Merge pull request #23 from glrs/feature/10x-dev

Update to interact with YggDB and follow AbstractProject changes

lib/realms/tenx/run_sample.py

@@ -39,6 +39,8 @@ def __init__(
         self.run_sample_id: str = sample_id
         self.lab_samples: List[Any] = lab_samples
         self.project_info: Dict[str, Any] = project_info or {}
+        # TODO: ensure project_id is always available
+        self.project_id = self.project_info.get("project_id", "")
         self.config: Mapping[str, Any] = config or {}
         self.ydm: Any = yggdrasil_db_manager
 
@@ -93,9 +95,8 @@ def status(self, value: str) -> None:
             value (str): The new status value.
         """
         self._status = value
-        # self.ydm.update_sample_status(
-        #     self.project_info.get("project_id", ""), self.id, value
-        # )
+        # Update the status in the database
+        self.ydm.update_sample_status(self.project_id, self.id, value)
 
     def collect_reference_genomes(self) -> Optional[Dict[str, str]]:
         """Collect reference genomes from lab samples and ensure consistency.

lib/realms/tenx/tenx_project.py

@@ -31,9 +31,10 @@ def __init__(self, doc: Dict[str, Any], yggdrasil_db_manager: Any) -> None:
         self.ydm: Any = yggdrasil_db_manager
 
         # TODO: Might need to check required fields for each different method, if they differ
-        self.proceed: bool = self._check_required_fields()
+        self.proceed: bool = self.check_required_fields()
 
         if self.proceed:
+            self.initialize_project_in_db()
             # Extract metadata from project document
             self.project_info: Dict[str, Any] = self._extract_project_info()
 
@@ -152,7 +153,7 @@ def is_supported_organism(self, organism: str) -> bool:
         gex_organisms = reference_mapping.get("gex", {}).keys()
         return organism in gex_organisms
 
-    def _check_required_fields(self) -> bool:
+    def check_required_fields(self) -> bool:
         """Check if the document contains all required fields.
 
         Returns:
@@ -411,6 +412,8 @@ async def launch(self):
             logging.warning("No samples found for processing. Returning...")
             return
 
+        self.add_samples_to_project_in_db()
+
         logging.info(f"Considered samples: {[sample.id for sample in self.samples]}")
         logging.info(f"Sample features: {[sample.features for sample in self.samples]}")