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

* remove dead code

* rename geneset to gene_set

client/src/actions/annotation.js

@@ -411,7 +411,6 @@ export const saveGenesetsAction = () => async (dispatch, getState) => {
   const tid = (lastTid ?? 0) + 1;
   const genesets = [];
   for (const [name, gs] of lastGenesets) {
-    // const genes = Array.from(gs.genes.values());
     const genes = [];
     for (const g of gs.genes.values()) {
       genes.push({

local_server/cli/launch.py

@@ -42,7 +42,7 @@ def annotation_args(func):
         multiple=False,
         metavar="<directory path>",
         help="Directory of where to save output annotations; filename will be specified in the application. "
-        "Incompatible with --annotations-file and --genesets-file.",
+        "Incompatible with --annotations-file and --gene-sets-file.",
     )
     @click.option(
         "--experimental-annotations-ontology",
@@ -59,16 +59,16 @@ def annotation_args(func):
         help="Location of OBO file defining cell annotation autosuggest terms.",
     )
     @click.option(
-        "--disable-genesets-save",
+        "--disable-gene-sets-save",
         is_flag=True,
-        default=DEFAULT_CONFIG.dataset_config.user_annotations__genesets__readonly,
+        default=DEFAULT_CONFIG.dataset_config.user_annotations__gene_sets__readonly,
         show_default=False,
         help="Disable saving gene sets. If disabled, users will be able to make changes to gene sets but all "
         "changes will be lost on browser refresh.",
     )
     @click.option(
-        "--genesets-file",
+        "--gene-sets-file",
-        default=DEFAULT_CONFIG.dataset_config.user_annotations__local_file_csv__genesets_file,
+        default=DEFAULT_CONFIG.dataset_config.user_annotations__local_file_csv__gene_sets_file,
         show_default=True,
         multiple=False,
         metavar="<path>",
@@ -334,8 +334,8 @@ def launch(
     disable_annotations,
     annotations_file,
     user_generated_data_dir,
-    genesets_file,
+    gene_sets_file,
-    disable_genesets_save,
+    disable_gene_sets_save,
     backed,
     disable_diffexp,
     experimental_annotations_ontology,
@@ -394,8 +394,8 @@ def launch(
             user_annotations__enable=not disable_annotations,
             user_annotations__local_file_csv__file=annotations_file,
             user_annotations__local_file_csv__directory=user_generated_data_dir,
-            user_annotations__local_file_csv__genesets_file=genesets_file,
+            user_annotations__local_file_csv__gene_sets_file=gene_sets_file,
-            user_annotations__genesets__readonly=disable_genesets_save,
+            user_annotations__gene_sets__readonly=disable_gene_sets_save,
             user_annotations__ontology__enable=experimental_annotations_ontology,
             user_annotations__ontology__obo_location=experimental_annotations_ontology_obo,
             presentation__max_categories=max_category_items,

local_server/common/annotations/annotations.py

@@ -21,15 +21,15 @@ class Annotations(metaclass=ABCMeta):
     def user_annotations_enabled(self):
         return self.config.get("user-annotations", False)
 
-    def genesets_save_enabled(self):
+    def gene_sets_save_enabled(self):
         return self.config.get("genesets-save", False)
 
     def check_user_annotations_enabled(self):
         if not self.user_annotations_enabled():
             raise DisabledFeatureError("User annotations are disabled.")
 
-    def check_genesets_save_enabled(self):
+    def check_gene_sets_save_enabled(self):
-        if not self.genesets_save_enabled():
+        if not self.gene_sets_save_enabled():
             raise DisabledFeatureError("User genesets save is disabled.")
 
     def load_ontology(self, path):
@@ -80,12 +80,12 @@ class Annotations(metaclass=ABCMeta):
         pass
 
     @abstractmethod
-    def read_genesets(self, data_adaptor):
+    def read_gene_sets(self, data_adaptor):
         """Return the genesets from persistent storage """
         pass
 
     @abstractmethod
-    def write_genesets(self, gs, data_adaptor):
+    def write_gene_sets(self, gs, data_adaptor):
         """Write the genesets (gs) to a persistent storage such that it can later be read"""
         pass
 
