Fixing the docker return character issues (by moving from native vers…

…ion to the command line based command runner)

src/tes-server/server.go

@@ -3,8 +3,6 @@ package main
 import (
 	"flag"
 	"fmt"
-	"tes/server"
-	"tes/ga4gh"
 	"github.com/gorilla/mux"
 	"github.com/grpc-ecosystem/grpc-gateway/runtime"
 	"golang.org/x/net/context"
@@ -14,6 +12,8 @@ import (
 	"os"
 	"path/filepath"
 	"runtime/debug"
+	"tes/ga4gh"
+	"tes/server"
 )
 
 func main() {

src/tes-worker/worker.go

@@ -2,13 +2,13 @@ package main
 
 import (
 	"flag"
-	"tes/worker"
-	"tes/server/proto"
 	uuid "github.com/nu7hatch/gouuid"
 	"google.golang.org/grpc"
 	"log"
 	"os"
 	"path/filepath"
+	"tes/server/proto"
+	"tes/worker"
 	"time"
 )
 

src/tes/server/task_boltdb.go

@@ -2,14 +2,14 @@ package tes_server
 
 import (
 	"fmt"
-	"tes/server/proto"
-	"tes/ga4gh"
 	"github.com/boltdb/bolt"
 	proto "github.com/golang/protobuf/proto"
 	uuid "github.com/nu7hatch/gouuid"
 	"golang.org/x/net/context"
 	"log"
 	"strings"
+	"tes/ga4gh"
+	"tes/server/proto"
 )
 
 var TASK_BUCKET = []byte("tasks")

src/tes/server/task_server.go

@@ -1,11 +1,11 @@
 package tes_server
 
 import (
-	"tes/server/proto"
-	"tes/ga4gh"
 	"google.golang.org/grpc"
 	"log"
 	"net"
+	"tes/ga4gh"
+	"tes/server/proto"
 )
 
 /// Common GA4GH server, multiple services could be placed into the same server

src/tes/worker/docker.go

@@ -0,0 +1,52 @@
+package tes_taskengine_worker
+
+import (
+	"log"
+	"os"
+	"os/exec"
+	"strings"
+	"syscall"
+)
+
+func NewDockerEngine() *DockerCmd {
+	return &DockerCmd{}
+}
+
+type DockerCmd struct {
+}
+
+func (self DockerCmd) Run(containerName string, args []string,
+	binds []string, workdir string, remove bool, stdout *os.File, stderr *os.File) (int, error) {
+
+	log.Printf("Docker Binds: %s", binds)
+
+	docker_args := []string{"run", "--rm", "-i", "-w", workdir}
+
+	for _, i := range binds {
+		docker_args = append(docker_args, "-v", i)
+	}
+	docker_args = append(docker_args, containerName)
+	docker_args = append(docker_args, args...)
+	log.Printf("Runner docker %s", strings.Join(args, " "))
+
+	cmd := exec.Command("docker", docker_args...)
+
+	if stdout != nil {
+		cmd.Stdout = stdout
+	}
+	if stderr != nil {
+		cmd.Stderr = stderr
+	}
+	cmd_err := cmd.Run()
+	exitStatus := 0
+	if exiterr, ok := cmd_err.(*exec.ExitError); ok {
+		if status, ok := exiterr.Sys().(syscall.WaitStatus); ok {
+			exitStatus = status.ExitStatus()
+			log.Printf("Exit Status: %d", exitStatus)
+		}
+	} else {
+		log.Printf("cmd.Run: %v", cmd_err)
+	}
+
+	return exitStatus, nil
+}

src/tes/worker/engine.go

@@ -2,8 +2,8 @@ package tes_taskengine_worker
 
 import (
 	"fmt"
-	"tes/ga4gh"
 	"os"
+	"tes/ga4gh"
 )
 
 const HEADER_SIZE = int64(102400)

src/tes/worker/file_client.go

@@ -2,12 +2,12 @@ package tes_taskengine_worker
 
 import (
 	"fmt"
-	"tes/server/proto"
-	"tes/ga4gh"
 	"golang.org/x/net/context"
 	"io/ioutil"
 	"os"
 	"path"
+	"tes/ga4gh"
+	"tes/server/proto"
 )
 
 type FileMapper struct {

src/tes/worker/fork_engine.go

@@ -1,12 +1,12 @@
 package tes_taskengine_worker
 
 import (
-	"tes/server/proto"
-	"tes/ga4gh"
 	context "golang.org/x/net/context"
 	"log"
 	"os"
 	"sync/atomic"
+	"tes/ga4gh"
+	"tes/server/proto"
 	"time"
 	//proto "github.com/golang/protobuf/proto"
 )

tests/common_test_util.py

@@ -20,19 +20,19 @@ def setUp(self):
         if not os.path.exists("./test_tmp"):
             os.mkdir("test_tmp")
         self.task_server = None
-        f, db_path = tempfile.mkstemp(dir="./test_tmp", prefix="ga4hg_task_db.")
+        f, db_path = tempfile.mkstemp(dir="./test_tmp", prefix="tes_task_db.")
         os.close(f)
         self.storage_dir = db_path + ".storage"
         self.volume_dir = db_path + ".volumes"
         os.mkdir(self.storage_dir)
         os.mkdir(self.volume_dir)
-        cmd = ["./bin/ga4gh-taskserver", "-db", db_path]
+        cmd = ["./bin/tes-server", "-db", db_path]
         logging.info("Running %s" % (" ".join(cmd)))
         self.task_server = subprocess.Popen(cmd)
         time.sleep(3)
 
         self.task_worker = None
-        cmd = ["./bin/ga4gh-worker", "-volumes", self.volume_dir, "-storage", self.storage_dir]
+        cmd = ["./bin/tes-worker", "-volumes", self.volume_dir, "-storage", self.storage_dir]
         logging.info("Running %s" % (" ".join(cmd)))
         self.task_worker = subprocess.Popen(cmd)