Uploader

NL-BIOMERO

@@ -0,0 +1 @@
+../NL-BIOMERO

omero-init.sh

@@ -7,6 +7,7 @@ CONTAINER_NAME="nl-biomero-omeroweb-1"
 # Command to execute inside the container
 # COMMAND1="/usr/local/bin/entrypoint.sh"
 COMMAND0="chmod a+w /opt/omero/web/OMERO.web/var/static"
+COMMAND0B="git config --global --add safe.directory /opt/omero/web/OMERO.biomero"
 
 COMMAND1="/opt/omero/web/venv3/bin/python -m pip install -e /opt/omero/web/OMERO.biomero"
 COMMAND2="/opt/omero/web/venv3/bin/omero-biomero-setup"
@@ -15,6 +16,7 @@ COMMAND3="/opt/omero/web/venv3/bin/omero web stop || true; rm -f /opt/omero/web/
 COMMAND4="/opt/omero/web/OMERO.biomero/startup.sh"
 
 docker exec --user root "$CONTAINER_NAME" sh -c "$COMMAND0"
+docker exec --user root "$CONTAINER_NAME" sh -c "$COMMAND0B"
 docker exec --user root "$CONTAINER_NAME" sh -c "$COMMAND1"
 docker exec --user root "$CONTAINER_NAME" sh -c "$COMMAND2"
 docker exec --user omero-web "$CONTAINER_NAME" sh -c "$COMMAND3"

omero-update.sh

@@ -8,7 +8,8 @@ CONTAINER_NAME="nl-biomero-omeroweb-1"
 COMMAND0="chmod a+w /opt/omero/web/OMERO.web/var/static"
 COMMAND1="/opt/omero/web/venv3/bin/pip install -e /opt/omero/web/OMERO.biomero"
 COMMAND2="/opt/omero/web/venv3/bin/omero-biomero-setup"
-COMMAND3="/opt/omero/web/venv3/bin/omero web stop"
+COMMAND3="/opt/omero/web/venv3/bin/omero web stop || true; rm -f /opt/omero/web/OMERO.web/var/django.pid"
+
 COMMAND4="/opt/omero/web/OMERO.biomero/startup.sh"
 
 docker exec --user root "$CONTAINER_NAME" sh -c "$COMMAND2"

omero_biomero/admin_views.py

@@ -3,13 +3,16 @@
 import json
 import logging
 import os
+import logging
+import os
 
 from biomero import SlurmClient
 from collections import defaultdict
 from configupdater import ConfigUpdater, Comment
 from django.http import JsonResponse, HttpResponseBadRequest
 from django.views.decorators.http import require_http_methods
 from omeroweb.webclient.decorators import login_required
+from .settings import CONFIG_FILE_PATH
 
 logger = logging.getLogger(__name__)
 
@@ -44,6 +47,21 @@ def admin_config(request, conn=None, **kwargs):
                 section: dict(configs.items(section)) for section in configs.sections()
             }
 
+            # Load the JSON configuration file (biomero-config.json)
+            json_config = {}
+            if os.path.exists(CONFIG_FILE_PATH):
+                try:
+                    with open(CONFIG_FILE_PATH, "r") as f:
+                        json_config = json.load(f)
+                except Exception as e:
+                    logger.error(f"Error reading JSON config: {str(e)}")
+
+            # Merge JSON config into config_dict
+            # Note: JSON config allows nested dicts, while INI is flat (section -> key/value)
+            # We assume top-level keys in JSON correspond to sections or specific config groups
+            for key, value in json_config.items():
+                config_dict[key] = value
+
             return JsonResponse({"config": config_dict})
         except Exception as e:
             logger.error(f"Error retrieving BIOMERO config: {str(e)}")
@@ -86,8 +104,58 @@ def generate_model_comment(key):
                     c = "# Adding or overriding job value for this workflow"
                 return c
 
