Feature/couchdb

lib/couchdb/document.py

@@ -45,6 +45,9 @@ def from_dict(cls, data: Dict[str, Any]) -> "YggdrasilDocument":
         # Samples
         instance.samples = data.get("samples", [])
 
+        # User info
+        instance.user_info = data.get("user_info", {})
+
         # Delivery info
         instance.delivery_info = data.get("delivery_info", {})
         if "delivery_results" not in instance.delivery_info:
@@ -78,6 +81,7 @@ def __init__(self, project_id: str, projects_reference: str, method: str) -> Non
         self.samples: List[Dict[str, Any]] = []
         self.delivery_info: Dict[str, Any] = {"delivery_results": []}
         self.ngi_report: List[Dict[str, Any]] = []
+        self.user_info: Dict[str, Dict[str, Optional[str]]] = {}
 
     def to_dict(self) -> Dict[str, Any]:
         """Converts the YggdrasilDocument to a dictionary.
@@ -96,8 +100,37 @@ def to_dict(self) -> Dict[str, Any]:
             "samples": self.samples,
             "delivery_info": self.delivery_info,
             "ngi_report": self.ngi_report,
+            "user_info": self.user_info,
         }
 
+    # ---------------------------
+    # USER INFO
+    # ---------------------------
+
+    def set_user_info(self, updated_info: Dict[str, Dict[str, Optional[str]]]) -> None:
+        """
+        Updates self.user_info with the nested dictionary provided.
+
+        Example updated_info:
+        {
+            "owner": {
+            "email": "[email protected]",
+            "name": "Owner Name"
+            },
+            "pi": {
+            "email": "[email protected]",
+            "name": "PI Name"
+            }
+        }
+        """
+        for role, sub_dict in updated_info.items():
+            if role not in self.user_info:
+                # If the doc didn't have that role yet, create a blank dict
+                self.user_info[role] = {}
+            # Copy keys like "email", "name"
+            for key, val in sub_dict.items():
+                self.user_info[role][key] = val or ""
+
     # ------------------------------------------------------------------------
     # SAMPLES
     # ------------------------------------------------------------------------

lib/couchdb/manager.py

@@ -203,25 +203,71 @@ def __init__(self) -> None:
         super().__init__("yggdrasil")
 
     def create_project(
-        self, project_id: str, projects_reference: str, method: str
+        self,
+        project_id: str,
+        projects_reference: str,
+        method: str,
+        user_info: Optional[Dict[str, Dict[str, Optional[str]]]] = None,
+        sensitive: Optional[bool] = True,
     ) -> YggdrasilDocument:
         """Creates a new project document in the database.
 
         Args:
             project_id (str): The project ID.
             projects_reference (str): Reference to the original project document.
             method (str): The library construction method.
+            user_info (Optional[Dict[str, Dict[str, str]]]): Nested dict of user info,
+                e.g. {"owner": {"email": "...", "name": "..."}, ...}.
+            sensitive (bool): True if data is sensitive. Defaults to True.
 
         Returns:
             YggdrasilDocument: The newly created project document.
         """
         new_document = YggdrasilDocument(
             project_id=project_id, projects_reference=projects_reference, method=method
         )
+
+        # If we have user info, populate it into new_document.user_info
+        # TODO: Make sure the PI and the owner are always set | Either here or upon delivery
+        if user_info:
+            new_document.user_info = user_info
+
+        # Set sensitive flag to True by default (better safe than sorry)
+        new_document.delivery_info["sensitive"] = sensitive
+
         self.save_document(new_document)
         logging.info(f"New project with ID '{project_id}' created successfully.")
         return new_document
 
+    def sync_project_metadata(
+        self,
+        project_id: str,
+        user_info: Dict[str, Dict[str, Optional[str]]],
+        is_sensitive: bool,
+    ) -> None:
+        """
+        Fetches the project doc from YggdrasilDB, updates user_info & sensitive,
+        then saves it back.
+        """
+        doc_dict = self.get_document_by_project_id(project_id)
+        if not doc_dict:
+            logging.warning(f"No project '{project_id}' found to update.")
+            return
+
+        ygg_doc = YggdrasilDocument.from_dict(doc_dict)
+
+        # Update user_info
+        ygg_doc.set_user_info(user_info)
+
+        # Update sensitive
+        ygg_doc.delivery_info["sensitive"] = is_sensitive
+
+        # Save
+        self.save_document(ygg_doc)
+        logging.info(
+            f"Synced project '{project_id}' with necessary metadata from projectsDB."
+        )
+
     def save_document(self, document: YggdrasilDocument) -> None:
         try:
             existing_doc = self.db.get(document._id)