fix pipeline_type for pipestat usage with consolidated pipelines, fix…

… remaning tests
pepkit · Jun 27, 2024 · 2d2475b · 2d2475b
1 parent 168f012
commit 2d2475b
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Showing 4 changed files with 16 additions and 15 deletions.
diff --git a/looper/cli_pydantic.py b/looper/cli_pydantic.py
@@ -243,7 +243,7 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
         # Check at the beginning if user wants to use pipestat and pipestat is configurable
         is_pipestat_configured = (
             prj._check_if_pipestat_configured(pipeline_type=PipelineLevel.PROJECT.value)
-            if getattr(subcommand_args, "project", None)
+            if getattr(subcommand_args, "project", None) or subcommand_name == "runp"
             else prj._check_if_pipestat_configured()
         )
 

diff --git a/looper/project.py b/looper/project.py
@@ -413,10 +413,12 @@ def _get_pipestat_configuration(self, pipeline_type=PipelineLevel.SAMPLE.value):
                 pipestat_config_path = self._check_for_existing_pipestat_config(piface)
 
                 if not pipestat_config_path:
-                    self._create_pipestat_config(piface)
+                    self._create_pipestat_config(piface, pipeline_type)
                 else:
                     piface.psm = PipestatManager(
-                        config_file=pipestat_config_path, multi_pipelines=True
+                        config_file=pipestat_config_path,
+                        multi_pipelines=True,
+                        pipeline_type="sample",
                     )
 
         elif pipeline_type == PipelineLevel.PROJECT.value:
@@ -426,10 +428,12 @@ def _get_pipestat_configuration(self, pipeline_type=PipelineLevel.SAMPLE.value):
                 )
 
                 if not pipestat_config_path:
-                    self._create_pipestat_config(prj_piface)
+                    self._create_pipestat_config(prj_piface, pipeline_type)
                 else:
                     prj_piface.psm = PipestatManager(
-                        config_file=pipestat_config_path, multi_pipelines=True
+                        config_file=pipestat_config_path,
+                        multi_pipelines=True,
+                        pipeline_type="project",
                     )
         else:
             _LOGGER.error(
@@ -469,7 +473,7 @@ def _check_for_existing_pipestat_config(self, piface):
         else:
             return None
 
-    def _create_pipestat_config(self, piface):
+    def _create_pipestat_config(self, piface, pipeline_type):
         """
         Each piface needs its own config file and associated psm
         """
@@ -512,11 +516,10 @@ def _create_pipestat_config(self, piface):
             pipestat_config_dict.update({"pipeline_name": piface.data["pipeline_name"]})
         else:
             pipeline_name = None
-        if "pipeline_type" in piface.data:
-            pipestat_config_dict.update({"pipeline_type": piface.data["pipeline_type"]})
 
         # Warn user if there is a mismatch in pipeline_names from sources!!!
         if pipeline_name != output_schema_pipeline_name:
+            # TODO Raise exception here.
             _LOGGER.warning(
                 msg=f"Pipeline name mismatch detected. Pipeline interface: {pipeline_name}  Output schema: {output_schema_pipeline_name}  Defaulting to pipeline_interface value."
             )

diff --git a/tests/smoketests/test_run.py b/tests/smoketests/test_run.py
@@ -162,8 +162,7 @@ def test_looper_single_pipeline(self, prep_temp_pep):
         with mod_yaml_data(tp) as config_data:
 
             pifaces = config_data[PIPELINE_INTERFACES_KEY]
-            config_data[PIPELINE_INTERFACES_KEY]["sample"] = pifaces["sample"][1]
-            del config_data[PIPELINE_INTERFACES_KEY]["project"]
+            config_data[PIPELINE_INTERFACES_KEY] = pifaces[0]
 
         x = test_args_expansion(tp, "run")
         try:
@@ -193,7 +192,7 @@ def test_looper_cli_pipeline(self, prep_temp_pep):
         tp = prep_temp_pep
         with mod_yaml_data(tp) as config_data:
             pifaces = config_data[PIPELINE_INTERFACES_KEY]
-            pi_pth = pifaces["sample"][1]
+            pi_pth = pifaces[1]
         x = test_args_expansion(tp, "run", ["--sample-pipeline-interfaces", pi_pth])
         try:
             result = main(test_args=x)
@@ -224,7 +223,7 @@ def test_looper_pipeline_not_found(self, prep_temp_pep):
         """
         tp = prep_temp_pep
         with mod_yaml_data(tp) as config_data:
-            config_data[PIPELINE_INTERFACES_KEY]["sample"] = ["bogus"]
+            config_data[PIPELINE_INTERFACES_KEY] = ["bogus"]
         x = test_args_expansion(tp, "run")
         try:
             result = main(test_args=x)
@@ -344,10 +343,9 @@ def test_looper_single_pipeline(self, prep_temp_pep):
 
         with mod_yaml_data(tp) as config_data:
             # Modifying in this way due to https://github.com/pepkit/looper/issues/474
-            config_data[PIPELINE_INTERFACES_KEY]["project"] = os.path.join(
+            config_data[PIPELINE_INTERFACES_KEY] = os.path.join(
                 os.path.dirname(tp), "pipeline/pipeline_interface1_project.yaml"
             )
-            del config_data[PIPELINE_INTERFACES_KEY]["sample"]
 
         print(tp)
         x = test_args_expansion(tp, "runp")

diff --git a/tests/test_comprehensive.py b/tests/test_comprehensive.py
@@ -123,7 +123,7 @@ def test_comprehensive_looper_pipestat(prep_temp_pep_pipestat):
 
     try:
         result = main(test_args=x)
-        assert result == {"example_pipestat_project_pipeline": {"project": "unknown"}}
+        assert result == {"example_pipestat_pipeline": {"project": "unknown"}}
 
     except Exception:
         raise pytest.fail("DID RAISE {0}".format(Exception))