Spec 23821 : Python API for saveBatch

fixed a bug in save_batch and added sample files for load/save using the API

Author: labkey-ians

labkey/experiment.py

@@ -240,7 +240,8 @@ def from_data(data):
 
     def to_json(self):
         data = super(Run, self).to_json()
-        data['dataInputs'] = self.data_inputs
+
+        data['dataInputs'] = [data_input.to_json() for data_input in self.data_inputs]
         data['dataRows'] = self.data_rows
         data['experiments'] = self.experiments
         data['filePathRoot'] = self.file_path_root
@@ -256,24 +257,45 @@ def __init__(self, **kwargs):
 
         self.source_protocol = kwargs.pop('source_protocol', kwargs.pop('sourceProtocol', None))
         self.run = kwargs.pop('run', None)  # TODO Check if this should be a Run instance
-        self.target_applications = kwargs.pop('target_applications', kwargs.pop('targetApplications'), None)
-        self.successor_runs = kwargs.pop('successor_runs', kwargs.pop('sucessorRuns', None))  # sic
+        self.target_applications = kwargs.pop('target_applications', kwargs.pop('targetApplications', None))
+        self.successor_runs = kwargs.pop('successor_runs', kwargs.pop('successorRuns', kwargs.pop('sucessorRuns', None)))  # sic
         self.cpas_type = kwargs.pop('cpas_type', kwargs.pop('cpasType', None))
 
     @staticmethod
     def from_data(data):
         return ProtocolOutput(**data)
 
+    def to_json(self):
+        data = super(ProtocolOutput, self).to_json()
+
+        data['sourceProtocol'] = self.source_protocol
+        data['run'] = self.run
+        data['targetApplications'] = self.target_applications
+        data['sucessorRuns'] = self.successor_runs
+        data['cpasType'] = self.cpas_type
+
+        return data
+
 
 class Data(ProtocolOutput):
     def __init__(self, **kwargs):
         super(Data, self).__init__(**kwargs)
 
         self.data_type = kwargs.pop('data_type', kwargs.pop('dataType', None))
         self.data_file_url = kwargs.pop('data_file_url', kwargs.pop('dataFileURL', None))
-        self.pipeline_path = kwargs.pop('pipeline_path', kwargs.pop('pipeline_path', None))
+        self.pipeline_path = kwargs.pop('pipeline_path', kwargs.pop('pipelinePath', None))
         self.role = kwargs.pop('role', None)
 
     @staticmethod
     def from_data(data):
         return Data(**data)
+
+    def to_json(self):
+        data = super(Data, self).to_json()
+
+        data['dataFileURL'] = self.data_file_url
+        data['dataType'] = self.data_type
+        data['pipelinePath'] = self.pipeline_path
+        data['role'] = self.role
+
+        return data

samples/load_batch_example.py

@@ -0,0 +1,18 @@
+# Sample to get a batch
+
+from labkey.utils import create_server_context
+from labkey.experiment import load_batch
+
+print("Create a server context")
+project_name = 'ModuleAssayTest'  # Project folder name
+server_context = create_server_context('localhost:8080', project_name, 'labkey', use_ssl=False)
+
+print("Load an Assay batch from the server")
+assay_id = 1168  # provide one from your server
+batch_id = 95  # provide one from your server
+run_group = load_batch(assay_id, batch_id, server_context)
+
+if run_group is not None:
+    print("Batch Id: " + str(run_group.id))
+    print("Created By: " + run_group.created_by)
+

samples/save_batch_example.py

@@ -0,0 +1,49 @@
+# Sample code to submit a single batch of Assay data containing a run with three rows of data
+
+from labkey.utils import create_server_context
+from labkey.experiment import save_batch, save_batches, Batch, Run
+
+assay_id = 1168  # provide one from your server. rowid from the URL query parameters
+
+print("Create a server context")
+project_name = 'ModuleAssayTest'
+server_context = create_server_context('localhost:8080', project_name, 'labkey', use_ssl=False)
+
+# Run data rows
+dataRows = [
+    {
+        # ColumnName : Value
+        "SampleId": "Monkey 1"
+        , "TimePoint": "2008/11/02 11:22:33"
+        , "DoubleData": 4.5
+        , "HiddenData": "another data point"
+    }, {
+        "SampleId": "Monkey 2"
+        , "TimePoint": "2008/11/02 14:00:01"
+        , "DoubleData": 3.1
+        , "HiddenData": "fozzy bear"
+    }, {
+        "SampleId": "Monkey 3"
+        , "TimePoint": "2008/11/02 14:00:01"
+        , "DoubleData": 1.5
+        , "HiddenData": "jimbo"
+    }
+]
+
+# Generate the Run object(s)
+runTest = Run()
+runTest.name = 'python upload'
+runTest.data_rows = dataRows
+runTest.properties['RunFieldName'] = 'Run Field Value'
+
+# Generate the Batch object(s)
+batch = Batch()
+batch.runs = [runTest]
+batch.name = 'python batch'
+batch.properties['PropertyName'] = 'Property Value'
+
+# Execute save api
+RESULT = save_batch(assay_id, batch, server_context)
+# RESULT = save_batches(assay_id, [batch1, batch2], server_context)
+print(RESULT.id)
+