import/export user constraints

Author: bgoli

src/CBConfig.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBConfig.py 631 2017-11-03 16:09:23Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBConfig.py 637 2017-12-15 11:34:59Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -37,13 +37,13 @@
 # release
 
 try:
-    STATUS = '$Rev: 631 $'.replace('Rev: ', '').replace('$', '').strip()
+    STATUS = '$Rev: 637 $'.replace('Rev: ', '').replace('$', '').strip()
 except Exception:
     STATUS = ''
 
 __CBCONFIG__ = {'VERSION_MAJOR' : 0,
                 'VERSION_MINOR' : 7,
-                'VERSION_MICRO' : 19,
+                'VERSION_MICRO' : 20,
                 'VERSION_STATUS' : STATUS,
                 'VERSION' : None,
                 'DEBUG' : False,

src/CBModel.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBModel.py 636 2017-12-13 20:05:01Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBModel.py 640 2017-12-18 18:13:40Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -34,7 +34,7 @@
 from __future__ import absolute_import
 #from __future__ import unicode_literals
 
-import numpy, re, time, weakref, copy, json, ast
+import numpy, re, time, weakref, copy, json, ast, os
 
 try:
     from urllib2 import quote as urlquote
@@ -2886,6 +2886,33 @@ def exportFVAdata(self):
         # investigate the use of numpy index arrays here
         raise NotImplementedError
 
+    def importUserConstraints(self, filename):
+        """
+        Exports user constraints in json
+
+        """
+        F = open(filename, 'r')
+        #din = json.load(F)
+        self.user_constraints = json.load(F)
+        #key = os.path.split(self.sourcefile)[-1]
+        #F.close()
+        #if key in din:
+            #self.user_constraints = din[key]
+        #else:
+            #print('ERROR: constraints refers to file \"{}\" whereas this is file \"{}\"'.format(list(din.keys())[0], key))
+            #return False
+        return True
+
+    def exportUserConstraints(self, filename):
+        """
+        Exports user constraints in json
+
+        """
+        F = open(filename, 'w')
+        #json.dump({os.path.split(self.sourcefile)[-1] : self.user_constraints}, F, indent=2)
+        json.dump(self.user_constraints, F, indent=2)
+        F.close()
+
     def createGroup(self, gid):
         """
         Create an empty group with

src/CBXML.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: CBXML.py 629 2017-10-24 22:01:14Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBXML.py 640 2017-12-18 18:13:40Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -2553,6 +2553,11 @@ def sbml_writeSBML3FBC(fba, fname, directory=None, sbml_level_version=(3,1), aut
         F.close()
         print('Model exported as: {}'.format(fname))
 
+
+    # bgoli: temporary (until incorporated into FBC stadard) solution to store the constraints in a separate json file
+    if fba.user_constraints is not None and len(fba.user_constraints) >= 1:
+        fba.exportUserConstraints(fname+'.user_constraints.json')
+
     if VALIDATE:
         sbml_setValidationOptions(cs3.doc, level='full')
         print('\nPerforming validation on output SBML ...\n')

src/__init__.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: [email protected]
-Last edit: $Author: bgoli $ ($Id: __init__.py 633 2017-11-06 09:57:54Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: __init__.py 640 2017-12-18 18:13:40Z bgoli $)
 
 """
 #
@@ -94,7 +94,6 @@
 SED = PyscesSED.SEDCBMPY
 
 try:
-    from . import nosetests
     __test_dir__ = os.path.join(__CBCONFIG__['CBMPY_DIR'], 'nosetests')
     test_set = 1
     test_bundle = os.path.join(__test_dir__, 'cbmpy_test_bundle_v{}.zip.py'.format(test_set))
@@ -107,6 +106,7 @@
         zfile.close()
         #os.remove(test_bundle)
         del zipfile, zfile
+    from . import nosetests
     test = nosetests.run
     del nosetests, test_bundle, test_file, test_set
 except ImportError: