Add support for plate metadata in assay saveBatch API #31

Author: labkey-klum

labkey/experiment.py

@@ -186,6 +186,7 @@ def __init__(self, **kwargs):
         self.material_inputs = kwargs.pop('material_inputs', kwargs.pop('materialInputs', []))
         self.material_outputs = kwargs.pop('material_outputs', kwargs.pop('materialOutputs', []))
         self.object_properties = kwargs.pop('object_properties', kwargs.pop('objectProperties', []))
+        self.plate_metadata = kwargs.pop('plate_metadata', None)
 
         # TODO: initialize protocol
         # self._protocol = None
@@ -212,6 +213,7 @@ def to_json(self):
         data['filePathRoot'] = self.file_path_root
         data['materialInputs'] = self.material_inputs
         data['materialOutputs'] = self.material_outputs
+        data['plateMetadata'] = self.plate_metadata
 
         return data
 

samples/experiment_platemetadata_example.py

@@ -0,0 +1,75 @@
+#
+# Copyright (c) 2018 LabKey Corporation
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+from __future__ import unicode_literals
+
+from labkey.utils import create_server_context
+from labkey.experiment import Batch, Run, load_batch, save_batch
+
+labkey_server = 'localhost:8080'
+project_name = 'assays'  # Project folder name
+context_path = 'labkey'
+server_context = create_server_context(labkey_server, project_name, context_path, use_ssl=False)
+
+assay_id = 310  # provide one from your server
+
+###################
+# Save an Assay batch
+###################
+
+# Generate the Run object(s)
+runTest = Run()
+runTest.name = 'python upload'
+runTest.data_rows = [{
+    # ColumnName: Value
+    'ParticipantId' : '1234',
+    'VisitId' : 111,
+    'WellLocation' : 'A1'
+}, {
+    'ParticipantId' : '5678',
+    'VisitId' : 222,
+    'WellLocation' : 'B11'
+}, {
+    'ParticipantId' : '9123',
+    'VisitId' : 333,
+    'WellLocation' : 'F12'
+}]
+
+# Assays that are configured for plate support have a required run property for the plate template, this is the plate template lsid
+runTest.properties['PlateTemplate'] = 'urn:lsid:labkey.com:PlateTemplate.Folder-6:d8bbec7d-34cd-1038-bd67-b3bd777822f8'
+
+# The assay plate metadata is a specially formatted JSON object to map properties to the well groups
+runTest.plate_metadata = {
+    'control' : {
+      'positive' : {'dilution':  0.005},
+      'negative' : {'dilution':  1.0}
+    },
+    'sample' : {
+      'SA01' : {'dilution': 1.0, 'Barcode' : 'BC_111', 'Concentration' : 0.0125},
+      'SA02' : {'dilution': 2.0, 'Barcode' : 'BC_222'},
+      'SA03' : {'dilution': 3.0, 'Barcode' : 'BC_333'},
+      'SA04' : {'dilution': 4.0, 'Barcode' : 'BC_444'}
+    }
+  }
+
+# Generate the Batch object(s)
+batch = Batch()
+batch.runs = [runTest]
+batch.name = 'python batch'
+batch.properties['PropertyName'] = 'Property Value'
+
+# Execute save api
+saved_batch = save_batch(server_context, assay_id, batch)
+

test/test_experiment_api.py

@@ -104,7 +104,7 @@ def setUp(self):
         self.service = MockSaveBatch()
         self.expected_kwargs = {
             'expected_args': [self.service.get_server_url()],
-            'data': '{"assayId": 12345, "batches": [{"batchProtocolId": 0, "comment": null, "created": null, "createdBy": null, "modified": null, "modifiedBy": null, "name": null, "properties": {"PropertyName": "Property Value"}, "runs": [{"comment": null, "created": null, "createdBy": null, "dataInputs": [], "dataRows": [], "experiments": [], "filePathRoot": null, "materialInputs": [], "materialOutputs": [], "modified": null, "modifiedBy": null, "name": "python upload", "properties": {"RunFieldName": "Run Field Value"}}]}]}',
+            'data': '{"assayId": 12345, "batches": [{"batchProtocolId": null, "comment": null, "created": null, "createdBy": null, "modified": null, "modifiedBy": null, "name": null, "properties": {"PropertyName": "Property Value"}, "runs": [{"comment": null, "created": null, "createdBy": null, "dataInputs": [], "dataRows": [], "experiments": [], "filePathRoot": null, "materialInputs": [], "materialOutputs": [], "modified": null, "modifiedBy": null, "name": "python upload", "plateMetadata": null, "properties": {"RunFieldName": "Run Field Value"}}]}]}',
             'headers': {'Content-type': 'application/json', 'Accept': 'text/plain'},
             'timeout': 300
         }