From de00af2c96b3cb3fa03f330814c947036135b30f Mon Sep 17 00:00:00 2001
From: tcezard <timothee.cezard@ed.ac.uk>
Date: Tue, 12 Mar 2019 12:43:28 +0000
Subject: [PATCH 1/2] change rework-step value's type  to match the API
 requirement

---
 pyclarity_lims/descriptors.py | 12 ++++++++----
 tests/test_descriptors.py     |  7 +++++--
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/pyclarity_lims/descriptors.py b/pyclarity_lims/descriptors.py
index 91e2a4d5..c29c8a21 100644
--- a/pyclarity_lims/descriptors.py
+++ b/pyclarity_lims/descriptors.py
@@ -278,7 +278,7 @@ class XmlAction(XmlElementAttributeDict):
     action: The type of action to perform. (leave, repeat, remove, review, complete, store, nextstep, rework, completerepeat, unknown)
     """
     def _parse_element(self, element, **kwargs):
-        from pyclarity_lims.entities import Artifact, ProtocolStep
+        from pyclarity_lims.entities import Artifact, ProtocolStep, Step
         for k, v in element.attrib.items():
 
             if k == 'artifact-uri':
@@ -287,12 +287,16 @@ def _parse_element(self, element, **kwargs):
             elif k in ('step-uri', 'rework-step-uri'):
                 k = k[:-(len('-uri'))]
                 v = ProtocolStep(self.instance.lims, uri=v)
+            elif k == 'rework-step-uri':
+                k = k[:-(len('-uri'))]
+                v = Step(self.instance.lims, uri=v)
             dict.__setitem__(self, k, v)
 
     def _setitem(self, key, value):
-        from pyclarity_lims.entities import Artifact, ProtocolStep
-        if (key in ['artifact'] and isinstance(value, Artifact)) or \
-           (key in ['step', 'rework-step'] and isinstance(value, ProtocolStep)):
+        from pyclarity_lims.entities import Artifact, ProtocolStep, Step
+        if key == 'artifact' and isinstance(value, Artifact) or \
+                key == 'step' and isinstance(value, ProtocolStep) or \
+                key == 'rework-step' and isinstance(value, Step):
             key += '-uri'
             value = value.uri
         elif key in ['action']:
diff --git a/tests/test_descriptors.py b/tests/test_descriptors.py
index 2523475c..407b430e 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, Process
+from pyclarity_lims.entities import Artifact, ProtocolStep, Container, Process, Step
 from pyclarity_lims.lims import Lims
 from tests import elements_equal
 
@@ -780,7 +780,7 @@ class TestXmlAction(TestCase):
     def setUp(self):
         et = ElementTree.fromstring('''<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
                 <test-entry>
-                <next-action step-uri="{url}/prt/1/stp/1" action="nextstep" artifact-uri="{url}/arts/a1"/>
+                <next-action step-uri="{url}/prt/1/stp/1" rework-step-uri="{url}/steps/1" action="nextstep" artifact-uri="{url}/arts/a1"/>
                 </test-entry>'''.format(url='http://testgenologics.com:4040'))
 
         et1 = ElementTree.fromstring('''<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
@@ -797,6 +797,7 @@ def test_parse(self):
         assert action['action'] == 'nextstep'
         assert action['step'] == ProtocolStep(self.lims, uri='http://testgenologics.com:4040/prt/1/stp/1')
         assert action['artifact'] == Artifact(self.lims, uri='http://testgenologics.com:4040/arts/a1')
+        assert action['rework-step'] == Step(self.lims, uri='http://testgenologics.com:4040/steps/1')
 
     def test_set(self):
         action = XmlAction(self.instance_empty, tag='next-action')
@@ -804,6 +805,8 @@ def test_set(self):
         assert action.instance.root.find('next-action').attrib['step-uri'] == 'http://testgenologics.com:4040/prt/1/stp/1'
         action['action'] = 'nextstep'
         assert action.instance.root.find('next-action').attrib['action'] == 'nextstep'
+        action['rework-step'] = Step(self.lims, uri='http://testgenologics.com:4040/steps/1')
+        assert action.instance.root.find('next-action').attrib['rework-step-uri'] == 'http://testgenologics.com:4040/steps/1'
 
         with pytest.raises(KeyError):
             action['whatever'] = 'youwant'

From 0bdeaacbc9ade637d3544521cb1c7dd4b9c9e1a5 Mon Sep 17 00:00:00 2001
From: tcezard <timothee.cezard@ed.ac.uk>
Date: Wed, 13 Mar 2019 15:49:08 +0000
Subject: [PATCH 2/2] ensure the rework_step-uri is actually set to Step in
 rework

---
 pyclarity_lims/descriptors.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyclarity_lims/descriptors.py b/pyclarity_lims/descriptors.py
index c29c8a21..6ac85650 100644
--- a/pyclarity_lims/descriptors.py
+++ b/pyclarity_lims/descriptors.py
@@ -284,7 +284,7 @@ def _parse_element(self, element, **kwargs):
             if k == 'artifact-uri':
                 k = 'artifact'
                 v = Artifact(self.instance.lims, uri=v)
-            elif k in ('step-uri', 'rework-step-uri'):
+            elif k == 'step-uri':
                 k = k[:-(len('-uri'))]
                 v = ProtocolStep(self.instance.lims, uri=v)
             elif k == 'rework-step-uri':