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Add pretty option to dump operator [ci fast]
Signed-off-by: Paolo Di Tommaso <[email protected]>
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82 changes: 82 additions & 0 deletions
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modules/nextflow/src/main/groovy/nextflow/extension/DumpHelper.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
| /* | ||
| * Copyright 2020-2022, Seqera Labs | ||
| * | ||
| * Licensed 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 nextflow.extension | ||
|
|
||
| import java.nio.file.Path | ||
|
|
||
| import groovy.json.JsonBuilder | ||
| import groovy.json.JsonOutput | ||
| import groovy.transform.CompileStatic | ||
| import nextflow.extension.FilesEx | ||
| import org.codehaus.groovy.runtime.InvokerHelper | ||
| /** | ||
| * Helper converters for {@link DumpOp} operator | ||
| * | ||
| * @author : jorge <[email protected]> | ||
| */ | ||
| @CompileStatic | ||
| class DumpHelper { | ||
|
|
||
| static def deepReplaceToString(root, replaceNullWith = "") { | ||
| if (root instanceof List) { | ||
| root.collect { | ||
| if (it instanceof Map) { | ||
| deepReplaceToString(it, replaceNullWith) | ||
| } else if (it instanceof List) { | ||
| deepReplaceToString(it, replaceNullWith) | ||
| } else if (it == null) { | ||
| replaceNullWith | ||
| } else if (it instanceof Path) { | ||
| FilesEx.toUriString(it) | ||
| } else { | ||
| it.toString() | ||
| } | ||
| } | ||
| } | ||
| else if (root instanceof Map) { | ||
| root.each { | ||
| if (it.value instanceof Map) { | ||
| deepReplaceToString(it.value, replaceNullWith) | ||
| } else if (it.value instanceof List) { | ||
| it.value = deepReplaceToString(it.value, replaceNullWith) | ||
| } else if (it.value == null) { | ||
| it.value = replaceNullWith | ||
| } else if (it.value instanceof Path) { | ||
| return FilesEx.toUriString((Path)it.value) | ||
| } else { | ||
| it.value = it.value.toString() | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
|
||
| static String prettyPrint(input){ | ||
| if (input instanceof Map) { | ||
| def converted = deepReplaceToString(input) | ||
| return JsonOutput.prettyPrint(JsonOutput.toJson(converted)) | ||
| } else if (input instanceof List) { | ||
| def converted = deepReplaceToString(input) | ||
| return new JsonBuilder(converted).toPrettyString() | ||
| } else if (input instanceof Path) { | ||
| return FilesEx.toUriString(input) | ||
| } else { | ||
| return InvokerHelper.inspect(input) | ||
| } | ||
| } | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -22,6 +22,9 @@ import nextflow.Session | |
| import spock.lang.Specification | ||
| import spock.lang.Unroll | ||
| import test.OutputCapture | ||
|
|
||
| import java.nio.file.Path | ||
|
|
||
| /** | ||
| * | ||
| * @author Paolo Di Tommaso <[email protected]> | ||
|
|
@@ -40,7 +43,7 @@ class DumpOpTest extends Specification { | |
| new Session(dumpChannels: ['*']) | ||
|
|
||
| when: | ||
| def result = Channel.from(1,2,3).dump() | ||
| def result = Channel.from(1, 2, 3).dump() | ||
| then: | ||
| result.val == 1 | ||
| result.val == 2 | ||
|
|
@@ -58,7 +61,7 @@ class DumpOpTest extends Specification { | |
| new Session(dumpChannels: ['*']) | ||
|
|
||
| when: | ||
| def result = Channel.from(1,2,3).dump { it * it } | ||
| def result = Channel.from(1, 2, 3).dump { it * it } | ||
| then: | ||
| result.val == 1 | ||
| result.val == 2 | ||
|
|
@@ -76,7 +79,7 @@ class DumpOpTest extends Specification { | |
| new Session(dumpChannels: ['*']) | ||
|
|
||
| when: | ||
| def result = Channel.from(1,2,3).dump(tag:'foo') | ||
| def result = Channel.from(1, 2, 3).dump(tag: 'foo') | ||
| then: | ||
| result.val == 1 | ||
| result.val == 2 | ||
|
|
@@ -89,7 +92,7 @@ class DumpOpTest extends Specification { | |
| } | ||
|
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||
| @Unroll | ||
| def 'should validate isEnabled when tag=#tag and names=#names' () { | ||
| def 'should validate isEnabled when tag=#tag and names=#names'() { | ||
|
|
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| given: | ||
| def op = new DumpOp(tag: tag, dumpNames: names.tokenize(',')) | ||
|
|
@@ -98,16 +101,61 @@ class DumpOpTest extends Specification { | |
| op.isEnabled() == expected | ||
|
|
||
| where: | ||
| tag | names | expected | ||
| 'foo' | 'foo' | true | ||
| 'foo' | '*' | true | ||
| 'foo' | 'bar' | false | ||
| 'foo' | 'f' | false | ||
| 'foo' | 'f*' | true | ||
| 'bar' | 'f*' | false | ||
| 'bar' | 'f*,b*' | true | ||
| null | '*' | true | ||
| tag | names | expected | ||
| 'foo' | 'foo' | true | ||
| 'foo' | '*' | true | ||
| 'foo' | 'bar' | false | ||
| 'foo' | 'f' | false | ||
| 'foo' | 'f*' | true | ||
| 'bar' | 'f*' | false | ||
| 'bar' | 'f*,b*' | true | ||
| null | '*' | true | ||
|
|
||
| } | ||
|
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| @Unroll | ||
| def 'should pretty print channel with items #items'() { | ||
|
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| given: | ||
| new Session(dumpChannels: ['*']) | ||
|
|
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| when: | ||
| def result = Channel.of(items).dump(tag: 'foo', pretty: true) | ||
|
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| then: | ||
| result.val | ||
| result.val == Channel.STOP | ||
| capture.toString().contains(expected) | ||
|
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| where: | ||
| items | expected | ||
| 'a string' | "[DUMP: foo] 'a string'" | ||
| 123123 | '[DUMP: foo] 123123' | ||
| ['a', 'b'] | '"a",' | ||
| ['a': 'b'] | '"a": "b"' | ||
| ['a': Path.of('b')] | '"a": "b"' | ||
| ['a': [b: Path.of('c')]] | '"b": "c"' | ||
| } | ||
|
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| def 'should pretty print a complex channel'() { | ||
|
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| given: | ||
| new Session(dumpChannels: ['*']) | ||
|
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| when: | ||
| def result = Channel.of([ | ||
| id : 'test', | ||
| samples: [ | ||
| [id: 'S1', path: '/path/to/s1'], | ||
| [id: 'S2', path: '/path/to/s2'], | ||
| [id: 'S3', path: '/path/to/s3'] | ||
| ] | ||
| ]).dump(tag: 'foo', pretty: true) | ||
|
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| then: | ||
| result.val | ||
| result.val == Channel.STOP | ||
| capture.toString().contains('"path": "/path/to/s1"') | ||
| } | ||
|
|
||
| } | ||