feat: 42 audit get automated code coverage working (#234)

CHANGELOG.md

@@ -1,5 +1,15 @@
 # Changelog
 
+## [0.8.1] UNRELEASED
+
+- Fix bug in path extraction from S3 URIs
+
+## [0.8.0] 2024-08-31
+
+- Add and improve code coverage using jacoco
+- Support S3 URIs as an overlay plugin
+- Fix bug with pathless input URIs
+
 ## [0.7.17] UNRELEASED
 
 - support ChunkedChecksums

Makefile

@@ -49,11 +49,21 @@ check:
 
 .PHONY: clean test test-all all pkg-test tower-test
 
-test: clean compile check #coverage
+test: clean compile check verifyCoverage
 
-test-nextflow: clean nextflow-git compile check #coverage
+test-nextflow: clean nextflow-git compile check
 
-test-all: clean compile-all check #coverage
+test-all: clean compile-all check coverage
+
+coverage:
+	./gradlew jacocoTestReport
+	open plugins/nf-quilt/build/reports/jacoco/test/html/index.html
+
+verifyCoverage:
+	./gradlew jacocoTestCoverageVerification
+
+groovysh:
+	./gradlew -q --no-daemon --console=plain --init-script groovysh-task.gradle groovysh
 
 #
 # Create packages

gradle-groovysh-init.gradle

@@ -0,0 +1,49 @@
+gradle.projectsLoaded {
+    rootProject {
+        afterEvaluate { project ->
+            if (!project.repositories.any{it.name == 'MavenRepo'}) {
+                project.repositories {
+                    // To be able to load org.codehaus.groovy:groovy-groovysh
+                    mavenCentral()
+                }
+            }
+
+            project.configurations {
+                groovyshdependencies
+            }
+
+            project.dependencies {
+                groovyshdependencies("org.codehaus.groovy:groovy-groovysh:${GroovySystem.version}") {
+                    exclude group: 'org.codehaus.groovy'
+                }
+            }
+
+            project.tasks.register('groovysh') {
+                group 'debug'
+                description 'Runs an interactive shell in the context of the project.'
+                doLast {
+                    URLClassLoader groovyObjectClassLoader = GroovyObject.class.classLoader
+                    def groovyshClass
+                    def groovyShell
+
+                    // Add dependency jars to classloader
+                    configurations.groovyshdependencies.each {File file ->
+                        groovyObjectClassLoader.addURL(file.toURL())
+                    }
+                    Class.forName('jline.console.history.FileHistory', true, groovyObjectClassLoader)
+                    groovyshClass = Class.forName('org.codehaus.groovy.tools.shell.Groovysh', true, groovyObjectClassLoader)
+
+                    if (groovyshClass) {
+                        groovyShell = groovyshClass.newInstance()
+                    }
+                    if (groovyShell) {
+                        groovyShell.interp.context.variables.put("gradle", gradle)
+                        groovyShell.interp.context.variables.put("settings", gradle.settings)
+                        groovyShell.interp.context.variables.put("project", project)
+                        groovyShell.run('')
+                    }
+                }
+            }
+        }
+    }
+}

groovysh-task.gradle

@@ -0,0 +1,54 @@
+gradle.projectsLoaded {
+    rootProject {
+        afterEvaluate { project ->
+            if (!project.repositories.any{it.name == 'MavenRepo'}) {
+                project.repositories {
+                    // To be able to load org.apache.groovy:groovy-groovysh and dependencies
+                    mavenCentral {
+                        content {
+                            includeGroup 'org.apache.groovy'
+                            includeGroup 'jline'
+                            includeGroup 'com.github.javaparser'
+                            includeGroup 'org.ow2.asm'
+                            includeGroup 'org.abego.treelayout'
+                            includeGroup 'org.apache.ivy'
+                        }
+                    }
+                }
+            }
+            project.configurations {
+                groovyshdependencies
+            }
+
+            project.dependencies {
+                groovyshdependencies "org.apache.groovy:groovy-groovysh:4.0.13"
+            }
+
+            project.tasks.register('groovysh') {
+                group 'debug'
+                description 'Runs an interactive shell in the context of the project. Use :inspect command to inspect project, gradle, settings or other objects.'
+                doLast {
+                    URLClassLoader groovyshClassLoader = new URLClassLoader();
+                    configurations.groovyshdependencies.each {File file ->
+                        groovyshClassLoader.addURL(file.toURI().toURL())
+                    }
+
+                    def fileHistoryClass
+                    def groovyshClass
+                    def groovyShell
+                    fileHistoryClass = Class.forName('jline.console.history.FileHistory', true, groovyshClassLoader)
+                    groovyshClass = Class.forName('org.apache.groovy.groovysh.Groovysh', true, groovyshClassLoader)
+                    if (groovyshClass) {
+                        groovyShell = groovyshClass.newInstance()
+                        if (groovyShell) {
+                            groovyShell.interp.context.variables.put("gradle", gradle)
+                            groovyShell.interp.context.variables.put("settings", gradle.settings)
+                            groovyShell.interp.context.variables.put("project", project)
+                            groovyShell.run('# Available objects: gradle, settings, project\n# Try :inspect project')
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

