Merge pull request #9279 from bernt-matthias/topic/inputs-multiple-test

extend config file inputs tests

lib/galaxy/tools/parameters/wrapped_json.py

@@ -11,15 +11,15 @@ def json_wrap(inputs, input_values, as_dict=None, handle_files="skip"):
 
     for input in inputs.values():
         input_name = input.name
-        value = input_values[input_name]
-        json_value = _json_wrap_input(input, value, handle_files=handle_files)
+        value_wrapper = input_values[input_name]
+        json_value = _json_wrap_input(input, value_wrapper, handle_files=handle_files)
         if json_value is SKIP_INPUT:
             continue
         as_dict[input_name] = json_value
     return as_dict
 
 
-def _json_wrap_input(input, value, handle_files="skip"):
+def _json_wrap_input(input, value_wrapper, handle_files="skip"):
     input_type = input.type
 
     def _data_input_to_path(v):
@@ -30,13 +30,13 @@ def _json_wrap_input(input, value, handle_files="skip"):
 
     if input_type == "repeat":
         repeat_job_value = []
-        for d in value:
+        for d in value_wrapper:
             repeat_instance_job_value = {}
             json_wrap(input.inputs, d, repeat_instance_job_value, handle_files=handle_files)
             repeat_job_value.append(repeat_instance_job_value)
         json_value = repeat_job_value
     elif input_type == "conditional":
-        values = value
+        values = value_wrapper
         current = values["__current_case__"]
         conditional_job_value = {}
         json_wrap(input.cases[current].inputs, values, conditional_job_value, handle_files=handle_files)
@@ -46,29 +46,29 @@ def _json_wrap_input(input, value, handle_files="skip"):
         conditional_job_value[test_param_name] = test_value
         json_value = conditional_job_value
     elif input_type == "section":
-        values = value
+        values = value_wrapper
         section_job_value = {}
         json_wrap(input.inputs, values, section_job_value, handle_files=handle_files)
         json_value = section_job_value
     elif input_type == "data" and input.multiple:
         if handle_files == "paths":
-            json_value = list(map(_data_input_to_path, value))
+            json_value = list(map(_data_input_to_path, value_wrapper))
         elif handle_files == "skip":
             return SKIP_INPUT
         else:
             raise NotImplementedError()
     elif input_type == "data":
         if handle_files == "paths":
-            json_value = _data_input_to_path(value)
+            json_value = _data_input_to_path(value_wrapper)
         elif handle_files == "skip":
             return SKIP_INPUT
         elif handle_files == "OBJECT":
-            if value:
-                if isinstance(value, list):
-                    value = value[0]
-                json_value = _hda_to_object(value)
+            if value_wrapper:
+                if isinstance(value_wrapper, list):
+                    value_wrapper = value_wrapper[0]
+                json_value = _hda_to_object(value_wrapper)
                 if input.load_contents:
-                    with open(str(value), mode='rb') as fh:
+                    with open(str(value_wrapper), mode='rb') as fh:
                         json_value['contents'] = fh.read(input.load_contents).decode('utf-8', errors='replace')
                 return json_value
             else:
@@ -79,20 +79,25 @@ def _json_wrap_input(input, value, handle_files="skip"):
         if handle_files == "skip":
             return SKIP_INPUT
         raise NotImplementedError()
-    elif input_type in ["select", "text", "color", "hidden"]:
-        json_value = _cast_if_not_none(value, str)
+    elif input_type in ["text", "color", "hidden"]:
+        json_value = _cast_if_not_none(value_wrapper, str)
     elif input_type == "float":
-        json_value = _cast_if_not_none(value, float, empty_to_none=True)
+        json_value = _cast_if_not_none(value_wrapper, float, empty_to_none=True)
     elif input_type == "integer":
-        json_value = _cast_if_not_none(value, int, empty_to_none=True)
+        json_value = _cast_if_not_none(value_wrapper, int, empty_to_none=True)
     elif input_type == "boolean":
-        json_value = _cast_if_not_none(value, bool)
+        json_value = _cast_if_not_none(value_wrapper, bool)
+    elif input_type == "select":
+        if input.multiple:
+            json_value = [_ for _ in _cast_if_not_none(value_wrapper.value, list)]
+        else:
+            json_value = _cast_if_not_none(value_wrapper.value, str)
     elif input_type == "data_column":
         # value is a SelectToolParameterWrapper()
         if input.multiple:
-            json_value = [int(_) for _ in _cast_if_not_none(value.value, list)]
+            json_value = [int(_) for _ in _cast_if_not_none(value_wrapper.value, list)]
         else:
-            json_value = [_cast_if_not_none(value.value, int)]
+            json_value = [_cast_if_not_none(value_wrapper.value, int)]
     else:
         raise NotImplementedError("input_type [%s] not implemented" % input_type)
 

test-data/configfile.json

@@ -1 +0,0 @@
-{"col": [11]}

test/functional/tools/column_param_configfile.xml

@@ -1,13 +1,29 @@
 <tool id="column_param_configfile" name="Column Param into configfile" >
-  <command>
-cat '$inputs' > '$output1'
-  </command>
+  <command detect_errors="exit_code"><![CDATA[
+    python $check_inputs inputs.json
+  ]]></command>
   <configfiles>
-    <inputs name="inputs" />
+    <inputs name="inputs" filename="inputs.json" />
+      <configfile name="check_inputs"><![CDATA[
+import json
+import sys
+
+input_json_path = sys.argv[1]
+as_dict = json.load(open(input_json_path, "r"))
+
+def assert_equals(x, y):
+    assert x == y, "%s[%s] != %s[%s] " % (x, type(x), y, type(y))
+
+assert_equals(as_dict["col"], [11])
+assert_equals(as_dict["col_mult"], [1,2,3])
+with open("$output1", "w") as f:
+    f.write("okay\n")
+]]></configfile>
   </configfiles>
   <inputs>
     <param type="data" format="tabular" name="input1" label="Input 1" />
-    <param name="col" type="data_column" data_ref="input1" label="Column to Use" />
+    <param name="col" type="data_column" data_ref="input1" label="Column to Use"/>
+    <param name="col_mult" type="data_column" data_ref="input1" label="Columns to Use" multiple="true"/>
   </inputs>
   <outputs>
     <data name="output1" format="data" />
@@ -16,7 +32,12 @@ cat '$inputs' > '$output1'
     <test>
       <param name="input1" value="11.tabular" />
       <param name="col" value="11" />
-      <output name="output1" file="configfile.json"/>
+      <param name="col_mult" value="1,2,3" />
+      <output name="output1">
+        <assert_contents>
+          <has_line line="okay" />
+        </assert_contents>
+      </output>
     </test>
   </tests>
 </tool>

test/functional/tools/inputs_as_json.xml

@@ -1,7 +1,8 @@
 <tool id="inputs_as_json" name="inputs_as_json" version="1.0.0">
-    <command detect_errors="exit_code">
+    <command detect_errors="exit_code"><![CDATA[
+        cat inputs.json &&
         python $check_inputs inputs.json $test_case
-    </command>
+    ]]></command>
     <configfiles>
         <inputs name="inputs" filename="inputs.json" />
         <!-- Can specify with fixed path in working directory instead:
@@ -15,9 +16,8 @@ input_json_path = sys.argv[1]
 test_case = sys.argv[2]
 as_dict = json.load(open(input_json_path, "r"))
 
-
 def assert_equals(x, y):
-    assert x == y, "%s != %s" % (x, y)
+    assert x == y, "%s[%s] != %s[%s] " % (x, type(x), y, type(y))
 
