Fix Allow nextflow to handle http protocol for Singularity images #1791

nextflow-io · Nov 12, 2020 · 9479d69 · 9479d69
1 parent 48357c2
commit 9479d69
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Showing 2 changed files with 29 additions and 3 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy
@@ -18,6 +18,7 @@
 package nextflow.container
 import java.nio.file.Path
 import java.nio.file.Paths
+import java.util.regex.Pattern
 
 import groovy.transform.PackageScope
 import nextflow.util.Escape
@@ -62,8 +63,7 @@ class ContainerHandler {
             final normalizedImageName = normalizeSingularityImageName(imageName)
             if( !config.isEnabled() || !normalizedImageName )
                 return normalizedImageName
-            final formats = ['docker', 'docker-daemon', 'shub', 'library']
-            final requiresCaching =  formats.any { normalizedImageName.startsWith(it) }
+            final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
             final result = requiresCaching ? createCache(this.config, normalizedImageName) : normalizedImageName
             Escape.path(result)
         }
@@ -157,6 +157,9 @@ class ContainerHandler {
         return imageName
     }
 
+
+    public static final Pattern IMAGE_URL_PREFIX = ~/^[^\/:\. ]+:\/\/(.*)/
+
     /**
      * Normalize Singularity image name resolving the absolute path or
      * adding `docker://` prefix when required
@@ -179,7 +182,7 @@ class ContainerHandler {
         }
 
         // check if matches a protocol scheme such as `docker://xxx`
-        if( img =~ '^[^/:\\. ]+://(.*)' ) {
+        if( img =~ IMAGE_URL_PREFIX ) {
             return img
         }
 

diff --git a/modules/nextflow/src/test/groovy/nextflow/container/ContainerHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/ContainerHandlerTest.groovy
@@ -108,6 +108,8 @@ class ContainerHandlerTest extends Specification {
         'foo.img'                  | 'docker://foo.img'
         'quay.io/busybox'          | 'docker://quay.io/busybox'
         'library://library/default/debian:7'    | 'library://library/default/debian:7'
+        'http://reg.io/v1/alpine:latest'        | 'http://reg.io/v1/alpine:latest'
+        'https://reg.io/v1/alpine:latest'       | 'https://reg.io/v1/alpine:latest'
     }
 
     def 'test singularity relative path exists' () {
@@ -226,4 +228,25 @@ class ContainerHandlerTest extends Specification {
         1 * handler.createCache(_,IMAGE) >> '/some/path/foo.img'
         result == '/some/path/foo.img'
     }
+
+    def 'should invoke singularity cache' () {
+        given:
+        def handler = Spy(ContainerHandler,constructorArgs:[[engine: 'singularity', enabled: true]])
+
+        when:
+        def result = handler.normalizeImageName(IMG)
+        then:
+        TIMES * handler.createCache(_, NORM) >> EXPECTED
+
+        then:
+        result == EXPECTED
+
+        where:
+        IMG                     | NORM                  | TIMES | EXPECTED
+        'foo'                   | 'docker://foo'        | 1     | '/local/img/foo'
+        'library://foo:latest'  | 'library://foo:latest'| 1     | '/local/img/foo.img'
+        'http://bar:latest'     | 'http://bar:latest'   | 1     | '/local/http/foo.img'
+        'https://bar:latest'    | 'https://bar:latest'  | 1     | '/local/https/foo.img'
+        '/some/container.img'   | '/some/container.img' | 0     | '/some/container.img'
+    }
 }