test: small csv from nicj into microreact

bacpop · Dec 9, 2024 · 41fca0f · 41fca0f
1 parent 0a063d0
commit 41fca0f
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Showing 5 changed files with 7,125 additions and 2 deletions.
diff --git a/beebop/app.py b/beebop/app.py
@@ -255,6 +255,7 @@ def run_poppunk_internal(sketches: dict,
     db_fs = DatabaseFileStore(
         f"{dbs_location}/{species_args.dbname}",
         species_args.external_clusters_file,
+        species_args.db_metadata_file,
     )
 
     # store json sketches in storage, and store an initial output_cluster file

diff --git a/beebop/filestore.py b/beebop/filestore.py
@@ -227,7 +227,10 @@ class DatabaseFileStore:
     Filestore that provides paths to the database
     """
     def __init__(
-        self, full_path: str, external_clusters_file: Optional[str] = None
+        self,
+        full_path: str,
+        external_clusters_file: Optional[str] = None,
+        db_metadata_file: Optional[str] = None,
     ):
         """
         :param full_path: [path to database]
@@ -244,3 +247,8 @@ def __init__(
             if external_clusters_file
             else None
         )
+        self.metadata = (
+            str(PurePath("beebop", "resources", db_metadata_file))
+            if db_metadata_file
+            else None
+        )
diff --git a/beebop/poppunkWrapper.py b/beebop/poppunkWrapper.py
@@ -101,7 +101,7 @@ def create_microreact(self, cluster: str, internal_cluster: str) -> None:
             previous_distances=None,
             network_file=self.fs.network_file(self.p_hash),
             gpu_graph=self.args.visualise.gpu_graph,
-            info_csv=self.args.visualise.info_csv,
+            info_csv=self.db_fs.metadata,
             rapidnj=shutil.which('rapidnj'),
             api_key=None,
             tree=self.args.visualise.tree,