Merge pull request #33 from fubar2/master

README.rst

@@ -20,6 +20,9 @@ License
 
 Changelog
 ---------
+-  0.4.13
+
+   - Add TestOutputCollection, TestRepeat and tests (thanks @fubar2)
 
 -  0.4.12
 

examples/example.py

@@ -104,6 +104,12 @@
 test_a.append(param)
 test_out = gxtp.TestOutput(name="output", value="file.out")
 test_a.append(test_out)
+coll_out = gxtp.TestOutputCollection(name="pdf_out")
+test_a.append(coll_out)
+rep_out = gxtp.TestRepeat(name="testrepeat")
+param = gxtp.TestParam("repeatchild", value="foo")
+rep_out.append(param)
+test_a.append(rep_out)
 tool.tests.append(test_a)
 
 

examples/tool.xml

@@ -67,6 +67,10 @@ select_local $select_local
     <test>
       <param name="float" value="5.4"/>
       <output name="output" value="file.out"/>
+      <output_collection name="pdf_out"/>
+      <test_repeat name="testrepeat">
+        <param name="repeatchild" value="foo"/>
+      </test_repeat>
     </test>
   </tests>
   <help><![CDATA[HI]]></help>

galaxyxml/__init__.py

@@ -1,6 +1,6 @@
 from builtins import (
-    str,
-    object
+    object,
+    str
 )
 
 from lxml import etree

galaxyxml/tool/import_xml.py

@@ -698,6 +698,60 @@ def _load_output(self, test_root, output_root):
             )
         )
 
+    def _load_output_collection(self, test_root, output_root):
+        """
+        Add <output_collection> to the <test>.
+
+        :param root: <test> root to append <output> to.
+        :param repeat_root: root of <output_collection> tag.
+        :param repeat_root: :class:`xml.etree._Element`
+        """
+        test_root.append(
+            gxtp.TestOutputCollection(
+                name=output_root.attrib.get("name", None),
+                ftype=output_root.attrib.get("ftype", None),
+                sort=output_root.attrib.get("sort", None),
+                value=output_root.attrib.get("value", None),
+                compare=output_root.attrib.get("compare", None),
+                lines_diff=output_root.attrib.get("lines_diff", None),
+                delta=output_root.attrib.get("delta", None),
+            )
+        )
+
+    def _load_repeat(self, root, repeat_root):
+        """
+        Add <test_repeat> to the <test>.
+
+        :param root: <test> root to append <output> to.
+        :param output_root: root of <test_repeat> tag.
+        :param output_root: :class:`xml.etree._Element`
+        """
+
+        repeat = gxtp.TestRepeat(
+            repeat_root.attrib.get("name", None),
+            repeat_root.attrib.get("title",None),
+            min=repeat_root.attrib.get("min", None),
+            max=repeat_root.attrib.get("max", None),
+            default=repeat_root.attrib.get("default", None)
+        )
+        # Deal with child nodes
+        self.load_inputs(repeat, repeat_root)
+        root.append(repeat)
+
+    def load_inputs(self, repeat, repeat_root):
+        """
+        Add children to repeat for test
+
+        :param repeat_root: repeat to attach inputs to.
+        :param repeat: root of <repeat> tag.
+        :type repeat_root: :class:`xml.etree._Element`
+        """
+        for rep_child in repeat_root:
+            try:
+                getattr(self, "_load_{}".format(rep_child.tag))(repeat, rep_child)
+            except AttributeError:
+                logger.warning(rep_child.tag + " tag is not processed for <" + repeat_root.tag + "> tag.")
+
     def load_tests(self, root, tests_root):
         """
         Add <tests> to the root.

galaxyxml/tool/parameters/__init__.py

@@ -1,12 +1,13 @@
+import logging
 from builtins import (
-    str,
-    object
+    object,
+    str
 )
-import logging
+
+from galaxy.tool_util.parser.util import _parse_name
 
 from galaxyxml import Util
 
-from galaxy.tool_util.parser.util import _parse_name
 from lxml import etree
 
 logging.basicConfig(level=logging.INFO)
@@ -859,6 +860,8 @@ class Test(XMLParam):
     def acceptable_child(self, child):
         return isinstance(child, TestParam) \
             or isinstance(child, TestOutput) \
+            or isinstance(child, TestOutputCollection) \
+            or isinstance(child, TestRepeat) \
             or isinstance(child, Expand)
 
 
@@ -891,6 +894,66 @@ def __init__(
         super(TestOutput, self).__init__(**params)
 
 
+class TestOutputCollection(XMLParam):
+    name = "output_collection"
+
+    def __init__(
+        self,
+        name=None,
+        ftype=None,
+        sort=None,
+        value=None,
+        compare=None,
+        lines_diff=None,
+        delta=None,
+        **kwargs,
+    ):
+        params = Util.clean_kwargs(locals().copy())
+        super(TestOutputCollection, self).__init__(**params)
+
+    def command_line_before(self, mako_path):
+        return "<output_collection name = '%s'>" % self.name
+
+    def command_line_after(self):
+        return "</output_collection>"
+
+    def command_line_actual(self, mako_path):
+
+        return ""
+
+class TestRepeat(XMLParam):
+    name = "repeat"
+
+    def __init__(
+        self,
+        name=None,
+        ftype=None,
+        sort=None,
+        value=None,
+        compare=None,
+        lines_diff=None,
+        delta=None,
+        **kwargs,
+    ):
+        params = Util.clean_kwargs(locals().copy())
+        super(TestRepeat, self).__init__(**params)
+
+    def acceptable_child(self, child):
+        return issubclass(type(child), TestParam)
+
+    def command_line_before(self, mako_path):
+        return "<repeat name = '%s'>" % self.name
+
+    def command_line_after(self):
+        return "</repeat>"
+
+    def command_line_actual(self, mako_path):
+        lines = []
+        for child in self.children:
+            lines.append(child.command_line())
+        return "\n".join(lines)
+
+
 class Citations(XMLParam):
     name = "citations"
 

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name="galaxyxml",
-    version="0.4.12",
+    version="0.4.13",
     description="Galaxy XML generation library",
     author="Helena Rasche",
     author_email="[email protected]",

test/import_xml.xml

@@ -71,6 +71,10 @@
     <test>
       <param name="sequence" value="seq.fasta"/>
       <output file="file.gbk" name="genbank"/>
+      <output_collection name="pdf_out"></output_collection>
+      <repeat name="test_repeat">
+          <param name="repeatchild" value="foo"/>
+      </repeat>
     </test>
   </tests>
   <help><![CDATA[help]]></help>

test/unit_test_import_xml.py

@@ -192,3 +192,14 @@ def test_load_output(self):
         output = self.tool.tests.children[0].node[1]
         self.assertEqual(output.attrib["file"], "file.gbk")
         self.assertEqual(output.attrib["name"], "genbank")
+
+    def test_collection_output(self):
+        output = self.tool.tests.children[0].node[2]
+        self.assertEqual(output.attrib["name"], "pdf_out")
+
+    def test_repeat(self):
+        repeat = self.tool.tests.children[0].node[3]
+        self.assertEqual(repeat.attrib["name"],"test_repeat")
+        # test param within repeat
+        self.assertEqual(repeat[0].attrib["name"], "repeatchild")
+        self.assertEqual(repeat[0].attrib["value"], "foo")