CWLUtil test cases
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/commit/c191822b Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/c191822b Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/c191822b Branch: refs/heads/cwl-browse Commit: c191822b801d47c9f71a1535422b226ac90e0b44 Parents: c815a14 Author: ThilinaManamgoda <[email protected]> Authored: Mon Jul 4 23:36:17 2016 +0530 Committer: ThilinaManamgoda <[email protected]> Committed: Mon Jul 4 23:36:17 2016 +0530 ---------------------------------------------------------------------- taverna-cwl-utilities/CWLFiles/customtool1.cwl | 67 ++++++++++++ .../CWLFiles/customtoolrecord.cwl | 41 ++++++++ taverna-cwl-utilities/pom.xml | 7 ++ .../apache/taverna/cwl/utilities/CWLUtil.java | 14 ++- .../taverna/cwl/utilities/CWLUtilTest.java | 103 +++++++++++++++++++ 5 files changed, 227 insertions(+), 5 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/c191822b/taverna-cwl-utilities/CWLFiles/customtool1.cwl ---------------------------------------------------------------------- diff --git a/taverna-cwl-utilities/CWLFiles/customtool1.cwl b/taverna-cwl-utilities/CWLFiles/customtool1.cwl new file mode 100644 index 0000000..227ba16 --- /dev/null +++ b/taverna-cwl-utilities/CWLFiles/customtool1.cwl @@ -0,0 +1,67 @@ +################################################################################ +# 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. +################################################################################# + + +#!/usr/bin/env cwl-runner + +class: CommandLineTool +cwlVersion: cwl:draft-3 + +$namespaces: + edam: http://edamontology.org/ + +inputs: + - id: input_1 + type: int + label: input 1 testing label + description: this is a short description of input 1 + format: edam:format_2323 + + - id: input_2 + type: + type: array + items: int + label: input 2 testing label + description: this is a short description of input 2 + format: $expression + + - id: input_3 + type: String + label: input 3 testing label + description: this is a short description of input 3 + format: noNameSpace:testing + +outputs: + - id: output_1 + type: int + label: output 1 testing label + description: this is a short description of output 1 + format: just a string + + - id: output_2 + type: String + label: output 2 testing label + description: this is a short description of output 2 + format: ["edam:format_2323", just a string] + +label: This is a short description of the tool + +description: | + This is a much longer description of the tool. This can be displayed in + the service detail panel + +basecommand: echo http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/c191822b/taverna-cwl-utilities/CWLFiles/customtoolrecord.cwl ---------------------------------------------------------------------- diff --git a/taverna-cwl-utilities/CWLFiles/customtoolrecord.cwl b/taverna-cwl-utilities/CWLFiles/customtoolrecord.cwl new file mode 100644 index 0000000..f008bdb --- /dev/null +++ b/taverna-cwl-utilities/CWLFiles/customtoolrecord.cwl @@ -0,0 +1,41 @@ +################################################################################ +# 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. +################################################################################# + +#!/usr/bin/env cwl-runner + +class: CommandLineTool +cwlVersion: cwl:draft-3 + +inputs: + - id: input_1 + type: record + + - id: input_2 + type: + type: array + items: int + - id: input_3 + type: String + +outputs: + - id: output_1 + type: int + + - id: ouput_2 + type: String + +basecommand: echo http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/c191822b/taverna-cwl-utilities/pom.xml ---------------------------------------------------------------------- diff --git a/taverna-cwl-utilities/pom.xml b/taverna-cwl-utilities/pom.xml index 5316b02..0eb2095 100644 --- a/taverna-cwl-utilities/pom.xml +++ b/taverna-cwl-utilities/pom.xml @@ -20,5 +20,12 @@ <artifactId>taverna-cwl-utilities</artifactId> <packaging>bundle</packaging> <name>Apache Taverna CWL Activity</name> +<dependencies> +<dependency> + <groupId>org.yaml</groupId> + <artifactId>snakeyaml</artifactId> + <version>1.17</version> + </dependency> +</dependencies> </project> http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/c191822b/taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/CWLUtil.java ---------------------------------------------------------------------- diff --git a/taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/CWLUtil.java b/taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/CWLUtil.java index a7d944b..300891f 100644 --- a/taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/CWLUtil.java +++ b/taverna-cwl-utilities/src/main/java/org/apache/taverna/cwl/utilities/CWLUtil.java @@ -34,6 +34,10 @@ public class CWLUtil { processNameSpace(); } + public LinkedHashMap