Merge pull request #180 from jonls/cache-native-model

Split reader part of NativeModel into ModelReader

psamm/balancecheck.py

@@ -53,11 +53,11 @@ def charge_balance(model):
     """
 
     compound_charge = {}
-    for compound in model.parse_compounds():
-        if hasattr(compound, 'charge') and compound.charge is not None:
+    for compound in model.compounds:
+        if compound.charge is not None:
             compound_charge[compound.id] = compound.charge
 
-    for reaction in model.parse_reactions():
+    for reaction in model.reactions:
         charge = reaction_charge(reaction.equation, compound_charge)
         yield reaction, charge
 
@@ -101,7 +101,7 @@ def formula_balance(model):
 
     # Mapping from compound id to formula
     compound_formula = {}
-    for compound in model.parse_compounds():
+    for compound in model.compounds:
         if compound.formula is not None:
             try:
                 f = Formula.parse(compound.formula).flattened()
@@ -111,5 +111,5 @@ def formula_balance(model):
                     'Error parsing formula for compound {}: {}'.format(
                         compound.id, compound.formula), exc_info=True)
 
-    for reaction in model.parse_reactions():
+    for reaction in model.reactions:
         yield reaction, reaction_formula(reaction.equation, compound_formula)

psamm/command.py

@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with PSAMM.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Copyright 2014-2015  Jon Lund Steffensen <jon_steffensen@uri.edu>
+# Copyright 2014-2017  Jon Lund Steffensen <jon_steffensen@uri.edu>
 
 """Command line interface.
 
@@ -40,9 +40,8 @@
 from six import add_metaclass, iteritems, itervalues, text_type
 
 from . import __version__ as package_version
-from .datasource.native import NativeModel
+from .datasource import native
 from .lpsolver import generic
-from . import util
 
 logger = logging.getLogger(__name__)
 
@@ -76,15 +75,11 @@ def __init__(self, model, args):
         self._model = model
         self._args = args
 
-        name = self._model.name
-        if name is None:
-            name = text_type(self._model.context)
-        logger.info('Model: {}'.format(name))
+        if self._model.name is not None:
+            logger.info('Model: {}'.format(self._model.name))
 
-        if self._model.context is not None:
-            version = util.git_try_describe(self._model.context.basepath)
-            if version is not None:
-                logger.info('Model Git version: {}'.format(version))
+        if self._model.version_string is not None:
+            logger.info('Model version: {}'.format(self._model.version_string))
 
     @classmethod
     def init_parser(cls, parser):
@@ -552,10 +547,10 @@ def main(command_class=None, args=None):
     parsed_args = parser.parse_args(args)
 
     # Load model definition
-    model = NativeModel.load_model_from_path(parsed_args.model)
+    reader = native.ModelReader.reader_from_path(parsed_args.model)
 
     # Instantiate command with model and run
-    command = parsed_args.command(model, parsed_args)
+    command = parsed_args.command(reader.create_model(), parsed_args)
     try:
         command.run()
     except CommandError as e:

psamm/commands/chargecheck.py

@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with PSAMM.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Copyright 2014-2015  Jon Lund Steffensen <jon_steffensen@uri.edu>
+# Copyright 2014-2017  Jon Lund Steffensen <jon_steffensen@uri.edu>
 
 from __future__ import unicode_literals
 
@@ -49,10 +49,10 @@ def run(self):
         """Run charge balance command"""
 
         # Load compound information
-        compound_name = {}
-        for compound in self._model.parse_compounds():
-            compound_name[compound.id] = (
-                compound.name if compound.name is not None else compound.id)
+        def compound_name(id):
+            if id not in self._model.compounds:
+                return id
+            return self._model.compounds[id].properties.get('name', id)
 
         # Create a set of excluded reactions
         exclude = set(self._args.exclude)
@@ -71,8 +71,7 @@ def run(self):
                 unchecked += 1
             elif abs(charge) > self._args.epsilon:
                 unbalanced += 1
-                rxt = reaction.equation.translated_compounds(
-                    lambda x: compound_name.get(x, x))
+                rxt = reaction.equation.translated_compounds(compound_name)
                 print('{}\t{}\t{}'.format(reaction.id, charge, rxt))
 
         logger.info('Unbalanced reactions: {}/{}'.format(unbalanced, count))

psamm/commands/console.py

@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with PSAMM.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Copyright 2014-2015  Jon Lund Steffensen <jon_steffensen@uri.edu>
+# Copyright 2014-2017  Jon Lund Steffensen <jon_steffensen@uri.edu>
 
 from __future__ import unicode_literals
 

psamm/commands/duplicatescheck.py

@@ -80,7 +80,7 @@ def run(self):
 
         # Create dictonary of signatures
         database_signatures = {}
-        for entry in self._model.parse_reactions():
+        for entry in self._model.reactions:
             signature = reaction_signature(
                 entry.equation, direction=self._args.compare_direction,
                 stoichiometry=self._args.compare_stoichiometry)

psamm/commands/excelexport.py

@@ -20,10 +20,9 @@
 
 import logging
 
-from six import text_type
+from six import text_type, itervalues
 
 from ..command import Command
-from .. import util
 
 try:
     import xlsxwriter
@@ -52,36 +51,29 @@ def run(self):
         workbook = xlsxwriter.Workbook(self._args.file)
         reaction_sheet = workbook.add_worksheet(name='Reactions')
 
-        git_version = None
-        if self._model.context is not None:
-            git_version = util.git_try_describe(self._model.context.basepath)
-
         property_set = set()
-        for reaction in model.parse_reactions():
+        for reaction in model.reactions:
             property_set.update(reaction.properties)
         property_list = list(property_set)
         property_list_sorted = sorted(property_list,
                                       key=lambda x: (x != 'id',
                                                      x != 'equation', x))
-        model_reactions = set(model.parse_model())
+        model_reactions = set(model.model)
         for z, i in enumerate(property_list_sorted + ['in_model']):
             reaction_sheet.write_string(0, z, text_type(i))
-        for x, i in enumerate(model.parse_reactions()):
+        for x, i in enumerate(model.reactions):
             for y, j in enumerate(property_list_sorted):
-                reaction_sheet.write_string(
-                    x+1, y, text_type(i.properties.get(j)))
-            if (not model.has_model_definition() or
-                    i.id in model_reactions):
-                reaction_sheet.write_string(
-                    x+1, len(property_list_sorted), 'True')
-            else:
-                reaction_sheet.write_string(
-                    x+1, len(property_list_sorted), 'False')
+                value = i.properties.get(j)
+                if value is not None:
+                    reaction_sheet.write_string(x+1, y, text_type(value))
+            reaction_sheet.write_string(
+                x+1, len(property_list_sorted),
+                text_type(i.id in model_reactions))
 
         compound_sheet = workbook.add_worksheet(name='Compounds')
 
         compound_set = set()
-        for compound in model.parse_compounds():
+        for compound in model.compounds:
             compound_set.update(compound.properties)
 
         compound_list_sorted = sorted(compound_set,
@@ -92,17 +84,14 @@ def run(self):
         model_compounds = set(x.name for x in metabolic_model.compounds)
         for z, i in enumerate(compound_list_sorted + ['in_model']):
             compound_sheet.write_string(0, z, text_type(i))
-        for x, i in enumerate(model.parse_compounds()):
+        for x, i in enumerate(model.compounds):
             for y, j in enumerate(compound_list_sorted):
-                compound_sheet.write_string(
-                    x+1, y, text_type(i.properties.get(j)))
-            if (not self._model.has_model_definition() or
-                    i.id in model_compounds):
-                compound_sheet.write_string(
-                    x+1, len(compound_list_sorted), 'True')
-            else:
-                compound_sheet.write_string(
-                    x+1, len(compound_list_sorted), 'False')
+                value = i.properties.get(j)
+                if value is not None:
+                    compound_sheet.write_string(x+1, y, text_type(value))
+            compound_sheet.write_string(
+                x+1, len(compound_list_sorted),
+                text_type(i.id in model_compounds))
 
         exchange_sheet = workbook.add_worksheet(name='Exchange')
 
@@ -114,9 +103,9 @@ def run(self):
         default_flux = model.default_flux_limit
 
         for x, (compound, reaction, lower, upper) in enumerate(
-                model.parse_exchange()):
+                itervalues(model.exchange)):
             if lower is None:
-                lower = -1 * default_flux
+                lower = -default_flux
 
             if upper is None:
                 upper = default_flux
@@ -132,7 +121,7 @@ def run(self):
         limits_sheet.write_string(0, 1, 'Lower Limit')
         limits_sheet.write_string(0, 2, 'Upper Limit')
 
-        for x, limit in enumerate(model.parse_limits()):
+        for x, limit in enumerate(itervalues(model.limits)):
             reaction_id, lower, upper = limit
             if lower is None:
                 lower = -default_flux
@@ -151,7 +140,8 @@ def run(self):
             1, 0, ('Biomass Reaction: {}'.format(model.biomass_reaction)))
         model_info.write(
             2, 0, ('Default Flux Limits: {}'.format(model.default_flux_limit)))
-        if git_version is not None:
-            model_info.write(3, 0, ('Git version: {}'.format(git_version)))
+        if model.version_string is not None:
+            model_info.write(
+                3, 0, ('Version: {}'.format(model.version_string)))
 
         workbook.close()

psamm/commands/fastgapfill.py

@@ -59,10 +59,10 @@ def run(self):
         solver = self._get_solver()
 
