add find_data_object method

nmdc_automation/api/nmdcapi.py

@@ -368,14 +368,22 @@ def run_query(self, query):
         return resp.json()
 
     # The find endpoints don't require a token
-    def get_planned_process(self, id: str) -> Optional[dict]:
+    def find_planned_process(self, id: str) -> Optional[dict]:
         url = f"{self._base_url}planned_processes/{id}"
         resp = requests.get(url)
         if resp.status_code == 404:
             return None
         resp.raise_for_status()
         return resp.json()
 
+    def find_data_object(self, id: str) -> Optional[dict]:
+        url = f"{self._base_url}data_objects/{id}"
+        resp = requests.get(url)
+        if resp.status_code == 404:
+            return None
+        resp.raise_for_status()
+        return resp.json()
+
 
 # TODO - This is deprecated and should be removed along with the re_iding code that uses it
 class NmdcRuntimeUserApi:

nmdc_automation/run_process/run_import.py

@@ -59,22 +59,15 @@ def import_projects(import_file, import_yaml, site_configuration, iteration):
 
         # Nucleotide sequencing data
         logger.info(f"Checking for existing nucleotide_sequencing_id: {nucleotide_sequencing_id}")
-        nucleotide_sequencing = runtime.get_planned_process(nucleotide_sequencing_id)
+        nucleotide_sequencing = runtime.find_planned_process(nucleotide_sequencing_id)
         if not nucleotide_sequencing:
-            logger.error(f"nucleotide_sequencing_id {nucleotide_sequencing_id} not found")
-            continue
-        # Check if the nucleotide sequencing has outputs
-        sequence_data = nucleotide_sequencing.get("has_output", [])
-        if sequence_data:
-            logger.info(f"nucleotide_sequencing_id {nucleotide_sequencing_id} has outputs")
-            logger.info(f"Output data objects: {sequence_data}")
-            continue
-        else:
-            logger.info(f"nucleotide_sequencing_id {nucleotide_sequencing_id} has no outputs")
-            # link sequencing data files and create data objects
-            # Initialize the db with the sequencing data object and create an update to be applied
+            raise Exception(f"nucleotide_sequencing_id {nucleotide_sequencing_id} not found")
 
+        if _nucleotide_sequencing_has_output(nucleotide_sequencing, nucleotide_sequencing_id):
+            logger.info(f"nucleotide_sequencing_id {nucleotide_sequencing_id} already has output: {nucleotide_sequencing['has_output']}")
+            continue
 
+        logger.info(f"Mapping sequencing data for nucleotide_sequencing_id: {nucleotide_sequencing_id}")
 
         # Initialize the db with the sequencing data and create an update to be applied
         # to the sequencing data generation has_output list
@@ -127,6 +120,24 @@ def import_projects(import_file, import_yaml, site_configuration, iteration):
         # gc.collect()
 
 
+def _nucleotide_sequencing_has_output(nucleotide_sequencing, nucleotide_sequencing_id) -> bool:
+    """
+    Check if the nucleotide sequencing has an output and if it is an NMDC data object.
+    """
+    seq_has_output = nucleotide_sequencing.get("has_output", [])
+    if seq_has_output:
+        # Raise an exception if there is more than one output or if the output is not an NMDC data object
+        if len(seq_has_output) > 1:
+            raise Exception(f"nucleotide_sequencing_id {nucleotide_sequencing_id} has more than one output")
+        seq_do_id = seq_has_output[0]
+        if not seq_do_id.startswith("nmdc:dobj-"):
+            raise Exception(f"nucleotide_sequencing_id {nucleotide_sequencing_id} has a non-NMDC output")
+
+        logger.info(f"nucleotide_sequencing_id {nucleotide_sequencing_id} has output {seq_do_id}")
+        return True
+    else:
+        logger.info(f"nucleotide_sequencing_id {nucleotide_sequencing_id} has no outputs")
+        return False
 
 
 @lru_cache(maxsize=None)