@@ -95,16 +95,16 @@ class Annotations(metaclass=ABCMeta):
         pass
 
     Genesets_Header = [
-        "geneset_name",
+        "gene_set_name",
-        "geneset_description",
+        "gene_set_description",
         "gene_symbol",
         "gene_description",
     ]
 
     @staticmethod
-    def genesets_to_csv(genesets):
+    def gene_sets_to_csv(genesets):
         """
-        Convert the internal genesets format (returned by read_geneset) into
+        Convert the internal genesets format (returned by read_gene_set) into
         the simple Tidy CSV.
         """
         from io import StringIO
@@ -136,9 +136,9 @@ class Annotations(metaclass=ABCMeta):
             return sio.getvalue()
 
     @staticmethod
-    def genesets_to_response(genesets):
+    def gene_sets_to_response(genesets):
         """
-        Convert the internal genesets format (returned by read_geneset) into
+        Convert the internal genesets format (returned by read_gene_set) into
         the dict expected by the JSON REST API
         """
         return list(genesets.values())

local_server/common/annotations/local_file_csv.py

@@ -17,14 +17,14 @@ from local_server.common.errors import AnnotationsError, ObsoleteRequest
 class AnnotationsLocalFile(Annotations):
     CXG_ANNO_COLLECTION = "cxg_anno_collection"
 
-    def __init__(self, config, output_dir, label_output_file, genesets_output_file):
+    def __init__(self, config, output_dir, label_output_file, gene_sets_output_file):
         super().__init__(config)
         self.output_dir = output_dir
         self.label_output_file = label_output_file
-        self.genesets_output_file = genesets_output_file
+        self.gene_sets_output_file = gene_sets_output_file
         # lock used to protect label file write ops
         self.label_lock = threading.RLock()
-        self.genesets_lock = threading.RLock()
+        self.gene_sets_lock = threading.RLock()
 
         # cache the most recent annotations.
         self.last_fname = None
@@ -105,29 +105,29 @@ class AnnotationsLocalFile(Annotations):
             self.last_fname = fname
             self.last_labels = df
 
-    def read_genesets(self, data_adaptor, context=None):
+    def read_gene_sets(self, data_adaptor, context=None):
         if has_request_context():
             if not current_app.auth.is_user_authenticated():
                 return ({}, self.last_geneset_tid)
 
         fname = self._get_genesets_filename(data_adaptor)
-        genesets = {}
+        gene_sets = {}
         tid = None
-        with self.genesets_lock:
+        with self.gene_sets_lock:
             tid = self.last_geneset_tid  # inside the critical section
             if fname is not None and os.path.exists(fname) and os.path.getsize(fname) > 0:
                 with open(fname, newline="") as f:
-                    genesets = read_geneset_tidycsv(f, context)
+                    gene_sets = read_gene_set_tidycsv(f, context)
 
-        return (genesets, tid)
+        return (gene_sets, tid)
 
-    def write_genesets(self, genesets, tid, data_adaptor):
+    def write_gene_sets(self, gene_sets, tid, data_adaptor):
-        self.check_genesets_save_enabled()  # raises
+        self.check_gene_sets_save_enabled()  # raises
 
         if type(tid) != int or tid < 0:
             raise ValueError("tid must be a positive integer")
 
-        with self.genesets_lock:
+        with self.gene_sets_lock:
             # skip if the request is stale
             if tid is not None:
                 if tid <= self.last_geneset_tid:
@@ -137,7 +137,7 @@ class AnnotationsLocalFile(Annotations):
             lastmod = data_adaptor.get_last_mod_time()
             lastmodstr = "'unknown'" if lastmod is None else lastmod.isoformat(timespec="seconds")
             header = (
-                f"# Geneset generated on {datetime.now().isoformat(timespec='seconds')} "
+                f"# Gene set generated on {datetime.now().isoformat(timespec='seconds')} "
                 f"using cellxgene version {cellxgene_version}\n"
                 f"# Input data file was {data_adaptor.get_location()}, "
                 f"which was last modified on {lastmodstr}\n"
@@ -147,7 +147,7 @@ class AnnotationsLocalFile(Annotations):
             self._backup(fname)
             with open(fname, "w", newline="") as f:
                 f.write(header)
-                f.write(self.genesets_to_csv(genesets))
+                f.write(self.gene_sets_to_csv(gene_sets))
 
     def _get_userdata_idhash(self, data_adaptor):
         """
@@ -163,7 +163,7 @@ class AnnotationsLocalFile(Annotations):
         if self.output_dir:
             return self.output_dir
 
