Merge branch 'bacpop-207-csv-microreact' of https://github.com/bacpop…

…/beebop_py into bacpop-205-fix-network
bacpop · Dec 16, 2024 · 95482ce · 95482ce
2 parents eb5799b + 41fca0f
commit 95482ce
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Showing 5 changed files with 7,126 additions and 3 deletions.
diff --git a/beebop/app.py b/beebop/app.py
@@ -257,6 +257,7 @@ def run_poppunk_internal(sketches: dict,
     full_db_fs = DatabaseFileStore(
         f"{dbs_location}/{species_args.fulldb}",
         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
@@ -276,7 +276,10 @@ class DatabaseFileStore:
     """
 
     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]
@@ -295,3 +298,8 @@ 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
@@ -110,8 +110,8 @@ def create_microreact(self, cluster: str, internal_cluster: str) -> None:
             previous_distances=None,
             network_file=None,
             gpu_graph=self.args.visualise.gpu_graph,
-            info_csv=self.args.visualise.info_csv,
-            rapidnj=shutil.which("rapidnj"),
+            info_csv=self.db_fs.metadata,
+            rapidnj=shutil.which('rapidnj'),
             api_key=None,
             tree=self.args.visualise.tree,
             mst_distances=self.args.visualise.mst_distances,