Merge c334fd9 into 0aac6ad

pyclarity_lims/entities.py

@@ -875,7 +875,7 @@ def set_placements(self, output_containers, output_placement_list):
         self.placement.root = self.placement.post()
 
     @classmethod
-    def create(cls, lims, protocol_step, inputs, container_type_name=None, reagent_category=None, **kwargs):
+    def create(cls, lims, protocol_step, inputs, container_type_name=None, reagent_category=None, replicates=1, **kwargs):
         """
         Create a new instance of a Step. This method will start a step from queued artifacts.
 
@@ -885,6 +885,7 @@ def create(cls, lims, protocol_step, inputs, container_type_name=None, reagent_c
         :param container_type_name: optional name of the type of container that this step use for its output.
                                     if omitted it uses the required type from the ProtocolStep if there is only one.
         :param reagent_category: optional reagent_category.
+        :param replicates: int or list of int specifying the number of replicates for each inputs.
         """
         instance = super(Step, cls)._create(lims, **kwargs)
         # Check configuratio of the step
@@ -910,12 +911,17 @@ def create(cls, lims, protocol_step, inputs, container_type_name=None, reagent_c
             reagent_category_node = ElementTree.SubElement(instance.root, 'reagent_category')
             reagent_category_node.text = reagent_category
 
+        if isinstance(replicates, int):
+            replicates = [replicates] * len(inputs)
+        assert len(replicates) == len(inputs)
         inputs_node = ElementTree.SubElement(instance.root, 'inputs')
-        for artifact in inputs:
+        for i, artifact in enumerate(inputs):
             if not isinstance(artifact, Artifact):
                 raise TypeError('Input must be of type Artifact not %s.' % type(artifact))
             input_node = ElementTree.SubElement(inputs_node, 'input')
             input_node.attrib['uri'] = artifact.uri
+            if replicates:
+                input_node.attrib['replicates'] = str(replicates[i])
         data = lims.tostring(ElementTree.ElementTree(instance.root))
         instance.root = lims.post(uri=lims.get_uri(cls._URI), data=data)
         instance._uri = instance.root.attrib['uri']

tests/test_entities.py

@@ -274,6 +274,35 @@ def test_create(self):
         )
         with patch('pyclarity_lims.lims.requests.post',
                    return_value=Mock(content=self.step_xml, status_code=201)) as patch_post:
+            Step.create(self.lims, protocol_step=protocol_step, inputs=inputs, replicates=[1, 2])
+            data = '''<?xml version='1.0' encoding='utf-8'?>
+            <stp:step-creation xmlns:stp="http://genologics.com/ri/step">
+                <configuration uri="http://testgenologics.com:4040/api/v2/configuration//protocols/p1/steps/p1s1">
+                    My fancy step
+                </configuration>
+                <container-type>Tube</container-type>
+                <inputs>
+                    <input uri="http://testgenologics.com:4040/api/v2/artifacts/a1" replicates="1"/>
+                    <input uri="http://testgenologics.com:4040/api/v2/artifacts/a2" replicates="2"/>
+                </inputs>
+            </stp:step-creation>
+            '''
+            assert elements_equal(ElementTree.fromstring(patch_post.call_args_list[0][1]['data']), ElementTree.fromstring(data))
+
+    def test_create2(self):
+        inputs = [
+            Mock(spec=Artifact, lims=self.lims, uri='http://testgenologics.com:4040/api/v2/artifacts/a1'),
+            Mock(spec=Artifact, lims=self.lims, uri='http://testgenologics.com:4040/api/v2/artifacts/a2')
+        ]
+        protocol_step = NamedMock(
+            spec=ProtocolStep,
+            real_name='My fancy step',
+            uri='http://testgenologics.com:4040/api/v2/configuration//protocols/p1/steps/p1s1',
+            permittedcontainers=['Tube']
+        )
+        with patch('pyclarity_lims.lims.requests.post',
+                   return_value=Mock(content=self.step_xml, status_code=201)) as patch_post:
+            # replicates default to 1
             Step.create(self.lims, protocol_step=protocol_step, inputs=inputs)
             data = '''<?xml version='1.0' encoding='utf-8'?>
             <stp:step-creation xmlns:stp="http://genologics.com/ri/step">
@@ -282,13 +311,14 @@ def test_create(self):
                 </configuration>
                 <container-type>Tube</container-type>
                 <inputs>
-                    <input uri="http://testgenologics.com:4040/api/v2/artifacts/a1" />
-                    <input uri="http://testgenologics.com:4040/api/v2/artifacts/a2" />
+                    <input uri="http://testgenologics.com:4040/api/v2/artifacts/a1" replicates="1"/>
+                    <input uri="http://testgenologics.com:4040/api/v2/artifacts/a2" replicates="1"/>
                 </inputs>
             </stp:step-creation>
             '''
             assert elements_equal(ElementTree.fromstring(patch_post.call_args_list[0][1]['data']), ElementTree.fromstring(data))
 
+
     def test_parse_entity(self):
         with patch('requests.Session.get', return_value=Mock(content=self.step_xml, status_code=200)):
             s = Step(self.lims, id='s1')
@@ -404,5 +434,3 @@ def test_create_entity(self):
             </location>
             </smp:samplecreation>'''
             assert elements_equal(ElementTree.fromstring(patch_post.call_args_list[0][1]['data']), ElementTree.fromstring(data))
-
-