Merge branch 'dev' into master

Author: mwatts15

owmeta-data-bundle.yml

@@ -1,13 +1,13 @@
 ---
 id: openworm/owmeta-data
 name: owmeta data bundle
-version: 4
+version: 6
 description: Bundle for OpenWorm data
 patterns:
     - http://data.openworm.org/sci/data_sources/DataWithEvidenceDataSource#bently_expression/context_for?*
     - http://data.openworm.org/sci/data_sources/DataWithEvidenceDataSource#neurons/context_for?*
     - http://data.openworm.org/sci/data_sources/DataWithEvidenceDataSource#cells/context_for?*
-includes: 
+includes:
     - http://openworm.org/data
     - http://openworm.org/data-data:
         empty: true
@@ -63,7 +63,7 @@ includes:
 
 dependencies:
     - id: openworm/owmeta-schema
-      version: 2
+      version: 3
       #excludes:
           #- http://www.w3.org/1999/02/22-rdf-syntax-ns
       #merges:

owmeta-schema-bundle.yml

@@ -1,9 +1,9 @@
 ---
 id: openworm/owmeta-schema
 name: owmeta schema bundle
-version: 2 
+version: 3
 description: Bundle for OpenWorm schema for scientific data
-includes: 
+includes:
     - http://schema.openworm.org/2020/07/sci
     - http://schema.openworm.org/2020/07/sci/bio
 dependencies:

owmeta/__init__.py

@@ -13,7 +13,7 @@
 """
 
 from __future__ import print_function
-__version__ = '0.12.0'
+__version__ = '0.12.1'
 __author__ = 'OpenWorm.org authors and contributors'
 
 import logging

owmeta/data_trans/connections.py

@@ -15,7 +15,7 @@
 from ..document import Document
 from ..evidence import Evidence
 from ..neuron import Neuron
-from ..muscle import Muscle
+from ..muscle import Muscle, BodyWallMuscle
 from ..worm import Worm
 from ..network import Network
 
@@ -110,7 +110,7 @@ def translate(self, data_source, neurons_source, muscles_source):
         res.evidence_context(Evidence)(key="emmons2015",
                 reference=doc,
                 supports=docctx.rdf_object)
-        with docctx(Neuron, Muscle, Cell, Connection) as ctx:
+        with docctx(Neuron, Muscle, BodyWallMuscle, Cell, Connection) as ctx:
             res.data_context.add_import(ctx.context)
             with open(data_source.full_path()) as csvfile:
                 edge_reader = csv.reader(csvfile)
@@ -125,25 +125,22 @@ def translate(self, data_source, neurons_source, muscles_source):
                     elif syn_type == 'chemical':
                         syn_type = 'send'
 
+                    source_is_bwm = 'BWM' in source.upper()
+                    target_is_bwm = 'BWM' in target.upper()
+
                     source = normalize_cell_name(source).upper()
                     target = normalize_cell_name(target).upper()
 
                     weight = int(weight)
 
-                    # remove BMW from Body Wall Muscle cells
-                    if 'BWM' in source:
-                        source = normalize_muscle(source)
-                    if 'BWM' in target:
-                        target = normalize_muscle(target)
-
                     # change certain muscle names to names in wormbase
                     if source in changed_muscles:
                         source = changed_muscle(source)
                     if target in changed_muscles:
                         target = changed_muscle(target)
 
-                    sources = convert_to_cell(ctx, source, muscles, neurons)
-                    targets = convert_to_cell(ctx, target, muscles, neurons)
+                    sources = convert_to_cell(ctx, source, muscles, neurons, source_is_bwm)
+                    targets = convert_to_cell(ctx, target, muscles, neurons, target_is_bwm)
 
                     for s in sources:
                         for t in targets:
@@ -241,16 +238,21 @@ def translate(self, data_source, neurotransmitter_source):
         return res
 
 
-def convert_to_cell(ctx, name, muscles, neurons):
+def convert_to_cell(ctx, name, muscles, neurons, is_bwm):
     ret = []
     res = None
     res2 = None
     if name in neurons:
         res = ctx.Neuron(name)
-    elif name in muscles:
-        res = ctx.Muscle(name)
     elif name in TO_EXPAND_MUSCLES:
+        # All of the muscle cell types we need to expand are pharyngeal, so no need to
+        # pass through is_bwm
         res, res2 = expand_muscle(ctx, name)
+    elif name in muscles:
+        if is_bwm:
+            res = ctx.BodyWallMuscle(name)
+        else:
+            res = ctx.Muscle(name)
     elif name in OTHER_CELLS:
         res = ctx.Cell(name)
 
