Merge remote-tracking branch 'origin/experiment' into experiment

# Conflicts:
#	labkey/query.py

Author: labkey-ians

labkey/experiment.py

@@ -32,7 +32,7 @@
 # print("Load an Assay batch from the server")
 # assay_id = # provide one from your server
 # batch_id = # provide one from your server
-# run_group = load_batch(assay_id, batch_id, server_context)
+# run_group = load_batch(server_context, assay_id, batch_id)
 #
 # if run_group is not None:
 # 	print("Batch Id: " + str(run_group.id))
@@ -44,23 +44,24 @@
 # 	run_group.properties[batch_property_name] = batch_property_value
 #
 # 	print("Save the batch")
-# 	save_batch(assay_id, run_group, server_context)
+# 	save_batch(server_context, assay_id, run_group)
 
 # --------
 # /EXAMPLE
 
 # TODO Incorporate logging
 
-def load_batch(assay_id, batch_id, server_context):
+def load_batch(server_context, assay_id, batch_id):
     """
     Loads a batch from the server.
+    :param server_context: A LabKey server context. See utils.create_server_context.
     :param assay_id: The protocol id of the assay from which to load a batch.
     :param batch_id:
-    :param server_context: A LabKey server context. See utils.create_server_context.
     :return:
     """
-    load_batch_url = build_url('assay', 'getAssayBatch.api', server_context)
+    load_batch_url = build_url(server_context, 'assay', 'getAssayBatch.api')
     session = server_context['session']
+    loaded_batch = None
 
     payload = {
         'assayId': assay_id,
@@ -76,39 +77,38 @@ def load_batch(assay_id, batch_id, server_context):
         response = session.post(load_batch_url, data=json.dumps(payload), headers=headers)
         json_body = handle_response(response)
         if json_body is not None:
-            return Batch.from_data(json_body['batch'])
+            loaded_batch = Batch.from_data(json_body['batch'])
     except SSLError as e:
         raise Exception("Failed to match server SSL configuration. Failed to load batch.")
 
-    return None
+    return loaded_batch
 
 
-def save_batch(assay_id, batch, server_context):
+def save_batch(server_context, assay_id, batch):
     """
     Saves a modified batch.
+    :param server_context: A LabKey server context. See utils.create_server_context.
     :param assay_id: The assay protocol id.
     :param batch: The Batch to save.
-    :param server_context: A LabKey server context. See utils.create_server_context.
     :return:
     """
-    result = save_batches(assay_id,[batch],server_context)
+    result = save_batches(server_context, assay_id, [batch])
 
     if result is not None:
         return result[0]
-    else:
-        return None
+    return None
 
 
-def save_batches(assay_id, batches, server_context):
+def save_batches(server_context, assay_id, batches):
     """
     Saves a modified batches.
-    :param assay_id: The assay protocol id.
-    :param batch: The Batch(es) to save.
     :param server_context: A LabKey server context. See utils.create_server_context.
+    :param assay_id: The assay protocol id.
+    :param batches: The Batch(es) to save.
     :return:
     """
 
-    save_batch_url = build_url('assay', 'saveAssayBatch.api', server_context)
+    save_batch_url = build_url(server_context, 'assay', 'saveAssayBatch.api')
     session = server_context['session']
 
     json_batches = []
@@ -145,7 +145,7 @@ def save_batches(assay_id, batches, server_context):
 
 class ExpObject(object):
     def __init__(self, **kwargs):
-        self.lsid = kwargs.pop('lsid', None)
+        self.lsid = kwargs.pop('lsid', None)  # Life Science identifier
         self.name = kwargs.pop('name', None)
         self.id = kwargs.pop('id', 0)
         self.row_id = self.id

labkey/query.py

@@ -58,9 +58,8 @@ class Pagination(Enum):
     all = 3
     none = 4
 
-
-def delete_rows(schema_name, query_name, rows, server_context, container_path=None):
-    url = build_url('query', 'deleteRows.api', server_context, container_path=container_path)
+def delete_rows(server_context, schema_name, query_name, rows, container_path=None):
+    url = build_url(server_context, 'query', 'deleteRows.api', container_path=container_path)
 
     payload = {
         'schemaName': schema_name,
@@ -72,9 +71,9 @@ def delete_rows(schema_name, query_name, rows, server_context, container_path=No
     return delete_rows_response
 