         # Load compound information
-        compound_name = {}
-        for compound in self._model.parse_compounds():
-            compound_name[compound.id] = (
-                compound.name if compound.name is not None else compound.id)
+        def compound_name(id):
+            if id not in self._model.compounds:
+                return id
+            return self._model.compounds[id].properties.get('name', id)
 
         # TODO: The exchange and transport reactions have tuple names. This
         # means that in Python 3 the reactions can no longer be directly
@@ -106,15 +106,13 @@ def reaction_key(r):
 
         for reaction_id in sorted(self._mm.reactions):
             rx = self._mm.get_reaction(reaction_id)
-            rxt = rx.translated_compounds(
-                lambda x: compound_name.get(x, x))
+            rxt = rx.translated_compounds(compound_name)
             print('{}\t{}\t{}\t{}'.format(reaction_id, 'Model', 0, rxt))
 
         for rxnid in sorted(induced, key=reaction_key):
             if self._mm.has_reaction(rxnid):
                 continue
             rx = model_extended.get_reaction(rxnid)
-            rxt = rx.translated_compounds(
-                lambda x: compound_name.get(x, x))
+            rxt = rx.translated_compounds(compound_name)
             print('{}\t{}\t{}\t{}'.format(
                 rxnid, 'Add', weights.get(rxnid, 1), rxt))

psamm/commands/fba.py

@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with PSAMM.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Copyright 2014-2015  Jon Lund Steffensen <jon_steffensen@uri.edu>
+# Copyright 2014-2017  Jon Lund Steffensen <jon_steffensen@uri.edu>
 
 from __future__ import unicode_literals
 
@@ -47,18 +47,16 @@ def run(self):
         """Run flux analysis command."""
 
         # Load compound information
-        compound_name = {}
-        for compound in self._model.parse_compounds():
-            if 'name' in compound.properties:
-                compound_name[compound.id] = compound.properties['name']
-            elif compound.id not in compound_name:
-                compound_name[compound.id] = compound.id
+        def compound_name(id):
+            if id not in self._model.compounds:
+                return id
+            return self._model.compounds[id].properties.get('name', id)
 
         # Reaction genes information
-        reaction_genes = {}
-        for reaction in self._model.parse_reactions():
-            if 'genes' in reaction.properties:
-                reaction_genes[reaction.id] = reaction.properties['genes']
+        def reaction_genes_string(id):
+            if id not in self._model.reactions:
+                return ''
+            return self._model.reactions[id].properties.get('genes', '')
 
         reaction = self._get_objective()
         if not self._mm.has_reaction(reaction):
@@ -83,9 +81,8 @@ def run(self):
 
             if abs(flux) > self._args.epsilon or self._args.all_reactions:
                 rx = self._mm.get_reaction(reaction_id)
-                rx_trans = rx.translated_compounds(
-                    lambda x: compound_name.get(x, x))
-                genes = reaction_genes.get(reaction_id, '')
+                rx_trans = rx.translated_compounds(compound_name)
+                genes = reaction_genes_string(reaction_id)
                 print('{}\t{}\t{}\t{}'.format(
                     reaction_id, flux, rx_trans, genes))
 

psamm/commands/fluxcheck.py

@@ -13,7 +13,7 @@
 # You should have received a copy of the GNU General Public License
 # along with PSAMM.  If not, see <http://www.gnu.org/licenses/>.
 #
-# Copyright 2014-2015  Jon Lund Steffensen <jon_steffensen@uri.edu>
+# Copyright 2014-2017  Jon Lund Steffensen <jon_steffensen@uri.edu>
 
 from __future__ import unicode_literals
 
@@ -63,12 +63,10 @@ def run(self):
         """Run flux consistency check command"""
 
         # Load compound information
-        compound_name = {}
-        for compound in self._model.parse_compounds():
-            if 'name' in compound.properties:
-                compound_name[compound.id] = compound.properties['name']
-            elif compound.id not in compound_name:
-                compound_name[compound.id] = compound.id
+        def compound_name(id):
+            if id not in self._model.compounds:
+                return id
+            return self._model.compounds[id].properties.get('name', id)
 
         epsilon = self._args.epsilon
 
@@ -148,8 +146,7 @@ def run(self):
 
             if reaction in inconsistent:
                 rx = self._mm.get_reaction(reaction)
-                rxt = rx.translated_compounds(
-                    lambda x: compound_name.get(x, x))
+                rxt = rx.translated_compounds(compound_name)
                 print('{}\t{}'.format(reaction, rxt))
 
         logger.info('Model has {}/{} inconsistent internal reactions'