fix getitem implementation, add test #99

pipestat/pipestat.py

@@ -220,7 +220,7 @@ def __str__(self):
         res += f"\nStatus Schema key: {self.cfg[STATUS_SCHEMA_KEY]}"
         res += f"\nResults formatter: {str(self.cfg[RESULT_FORMATTER].__name__)}"
         res += f"\nResults schema source: {self.cfg[SCHEMA_PATH]}"
-        res += f"\nStatus schema source: {self.status_schema_source}"
+        res += f"\nStatus schema source: {self.cfg[STATUS_SCHEMA_SOURCE_KEY]}"
         res += f"\nRecords count: {self.record_count}"
         if self.cfg[SCHEMA_PATH] is not None:
             high_res = self.highlighted_results
@@ -231,15 +231,15 @@ def __str__(self):
         return res
 
     def __getitem__(self, key):
-        # return self.cfg[self._keytransform(key)]
-        print(key)
+        # This is a wrapper for the retrieve function:
+        result = self.retrieve(record_identifier=key)
+        return result
 
     def __setitem__(self, key, value):
         # This is a wrapper for the report function:
         result = self.report(record_identifier=key, values=value)
         return result
 
-
     def __delitem__(self, key):
         del self.cfg[self._keytransform(key)]
 
@@ -488,7 +488,7 @@ def remove(
         :return bool: whether the result has been removed
         """
 
-        r_id = record_identifier or self.record_identifier
+        r_id = record_identifier or self.cfg[RECORD_IDENTIFIER]
         return self.backend.remove(
             record_identifier=r_id,
             result_identifier=result_identifier,
@@ -518,7 +518,7 @@ def report(
         :return str reported_results: return list of formatted string
         """
 
-        result_formatter = result_formatter or self[RESULT_FORMATTER]
+        result_formatter = result_formatter or self.cfg[RESULT_FORMATTER]
         values = deepcopy(values)
         r_id = record_identifier or self.cfg[RECORD_IDENTIFIER]
         if r_id is None:
@@ -595,7 +595,7 @@ def retrieve(
                     record_identifier, result_identifier, limit, offset
                 )
 
-        r_id = record_identifier or self.record_identifier
+        r_id = record_identifier or self.cfg[RECORD_IDENTIFIER]
 
         return self.backend.retrieve(r_id, result_identifier)
 

pipestat/reports.py

@@ -384,7 +384,7 @@ def create_sample_html(self, sample_stats, navbar, footer, sample_name):
                 flag = flag_dict["flag"]
         highlighted_results = fetch_pipeline_results(
             project=self.prj,
-            pipeline_name=self.prj.pipeline_name,
+            pipeline_name=self.prj.cfg[PIPELINE_NAME],
             sample_name=sample_name,
             inclusion_fun=lambda x: x == "file",
             highlighted=True,
@@ -482,7 +482,7 @@ def create_index_html(self, navbar, footer):
         # Add stats_summary.tsv button link
         stats_file_path = get_file_for_project(
             prj=self.prj,
-            pipeline_name=self.prj.pipeline_name,
+            pipeline_name=self.prj.cfg[PIPELINE_NAME],
             appendix="stats_summary.tsv",
             reportdir=self.reports_dir,
         )
@@ -495,7 +495,7 @@ def create_index_html(self, navbar, footer):
         # Add objects_summary.yaml button link
         objs_file_path = get_file_for_project(
             prj=self.prj,
-            pipeline_name=self.prj.pipeline_name,
+            pipeline_name=self.prj.cfg[PIPELINE_NAME],
             appendix="objs_summary.yaml",
             reportdir=self.reports_dir,
         )
@@ -548,7 +548,7 @@ def create_index_html(self, navbar, footer):
         )
         # Create status page with each sample's status listed
         status_tab = create_status_table(
-            pipeline_name=self.prj.pipeline_name,
+            pipeline_name=self.prj.cfg[PIPELINE_NAME],
             project=self.prj,
             pipeline_reports_dir=self.pipeline_reports,
         )
@@ -571,8 +571,8 @@ def create_index_html(self, navbar, footer):
             columns=columns,
             columns_json=dumps(columns),
             table_row_data=table_row_data,
-            project_name=self.prj.project_name,
-            pipeline_name=self.prj.pipeline_name,
+            project_name=self.prj.cfg[PROJECT_NAME],
+            pipeline_name=self.prj.cfg[PIPELINE_NAME],
             stats_json=self._stats_to_json_str(),
             footer=footer,
             amendments="",
@@ -619,7 +619,7 @@ def _stats_to_json_str(self):
             results[sample_name] = fetch_pipeline_results(
                 project=self.prj,
                 sample_name=sample_name,
-                pipeline_name=self.prj.pipeline_name,
+                pipeline_name=self.prj.cfg[PIPELINE_NAME],
                 inclusion_fun=lambda x: x not in OBJECT_TYPES,
                 casting_fun=str,
             )
@@ -983,10 +983,10 @@ def get_file_for_project(prj, pipeline_name, appendix=None, directory=None, repo
         output_dir = output_dir or results_file_path or config_path
         output_dir = os.path.dirname(output_dir)
         reportdir = os.path.join(output_dir, "reports")
-    if prj["project_name"] is None:
+    if prj.cfg["project_name"] is None:
         fp = os.path.join(reportdir, directory or "", f"NO_PROJECT_NAME_{pipeline_name}")
     else:
-        fp = os.path.join(reportdir, directory or "", f"{prj['project_name']}_{pipeline_name}")
+        fp = os.path.join(reportdir, directory or "", f"{prj.cfg['project_name']}_{pipeline_name}")
 
