diff --git a/AUTHROS b/AUTHROS
new file mode 100644
index 0000000000000000000000000000000000000000..f568c742ebe5fc90330f250c3c5e035224fed581
--- /dev/null
+++ b/AUTHROS
@@ -0,0 +1,9 @@
+Upinder S. Bhalla Primary Architect
+Niraj Dudani Neuronal solver
+Subhasis Ray Python interface
+Aditya Gilra NeuroML support
+Aviral Goel Moogli
+HarshaRani. G.V Designing of Website,read and write SBML and
+ Graphical User Interface for moose
+Dilawar Singh Packaging, BOOST solvers
+Dharma Teja GPU parallelization using CUDA
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 390904c58e1e4ebd1f8a9c4e1337014f7676d173..916c01176ab45eb8065bdd9a9aab2fd63dad81be 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,5 +1,5 @@
set(CMAKE_LEGACY_CYGWIN_WIN32 0)
-cmake_minimum_required(VERSION 2.6.0 FATAL_ERROR)
+cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
if(COMMAND cmake_policy)
cmake_policy(SET CMP0003 NEW)
@@ -11,9 +11,11 @@ endif(COMMAND cmake_policy)
project(MOOSE)
+set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake_modules")
include(CheckCXXCompiler.cmake)
include(CheckIncludeFileCXX)
include(FindPkgConfig)
+include(GetRevision)
# If from command line, version info is not passed, use the git to generate a
# version file. If GIT fails, use the previous known version.
@@ -27,14 +29,14 @@ if( (NOT MOOSE_VERSION) AND GIT_EXEC)
OUTPUT_VARIABLE MOOSE_VERSION
OUTPUT_STRIP_TRAILING_WHITESPACE
)
- message(STATUS "+ Writing ${MOOSE_VERSION} to ${VERSION_FILE}" )
- file(WRITE ${VERSION_FILE} ${MOOSE_VERSION})
-elseif( (NOT MOOSE_VERSION) AND (NOT GIT_EXEC) )
- message(STATUS "+ Reading ${VERSION_FILE}" )
- file(READ ${VERSION_FILE} GIT_VERSION_OUTPUT )
+endif( )
+
+# Default to current date.
+if( (NOT MOOSE_VERSION) )
+ NOW(TIMESTAMP)
+ set(MOOSE_VERSION "nightly-${TIMESTAMP}" )
elseif(MOOSE_VERSION)
message(STATUS "+ Using user specified VERSION = ${MOOSE_VERSION}" )
- file(WRITE ${VERSION_FILE} ${MOOSE_VERSION})
else()
message(FATAL_ERROR "Could not determine MOOSE_VERSION" )
endif( )
@@ -42,6 +44,10 @@ endif( )
add_definitions( -DMOOSE_VERSION="${MOOSE_VERSION}")
message( STATUS "MOOSE Version ${MOOSE_VERSION}" )
+# Write VERSION to a file VERSION so that setup.py can use it.
+message(STATUS "+ Writing ${MOOSE_VERSION} to ${VERSION_FILE}" )
+file(WRITE ${VERSION_FILE} ${MOOSE_VERSION} )
+
# This snippet is from LLVM project.
# Sanity check our source directory to make sure that we are not trying to
# generate an in-tree build (unless on MSVC_IDE, where it is ok), and to make
@@ -98,9 +104,6 @@ option(WITH_MPI "Enable Openmpi support" OFF)
option(WITH_BOOST "Use boost library instead of GSL" OFF)
option(WITH_GSL "Use gsl-library. Alternative is WITH_BOOST" ON)
-################################# CMKAE MACROS #################################
-
-set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake_modules")
############################ BUILD CONFIGURATION #################################
diff --git a/basecode/global.h b/basecode/global.h
index 9b06b2820245f1ef4d8fd0639be1b3e6f42a5a13..692bb71cbd15adfc81d6470f830cba0600a50c11 100644
--- a/basecode/global.h
+++ b/basecode/global.h
@@ -48,9 +48,6 @@ extern unsigned int totalTests;
#define TEST_END totalTests++; \
cout << std::right << setw(20) << "test of " << SIMPLE_CURRENT_FUNCTION << " finished.";
-/*-----------------------------------------------------------------------------
- * Global functions in namespace moose
- *-----------------------------------------------------------------------------*/
#define MISSING_BRACKET_AT_END -1
#define EMPTY_PATH -2
#define SPACES_AT_THE_BEGINING -3
@@ -59,6 +56,9 @@ extern unsigned int totalTests;
#define BAD_CHARACTER_IN_PATH -6
+/*-----------------------------------------------------------------------------
+ * Global functions in namespace moose
+ *-----------------------------------------------------------------------------*/
namespace moose
{
diff --git a/cmake_modules/GetRevision.cmake b/cmake_modules/GetRevision.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..41c991cb8a6e06d71b82eb08b0705ab085b37366
--- /dev/null
+++ b/cmake_modules/GetRevision.cmake
@@ -0,0 +1,20 @@
+CMAKE_MINIMUM_REQUIRED(VERSION 2.6.3)
+
+MACRO(NOW RESULT)
+ IF(CMAKE_VERSION VERSION_GREATER "2.8.10")
+ STRING(TIMESTAMP ${RESULT} "%Y%m%d")
+ ELSE()
+ IF(WIN32)
+ EXECUTE_PROCESS(COMMAND "wmic" "os" "get" "localdatetime" OUTPUT_VARIABLE DATETIME)
+ IF(NOT DATETIME MATCHES "ERROR")
+ STRING(REGEX REPLACE ".*\n([0-9][0-9][0-9][0-9])([0-9][0-9])([0-9][0-9])([0-9][0-9])([0-9][0-9])([0-9][0-9]).*" "\\1-\\2-\\3 \\4:\\5:\\6" ${RESULT} "${DATETIME}")
+ ENDIF()
+ ELSEIF(UNIX)
+ EXECUTE_PROCESS(COMMAND "date" "+%Y%m%d" OUTPUT_VARIABLE DATETIME)
+ STRING(REGEX REPLACE "([0-9: -]+).*" "\\1" ${RESULT} "${DATETIME}")
+ ELSE()
+ MESSAGE(SEND_ERROR "date not implemented")
+ SET(${RESULT} "00000000")
+ ENDIF()
+ ENDIF()
+ENDMACRO()
diff --git a/python/moose/SBML/readSBML.py b/python/moose/SBML/readSBML.py
index 2765c5e045a4d600aea8a23c0398e422c8bd5c96..6a627054181e6d06e26ed7a4e2db2317cd962b25 100644
--- a/python/moose/SBML/readSBML.py
+++ b/python/moose/SBML/readSBML.py
@@ -10,10 +10,10 @@
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment,
** also known as GENESIS 3 base code.
-** copyright (C) 2003-2016 Upinder S. Bhalla. and NCBS
+** copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
Created : Thu May 12 10:19:00 2016(+0530)
Version
-Last-Updated: Wed Sep 28
+Last-Updated: Tue Feb 10 2017
By:
**********************************************************************/
@@ -23,8 +23,8 @@ import sys
import os.path
import collections
import moose
-
-
+from validation import validateModel
+import re
'''
TODO in
-Compartment
@@ -57,13 +57,13 @@ try:
except ImportError:
pass
-
def mooseReadSBML(filepath, loadpath, solver="ee"):
global foundLibSBML_
if not foundLibSBML_:
print('No python-libsbml found.'
'\nThis module can be installed by following command in terminal:'
- '\n\t easy_install python-libsbl'
+ '\n\t easy_install python-libsbml'
+ '\n\t apt-get install python-libsbml'
)
return None
@@ -74,12 +74,9 @@ def mooseReadSBML(filepath, loadpath, solver="ee"):
with open(filepath, "r") as filep:
filep = open(filepath, "r")
document = libsbml.readSBML(filepath)
- num_errors = document.getNumErrors()
- if (num_errors > 0):
- print("Encountered the following SBML errors:")
- document.printErrors()
- return moose.element('/')
- else:
+ tobecontinue = False
+ tobecontinue = validateModel(document)
+ if tobecontinue:
level = document.getLevel()
version = document.getVersion()
print(("\n" + "File: " + filepath + " (Level " +
@@ -120,17 +117,19 @@ def mooseReadSBML(filepath, loadpath, solver="ee"):
return moose.element('/')
else:
baseId = moose.Neutral(loadpath)
+ basePath = baseId
# All the model will be created under model as
# a thumbrule
- basePath = moose.Neutral(
- baseId.path + '/model')
+ basePath = moose.Neutral(baseId.path + '/model')
# Map Compartment's SBML id as key and value is
# list of[ Moose ID and SpatialDimensions ]
global comptSbmlidMooseIdMap
global warning
warning = " "
+ global msg
+ msg = " "
comptSbmlidMooseIdMap = {}
- print(("modelPath:" + basePath.path))
+ #print(("modelPath:" + basePath.path))
globparameterIdValue = {}
modelAnnotaInfo = {}
mapParameter(model, globparameterIdValue)
@@ -138,8 +137,10 @@ def mooseReadSBML(filepath, loadpath, solver="ee"):
basePath, model, comptSbmlidMooseIdMap)
if errorFlag:
specInfoMap = {}
- errorFlag = createSpecies(
+ errorFlag,warning = createSpecies(
basePath, model, comptSbmlidMooseIdMap, specInfoMap, modelAnnotaInfo)
+ #print(errorFlag,warning)
+
if errorFlag:
errorFlag = createRules(
model, specInfoMap, globparameterIdValue)
@@ -148,7 +149,7 @@ def mooseReadSBML(filepath, loadpath, solver="ee"):
model, specInfoMap, modelAnnotaInfo, globparameterIdValue)
getModelAnnotation(
model, baseId, basePath)
-
+
if not errorFlag:
print(msg)
# Any time in the middle if SBML does not read then I
@@ -157,7 +158,11 @@ def mooseReadSBML(filepath, loadpath, solver="ee"):
# built which is not correct print "Deleted rest of the
# model"
moose.delete(basePath)
- return baseId
+ basePath = moose.Shell('/')
+ return basePath
+ else:
+ print("Validation failed while reading the model.")
