Merge branch 'update-nmdc_metadata_gen' into 'master'

Update nmdc metadata gen See merge request mass-spectrometry/enviroms!1
EMSL-Computing · Feb 14, 2024 · 00a0892 · 00a0892
2 parents 548fa37 + aa197c1
commit 00a0892
Showing 1 changed file with 24 additions and 16 deletions.
diff --git a/enviroMS/nmdc_metadata_gen.py b/enviroMS/nmdc_metadata_gen.py
@@ -15,9 +15,18 @@
 
 env_mediums = {'ENVO_00002042': 'surface water',
                'ENVO_00002007': 'sediment',
+               'ENVO:00001998': 'soil'
                }
-env_local_scales = {'ENVO_00000022': 'river'}    
-env_broad_scales = {'ENVO_01000253': 'freshwater river biome'}    
+env_local_scales = {'ENVO_00000022': 'river',
+                    'ENVO:01000861': 'area of dwarf scrub',
+                    'ENVO:00000516': 'hummock',
+                    'ENVO:01000869': 'area of scrub',
+                    'ENVO:01000887': 'area of sedge- and forb-dominated herbaceous vegetation',
+                    'ENVO:01001370': 'tundra ecosystem'
+                    }    
+env_broad_scales = {'ENVO_01000253': 'freshwater river biome',
+                    'ENVO:00000446': 'terrestrial biome'
+                    }    
 
 
 @dataclass
@@ -39,16 +48,16 @@ class DataObject:
     nom_raw_data_object_type:str = "Direct Infusion FT ICR-MS Raw Data"
     nom_raw_data_object_description:str = "Raw 21T Direct Infusion Data"
     nom_dp_data_object_type:str = "FT ICR-MS Analysis Results"
-    nom_dp_data_object_description:str = "EnviroMS FT ICR-MS natural organic matter workflow molecular formula assignment output details",
+    nom_dp_data_object_description:str = "EnviroMS FT ICR-MS natural organic matter workflow molecular formula assignment output details"
 
 @dataclass
-class BioSample:
+class Biosample:
     pass
 
 @dataclass
 class NMDC_Types: 
 
-    BioSample:str = "nmdc:BioSample"
+    Biosample:str = "nmdc:Biosample"
     OmicsProcessing:str = "nmdc:OmicsProcessing"
     NomAnalysisActivity:str = "nmdc:NomAnalysisActivity"
     DataObject:str = "nmdc:DataObject"
@@ -93,7 +102,7 @@ def mint_nmdc_id(type:NMDC_Types, how_many:int = 1) -> List[str]:
 
 def get_biosample_object(emsl_metadata:EMSL_Metadata) -> nmdc.Biosample:
 
-    nmdc_id = mint_nmdc_id({'id': NMDC_Types.BioSample})[0]
+    nmdc_id = mint_nmdc_id({'id': NMDC_Types.Biosample})[0]
 
     env_medium = {
                  'has_raw_value': emsl_metadata.env_medium,
@@ -121,14 +130,14 @@ def get_biosample_object(emsl_metadata:EMSL_Metadata) -> nmdc.Biosample:
                 "longitude": emsl_metadata.longitude,
             }
 
-    collection_date = { 'has_raw_value': emsl_metadata.collection_date}
+    collection_date = {'has_raw_value': emsl_metadata.collection_date}
 
     geo_loc_name =  {'has_raw_value': emsl_metadata.geo_loc_name}
 
     data_dict = {'id': nmdc_id,
                 'env_medium' : env_medium,
                 'env_local_scale' : env_local_scale,
-                'env_broad_scales_data' : env_broad_scale,
+                'env_broad_scale' : env_broad_scale,
                 'lat_lon': lat_lon,
                 'location': emsl_metadata.location,
                 'ecosystem_type': emsl_metadata.ecosystem_type,
@@ -228,21 +237,21 @@ def create_nmdc_metadata(raw_data_path:Path, data_product_path:Path, base_url:st
 
     if not biosample_id:
 
-        biosample_id = mint_nmdc_id({'id': NMDC_Types.BioSample})[0]
+        biosample_id = mint_nmdc_id({'id': NMDC_Types.Biosample})[0]
         bioSample = get_biosample_object(emsl_metadata)
         biosample_id = bioSample.id
 
     else:
 
         ''' needs to finish the logic for creating biosamples, this will fail because it is missing some required fields'''
-        bioSample =  nmdc.BioSample(id=biosample_id)
+        bioSample =  nmdc.Biosample(id=biosample_id)
 
     omicsProcessing = get_omics_processing(raw_data_path,
                                            OmicsProcessing.nom_12T_instrument_name,
-                                           biosample_id, None, 
+                                           biosample_id, 'nmdc:placeholder', 
                                            OmicsProcessing.nom_omics_processing_type,
                                            OmicsProcessing.nom_omics_processing_description,
-                                           emsl_metadata.nmdc_study_id
+                                           emsl_metadata.nmdc_study 
                                            )
 
     rawDataObject = get_data_object(raw_data_path, base_url + 'nom/grow/raw/', 
@@ -252,7 +261,7 @@ def create_nmdc_metadata(raw_data_path:Path, data_product_path:Path, base_url:st
 
     nomAnalysisActivity = get_nom_analysis_activity(NomAnalysisActivity.cluster_name,
                                                 NomAnalysisActivity.codebase_url,
-                                                rawDataObject.id, None, False, 
+                                                rawDataObject.id, 'nmdc:placeholder', False, 
                                                 omicsProcessing.id,
                                                 NomAnalysisActivity.nom_12T_instrument_name)
 
@@ -262,9 +271,8 @@ def create_nmdc_metadata(raw_data_path:Path, data_product_path:Path, base_url:st
                                     description =DataObject.nom_dp_data_object_description)
 
     #circular dependencies : great! 
-    nomAnalysisActivity.has_input = rawDataObject.id
-    nomAnalysisActivity.has_output = dataProductDataObject.id
-    omicsProcessing.has_output = rawDataObject.id
+    nomAnalysisActivity.has_output = [dataProductDataObject.id]
+    omicsProcessing.has_output = [rawDataObject.id]
 
     nom_metadata_db.biosample_set.append(bioSample)
     nom_metadata_db.data_object_set.append(rawDataObject)