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mr-cmr-c
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add more tests (#35)
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‎src/test/java/org/w3id/cwl/cwl1_2/utils/ExamplesTest.java

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@@ -7642,4 +7642,59 @@ public void testvalid_listing_deep2ByMap() throws Exception {
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doc = (java.util.Map<String, Object>) YamlUtils.mapFromString(yaml);
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RootLoader.loadDocument(doc);
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}
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@org.junit.Test(expected = ValidationException.class)
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public void testvalid_rename_inputsByString() throws Exception {
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String path = java.nio.file.Paths.get(".").toAbsolutePath().normalize().toString();
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String baseUri = Uris.fileUri(path) + "/";
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java.net.URL url = getClass().getResource("valid_rename-inputs.cwl");
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java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI());
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String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8");
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RootLoader.loadDocument(yaml, baseUri);
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}
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@org.junit.Test(expected = ValidationException.class)
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public void testvalid_rename_inputsByPath() throws Exception {
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java.net.URL url = getClass().getResource("valid_rename-inputs.cwl");
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java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI());
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RootLoader.loadDocument(resPath);
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}
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@org.junit.Test(expected = ValidationException.class)
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public void testvalid_rename_inputsByMap() throws Exception {
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java.net.URL url = getClass().getResource("valid_rename-inputs.cwl");
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java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI());
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String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8");
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java.util.Map<String, Object> doc;
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doc = (java.util.Map<String, Object>) YamlUtils.mapFromString(yaml);
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RootLoader.loadDocument(doc);
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}
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@org.junit.Test
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public void testvalid_rename_outputsByString() throws Exception {
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String path = java.nio.file.Paths.get(".").toAbsolutePath().normalize().toString();
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String baseUri = Uris.fileUri(path) + "/";
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java.net.URL url = getClass().getResource("valid_rename-outputs.cwl");
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java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI());
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String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8");
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RootLoader.loadDocument(yaml, baseUri);
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}
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@org.junit.Test
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public void testvalid_rename_outputsByPath() throws Exception {
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java.net.URL url = getClass().getResource("valid_rename-outputs.cwl");
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java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI());
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RootLoader.loadDocument(resPath);
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}
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@org.junit.Test
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public void testvalid_rename_outputsByMap() throws Exception {
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java.net.URL url = getClass().getResource("valid_rename-outputs.cwl");
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java.nio.file.Path resPath = java.nio.file.Paths.get(url.toURI());
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String yaml = new String(java.nio.file.Files.readAllBytes(resPath), "UTF8");
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java.util.Map<String, Object> doc;
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doc = (java.util.Map<String, Object>) YamlUtils.mapFromString(yaml);
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RootLoader.loadDocument(doc);
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}
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}

‎src/test/resources/org/w3id/cwl/cwl1_2/utils/rename-inputs.yml

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inputWithSecondary:
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class: File
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location: secondary_file_test.txt

‎src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_rename-inputs.cwl

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#!/usr/bin/env cwl-runner
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id: InputSecondaryFileConformanceTest
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baseCommand:
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- ls
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class: CommandLineTool
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cwlVersion: v1.2
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doc: |
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Simple test to confirm the implementation of expressions returning a File within a CommandInputParameter.secondaryFile field.
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Use GREP to filter the result from ls to ensure we only get the secondary files in there.
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Related links:
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- Issue: https://github.com/common-workflow-language/cwltool/issues/1232
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- PR: https://github.com/common-workflow-language/cwltool/pull/1233
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- Discourse: https://cwl.discourse.group/t/ask-cwl-to-rename-a-secondary-file/72
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inputs:
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- id: inputWithSecondary
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type: File
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doc: |
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This input will with a secondary file `.accessory`. You could create these files (and its accessory) with:
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```bash
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touch secondary_file_test.txt
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touch secondary_file_test.txt.accessory
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```
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secondaryFiles:
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- .accessory
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- |
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${
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function resolveSecondary(base, secPattern) {
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if (secPattern[0] == '^') {
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var spl = base.split('.');
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var endIndex = spl.length > 1 ? spl.length - 1 : 1;
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return resolveSecondary(spl.slice(undefined, endIndex).join("."), secPattern.slice(1));
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}
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return base + secPattern;
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}
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return [{
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"class": "File",
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"location": self.secondaryFiles[0].location,
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"basename": resolveSecondary(self.basename, '^.accessory')
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}];
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}
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arguments:
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- valueFrom: "|"
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shellQuote: false
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position: 0
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- valueFrom: "grep"
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position: 1
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- valueFrom: "secondary"
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position: 2
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outputs:
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- id: output_file
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type: stdout
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stdout: result
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requirements:
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InlineJavascriptRequirement: {}
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ShellCommandRequirement: {}
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InitialWorkDirRequirement:
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listing:
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- $(inputs.inputWithSecondary)

‎src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_rename-outputs.cwl

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#!/usr/bin/env cwl-runner
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id: OutputSecondaryFileConformanceTest
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baseCommand:
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- ls
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class: CommandLineTool
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cwlVersion: v1.2
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doc: |
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Simple test to confirm the implementation of expressions returning a File within a CommandOutputParameter.secondaryFile field.
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Related links:
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- Issue: https://github.com/common-workflow-language/cwltool/issues/1232
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- PR: https://github.com/common-workflow-language/cwltool/pull/1233
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- Discourse: https://cwl.discourse.group/t/ask-cwl-to-rename-a-secondary-file/72
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inputs: []
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outputs:
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- id: output_file
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label: out
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outputBinding:
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glob: "*.txt"
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secondaryFiles: |
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${
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function resolveSecondary(base, secPattern) {
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if (secPattern[0] == "^") {
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var spl = base.split(".");
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var endIndex = spl.length > 1 ? spl.length - 1 : 1;
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return resolveSecondary(spl.slice(undefined, endIndex).join("."), secPattern.slice(1));
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}
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return base + secPattern;
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}
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return [
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{
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"class": "File",
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"path": resolveSecondary(self.path, "^.accessory"),
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"basename": resolveSecondary(self.basename, ".accessory")
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}
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];
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}
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type: File
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requirements:
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InlineJavascriptRequirement: {}
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InitialWorkDirRequirement:
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listing:
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- entry: ""
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entryname: secondary_file_test.txt
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writable: true
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- entry: ""
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entryname: secondary_file_test.accessory
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writable: true

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