+ return moose.element('/')
def setupEnzymaticReaction(enz, groupName, enzName,
@@ -168,7 +173,6 @@ def setupEnzymaticReaction(enz, groupName, enzName,
cplx = (modelAnnotaInfo[groupName]["complex"])
cplx = str(idBeginWith(cplx))
complx = moose.element(specInfoMap[cplx]["Mpath"].path)
-
enzyme_ = moose.Enz(enzParent.path + '/' + enzName)
moose.move(complx, enzyme_)
moose.connect(enzyme_, "cplx", complx, "reac")
@@ -284,7 +288,7 @@ def getModelAnnotation(obj, baseId, basepath):
for plots in plotlist:
plots = plots.replace(" ", "")
plotorg = plots
- if moose.exists(basepath.path + plotorg):
+ if( moose.exists(basepath.path + plotorg) and isinstance(moose.element(basepath.path+plotorg),moose.PoolBase)) :
plotSId = moose.element(
basepath.path + plotorg)
# plotorg = convertSpecialChar(plotorg)
@@ -299,8 +303,7 @@ def getModelAnnotation(obj, baseId, basepath):
if not fullPath in tablelistname:
tab = moose.Table2(fullPath)
tablelistname.append(fullPath)
- moose.connect(
- tab, "requestOut", plotSId, "getConc")
+ moose.connect(tab, "requestOut", plotSId, "getConc")
def getObjAnnotation(obj, modelAnnotationInfo):
@@ -333,6 +336,8 @@ def getObjAnnotation(obj, modelAnnotationInfo):
annotateMap[nodeName] = nodeValue
if nodeName == "textColor":
annotateMap[nodeName] = nodeValue
+ if nodeName == "Group":
+ annotateMap[nodeName] = nodeValue
return annotateMap
@@ -457,7 +462,14 @@ def createReaction(model, specInfoMap, modelAnnotaInfo, globparameterIdValue):
for ritem in range(0, model.getNumReactions()):
reactionCreated = False
groupName = ""
+
reac = model.getReaction(ritem)
+ group = ""
+ reacAnnoInfo = {}
+ reacAnnoInfo = getObjAnnotation(reac, modelAnnotaInfo)
+ if "Group" in reacAnnoInfo:
+ group = reacAnnoInfo["Group"]
+
if (reac.isSetId()):
rId = reac.getId()
if (reac.isSetName()):
@@ -509,9 +521,7 @@ def createReaction(model, specInfoMap, modelAnnotaInfo, globparameterIdValue):
nummodifiers = reac.getNumModifiers()
if not (numRcts and numPdts):
- print(
- rName,
- " : Substrate and Product is missing, we will be skiping creating this reaction in MOOSE")
+ print("Warning: %s" %(rName)," : Substrate or Product is missing, we will be skiping creating this reaction in MOOSE")
reactionCreated = False
elif (reac.getNumModifiers() > 0):
reactionCreated, reaction_ = setupMMEnzymeReaction(
@@ -529,6 +539,11 @@ def createReaction(model, specInfoMap, modelAnnotaInfo, globparameterIdValue):
sp = react.getSpecies()
sp = str(idBeginWith(sp))
speCompt = specInfoMap[sp]["comptId"].path
+ if group:
+ if moose.exists(speCompt+'/'+group):
+ speCompt = speCompt+'/'+group
+ else:
+ speCompt = (moose.Neutral(speCompt+'/'+group)).path
reaction_ = moose.Reac(speCompt + '/' + rName)
reactionCreated = True
reactSBMLIdMooseId[rName] = {
@@ -758,10 +773,12 @@ def createRules(model, specInfoMap, globparameterIdValue):
exp = rule.getFormula()
for mem in ruleMemlist:
if (mem in specInfoMap):
- exp1 = exp.replace(mem, str(speFunXterm[mem]))
+ #exp1 = exp.replace(mem, str(speFunXterm[mem]))
+ exp1 = re.sub(r'\b%s\b'% (mem), speFunXterm[mem], exp)
exp = exp1
elif(mem in globparameterIdValue):
- exp1 = exp.replace(mem, str(globparameterIdValue[mem]))
+ #exp1 = exp.replace(mem, str(globparameterIdValue[mem]))
+ exp1 = re.sub(r'\b%s\b'% (mem), globparameterIdValue[mem], exp)
exp = exp1
else:
print("Math expression need to be checked")
@@ -805,12 +822,17 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
# - Need to add group name if exist in pool
# - Notes
# print "species "
-
if not (model.getNumSpecies()):
- return False
+ return (False,"number of species is zero")
else:
for sindex in range(0, model.getNumSpecies()):
spe = model.getSpecies(sindex)
+ group = ""
+ specAnnoInfo = {}
+ specAnnoInfo = getObjAnnotation(spe, modelAnnotaInfo)
+ if "Group" in specAnnoInfo:
+ group = specAnnoInfo["Group"]
+
sName = None
sId = spe.getId()
if spe.isSetName():
@@ -829,7 +851,11 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
hasonlySubUnit = spe.getHasOnlySubstanceUnits()
# "false": is {unit of amount}/{unit of size} (i.e., concentration or density).
# "true": then the value is interpreted as having a unit of amount only.
-
+ if group:
+ if moose.exists(comptEl+'/'+group):
+ comptEl = comptEl+'/'+group
+ else:
+ comptEl = (moose.Neutral(comptEl+'/'+group)).path
if (boundaryCondition):
poolId = moose.BufPool(comptEl + '/' + sName)
else:
@@ -837,13 +863,13 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
if (spe.isSetNotes):
pullnotes(spe, poolId)
- specAnnoInfo = {}
- specAnnoInfo = getObjAnnotation(spe, modelAnnotaInfo)
+
if specAnnoInfo:
if not moose.exists(poolId.path + '/info'):
poolInfo = moose.Annotator(poolId.path + '/info')
else:
poolInfo = moose.element(poolId.path + '/info')
+
for k, v in list(specAnnoInfo.items()):
if k == 'xCord':
poolInfo.x = float(v)
@@ -876,8 +902,7 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
initvalue = initvalue * unitfactor
elif spe.isSetInitialConcentration():
initvalue = spe.getInitialConcentration()
- print(
- " Since hasonlySubUnit is true and concentration is set units are not checked")
+ print(" Since hasonlySubUnit is true and concentration is set units are not checked")
poolId.nInit = initvalue
elif hasonlySubUnit == False:
@@ -885,8 +910,7 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
if spe.isSetInitialAmount():
initvalue = spe.getInitialAmount()
# initAmount is set we need to convert to concentration
- initvalue = initvalue / \
- comptSbmlidMooseIdMap[comptId]["size"]
+ initvalue = initvalue / comptSbmlidMooseIdMap[comptId]["size"]
elif spe.isSetInitialConcentration():
initvalue = spe.getInitialConcentration()
@@ -907,13 +931,14 @@ def createSpecies(basePath, model, comptSbmlidMooseIdMap,
if (rule_variable == sId):
found = True
break
+
if not (found):
print(
"Invalid SBML: Either initialConcentration or initialAmount must be set or it should be found in assignmentRule but non happening for ",
sName)
- return False
+ return (False,"Invalid SBML: Either initialConcentration or initialAmount must be set or it should be found in assignmentRule but non happening for ",sName)
- return True
+ return (True," ")
def transformUnit(unitForObject, hasonlySubUnit=False):
@@ -995,7 +1020,7 @@ def createCompartment(basePath, model, comptSbmlidMooseIdMap):
# ToDoList : Check what should be done for the spaitialdimension is 2 or
# 1, area or length
if not(model.getNumCompartments()):
- return False
+ return False,
else:
for c in range(0, model.getNumCompartments()):
compt = model.getCompartment(c)
@@ -1115,19 +1140,25 @@ def findCompartment(element):
return element
if __name__ == "__main__":
-
- filepath = sys.argv[1]
- path = sys.argv[2]
-
- f = open(filepath, 'r')
-
- if path == '':
- loadpath = filepath[filepath.rfind('/'):filepath.find('.')]