-        output_file = self.label_output_file or self.genesets_output_file
+        output_file = self.label_output_file or self.gene_sets_output_file
         if output_file:
             return os.path.dirname(os.path.abspath(output_file))
 
@@ -177,9 +177,9 @@ class AnnotationsLocalFile(Annotations):
         return self._get_filename(data_adaptor, "celllabels")
 
     def _get_genesets_filename(self, data_adaptor):
-        """ return the current genesets file name """
+        """ return the current gene sets file name """
-        if self.genesets_output_file:
+        if self.gene_sets_output_file:
-            return self.genesets_output_file
+            return self.gene_sets_output_file
 
         return self._get_filename(data_adaptor, "genesets")
 
@@ -236,7 +236,7 @@ class AnnotationsLocalFile(Annotations):
     def update_parameters(self, parameters, data_adaptor):
         params = {}
         params["annotations"] = self.user_annotations_enabled()
-        params["annotations_genesets_readonly"] = not self.genesets_save_enabled()
+        params["annotations_genesets_readonly"] = not self.gene_sets_save_enabled()
         params["user_annotation_collection_name_enabled"] = True
 
         if self.ontology_data:
@@ -263,7 +263,7 @@ class AnnotationsLocalFile(Annotations):
         parameters.update(params)
 
 
-def read_geneset_tidycsv(f, context=None):
+def read_gene_set_tidycsv(f, context=None):
     """
     Read & parse the Tidy CSV format, applying validation checks for mandatory
     values, and de-duping rules.
@@ -271,9 +271,9 @@ def read_geneset_tidycsv(f, context=None):
     Format is a four-column CSV, with a mandatory header row, and optional "#" prefixed
     comments.  Format:
 
-        geneset_name, geneset_description, gene_symbol, gene_description
+        gene_set_name, gene_set_description, gene_symbol, gene_description
 
-    geneset_name and gene_symbol must be non-null; others are optional.
+    gene_set_name must be non-null; others are optional.
 
     Returns: a dictionary of the shape (values in angle-brackets vary):
 
@@ -305,7 +305,7 @@ def read_geneset_tidycsv(f, context=None):
     messagefn = context["messagefn"] if context else (lambda x: None)
 
     reader = csv.reader(f, dialect=myDialect())
-    genesets = {}
+    gene_sets = {}
     haveReadHeader = False
     lineno = 0
     for row in reader:
@@ -329,10 +329,10 @@ def read_geneset_tidycsv(f, context=None):
         if (not gene_symbol) and gene_description:
             messagefn(f"Warning: Missing gene name in geneset name {geneset_name} on line {lineno}.")
 
-        if geneset_name in genesets:
+        if geneset_name in gene_sets:
-            gs = genesets[geneset_name]
+            gs = gene_sets[geneset_name]
         else:
-            gs = genesets[geneset_name] = {
+            gs = gene_sets[geneset_name] = {
                 "geneset_name": geneset_name,
                 "geneset_description": geneset_description,
                 "genes": [],
@@ -349,4 +349,4 @@ def read_geneset_tidycsv(f, context=None):
                 }
             )
 
-    return genesets
+    return gene_sets

local_server/common/config/client_config.py

@@ -45,7 +45,7 @@ def get_client_config(app_config, data_adaptor):
         "annotations_file": None,
         "annotations_dir": None,
         "annotations_genesets": True,  # feature flag
-        "annotations_genesets_readonly": dataset_config.user_annotations__genesets__readonly,
+        "annotations_genesets_readonly": dataset_config.user_annotations__gene_sets__readonly,
         "annotations_genesets_summary_methods": ["mean"],
         "annotations_cell_ontology_enabled": False,
         "annotations_cell_ontology_obopath": None,

