pyOperator(script: 'echo_kwargs.py')
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.view { result ->
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assert result == [a: 1, b: 2]
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println "[TEST] dict roundtrip: $result"
101+
}
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103+
Channel.of('/tmp/example.txt')
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.pyOperator(script: 'echo_kwargs.py')
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.view { result ->
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assert result.value.toString() == '/tmp/example.txt'
107+
println "[TEST] path roundtrip: $result"
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}
109+
110+
Channel.of(java.time.Duration.ofSeconds(90))
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.pyOperator(script: 'echo_kwargs.py')
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.view { result ->
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assert result.value.toString() == 'PT1M30S' || result.value.seconds == 90
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println "[TEST] duration roundtrip: $result"
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}
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117+
Channel.of(Duration.of(90000))
118+
.pyOperator(script: 'echo_kwargs.py')
119+
.view { result ->
120+
assert result.value.toString() == 'PT1M30S' || result.value.seconds == 90
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println "[TEST] duration roundtrip: $result"
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}
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Channel.of(10241024)
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.pyOperator(script: 'echo_kwargs.py', type: 'memory')
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.view { result ->
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// memory is returned as int, check value
128+
assert result.value == 10241024
129+
println "[TEST] memory roundtrip: $result"
130+
}
131+
132+
Channel.of([82, 17, 49])
133+
.pyOperator(script: 'echo_kwargs.py', type: 'version')
134+
.view { result ->
135+
// version is returned as list, check value
136+
assert result.value == [82, 17, 49]
137+
println "[TEST] version roundtrip: $result"
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}
32139
}

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