-            # Update the config with new values
+            # Separate settings for JSON config and INI config
+            json_config_updates = {}
+            ini_config_updates = {}
+
+            # Define sections that belong in the JSON configuration
+            JSON_SECTIONS = [
+                "UPLOADER",
+                "PREPROCESSING_CONFIG",
+                "PREPROCESSING_EXTENSION_MAP",
+                "FILE_OR_EXTENSION_PATTERNS_EXCLUSIVE",
+                "UPLOADER_NESTED_FILE_EXTENSIONS",
+                "group_mappings",
+            ]
+
             for section, settingsd in config_data.items():
+                if section in JSON_SECTIONS:
+                    json_config_updates[section] = settingsd
+                else:
+                    ini_config_updates[section] = settingsd
+
+            # --- Save JSON Config ---
+            if json_config_updates:
+                try:
+                    current_json_config = {}
+                    if os.path.exists(CONFIG_FILE_PATH):
+                        with open(CONFIG_FILE_PATH, "r") as f:
+                            current_json_config = json.load(f) or {}
+
+                    # Update with new values
+                    for key, value in json_config_updates.items():
+                        current_json_config[key] = value
+
+                    # Ensure directory exists
+                    config_dir = os.path.dirname(CONFIG_FILE_PATH)
+                    if config_dir and not os.path.exists(config_dir):
+                        os.makedirs(config_dir, exist_ok=True)
+
+                    with open(CONFIG_FILE_PATH, "w") as f:
+                        json.dump(current_json_config, f, indent=2)
+                    logger.info(f"JSON configuration saved to {CONFIG_FILE_PATH}")
+                except Exception as e:
+                    logger.error(f"Failed to save JSON config: {str(e)}")
+                    # We might want to return an error here, but let's see if INI save works first?
+                    # Or fail immediately? Let's fail if we can't save the requested changes.
+                    return JsonResponse(
+                        {"error": f"Failed to save JSON configuration: {str(e)}"},
+                        status=500,
+                    )
+
+            # --- Save INI Config ---
+            # Update the config with new values
+            for section, settingsd in ini_config_updates.items():
                 if not isinstance(settingsd, dict):
                     raise ValueError(
                         f"Section '{section}' must contain key-value pairs."
@@ -196,10 +264,25 @@ def generate_model_comment(key):
             changelog_section.add_after.comment(change_comment)
 
             # Save the updated configuration while preserving comments
-            with open(config_path, "w") as config_file:
-                config.write(config_file)
+            try:
+                with open(config_path, "w") as config_file:
+                    config.write(config_file)
+                logger.info(f"Configuration saved successfully to {config_path}")
+            except PermissionError:
+                logger.error(
+                    f"Permission denied writing to {config_path}. Skipping INI save."
+                )
+                if not json_config_updates:
+                    # If we only tried to save INI and failed, that's an error.
+                    # If we saved JSON but failed INI, we might want to warn or just succeed partially.
+                    # For now, if we have mix, and INI fails, we report error?
+                    # But the user might be toggling UPLOADER (JSON) and not caring about Slurm (INI).
+                    # So if json_config_updates succeeded, we can treat it as partial success.
+                    pass
+            except Exception as e:
+                logger.error(f"Error saving INI config: {e}")
+                raise e
 
-            logger.info(f"Configuration saved successfully to {config_path}")
             return JsonResponse(
                 {"message": "Configuration saved successfully", "path": config_path},
                 status=200,

omero_biomero/biomero_views.py

@@ -11,6 +11,7 @@
 )
 from .settings import (
     BASE_DIR,
+    UPLOADER_ALLOWED_FILE_EXTENSIONS,
 )
 
 logger = logging.getLogger(__name__)
@@ -87,5 +88,6 @@ def biomero(request, conn=None, **kwargs):
         "app_name": "biomero",
         "importer_enabled": importer_enabled,
         "analyzer_enabled": analyzer_enabled,
+        "uploader_allowed_file_extensions": UPLOADER_ALLOWED_FILE_EXTENSIONS,
     }
     return context