From 85159560d27d46b9e04adae9455bf17e0d6a8931 Mon Sep 17 00:00:00 2001
From: tcezard <timothee.cezard@ed.ac.uk>
Date: Thu, 14 Feb 2019 12:05:20 +0000
Subject: [PATCH] Add creation of input-output-map entry

---
 pyclarity_lims/descriptors.py | 34 +++++++++++++++++++++++++++++-----
 tests/test_descriptors.py     | 22 +++++++++++++++++++++-
 2 files changed, 50 insertions(+), 6 deletions(-)

diff --git a/pyclarity_lims/descriptors.py b/pyclarity_lims/descriptors.py
index 46e80c22..91e2a4d5 100644
--- a/pyclarity_lims/descriptors.py
+++ b/pyclarity_lims/descriptors.py
@@ -664,16 +664,40 @@ def _get_dict(self, lims, node):
                 result[key] = node.attrib[key]
             except KeyError:
                 pass
-            for uri in ['uri', 'post-process-uri']:
-                try:
-                    result[uri] = Artifact(lims, uri=node.attrib[uri])
-                except KeyError:
-                    pass
+        for uri in ['uri', 'post-process-uri']:
+            try:
+                result[uri] = Artifact(lims, uri=node.attrib[uri])
+            except KeyError:
+                pass
         node = node.find('parent-process')
         if node is not None:
             result['parent-process'] = Process(lims, node.attrib['uri'])
         return result
 
+    def _set_dict(self, element, value_dict):
+        for key in ['limsid', 'output-type', 'output-generation-type']:
+            if key in value_dict:
+                element.attrib[key] = value_dict[key]
+        for key in ['uri', 'post-process-uri']:
+            if key in value_dict:
+                element.attrib[key] = value_dict[key].uri
+        if 'parent-process' in value_dict:
+            node = ElementTree.SubElement(element, 'parent-process')
+            node.attrib['uri'] = value_dict['parent-process'].uri
+
+    def _create_new_node(self, value ):
+        if not isinstance(value, tuple):
+            raise TypeError('You need to provide a tuple not %s' % (type(value)))
+        if len(value) != 2:
+            raise TypeError('You need to provide a tuple with 2 values, found %s' % len(value))
+        input_dict, output_dict = value
+        node = ElementTree.Element(self.tag)
+        input_element = ElementTree.SubElement(node, 'input')
+        output_element = ElementTree.SubElement(node, 'output')
+        self._set_dict(input_element, input_dict)
+        self._set_dict(output_element, output_dict)
+        return node
+
 
 class OutputPlacementList(TagXmlList):
     """This is a list of output placements as found in the StepPlacement. The list contains tuples organised as follows:
diff --git a/tests/test_descriptors.py b/tests/test_descriptors.py
index 6873caf3..2523475c 100644
--- a/tests/test_descriptors.py
+++ b/tests/test_descriptors.py
@@ -11,7 +11,7 @@
     StringDictionaryDescriptor, IntegerDescriptor, BooleanDescriptor, UdfDictionary, EntityDescriptor, \
     InputOutputMapList, EntityListDescriptor, PlacementDictionary, EntityList, SubTagDictionary, ExternalidList,\
     XmlElementAttributeDict, XmlAttributeList, XmlReagentLabelList, XmlPooledInputDict, XmlAction, QueuedArtifactList
-from pyclarity_lims.entities import Artifact, ProtocolStep, Container
+from pyclarity_lims.entities import Artifact, ProtocolStep, Container, Process
 from pyclarity_lims.lims import Lims
 from tests import elements_equal
 
@@ -663,6 +663,26 @@ def test___get__(self):
         assert sorted(res[0][0].keys()) == sorted(expected_keys_input)
         assert sorted(res[0][1].keys()) == sorted(expected_keys_ouput)
 
+    def test_create(self):
+        et = ElementTree.fromstring("""<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+        <test-entry xmlns:udf="http://genologics.com/ri/userdefined">
+        </test-entry>""")
+        lims = Mock(cache={})
+        instance = Mock(root=et, lims=lims)
+        res = self.IO_map.__get__(instance, None)
+        input_dict = {'uri': Artifact(lims, uri='input_uri'), 'limsid': 'a1', 'parent-process': Process(lims, uri='p_uri')}
+        output_dict = {'uri': Artifact(lims, uri='output_uri'), 'limsid': 'a2', 'output-type': 'PerInput'}
+        res.append((input_dict, output_dict))
+        assert len(et) == 1
+        node = et.find('input-output-map')
+        assert len(node) == 2  # input and output
+        assert node.find('input').attrib['uri'] == 'input_uri'
+        assert node.find('input').attrib['limsid'] == 'a1'
+        assert node.find('input').find('parent-process').attrib['uri'] == 'p_uri'
+        assert node.find('output').attrib['uri'] == 'output_uri'
+        assert node.find('output').attrib['limsid'] == 'a2'
+        assert node.find('output').attrib['output-type'] == 'PerInput'
+
 
 class TestExternalidList(TestCase):
     def setUp(self):