Merge pull request #17 from EdinburghGenomics/fixactions

Fixactions

pyclarity_lims/descriptors.py

@@ -270,25 +270,30 @@ class XmlAction(XmlElementAttributeDict):
     artifact: The Artifact associated with this Action
     step: The next step associated with this action
     rework-step: The step associated with this action when the Artifact need to be requeued
+    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, Step
+        from pyclarity_lims.entities import Artifact, ProtocolStep
         for k, v in element.attrib.items():
+
             if k == 'artifact-uri':
                 k = 'artifact'
                 v = Artifact(self.instance.lims, uri=v)
-            elif k == 'step-uri':
-                k = 'step'
-                v = Step(self.instance.lims, uri=v)
-            elif k == 'rework-step-uri':
-                k = 'rework-step'
-                v = Step(self.instance.lims, uri=v)
+            elif k in ('step-uri', 'rework-step-uri'):
+                k = k[:-(len('-uri'))]
+                v = ProtocolStep(self.instance.lims, uri=v)
             dict.__setitem__(self, k, v)
 
     def _setitem(self, key, value):
-        if key in ['artifact', 'step', 'rework-step']:
-            key = key + '-uri'
+        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)):
+            key += '-uri'
             value = value.uri
+        elif key in ['action']:
+            pass
+        else:
+            raise KeyError('%s Is not a supported key for next action' % key)
         self._elems[0].attrib[key] = value
 
     def _delitem(self, key):

pyclarity_lims/entities.py

@@ -655,19 +655,32 @@ def get_selected_containers(self):
 
 
 class StepActions(Entity):
-    """Actions associated with a step"""
+    """Actions associated with the end of the step"""
     _escalation = None
     next_actions = MutableDescriptor(XmlActionList)
     """
     List of dict that representing an action for an artifact. They keys of the dict are:
       - artifact: The :py:class:`artifact <pyclarity_lims.entities.Artifact>` associated with this Action
       - step: The next :py:class:`step <pyclarity_lims.entities.Step>` associated with this action
-      - rework-step: The :py:class:`step <pyclarity_lims.entities.Step>` associated with this action when the Artifact need to be requeued"""
+      - rework-step: The :py:class:`step <pyclarity_lims.entities.Step>` associated with this action when the Artifact need to be requeued
+      - action: The type of action to perform.
+        - leave: Leave the sample in the QC protocol.
+        - repeat: Repeat this step.
+        - remove: Remove from workflow.
+        - review: Request manager review.
+        - complete: Mark protocol as complete.
+        - store: Store for later.
+        - nextstep: Continue to the next step.
+        - rework: Rework from an earlier step.
+        - completerepeat: Complete and Repeat
+        - unknown: The action is unknown.
+        """
     step = None # See bottom of the file
     """:py:class:`Step <pyclarity_lims.entities.Step>` associated with the actions."""
 
     @property
     def escalation(self):
+        # TODO: Convert to using descriptor and document
         if not self._escalation:
             self.get()
             self._escalation = {}

tests/test_descriptors.py

@@ -9,10 +9,10 @@
 from pyclarity_lims.descriptors import StringDescriptor, StringAttributeDescriptor, StringListDescriptor, \
     StringDictionaryDescriptor, IntegerDescriptor, BooleanDescriptor, UdfDictionary, EntityDescriptor, \
     InputOutputMapList, EntityListDescriptor, PlacementDictionary, EntityList, SubTagDictionary, ExternalidList,\
-    XmlElementAttributeDict, XmlAttributeList, XmlReagentLabelList, XmlPooledInputDict
-from pyclarity_lims.entities import Artifact
+    XmlElementAttributeDict, XmlAttributeList, XmlReagentLabelList, XmlPooledInputDict, XmlAction
+from pyclarity_lims.entities import Artifact, ProtocolStep
 from pyclarity_lims.lims import Lims
-from tests import  elements_equal
+from tests import elements_equal
 
 if version_info[0] == 2:
     from mock import Mock
@@ -94,7 +94,7 @@ def setUp(self):
 
     def test__get__(self):
         bd = self._make_desc(BooleanDescriptor, 'istest')
-        assert bd.__get__(self.instance, None) == True
+        assert bd.__get__(self.instance, None)
 
     def test__set__(self):
         bd = self._make_desc(BooleanDescriptor, 'istest')
@@ -246,6 +246,7 @@ def test__set__(self):
         assert isinstance(res, dict)
         assert res['mykey1'] == 'myvalue1'
 
+
 class TestUdfDictionary(TestCase):
     def setUp(self):
         et = ElementTree.fromstring("""<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
@@ -345,8 +346,7 @@ def test___delitem__(self):
         del self.dict1['test']
         with pytest.raises(KeyError):
             self.dict1['test']
-        assert self._get_udf_value(self.dict1, 'test') == None
-
+        assert self._get_udf_value(self.dict1, 'test') is None
 
     def test_items(self):
         pass
@@ -500,6 +500,7 @@ def test___setitem__(self):
         assert len(self.dict1) == 3
         assert len(self.dict1.rootnode(self.dict1.instance)) == 3
 
+
 class TestEntityList(TestCase):
 
     def setUp(self):
@@ -600,7 +601,6 @@ def test___get__(self):
         assert sorted(res[0][1].keys()) == sorted(expected_keys_ouput)
 
 
-
 class TestExternalidList(TestCase):
 
     def setUp(self):
@@ -648,7 +648,7 @@ def setUp(self):
     def test_get(self):
         al = XmlAttributeList(self.instance1, tag='test-tag', nesting=['test-tags'])
         assert al[0] == {'attrib1': 'value1', 'attrib2':'value2'}
-        assert al[1] == {'attrib1': 'value11', 'attrib2':'value12', 'attrib3':'value13'}
+        assert al[1] == {'attrib1': 'value11', 'attrib2': 'value12', 'attrib3':'value13'}
 
     def test_append(self):
         el = XmlAttributeList(self.instance1, tag='test-tag', nesting=['test-tags'])
@@ -694,3 +694,37 @@ def test_append(self):
             rl.instance.root.findall('reagent-label')[1],
             ElementTree.fromstring('''<reagent-label name="another label"/>''')
         )
+
+
+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"/>
+                </test-entry>'''.format(url='http://testgenologics.com:4040'))
+
+        et1 = ElementTree.fromstring('''<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+        <test-entry>
+        <next-action artifact-uri="{url}/arts/a1"/>
+        </test-entry>'''.format(url='http://testgenologics.com:4040'))
+
+        self.lims = Lims('http://testgenologics.com:4040', username='test', password='password')
+        self.instance1 = Mock(root=et, lims=self.lims)
+        self.instance_empty = Mock(root=et1, lims=self.lims)
+
+    def test_parse(self):
+        action = XmlAction(self.instance1, tag='next-action')
+        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')
+
+    def test_set(self):
+        action = XmlAction(self.instance_empty, tag='next-action')
+        action['step'] = ProtocolStep(self.lims, uri='http://testgenologics.com:4040/prt/1/stp/1')
+        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'
+
+        with pytest.raises(KeyError):
+            action['whatever'] = 'youwant'