- else:
- loadpath = path
-
- read = mooseReadSBML(filepath, loadpath)
- if read:
- print(" Read to path", loadpath)
+ try:
+ sys.argv[1]
+ except IndexError:
+ print("Filename or path not given")
+ exit(0)
else:
- print(" could not read SBML to MOOSE")
+ filepath = sys.argv[1]
+ if not os.path.exists(filepath):
+ print("Filename or path does not exist",filepath)
+
+ else:
+ try:
+ sys.argv[2]
+ except :
+ modelpath = filepath[filepath.rfind('/'):filepath.find('.')]
+ else:
+ modelpath = sys.argv[2]
+ read = mooseReadSBML(filepath, modelpath)
+ if read:
+ print(" Model read to moose path "+ modelpath)
+ else:
+ print(" could not read SBML to MOOSE")
\ No newline at end of file
diff --git a/python/moose/SBML/validation.py b/python/moose/SBML/validation.py
new file mode 100644
index 0000000000000000000000000000000000000000..41ab4140b6a1a1ae659d2738fd0471e793756fcb
--- /dev/null
+++ b/python/moose/SBML/validation.py
@@ -0,0 +1,95 @@
+foundLibSBML_ = False
+try:
+ from libsbml import *
+ foundLibSBML_ = True
+except Exception as e:
+ pass
+
+def validateModel(sbmlDoc):
+ if sbmlDoc.getNumErrors() > 0:
+ tobecontinued = False
+ for i in range(0,sbmlDoc.getNumErrors()):
+ print (sbmlDoc.getError(i).getMessage())
+ return False
+
+ if (not sbmlDoc):
+ print("validateModel: given a null SBML Document")
+ return False
+
+ consistencyMessages = ""
+ validationMessages = ""
+ noProblems = True
+ numCheckFailures = 0
+ numConsistencyErrors = 0
+ numConsistencyWarnings = 0
+ numValidationErrors = 0
+ numValidationWarnings = 0
+ # Once the whole model is done and before it gets written out,
+ # it's important to check that the whole model is in fact complete,
+ # consistent and valid.
+ numCheckFailures = sbmlDoc.checkInternalConsistency()
+ if (numCheckFailures > 0):
+ for i in range(0, numCheckFailures):
+ sbmlErr = sbmlDoc.getError(i)
+ if (sbmlErr.isFatal() or sbmlErr.isError()):
+ noProblems = False
+ numConsistencyErrors += 1
+ else:
+ numConsistencyWarnings += 1
+ constStr = sbmlDoc.printErrors()
+ if sbmlDoc.printErrors():
+ consistencyMessages = constStr
+
+ # If the internal checks fail, it makes little sense to attempt
+ # further validation, because the model may be too compromised to
+ # be properly interpreted.
+
+ if (numConsistencyErrors > 0):
+ consistencyMessages += "Further validation aborted."
+ else:
+ numCheckFailures = sbmlDoc.checkConsistency()
+ validationMessages;
+ #numCheckFailures = sbmlDoc.checkL3v1Compatibility()
+ if (numCheckFailures > 0):
+ for i in range(0, (numCheckFailures)):
+ consistencyMessages = sbmlDoc.getErrorLog().toString()
+ sbmlErr = sbmlDoc.getError(i)
+ if (sbmlErr.isFatal() or sbmlErr.isError()):
+ noProblems = False
+ numValidationErrors += 1
+ else:
+ numValidationWarnings += 1
+
+ warning = sbmlDoc.getErrorLog().toString()
+ oss = sbmlDoc.printErrors()
+ validationMessages = oss
+
+ if (noProblems):
+ return True
+ else:
+ if consistencyMessages is None:
+ consistencyMessages = ""
+ if consistencyMessages != "":
+ print("consistency Warning: " + consistencyMessages)
+
+ if (numConsistencyErrors > 0):
+ print("ERROR: encountered " +str(numConsistencyErrors) +" consistency error in model " +sbmlDoc.getModel().getId() +"'.")
+
+ if (numConsistencyWarnings > 0):
+ print("Notice: encountered " +str(numConsistencyWarnings) +" consistency warning in model " +sbmlDoc.getModel().getId() +"'.")
+
+ if (numValidationErrors > 0):
+ print("ERROR: encountered " + str(numValidationErrors) + " validation error in model " +sbmlDoc.getModel().getId() + "'.")
+ if (numValidationWarnings > 0):
+ print("Notice: encountered " +str(numValidationWarnings) +" validation warning in model " +sbmlDoc.getModel().getId() +"'.")
+
+ if validationMessages:
+ print(validationMessages)
+
+ return False
+ # return ( numConsistencyErrors == 0 and numValidationErrors == 0,
+ # consistencyMessages)
+
+if __name__ == '__main__':
+ sbmlDoc = libsbml.readSBML('00001-sbml-l3v1.xml')
+ validateModel(sbmlDoc)
diff --git a/python/moose/SBML/writeSBML.py b/python/moose/SBML/writeSBML.py
index 3057f1002b3d356114f579a195a97c0804f568b1..90400306877ebe14cb5fccc4e7c42211d648ae20 100644
--- a/python/moose/SBML/writeSBML.py
+++ b/python/moose/SBML/writeSBML.py
@@ -9,26 +9,28 @@
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment,
** also known as GENESIS 3 base code.
-** copyright (C) 2003-2016 Upinder S. Bhalla. and NCBS
+** copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
Created : Friday May 27 12:19:00 2016(+0530)
Version
-Last-Updated: Thursday Oct 27 11:20:00 2016(+0530)
- By:
+Last-Updated: Wed Jan 11 15:20:00 2017(+0530)
+ By:
**********************************************************************/
/****************************
'''
-
-import moose
+import sys
import re
from collections import Counter
-import networkx as nx
-import matplotlib.pyplot as plt
-import sys
+
+import moose
+from validation import validateModel
+from moose.chemUtil.chemConnectUtil import *
+from moose.chemUtil.graphUtils import *
+
# ToDo:
-# Table should be written
-# Group's should be added
+# Table should be written
+# Group's should be added
# boundary condition for buffer pool having assignment statment constant
# shd be false
@@ -41,12 +43,14 @@ except Exception as e:
def mooseWriteSBML(modelpath, filename, sceneitems={}):
global foundLibSBML_
+ msg = " "
if not foundLibSBML_:
print('No python-libsbml found.'
