[wip] adding analysis directory name to the config path

babs/base.py

@@ -29,6 +29,21 @@
 )
 
 CONFIG_SECTIONS = ['processing_level', 'queue', 'input_datasets', 'container']
+
+
+def _find_analysis_dirname(project_root, default='analysis'):
+    """Find the analysis directory name inside project_root.
+
+    First checks if code/babs_proj_config.yaml exists directly in project_root (dirname='.'),
+    then scans subdirectories. Falls back to default if none found (e.g. during babs init).
+    """
+    if op.exists(project_root):
+        if op.exists(op.join(project_root, 'code/babs_proj_config.yaml')):
+            return '.'
+        for entry in os.scandir(project_root):
+            if entry.is_dir() and op.exists(op.join(entry.path, 'code/babs_proj_config.yaml')):
+                return entry.name
+    return default
 EMPTY_JOB_STATUS_DF = pd.DataFrame(
     columns=['sub_id', 'ses_id', 'task_id', 'job_id', 'has_results']
 )
@@ -101,19 +116,19 @@ def __init__(self, project_root):
         # attributes:
         self.project_root = str(project_root)
 
-        self.analysis_path = op.join(self.project_root, 'analysis')
         self._analysis_datalad_handle = None
-
-        self.config_path = op.join(self.analysis_path, 'code/babs_proj_config.yaml')
+        self.output_ria_data_dir = None  # not known yet before output_ria is created
+        self.analysis_dataset_id = None  # to update later
 
         self.input_ria_path = op.join(self.project_root, 'input_ria')
         self.output_ria_path = op.join(self.project_root, 'output_ria')
 
         self.input_ria_url = 'ria+file://' + self.input_ria_path
         self.output_ria_url = 'ria+file://' + self.output_ria_path
 
-        self.output_ria_data_dir = None  # not known yet before output_ria is created
-        self.analysis_dataset_id = None  # to update later
+        self.analysis_path = op.join(self.project_root, _find_analysis_dirname(self.project_root))
+
+        self.config_path = op.join(self.analysis_path, 'code/babs_proj_config.yaml')
 
         self.list_sub_path_rel = 'code/processing_inclusion.csv'
         self.list_sub_path_abs = op.join(self.analysis_path, self.list_sub_path_rel)
@@ -161,11 +176,18 @@ def _apply_config(self) -> None:
         self.queue = validate_queue(config_yaml['queue'])
         self.container = config_yaml['container']
 
+        if 'input_ria_path' in config_yaml:
+            self.input_ria_path = config_yaml['input_ria_path']
+            self.input_ria_url = 'ria+file://' + self.input_ria_path
+        if 'output_ria_path' in config_yaml:
+            self.output_ria_path = config_yaml['output_ria_path']
+            self.output_ria_url = 'ria+file://' + self.output_ria_path
+
         # Check the output RIA:
         self.wtf_key_info(flag_output_ria_only=True)
 
         self.input_datasets = InputDatasets(self.processing_level, config_yaml['input_datasets'])
-        self.input_datasets.update_abs_paths(Path(self.project_root) / 'analysis')
+        self.input_datasets.update_abs_paths(Path(self.analysis_path))
 
     def _update_inclusion_dataframe(
         self, initial_inclusion_df: pd.DataFrame | None = None

babs/bootstrap.py

@@ -92,9 +92,25 @@ def babs_bootstrap(
         self.queue = validate_queue(queue)
         system = System(self.queue)
 
+        # Override analysis_path if analysis_dirname is specified in container_config:
+        analysis_dirname = babs_config.get('analysis_dirname', 'analysis')
+        self.analysis_path = op.join(self.project_root, analysis_dirname)
+        self.config_path = op.join(self.analysis_path, 'code/babs_proj_config.yaml')
+        self.list_sub_path_abs = op.join(self.analysis_path, self.list_sub_path_rel)
+        self.job_status_path_abs = op.join(self.analysis_path, self.job_status_path_rel)
+        self.job_submit_path_abs = op.join(self.analysis_path, 'code/job_submit.csv')
+
+        # Override input/output RIA paths if specified in container_config:
+        if 'input_ria' in babs_config:
+            self.input_ria_path = babs_config['input_ria']
+            self.input_ria_url = 'ria+file://' + self.input_ria_path
+        if 'output_ria' in babs_config:
+            self.output_ria_path = babs_config['output_ria']
+            self.output_ria_url = 'ria+file://' + self.output_ria_path
+
         # Create `analysis` folder: -----------------------------
         print('DataLad version: ' + get_datalad_version())
-        print('\nCreating `analysis` folder (also a datalad dataset)...')
+        print(f'\nCreating `{analysis_dirname}` folder (also a datalad dataset)...')
         self._analysis_datalad_handle = dlapi.create(
             self.analysis_path, cfg_proc='yoda', annex=True
         )
@@ -144,6 +160,9 @@ def babs_bootstrap(
                 template.render(
                     processing_level=self.processing_level,
                     queue=self.queue,
+                    analysis_dirname=analysis_dirname,
+                    input_ria_path=self.input_ria_path,
+                    output_ria_path=self.output_ria_path,
                     input_ds=self.input_datasets,
                     container_name=container_name,
                     container_ds=container_ds,

babs/templates/babs_proj_config.yaml.jinja2

@@ -1,5 +1,8 @@
 processing_level: '{{ processing_level }}'
 queue: '{{ queue }}'
+analysis_dirname: '{{ analysis_dirname }}'
+input_ria_path: '{{ input_ria_path }}'
+output_ria_path: '{{ output_ria_path }}'
 
 # input dataset's name(s)
 input_datasets: