Initial wip for pepkit/looper#82

pipestat/reports.py

@@ -647,6 +647,17 @@ def create_index_html(self, navbar, footer):
         )
 
         project_objects = self.create_project_objects()
+
+        if self.looper_samples:
+            try:
+                sources = self.looper_samples[0]._mapped_attr["_project"].config["sample_modifiers"]['derive']['sources']
+                derived_table = self.create_derived_table(derived_attributes=sources)
+            except KeyError:
+                # No sample modifers or sources, so just pass
+                derived_table = None
+        else:
+            derived_table = None
+
         columns = ["Record Identifiers"] + list(sorted_sample_stat_results.keys())
         template_vars = dict(
             navbar=navbar,
@@ -668,6 +679,16 @@ def create_index_html(self, navbar, footer):
             render_jinja_template("index.html", self.jinja_env, template_vars),
         )
 
+    def create_derived_table(self, derived_attributes):
+        print("Placeholder")
+        if derived_attributes:
+            for k,v in derived_attributes.items():
+                print(f"{k}     {v}")
+
+
+        return None
+
+
     def create_project_objects(self):
         """
         Render available project level outputs defined in the

tests/test_pipestat.py

@@ -2132,3 +2132,36 @@ def test_multi_results_summarize(
             psm.summarize()
             data = YAMLConfigManager(filepath=os.path.join(temp_dir, "aggregate_results.yaml"))
             assert r_id in data[psm.pipeline_name][psm.pipeline_type].keys()
+
+    @pytest.mark.parametrize("backend", ["file"])
+    def test_temp(
+        self,
+        config_file_path,
+        results_file_path,
+        recursive_schema_file_path,
+        backend,
+        range_values,
+    ):
+        # This is for temporary PEATAC testing for determining summarize function
+        with TemporaryDirectory() as d, ContextManagerDBTesting(DB_URL):
+            temp_dir = d
+            # single_results_file_path = "{record_identifier}/results.yaml"
+            # results_file_path = os.path.join(temp_dir, single_results_file_path)
+            # args = dict(schema_path=recursive_schema_file_path, database_only=False)
+            # n = 3
+            config_file_path = "/home/drc/pepatac_tutorial/processed/looper_pipestat_config.yaml"
+
+            # for i in range_values[:n]:
+            #     r_id = i[0]
+            #     val = i[1]
+            #     backend_data = {"record_identifier": r_id, "results_file_path": results_file_path}
+            #     args.update(backend_data)
+            #     psm = SamplePipestatManager(**args)
+            #     psm.report(record_identifier=r_id, values=val, force_overwrite=True)
+            psm = PipestatManager(config_file=config_file_path)
+            reportlink = psm.summarize()
+            print(reportlink)
+            statstsv = psm.table()
+            print(statstsv)
+            # data = YAMLConfigManager(filepath=os.path.join(temp_dir, "aggregate_results.yaml"))
+            # assert r_id in data[psm.pipeline_name][psm.pipeline_type].keys()