rename "geneset" to "gene set" in CLI (#2088)

* remove dead code

* rename geneset to gene_set

local_server/test/fixtures/dataset_config_outline.py

@@ -16,12 +16,12 @@ dataset:
     local_file_csv:
       directory: {local_file_csv_directory}
       file: {local_file_csv_file}
-      genesets_file: {local_file_csv_genesets_file}
+      gene_sets_file: {local_file_csv_gene_sets_file}
     ontology:
       enable: {ontology_enabled}
       obo_location: {obo_location}
-    genesets:
-      readonly: {genesets_readonly}
+    gene_sets:
+      readonly: {gene_sets_readonly}
 
   embeddings:
     names: {embedding_names}

local_server/test/fixtures/pbmc3k-genesets.csv

@@ -1,12 +1,12 @@
 # Test fixture
-geneset_name, geneset_description, gene_symbol, gene_description
-first geneset name,,F5, a gene_description
-first geneset name,a description, NO_SUCH_GENE, non-existent gene
-first geneset name,a description, F5, duplicate gene
-first geneset name, a description, SUMO3,
-first geneset name,, SRM,
-second geneset,,RER1
-second geneset,,SIK1
-third geneset,,NO_SUCH_GENE
-fourth_geneset,fourth description,,gene intentionally missing
+gene_set_name, gene_set_description, gene_symbol, gene_description
+first gene set name,,F5, a gene_description
+first gene set name,a description, NO_SUCH_GENE, non-existent gene
+first gene set name,a description, F5, duplicate gene
+first gene set name, a description, SUMO3,
+first gene set name,, SRM,
+second gene set,,RER1
+second gene set,,SIK1
+third gene set,,NO_SUCH_GENE
+fourth_gene_set,fourth description,,gene intentionally missing
 fifth_dataset,,,

local_server/test/unit/auth/test_auth.py

@@ -14,7 +14,7 @@ class AuthTest(unittest.TestCase):
         app_config = AppConfig()
         app_config.update_server_config(app__flask_secret_key="secret")
         app_config.update_server_config(authentication__type=None, single_dataset__datapath=self.dataset_datapath)
-        app_config.update_dataset_config(user_annotations__enable=False, user_annotations__genesets__readonly=True)
+        app_config.update_dataset_config(user_annotations__enable=False, user_annotations__gene_sets__readonly=True)
 
         app_config.complete_config()
 

local_server/test/unit/common/config/__init__.py

@@ -92,10 +92,10 @@ class ConfigTests(unittest.TestCase):
         hosted_file_directory="null",
         local_file_csv_directory="null",
         local_file_csv_file="null",
-        local_file_csv_genesets_file="null",
+        local_file_csv_gene_sets_file="null",
         ontology_enabled="false",
         obo_location="null",
-        genesets_readonly="false",
+        gene_sets_readonly="false",
         embedding_names=[],
         enable_reembedding="false",
         enable_difexp="true",
@@ -144,10 +144,10 @@ class ConfigTests(unittest.TestCase):
             hosted_file_directory=hosted_file_directory,
             local_file_csv_directory=local_file_csv_directory,
             local_file_csv_file=local_file_csv_file,
-            local_file_csv_genesets_file=local_file_csv_genesets_file,
+            local_file_csv_gene_sets_file=local_file_csv_gene_sets_file,
             ontology_enabled=ontology_enabled,
             obo_location=obo_location,
-            genesets_readonly=genesets_readonly,
+            gene_sets_readonly=gene_sets_readonly,
             embedding_names=embedding_names,
             enable_reembedding=enable_reembedding,
             enable_difexp=enable_difexp,
@@ -182,10 +182,10 @@ class ConfigTests(unittest.TestCase):
         hosted_file_directory="null",
         local_file_csv_directory="null",
         local_file_csv_file="null",
-        local_file_csv_genesets_file="null",
+        local_file_csv_gene_sets_file="null",
         ontology_enabled="false",
         obo_location="null",
-        genesets_readonly="false",
+        gene_sets_readonly="false",
         embedding_names=[],
         enable_reembedding="false",
         enable_difexp="true",

local_server/test/unit/common/test_api.py

@@ -388,7 +388,7 @@ class EndPointsAnndata(unittest.TestCase, EndPoints):
             [
                 f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
                 "--disable-annotations",
-                "--disable-genesets-save",
+                "--disable-gene-sets-save",
                 "--experimental-enable-reembedding",
             ],
         )
@@ -465,7 +465,7 @@ class EndPointsAnnDataGenesets(unittest.TestCase, EndPoints):
             [
                 f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
                 "--disable-annotations",
-                "--genesets-file",
+                "--gene-sets-file",
                 genesets_file,
             ],
         )
@@ -496,7 +496,7 @@ class EndPointsAnnDataGenesets(unittest.TestCase, EndPoints):
                             {"gene_description": "", "gene_symbol": "SRM"},
                         ],
                         "geneset_description": "a description",
-                        "geneset_name": "first geneset name",
+                        "geneset_name": "first gene set name",
                     },
                     {
                         "genes": [
@@ -504,10 +504,10 @@ class EndPointsAnnDataGenesets(unittest.TestCase, EndPoints):
                             {"gene_description": "", "gene_symbol": "SIK1"},
                         ],
                         "geneset_description": "",
-                        "geneset_name": "second geneset",
+                        "geneset_name": "second gene set",
                     },
-                    {"genes": [], "geneset_description": "", "geneset_name": "third geneset"},
-                    {"genes": [], "geneset_description": "fourth description", "geneset_name": "fourth_geneset"},
+                    {"genes": [], "geneset_description": "", "geneset_name": "third gene set"},
+                    {"genes": [], "geneset_description": "fourth description", "geneset_name": "fourth_gene_set"},
                     {"genes": [], "geneset_description": "", "geneset_name": "fifth_dataset"},
                 ],
                 "tid": 0,
@@ -522,14 +522,14 @@ class EndPointsAnnDataGenesets(unittest.TestCase, EndPoints):
         self.assertEqual(result.headers["Content-Type"], "text/csv")
         self.assertEqual(
             result.text,
-            """geneset_name,geneset_description,gene_symbol,gene_description\r
-first geneset name,a description,F5,a gene_description\r
-first geneset name,a description,SUMO3,\r
-first geneset name,a description,SRM,\r
-second geneset,,RER1,\r
-second geneset,,SIK1,\r
-third geneset,,,\r
-fourth_geneset,fourth description,,\r
+            """gene_set_name,gene_set_description,gene_symbol,gene_description\r
+first gene set name,a description,F5,a gene_description\r
+first gene set name,a description,SUMO3,\r
+first gene set name,a description,SRM,\r
+second gene set,,RER1,\r
+second gene set,,SIK1,\r
+third gene set,,,\r
+fourth_gene_set,fourth description,,\r
 fifth_dataset,,,\r
 """,
         )