Allow including paths in inputs json files.

2026-10-24 12:13:33 +08:00 · 2018-07-05 11:05:15 -04:00
parent e33427a3b7
commit 019f088543
6 changed files with 168 additions and 10 deletions
@@ -803,7 +803,8 @@ class Tool(Dictifiable):
                name = inputs_elem.get("name")
                filename = inputs_elem.get("filename", None)
                format = inputs_elem.get("format", "json")
-                content = dict(format=format)
+                data_style = inputs_elem.get("data_style", "skip")
+                content = dict(format=format, handle_files=data_style)
                self.config_files.append((name, filename, content))
            for conf_elem in conf_parent_elem.findall("configfile"):
                name = conf_elem.get("name")
@@ -561,12 +561,13 @@ class ToolEvaluator(object):
            return content, True

        content_format = content["format"]
+        handle_files = content["handle_files"]
        if content_format != "json":
            template = "Galaxy can only currently convert inputs to json, format [%s] is unhandled"
            message = template % content_format
            raise Exception(message)

-        return json.dumps(wrapped_json.json_wrap(self.tool.inputs, self.param_dict)), False
+        return json.dumps(wrapped_json.json_wrap(self.tool.inputs, self.param_dict, handle_files=handle_files)), False

    def __write_workdir_file(self, config_filename, content, context, is_template=True):
        if is_template:
@@ -5,7 +5,7 @@ log = logging.getLogger(__name__)
 SKIP_INPUT = object()


-def json_wrap(inputs, input_values, as_dict=None, handle_files="SKIP"):
+def json_wrap(inputs, input_values, as_dict=None, handle_files="skip"):
    if as_dict is None:
        as_dict = {}

@@ -19,8 +19,15 @@ def json_wrap(inputs, input_values, as_dict=None, handle_files="SKIP"):
    return as_dict


-def _json_wrap_input(input, value, handle_files="SKIP"):
+def _json_wrap_input(input, value, handle_files="skip"):
    input_type = input.type
+
+    def _data_input_to_path(v):
+        path = _cast_if_not_none(v, str)
+        if path == "None":
+            path = None
+        return path
+
    if input_type == "repeat":
        repeat_job_value = []
        for d in value:
@@ -44,15 +51,21 @@ def _json_wrap_input(input, value, handle_files="SKIP"):
        json_wrap(input.inputs, values, section_job_value)
        json_value = section_job_value
    elif input_type == "data" and input.multiple:
-        if handle_files == "SKIP":
+        if handle_files == "paths":
+            json_value = list(map(_data_input_to_path, value))
+        elif handle_files == "skip":
            return SKIP_INPUT
-        raise NotImplementedError()
+        else:
+            raise NotImplementedError()
    elif input_type == "data":
-        if handle_files == "SKIP":
+        if handle_files == "paths":
+            json_value = _data_input_to_path(value)
+        elif handle_files == "skip":
            return SKIP_INPUT
-        raise NotImplementedError()
+        else:
+            raise NotImplementedError()
    elif input_type == "data_collection":
-        if handle_files == "SKIP":
+        if handle_files == "skip":
            return SKIP_INPUT
        raise NotImplementedError()
    elif input_type in ["select", "text", "color", "hidden"]:
@@ -4549,7 +4549,7 @@ the path to the file created with this directive.</xs:documentation>
      <xs:documentation xml:lang="en"><![CDATA[

 This tag set is contained within the <configfiles> tag set. It tells Galaxy to
-write out a JSON representation of the tool parameters .
+write out a JSON representation of the tool parameters.

 *Example*

@@ -4573,6 +4573,9 @@ the specified name (i.e. ``inputs.json``).

