Merge pull request #316 from mskcc/release/1.28.0

Release 1.28.0

orchestrator/tasks.py

@@ -275,15 +275,16 @@ def terminate_job(job):
 
 
 def set_permission(job):
-    root_dir = job.base_dir
+    first_dir = job.root_dir.replace(job.base_dir, "").split("/")[0]
+    permissions_dir = "/".join([job.base_dir, first_dir]).replace("//", "/")
     permission_str = job.root_permission
     try:
         permission_octal = int(permission_str, 8)
     except Exception:
         raise TypeError("Could not convert %s to permission octal" % str(permission_str))
     try:
-        os.chmod(root_dir, permission_octal)
-        for root, dirs, files in os.walk(root_dir):
+        os.chmod(permissions_dir, permission_octal)
+        for root, dirs, files in os.walk(permissions_dir):
             for single_dir in dirs:
                 if oct(os.lstat(os.path.join(root, single_dir)).st_mode)[-3:] != permission_octal:
                     logger.info(f"Setting permissions for {os.path.join(root, single_dir)}")
@@ -293,7 +294,7 @@ def set_permission(job):
                     logger.info(f"Setting permissions for {os.path.join(root, single_file)}")
                     os.chmod(os.path.join(root, single_file), permission_octal)
     except Exception:
-        raise RuntimeError("Failed to change permission of directory %s" % root_dir)
+        raise RuntimeError("Failed to change permission of directory %s" % permissions_dir)
 
 
 # Cleaning jobs

orchestrator/tests/test_tasks.py

@@ -405,7 +405,7 @@ def test_permission(self):
                     }
                 },
                 root_dir=temp_path,
-                base_dir=temp_path,
+                base_dir="/".join(temp_path.split("/")[:-1]) + "/",
                 root_permission=expected_permission,
                 external_id="ext_id",
                 status=Status.COMPLETED,
@@ -428,6 +428,7 @@ def test_permission_wrong_permission(self):
                         }
                     },
                     root_dir=temp_path,
+                    base_dir="/".join(temp_path.split("/")[:-1]) + "/",
                     root_permission=expected_permission,
                     external_id="ext_id",
                     status=Status.COMPLETED,

ridgeback/__init__.py

@@ -1 +1 @@
-__version__ = "1.27.1"
+__version__ = "1.28.0"

tests/test_commandline.py

@@ -2,9 +2,8 @@
 Tests for commandline status handling
 """
 import os
-from shutil import unpack_archive, copytree
+from shutil import unpack_archive, copytree, copy
 import tempfile
-import requests
 from django.test import TestCase, override_settings
 import toil
 from orchestrator.models import Job, Status, PipelineType, CommandLineToolJob
@@ -16,24 +15,19 @@ class TestToil(TestCase):
     Test toil track functions
     """
 
-    def download_toil_mock(self, toil_version):
+    def get_toil_mock(self, toil_version):
         """
         Download TOIL mock data from s3
         """
-        download_url = "https://toilmock.s3.amazonaws.com/toil_%s.tar.gz" % toil_version
-        download_path = "toil_%s.tar.gz" % toil_version
+        resource_name = "toil_%s.tar.gz" % toil_version
+        resource_path = os.path.join(os.path.dirname(__file__), "data", resource_name)
         folder_path = "toil_%s" % toil_version
-        download_full_path = os.path.join(self.mock_dir.name, download_path)
         self.mock_full_path = os.path.join(self.mock_dir.name, folder_path)
-        if not os.path.exists(download_full_path):
-            response = requests.get(download_url, stream=True)
-            if response.status_code == 200:
-                with open(download_full_path, "wb") as download:
-                    download.write(response.raw.read())
-            else:
-                raise Exception("Could not download TOIL mock data from: %s" % download_url)
+        if not os.path.exists(resource_path):
+            raise Exception("Could not find TOIL mock data from: %s" % resource_path)
         if not os.path.exists(self.mock_full_path):
-            unpack_archive(download_full_path, self.mock_dir.name)
+            copy(resource_path, self.mock_dir.name)
+            unpack_archive(resource_path, self.mock_dir.name)
 
     def setUp(self):
         Job.objects.all().delete()
@@ -50,7 +44,7 @@ def setUp(self):
             status=Status.RUNNING,
         )
         self.job.save()
-        self.download_toil_mock(self.toil_version)
+        self.get_toil_mock(self.toil_version)
 
     def tearDown(self):
         self.mock_dir.cleanup()