getNameSpace() { + return nameSpace; + } + public void processNameSpace() { if (cwlFile.containsKey("$namespaces")) { @@ -58,7 +62,7 @@ public class CWLUtil { return processdetails(cwlFile.get(OUTPUTS)); } - private HashMap<String, Integer> process(Object inputs) { + public HashMap<String, Integer> process(Object inputs) { HashMap<String, Integer> result = new HashMap<>(); @@ -131,7 +135,7 @@ public class CWLUtil { return result; } - private void extractLabel(Map input, PortDetail detail) { + public void extractLabel(Map input, PortDetail detail) { if (input != null) if (input.containsKey(LABEL)) { detail.setLabel((String) input.get(LABEL)); @@ -140,7 +144,7 @@ public class CWLUtil { } } - private void extractDescription(Map input, PortDetail detail) { + public void extractDescription(Map input, PortDetail detail) { if (input != null) if (input.containsKey(DESCRIPTION)) { detail.setDescription((String) input.get(DESCRIPTION)); @@ -149,7 +153,7 @@ public class CWLUtil { } } - private void extractFormat(Map input, PortDetail detail) { + public void extractFormat(Map input, PortDetail detail) { if (input != null) if (input.containsKey(FORMAT)) { @@ -170,7 +174,7 @@ public class CWLUtil { } } - private void figureOutFormats(String formatInfoString, PortDetail detail) { + public void figureOutFormats(String formatInfoString, PortDetail detail) { if (formatInfoString.startsWith("$")) { detail.addFormat(formatInfoString); http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/c191822b/taverna-cwl-utilities/src/test/java/org/apache/taverna/cwl/utilities/CWLUtilTest.java ---------------------------------------------------------------------- diff --git a/taverna-cwl-utilities/src/test/java/org/apache/taverna/cwl/utilities/CWLUtilTest.java b/taverna-cwl-utilities/src/test/java/org/apache/taverna/cwl/utilities/CWLUtilTest.java new file mode 100644 index 0000000..6f5a4ad --- /dev/null +++ b/taverna-cwl-utilities/src/test/java/org/apache/taverna/cwl/utilities/CWLUtilTest.java @@ -0,0 +1,103 @@ +package org.apache.taverna.cwl.utilities; + +import static org.junit.Assert.*; + +import java.io.FileInputStream; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashMap; +import java.util.LinkedHashMap; +import java.util.Map; +import java.util.stream.Stream; + +import org.junit.Before; +import org.junit.Test; +import org.yaml.snakeyaml.Yaml; + +public class CWLUtilTest { + Map cwlFile; + CWLUtil cwlUtil; + Map input; + + @Before + public void setUp() throws Exception { + Yaml reader = new Yaml(); + Path path = Paths.get("CWLFiles", "customtool1.cwl"); + cwlFile = (Map) reader.load(new FileInputStream(path.toFile())); + cwlUtil = new CWLUtil(cwlFile); + input = ((ArrayList<Map>) cwlFile.get("inputs")).get(0); + } + + @Test + public void processNameSpaceTest() { + LinkedHashMap nameSpace = cwlUtil.getNameSpace(); + + assertEquals(1, nameSpace.size()); + assertTrue(nameSpace.containsKey("edam")); + assertEquals("http://edamontology.org/";, nameSpace.get("edam")); + } + + @Test + public void extractLabelTest() { + PortDetail detail = new PortDetail(); + + cwlUtil.extractLabel(null, detail); + assertEquals(null, detail.getLabel()); + + cwlUtil.extractLabel(input, detail); + assertEquals("input 1 testing label", detail.getLabel()); + + } + + @Test + public void extractDescriptionTest() { + PortDetail detail = new PortDetail(); + + cwlUtil.extractDescription(null, detail); + assertEquals(null, detail.getDescription()); + + cwlUtil.extractDescription(input, detail); + assertEquals("this is a short description of input 1", detail.getDescription()); + + } + + @Test + public void figureOutFormatsTest() { + PortDetail detail = new PortDetail(); + detail.setFormat(new ArrayList<String>()); + cwlUtil.figureOutFormats("edam:1245", detail); + assertEquals("http://edamontology.org/1245";, detail.getFormat().get(0)); + + cwlUtil.figureOutFormats("$formatExpression", detail); + assertEquals("$formatExpression", detail.getFormat().get(1)); + + // format that doesn't defined in the name space + + cwlUtil.figureOutFormats("formatkey: not Defined", detail); + assertEquals("formatkey: not Defined", detail.getFormat().get(2)); + } + + @Test + public void processTest() { + + HashMap<String, Integer> actual = cwlUtil.process(((ArrayList<Map>) cwlFile.get("inputs"))); + + HashMap<String, Integer> expected = new HashMap<>(); + expected.put("input_1", 0); + expected.put("input_2", 1); + expected.put("input_3", 0); + for (Map.Entry<String, Integer> input : expected.entrySet()) { + assertEquals(input.getValue(), actual.get(input.getKey())); + } + + actual = cwlUtil.process(((ArrayList<Map>) cwlFile.get("outputs"))); + expected = new HashMap<>(); + expected.put("output_1", 0); + expected.put("output_2", 0); + for (Map.Entry<String, Integer> input : expected.entrySet()) { + assertEquals(input.getValue(), actual.get(input.getKey())); + } + } +}