     if hasattr(prj, "amendments") and getattr(prj, "amendments"):
         fp += f"_{'_'.join(prj.amendments)}"
@@ -1040,7 +1040,7 @@ def _create_stats_objs_summaries(prj, pipeline_name) -> List[str]:
     reported_stats = []
     stats = []
 
-    if prj.pipeline_type == "sample":
+    if prj.cfg[PIPELINE_TYPE] == "sample":
         columns = ["Sample Index", "Sample Name", "Results"]
     else:
         columns = ["Sample Index", "Project Name", "Sample Name", "Results"]
@@ -1051,7 +1051,7 @@ def _create_stats_objs_summaries(prj, pipeline_name) -> List[str]:
         record_index += 1
         record_name = record
 
-        if prj.pipeline_type == "sample":
+        if prj.cfg[PIPELINE_TYPE] == "sample":
             reported_stats = [record_index, record_name]
             rep_data = prj.retrieve(record_identifier=record_name)
         else:

tests/test_pipestat.py

@@ -204,13 +204,13 @@ def test_report_basic(
     )
     @pytest.mark.parametrize("backend", ["file", "db"])
     def test_report_setitem(
-            self,
-            rec_id,
-            val,
-            config_file_path,
-            schema_file_path,
-            results_file_path,
-            backend,
+        self,
+        rec_id,
+        val,
+        config_file_path,
+        schema_file_path,
+        results_file_path,
+        backend,
     ):
         with NamedTemporaryFile() as f, ContextManagerDBTesting(DB_URL):
             results_file_path = f.name
@@ -222,16 +222,16 @@ def test_report_setitem(
             )
             args.update(backend_data)
             psm = SamplePipestatManager(**args)
-            #psm.report(record_identifier=rec_id, values=val, force_overwrite=True)
+            # psm.report(record_identifier=rec_id, values=val, force_overwrite=True)
             psm[rec_id] = val
             if backend == "file":
                 print(psm.backend._data[STANDARD_TEST_PIPE_ID])
                 print("Test if", rec_id, " is in ", psm.backend._data[STANDARD_TEST_PIPE_ID])
                 assert rec_id in psm.backend._data[STANDARD_TEST_PIPE_ID][PROJECT_SAMPLE_LEVEL]
                 print("Test if", list(val.keys())[0], " is in ", rec_id)
                 assert (
-                        list(val.keys())[0]
-                        in psm.backend._data[STANDARD_TEST_PIPE_ID][PROJECT_SAMPLE_LEVEL][rec_id]
+                    list(val.keys())[0]
+                    in psm.backend._data[STANDARD_TEST_PIPE_ID][PROJECT_SAMPLE_LEVEL][rec_id]
                 )
                 if backend == "file":
                     assert_is_in_files(results_file_path, str(list(val.values())[0]))
@@ -438,6 +438,40 @@ def test_retrieve_basic(
             # Test Retrieve Whole Record
             assert isinstance(psm.retrieve(record_identifier=rec_id), Mapping)
 
+    @pytest.mark.parametrize(
+        ["rec_id", "val"],
+        [
+            ("sample1", {"name_of_something": "test_name"}),
+            ("sample1", {"number_of_things": 2}),
+        ],
+    )
+    @pytest.mark.parametrize("backend", ["file", "db"])
+    def test_retrieve_getitem(
+        self,
+        rec_id,
+        val,
+        config_file_path,
+        results_file_path,
+        schema_file_path,
+        backend,
+    ):
+        with NamedTemporaryFile() as f, ContextManagerDBTesting(DB_URL):
+            results_file_path = f.name
+            args = dict(schema_path=schema_file_path, database_only=False)
+            backend_data = (
+                {"config_file": config_file_path}
+                if backend == "db"
+                else {"results_file_path": results_file_path}
+            )
+            args.update(backend_data)
+            psm = SamplePipestatManager(**args)
+            psm.report(record_identifier=rec_id, values=val, force_overwrite=True)
+            retrieved_val = psm[rec_id]
+            # Test Retrieve Basic
+            assert str(retrieved_val[str(list(retrieved_val.keys())[0])]) == str(
+                list(val.values())[0]
+            )
+
     @pytest.mark.parametrize("backend", ["file", "db"])
     def test_retrieve_multiple(
         self,