 
-def execute_sql(schema_name, sql, server_context, container_path=None,
+def execute_sql(server_context, schema_name, sql, container_path=None,
                 max_rows=None, sort=None, offset=None, container_filter=None):
-    url = build_url('query', 'executeSql.api', server_context, container_path=container_path)
+    url = build_url(server_context, 'query', 'executeSql.api', container_path=container_path)
 
     payload = {
         'schemaName': schema_name,
@@ -97,8 +96,8 @@ def execute_sql(schema_name, sql, server_context, container_path=None,
     return execute_sql_response
 
 
-def insert_rows(schema_name, query_name, rows, server_context, container_path=None):
-    url = build_url('query', 'insertRows.api', server_context, container_path=container_path)
+def insert_rows(server_context, schema_name, query_name, rows, container_path=None):
+    url = build_url(server_context, 'query', 'insertRows.api', container_path=container_path)
 
     payload = {
         'schemaName': schema_name,
@@ -111,8 +110,7 @@ def insert_rows(schema_name, query_name, rows, server_context, container_path=No
 
 
 # TODO: Support all the properties
-def select_rows(schema_name, query_name, server_context,
-                view_name=None,
+def select_rows(server_context, schema_name, query_name, view_name=None,
                 filter_array=None,
                 container_path=None,
                 columns=None,
@@ -130,10 +128,11 @@ def select_rows(schema_name, query_name, server_context,
                 required_version=None
                 ):
     # TODO: Support data_region_name
-    url = build_url('query', 'getQuery.api', server_context, container_path=container_path)
+    url = build_url(server_context, 'query', 'getQuery.api', container_path=container_path)
+
     payload = {
         'schemaName': schema_name,
-        'query.queryName': query_name,
+        'query.queryName': query_name
     }
 
     # TODO: Roll these checks up
@@ -185,8 +184,8 @@ def select_rows(schema_name, query_name, server_context,
     return select_rows_response
 
 
-def update_rows(schema_name, query_name, rows, server_context, container_path=None):
-    url = build_url('query', 'updateRows.api', server_context, container_path=container_path)
+def update_rows(server_context, schema_name, query_name, rows, container_path=None):
+    url = build_url(server_context, 'query', 'updateRows.api', container_path=container_path)
 
     payload = {
         'schemaName': schema_name,
@@ -205,5 +204,3 @@ def _make_request(server_context, url, payload):
         return handle_response(raw_response)
     except SSLError as e:
         raise Exception('Failed to match server SSL configuration. Ensure the server_context is configured correctly.')
-
-

labkey/utils.py

@@ -33,7 +33,16 @@ def init_poolmanager(self, connections, maxsize, block=False):
 
 
 def create_server_context(domain, container_path, context_path=None, use_ssl=True):
-    # TODO: Document
+    """
+    Create a LabKey server context. This context is used to encapsulate properties
+    about the LabKey server that is being requested against. This includes, but is not limited to,
+    the domain, container_path, and if the server is using SSL.
+    :param domain:
+    :param container_path:
+    :param context_path:
+    :param use_ssl:
+    :return:
+    """
     server_context = dict(domain=domain, container_path=container_path, context_path=context_path)
 
     if use_ssl:
@@ -55,13 +64,13 @@ def create_server_context(domain, container_path, context_path=None, use_ssl=Tru
     return server_context
 
 
-def build_url(controller, action, server_context, container_path=None):
+def build_url(server_context, controller, action, container_path=None):
     """
     Builds a URL from a controller and an action. Users the server context to determine domain,
     context path, container, etc.
+    :param server_context: A LabKey server context. See utils.create_server_context.
     :param controller: The controller to use in building the URL
     :param action: The action to use in building the URL
-    :param server_context:
     :param container_path:
     :return:
     """

samples/load_batch_example.py

@@ -10,7 +10,7 @@
 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)
+run_group = load_batch(server_context, assay_id, batch_id)
 
 if run_group is not None:
     print("Batch Id: " + str(run_group.id))

samples/save_batch_example.py

@@ -13,20 +13,20 @@
 dataRows = [
     {
         # ColumnName : Value
-        "SampleId": "Monkey 1"
-        , "TimePoint": "2008/11/02 11:22:33"
-        , "DoubleData": 4.5
-        , "HiddenData": "another data point"
+        "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 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"
+        "SampleId": "Monkey 3",
+        "TimePoint": "2008/11/02 14:00:01",
+        "DoubleData": 1.5,
+        "HiddenData": "jimbo"
     }
 ]
 
@@ -43,7 +43,7 @@
 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)
+RESULT = save_batch(server_context, assay_id, batch)
+# RESULT = save_batches(server_context, assay_id, [batch1, batch2])
 print(RESULT.id)