Starting on #319

OpenWormData/scripts/insert_worm.py

@@ -67,7 +67,14 @@ def upload_ionchannels():
                 c.gene_name(gene_name)
                 c.gene_WB_ID(gene_WB_ID)
                 c.description(description)
-                c.expression_pattern(expression_pattern)
+                patterns = expression_pattern.split(r' | ')
+                regex = re.compile(r' *\[([^\]]+)\] *(.*) *')
+
+                matches = [regex.match(pat) for pat in patterns]
+                patterns = [P.ExpressionPattern(wormbaseID=m.group(1), description=m.group(2)) for m in matches if m is not None]
+                for pat in patterns:
+                    c.expression_pattern(pat)
+
                 c.save()
         print ("uploaded ion_channel")
     except Exception:
@@ -77,33 +84,15 @@ def upload_ionchannels():
 def upload_channelneuron_association():
     print ("uploading the channel neuron association")
     try:
-        net = NETWORK
         with open(CHANNEL_NEURON_SOURCE, 'rb') as f:
             reader = csv.reader(f, delimiter='\t')
-            rows = 0
+            heading = skip_to_header(reader)
             for row in reader:
-                neuronlist = []
-                if rows < 3:
-                    rows += 1
-                    continue
-                elif rows == 3:
-                    heading = row
-                    rows += 1
-                    continue
-                rows += 1
-
-                cols = 0
-                for col in row:
-                    if cols >= 0 and cols <= 101:
-                        cols += 1
-                    else:
-                        if col == '1' or col == '2':
-                            neuronlist.append(heading[cols])
-                        cols += 1
+                neuronlist = extract_neuron_names(heading, row)
                 ch = P.Channel(name=str(row[0]))
                 for neuron in neuronlist:
                     n = P.Neuron(name=str(neuron))
-                    net.neuron(n)
+                    NETWORK.neuron(n)
                     ch.appearsIn(n)
         print ("uploaded channel neuron association")
     except Exception:
@@ -113,39 +102,58 @@ def upload_channelneuron_association():
 def upload_channelmuscle_association():
     print ("uploading the channel muscle association")
     try:
-        w = WORM
         with open(CHANNEL_MUSCLE_SOURCE, 'rb') as f:
             reader = csv.reader(f, delimiter='\t')
-            rows = 0
+            heading = skip_to_header(reader)
             for row in reader:
-                musclelist = []
-                if rows < 3:
-                    rows += 1
-                    continue
-                elif rows == 3:
-                    heading = row
-                    rows += 1
-                    continue
-                rows += 1
-
-                cols = 0
-                for col in row:
-                    if cols >= 0 and cols <= 6:
-                        cols += 1
-                    else:
-                        if col == '1' or col == '2':
-                            musclelist.append(heading[cols])
-                        cols += 1
+                musclelist = extract_muscle_names(heading, row)
                 ch = P.Channel(name=str(row[0]))
                 for muscle in musclelist:
                     m = P.Muscle(name=str(muscle))
-                    w.muscle(m)
+                    WORM.muscle(m)
                     ch.appearsIn(m)
         print ("uploaded channel muscle association")
     except Exception:
         traceback.print_exc()
 
 
+def extract_neuron_names(heading, row):
+    neuronlist = []
+    cols = 0
+    for col in row:
+        if cols >= 0 and cols <= 101:
+            cols += 1
+        else:
+            if col == '1' or col == '2':
+                neuronlist.append(heading[cols])
+            cols += 1
+    return neuronlist
+
+
+def extract_muscle_names(heading, row):
+    musclelist = []
+    cols = 0
+    for col in row:
+        if cols >= 0 and cols <= 6:
+            cols += 1
+        else:
+            if col == '1' or col == '2':
+                musclelist.append(heading[cols])
+            cols += 1
+    return musclelist
+
+
+def skip_to_header(reader):
+    heading = None
+    rows = 0
+    for row in reader:
+        if rows == 3:
+            heading = row
+            break
+        rows += 1
+    return heading
+
+
 def upload_muscles():
     """ Upload muscles and the neurons that connect to them
     """
@@ -646,16 +654,16 @@ def do_insert(config="default.conf", logging=False):
         WORM.neuron_network(NETWORK)
         NETWORK.worm(WORM)
 
