+
+func (s *TestSuite) TestFullRunWithAPI(c *C) {
+ os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
+ defer os.Unsetenv("ARVADOS_API_HOST")
+ api, _, _ := FullRunHelper(c, `{
+ "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {"API": true}
+}`, nil, 0, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "test.arvados.org\n"), Equals, true)
+ c.Check(api.CalledWith("container.output", "d41d8cd98f00b204e9800998ecf8427e+0"), NotNil)
+}
+
+func (s *TestSuite) TestFullRunSetOutput(c *C) {
+ os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
+ defer os.Unsetenv("ARVADOS_API_HOST")
+ api, _, _ := FullRunHelper(c, `{
+ "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {"API": true}
+}`, nil, 0, func(t *TestDockerClient) {
+ t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122"
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil)
+}
+
+func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "/tmp/foo": {"kind": "collection",
+ "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54",
+ "exclude_from_output": true
+ },
+ "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
+
+ api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
+}
+
+func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/file2_in_main.txt"},
+ "/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1"},
+ "/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/file2_in_subdir1.txt"},
+ "/tmp/foo/baz/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"},
+ "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{
+ "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt",
+ "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
+ "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
+ }
+
+ api, runner, realtemp := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(runner.Binds, DeepEquals, []string{realtemp + "/2:/tmp",
+ realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
+ realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
+ realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
+ realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro",
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ for _, v := range api.Content {
+ if v["collection"] != nil {
+ c.Check(v["ensure_unique_name"], Equals, true)
+ collection := v["collection"].(arvadosclient.Dict)
+ if strings.Index(collection["name"].(string), "output") == 0 {
+ manifest := collection["manifest_text"].(string)
+
+ c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
+./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 9:18:bar 9:18:sub1file2
+./foo/baz 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2
+./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
+./foo/sub1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
+`)
+ }
+ }
+ }
+}
+
+func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt"},
+ "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{
+ "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
+ }
+
+ api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ for _, v := range api.Content {
+ if v["collection"] != nil {
+ collection := v["collection"].(arvadosclient.Dict)
+ if strings.Index(collection["name"].(string), "output") == 0 {
+ manifest := collection["manifest_text"].(string)
+
+ c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
+./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 10:17:bar
+`)
+ }
+ }
+ }
+}
+
+func (s *TestSuite) TestOutputSymlinkToInput(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "/keep/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path": "/subdir1/file2_in_subdir1.txt"},
+ "/keep/foo2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{
+ "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
+ }
+
+ api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ os.Symlink("/keep/foo/sub1file2", t.realTemp+"/2/baz")
+ os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/2/baz2")
+ os.Symlink("/keep/foo2/subdir1", t.realTemp+"/2/baz3")
+ os.Mkdir(t.realTemp+"/2/baz4", 0700)
+ os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/2/baz4/baz5")
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ for _, v := range api.Content {
+ if v["collection"] != nil {
+ collection := v["collection"].(arvadosclient.Dict)
+ if strings.Index(collection["name"].(string), "output") == 0 {
+ manifest := collection["manifest_text"].(string)
+ c.Check(manifest, Equals, `. 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:baz 9:18:baz2
+./baz3 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
+./baz3/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
+./baz4 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:baz5
+`)
+ }
+ }
+ }
+}
+
+func (s *TestSuite) TestOutputError(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{}
+
+ api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ os.Symlink("/etc/hosts", t.realTemp+"/2/baz")
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
+}
+
+func (s *TestSuite) TestStdinCollectionMountPoint(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "stdin": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367", "path": "/file1_in_main.txt"},
+ "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{
+ "b0def87f80dd594d4675809e83bd4f15+367/file1_in_main.txt",
+ }
+
+ api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ for _, v := range api.Content {
+ if v["collection"] != nil {
+ collection := v["collection"].(arvadosclient.Dict)
+ if strings.Index(collection["name"].(string), "output") == 0 {
+ manifest := collection["manifest_text"].(string)
+ c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
+`)
+ }
+ }
+ }
+}
+
+func (s *TestSuite) TestStdinJsonMountPoint(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "stdin": {"kind": "json", "content": "foo"},
+ "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ for _, v := range api.Content {
+ if v["collection"] != nil {
+ collection := v["collection"].(arvadosclient.Dict)
+ if strings.Index(collection["name"].(string), "output") == 0 {
+ manifest := collection["manifest_text"].(string)
+ c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
+`)
+ }
+ }
+ }
+}
+
+func (s *TestSuite) TestStderrMount(c *C) {
+ api, _, _ := FullRunHelper(c, `{
+ "command": ["/bin/sh", "-c", "echo hello;exit 1"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": ".",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"},
+ "stdout": {"kind": "file", "path": "/tmp/a/out.txt"},
+ "stderr": {"kind": "file", "path": "/tmp/b/err.txt"}},
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+}`, nil, 1, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, "hello\n"))
+ t.logWriter.Write(dockerLog(2, "oops\n"))
+ t.logWriter.Close()
+ })
+
+ final := api.CalledWith("container.state", "Complete")
+ c.Assert(final, NotNil)
+ c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
+ c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
+
+ c.Check(api.CalledWith("collection.manifest_text", "./a b1946ac92492d2347c6235b4d2611184+6 0:6:out.txt\n./b 38af5c54926b620264ab1501150cf189+5 0:5:err.txt\n"), NotNil)
+}