Merge pull request #46 from glrs/feature/couchdb

Feature/couchdb

lib/couchdb/yggdrasil_db_manager.py

@@ -158,43 +158,76 @@ def check_project_exists(self, project_id: str) -> bool:
 
     @auto_load_and_save
     def add_sample(
-        self, ygg_doc: YggdrasilDocument, sample_id: str, status: str = "pending"
+        self, _doc_injected: YggdrasilDocument, sample_id: str, status: str = "pending"
     ):
         """
-        Adds a sample to the given YggdrasilDocument and
-        relies on the decorator to fetch & save the doc.
+        IMPORTANT: This method is decorated by @auto_load_and_save,
+        so you must call it like:
+
+            add_sample(<project_id>, <sample_id>, <status>)
+
+        The decorator will fetch the YggdrasilDocument and pass it here as '_doc_injected'.
+
+        ---
+
+        Adds a sample to a project.
+
+        Args:
+            _doc_injected (YggdrasilDocument): The Yggdrasil document (injected by the decorator).
+            sample_id (str): The sample ID.
+            status (str): The status of the sample. Defaults to "pending".
         """
-        ygg_doc.add_sample(sample_id=sample_id, status=status)
+        _doc_injected.add_sample(sample_id=sample_id, status=status)
         logging.info(f"Sample '{sample_id}' added with status '{status}'.")
 
     @auto_load_and_save
     def update_sample_status(
-        self, ygg_doc: YggdrasilDocument, sample_id: str, status: str
+        self, _doc_injected: YggdrasilDocument, sample_id: str, status: str
     ) -> None:
-        """Updates the status of a sample within a project.
+        """
+        IMPORTANT: This method is decorated by @auto_load_and_save,
+        so you must call it like:
+
+            update_sample_status(<project_id>, <sample_id>, <status>)
+
+        The decorator will fetch the YggdrasilDocument and pass it here as '_doc_injected'.
+
+        ---
+
+        Updates the status of a sample within a project.
 
         Args:
-            project_id (str): The project ID.
+            _doc_injected (YggdrasilDocument): The Yggdrasil document (injected by the decorator).
             sample_id (str): The sample ID.
             status (str): The new status for the sample.
         """
-        ygg_doc.update_sample_status(sample_id=sample_id, status=status)
+        _doc_injected.update_sample_status(sample_id=sample_id, status=status)
         logging.info(f"Sample '{sample_id}' status updated to '{status}'.")
 
     @auto_load_and_save
     def add_ngi_report_entry(
         self,
-        ygg_doc: YggdrasilDocument,
+        _doc_injected: YggdrasilDocument,
         report_data: Dict[str, Any],
     ) -> bool:
-        """Adds an NGI report entry to the given YggdrasilDocument.
+        """
+        IMPORTANT: This method is decorated by @auto_load_and_save,
+        so you must call it like:
+
+            add_ngi_report_entry(<project_id>, <report_data>)
+
+        The decorator will fetch the YggdrasilDocument and pass it here as '_doc_injected'.
+
+        ---
+
+        Adds an NGI report entry to a project.
 
         Args:
-            ygg_doc (YggdrasilDocument): The Yggdrasil document.
+            _doc_injected (YggdrasilDocument): The Yggdrasil document (injected by the decorator).
             report_data (Dict[str, Any]): The NGI report data.
         """
-        if not ygg_doc.add_ngi_report_entry(report_data):
-            logging.info("NGI report entry failed to be added to the document.")
+        if not _doc_injected.add_ngi_report_entry(report_data):
+            logging.warning("NGI report entry failed to be added to the document.")
             return False
         logging.info("NGI report entry added to the document.")
         return True

lib/couchdb/yggdrasil_document.py

@@ -288,6 +288,9 @@ def sync_project_metadata(
         # Update sensitive
         self.delivery_info["sensitive"] = is_sensitive
 
+        # NOTE: Hardcoded for now, may be configurable in the future
+        # self.delivery_info["partial_delivery_allowed"] = False
+
     def update_project_status(self, new_status: str) -> None:
         """Updates the overall project status. If 'completed', set end_date."""
         self.project_status = new_status
@@ -382,7 +385,7 @@ def add_ngi_report_entry(self, report_data: Dict[str, Any]) -> bool:
           "date_created": "2025-02-02_10:20:30",
           "signee": "",
           "date_signed": "",
-          "approved": False,
+          "rejected": False,
           "samples_included": [...]
         }
         """
@@ -391,7 +394,7 @@ def add_ngi_report_entry(self, report_data: Dict[str, Any]) -> bool:
             "date_created",
             "signee",
             "date_signed",
-            "approved",
+            "rejected",
             "samples_included",
         }
         if isinstance(report_data, dict) and required_keys.issubset(report_data.keys()):