updated miriam registry

Author: bgoli

cbmpy-tools/miriam-tools/miriamids.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: bgoli@users.sourceforge.net
-Last edit: $Author: bgoli $ ($Id: CBModel.py 505 2016-10-20 15:46:12Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBModel.py 518 2016-11-07 17:40:44Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -37,9 +37,10 @@
 import numpy, re, time, weakref, copy, json, urllib2
 
 try:
-    import pickle
-except ImportError:
     import cPickle as pickle
+except ImportError:
+    import pickle
+
 
 HAVE_SYMPY = False
 try:
@@ -99,6 +100,8 @@ def __getstate__(self):
         """
         Internal method that should allow our weakrefs to be 'picklable'
 
+        # overloaded by Model
+
         """
 
         if '__objref__' not in self.__dict__:
@@ -322,17 +325,21 @@ def serialize(self, protocol=0):
          - *protocol* [default=0] serialize to a string or binary if required,
                       see pickle module documentation for details
 
+        # overloaded in Model
+
         """
         return pickle.dumps(self, protocol=protocol)
 
-    def serializeToDisk(self, filename, protocol=0):
+    def serializeToDisk(self, filename, protocol=2):
         """
         Serialize to disk using pickle protocol:
 
          - *filename* the name of the output file
-         - *protocol* [default=0] serialize to a string or binary if required,
+         - *protocol* [default=2] serialize to a string or binary if required,
                       see pickle module documentation for details
 
+        # overloaded in Model
+
         """
         F = file(filename, 'wb')
         pickle.dump(self, F, protocol=protocol)
@@ -555,6 +562,9 @@ def clone(self):
         cpy.__setModelSelf__()
         cpy.__setGlobalIdStore__()
         cpy.__populateGlobalIdStore__()
+        # TODO: try make the global ID store work exclusively with __setState__ and __getState__ for both clone/serialise
+        self.__setGlobalIdStore__()
+        self.__populateGlobalIdStore__()
 
         print('Model clone time: {}'.format(time.time()-tzero))
         return cpy
@@ -641,6 +651,21 @@ def __unsetModelSelf__(self):
         for p in self.parameters:
             p.__unsetObjRef__()
 
+    def __getstate__(self):
+        """
+        Internal method that should allow our weakrefs to be 'picklable'
+
+        # overloaded by Model
+
+        """
+
+        self.__global_id__ = None
+        if '__objref__' not in self.__dict__:
+            return self.__dict__
+        else:
+            cpy = self.__dict__.copy()
+            cpy['__objref__'] = None
+            return cpy
 
     def __setstate__(self, dic):
         """
@@ -649,6 +674,40 @@ def __setstate__(self, dic):
         """
         self.__dict__ = dic
         self.__setModelSelf__()
+        self.__setGlobalIdStore__()
+        self.__populateGlobalIdStore__()
+
+    def serialize(self, protocol=0):
+        """
+        Serialize object, returns a string by default
+
+         - *protocol* [default=0] serialize to a string or binary if required,
+                      see pickle module documentation for details
+
+        # overloaded in CBModel
+
+        """
+        s = pickle.dumps(self, protocol=protocol)
+        self.__setGlobalIdStore__()
+        self.__populateGlobalIdStore__()
+        return s
+
+    def serializeToDisk(self, filename, protocol=2):
+        """
+        Serialize to disk using pickle protocol:
+
+         - *filename* the name of the output file
+         - *protocol* [default=2] serialize to a string or binary if required,
+                      see pickle module documentation for details
+
+        # overloaded in CBModel
+
+        """
+        F = file(filename, 'wb')
+        pickle.dump(self, F, protocol=protocol)
+        F.close()
+        self.__setGlobalIdStore__()
+        self.__populateGlobalIdStore__()
 
     def addMIRIAMannotation(self, qual, entity, mid):
         """

cbmpy-tools/miriam-tools/miriamresources.xml

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: bgoli@users.sourceforge.net
-Last edit: $Author: bgoli $ ($Id: CBMultiCore.py 515 2016-11-07 14:20:11Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBMultiCore.py 518 2016-11-07 17:40:44Z bgoli $)
 
 """
 
@@ -41,14 +41,14 @@
 MULTIFVAFILE = __file__.replace('CBMultiCore', '_multicorefva')
 del _multicorefva
 
-try:
-    from . import _multicoreenvfva
-    MULTIENVFVAFILE = __file__.replace('CBMultiCore','_multicoreenvfva')
-    del _multicoreenvfva
-    HAVE_MULTIENV = True
-except ImportError as ex:
-    print(ex)
-    HAVE_MULTIENV = False
+#try:
+    #from . import _multicoreenvfva
+    #MULTIENVFVAFILE = __file__.replace('CBMultiCore','_multicoreenvfva')
+    #del _multicoreenvfva
+    #HAVE_MULTIENV = True
+#except ImportError as ex:
+    #print(ex)
+    #HAVE_MULTIENV = False
 
 from .CBConfig import __CBCONFIG__ as __CBCONFIG__
 
@@ -101,110 +101,47 @@ def runMultiCoreFVA(fba, selected_reactions=None, pre_opt=True, tol=None, objF2c
             REAC.reduced_costs = fva[R][1]
     return fva, fvan
 
-if HAVE_MULTIENV:
-    def runMultiCoreMultiEnvFVA(lp, selected_reactions=None, tol=None, rhs_sense='lower', optPercentage=100.0, work_dir=None, debug=False, procs=2):
-        """
-        Run a multicore FVA where:
-
-         - *lp* is a multienvironment lp model instance
-         - *procs* [default=2] number of processing threads (optimum seems to be about the number of physical cores)
-
-        """
-        fN = os.path.join(work_dir, str(time.time()).split('.')[0])
-        lp.write(fN+'.lp', filetype='lp')
-        MEargs = [fN+'.lp', selected_reactions, tol, rhs_sense, optPercentage, work_dir, debug]
-        print(MEargs)
-        print(fN)
-        F = file(fN, 'wb')
-        pickle.dump(MEargs, F, protocol=-1)
-        F.close()
-        subprocess.call(['python', MULTIENVFVAFILE, str(procs), fN])
-        F = file(fN, 'rb')
-        res = pickle.load(F)
-        F.close()
-        os.remove(fN)
-
-        fva = res[0]
-        fvan = res[1]
-
-        if len(fva) == 1:
-            fva = fva[0]
-            fvan = fvan[0]
-        elif len(fva) > 1:
-            fva = numpy.vstack(fva)
-            fvan2 = []
-            for n_ in fvan:
-                fvan2 += n_
-            fvan = fvan2
-
-        return fva, fvan
-else:
-    def runMultiCoreMultiEnvFVA(lp, selected_reactions=None, tol=None, rhs_sense='lower', optPercentage=100.0, work_dir=None, debug=False, procs=2):
-        raise RuntimeError('\nMultiCore module not present')
-
-
-
-
-# look at using if __name__ != '__main__'
-
-"""
-import os, time, math, pickle
-import multiprocessing
-import CBSolver, CBMultiCore
-
-def funcFVA(x,r):
-    try:
-        fva, fvan = CBSolver.FluxVariabilityAnalysis(x, selected_reactions=r, pre_opt=True, quiet=True, oldlpgen=False)
-    except Exception as ex:
-        print ex
-        fva = fvan = None
-        raise RuntimeError(ex)
-    return fva, fvan
-
-def multiCoreFVA(fvamod, procs=2, timeout=None):
-    #assert procs >= 2, '\nMinimum 2 processes required'
-    rid = fvamod.getReactionIds()
-    PRs = [d_[0] for d_ in list(CBMultiCore.grouper(int(math.ceil(len(rid)/float(procs))), range(len(rid))))]
-    print procs, len(PRs), PRs
-
-    s2time = time.time()
-    TP = multiprocessing.Pool(processes=procs)
-    results = []
-    if procs == 1:
-        results.append(TP.apply_async(funcFVA, (fvamod.clone(), rid)))
-    else:
-        for p_ in range(len(PRs)-1):
-            print '%s -> %s' % (PRs[p_], PRs[p_+1])
-            results.append(TP.apply_async(funcFVA, (fvamod.clone(), rid[PRs[p_]:PRs[p_+1]])))
-        results.append(TP.apply_async(funcFVA, (fvamod.clone(), rid[PRs[-1]:])))
-    fva = []
-    fvan = []
-    for r_ in results:
-        out = r_.get(timeout)
-        fva.append(out[0])
-        fvan.append(out[1])
-    e2time = time.time()
-    del results
-
-    print '\nMulticore FVA took: %.2f min (%s processes)' % ((e2time-s2time)/60., procs)
-    return fva, fvan
-
-
-if __name__ == '__main__':
-    print os.sys.argv
+#if HAVE_MULTIENV:
+    #def runMultiCoreMultiEnvFVA(lp, selected_reactions=None, tol=None, rhs_sense='lower', optPercentage=100.0, work_dir=None, debug=False, procs=2):
+        #"""
+        #Run a multicore FVA where:
+
+         #- *lp* is a multienvironment lp model instance
+         #- *procs* [default=2] number of processing threads (optimum seems to be about the number of physical cores)
+
+        #"""
+        #fN = os.path.join(work_dir, str(time.time()).split('.')[0])
+        #lp.write(fN+'.lp', filetype='lp')
+        #MEargs = [fN+'.lp', selected_reactions, tol, rhs_sense, optPercentage, work_dir, debug]
+        #print(MEargs)
+        #print(fN)
+        #F = file(fN, 'wb')
+        #pickle.dump(MEargs, F, protocol=-1)
+        #F.close()
+        #subprocess.call(['python', MULTIENVFVAFILE, str(procs), fN])
+        #F = file(fN, 'rb')
+        #res = pickle.load(F)
+        #F.close()
+        #os.remove(fN)
+
+        #fva = res[0]
+        #fvan = res[1]
+
+        #if len(fva) == 1:
+            #fva = fva[0]
+            #fvan = fvan[0]
+        #elif len(fva) > 1:
+            #fva = numpy.vstack(fva)
+            #fvan2 = []
+            #for n_ in fvan:
+                #fvan2 += n_
+            #fvan = fvan2
+
+        #return fva, fvan
+#else:
+    #def runMultiCoreMultiEnvFVA(lp, selected_reactions=None, tol=None, rhs_sense='lower', optPercentage=100.0, work_dir=None, debug=False, procs=2):
+        #raise RuntimeError('\nMultiCore module not present')
 
