Compose now adds nf config

Jote now checks for local nf config

Author: Alan Christie

src/jote/compose.py

@@ -35,6 +35,13 @@
     cpus: {cpus}.0
 """
 
+_NF_CONFIG_CONTENT: str = """
+docker {
+  enabled = true
+  runOptions = '-u $(id -u):$(id -g)'
+}
+"""
+
 
 def _get_docker_compose_version() -> str:
 
@@ -66,6 +73,7 @@ def __init__(self, collection: str,
                  job: str,
                  test: str,
                  image: str,
+                 image_type: str,
                  memory: str,
                  cores: int,
                  project_directory: str,
@@ -85,6 +93,7 @@ def __init__(self, collection: str,
         self._job: str = job
         self._test: str = test
         self._image: str = image
+        self._image_type: str = image_type
         self._cores: int = cores
         self._project_directory: str = project_directory
         self._working_directory: str = working_directory
@@ -121,7 +130,9 @@ def create(self) -> str:
             Compose._COMPOSE_VERSION = _get_docker_compose_version()
             print(f'# docker-compose ({Compose._COMPOSE_VERSION})')
 
-        # Make the test directory...
+        # Make the test directory
+        # (where the test is launched from)
+        # and the project directory (a /project sud-directory of test)
         test_path = self.get_test_path()
         project_path: str = self.get_test_project_path()
         inst_path: str = f'{project_path}/{INSTANCE_DIRECTORY}'
@@ -152,6 +163,14 @@ def create(self) -> str:
         with open(compose_path, 'wt', encoding='UTF-8') as compose_file:
             compose_file.write(compose_content)
 
+        if self._image_type == 'nextflow':
+            # Write a nextflow config to the project path
+            # (this is where the non-container-based nextflow is executed)
+            # and where nextflow will, by default, look for the config.
+            nf_cfg_path: str = f'{project_path}/nextflow.config'
+            with open(nf_cfg_path, 'wt', encoding='UTF-8') as nf_cfg_file:
+                nf_cfg_file.write(_NF_CONFIG_CONTENT)
+
         print('# Created')
 
         return project_path

src/jote/jote.py

@@ -40,6 +40,11 @@
 _IMAGE_TYPE_NEXTFLOW: str = 'nextflow'
 _DEFAULT_IMAGE_TYPE: str = _IMAGE_TYPE_SIMPLE
 
+# User HOME directory.
+# Used to check for netflow files if nextflow is executed.
+# The user CANNOT have any pf their own nextflow config.
+_USR_HOME: str = os.environ.get('HOME', '')
+
 
 def _print_test_banner(collection: str,
                        job_name: str,
@@ -304,6 +309,17 @@ def _run_nextflow(command: str, project_path: str)\
     assert command
     assert project_path
 
+    # The user cannot have a nextflow config in their home directory.
+    # Nextflow looks here and any config will be merged with the test config.
+    if _USR_HOME:
+        home_config: str = os.path.join(_USR_HOME, '.nextflow', 'config')
+        if os.path.exists(home_config) and os.path.isfile(home_config):
+            print('! FAILURE')
+            print('! A nextflow test but'
+                  f' you have your own config file ({home_config})')
+            print('! You cannot test Jobs and have your own config file')
+            return 1, '', ''
+
     cwd = os.getcwd()
     os.chdir(project_path)
 
@@ -502,6 +518,7 @@ def _test(args: argparse.Namespace,
                                 job,
                                 job_test_name,
                                 job_image,
+                                job_image_type,
                                 job_image_memory,
                                 job_image_cores,
                                 job_project_directory,