'\nThis module can be installed by following command in terminal:'
- '\n\t easy_install python-libsbl'
+ '\n\t easy_install python-libsbml or'
+ '\n\t apt-get install python-libsbml'
)
- return -1, msg
+ return -2, "Could not save the model in to SBML file. \nThis module can be installed by following command in terminal: \n\t easy_install python-libsbml or \n\t apt-get install python-libsbml",''
sbmlDoc = SBMLDocument(3, 1)
filepath, filenameExt = os.path.split(filename)
@@ -57,12 +61,11 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
# validatemodel
sbmlOk = False
- global spe_constTrue, cmin, cmax
+ global spe_constTrue
spe_constTrue = []
global nameList_
nameList_ = []
-
- autoCoordinateslayout = False
+ positionInfoexist = False
xmlns = XMLNamespaces()
xmlns.add("http://www.sbml.org/sbml/level3/version1")
xmlns.add("http://www.moose.ncbs.res.in", "moose")
@@ -74,55 +77,57 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
cremodel_.setExtentUnits("substance")
cremodel_.setSubstanceUnits("substance")
neutralNotes = ""
+
specieslist = moose.wildcardFind(modelpath + '/##[ISA=PoolBase]')
- neutralPath = getGroupinfo(specieslist[0])
- if moose.exists(neutralPath.path + '/info'):
- neutralInfo = moose.element(neutralPath.path + '/info')
- neutralNotes = neutralInfo.notes
- if neutralNotes != "":
- cleanNotes = convertNotesSpecialChar(neutralNotes)
- notesString = "<body xmlns=\"http://www.w3.org/1999/xhtml\">\n \t \t" + \
- neutralNotes + "\n\t </body>"
- cremodel_.setNotes(notesString)
- srcdesConnection = {}
- cmin, cmax = 0, 1
+ if specieslist:
+ neutralPath = getGroupinfo(specieslist[0])
+ if moose.exists(neutralPath.path + '/info'):
+ neutralInfo = moose.element(neutralPath.path + '/info')
+ neutralNotes = neutralInfo.notes
+ if neutralNotes != "":
+ cleanNotes = convertNotesSpecialChar(neutralNotes)
+ notesString = "<body xmlns=\"http://www.w3.org/1999/xhtml\">\n \t \t" + \
+ neutralNotes + "\n\t </body>"
+ cremodel_.setNotes(notesString)
+ srcdesConnection = {}
if not bool(sceneitems):
- autoCoordinateslayout = True
- srcdesConnection = setupItem(modelpath)
- meshEntry = setupMeshObj(modelpath)
- cmin, cmax, sceneitems = autoCoordinates(
- meshEntry, srcdesConnection)
-
+ meshEntry,xmin,xmax,ymin,ymax,positionInfoexist,sitem = setupMeshObj(modelpath)
+ #moose.coordinateUtil.setupItem(modelpath,srcdesConnection)
+ setupItem(modelpath,srcdesConnection)
+ if not positionInfoexist:
+ autoCoordinates(meshEntry,srcdesConnection)
+
writeUnits(cremodel_)
modelAnno = writeSimulationAnnotation(modelpath)
if modelAnno:
cremodel_.setAnnotation(modelAnno)
+
compartexist = writeCompt(modelpath, cremodel_)
- species = writeSpecies(
- modelpath,
- cremodel_,
- sbmlDoc,
- sceneitems,
- autoCoordinateslayout)
- if species:
- writeFunc(modelpath, cremodel_)
- writeReac(modelpath, cremodel_, sceneitems, autoCoordinateslayout)
- writeEnz(modelpath, cremodel_, sceneitems, autoCoordinateslayout)
-
- consistencyMessages = ""
- SBMLok = validateModel(sbmlDoc)
- if (SBMLok):
- writeTofile = filepath + "/" + filename + '.xml'
- writeSBMLToFile(sbmlDoc, writeTofile)
- return True, consistencyMessages, writeTofile
-
- if (not SBMLok):
- cerr << "Errors encountered " << endl
- return -1, consistencyMessages
-
-
-def writeEnz(modelpath, cremodel_, sceneitems, autoCoordinateslayout):
+ if compartexist == True:
+ species = writeSpecies( modelpath,cremodel_,sbmlDoc,sceneitems)
+ if species:
+ writeFunc(modelpath, cremodel_)
+ writeReac(modelpath, cremodel_, sceneitems)
+ writeEnz(modelpath, cremodel_, sceneitems)
+ consistencyMessages = ""
+ SBMLok = validateModel(sbmlDoc)
+ if (SBMLok):
+ writeTofile = filepath + "/" + filename + '.xml'
+ writeSBMLToFile(sbmlDoc, writeTofile)
+ return True, consistencyMessages, writeTofile
+
+ if (not SBMLok):
+ cerr << "Errors encountered " << endl
+ return -1, consistencyMessages
+ else:
+ return False, "Atleast one compartment should exist to write SBML"
+
+def calPrime(x):
+ prime = int((20 * (float(x - cmin) / float(cmax - cmin))) - 10)
+ return prime
+
+def writeEnz(modelpath, cremodel_, sceneitems):
for enz in moose.wildcardFind(modelpath + '/##[ISA=EnzBase]'):
enzannoexist = False
enzGpnCorCol = " "
@@ -135,25 +140,26 @@ def writeEnz(modelpath, cremodel_, sceneitems, autoCoordinateslayout):
notesE = Anno.notes
element = moose.element(enz)
ele = getGroupinfo(element)
- if ele.className == "Neutral" or sceneitems[
- element] or Anno.color or Anno.textColor:
- enzannoexist = True
-
+ if element.className == "Neutral" or sceneitems or Anno.x or Anno.y:
+ enzannoexist = True
if enzannoexist:
+ enzAnno = "<moose:ModelAnnotation>\n"
if ele.className == "Neutral":
- enzGpnCorCol = "<moose:Group> " + ele.name + " </moose:Group>\n"
- if sceneitems[element]:
- v = sceneitems[element]
- if autoCoordinateslayout == False:
- enzGpnCorCol = enzGpnCorCol + "<moose:xCord>" + \
- str(v['x']) + "</moose:xCord>\n" + \
- "<moose:yCord>" + str(v['y']) + "</moose:yCord>\n"
- elif autoCoordinateslayout == True:
- x = calPrime(v['x'])
- y = calPrime(v['y'])
- enzGpnCorCol = enzGpnCorCol + "<moose:xCord>" + \
- str(x) + "</moose:xCord>\n" + \
- "<moose:yCord>" + str(y) + "</moose:yCord>\n"
+ enzGpnCorCol = "<moose:Group>" + ele.name + "</moose:Group>\n"
+ if sceneitems:
+ #Saved from GUI, then scene co-ordinates are passed
+ enzGpnCorCol = enzGpnCorCol + "<moose:xCord>" + \
+ str(sceneitems[enz]['x']) + "</moose:xCord>\n" + \
+ "<moose:yCord>" + \
+ str(sceneitems[enz]['y'])+ "</moose:yCord>\n"
+ else:
+ #Saved from cmdline,genesis coordinates are kept as its
+ # SBML, cspace, python, then auto-coordinates are done
+ #and coordinates are updated in moose Annotation field
+ enzGpnCorCol = enzGpnCorCol + "<moose:xCord>" + \
+ str(Anno.x) + "</moose:xCord>\n" + \
+ "<moose:yCord>" + \
+ str(Anno.y)+ "</moose:yCord>\n"
if Anno.color:
enzGpnCorCol = enzGpnCorCol + "<moose:bgColor>" + Anno.color + "</moose:bgColor>\n"
if Anno.textColor:
@@ -501,7 +507,7 @@ def listofname(reacSub, mobjEnz):
nameList_.append(clean_name)
-def writeReac(modelpath, cremodel_, sceneitems, autoCoordinateslayout):
+def writeReac(modelpath, cremodel_, sceneitems):
for reac in moose.wildcardFind(modelpath + '/##[ISA=ReacBase]'):
reacSub = reac.neighbors["sub"]
reacPrd = reac.neighbors["prd"]
@@ -537,34 +543,34 @@ def writeReac(modelpath, cremodel_, sceneitems, autoCoordinateslayout):
reaction.setNotes(notesStringR)
element = moose.element(reac)
ele = getGroupinfo(element)
- if ele.className == "Neutral" or sceneitems[
- element] or Anno.color or Anno.textColor:
+ if element.className == "Neutral" or sceneitems or Anno.x or Anno.y:
reacannoexist = True
if reacannoexist:
reacAnno = "<moose:ModelAnnotation>\n"
if ele.className == "Neutral":
reacAnno = reacAnno + "<moose:Group>" + ele.name + "</moose:Group>\n"
- if sceneitems[element]:
- v = sceneitems[element]
- if autoCoordinateslayout == False:
- reacAnno = reacAnno + "<moose:xCord>" + \
- str(v['x']) + "</moose:xCord>\n" + \
+ if sceneitems:
+ #Saved from GUI, then scene co-ordinates are passed
+ reacAnno = reacAnno + "<moose:xCord>" + \
+ str(sceneitems[reac]['x']) + "</moose:xCord>\n" + \
+ "<moose:yCord>" + \
+ str(sceneitems[reac]['y'])+ "</moose:yCord>\n"
+ else:
+ #Saved from cmdline,genesis coordinates are kept as its
