Refactor Tool._populate for reuse of hook checks.

Author: jmchilton

lib/galaxy/tools/__init__.py

@@ -1972,17 +1972,21 @@ def _populate(
                 simple_errors=False,
                 input_format=input_format,
             )
-            # If the tool provides a `validate_input` hook, call it.
-            validate_input = self.get_hook("validate_input")
-            if validate_input:
-                # hooks are so terrible ... this is specifically for https://github.com/galaxyproject/tools-devteam/blob/main/tool_collections/gops/basecoverage/operation_filter.py
-                legacy_non_dce_params = {
-                    k: v.hda if isinstance(v, model.DatasetCollectionElement) and v.hda else v
-                    for k, v in params.items()
-                }
-                validate_input(request_context, errors, legacy_non_dce_params, self.inputs)
+            self._handle_validate_input_hook(request_context, params, errors)
         return params, errors
 
+    def _handle_validate_input_hook(
+        request_context, params: ToolStateJobInstancePopulatedT, errors: ParameterValidationErrorsT
+    ):
+        # If the tool provides a `validate_input` hook, call it.
+        validate_input = self.get_hook("validate_input")
+        if validate_input:
+            # hooks are so terrible ... this is specifically for https://github.com/galaxyproject/tools-devteam/blob/main/tool_collections/gops/basecoverage/operation_filter.py
+            legacy_non_dce_params = {
+                k: v.hda if isinstance(v, model.DatasetCollectionElement) and v.hda else v for k, v in params.items()
+            }
+            validate_input(request_context, errors, legacy_non_dce_params, self.inputs)
+
     def completed_jobs(
         self, trans, use_cached_job: bool, all_params: List[ToolStateJobInstancePopulatedT]
     ) -> Dict[int, Optional[model.Job]]:

lib/galaxy/tools/parameters/__init__.py

@@ -389,53 +389,6 @@ def populate_state(
 ):
     """
     Populates nested state dict from incoming parameter values.
-    >>> from galaxy.util import XML
-    >>> from galaxy.util.bunch import Bunch
-    >>> from galaxy.tools.parameters.basic import TextToolParameter, BooleanToolParameter
-    >>> from galaxy.tools.parameters.grouping import Repeat
-    >>> trans = Bunch(workflow_building_mode=False)
-    >>> a = TextToolParameter(None, XML('<param name="a"/>'))
-    >>> b = Repeat('b')
-    >>> b.min = 0
-    >>> b.max = 1
-    >>> c = TextToolParameter(None, XML('<param name="c"/>'))
-    >>> d = Repeat('d')
-    >>> d.min = 0
-    >>> d.max = 1
-    >>> e = TextToolParameter(None, XML('<param name="e"/>'))
-    >>> f = Conditional('f')
-    >>> g = BooleanToolParameter(None, XML('<param name="g"/>'))
-    >>> h = TextToolParameter(None, XML('<param name="h"/>'))
-    >>> i = TextToolParameter(None, XML('<param name="i"/>'))
-    >>> b.inputs = dict([('c', c), ('d', d)])
-    >>> d.inputs = dict([('e', e), ('f', f)])
-    >>> f.test_param = g
-    >>> f.cases = [Bunch(value='true', inputs= { 'h': h }), Bunch(value='false', inputs= { 'i': i })]
-    >>> inputs = dict([('a',a),('b',b)])
-    >>> flat = dict([('a', 1), ('b_0|c', 2), ('b_0|d_0|e', 3), ('b_0|d_0|f|h', 4), ('b_0|d_0|f|g', True)])
-    >>> state = {}
-    >>> populate_state(trans, inputs, flat, state, check=False)
-    >>> print(state['a'])
-    1
-    >>> print(state['b'][0]['c'])
-    2
-    >>> print(state['b'][0]['d'][0]['e'])
-    3
-    >>> print(state['b'][0]['d'][0]['f']['h'])
-    4
-    >>> # now test with input_format='21.01'
-    >>> nested = {'a': 1, 'b': [{'c': 2, 'd': [{'e': 3, 'f': {'h': 4, 'g': True}}]}]}
-    >>> state_new = {}
-    >>> populate_state(trans, inputs, nested, state_new, check=False, input_format='21.01')
-    >>> print(state_new['a'])
-    1
-    >>> print(state_new['b'][0]['c'])
-    2
-    >>> print(state_new['b'][0]['d'][0]['e'])
-    3
-    >>> print(state_new['b'][0]['d'][0]['f']['h'])
-    4
-
     """
     if errors is None:
         errors = {}

test/unit/app/tools/test_populate_state.py

@@ -0,0 +1,55 @@
+from galaxy.util import XML
+from galaxy.util.bunch import Bunch
+from galaxy.app_unittest_utils.galaxy_mock import MockTrans
+from galaxy.app_unittest_utils.tools_support import UsesTools
+from galaxy.tools.parameters import populate_state
+from galaxy.tools.parameters.basic import (
+    BooleanToolParameter,
+    TextToolParameter,
+)
+from galaxy.tools.parameters.grouping import (
+    Conditional,
+    Repeat,
+)
+from galaxy.tool_util.unittest_utils import functional_test_tool_path
+from galaxy.util.unittest import TestCase
+
+
+trans = Bunch(workflow_building_mode=False)
+
+
+def test_populate_state():
+    
+    a = TextToolParameter(None, XML('<param name="a"/>'))
+    b = Repeat('b')
+    b.min = 0
+    b.max = 1
+    c = TextToolParameter(None, XML('<param name="c"/>'))
+    d = Repeat('d')
+    d.min = 0
+    d.max = 1
+    e = TextToolParameter(None, XML('<param name="e"/>'))
+    f = Conditional('f')
+    g = BooleanToolParameter(None, XML('<param name="g"/>'))
+    h = TextToolParameter(None, XML('<param name="h"/>'))
+    i = TextToolParameter(None, XML('<param name="i"/>'))
+    b.inputs = dict([('c', c), ('d', d)])
+    d.inputs = dict([('e', e), ('f', f)])
+    f.test_param = g
+    f.cases = [Bunch(value='true', inputs= { 'h': h }), Bunch(value='false', inputs= { 'i': i })]
+    inputs = dict([('a',a),('b',b)])
+    flat = dict([('a', 1), ('b_0|c', 2), ('b_0|d_0|e', 3), ('b_0|d_0|f|h', 4), ('b_0|d_0|f|g', True)])
+    state = {}
+    populate_state(trans, inputs, flat, state, check=False)
+    assert state['a'] == 1
+    assert state['b'][0]['c'] == 2
+    assert state['b'][0]['d'][0]['e'] == 3
+    assert state['b'][0]['d'][0]['f']['h'] == 4
+    # now test with input_format='21.01'
+    nested = {'a': 1, 'b': [{'c': 2, 'd': [{'e': 3, 'f': {'h': 4, 'g': True}}]}]}
+    state_new = {}
+    populate_state(trans, inputs, nested, state_new, check=False, input_format='21.01')
+    assert state_new['a'] == 1
+    assert state_new['b'][0]['c'] == 2
+    assert state_new['b'][0]['d'][0]['e'] == 3
+    assert state_new['b'][0]['d'][0]['f']['h'] == 4