Merge pull request #39 from mvdbeek/mulled_mount_test_files

Add possibility to mount in test-files during conda testing

galaxy/tools/deps/mulled/invfile.lua

@@ -34,6 +34,12 @@ for i = 1, #binds_table do
     table.insert(bind_args, binds_table[i])
 end
 
+local test_bind_args = {}
+local test_binds_table = VAR.TEST_BINDS:split(",")
+for i = 1, #test_binds_table do
+    table.insert(test_bind_args, test_binds_table[i])
+end
+
 inv.task('build')
     .using('continuumio/miniconda:latest')
         .withHostConfig({binds = {"build:/data"}})
@@ -49,10 +55,18 @@ inv.task('build')
         .inImage('bgruening/busybox-bash:0.1')
         .as(repo)
 
-inv.task('test')
-    .using(repo)
-    .withConfig({entrypoint = {'/bin/sh', '-c'}})
-    .run(VAR.TEST)
+if VAR.TEST_BINDS == '' then
+    inv.task('test')
+        .using(repo)
+        .withConfig({entrypoint = {'/bin/sh', '-c'}})
+        .run(VAR.TEST)
+else
+    inv.task('test')
+        .using(repo)
+        .withHostConfig({binds = test_bind_args})
+        .withConfig({entrypoint = {'/bin/sh', '-c'}})
+        .run(VAR.TEST)
+end
 
 inv.task('push')
     .push(repo)

galaxy/tools/deps/mulled/mulled_build.py

@@ -34,6 +34,7 @@
 DEFAULT_CHANNELS = [DEFAULT_CHANNEL] + DEFAULT_EXTRA_CHANNELS
 DEFAULT_REPOSITORY_TEMPLATE = "quay.io/${namespace}/${image}"
 DEFAULT_BINDS = ["build/dist:/usr/local/"]
+DEFAULT_WORKING_DIR = '/source/'
 IS_OS_X = _platform == "darwin"
 INVOLUCRO_VERSION = "1.1.2"
 
@@ -113,7 +114,7 @@ def conda_versions(pkg_name, file_name):
 def mull_targets(
     targets, involucro_context=None,
     command="build", channels=DEFAULT_CHANNELS, namespace="mulled",
-    test='true', image_build=None, name_override=None,
+    test='true', test_files=None, image_build=None, name_override=None,
     repository_template=DEFAULT_REPOSITORY_TEMPLATE, dry_run=False,
     binds=DEFAULT_BINDS
 ):
@@ -144,6 +145,18 @@ def mull_targets(
         '-set', "BINDS='%s'" % bind_str,
         command,
     ]
+    if test_files:
+        test_bind = []
+        for test_file in test_files:
+            if ':' not in test_file:
+                if os.path.exists(test_file):
+                    test_bind.append("%s:%s/%s" % (test_file, DEFAULT_WORKING_DIR, test_file))
+            else:
+                if os.path.exists(test_file.split(':')[0]):
+                    test_bind.append(test_file)
+        if test_bind:
+            involucro_args.insert(6, '-set')
+            involucro_args.insert(7, "TEST_BINDS='%s'" % ",".join(test_bind))
     print(" ".join(involucro_context.build_command(involucro_args)))
     if not dry_run:
         ensure_installed(involucro_context, True)
@@ -252,6 +265,9 @@ def args_to_mull_targets_kwds(args):
         kwds["dry_run"] = args.dry_run
     if hasattr(args, "test"):
         kwds["test"] = args.test
+    if hasattr(args, "test_files"):
+        if args.test_files:
+            kwds["test_files"] = args.test_files.split(",")
     if hasattr(args, "channel"):
         channels = [args.channel]
         if hasattr(args, "extra_channels"):
@@ -276,6 +292,8 @@ def main(argv=None):
     parser.add_argument('targets', metavar="TARGETS", default=None, help="Build a single container with specific package(s).")
     parser.add_argument('--repository-name', dest="repository_name", default=None, help="Name of mulled container (leave blank to auto-generate based on packages - recommended).")
     parser.add_argument('--test', help='Provide a test command for the container.')
+    parser.add_argument('--test-files', help='Provide test-files that may be required to run the test command. Individual mounts are separated by comma.'
+                                             'The source:dest docker syntax is respected. If relative file paths are given, files will be mounted in /source/<relative_file_path>')
     args = parser.parse_args()
     targets = target_str_to_targets(args.targets)
     sys.exit(mull_targets(targets, **args_to_mull_targets_kwds(args)))