@@ -266,28 +268,15 @@ def add_synapse(ctx, source, target, weight, syn_type):
     c = ctx.Connection(pre_cell=source, post_cell=target,
                        number=weight, syntype=syn_type)
 
-    if isinstance(source, ctx.Neuron) and isinstance(target, ctx.Neuron):
+    if isinstance(source, Neuron) and isinstance(target, Neuron):
         c.termination('neuron')
-    elif isinstance(source, ctx.Neuron) and isinstance(target, ctx.Muscle) or \
-            isinstance(source, ctx.Muscle) and isinstance(target, ctx.Neuron):
+    elif isinstance(source, Neuron) and isinstance(target, Muscle) or \
+            isinstance(source, Muscle) and isinstance(target, Neuron):
         c.termination('muscle')
 
     return c
 
 
-# to normalize certian body wall muscle cell names
-SEARCH_STRING_MUSCLE = re.compile(r'\w+[BWM]+\w+')
-REPLACE_STRING_MUSCLE = re.compile(r'[BWM]+')
-
-
-def normalize_muscle(name):
-    # normalize names of Body Wall Muscles
-    # if there is 'BWM' in the name, remove it
-    if re.match(SEARCH_STRING_MUSCLE, name):
-        name = REPLACE_STRING_MUSCLE.sub('', name)
-    return name
-
-
 MUSCLES = {
     'ANAL': 'MU_ANAL',
     'INTR': 'MU_INT_R',

owmeta/data_trans/wormbase.py

@@ -10,7 +10,7 @@
 from ..utils import normalize_cell_name
 from ..channel import Channel, ExpressionPattern
 from ..evidence import Evidence
-from ..muscle import Muscle
+from ..muscle import Muscle, BodyWallMuscle
 from ..network import Network
 from ..neuron import Neuron
 from ..cell import Cell
@@ -177,19 +177,25 @@ def translate(self, data_source):
                 doc_ctx = res.data_context_for(document=doc)
                 ctx.Evidence(reference=doc, supports=doc_ctx.rdf_object)
 
-            with doc_ctx(Worm=Worm, Muscle=Muscle, Network=Network, Neuron=Neuron, Cell=Cell) as ctx:
+            with doc_ctx(Worm=Worm,
+                         BodyWallMuscle=BodyWallMuscle,
+                         Muscle=Muscle,
+                         Network=Network,
+                         Neuron=Neuron,
+                         Cell=Cell) as ctx:
                 w = ctx.Worm()
                 n = ctx.Network()
                 n.worm(w)
 
                 for line in csvreader:
                     cell = None
-                    if (line['Body wall muscles'] or
-                            line['Pharynx muscles'] or
-                            line['Other muscles']):  # muscle's marked in these columns
+                    if line['Body wall muscles']:
+                        cell = ctx.BodyWallMuscle()
+                        w.muscle(cell)
+                    elif line['Pharynx muscles'] or line['Other muscles']:
                         cell = ctx.Muscle()
                         w.muscle(cell)
-                    elif line['Neurons (no male-specific cells)']:  # neurons marked in this column
+                    elif line['Neurons (no male-specific cells)']:
                         cell = ctx.Neuron()
                         cell.wormbaseID(line['WormBase ID'])
                         n.neuron(cell)

owmeta/muscle.py

@@ -5,8 +5,8 @@
 
 
 class Muscle(Cell):
-
-    """A single muscle cell.
+    """
+    A single muscle cell.
 
     See what neurons innervate a muscle:
 
@@ -31,3 +31,11 @@ class Muscle(Cell):
 
     receptor = Alias(receptors)
     ''' Alias to `receptors` '''
+
+
+class BodyWallMuscle(Muscle):
+    '''
+    A somatic muscle cell that lies close under the skin and basal lamina of C. elegans
+    and allows the worm to move
+    '''
+    class_context = Cell.class_context

save_data.py

@@ -48,14 +48,6 @@ def __init__(self):
         self.owm = OWM()
         self.ctx = self.owm.default_context.stored
 
-    def muscles(self):
-        muscles = self.owm.translate(MuscleWormBaseCSVTranslator(),
-                data_sources=[WormBaseCSVDataSource(key='wormbase_celegans_cells')],
-                output_key='muscles')
-        self.ctx(muscles).description(
-                "Contains descriptions of C. elegans muscles and is the"
-                " principle such list for OpenWorm")
-
     def neurons(self):
         neurons = self.owm.translate(NeuronCSVDataTranslator(),
                 data_sources=[NeuronCSVDataSource(key='neurons')],