add check for sample IDs

micom-dev · Aug 2, 2024 · 8669cda · 8669cda
1 parent 42d7ceb
commit 8669cda
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diff --git a/NEWS.md b/NEWS.md
@@ -11,6 +11,9 @@ Limit logger default change to workflows only.
 
 Make some attempts to clean the taxon name in interactions.
 
+Workflows accepting per sample media will now raise an error if the medium is missing
+samples.
+
 ### 0.36.1
 
 Fixes a crash in the `minimal_media` workflow when growth rates are infeasible.

diff --git a/micom/workflows/media.py b/micom/workflows/media.py
@@ -22,6 +22,11 @@ def process_medium(medium, samples):
             m["sample_id"] = s
             meds.append(m)
         medium = pd.concat(meds, axis=0)
+    elif not all(s in medium.sample_id.unique() for s in samples):
+        missing = [s for s in samples if s not in medium.sample_id.unique()]
+        raise ValueError(
+            "The medium is missing samples from the manifest: {', '.join(missing)}."
+        )
     return medium.drop_duplicates(subset=["reaction", "sample_id"])