Add references attribute to various classes

wc_kb/__init__.py

@@ -14,9 +14,9 @@
                    PolymerSpeciesType,
                    ComplexSpeciesType,
                    DnaSpeciesType,
-                   RnaType,                   
+                   RnaType,
                    PolymerLocus,
-                   GeneType,                   
+                   GeneType,
                    Reaction,
                    Species,
                    SpeciesCoefficient,
@@ -34,6 +34,7 @@
                    RateLawEquation,
                    Reference,
                    DatabaseReference)
+
 from .prokaryote_schema import (RnaSpeciesType,
                                 ProteinSpeciesType,
                                 GeneLocus,

wc_kb/core.py

@@ -480,11 +480,12 @@ def deserialize(self, value, objects, decoded=None):
 
             spec_type_id = spec_coeff_match[5]
 
-            try:
+            try:                
                 if spec_type_id in objects[ProteinSpeciesType]:
                     spec_type = objects[ProteinSpeciesType][spec_type_id]
                 elif spec_type_id in objects[RnaSpeciesType]:
                     spec_type = objects[RnaSpeciesType][spec_type_id]
+
                 elif spec_type_id in objects[ComplexSpeciesType]:
                     spec_type = objects[ComplexSpeciesType][spec_type_id]
                 elif spec_type_id in objects[DnaSpeciesType]:
@@ -728,8 +729,8 @@ class KnowledgeBaseObject(obj_model.Model):
     """
     id = obj_model.SlugAttribute(primary=True, unique=True)
     name = obj_model.StringAttribute()
-    comments = obj_model.StringAttribute()    
-    
+    comments = obj_model.StringAttribute()
+
 
 class KnowledgeBase(KnowledgeBaseObject):
     """ A knowledge base
@@ -768,7 +769,7 @@ class Cell(KnowledgeBaseObject):
         knowledge_base (:obj:`KnowledgeBase`): knowledge base
         taxon (:obj:`int`): NCBI taxon identifier
 
-    Related attributes:        
+    Related attributes:
         compartments (:obj:`list` of :obj:`Compartment`): compartments
         species_types (:obj:`list` of :obj:`SpeciesType`): species types
         observables (:obj:'list' or :obj: 'Observable') : observables
@@ -782,7 +783,7 @@ class Cell(KnowledgeBaseObject):
     class Meta(obj_model.Model.Meta):
         attribute_order = ('id', 'name', 'taxon', 'comments')
         tabular_orientation = obj_model.TabularOrientation.column
-   
+
 
 class Compartment(KnowledgeBaseObject):
     """ Knowledge of a subcellular compartment
@@ -791,7 +792,7 @@ class Compartment(KnowledgeBaseObject):
         cell (:obj:`Cell`): cell
         volumetric_fraction (:obj:`float`): average volumetric fraction relative to the cell volume
         references (:obj:`list` of :obj:`Reference`): references
-        
+ 
     Related attributes:
         reaction_participants (:obj:`list` of :obj:`ReactionParticipant`): reaction participants
     """

wc_kb/io.py

@@ -54,7 +54,7 @@ def run(self, knowledge_base, core_path, seq_path, set_repo_metadata_from_path=T
             knowledge_base (:obj:`core.KnowledgeBase`): knowledge base
             core_path (:obj:`str`): path to save core knowledge base
             seq_path (:obj:`str`): path to save genome sequence
-            set_repo_metadata_from_path (:obj:`bool`, optional): if :obj:`True`, set the Git repository metadata (URL, 
+            set_repo_metadata_from_path (:obj:`bool`, optional): if :obj:`True`, set the Git repository metadata (URL,
                 branch, revision) for the knowledge base from the parent directory of :obj:`core_path`
 
         Raises:
@@ -119,7 +119,7 @@ def run(self, knowledge_base, core_path, seq_path, set_repo_metadata_from_path=T
 
     @classmethod
     def validate_implicit_relationships(cls):
-        """ Check that relationships to :obj:`core.KnowledgeBase` and :obj:`core.Cell` do not need to be explicitly written to 
+        """ Check that relationships to :obj:`core.KnowledgeBase` and :obj:`core.Cell` do not need to be explicitly written to
         workbooks because they can be inferred by :obj:`Reader.run`
 
         Raises:
@@ -150,13 +150,13 @@ def validate_implicit_relationships(cls):
 class Reader(object):
     """ Read knowledge base from file(s) """
 
-    @wc_utils.cache.memoize(filename_args=[1, 2])
+    #@wc_utils.cache.memoize(filename_args=[1, 2])
     def run(self, core_path, seq_path, strict=True):
         """ Read knowledge base from file(s)
 
         Args:
             core_path (:obj:`str`): path to core knowledge base
-            seq_path (:obj:`str`): path to genome sequence            
+            seq_path (:obj:`str`): path to genome sequence
             strict (:obj:`bool`, optional): if :obj:`True`, validate that the the model file(s) strictly follow the
                 :obj:`obj_model` serialization format:
 
@@ -171,7 +171,7 @@ def run(self, core_path, seq_path, strict=True):
             :obj:`core.KnowledgeBase`: knowledge base
 
         Raises:
-            :obj:`ValueError`: if :obj:`core_path` 
+            :obj:`ValueError`: if :obj:`core_path`
 
                 * Defines multiple knowledge bases or cells
                 * Represents objects that cannot be linked to a knowledge base and/or cell
@@ -284,7 +284,7 @@ def create_template(core_path, seq_path, set_repo_metadata_from_path=True):
     Args:
         core_path (:obj:`str`): path to save temploate of core knowledge base
         seq_path (:obj:`str`): path to save genome sequence
-        set_repo_metadata_from_path (:obj:`bool`, optional): if :obj:`True`, set the Git repository metadata (URL, 
+        set_repo_metadata_from_path (:obj:`bool`, optional): if :obj:`True`, set the Git repository metadata (URL,
             branch, revision) for the knowledge base from the parent directory of :obj:`core_path`
     """
     kb = core.KnowledgeBase(

wc_kb/prokaryote_schema.py

@@ -294,4 +294,4 @@ class GeneLocus(schema_core.PolymerLocus):
     class Meta(obj_model.Model.Meta):
         attribute_order = ('id', 'polymer', 'name', 'symbol',
                            'type', 'strand', 'start', 'end', 'comments', 'references')
-
+