Add functionality to authenticate via MetabRef API token

configuration/gcms_metams.toml

@@ -5,3 +5,4 @@ nmdc_metadata_path = "configuration/nmdc_metadata.json"
 output_directory = "output"
 output_filename = "output"
 output_type = "csv"
+metabref_token_path = "configuration/metabref.token"

metaMS/cli.py

@@ -31,6 +31,7 @@ def cli():
 @click.argument("output_type", required=True, type=str)
 @click.argument("corems_toml_path", required=True, type=str)
 @click.argument("nmdc_metadata_path", required=True, type=str)
+@click.argument("metabref_token_path", required=True, type=str)
 @click.option("--jobs", "-j", default=4, help="'cpu's'")
 def run_gcms_wdl_workflow(
     file_paths,
@@ -40,6 +41,7 @@ def run_gcms_wdl_workflow(
     output_type,
     corems_toml_path,
     nmdc_metadata_path,
+    metabref_token_path,
     jobs,
 ):
     """Run the GCMS workflow\n
@@ -56,6 +58,7 @@ def run_gcms_wdl_workflow(
         output_filename,
         output_type,
         corems_toml_path,
+        metabref_token_path,
         jobs,
     )
 

metaMS/gcmsWorkflow.py

@@ -54,6 +54,9 @@ class WorkflowParameters:
     output_filename: str = "data/..."
     output_type: str = "csv"
 
+    # Token
+    metabref_token_path: str = "configuration/..."
+
 
 def worker(args):
     """
@@ -72,6 +75,7 @@ def run_gcms_metabolomics_workflow_wdl(
     output_filename,
     output_type,
     corems_toml_path,
+    metabref_token_path,
     jobs,
     db_path=None,
 ):
@@ -92,6 +96,8 @@ def run_gcms_metabolomics_workflow_wdl(
         Output extension.
     corems_toml_path : str
         CoreMS configuration.
+    metabref_token_path : str
+        Token to authenticate MetabRef database access.
     jobs : int
         Number of concurrent jobs.
     [unused] db_path : str
@@ -109,6 +115,7 @@ def run_gcms_metabolomics_workflow_wdl(
     workflow_params.output_filename = output_filename
     workflow_params.output_type = output_type
     workflow_params.corems_toml_path = corems_toml_path
+    workflow_params.metabref_token_path = metabref_token_path
 
     # Load CoreMS settings
     click.echo("Loading CoreMS settings from %s" % workflow_params.corems_toml_path)
@@ -128,6 +135,7 @@ def run_gcms_metabolomics_workflow_wdl(
     )
 
     # Load FAMEs calibration reference
+    MetabRefGCInterface().set_token(workflow_params.metabref_token_path)
     fames_ref_sql = MetabRefGCInterface().get_fames(format="sql")
 
     # Compute RT:RI pairs
@@ -183,9 +191,8 @@ def run_nmdc_metabolomics_workflow(workflow_params_file, jobs):
     )
 
     # Load FAMEs calibration reference
-    fames_ref_sql = EI_LowRes_SQLite(
-        url=workflow_params.calibration_reference_path
-    )
+    MetabRefGCInterface().set_token(workflow_params.metabref_token_path)
+    fames_ref_sql = MetabRefGCInterface().get_fames(format='sql')
 
     # Compute RT:RI pairs
     rt_ri_pairs = get_rt_ri_pairs(gcms_cal_obj, sql_obj=fames_ref_sql)
@@ -253,6 +260,7 @@ def run_gcms_metabolomics_workflow(workflow_params_file, jobs):
     )
 
     # Load FAMEs calibration reference
+    MetabRefGCInterface().set_token(workflow_params.metabref_token_path)
     fames_ref_sql = MetabRefGCInterface().get_fames(format="sql")
 
     # Compute RT:RI pairs

wdl/metaMS_gcms.wdl

@@ -19,6 +19,7 @@ task runMetaMSGCMS {
         String output_type
         File corems_toml_path
         File nmdc_metadata_path
+        File metabref_token_path
         Int jobs_count
     }
 
@@ -31,6 +32,7 @@ task runMetaMSGCMS {
             ${output_type} \
             ${corems_toml_path} \
             ${nmdc_metadata_path} \
+            ${metabref_token_path} \
             --jobs ${jobs_count}
     }