-    cores = int(os.sys.argv[1])
-    F = file(os.sys.argv[2],'rb')
-    cmod = pickle.load(F)
-    F.close()
 
 
-    CBSolver.analyzeModel(cmod, oldlpgen=False)
-    res = multiCoreFVA(cmod, procs=cores)
-
-    F = file(os.sys.argv[2], 'wb')
-    pickle.dump(res, F, protocol=-1)
-    F.flush()
-    F.close()
 
-"""

src/CBModel.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: bgoli@users.sourceforge.net
-Last edit: $Author: bgoli $ ($Id: CBTools.py 515 2016-11-07 14:20:11Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBTools.py 518 2016-11-07 17:40:44Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -98,6 +98,17 @@ def deSerialize(s):
     """
     return pickle.loads(s)
 
+def deSerializeFromDisk(filename):
+    """
+    Loads a serialised Python pickle from *filename* returns the Python object(s)
+
+    """
+    assert os.path.exists(filename), '\nFile \"{}\" does not exist'.format(filename)
+    F = file(filename, 'rb')
+    obj = pickle.load(F)
+    F.close()
+    return obj
+
 def addStoichToFBAModel(fm):
     """
     Build stoichiometry: this method has been refactored into the model class - cmod.buildStoichMatrix()

src/CBMultiCore.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: bgoli@users.sourceforge.net
-Last edit: $Author: bgoli $ ($Id: CBXML.py 515 2016-11-07 14:20:11Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: CBXML.py 520 2016-11-07 21:10:45Z bgoli $)
 
 """
 ## gets rid of "invalid variable name" info
@@ -3726,15 +3726,15 @@ def sbml_readSBML3FBC(fname, work_dir=None, return_sbml_model=False, xoptions={}
             else:
                 print('Gene {} is not part of a GPR association. Will create anyway!'.format(g_))
                 non_gpr_genes.append(g_)
-        # TODO: this is a corner case I'll deal with it better later, non GPR associated genes are added as inactive gene objects
+
         for ng_ in non_gpr_genes:
             G = CBModel.Gene(ng_, label=GENE_D[ng_]['label'], active=False)
             G.annotation = GENE_D[ng_]['annotation']
             G.__sbo_term__ = GENE_D[ng_]['sbo']
             G.miriam = GENE_D[ng_]['miriam']
             G.setNotes(GENE_D[ng_]['notes'])
             print('WARNING: Non-gpr gene detected.', G.getId(), G.getLabel(), fm.getId())
-            raise RuntimeError()
+            #raise RuntimeError()
 
     if DEBUG: print('GPR build: {}'.format(round(time.time() - time0, 3)))
     time0 = time.time()

src/CBTools.py

@@ -19,7 +19,7 @@
 
 Author: Brett G. Olivier
 Contact email: bgoli@users.sourceforge.net
-Last edit: $Author: bgoli $ ($Id: __init__.py 515 2016-11-07 14:20:11Z bgoli $)
+Last edit: $Author: bgoli $ ($Id: __init__.py 518 2016-11-07 17:40:44Z bgoli $)
 
 """
 ##
@@ -87,6 +87,7 @@
 NAN = float('nan')
 
 from . import CBModel, CBDataStruct, CBModelTools, CBRead, CBReadtxt, CBTools, CBVersion, CBWrite, CBXML, CBNetDB, CBPlot
+from .CBTools import deSerialize, deSerializeFromDisk
 from . import PyscesSED
 SED = PyscesSED.SEDCBMPY