updates for TES v0.3.0

ohsu-comp-bio · Nov 17, 2017 · b52f319 · b52f319
1 parent bbdd4aa
commit b52f319
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Showing 4 changed files with 22 additions and 19 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -17,7 +17,7 @@ install:
   - python setup.py install
 
 before_script:
-  - wget https://github.com/ohsu-comp-bio/funnel/releases/download/0.3.0/funnel-linux-amd64-0.3.0.tar.gz -O /opt/funnel.tar.gz
+  - wget -O /opt/funnel.tar.gz https://github.com/ohsu-comp-bio/funnel/releases/download/0.4.1/funnel-linux-amd64-0.4.1.tar.gz
   - tar -zxvf /opt/funnel.tar.gz -C /opt
   - export PATH=$PATH:/opt
   - docker pull python:2.7

diff --git a/tesseract/future.py b/tesseract/future.py
@@ -52,7 +52,8 @@ def running(self):
 
     def done(self):
         r = self.__client.get_task(self.__id, "MINIMAL")
-        return r.state in ["COMPLETE", "ERROR", "SYSTEM_ERROR", "CANCELED"]
+        return r.state in ["COMPLETE", "EXECUTOR_ERROR", "SYSTEM_ERROR",
+                           "CANCELED"]
 
     def cancel(self):
         self.__result.cancel()

diff --git a/tesseract/tesseract.py b/tesseract/tesseract.py
@@ -32,10 +32,10 @@ class Tesseract(object):
     )
     timeout = attrib(default=30, validator=instance_of(int))
     input_files = attrib(
-        default=Factory(list), validator=tes.models.list_of(tes.TaskParameter)
+        default=Factory(list), validator=tes.models.list_of(tes.Input)
     )
     output_files = attrib(
-        default=Factory(list), validator=tes.models.list_of(tes.TaskParameter)
+        default=Factory(list), validator=tes.models.list_of(tes.Output)
     )
     cpu_cores = attrib(default=None, validator=optional(instance_of(int)))
     ram_gb = attrib(
@@ -155,7 +155,7 @@ def with_input(self, url, path):
             )
 
         self.input_files.append(
-            tes.TaskParameter(
+            tes.Input(
                 path=os.path.join("/tmp/tesseract", re.sub("^./", "", path)),
                 url=url,
                 type="FILE"
@@ -178,7 +178,7 @@ def with_output(self, path):
 
         run_id = self.__get_id()
         self.output_files.append(
-            tes.TaskParameter(
+            tes.Output(
                 path=os.path.join("/tmp/tesseract", re.sub("^./", "", path)),
                 url=self.file_store.generate_url(
                     os.path.join(run_id, re.sub("^./|^/", "", path))
@@ -249,21 +249,21 @@ def _create_task_msg(self, input_cp_url, output_cp_url):
         task = tes.Task(
             name="tesseract remote execution",
             inputs=self.input_files + [
-                tes.TaskParameter(
+                tes.Input(
                     name="pickled function",
                     url=input_cp_url,
                     path="/tmp/tesseract/func.pickle",
                     type="FILE"
                 ),
-                tes.TaskParameter(
+                tes.Input(
                     name="tesseract runner script",
                     path="/tmp/tesseract/tesseract.py",
                     type="FILE",
-                    contents=str(runner)
+                    content=str(runner)
                 )
             ],
             outputs=self.output_files + [
-                tes.TaskParameter(
+                tes.Output(
                     name="pickled result",
                     url=output_cp_url,
                     path="/tmp/tesseract/result.pickle",
@@ -273,12 +273,12 @@ def _create_task_msg(self, input_cp_url, output_cp_url):
             resources=tes.Resources(
                 cpu_cores=self.cpu_cores,
                 ram_gb=self.ram_gb,
-                size_gb=self.disk_gb
+                disk_gb=self.disk_gb
             ),
             executors=[
                 tes.Executor(
-                    image_name=self.docker,
-                    cmd=["sh", "-c", cmd],
+                    image=self.docker,
+                    command=["sh", "-c", cmd],
                     stdout="/tmp/tesseract/stdout",
                     stderr="/tmp/tesseract/stderr",
                     workdir="/tmp/tesseract"

diff --git a/tests/test_tesseract.py b/tests/test_tesseract.py
@@ -65,13 +65,15 @@ def test_with_input(self):
         r.with_input("file:///tmp/input", "/mnt/input")
         r.with_input("file:///tmp/input2", "./input2")
         expected = [
-            tes.TaskParameter(
+            tes.Input(
                 url="file:///tmp/input",
-                path="/mnt/input"
+                path="/mnt/input",
+                type="FILE"
             ),
-            tes.TaskParameter(
+            tes.Input(
                 url="file:///tmp/input2",
-                path="/tmp/tesseract/input2"
+                path="/tmp/tesseract/input2",
+                type="FILE"
             )
         ]
         print("ACTUAL", r.input_files)
@@ -93,12 +95,12 @@ def test_with_output(self):
         r.with_output("./output.txt")
         r.with_output("/mnt/output.txt")
         expected = [
-            tes.TaskParameter(
+            tes.Output(
                 path="/tmp/tesseract/output.txt",
                 url=r.file_store.generate_url("testid/output.txt"),
                 type="FILE"
             ),
-            tes.TaskParameter(
+            tes.Output(
                 path="/mnt/output.txt",
                 url=r.file_store.generate_url("testid/mnt/output.txt"),
                 type="FILE"