local_server/common/config/dataset_config.py

@@ -32,9 +32,9 @@ class DatasetConfig(BaseConfig):
             self.user_annotations__ontology__obo_location = default_config["user_annotations"]["ontology"][
                 "obo_location"
             ]
-            self.user_annotations__genesets__readonly = default_config["user_annotations"]["genesets"]["readonly"]
+            self.user_annotations__gene_sets__readonly = default_config["user_annotations"]["gene_sets"]["readonly"]
-            self.user_annotations__local_file_csv__genesets_file = default_config["user_annotations"]["local_file_csv"][
+            self.user_annotations__local_file_csv__gene_sets_file = default_config["user_annotations"]["local_file_csv"][
-                "genesets_file"
+                "gene_sets_file"
             ]
 
             self.embeddings__names = default_config["embeddings"]["names"]
@@ -99,15 +99,15 @@ class DatasetConfig(BaseConfig):
             "user_annotations__local_file_csv__file", (type(None), str)
         )
         self.validate_correct_type_of_configuration_attribute(
-            "user_annotations__local_file_csv__genesets_file", (type(None), str)
+            "user_annotations__local_file_csv__gene_sets_file", (type(None), str)
         )
         self.validate_correct_type_of_configuration_attribute("user_annotations__ontology__enable", bool)
         self.validate_correct_type_of_configuration_attribute(
             "user_annotations__ontology__obo_location", (type(None), str)
         )
-        self.validate_correct_type_of_configuration_attribute("user_annotations__genesets__readonly", bool)
+        self.validate_correct_type_of_configuration_attribute("user_annotations__gene_sets__readonly", bool)
 
-        if self.user_annotations__enable or not self.user_annotations__genesets__readonly:
+        if self.user_annotations__enable or not self.user_annotations__gene_sets__readonly:
             server_config = self.app_config.server_config
             if not self.app__authentication_enable:
                 raise ConfigurationError("user annotations requires authentication to be enabled")
@@ -134,7 +134,7 @@ class DatasetConfig(BaseConfig):
     def handle_local_file_csv_annotations(self, context):
         dirname = self.user_annotations__local_file_csv__directory
         filename = self.user_annotations__local_file_csv__file
-        genesets_filename = self.user_annotations__local_file_csv__genesets_file
+        genesets_filename = self.user_annotations__local_file_csv__gene_sets_file
 
         if dirname is not None and (filename is not None or genesets_filename is not None):
             raise ConfigurationError(
@@ -159,7 +159,7 @@ class DatasetConfig(BaseConfig):
 
         anno_config = {
             "user-annotations": self.user_annotations__enable,
-            "genesets-save": not self.user_annotations__genesets__readonly,
+            "genesets-save": not self.user_annotations__gene_sets__readonly,
         }
         self.user_annotations = AnnotationsLocalFile(anno_config, dirname, filename, genesets_filename)
 
@@ -170,9 +170,9 @@ class DatasetConfig(BaseConfig):
             data_adaptor = self.get_data_adaptor()
             if self.user_annotations__local_file_csv__file:
                 data_adaptor.check_new_labels(self.user_annotations.read_labels(data_adaptor))
-            if self.user_annotations__local_file_csv__genesets_file:
+            if self.user_annotations__local_file_csv__gene_sets_file:
                 try:
-                    data_adaptor.check_new_genesets(self.user_annotations.read_genesets(data_adaptor, context), context)
+                    data_adaptor.check_new_gene_sets(self.user_annotations.read_gene_sets(data_adaptor, context), context)
                 except (ValueError, AnnotationsError, KeyError) as e:
                     raise ConfigurationError(f"Unable to read genesets CSV file: {str(e)}") from e
 

local_server/common/rest.py

@@ -336,11 +336,11 @@ def genesets_get(request, data_adaptor):
 
     try:
         annotations = data_adaptor.dataset_config.user_annotations
-        (genesets, tid) = data_adaptor.check_new_genesets(annotations.read_genesets(data_adaptor))
+        (genesets, tid) = data_adaptor.check_new_gene_sets(annotations.read_gene_sets(data_adaptor))
 
         if preferred_mimetype == "text/csv":
             return make_response(
-                annotations.genesets_to_csv(genesets),
+                annotations.gene_sets_to_csv(genesets),
                 HTTPStatus.OK,
                 {
                     "Content-Type": "text/csv",
@@ -349,7 +349,7 @@ def genesets_get(request, data_adaptor):
             )
         else:
             return make_response(
-                jsonify({"genesets": annotations.genesets_to_response(genesets), "tid": tid}), HTTPStatus.OK
+                jsonify({"genesets": annotations.gene_sets_to_response(genesets), "tid": tid}), HTTPStatus.OK
             )
     except (ValueError, KeyError, AnnotationsError) as e:
         return abort_and_log(HTTPStatus.BAD_REQUEST, str(e))
@@ -357,7 +357,7 @@ def genesets_get(request, data_adaptor):
 
 def genesets_put(request, data_adaptor):
     annotations = data_adaptor.dataset_config.user_annotations
-    if not annotations.genesets_save_enabled():
+    if not annotations.gene_sets_save_enabled():
         return abort(HTTPStatus.NOT_IMPLEMENTED)
 
     anno_collection = request.args.get("annotation-collection-name", default=None)
@@ -373,8 +373,8 @@ def genesets_put(request, data_adaptor):
         if genesets is None:
             abort(HTTPStatus.BAD_REQUEST)
 
-        (gs, _) = data_adaptor.check_new_genesets((genesets, tid))
+        (gs, _) = data_adaptor.check_new_gene_sets((genesets, tid))
-        annotations.write_genesets(gs, tid, data_adaptor)
+        annotations.write_gene_sets(gs, tid, data_adaptor)
         return make_response(jsonify({"status": "OK"}), HTTPStatus.OK)
     except (ValueError, DisabledFeatureError, KeyError) as e:
         return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)

local_server/data_common/data_adaptor.py

@@ -262,7 +262,7 @@ class DataAdaptor(metaclass=ABCMeta):
 
         return labels_df
 
-    def check_new_genesets(self, args, context=None):
+    def check_new_gene_sets(self, args, context=None):
         """
         Check validity of gene sets, return if correct, else raise error.
         May also modify the gene set for conditions that should be resolved,

local_server/default_config.py

@@ -64,12 +64,12 @@ dataset:
     local_file_csv:
       directory: null
       file: null            # annotations file name
-      genesets_file: null   # gene sets file name
+      gene_sets_file: null  # gene sets file name
     ontology:
       enable: false
       obo_location: null
-    genesets:
+    gene_sets:
-      readonly: false      # genesets CRUD enabled/disabled
+      readonly: false       # gene sets CRUD enabled/disabled
 
   embeddings:
     names : []

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:
+    gene_sets:
-      readonly: {genesets_readonly}
+      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
+gene_set_name, gene_set_description, gene_symbol, gene_description
-first geneset name,,F5, a gene_description
+first gene set name,,F5, a gene_description
-first geneset name,a description, NO_SUCH_GENE, non-existent gene
+first gene set name,a description, NO_SUCH_GENE, non-existent gene
-first geneset name,a description, F5, duplicate gene
+first gene set name,a description, F5, duplicate gene
-first geneset name, a description, SUMO3,
+first gene set name, a description, SUMO3,
-first geneset name,, SRM,
+first gene set name,, SRM,
-second geneset,,RER1
+second gene set,,RER1
-second geneset,,SIK1
+second gene set,,SIK1
-third geneset,,NO_SUCH_GENE
+third gene set,,NO_SUCH_GENE
-fourth_geneset,fourth description,,gene intentionally missing
+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": "", "geneset_name": "third gene set"},
-                    {"genes": [], "geneset_description": "fourth description", "geneset_name": "fourth_geneset"},
+                    {"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
+            """gene_set_name,gene_set_description,gene_symbol,gene_description\r
-first geneset name,a description,F5,a gene_description\r
+first gene set name,a description,F5,a gene_description\r
-first geneset name,a description,SUMO3,\r
+first gene set name,a description,SUMO3,\r
-first geneset name,a description,SRM,\r
+first gene set name,a description,SRM,\r
-second geneset,,RER1,\r
+second gene set,,RER1,\r
-second geneset,,SIK1,\r
+second gene set,,SIK1,\r
-third geneset,,,\r
+third gene set,,,\r
-fourth_geneset,fourth description,,\r
+fourth_gene_set,fourth description,,\r
 fifth_dataset,,,\r
 """,
         )