Merge pull request #55 from PMCC-BioinformaticsCore/apply-prejanis-hook

Apply prejanis hook

janis_assistant/containers/base.py

@@ -1,6 +1,6 @@
 from abc import abstractmethod, ABC
 from enum import Enum
-from typing import Dict
+from typing import Dict, Optional
 
 
 class ContainerType(Enum):
@@ -41,7 +41,7 @@ def get_container_type():
 
     @staticmethod
     @abstractmethod
-    def test_available_by_getting_version() -> str:
+    def test_available_by_getting_version(command: Optional[str] = None) -> str:
         """
         Test if the container environment is available, raise the ContainerEnvNotFound if not.
         :return:

janis_assistant/containers/docker.py

@@ -1,5 +1,5 @@
 import subprocess
-from typing import Dict
+from typing import Dict, Optional
 
 from janis_core import Logger
 
@@ -31,7 +31,7 @@ def get_container_type():
         return ContainerType.docker
 
     @staticmethod
-    def test_available_by_getting_version() -> str:
+    def test_available_by_getting_version(command: Optional[str] = None) -> str:
         try:
             return subprocess.check_output(["docker", "-v"]).decode()
         except subprocess.CalledProcessError as e:

janis_assistant/containers/singularity.py

@@ -1,7 +1,7 @@
 import os
 import subprocess
 
-from typing import Dict
+from typing import Dict, Optional
 
 from janis_core import Logger
 
@@ -41,7 +41,7 @@ def get_build_instructions_for(containerlocation: str, docker: str):
         return ["singularity", "pull", containerlocation, "docker://" + docker]
 
     @staticmethod
-    def test_available_by_getting_version() -> str:
+    def test_available_by_getting_version(command: Optional[str] = None) -> str:
         try:
             version = subprocess.check_output(["singularity", "--version"]).decode()
             import re
@@ -58,8 +58,18 @@ def test_available_by_getting_version() -> str:
                 )
 
             return version
-        except subprocess.CalledProcessError as e:
-            raise Container.ContainerEnvNotFound("singularity", e)
+        # except subprocess.CalledProcessError as e:
+        #     raise Container.ContainerEnvNotFound("singularity", e)
+        except Exception as e:
+
+            if command is not None:
+                try:
+                    Logger.info("Trying to load singularity")
+                    subprocess.run(command, shell=True)
+                except Exception as e:
+                    raise Container.ContainerEnvNotFound("singularity", e)
+            else:
+                raise Container.ContainerEnvNotFound("singularity", e)
 
     def start_container(self):
 

janis_assistant/main.py

@@ -9,6 +9,7 @@
 import os
 import sys
 import time
+import subprocess
 from datetime import datetime
 from inspect import isclass
 from textwrap import dedent

janis_assistant/management/workflowmanager.py

@@ -288,8 +288,9 @@ def start_or_submit(self, run_in_background, watch=False):
 
         jc = metadb.prepared_job
         PreparedJob._instance = jc
+
         metadb.containertype = jc._container.__name__
-        metadb.containerversion = jc._container.test_available_by_getting_version()
+        metadb.containerversion = jc._container.test_available_by_getting_version(jc.template.template.setup_container_command())
 
         self.database.submission_metadata.save_changes()
 
@@ -310,6 +311,10 @@ def start_or_submit(self, run_in_background, watch=False):
             "--foreground",
             self.execution_dir,
         ]
+
+        if jc.template.template.prejanis_hook() is not None:
+            command = [f"{jc.template.template.prejanis_hook()};"] + command
+
         scriptdir = self.get_path_for_component(self.WorkflowManagerPath.configuration)
         logdir = self.get_path_for_component(self.WorkflowManagerPath.logs)
 

janis_assistant/templates/base.py

@@ -1,4 +1,5 @@
 import sys
+import os
 from abc import ABC, abstractmethod
 from datetime import datetime
 from typing import Type, Optional, List, Dict
@@ -223,6 +224,9 @@ def prepare_run_test_command(self, test_command: List[str]) -> Optional[List]:
         """
         return test_command
 
+    def setup_container_command(self):
+        return None
+
 
 class SingularityEnvironmentTemplate(EnvironmentTemplate, ABC):
     def __init__(

janis_assistant/templates/slurm.py

@@ -225,3 +225,6 @@ def submit_detatched_resume(
             logsdir=logsdir,
             **kwargs,
         )
+
+    def setup_container_command(self):
+        return self.singularity_load_instructions