+ # SBML, cspace, python, then auto-coordinates are done
+ #and coordinates are updated in moose Annotation field
+ reacAnno = reacAnno + "<moose:xCord>" + \
+ str(Anno.x) + "</moose:xCord>\n" + \
"<moose:yCord>" + \
- str(v['y']) + "</moose:yCord>\n"
- elif autoCoordinateslayout == True:
- x = calPrime(v['x'])
- y = calPrime(v['y'])
- reacAnno = reacAnno + "<moose:xCord>" + \
- str(x) + "</moose:xCord>\n" + \
- "<moose:yCord>" + str(y) + "</moose:yCord>\n"
+ str(Anno.y)+ "</moose:yCord>\n"
if Anno.color:
reacAnno = reacAnno + "<moose:bgColor>" + Anno.color + "</moose:bgColor>\n"
if Anno.textColor:
reacAnno = reacAnno + "<moose:textColor>" + \
Anno.textColor + "</moose:textColor>\n"
reacAnno = reacAnno + "</moose:ModelAnnotation>"
- # s1.appendAnnotation(XMLNode.convertStringToXMLNode(speciAnno))
reaction.setAnnotation(reacAnno)
+
kl_s, sRL, pRL, compt = "", "", "", ""
if not reacSub and not reacPrd:
@@ -712,8 +718,7 @@ def convertSpecialChar(str1):
return str1
-def writeSpecies(modelpath, cremodel_, sbmlDoc,
- sceneitems, autoCoordinateslayout):
+def writeSpecies(modelpath, cremodel_, sbmlDoc, sceneitems):
# getting all the species
for spe in moose.wildcardFind(modelpath + '/##[ISA=PoolBase]'):
sName = convertSpecialChar(spe.name)
@@ -785,28 +790,29 @@ def writeSpecies(modelpath, cremodel_, sbmlDoc,
cleanNotesS + "\n\t </body>"
s1.setNotes(notesStringS)
+
element = moose.element(spe)
ele = getGroupinfo(element)
- if ele.className == "Neutral" or sceneitems[
- element] or Anno.color or Anno.textColor:
+ if element.className == "Neutral" or Anno.color or Anno.textColor or sceneitems or Anno.x or Anno.y:
speciannoexist = True
if speciannoexist:
speciAnno = "<moose:ModelAnnotation>\n"
if ele.className == "Neutral":
speciAnno = speciAnno + "<moose:Group>" + ele.name + "</moose:Group>\n"
- if sceneitems[element]:
- v = sceneitems[element]
- if autoCoordinateslayout == False:
- speciAnno = speciAnno + "<moose:xCord>" + \
- str(v['x']) + "</moose:xCord>\n" + \
+ if sceneitems:
+ #Saved from GUI, then scene co-ordinates are passed
+ speciAnno = speciAnno + "<moose:xCord>" + \
+ str(sceneitems[spe]['x']) + "</moose:xCord>\n" + \
+ "<moose:yCord>" + \
+ str(sceneitems[spe]['y'])+ "</moose:yCord>\n"
+ else:
+ #Saved from cmdline,genesis coordinates are kept as its
+ # SBML, cspace, python, then auto-coordinates are done
+ #and coordinates are updated in moose Annotation field
+ speciAnno = speciAnno + "<moose:xCord>" + \
+ str(Anno.x) + "</moose:xCord>\n" + \
"<moose:yCord>" + \
- str(v['y']) + "</moose:yCord>\n"
- elif autoCoordinateslayout == True:
- x = calPrime(v['x'])
- y = calPrime(v['y'])
- speciAnno = speciAnno + "<moose:xCord>" + \
- str(x) + "</moose:xCord>\n" + \
- "<moose:yCord>" + str(y) + "</moose:yCord>\n"
+ str(Anno.y)+ "</moose:yCord>\n"
if Anno.color:
speciAnno = speciAnno + "<moose:bgColor>" + Anno.color + "</moose:bgColor>\n"
if Anno.textColor:
@@ -819,7 +825,8 @@ def writeSpecies(modelpath, cremodel_, sbmlDoc,
def writeCompt(modelpath, cremodel_):
# getting all the compartments
- for compt in moose.wildcardFind(modelpath + '/##[ISA=ChemCompt]'):
+ compts = moose.wildcardFind(modelpath + '/##[ISA=ChemCompt]')
+ for compt in compts:
comptName = convertSpecialChar(compt.name)
# converting m3 to litre
size = compt.volume * pow(10, 3)
@@ -836,7 +843,10 @@ def writeCompt(modelpath, cremodel_):
c1.setSize(size)
c1.setSpatialDimensions(ndim)
c1.setUnits('volume')
-
+ if compts:
+ return True
+ else:
+ return False
# write Simulation runtime,simdt,plotdt
def writeSimulationAnnotation(modelpath):
modelAnno = ""
@@ -867,18 +877,17 @@ def writeSimulationAnnotation(modelpath):
graphSpefound = True
if graphSpefound:
if not plots:
- #plots = ori[ori.find(q.name)-1:len(ori)]
- plots = '/' + q.name + '/' + name
+ plots = ori[ori.find(q.name)-1:len(ori)]
+ #plots = '/' + q.name + '/' + name
else:
- #plots = plots + "; "+ori[ori.find(q.name)-1:len(ori)]
- plots = plots + "; /" + q.name + '/' + name
+ plots = plots + "; "+ori[ori.find(q.name)-1:len(ori)]
+ #plots = plots + "; /" + q.name + '/' + name
if plots != " ":
modelAnno = modelAnno + "<moose:plots> " + plots + "</moose:plots>\n"
modelAnno = modelAnno + "</moose:ModelAnnotation>"
return modelAnno
-
def writeUnits(cremodel_):
unitVol = cremodel_.createUnitDefinition()
unitVol.setId("volume")
@@ -896,357 +905,28 @@ def writeUnits(cremodel_):
unit.setExponent(1.0)
unit.setScale(-3)
-
-def validateModel(sbmlDoc):
- # print " sbmlDoc ",sbmlDoc.toSBML()
- if (not sbmlDoc):
- print("validateModel: given a null SBML Document")
- return False
- consistencyMessages = ""
- validationMessages = ""
- noProblems = True
- numCheckFailures = 0
- numConsistencyErrors = 0
- numConsistencyWarnings = 0
- numValidationErrors = 0
- numValidationWarnings = 0
- # Once the whole model is done and before it gets written out,
- # it's important to check that the whole model is in fact complete,
- # consistent and valid.
- numCheckFailures = sbmlDoc.checkInternalConsistency()
- if (numCheckFailures > 0):
- noProblems = False
- for i in range(0, numCheckFailures):
- sbmlErr = sbmlDoc.getError(i)
- if (sbmlErr.isFatal() or sbmlErr.isError()):
- numConsistencyErrors += 1
- else:
- numConsistencyWarnings += 1
- constStr = sbmlDoc.printErrors()
- consistencyMessages = constStr
-
- # If the internal checks fail, it makes little sense to attempt
- # further validation, because the model may be too compromised to
- # be properly interpreted.
- if (numConsistencyErrors > 0):
- consistencyMessages += "Further validation aborted."
- else:
- numCheckFailures = sbmlDoc.checkConsistency()
- #numCheckFailures = sbmlDoc.checkL3v1Compatibility()
- if (numCheckFailures > 0):
- noProblems = False
- for i in range(0, (numCheckFailures)):
- consistencyMessages = sbmlDoc.getErrorLog().toString()
- sbmlErr = sbmlDoc.getError(i)
- if (sbmlErr.isFatal() or sbmlErr.isError()):
- numValidationErrors += 1
- else:
- numValidationWarnings += 1
- warning = sbmlDoc.getErrorLog().toString()
- oss = sbmlDoc.printErrors()
- validationMessages = oss
- if (noProblems):
- return True
- else:
- if consistencyMessages is None:
- consistencyMessages = ""
- if consistencyMessages != "":
- print(" consistency Warning: " + consistencyMessages)
-
- if (numConsistencyErrors > 0):
- if numConsistencyErrors == 1:
- t = ""
- else:
- t = "s"
- print(
- "ERROR: encountered " +
- numConsistencyErrors +
- " consistency error" +
- t +
- " in model '" +
- sbmlDoc.getModel().getId() +
- "'.")
- if (numConsistencyWarnings > 0):
- if numConsistencyWarnings == 1:
- t1 = ""
- else:
- t1 = "s"
- print(
- "Notice: encountered " +
- numConsistencyWarnings +
- " consistency warning" +
- t +
- " in model '" +
- sbmlDoc.getModel().getId() +
- "'.")
-
- if (numValidationErrors > 0):
- if numValidationErrors == 1:
- t2 = ""
- else:
- t2 = "s"
- print(
- "ERROR: encountered " +
- numValidationErrors +
- " validation error" +
- t2 +
- " in model '" +
- sbmlDoc.getModel().getId() +
- "'.")
- if (numValidationWarnings > 0):
- if numValidationWarnings == 1:
- t3 = ""
- else:
- t3 = "s"
-
- print(
- "Notice: encountered " +
- numValidationWarnings +
- " validation warning" +
- t3 +
- " in model '" +
- sbmlDoc.getModel().getId() +
- "'.")
