fix #211 spaces in html files

pipestat/reports.py

@@ -173,7 +173,7 @@ def create_object_parent_html(self, navbar, footer):
                 else ""
             )
             labels.append(f"<b>{key.replace('_', ' ')}</b>: {desc}")
-            page_path = os.path.join(self.pipeline_reports, f"{key}.html".lower())
+            page_path = os.path.join(self.pipeline_reports, f"{key}.html".replace(" ", "_").lower())
             pages.append(os.path.relpath(page_path, self.pipeline_reports))
 
         template_vars = dict(
@@ -364,7 +364,7 @@ def create_object_htmls(self, navbar, footer):
             os.makedirs(self.pipeline_reports)
         for file_result in file_results:
             links = []
-            html_page_path = os.path.join(self.pipeline_reports, f"{file_result}.html".lower())
+            html_page_path = os.path.join(self.pipeline_reports, f"{file_result}.html".replace(" ", "_").lower())
 
             pipeline_types = ["sample", "project"]
 
@@ -511,8 +511,7 @@ def create_sample_html(self, sample_stats, navbar, footer, sample_name):
         """
         if not os.path.exists(self.pipeline_reports):
             os.makedirs(self.pipeline_reports)
-        html_page = os.path.join(self.pipeline_reports, f"{sample_name}.html".lower())
-
+        html_page = os.path.join(self.pipeline_reports, f"{sample_name}.html".replace(" ", "_").lower())
         if self.prj.cfg["multi_result_files"] is True:
             self.prj.cfg["record_identifier"] = sample_name
             temp_result_file_path = mkabs(
@@ -978,7 +977,7 @@ 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(" ", "%20").lower()
+                self.pipeline_reports, (obj_id + ".html").replace(" ", "_").lower()
             )
             relpaths.append(_make_relpath(page_name, wd, context))
         return relpaths, displayable_ids
@@ -997,7 +996,7 @@ 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(" ", "%20").lower(),
+                    f"{sample_name}.html".replace(" ", "_").lower(),
                 )
                 relpaths.append(_make_relpath(page_name, wd, context))
                 sample_names.append(sample_name)

tests/data/output_schema_html_report.yaml

@@ -18,6 +18,9 @@ properties:
       switch_value:
         type: boolean
         description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras pharetra."
+      output file with spaces:
+        $ref: "#/$defs/file"
+        description: "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Fusce nec cursus nulla."
   samples:
     type: array
     items:

tests/test_pipestat.py

@@ -1339,6 +1339,54 @@ def test_zip_html_report_portable(
 
             assert len(zip_files) > 0
 
+    @pytest.mark.parametrize("backend", ["file", "db"])
+    def test_report_spaces_in_record_identifiers(
+        self,
+        config_file_path,
+        output_schema_html_report,
+        results_file_path,
+        backend,
+        values_project,
+    ):
+        with NamedTemporaryFile() as f, ContextManagerDBTesting(DB_URL):
+            results_file_path = f.name
+            args = dict(schema_path=output_schema_html_report, database_only=False)
+            backend_data = (
+                {"config_file": config_file_path}
+                if backend == "db"
+                else {"results_file_path": results_file_path}
+            )
+            args.update(backend_data)
+            # project level
+            psm = ProjectPipestatManager(**args)
+
+            for i in values_project:
+                for r, v in i.items():
+                    psm.report(
+                        record_identifier=r,
+                        values=v,
+                        force_overwrite=True,
+                    )
+                    psm.set_status(record_identifier=r, status_identifier="running")
+
+            # Add record with sspace in name
+            r = "SAMPLE Three WITH SPACES"
+            psm.report( record_identifier=r,
+                        values={'name_of_something': 'name of something string'},
+                        force_overwrite=True,)
+            psm.set_status(record_identifier=r, status_identifier="completed")
+            r = "SAMPLE FOUR WITH Spaces"
+            psm.report( record_identifier=r,
+                        values={'output file with spaces': {"path":"here is path", "title":"here is a title"}},
+                        force_overwrite=True,)
+
+            htmlreportpath = psm.summarize(amendment="")
+
+            directory_path = os.path.dirname(htmlreportpath)
+            all_files = os.listdir(directory_path)
+
+            assert "sample_three_with_spaces.html" in all_files
+            assert "output_file_with_spaces.html" in all_files
 
 @pytest.mark.skipif(not DB_DEPENDENCIES, reason="Requires dependencies")
 @pytest.mark.skipif(SERVICE_UNAVAILABLE, reason="requires service X to be available")