Ge/19

cellengine/Gates/ellipse_gate.py

@@ -1,13 +1,28 @@
-from custom_inherit import doc_inherit
-from .gate_util import common_gate_create, gate_style
+# from custom_inherit import doc_inherit
+from .gate_util import create_common_gate, gate_style
 from .. import _helpers
 
-@doc_inherit(common_gate_create, style=gate_style)
-def create_ellipse_gate(experiment_id, x_channel, y_channel, name,
-                        x, y, angle, major, minor, label=[], gid=None, locked=False,
-                        parent_population_id=None, parent_population=None,
-                        tailored_per_file=False, fcs_file_id=None,
-                        fcs_file=None, create_population=True):
+# @doc_inherit(create_common_gate, style=gate_style)
+def create_ellipse_gate(
+    experiment_id,
+    x_channel,
+    y_channel,
+    name,
+    x,
+    y,
+    angle,
+    major,
+    minor,
+    label=[],
+    gid=None,
+    locked=False,
+    parent_population_id=None,
+    parent_population=None,
+    tailored_per_file=False,
+    fcs_file_id=None,
+    fcs_file=None,
+    create_population=True,
+):
     """Creates an ellipse gate.
 
     Args:
@@ -33,22 +48,27 @@ def create_ellipse_gate(experiment_id, x_channel, y_channel, name,
         gid = _helpers.generate_id()
 
     model = {
-        'locked': locked,
-        'label': label,
-        'ellipse': {'angle': angle, 'major': major, 'minor': minor, 'center': [x, y]}
+        "locked": locked,
+        "label": label,
+        "ellipse": {"angle": angle, "major": major, "minor": minor, "center": [x, y]},
     }
 
     body = {
-        'experimentId': experiment_id,
-        'name': name,
-        'type': 'EllipseGate',
-        'gid': gid,
-        'xChannel': x_channel,
-        'yChannel': y_channel,
-        'parentPopulationId': parent_population_id,
-        'model': model
+        "experimentId": experiment_id,
+        "name": name,
+        "type": "EllipseGate",
+        "gid": gid,
+        "xChannel": x_channel,
+        "yChannel": y_channel,
+        "parentPopulationId": parent_population_id,
+        "model": model,
     }
 
-    return common_gate_create(experiment_id, body=body,
-            tailored_per_file=tailored_per_file, fcs_file_id=fcs_file_id,
-            fcs_file=fcs_file, create_population=create_population)
+    return create_common_gate(
+        experiment_id,
+        body=body,
+        tailored_per_file=tailored_per_file,
+        fcs_file_id=fcs_file_id,
+        fcs_file=fcs_file,
+        create_population=create_population,
+    )

cellengine/Gates/gate_util.py

@@ -5,8 +5,9 @@
 from .. import _helpers
 
 
-def common_gate_create(experiment_id, body, tailored_per_file, fcs_file_id,
-                       fcs_file, create_population):
+def create_common_gate(
+    experiment_id, body, tailored_per_file, fcs_file_id, fcs_file, create_population
+):
     """
     <Description>
 
@@ -46,36 +47,33 @@ def common_gate_create(experiment_id, body, tailored_per_file, fcs_file_id,
         Example:
             <Example>
     """
-    body = parse_fcs_file_args(experiment_id, body, tailored_per_file,
-                               fcs_file_id, fcs_file)
+    body = parse_fcs_file_args(
+        experiment_id, body, tailored_per_file, fcs_file_id, fcs_file
+    )
 
-    body = _helpers.convert_dict(body, 'snake_to_camel')
-    res = _helpers.base_create(gate.Gate,
-                               url="experiments/{0}/gates".format(experiment_id),
-                               expected_status=201,
-                               json=body, params={'createPopulation':
-                                                  create_population}
-                               )
-    return res
+    body = _helpers.convert_dict(body, "snake_to_camel")
+
+    return body
 
 
-def parse_fcs_file_args(experiment_id, body, tailored_per_file, fcs_file_id,
-                        fcs_file):
+def parse_fcs_file_args(experiment_id, body, tailored_per_file, fcs_file_id, fcs_file):
     """Find the fcs file ID if 'tailored_per_file' and either 'fcs_file' or
     'fcs_file_id' are specified."""
     if fcs_file is not None and fcs_file_id is not None:
         raise ValueError("Please specify only 'fcs_file' or 'fcs_file_id'.")
     if fcs_file is not None and tailored_per_file is True:  # lookup by name
         _file = get_fcsfile(experiment_id, name=fcs_file)
         fcs_file_id = _file._id
-    body['tailoredPerFile'] = tailored_per_file
-    body['fcsFileId'] = fcs_file_id
+    body["tailoredPerFile"] = tailored_per_file
+    body["fcsFileId"] = fcs_file_id
     return body
 
 
 def get_fcsfile(experiment_id, _id=None, name=None):
     if _id:
-        content = _helpers.base_get("experiments/{0}/fcsfiles/{1}".format(experiment_id, _id))
+        content = _helpers.base_get(
+            "experiments/{0}/fcsfiles/{1}".format(experiment_id, _id)
+        )
         content = FcsFile(properties=content)
     else:
         content = _helpers.load_fcsfile_by_name(experiment_id, name)
@@ -119,23 +117,25 @@ def create_gates(experiment_id=None, gates=None, create_all_populations=True):
     """
     prepared_gates = []
     for g in gates:
-        g.update({'_id': _helpers.generate_id()})
-        if 'gid' not in g.keys():
-            g.update({'gid': _helpers.generate_id()})
+        g.update({"_id": _helpers.generate_id()})
+        if "gid" not in g.keys():
+            g.update({"gid": _helpers.generate_id()})
         prepared_gates.append(g)
 
     new_gates = []
     for each_gate in prepared_gates:
         if create_all_populations is False:
-            create_populations = each_gate.get('create_population', False)
+            create_populations = each_gate.get("create_population", False)
         else:
             create_populations = create_all_populations
-        new_gate = common_gate_create(experiment_id=each_gate.get('experiment_id', experiment_id),
-                                 body=each_gate,
-                                 tailored_per_file=each_gate.get('tailored_per_file', False),
-                                 fcs_file_id=each_gate.get('fcs_file_id', None),
-                                 fcs_file=each_gate.get('fcs_file', None),
-                                 create_population=create_populations)
+        new_gate = create_common_gate(
+            experiment_id=each_gate.get("experiment_id", experiment_id),
+            body=each_gate,
+            tailored_per_file=each_gate.get("tailored_per_file", False),
+            fcs_file_id=each_gate.get("fcs_file_id", None),
+            fcs_file=each_gate.get("fcs_file", None),
+            create_population=create_populations,
+        )
         new_gates.append(new_gate)
 
     return new_gates
@@ -175,12 +175,14 @@ def delete_gates(experiment_id, _id=None, gid=None, exclude=None):
 
 
 def gate_style(prnt_doc, child_doc):
-    desc = child_doc[:child_doc.index('Args')].strip()
-    args = child_doc[child_doc.index('Args')+5:child_doc.index('Returns')].strip()
-    args = re.sub('\n', '\n    ', args)
-    returns = child_doc[child_doc.index('Returns')+10:child_doc.index('Example')].strip()
-    example = child_doc[child_doc.index('Example')+10:].strip()
-    keys = ['<Description>', '<Gate Args>', '<Returns>', '<Example>']
+    desc = child_doc[: child_doc.index("Args")].strip()
+    args = child_doc[child_doc.index("Args") + 5 : child_doc.index("Returns")].strip()
+    args = re.sub("\n", "\n    ", args)
+    returns = child_doc[
+        child_doc.index("Returns") + 10 : child_doc.index("Example")
+    ].strip()
+    example = child_doc[child_doc.index("Example") + 10 :].strip()
+    keys = ["<Description>", "<Gate Args>", "<Returns>", "<Example>"]
     sections = [desc, args, returns, example]
     docs = prnt_doc
     for key, section in zip(keys, sections):

cellengine/Gates/polygon_gate.py

@@ -1,15 +1,28 @@
 import numpy
-from custom_inherit import doc_inherit
-from .gate_util import common_gate_create, gate_style
+
+# from custom_inherit import doc_inherit
+from .gate_util import create_common_gate, gate_style
 from .. import _helpers
 
 
-@doc_inherit(common_gate_create, style=gate_style)
-def create_polygon_gate(experiment_id, x_channel, y_channel, name,
-                        x_vertices,  y_vertices, label=[], gid=None, locked=False,
-                        parent_population_id=None, parent_population=None,
-                        tailored_per_file=False, fcs_file_id=None,
-                        fcs_file=None, create_population=True):
+# @doc_inherit(create_common_gate, style=gate_style)
+def create_polygon_gate(
+    experiment_id,
+    x_channel,
+    y_channel,
+    name,
+    x_vertices,
+    y_vertices,
+    label=[],
+    gid=None,
+    locked=False,
+    parent_population_id=None,
+    parent_population=None,
+    tailored_per_file=False,
+    fcs_file_id=None,
+    fcs_file=None,
+    create_population=True,
+):
     """Creates a polygon gate.
 
     Args:
@@ -22,7 +35,7 @@ def create_polygon_gate(experiment_id, x_channel, y_channel, name,
         A PolygonGate object.
 
     Example:
-        experiment.create_polygon_gate(experiment_id, x_channel="FSC-A",
+        experiment.create_polygon_gate(x_channel="FSC-A",
         y_channel="FSC-W", name="my gate", x_vertices=[1, 2, 3], y_vertices=[4,
         5, 6])
     """
@@ -32,23 +45,27 @@ def create_polygon_gate(experiment_id, x_channel, y_channel, name,
         gid = _helpers.generate_id()
 
     model = {
-        'locked': locked,
-        'label': label,
-        'polygon': {'vertices': [[a, b] for (a, b) in zip(x_vertices, y_vertices)]}
+        "locked": locked,
+        "label": label,
+        "polygon": {"vertices": [[a, b] for (a, b) in zip(x_vertices, y_vertices)]},
     }
 
     body = {
-        'experimentId': experiment_id,
-        'name': name,
-        'type': 'PolygonGate',
-        'gid': gid,
-        'xChannel': x_channel,
-        'yChannel': y_channel,
-        'parentPopulationId': parent_population_id,
-        'model': model
+        "experimentId": experiment_id,
+        "name": name,
+        "type": "PolygonGate",
+        "gid": gid,
+        "xChannel": x_channel,
+        "yChannel": y_channel,
+        "parentPopulationId": parent_population_id,
+        "model": model,
     }
 
-    return common_gate_create(experiment_id, body=body,
-                              tailored_per_file=tailored_per_file,
-                              fcs_file_id=fcs_file_id, fcs_file=fcs_file,
-                              create_population=create_population)
+    return create_common_gate(
+        experiment_id,
+        body=body,
+        tailored_per_file=tailored_per_file,
+        fcs_file_id=fcs_file_id,
+        fcs_file=fcs_file,
+        create_population=create_population,
+    )