Remove Alt ID column from example csv

microbiomedata · Dec 19, 2024 · 95bc156 · 95bc156
1 parent 38db386
commit 95bc156
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Showing 2 changed files with 15 additions and 5 deletions.
diff --git a/metaMS/nmdc_lipidomics_metadata_generation/api_info_retriever.py b/metaMS/nmdc_lipidomics_metadata_generation/api_info_retriever.py
@@ -5,6 +5,16 @@
 class NMDCAPIInterface:
     """
     A generic interface for the NMDC runtime API.
+
+    Attributes
+    ----------
+    base_url : str
+        The base URL for the NMDC runtime API.
+
+    Methods
+    -------
+    validate_json(json_path: str) -> None:
+        Validates a json file using the NMDC json validate endpoint.
     """
 
     def __init__(self):

diff --git a/metaMS/nmdc_lipidomics_metadata_generation/example_metadata_file.csv b/metaMS/nmdc_lipidomics_metadata_generation/example_metadata_file.csv
@@ -1,5 +1,5 @@
-Biosample Id,Associated Study,Processing Type,Raw Data File,Raw Data Object Alt Id,Processed Data Directory,mass spec configuration name,lc config name,instrument used,processing institution,instrument analysis start date,instrument analysis end date,execution resource
-nmdc:biosamp:12-233,nmdc:sty-11-8fb6t785,MPLEX,/Users/zalm693/development/nmdc_ingest/example_lip_data/raw/raw_data_test1.raw,https://status.my.emsl.pnl.gov/view/1834807,/Users/zalm693/development/nmdc_ingest/example_lip_data/processed/sample1_ms1_processed,"EMSL lipidomics DDA mass spectrometry method, positive",EMSL metabolomics GC/MS mass spectrometry method,15T FT-ICR MS ,EMSL,01/22/2023,03/04/2024,EMSL-RZR
-nmdc:biosamp:12-233,nmdc:sty-11-8fb6t785,MPLEX,/Users/zalm693/development/nmdc_ingest/example_lip_data/raw/raw_data_test2.raw,https://status.my.emsl.pnl.gov/view/1834808,/Users/zalm693/development/nmdc_ingest/example_lip_data/processed/sample1_ms2_processed,"EMSL lipidomics DDA mass spectrometry method, negative",EMSL metabolomics GC/MS mass spectrometry method,12T FT-ICR MS ,EMSL,01/22/2023,03/04/2024,EMSL-RZR
-nmdc:biosamp:13-234,nmdc:sty-11-8fb6t785,MPLEX,/Users/zalm693/development/nmdc_ingest/example_lip_data/raw/raw_data_test3.raw,https://status.my.emsl.pnl.gov/view/1554801,/Users/zalm693/development/nmdc_ingest/example_lip_data/processed/sample2_ms1_processed,"EMSL lipidomics DDA mass spectrometry method, positive",EMSL metabolomics GC/MS mass spectrometry method,VOrbiETD04,EMSL,01/22/2023,03/04/2024,EMSL-RZR
-nmdc:biosamp:13-234,nmdc:sty-11-8fb6t785,MPLEX,/Users/zalm693/development/nmdc_ingest/example_lip_data/raw/raw_data_test4.raw,https://status.my.emsl.pnl.gov/view/1554809,/Users/zalm693/development/nmdc_ingest/example_lip_data/processed/sample2_ms2_processed,"EMSL lipidomics DDA mass spectrometry method, negative",EMSL metabolomics GC/MS mass spectrometry method,Agilent GC-MS (2009),EMSL,01/22/2023,03/04/2024,EMSL-RZR
+Biosample Id,Associated Study,Processing Type,Raw Data File,Processed Data Directory,mass spec configuration name,lc config name,instrument used,processing institution,instrument analysis start date,instrument analysis end date,execution resource
+nmdc:biosamp:12-233,nmdc:sty-11-8fb6t785,MPLEX,/Users/zalm693/development/nmdc_ingest/example_lip_data/raw/raw_data_test1.raw,/Users/zalm693/development/nmdc_ingest/example_lip_data/processed/sample1_ms1_processed,"EMSL lipidomics DDA mass spectrometry method, positive",EMSL metabolomics GC/MS mass spectrometry method,15T FT-ICR MS ,EMSL,1/22/23,3/4/24,EMSL-RZR
+nmdc:biosamp:12-233,nmdc:sty-11-8fb6t785,MPLEX,/Users/zalm693/development/nmdc_ingest/example_lip_data/raw/raw_data_test2.raw,/Users/zalm693/development/nmdc_ingest/example_lip_data/processed/sample1_ms2_processed,"EMSL lipidomics DDA mass spectrometry method, negative",EMSL metabolomics GC/MS mass spectrometry method,12T FT-ICR MS ,EMSL,1/22/23,3/4/24,EMSL-RZR
+nmdc:biosamp:13-234,nmdc:sty-11-8fb6t785,MPLEX,/Users/zalm693/development/nmdc_ingest/example_lip_data/raw/raw_data_test3.raw,/Users/zalm693/development/nmdc_ingest/example_lip_data/processed/sample2_ms1_processed,"EMSL lipidomics DDA mass spectrometry method, positive",EMSL metabolomics GC/MS mass spectrometry method,VOrbiETD04,EMSL,1/22/23,3/4/24,EMSL-RZR
+nmdc:biosamp:13-234,nmdc:sty-11-8fb6t785,MPLEX,/Users/zalm693/development/nmdc_ingest/example_lip_data/raw/raw_data_test4.raw,/Users/zalm693/development/nmdc_ingest/example_lip_data/processed/sample2_ms2_processed,"EMSL lipidomics DDA mass spectrometry method, negative",EMSL metabolomics GC/MS mass spectrometry method,Agilent GC-MS (2009),EMSL,1/22/23,3/4/24,EMSL-RZR