Merge pull request #35 from fubar2/master

Author: hexylena

README.rst

@@ -20,6 +20,10 @@ License
 
 Changelog
 ---------
+-  0.4.14
+
+   - Fix for TestRepeats (@fubar2)
+
 -  0.4.13
 
    - Add TestOutputCollection, TestRepeat and tests (thanks @fubar2)

examples/example.py

@@ -110,6 +110,14 @@
 param = gxtp.TestParam("repeatchild", value="foo")
 rep_out.append(param)
 test_a.append(rep_out)
+test_coll = gxtp.TestOutputCollection(name="pdf_out")
+test_elem = gxtp.TestOCElement(name="apdf",file="apdf",ftype="pdf")
+test_coll.append(test_elem)
+test_a.append(test_coll)
+rep_out = gxtp.TestRepeat(name="output_repeat")
+param = gxtp.TestOutput(name="repeatout", value="repeatfile.out")
+rep_out.append(param)
+test_a.append(rep_out)
 tool.tests.append(test_a)
 
 

examples/tool.xml

@@ -68,9 +68,15 @@ select_local $select_local
       <param name="float" value="5.4"/>
       <output name="output" value="file.out"/>
       <output_collection name="pdf_out"/>
-      <test_repeat name="testrepeat">
+      <repeat name="testrepeat">
         <param name="repeatchild" value="foo"/>
-      </test_repeat>
+      </repeat>
+      <output_collection name="pdf_out">
+        <element name="apdf" file="apdf" ftype="pdf"/>
+      </output_collection>
+      <repeat name="output_repeat">
+        <output name="repeatout" value="repeatfile.out"/>
+      </repeat>
     </test>
   </tests>
   <help><![CDATA[HI]]></help>

galaxyxml/tool/__init__.py

@@ -138,7 +138,7 @@ def export(self, keep_old_command=False):
             stdio_element = etree.SubElement(export_xml.root, "stdio")
             etree.SubElement(stdio_element, "exit_code", range="1:", level="fatal")
         try:
-            export_xml.append(export_xml.stdio)
+            export_xml.append(stdio_element)
         except Exception:
             export_xml.append(Expand(macro="stdio"))
 

galaxyxml/tool/import_xml.py

@@ -706,44 +706,59 @@ def _load_output_collection(self, test_root, output_root):
         :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),
-            )
+        collection = 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),
         )
+        # Deal with child nodes
+        self.load_inputs(collection, output_root)
+        test_root.append(collection)
 
-    def _load_repeat(self, root, repeat_root):
+    def _load_element(self, test_root, element_root):
         """
-        Add <test_repeat> to the <test>.
+        Add <element> 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`
+        :param repeat_root: root of <output_collection> tag.
+        :param repeat_root: :class:`xml.etree._Element`
         """
+        test_root.append(gxtp.TestOCElement(
+            name=element_root.attrib.get("name", None),
+            ftype=element_root.attrib.get("ftype", None),
+            file=element_root.attrib.get("file", None)
+        )
+        )
 
+    def _load_repeat(self, test_root, repeat_root):
+        """
+        Add <repeat> to the <test>.
+
+        :param root: <test> root to append <output> to.
+        :param output_root: root of <repeat> tag.
+        :param output_root: :class:`xml.etree._Element`
+        """
         repeat = gxtp.TestRepeat(
             repeat_root.attrib.get("name", None),
-            repeat_root.attrib.get("title",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)
+        test_root.append(repeat)
 
     def load_inputs(self, repeat, repeat_root):
         """
-        Add children to repeat for test
+        Add children to repeat/collection for test
 
         :param repeat_root: repeat to attach inputs to.
-        :param repeat: root of <repeat> tag.
+        :param repeat: root of <repeat> or <collection> tag.
         :type repeat_root: :class:`xml.etree._Element`
         """
         for rep_child in repeat_root:

galaxyxml/tool/parameters/__init__.py

@@ -13,6 +13,7 @@
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
+
 class XMLParam(object):
     name = "node"
 
@@ -69,7 +70,7 @@ def cli(self):
             lines.append(child.command_line())
         return "\n".join(lines)
 
-    def command_line(self, mako_path = None):
+    def command_line(self, mako_path=None):
         """
         genetate the command line for the node (and its childres)
 
@@ -355,7 +356,7 @@ def __init__(self, name, **kwargs):
         # We use kwargs instead of the usual locals(), so manually copy the
         # name to kwargs
         if name is not None:
-            kwargs = dict([("name", name)] + list(kwargs.items()) )
+            kwargs = dict([("name", name)] + list(kwargs.items()))
 