plugins/nf-quilt/build.gradle

@@ -20,6 +20,7 @@ plugins {
     id 'idea'
     id 'se.patrikerdes.use-latest-versions' version '0.2.18'
     id 'com.github.ben-manes.versions' version '0.51.0'
+    id 'jacoco'
 }
 
 useLatestVersions {
@@ -115,3 +116,29 @@ test {
     useJUnitPlatform()
 }
 
+jacocoTestReport {
+    dependsOn test // tests are required to run before generating the report
+}
+
+jacocoTestCoverageVerification {
+    dependsOn jacocoTestReport // tests are required to run before generating the report
+    violationRules {
+        rule {
+            limit {
+                minimum = 0.65
+            }
+        }
+
+        rule {
+            enabled = false
+            element = 'CLASS'
+            includes = ['org.gradle.*']
+
+            limit {
+                counter = 'LINE'
+                value = 'TOTALCOUNT'
+                maximum = 0.3
+            }
+        }
+    }
+}

plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy

@@ -114,6 +114,9 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
         log.debug "QuiltFileSystemProvider.download: ${remoteFile} -> ${localDestination}"
         QuiltPath qPath = asQuiltPath(remoteFile)
         Path cachedFile = qPath.localPath()
+        /*
+         * UNUSED: QuiltPackage is always installed
+         *
         QuiltPackage pkg = qPath.pkg()
         if (!pkg.installed) {
             log.info "download.install Quilt package: ${pkg}"
@@ -124,6 +127,7 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
             }
             log.info "download.installed Quilt package to: $dest"
         }
+        */
 
         if (!Files.exists(cachedFile)) {
             log.error "download: File ${cachedFile} not found"
@@ -164,6 +168,9 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
         if (Files.exists(cachedFile)) {
             throw new FileAlreadyExistsException(remoteDestination.toString())
         }
+        if (!Files.exists(localFile)) {
+            throw new NoSuchFileException(localFile.toString())
+        }
         Files.copy(localFile, cachedFile, options)
     }
 
@@ -418,9 +425,9 @@ class QuiltFileSystemProvider extends FileSystemProvider implements FileSystemTr
 
     @Override
     void copy(Path from, Path to, CopyOption... options) throws IOException {
-        // log.debug("Attempting `copy`: ${from} -> ${to}")
+        log.debug("Attempting `copy`: ${from} -> ${to}")
         assert provider(from) == provider(to)
-        if (from == to) {
+        if (from.toString() == to.toString()) {
             return // nothing to do -- just return
         }
 

plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy

@@ -23,6 +23,7 @@ import nextflow.Session
 import java.nio.file.Path
 import java.nio.file.Paths
 import groovy.transform.CompileDynamic
+import spock.lang.Ignore
 
 /**
  *
@@ -95,4 +96,55 @@ class QuiltObserverTest extends QuiltSpecification {
         '/bucket/file.ext' | 'quilt+s3://bucket#package=default_prefix%2fdefault_suffix&path=file.ext'
     }
 
