d03a89dc413d8f529778e5ad23b3e296dd2e99b2
mspeir
  Tue Jul 29 09:03:31 2025 -0700
fixing issue with cbScanpy not properly getting inMeta declared in scanpy.conf

diff --git src/cbPyLib/cellbrowser/cellbrowser.py src/cbPyLib/cellbrowser/cellbrowser.py
index bafab71..cde6e01 100755
--- src/cbPyLib/cellbrowser/cellbrowser.py
+++ src/cbPyLib/cellbrowser/cellbrowser.py
@@ -6742,31 +6742,31 @@
     conf["doLayouts"] = doLayouts
     conf["doLouvain"] = conf.get("doLouvain", True)
     conf["doPca"] = conf.get("doPca", True)
     conf["louvainNeighbors"] = int(conf.get("louvainNeighbors", 6))
     conf["louvainRes"] = float(conf.get("louvainRes", 1.0))
 
     conf["doMarkers"] = conf.get("doMarkers", True)
     if skipMarkers:
         conf["doMarkers"] = False
 
     conf["markerCount"] = int(conf.get("markerCount", 20))
     conf["inMeta"] = conf.get("inMeta", inMeta)
     conf["inCluster"] = conf.get("inCluster", inCluster)
 
     if conf["inMeta"]:
-        adata = addMetaToAnnData(adata, inMeta)
+        adata = addMetaToAnnData(adata, conf["inMeta"])
 
     sampleCount = len(adata.obs)
 
     bigDataset = False
     if sampleCount > 140000:
         bigDataset = True
 
     #useRaw = conf["useRaw"]
     #if useRaw and not bigDataset:
         #adata.raw = adata # this is doing much more than assigning, it calls implicitely a function that copies
         ## a few things around. See the anndata source code under basic.py
     #else:
         #bigDataset = True
         #logging.info("Big dataset: not keeping a .raw copy of the data to save memory during analysis")