From 5a650334dfc5fd4e72e78120e508a1d9acc37c80 Mon Sep 17 00:00:00 2001
From: Alok Saldanha <asaldanha@ip-192-168-0-69.ec2.internal>
Date: Thu, 6 Jul 2023 07:56:43 -0600
Subject: [PATCH] #81 moved gene set check into fileitem_source

---
 Changelog.md                                    |  4 ++++
 cellxgene_gateway/filecrawl.py                  | 12 ++----------
 cellxgene_gateway/items/file/fileitem_source.py |  3 +++
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/Changelog.md b/Changelog.md
index 2a93964..b8d8239 100644
--- a/Changelog.md
+++ b/Changelog.md
@@ -1,3 +1,7 @@
+# 0.3.11
+
+* #81 added support for gene sets via GATEWAY_ENABLE_GENE_SETS
+
 # 0.3.10
 
 * #65 Added GATEWAY_EXPIRE_SECONDS to set how long cellxgene servers can remain idle before being terminated.
diff --git a/cellxgene_gateway/filecrawl.py b/cellxgene_gateway/filecrawl.py
index 582afe8..f812091 100644
--- a/cellxgene_gateway/filecrawl.py
+++ b/cellxgene_gateway/filecrawl.py
@@ -20,23 +20,15 @@ def render_annotations(item, item_source):
         item_source.get_annotations_subpath(item), item_source.name
     )
     new_annotation = f"<a class='new' href='{url}'>new</a>"
-    non_gene_set_files = []
-    if item.annotations is not None:
-        # Do not also display files to store gene_sets. These should be loaded
-        # by clicking on the associated annotations file (i.e.  without the
-        # appended "_gene_sets")
-        for a in item.annotations:
-            if (len(a.name) < 10) or (a.name[-10:] != "_gene_sets"):
-                non_gene_set_files.append(a)
     annotations = (
         ", ".join(
             [
                 f"<a href='{CacheKey(item, item_source, a).view_url}/'>{a.name}</a>"
-                for a in non_gene_set_files
+                for a in item.annotations
             ]
         )
         + ", "
-        if non_gene_set_files
+        if item.annotations
         else ""
     )
     return " | annotations: " + annotations + new_annotation
diff --git a/cellxgene_gateway/items/file/fileitem_source.py b/cellxgene_gateway/items/file/fileitem_source.py
index 4ade4b9..38d0a8f 100644
--- a/cellxgene_gateway/items/file/fileitem_source.py
+++ b/cellxgene_gateway/items/file/fileitem_source.py
@@ -35,6 +35,8 @@ class FileItemSource(ItemSource):
     def name(self):
         return self._name or f"Files:{self.base_path}"
 
+    def is_gene_set(self, path:str) -> bool:
+        return ('_gene_sets' in path or '-gene-sets' in path) and path.endswith(self.annotation_file_suffix)
     def is_h5ad_file(self, path: str) -> bool:
         return path.endswith(self.h5ad_suffix) and os.path.isfile(path)
 
@@ -180,6 +182,7 @@ class FileItemSource(ItemSource):
                 self.make_fileitem_from_path(annotation, annotations_subpath, True)
                 for annotation in sorted(os.listdir(annotations_fullpath))
                 if annotation.endswith(self.annotation_file_suffix)
+                and not self.is_gene_set(annotation)
                 and os.path.isfile(os.path.join(annotations_fullpath, annotation))
             ]
         else: