replace spaces in names with %20 during html link generation

pipestat/backends/file_backend/filebackend.py

@@ -66,7 +66,6 @@ def __init__(
 
         self.determine_results_file(self.results_file_path)
 
-
     def determine_results_file(self, results_file_path: str) -> None:
         """Initialize or load results_file from given path
         :param str results_file_path: YAML file to report into, if file is
@@ -345,7 +344,6 @@ def report(
         # record_identifier = record_identifier or self.record_identifier
         record_identifier = record_identifier
 
-
         result_formatter = result_formatter or self.result_formatter
         results_formatted = []
         current_time = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
@@ -670,7 +668,7 @@ def _init_results_file(self) -> None:
     def aggregate_multi_results(self, results_directory):
         print(f"results directory {results_directory}")
         all_result_files = get_all_result_files(results_directory)
-        aggregate_results_file_path = os.path.join(results_directory,"aggregate_results.yaml")
+        aggregate_results_file_path = os.path.join(results_directory, "aggregate_results.yaml")
 
         # THIS WILL OVERWRITE self.results_file_path and self._data on the current psm!
         self.results_file_path = aggregate_results_file_path
@@ -683,9 +681,13 @@ def aggregate_multi_results(self, results_directory):
                 temp_data = YAMLConfigManager()
             if self.pipeline_name in temp_data:
                 if "project" in temp_data[self.pipeline_name]:
-                    self._data[self.pipeline_name]["project"].update(temp_data[self.pipeline_name]["project"])
+                    self._data[self.pipeline_name]["project"].update(
+                        temp_data[self.pipeline_name]["project"]
+                    )
                 if "sample" in temp_data[self.pipeline_name]:
-                    self._data[self.pipeline_name]["sample"].update(temp_data[self.pipeline_name]["sample"])
+                    self._data[self.pipeline_name]["sample"].update(
+                        temp_data[self.pipeline_name]["sample"]
+                    )
 
         with self._data as data_locked:
             data_locked.write()

pipestat/helpers.py

@@ -221,7 +221,6 @@ def force_symlink(file1, file2):
 
 
 def get_all_result_files(results_file_path):
-    files = glob.glob(results_file_path+'**/*.yaml')
+    files = glob.glob(results_file_path + "**/*.yaml")
     # get parent directory, glob all results files, build one results file return
     return files
-

pipestat/pipestat.py

@@ -198,12 +198,14 @@ def __init__(
             "pipeline_type", default="sample", override=pipeline_type
         )
 
-        self.cfg[FILE_KEY] = mk_abs_via_cfg(self.resolve_results_file_path(
-            self.cfg[CONFIG_KEY].priority_get(
-                "results_file_path",
-                env_var=ENV_VARS["results_file"],
-                override=results_file_path,
-            )),
+        self.cfg[FILE_KEY] = mk_abs_via_cfg(
+            self.resolve_results_file_path(
+                self.cfg[CONFIG_KEY].priority_get(
+                    "results_file_path",
+                    env_var=ENV_VARS["results_file"],
+                    override=results_file_path,
+                )
+            ),
             self.cfg["config_path"],
         )
 
@@ -290,16 +292,17 @@ def resolve_results_file_path(self, results_file_path):
         if results_file_path:
             assert isinstance(results_file_path, str), TypeError("Path is expected to be a str")
             if not self.record_identifier and "{record_identifier}" in results_file_path:
-                raise NotImplementedError(f"Must provide record identifier during PipestatManager creation for this results_file_path: {results_file_path}")
+                raise NotImplementedError(
+                    f"Must provide record identifier during PipestatManager creation for this results_file_path: {results_file_path}"
+                )
             self.cfg["unresolved_result_path"] = results_file_path
             return results_file_path.format(record_identifier=self.record_identifier)
         return results_file_path
-    def initialize_filebackend(self, record_identifier, results_file_path, flag_file_dir):
 
+    def initialize_filebackend(self, record_identifier, results_file_path, flag_file_dir):
         # Check if there will be multiple results_file_paths
         _LOGGER.debug(f"Determined file as backend: {results_file_path}")
 
-
         if self.cfg[DB_ONLY_KEY]:
             _LOGGER.debug(
                 "Running in database only mode does not make sense with a YAML file as a backend. "
@@ -760,7 +763,9 @@ def check_multi_results(self):
         if self.file and self.cfg["unresolved_result_path"] != self.file:
             if "{record_identifier}" in self.cfg["unresolved_result_path"]:
                 # assume there are multiple result files in sub-directories
-                results_directory = self.cfg["unresolved_result_path"].split("{record_identifier}")[0]
+                results_directory = self.cfg["unresolved_result_path"].split(
+                    "{record_identifier}"
+                )[0]
                 results_directory = mk_abs_via_cfg(results_directory, self.cfg["config_path"])
                 self.backend.aggregate_multi_results(results_directory)
 

pipestat/reports.py

@@ -638,7 +638,7 @@ def _get_navbar_dropdown_data_objects(self, objs, wd, context):
         for obj_id in objs:
             displayable_ids.append(obj_id.replace("_", " "))
             page_name = os.path.join(
-                self.pipeline_reports, (obj_id + ".html").replace(" ", "_").lower()
+                self.pipeline_reports, (obj_id + ".html").replace(" ", "%20").lower()
             )
             relpaths.append(_make_relpath(page_name, wd, context))
         return relpaths, displayable_ids
@@ -650,7 +650,7 @@ def _get_navbar_dropdown_data_samples(self, wd, context):
             sample_name = sample["record_identifier"]
             page_name = os.path.join(
                 self.pipeline_reports,
-                f"{sample_name}.html".replace(" ", "_").lower(),
+                f"{sample_name}.html".replace(" ", "%20").lower(),
             )
             relpaths.append(_make_relpath(page_name, wd, context))
             sample_names.append(sample_name)