get_workflow_default_param_value is based in step_index_in_current_s…

…ection (#269)

* get_workflow_default_param_value uses now step_index_in_current_section

* fixed tests

protzilla/run.py

@@ -262,7 +262,10 @@ def delete_step(self, section, index):
     def next_step(self, name=None):
         if not name:
             name = get_workflow_default_param_value(
-                self.workflow_config, *self.current_run_location(), "output_name"
+                self.workflow_config,
+                *self.current_run_location(),
+                self.step_index_in_current_section(),
+                "output_name",
             )
         try:
             parameters = self.current_parameters.get(self.calculated_method, {})

protzilla/run_helper.py

@@ -80,7 +80,12 @@ def get_parameters(run, section, step, method):
 
     for key, param_dict in parameters.items():
         workflow_default = get_workflow_default_param_value(
-            run.workflow_config, section, step, method, key
+            run.workflow_config,
+            section,
+            step,
+            method,
+            run.step_index_in_current_section(),
+            key,
         )
         if method in run.current_parameters and key in run.current_parameters[method]:
             param_dict["default"] = run.current_parameters[method][key]

protzilla/workflow_helper.py

@@ -55,17 +55,17 @@ def get_parameter_type(workflow_meta, section, step, method, param):
     return workflow_meta[section][step][method]["parameters"][param]["type"]
 
 
-def get_workflow_default_param_value(workflow_config, section, step, method, param):
-    # TODO 163: this should be based on step_index as there can be multiple steps with the same name
-    steps = workflow_config["sections"][section]["steps"]
-    for step_dict in steps:
-        if step_dict["name"] == step and step_dict["method"] == method:
-            if param in step_dict["parameters"]:
-                return step_dict["parameters"][param]
-            elif param in step_dict:
-                return step_dict[param]
-            else:
-                return None
+def get_workflow_default_param_value(
+    workflow_config, section, step, method, step_index_in_section, param
+):
+    step_dict = workflow_config["sections"][section]["steps"][step_index_in_section]
+    if step_dict["name"] == step and step_dict["method"] == method:
+        if param in step_dict["parameters"]:
+            return step_dict["parameters"][param]
+        elif param in step_dict:
+            return step_dict[param]
+        else:
+            return None
     return None
 
 

tests/protzilla/test_run.py

@@ -302,6 +302,7 @@ def test_name_step(example_workflow_short, tests_folder_name):
         "importing",
         "ms_data_import",
         "max_quant_import",
+        run.step_index_in_current_section(),
         "output_name",
     )
 

tests/protzilla/test_run_helper.py

@@ -1,5 +1,5 @@
 import copy
-from unittest.mock import MagicMock, Mock
+from unittest.mock import MagicMock, Mock, patch
 
 import pandas as pd
 import pytest
@@ -54,6 +54,7 @@ def test_get_parameters():
             }
         }
     }
+    run.step_index_in_current_section.return_value = 0
     expected = {
         "param1": {"default": "current1", "type": ""},
         "param2": {"default": "config2", "type": ""},
@@ -67,6 +68,7 @@ def test_get_parameters_no_side_effects(workflow_meta, example_workflow):
     run.workflow_meta = copy.deepcopy(workflow_meta)
     run.current_parameters = {"strategy": "median"}
     run.workflow_config = copy.deepcopy(example_workflow)
+    run.step_index_in_current_section.return_value = 5
     get_parameters(
         run, "data_preprocessing", "imputation", "simple_imputation_per_protein"
     )

tests/protzilla/test_workflow_helper.py

@@ -124,20 +124,23 @@ def test_get_workflow_default_param_value(example_workflow):
         "data_preprocessing",
         "filter_proteins",
         "samples_missing_filter",
+        0,
         "percentage",
     )
     output_name = get_workflow_default_param_value(
         example_workflow,
         "data_preprocessing",
         "normalisation",
         "median",
+        5,
         "output_name",
     )
     output_name_t_test = get_workflow_default_param_value(
         example_workflow,
         "data_analysis",
         "differential_expression",
         "t_test",
+        1,
         "output_name",
     )
 
@@ -152,6 +155,7 @@ def test_get_workflow_default_param_value_nonexistent(example_workflow_short):
         "data_preprocessing",
         "filter_samples",
         "protein_intensity_sum_filter",
+        0,
         "threshold",
     )
 
@@ -165,6 +169,7 @@ def test_test_get_workflow_default_param_value_no_side_effects(example_workflow)
         "data_preprocessing",
         "filter_proteins",
         "samples_missing_filter",
+        0,
         "percentage",
     )
     assert example_workflow == example_workflow_copy

ui/runs/fields.py

@@ -218,7 +218,10 @@ def make_name_field(allow_next, form, run, end_of_run):
     if end_of_run:
         return ""
     default = get_workflow_default_param_value(
-        run.workflow_config, *run.current_run_location(), "output_name"
+        run.workflow_config,
+        *run.current_run_location(),
+        run.step_index_in_current_section(),
+        "output_name",
     )
     if not default:
         default = ""