-
- print(validationMessages)
- return (numConsistencyErrors == 0 and numValidationErrors == 0)
- # return ( numConsistencyErrors == 0 and numValidationErrors == 0,
- # consistencyMessages)
-
-
-def setupItem(modelPath):
- '''This function collects information of what is connected to what. \
- eg. substrate and product connectivity to reaction's and enzyme's \
- sumtotal connectivity to its pool are collected '''
- # print " setupItem"
- sublist = []
- prdlist = []
- cntDict = {}
- zombieType = ['ReacBase', 'EnzBase', 'Function', 'StimulusTable']
- for baseObj in zombieType:
- path = '/##[ISA=' + baseObj + ']'
- if modelPath != '/':
- path = modelPath + path
- if ((baseObj == 'ReacBase') or (baseObj == 'EnzBase')):
- for items in moose.wildcardFind(path):
- sublist = []
- prdlist = []
- uniqItem, countuniqItem = countitems(items, 'subOut')
- subNo = uniqItem
- for sub in uniqItem:
- sublist.append((moose.element(sub), 's', countuniqItem[sub]))
-
- uniqItem, countuniqItem = countitems(items, 'prd')
- prdNo = uniqItem
- if (len(subNo) == 0 or len(prdNo) == 0):
- print("Substrate Product is empty ", " ", items)
- for prd in uniqItem:
- prdlist.append((moose.element(prd), 'p', countuniqItem[prd]))
-
- if (baseObj == 'CplxEnzBase'):
- uniqItem, countuniqItem = countitems(items, 'toEnz')
- for enzpar in uniqItem:
- sublist.append(
- (moose.element(enzpar), 't', countuniqItem[enzpar]))
-
- uniqItem, countuniqItem = countitems(items, 'cplxDest')
- for cplx in uniqItem:
- prdlist.append(
- (moose.element(cplx), 'cplx', countuniqItem[cplx]))
-
- if (baseObj == 'EnzBase'):
- uniqItem, countuniqItem = countitems(items, 'enzDest')
- for enzpar in uniqItem:
- sublist.append(
- (moose.element(enzpar), 't', countuniqItem[enzpar]))
- cntDict[items] = sublist, prdlist
- elif baseObj == 'Function':
- for items in moose.wildcardFind(path):
- sublist = []
- prdlist = []
- item = items.path + '/x[0]'
- uniqItem, countuniqItem = countitems(item, 'input')
- for funcpar in uniqItem:
- sublist.append(
- (moose.element(funcpar), 'sts', countuniqItem[funcpar]))
-
- uniqItem, countuniqItem = countitems(items, 'valueOut')
- for funcpar in uniqItem:
- prdlist.append(
- (moose.element(funcpar), 'stp', countuniqItem[funcpar]))
- cntDict[items] = sublist, prdlist
- else:
- for tab in moose.wildcardFind(path):
- tablist = []
- uniqItem, countuniqItem = countitems(tab, 'output')
- for tabconnect in uniqItem:
- tablist.append(
- (moose.element(tabconnect), 'tab', countuniqItem[tabconnect]))
- cntDict[tab] = tablist
- return cntDict
-
-
-def countitems(mitems, objtype):
- items = []
- # print "mitems in countitems ",mitems,objtype
- items = moose.element(mitems).neighbors[objtype]
- uniqItems = set(items)
- countuniqItems = Counter(items)
- return(uniqItems, countuniqItems)
-
-
-def setupMeshObj(modelRoot):
- ''' Setup compartment and its members pool,reaction,enz cplx under self.meshEntry dictionaries \
- self.meshEntry with "key" as compartment,
- value is key2:list where key2 represents moose object type,list of objects of a perticular type
- e.g self.meshEntry[meshEnt] = { 'reaction': reaction_list,'enzyme':enzyme_list,'pool':poollist,'cplx': cplxlist }
- '''
- meshEntry = {}
- if meshEntry:
- meshEntry.clear()
+if __name__ == "__main__":
+ try:
+ sys.argv[1]
+ except IndexError:
+ print("Filename or path not given")
+ exit(0)
else:
- meshEntry = {}
- meshEntryWildcard = '/##[ISA=ChemCompt]'
- if modelRoot != '/':
- meshEntryWildcard = modelRoot + meshEntryWildcard
- for meshEnt in moose.wildcardFind(meshEntryWildcard):
- mollist = []
- cplxlist = []
- mol_cpl = moose.wildcardFind(meshEnt.path + '/##[ISA=PoolBase]')
- funclist = moose.wildcardFind(meshEnt.path + '/##[ISA=Function]')
- enzlist = moose.wildcardFind(meshEnt.path + '/##[ISA=EnzBase]')
- realist = moose.wildcardFind(meshEnt.path + '/##[ISA=ReacBase]')
- tablist = moose.wildcardFind(meshEnt.path + '/##[ISA=StimulusTable]')
- if mol_cpl or funclist or enzlist or realist or tablist:
- for m in mol_cpl:
- if isinstance(moose.element(m.parent), moose.CplxEnzBase):
- cplxlist.append(m)
- elif isinstance(moose.element(m), moose.PoolBase):
- mollist.append(m)
-
- meshEntry[meshEnt] = {'enzyme': enzlist,
- 'reaction': realist,
- 'pool': mollist,
- 'cplx': cplxlist,
- 'table': tablist,
- 'function': funclist
- }
- return(meshEntry)
-
-
-def autoCoordinates(meshEntry, srcdesConnection):
- G = nx.Graph()
- for cmpt, memb in list(meshEntry.items()):
- for enzObj in find_index(memb, 'enzyme'):
- G.add_node(
- enzObj.path,
- label='',
- shape='ellipse',
- color='',
- style='filled',
- fontname='Helvetica',
- fontsize=12,
- fontcolor='blue')
- for cmpt, memb in list(meshEntry.items()):
- for poolObj in find_index(memb, 'pool'):
- #poolinfo = moose.element(poolObj.path+'/info')
- G.add_node(
- poolObj.path,
- label=poolObj.name,
- shape='box',
- color='',
- style='filled',
- fontname='Helvetica',
- fontsize=12,
- fontcolor='blue')
- for cplxObj in find_index(memb, 'cplx'):
- pass
- for reaObj in find_index(memb, 'reaction'):
- G.add_node(reaObj.path, label='', shape='record', color='')
-
- for inn, out in list(srcdesConnection.items()):
- if (inn.className == 'ZombieReac'):
- arrowcolor = 'green'
- elif(inn.className == 'ZombieEnz'):
- arrowcolor = 'red'
+ filepath = sys.argv[1]
+ if not os.path.exists(filepath):
+ print("Filename or path does not exist",filepath)
else:
- arrowcolor = 'blue'
- if isinstance(out, tuple):
- if len(out[0]) == 0:
- print(
- inn.className +
- ':' +
- inn.name +
- " doesn't have input message")
+ try:
+ sys.argv[2]
+ except :
+ modelpath = filepath[filepath.rfind('/'):filepath.find('.')]
else:
- for items in (items for items in out[0]):
- G.add_edge(moose.element(items[0]).path, inn.path)
-
- if len(out[1]) == 0:
- print(
- inn.className +
- ':' +
- inn.name +
- "doesn't have output mssg")
- else:
- for items in (items for items in out[1]):
- G.add_edge(inn.path, moose.element(items[0]).path)
+ modelpath = sys.argv[2]
+
+ moose.loadModel(filepath, modelpath, "gsl")
- elif isinstance(out, list):
- if len(out) == 0:
- print("Func pool doesn't have sumtotal")
+ written, c, writtentofile = mooseWriteSBML(modelpath, filepath)
+ if written:
+ print(" File written to ", writtentofile)
else:
- for items in (items for items in out):
- G.add_edge(moose.element(items[0]).path, inn.path)
- #from networkx.drawing.nx_agraph import graphviz_layout
- #position = graphviz_layout(G,prog='dot')
-
- position = nx.pygraphviz_layout(G, prog='dot')
- position = nx.spring_layout(G)
- #agraph = nx.to_agraph(G)
- #agraph.draw("~/out.png", format = 'png', prog = 'dot')
-
- sceneitems = {}
- xycord = []
- cmin = 0
- cmax = 0
- for key, value in list(position.items()):
- xycord.append(value[0])
- xycord.append(value[1])
- sceneitems[moose.element(key)] = {'x': value[0], 'y': value[1]}
- if len(xycord) > 0:
- cmin = min(xycord)
- cmax = max(xycord)
- return cmin, cmax, sceneitems
-
-
-def calPrime(x):
- prime = int((20 * (float(x - cmin) / float(cmax - cmin))) - 10)
- return prime
-
-
-def find_index(value, key):
- """ Value.get(key) to avoid expection which would raise if empty value in dictionary for a given key """
- if value.get(key) is not None:
- return value.get(key)
- else:
- raise ValueError('no dict with the key found')
-if __name__ == "__main__":
-
- filepath = sys.argv[1]
- path = sys.argv[2]
-
- f = open(filepath, 'r')
-
- if path == '':
- loadpath = filepath[filepath.rfind('/'):filepath.find('.')]