 if test_case == "1":
     assert_equals(as_dict["test_case"], 1)
@@ -27,6 +27,8 @@ if test_case == "1":
     assert_equals(as_dict["inttest"], 12456)
     assert_equals(as_dict["floattest"], 6.789)
     assert_equals(as_dict["radio_select"], "a_radio")
+    assert_equals(as_dict["optional_select"], None)
+    assert_equals(as_dict["optional_multiple_select"], [])
     assert_equals(as_dict["repeat"][0]["r"], "000000")
     assert_equals(as_dict["repeat"][1]["r"], "FFFFFF")
     assert_equals(as_dict["cond"]["more_text"], "fdefault")
@@ -40,6 +42,8 @@ elif test_case == "2":
     assert_equals(as_dict["inttest"], None)
     assert_equals(as_dict["floattest"], 1.0)
     assert_equals(as_dict["radio_select"], "a_radio")
+    assert_equals(as_dict["optional_select"], "a")
+    assert_equals(as_dict["optional_multiple_select"], ['a', 'b'])
     assert_equals(as_dict["repeat"][0]["r"], "000000")
     assert_equals(as_dict["cond"]["cond_test"], "second")
     assert_equals(as_dict["cond"]["more_text"], "sdefault")
@@ -63,6 +67,16 @@ with open("output", "w") as f:
             <option value="c_radio">C Radio</option>
         </param>
         <param name="data_input" type="data" optional="true" />
+        <param name="optional_select" type="select" optional="true">
+            <option value="a">A</option>
+            <option value="b">B</option>
+            <option value="c">C</option>
+        </param>
+        <param name="optional_multiple_select" type="select" optional="true" multiple="true">
+            <option value="a">A</option>
+            <option value="b">B</option>
+            <option value="c">C</option>
+        </param>
         <repeat name="repeat" title="Repeat" min="1">
             <param name="r" type="color" />
         </repeat>
@@ -114,6 +128,8 @@ with open("output", "w") as f:
             <param name="booltest" value="false" />
             <param name="booltest2" value="boolfalse" />
             <param name="data_input" value="simple_line.txt" />
+            <param name="optional_select" value="a"/>
+            <param name="optional_multiple_select" value="a,b"/>
             <!-- Testing null integers -->
             <!-- <param name="inttest" value="12456" /> -->
             <param name="r" value="000000" />

test/functional/tools/inputs_as_json_with_paths.xml

@@ -17,7 +17,7 @@ as_dict = json.load(open(input_json_path, "r"))
 
 
 def assert_equals(x, y):
-    assert x == y, "%s != %s" % (x, y)
+    assert x == y, "%s[%s] != %s[%s] " % (x, type(x), y, type(y))
 
 if test_case == "1":
     assert_equals(as_dict["test_case"], 1)
@@ -32,6 +32,7 @@ if test_case == "1":
     assert_equals(as_dict["cond"]["more_text"], "fdefault")
     assert_equals(as_dict["section_example"]["section_text"], "section_default")
     assert_equals(as_dict["data_input"], None)
+    assert_equals(as_dict["multiple_data_input"], [None])
 elif test_case == "2":
     assert_equals(as_dict["test_case"], 2)
     assert_equals(as_dict["text_test"], "bar")
@@ -46,6 +47,9 @@ elif test_case == "2":
     assert_equals(as_dict["section_example"]["section_text"], "section_default")
     data_input = as_dict["data_input"]
     assert data_input is not None
+    multiple_data_input = as_dict["multiple_data_input"]
+    assert type(multiple_data_input) is list
+    assert len(multiple_data_input) == 2
 
 with open("output", "w") as f:
     f.write("okay\n")
@@ -64,6 +68,7 @@ with open("output", "w") as f:
             <option value="c_radio">C Radio</option>
         </param>
         <param name="data_input" type="data" optional="true" />
+        <param name="multiple_data_input" type="data" optional="true" multiple="true" />
         <repeat name="repeat" title="Repeat" min="1">
             <param name="r" type="color" />
         </repeat>
@@ -115,6 +120,7 @@ with open("output", "w") as f:
             <param name="booltest" value="false" />
             <param name="booltest2" value="boolfalse" />
             <param name="data_input" value="simple_line.txt" />
+            <param name="multiple_data_input" value="simple_line.txt,simple_line_alternative.txt" />
             <!-- Testing null integers -->
             <!-- <param name="inttest" value="12456" /> -->
             <param name="r" value="000000" />