+    void 'should recover URI from onFilePublish QuiltPath'() {
+        given:
+        QuiltObserver observer = new QuiltObserver()
+        Path path = Paths.get(key)
+        Path quiltPath = QuiltPathFactory.parse(quilt_uri)
+        observer.onFilePublish(quiltPath, path)
+        String pkgKey = observer.pkgKey(quiltPath)
+        expect:
+        pkgKey == key
+        observer.uniqueURIs[key] == quilt_uri
+        observer.publishedURIs[key] == quilt_uri
+        where:
+        key | quilt_uri
+        'bucket/prefix/suffix' | 'quilt+s3://bucket#package=prefix%2fsuffix'
+    }
+
+    @Ignore('FIXME: handle onFilePublish with local Path')
+    void 'should extract URI from onFilePublish local Path'() {
+        given:
+        QuiltObserver observer = new QuiltObserver()
+        Path quiltPath = QuiltPathFactory.parse(quilt_uri)
+        Path path = Paths.get('/'+key)
+        observer.onFilePublish(path, quiltPath)
+        String pkgKey = observer.pkgKey(quiltPath)
+        expect:
+        pkgKey == key
+        observer.uniqueURIs[key] == quilt_uri
+        observer.publishedURIs[key] == quilt_uri
+        where:
+        key | quilt_uri
+        'bucket/prefix/suffix' | 'quilt+s3://bucket#package=prefix%2fsuffix'
+    }
+
+    void 'should not error on onFlowComplete'() {
+        given:
+        String quilt_uri = 'quilt+s3://bucket#package=prefix%2fsuffix'
+        QuiltObserver observer = new QuiltObserver()
+        QuiltPath qPath = QuiltPathFactory.parse(quilt_uri)
+        Session session = GroovyMock(Session) {
+            // getWorkflowMetadata() >> metadata
+            getParams() >> [outdir: quilt_uri]
+            isSuccess() >> false
+        }
+        observer.onFlowCreate(session)
+        observer.onFilePublish(qPath, qPath)
+        when:
+        observer.onFlowComplete()
+        then:
+        true
+    }
+
 }

plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy

@@ -17,6 +17,8 @@
 package nextflow.quilt.nio
 
 import nextflow.Session
+import nextflow.script.WorkflowMetadata
+
 import nextflow.quilt.QuiltSpecification
 import nextflow.quilt.QuiltProduct
 import nextflow.quilt.jep.QuiltParser
@@ -37,9 +39,16 @@ import spock.lang.Unroll
 @CompileDynamic
 class QuiltProductTest extends QuiltSpecification {
 
-    QuiltProduct makeProduct(String query=null) {
+    QuiltProduct makeProduct(String query=null, boolean success = false) {
         String subURL = query ? fullURL.replace('key=val&key2=val2', query) : fullURL
-        Session session = Mock(Session)
+        WorkflowMetadata metadata = GroovyMock(WorkflowMetadata) {
+            toMap() >> [start:'2022-01-01', complete:'2022-01-02']
+        }
+        Session session = GroovyMock(Session) {
+            getWorkflowMetadata() >> metadata
+            getParams() >> [outdir: subURL]
+            isSuccess() >> success
+        }
         QuiltPath path = QuiltPathFactory.parse(subURL)
         return new QuiltProduct(path, session)
     }
@@ -50,12 +59,23 @@ class QuiltProductTest extends QuiltSpecification {
             String query = QuiltParser.unparseQuery(meta)
             subURL = subURL.replace('#', "?${query}#")
         }
-        Session session = Mock(Session)
+        Session session = GroovyMock(Session)
         QuiltPath path = QuiltPathFactory.parse(subURL)
         return new QuiltProduct(path, session)
     }
 
-    void 'now should generate solid string for timestamp'() {
+    void 'should generate mocks from makeProduct'() {
+        given:
+        QuiltProduct product = makeProduct()
+
+        expect:
+        product
+        product.pkg
+        product.session != null
+        product.session.getWorkflowMetadata() != null
+    }
+
+    void 'should generate solid string for timestamp from now'() {
         when:
         def now = QuiltProduct.now()
         then:
@@ -216,4 +236,47 @@ class QuiltProductTest extends QuiltSpecification {
         Files.exists(Paths.get(sumPkg.packageDest().toString(), QuiltProduct.SUMMARY_FILE))
     }
 
+    void 'should getMetadata from Map'() {
+        given:
+        Map meta = [
+            'Name': 'QuiltPackageTest',
+            'Owner': 'Ernest',
+            'Date': '1967-10-08',
+            'Type': 'NGS'
+        ]
+        QuiltProduct product = makeProduct()
+        Map quilt_meta = product.getMetadata(meta)
+
+        expect:
+        quilt_meta != null
+    }
+
+    void 'should setupMeta from session'() {
+        given:
+        QuiltProduct product = makeProduct()
+        Map quilt_meta = product.setupMeta()
+
+        expect:
+        quilt_meta != null
+    }
+
+    void 'should throw error on publish'() {
+        given:
+        QuiltProduct product = makeProduct()
+
+        when:
+        product.publish()
+
+        then:
+        thrown(RuntimeException)
+    }
+
+    void 'should throw error if session.isSuccess'() {
+        when:
+        makeProduct(query: null, success: true)
+
+        then:
+        thrown(RuntimeException)
+    }
+
 }