 A contrived example of a tool that uses this is the test tool
 [inputs_as_json.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/inputs_as_json.xml).
+
+By default this file will not contain paths for data or collection inputs. To include simple
+paths for data parameters set the ``data_style`` attribute to ``paths`` (see [inputs_as_json_with_paths.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/inputs_as_json_with_paths.xml) for an example).
 ]]></xs:documentation>
    </xs:annotation>
    <xs:simpleContent>
@@ -4590,6 +4593,11 @@ response to this directive.
            <xs:documentation xml:lang="en">Path relative to the working directory of the tool for the inputs JSON file created in response to this directive.</xs:documentation>
          </xs:annotation>
        </xs:attribute>
+        <xs:attribute name="data_stype" type="xs:string">
+          <xs:annotation>
+            <xs:documentation xml:lang="en">Set to 'paths' to include dataset paths in the resulting file.</xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>
@@ -0,0 +1,134 @@
+<tool id="inputs_as_json_with_paths" name="inputs_as_json_with_paths" version="1.0.0" profile="18.09">
+    <command detect_errors="exit_code">
+        python '$check_inputs' '$inputs' $test_case
+    </command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths" />
+        <!-- Can specify with fixed path in working directory instead:
+        <inputs name="inputs" filename="input.json" />
+        -->
+        <configfile name="check_inputs"><![CDATA[
+import json
+import sys
+
+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)
+
+if test_case == "1":
+    assert_equals(as_dict["test_case"], 1)
+    assert_equals(as_dict["text_test"], "foo")
+    assert_equals(as_dict["booltest"], True)
+    assert_equals(as_dict["booltest2"], True)
+    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["repeat"][0]["r"], "000000")
+    assert_equals(as_dict["repeat"][1]["r"], "FFFFFF")
+    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)
+elif test_case == "2":
+    assert_equals(as_dict["test_case"], 2)
+    assert_equals(as_dict["text_test"], "bar")
+    assert_equals(as_dict["booltest"], False)
+    assert_equals(as_dict["booltest2"], False)
+    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["repeat"][0]["r"], "000000")
+    assert_equals(as_dict["cond"]["cond_test"], "second")
+    assert_equals(as_dict["cond"]["more_text"], "sdefault")
+    assert_equals(as_dict["section_example"]["section_text"], "section_default")
+    data_input = as_dict["data_input"]
+    assert data_input is not None
+
+with open("output", "w") as f:
+    f.write("okay\n")
+]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="test_case" type="integer" value="0" />
+        <param name="text_test" type="text" />
+        <param name="booltest" truevalue="booltrue" falsevalue="boolfalse" checked="false" type="boolean" />
+        <param name="booltest2" truevalue="booltrue" falsevalue="boolfalse" checked="false" type="boolean" />
+        <param name="inttest" type="integer" optional="true" />
+        <param name="floattest" value="1.0" type="float" />
+        <param name="radio_select" type="select" display="radio">
+            <option value="a_radio" selected="true">A Radio</option>
+            <option value="b_radio">B Radio</option>
+            <option value="c_radio">C Radio</option>
+        </param>
+        <param name="data_input" type="data" optional="true" />
+        <repeat name="repeat" title="Repeat" min="1">
+            <param name="r" type="color" />
+        </repeat>
+        <conditional name="cond">
+            <param name="cond_test" type="select">
+                <option value="first" selected="true">First</option>
+                <option value="second">Second</option>
+            </param>
+            <when value="first">
+                <param name="more_text" type="text" value="fdefault" />
+            </when>
+            <when value="second">
+                <param name="more_text" type="text" value="sdefault" />
+            </when> 
+        </conditional>
+        <section name="section_example" title="Section Example">
+            <param name="section_text" type="text" value="section_default" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_file1" from_work_dir="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="test_case" value="1" />
+            <param name="text_test" value="foo" />
+            <param name="booltest" value="true" />
+            <param name="booltest2" value="booltrue" />
+            <param name="inttest" value="12456" />
+            <param name="floattest" value="6.789" />
+            <repeat name="repeat">
+                <param name="r" value="000000"/>
+            </repeat>
+            <repeat name="repeat">
+                <param name="r" value="FFFFFF"/>
+            </repeat>
+            <conditional name="cond">
+                <param name="cond_test" value="first" />
+            </conditional>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="okay" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="test_case" value="2" />
+            <param name="text_test" value="bar" />
+            <param name="booltest" value="false" />
+            <param name="booltest2" value="boolfalse" />
+            <param name="data_input" value="simple_line.txt" />
+            <!-- Testing null integers -->
+            <!-- <param name="inttest" value="12456" /> -->
+            <param name="r" value="000000" />
+            <conditional name="cond">
+                <param name="cond_test" value="second" />
+            </conditional>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="okay" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        Test tool demonstrating the special inputs config file.
+    </help>
+</tool>
@@ -29,6 +29,7 @@
  <tool file="tool_provided_metadata_9.xml" />
  <tool file="empty_datasets.xml" />
  <tool file="inputs_as_json.xml" />
+  <tool file="inputs_as_json_with_paths.xml" />
  <tool file="dbkey_filter_input.xml" />
  <tool file="dbkey_filter_multi_input.xml" />
  <tool file="dbkey_output_action.xml" />