- else:
- loadpath = path
-
- moose.loadModel(filepath, loadpath, "gsl")
-
- written, c, writtentofile = mooseWriteSBML(loadpath, filepath)
- if written:
- print(" File written to ", writtentofile)
- else:
- print(" could not write model to SBML file")
+ print(" could not write model to SBML file")
diff --git a/python/moose/chemUtil/__init__.py b/python/moose/chemUtil/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..dce7080f0a0f57a421c2428821689fe824ff50a5
--- /dev/null
+++ b/python/moose/chemUtil/__init__.py
@@ -0,0 +1,3 @@
+from .add_Delete_ChemicalSolver import *
+from .chemConnectUtil import *
+from .graphUtils import autoCoordinates
diff --git a/python/moose/add_Delete_ChemicalSolver.py b/python/moose/chemUtil/add_Delete_ChemicalSolver.py
similarity index 94%
rename from python/moose/add_Delete_ChemicalSolver.py
rename to python/moose/chemUtil/add_Delete_ChemicalSolver.py
index f788118b7d20ad116c0a3323330ed20a598a712f..af9437b92dd886e39e4644a60f15579f3f76d525 100644
--- a/python/moose/add_Delete_ChemicalSolver.py
+++ b/python/moose/chemUtil/add_Delete_ChemicalSolver.py
@@ -1,5 +1,4 @@
-from . import _moose as moose
-
+import moose
def moosedeleteChemSolver(modelRoot):
"""Delete solvers from Chemical Compartment
@@ -25,11 +24,11 @@ def mooseaddChemSolver(modelRoot, solver):
comptinfo = moose.Annotator(moose.element(compt[0]).path + '/info')
previousSolver = comptinfo.solver
currentSolver = previousSolver
- if solver == "Gillespie":
+ if solver == "Gillespie" or solver == "gssa":
currentSolver = "gssa"
- elif solver == "Runge Kutta":
+ elif solver == "Runge Kutta" or solver == "gsl":
currentSolver = "gsl"
- elif solver == "Exponential Euler":
+ elif solver == "Exponential Euler" or solver == "ee":
currentSolver = "ee"
if previousSolver != currentSolver:
diff --git a/python/moose/chemUtil/chemConnectUtil.py b/python/moose/chemUtil/chemConnectUtil.py
new file mode 100644
index 0000000000000000000000000000000000000000..93d8be9d1442970c5ac748184f6743ba6810fc6b
--- /dev/null
+++ b/python/moose/chemUtil/chemConnectUtil.py
@@ -0,0 +1,181 @@
+import moose
+import numpy as np
+from collections import Counter
+
+def xyPosition(objInfo,xory):
+ try:
+ return(float(moose.element(objInfo).getField(xory)))
+ except ValueError:
+ return (float(0))
+
+def setupMeshObj(modelRoot):
+ ''' Setup compartment and its members pool,reaction,enz cplx under self.meshEntry dictionaries \
+ self.meshEntry with "key" as compartment,
+ value is key2:list where key2 represents moose object type,list of objects of a perticular type
+ e.g self.meshEntry[meshEnt] = { 'reaction': reaction_list,'enzyme':enzyme_list,'pool':poollist,'cplx': cplxlist }
+ '''
+ xmin = 0.0
+ xmax = 1.0
+ ymin = 0.0
+ ymax = 1.0
+ listOfitems = {}
+ positionInfoExist = True
+ meshEntry = {}
+ if meshEntry:
+ meshEntry.clear()
+ else:
+ meshEntry = {}
+ xcord = []
+ ycord = []
+ meshEntryWildcard = '/##[ISA=ChemCompt]'
+ if modelRoot != '/':
+ meshEntryWildcard = modelRoot+meshEntryWildcard
+ for meshEnt in moose.wildcardFind(meshEntryWildcard):
+ mollist = []
+ realist = []
+ enzlist = []
+ cplxlist = []
+ tablist = []
+ funclist = []
+
+ mol_cpl = moose.wildcardFind(meshEnt.path+'/##[ISA=PoolBase]')
+ funclist = moose.wildcardFind(meshEnt.path+'/##[ISA=Function]')
+ enzlist = moose.wildcardFind(meshEnt.path+'/##[ISA=EnzBase]')
+ realist = moose.wildcardFind(meshEnt.path+'/##[ISA=ReacBase]')
+ tablist = moose.wildcardFind(meshEnt.path+'/##[ISA=StimulusTable]')
+ if mol_cpl or funclist or enzlist or realist or tablist:
+ for m in mol_cpl:
+ if isinstance(moose.element(m.parent),moose.CplxEnzBase):
+ cplxlist.append(m)
+ objInfo = m.parent.path+'/info'
+ elif isinstance(moose.element(m),moose.PoolBase):
+ mollist.append(m)
+ objInfo =m.path+'/info'
+ if moose.exists(objInfo):
+ listOfitems[moose.element(moose.element(objInfo).parent)]={'x':xyPosition(objInfo,'x'),'y':xyPosition(objInfo,'y')}
+
+ xcord.append(xyPosition(objInfo,'x'))
+ ycord.append(xyPosition(objInfo,'y'))
+
+ getxyCord(xcord,ycord,funclist,listOfitems)
+ getxyCord(xcord,ycord,enzlist,listOfitems)
+ getxyCord(xcord,ycord,realist,listOfitems)
+ getxyCord(xcord,ycord,tablist,listOfitems)
+
+ meshEntry[meshEnt] = {'enzyme':enzlist,
+ 'reaction':realist,
+ 'pool':mollist,
+ 'cplx':cplxlist,
+ 'table':tablist,
+ 'function':funclist
+ }
+ positionInfoExist = not(len(np.nonzero(xcord)[0]) == 0 \
+ and len(np.nonzero(ycord)[0]) == 0)
+ if positionInfoExist:
+ xmin = min(xcord)
+ xmax = max(xcord)
+ ymin = min(ycord)
+ ymax = max(ycord)
+ return meshEntry,xmin,xmax,ymin,ymax,positionInfoExist,listOfitems
+
+def sizeHint(self):
+ return QtCore.QSize(800,400)
+
+def getxyCord(xcord,ycord,list1,listOfitems):
+ for item in list1:
+ # if isinstance(item,Function):
+ # objInfo = moose.element(item.parent).path+'/info'
+ # else:
+ # objInfo = item.path+'/info'
+ if not isinstance(item,moose.Function):
+ objInfo = item.path+'/info'
+ xcord.append(xyPosition(objInfo,'x'))
+ ycord.append(xyPosition(objInfo,'y'))
+ if moose.exists(objInfo):
+ listOfitems[moose.element(moose.element(objInfo).parent)]={'x':xyPosition(objInfo,'x'),'y':xyPosition(objInfo,'y')}
+
+def setupItem(modelPath,cntDict):
+ '''This function collects information of what is connected to what. \
+ eg. substrate and product connectivity to reaction's and enzyme's \
+ sumtotal connectivity to its pool are collected '''
+ #print " setupItem"
+ sublist = []
+ prdlist = []
+ zombieType = ['ReacBase','EnzBase','Function','StimulusTable']
+ for baseObj in zombieType:
+ path = '/##[ISA='+baseObj+']'
+ if modelPath != '/':
+ path = modelPath+path
+ if ( (baseObj == 'ReacBase') or (baseObj == 'EnzBase')):
+ for items in moose.wildcardFind(path):
+ sublist = []
+ prdlist = []
+ uniqItem,countuniqItem = countitems(items,'subOut')
+ subNo = uniqItem
+ for sub in uniqItem:
+ sublist.append((moose.element(sub),'s',countuniqItem[sub]))
+
+ uniqItem,countuniqItem = countitems(items,'prd')
+ prdNo = uniqItem
+ if (len(subNo) == 0 or len(prdNo) == 0):
+ print ("Substrate Product is empty ",path, " ",items)
+
+ for prd in uniqItem:
+ prdlist.append((moose.element(prd),'p',countuniqItem[prd]))
+
+ if (baseObj == 'CplxEnzBase') :
+ uniqItem,countuniqItem = countitems(items,'toEnz')
+ for enzpar in uniqItem:
+ sublist.append((moose.element(enzpar),'t',countuniqItem[enzpar]))
+
+ uniqItem,countuniqItem = countitems(items,'cplxDest')
+ for cplx in uniqItem:
+ prdlist.append((moose.element(cplx),'cplx',countuniqItem[cplx]))
+
+ if (baseObj == 'EnzBase'):
+ uniqItem,countuniqItem = countitems(items,'enzDest')
+ for enzpar in uniqItem:
+ sublist.append((moose.element(enzpar),'t',countuniqItem[enzpar]))
+ cntDict[items] = sublist,prdlist
+ elif baseObj == 'Function':
+ for items in moose.wildcardFind(path):
+ sublist = []
+ prdlist = []
+ item = items.path+'/x[0]'
+ uniqItem,countuniqItem = countitems(item,'input')
+ for funcpar in uniqItem:
+ sublist.append((moose.element(funcpar),'sts',countuniqItem[funcpar]))
+
+ uniqItem,countuniqItem = countitems(items,'valueOut')
+ for funcpar in uniqItem:
+ prdlist.append((moose.element(funcpar),'stp',countuniqItem[funcpar]))
+ cntDict[items] = sublist,prdlist
+
+ # elif baseObj == 'Function':
+ # #ZombieSumFunc adding inputs
+ # inputlist = []
+ # outputlist = []
+ # funplist = []
+ # nfunplist = []
+ # for items in moose.wildcardFind(path):
+ # for funplist in moose.element(items).neighbors['valueOut']:
+ # for func in funplist:
+ # funcx = moose.element(items.path+'/x[0]')
+ # uniqItem,countuniqItem = countitems(funcx,'input')
+ # for inPut in uniqItem:
+ # inputlist.append((inPut,'st',countuniqItem[inPut]))
+ # cntDict[func] = inputlist
+ else:
+ for tab in moose.wildcardFind(path):
+ tablist = []
+ uniqItem,countuniqItem = countitems(tab,'output')