-        upload_neurons()
-        upload_muscles()
+        # upload_neurons()
+        # upload_muscles()
         upload_ionchannels()
-        upload_channelneuron_association()
-        upload_channelmuscle_association()
-        attach_neuromlfiles_to_channel()
-        upload_lineage_and_descriptions()
-        upload_connections()
-        upload_receptors_types_neurotransmitters_neuropeptides_innexins()
-        upload_additional_receptors_neurotransmitters_neuropeptides_innexins()
+        # upload_channelneuron_association()
+        # upload_channelmuscle_association()
+        # attach_neuromlfiles_to_channel()
+        # upload_lineage_and_descriptions()
+        # upload_connections()
+        # upload_receptors_types_neurotransmitters_neuropeptides_innexins()
+        # upload_additional_receptors_neurotransmitters_neuropeptides_innexins()
 
         print("Saving...")
         WORM.save()

PyOpenWorm/__init__.py

@@ -80,7 +80,7 @@
 from .my_neuroml import NeuroML
 from .connection import Connection
 from .experiment import Experiment
-from .channel import Channel
+from .channel import Channel, ExpressionPattern
 from .channelworm import ChannelModel, PatchClampExperiment
 from .plot import Plot
 
@@ -114,6 +114,7 @@
     "Connection",
     "Experiment",
     "Channel",
+    "ExpressionPattern",
     "ChannelModel",
     "PatchClampExperiment",
     "Plot"]
@@ -270,6 +271,7 @@ def connect(configFile=False,
     SimpleProperty.register()
     Relationship.register()
     Channel.register()
+    ExpressionPattern.register()
     ChannelModel.register()
     Experiment.register()
     PatchClampExperiment.register()

PyOpenWorm/channel.py

@@ -1,3 +1,4 @@
+import rdflib as R
 from .pProperty import Property
 from .channelworm import ChannelModel
 from .dataObject import DataObject
@@ -100,7 +101,10 @@ def __init__(self, name=False, **kwargs):
         Channel.DatatypeProperty('description', self)
         Channel.DatatypeProperty('gene_name', self)
         Channel.DatatypeProperty('gene_WB_ID', self)
-        Channel.DatatypeProperty('expression_pattern', self)
+        Channel.ObjectProperty('expression_pattern',
+                               owner=self,
+                               multiple=True,
+                               value_type=ExpressionPattern)
         Channel.DatatypeProperty('neuroML_file', owner=self)
         Channel.DatatypeProperty('proteins', self, multiple=True)
         Channel.ObjectProperty('appearsIn', self, multiple=True,
@@ -123,3 +127,29 @@ def identifier(self):
         else:
             # name is already set, so we can make an identifier from it
             return self.make_identifier(self.name.defined_values[0])
+
+
+class ExpressionPattern(DataObject):
+    def __init__(self, wormbaseID=None, description=None, **kwargs):
+        super(ExpressionPattern, self).__init__(**kwargs)
+        ExpressionPattern.DatatypeProperty('wormbaseID', owner=self)
+        ExpressionPattern.DatatypeProperty('wormbaseURL', owner=self)
+        ExpressionPattern.DatatypeProperty('description', owner=self)
+
+        if wormbaseID:
+            self.wormbaseID(wormbaseID)
+            self.wormbaseURL(R.URIRef("http://www.wormbase.org/species/all/expr_pattern/"+wormbaseID))
+
+        if description:
+            self.description(description)
+
+    @property
+    def defined(self):
+        return super(ExpressionPattern, self).defined \
+                or self.wormbaseID.has_defined_value()
+
+    def identifier(self):
+        if super(ExpressionPattern, self).defined:
+            return super(ExpressionPattern, self).identifier()
+        else:
+            return self.make_identifier(self.wormbaseID.defined_values[0])