         # Handle positional parameters
         if "positional" in kwargs and kwargs["positional"]:
@@ -420,7 +421,7 @@ def mako_name(self, mako_path=None):
             if len(parent_identifiers) > 0:
                 parent_identifiers.append("")
             path = ".".join(parent_identifiers)
-        return "$"+ path + self.mako_identifier
+        return "$" + path + self.mako_identifier
 
     def flag(self):
         flag = "-" * self.num_dashes
@@ -492,7 +493,7 @@ def command_line(self, mako_path=None):
         for c in self.children[1:]:
             if len(c.children) == 0:
                 continue
-            lines.append('#if str(%s) == "%s"' %(self.children[0].mako_name(mako_path), c.value))
+            lines.append('#if str(%s) == "%s"' % (self.children[0].mako_name(mako_path), c.value))
             lines.append(c.cli())
             lines.append('#end if')
         return "\n".join(lines)
@@ -835,8 +836,18 @@ def __init__(
     def acceptable_child(self, child):
         return isinstance(child, OutputData) or isinstance(child, OutputFilter) or isinstance(child, DiscoverDatasets)
 
-    def command_line(self, mako_path):
-        return "## TODO CLI for OutputCollection %s" % self.name
+    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):
+        lines = []
+        for child in self.children:
+            lines.append(child.command_line())
+        return "\n".join(lines)
+
 
 class DiscoverDatasets(XMLParam):
     name = "discover_datasets"
@@ -894,6 +905,14 @@ def __init__(
         super(TestOutput, self).__init__(**params)
 
 
+class TestOCElement(XMLParam):
+    name = "element"
+
+    def __init__(self, name=None, file=None, ftype=None, **kwargs):
+        params = Util.clean_kwargs(locals().copy())
+        super(TestOCElement, self).__init__(**params)
+
+
 class TestOutputCollection(XMLParam):
     name = "output_collection"
 
@@ -911,15 +930,21 @@ def __init__(
         params = Util.clean_kwargs(locals().copy())
         super(TestOutputCollection, self).__init__(**params)
 
+    def acceptable_child(self, child):
+        return isinstance(child, TestOCElement)
+
     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):
+        lines = []
+        for child in self.children:
+            lines.append(child.command_line())
+        return "\n".join(lines)
 
-        return ""
 
 class TestRepeat(XMLParam):
     name = "repeat"
@@ -939,7 +964,9 @@ def __init__(
         super(TestRepeat, self).__init__(**params)
 
     def acceptable_child(self, child):
-        return issubclass(type(child), TestParam)
+        return issubclass(type(child), TestParam) \
+            or issubclass(type(child), TestOutput) \
+            or issubclass(type(child), TestOutputCollection)
 
     def command_line_before(self, mako_path):
         return "<repeat name = '%s'>" % self.name

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name="galaxyxml",
-    version="0.4.13",
+    version="0.4.14",
     description="Galaxy XML generation library",
     author="Helena Rasche",
     author_email="[email protected]",
@@ -20,5 +20,5 @@
         "Environment :: Console",
         "License :: OSI Approved :: Apache Software License",
     ],
-    data_files = [("", ["LICENSE.TXT"])]
+    data_files=[("", ["LICENSE.TXT"])]
 )

test/import_xml.xml

@@ -71,11 +71,21 @@
     <test>
       <param name="sequence" value="seq.fasta"/>
       <output file="file.gbk" name="genbank"/>
-      <output_collection name="pdf_out"></output_collection>
-      <repeat name="test_repeat">
+      <output_collection name="pdf_out">
+         <element name="apdf" file="apdf" ftype="pdf"/>
+      </output_collection>
+      <repeat name="testrepeat">
           <param name="repeatchild" value="foo"/>
       </repeat>
-    </test>
+      <repeat name="output_repeat">
+          <output file="outputchild" name="bar"/>
+      </repeat>
+      <repeat name="collection_repeat">
+          <output_collection name="collectionchild">
+              <element name="elementary" file="efile" ftype="txt"/>
+          </output_collection>
+      </repeat>
+      </test>
   </tests>
   <help><![CDATA[help]]></help>
   <citations>

test/unit_test_import_xml.py

@@ -199,7 +199,23 @@ def test_collection_output(self):
 
     def test_repeat(self):
         repeat = self.tool.tests.children[0].node[3]
-        self.assertEqual(repeat.attrib["name"],"test_repeat")
+        self.assertEqual(repeat.attrib["name"],"testrepeat")
         # test param within repeat
         self.assertEqual(repeat[0].attrib["name"], "repeatchild")
         self.assertEqual(repeat[0].attrib["value"], "foo")
+        # test output within repeat
+        output = self.tool.tests.children[0].node[4]
+        self.assertEqual(output.attrib["name"],"output_repeat")
+        self.assertEqual(output[0].attrib["file"], "outputchild")
+        self.assertEqual(output[0].attrib["name"], "bar")
+
+    def test_ocr(self):
+        # test outputcollection within repeat - who knows...
+        output = self.tool.tests.children[0].node[5]
+        self.assertEqual(output.attrib["name"],"collection_repeat")
+        collection = output[0]
+        self.assertEqual(collection.attrib["name"], "collectionchild")
+        element = collection[0]
+        self.assertEqual(element.attrib["name"], "elementary")
+        self.assertEqual(element.attrib["file"], "efile")
+        self.assertEqual(element.attrib["ftype"], "txt")