+ for tabconnect in uniqItem:
+ tablist.append((moose.element(tabconnect),'tab',countuniqItem[tabconnect]))
+ cntDict[tab] = tablist
+
+def countitems(mitems,objtype):
+ items = []
+ items = moose.element(mitems).neighbors[objtype]
+ uniqItems = set(items)
+ countuniqItems = Counter(items)
+ return(uniqItems,countuniqItems)
\ No newline at end of file
diff --git a/python/moose/chemUtil/graphUtils.py b/python/moose/chemUtil/graphUtils.py
new file mode 100644
index 0000000000000000000000000000000000000000..5bf05f54ace749c62ded010dc3c05f11efda52c9
--- /dev/null
+++ b/python/moose/chemUtil/graphUtils.py
@@ -0,0 +1,87 @@
+import moose
+
+pygraphvizFound_ = True
+try:
+ import pygraphviz as pgv
+except Exception as e:
+ pygraphvizFound_ = False
+
+def autoCoordinates(meshEntry,srcdesConnection):
+ global pygraphvizFound_
+ positionInfo = {}
+
+ if not pygraphvizFound_:
+ print( '[warn] python-pygraphviz could not be found.' )
+ print( '\tMOOSE Install pygraphviz to use this feature' )
+ return positionInfo
+
+ if meshEntry:
+ #G = nx.Graph()
+ G = pgv.AGraph()
+
+ for cmpt,memb in list(meshEntry.items()):
+ for enzObj in find_index(memb,'enzyme'):
+ #G.add_node(enzObj.path)
+ G.add_node(enzObj.path,label='',shape='ellipse',color='',style='filled',fontname='Helvetica',fontsize=12,fontcolor='blue')
+ for cmpt,memb in list(meshEntry.items()):
+ for poolObj in find_index(memb,'pool'):
+ #G.add_node(poolObj.path)
+ G.add_node(poolObj.path,label = poolObj.name,shape = 'box',color = '',style = 'filled',fontname = 'Helvetica',fontsize = 12,fontcolor = 'blue')
+ for cplxObj in find_index(memb,'cplx'):
+ G.add_node(cplxObj.path)
+ G.add_node(cplxObj.path,label = cplxObj.name,shape = 'box',color = '',style = 'filled',fontname = 'Helvetica',fontsize = 12,fontcolor = 'blue')
+ #G.add_edge((cplxObj.parent).path,cplxObj.path)
+ for reaObj in find_index(memb,'reaction'):
+ #G.add_node(reaObj.path)
+ G.add_node(reaObj.path,label='',shape='circle',color='')
+
+ for inn,out in list(srcdesConnection.items()):
+ if (inn.className =='ZombieReac'): arrowcolor = 'green'
+ elif(inn.className =='ZombieEnz'): arrowcolor = 'red'
+ else: arrowcolor = 'blue'
+ if isinstance(out,tuple):
+ if len(out[0])== 0:
+ print( inn.className + ':' +inn.name + " doesn't have input message")
+ else:
+ for items in (items for items in out[0] ):
+ G.add_edge(moose.element(items[0]).path,inn.path)
+ if len(out[1]) == 0:
+ print(inn.className + ':' + inn.name + "doesn't have output mssg")
+ else:
+ for items in (items for items in out[1] ):
+ G.add_edge(inn.path,moose.element(items[0]).path)
+ elif isinstance(out,list):
+ if len(out) == 0:
+ print ("Func pool doesn't have sumtotal")
+ else:
+ for items in (items for items in out ):
+ G.add_edge(moose.element(items[0]).path,inn.path)
+
+ # if int( nx.__version__.split( '.' )[-1] ) >= 11:
+ # position = nx.spring_layout( G )
+ # else:
+ # position = nx.graphviz_layout(G, prog = 'dot')
+ # for item in position.items():
+ # xy = item[1]
+ # ann = moose.Annotator(item[0]+'/info')
+ # ann.x = xy[0]
+ # ann.y = xy[1]
+ # positioninfo[(moose.element(item[0]))] ={'x':float(xy[0]),'y':float(xy[1])}
+
+ G.layout()
+ for n in G.nodes():
+ value = str(n.attr['pos'])
+ valuelist = (value.split(','))
+ positionInfo[(moose.element(n))] ={'x':float(valuelist[0]),'y':float(valuelist[1])}
+ ann = moose.Annotator(moose.element(n).path+'/info')
+ ann.x = float(valuelist[0])
+ ann.y = float(valuelist[1])
+
+ return positionInfo
+
+def find_index(value, key):
+ """ Value.get(key) to avoid expection which would raise if empty value in dictionary for a given key """
+ if value.get(key) != None:
+ return value.get(key)
+ else:
+ raise ValueError('no dict with the key found')
diff --git a/python/moose/genesis/writeKkit.py b/python/moose/genesis/writeKkit.py
index 226fe2a319b000f199357f41a3fac3fdf0f85a73..2bd33e212590cad4216ca54e733b45bde7ad60b3 100644
--- a/python/moose/genesis/writeKkit.py
+++ b/python/moose/genesis/writeKkit.py
@@ -1,22 +1,27 @@
""" Chemical Signalling model loaded into moose can be save into Genesis-Kkit format """
__author__ = "Harsha Rani"
-__copyright__ = "Copyright 2015, Harsha Rani and NCBS Bangalore"
+__copyright__ = "Copyright 2017, Harsha Rani and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ = "Harsha Rani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
-
+__updated__ = "Feb 13 2017"
import sys
import random
-import moose
-import numpy as np
import re
-from collections import Counter
-import networkx as nx
-import matplotlib
+import moose
+from moose.chemUtil.chemConnectUtil import *
+from moose.chemUtil.graphUtils import *
+
+foundmatplotlib_ = False
+try:
+ import matplotlib
+ foundmatplotlib_ = True
+except Exception as e:
+ pass
GENESIS_COLOR_SEQUENCE = ((248, 0, 255), (240, 0, 255), (232, 0, 255), (224, 0, 255), (216, 0, 255), (208, 0, 255),
(200, 0, 255), (192, 0, 255), (184, 0, 255), (176, 0, 255), (168, 0, 255), (160, 0, 255), (152, 0, 255), (144, 0, 255),
@@ -38,264 +43,117 @@ GENESIS_COLOR_SEQUENCE = ((248, 0, 255), (240, 0, 255), (232, 0, 255), (224, 0,
#Todo : To be written
# --StimulusTable
-def mooseWriteKkit( modelpath, filename,sceneitems=None):
- if filename.rfind('.') != -1:
- filename = filename[:filename.rfind('.')]
- else:
- filename = filename[:len(filename)]
- filename = filename+'.g'
- global NA
- NA = 6.0221415e23
- global cmin,cmax,xmin,xmax,ymin,ymax
- cmin = 0
- cmax = 1
- xmin = 0
- xmax = 1
- ymin = 0
- ymax = 1
-
- compt = moose.wildcardFind(modelpath+'/##[ISA=ChemCompt]')
- maxVol = estimateDefaultVol(compt)
- f = open(filename, 'w')
-
- if sceneitems == None:
- srcdesConnection = {}
- setupItem(modelpath,srcdesConnection)
- meshEntry = setupMeshObj(modelpath)
- cmin,cmax,sceneitems = autoCoordinates(meshEntry,srcdesConnection)
- for k,v in list(sceneitems.items()):
- v = sceneitems[k]
- x1 = calPrime(v['x'])
- y1 = calPrime(v['y'])
- sceneitems[k]['x'] = x1
- sceneitems[k]['y'] = y1
- else:
- cs, xcord, ycord = [], [] ,[]
- for k,v in list(sceneitems.items()):
- xcord.append(v['x'])
- cs.append(v['x'])
- ycord.append(v['y'])
- cs.append(v['y'])
- xmin = min(xcord)
- xmax = max(xcord)
- ymin = min(ycord)
- ymax = max(ycord)
-
- cmin = min(cs)
- cmax = max(cs)
- writeHeader (f,maxVol)
-
- if (compt > 0):
- gtId_vol = writeCompartment(modelpath,compt,f)
- writePool(modelpath,f,gtId_vol,sceneitems)
- reacList = writeReac(modelpath,f,sceneitems)
- enzList = writeEnz(modelpath,f,sceneitems)
- writeSumtotal(modelpath,f)
- f.write("simundump xgraph /graphs/conc1 0 0 99 0.001 0.999 0\n"
- "simundump xgraph /graphs/conc2 0 0 100 0 1 0\n")
- tgraphs = moose.wildcardFind(modelpath+'/##[ISA=Table2]')
- first, second = " ", " "
- if tgraphs:
- first,second = writeplot(tgraphs,f)
- if first:
- f.write(first)
- f.write("simundump xgraph /moregraphs/conc3 0 0 100 0 1 0\n"
- "simundump xgraph /moregraphs/conc4 0 0 100 0 1 0\n")
- if second:
- f.write(second)
- f.write("simundump xcoredraw /edit/draw 0 -6 4 -2 6\n"
- "simundump xtree /edit/draw/tree 0 \\\n"
- " /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \"edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>\" auto 0.6\n"
- "simundump xtext /file/notes 0 1\n")
- storeReacMsg(reacList,f)
- storeEnzMsg(enzList,f)
- if tgraphs:
- storePlotMsgs(tgraphs,f)
- writeFooter1(f)
- writeNotes(modelpath,f)
- writeFooter2(f)
- return True
- else:
- print(("Warning: writeKkit:: No model found on " , modelpath))
+def mooseWriteKkit( modelpath, filename, sceneitems={}):
+ global foundmatplotlib_
+ if not foundmatplotlib_:
+ print('No maplotlib found.'
+ '\nThis module can be installed by following command in terminal:'
+ '\n\t sudo apt install python-maplotlib', "")
return False
-
-def calPrime(x):
- prime = int((20*(float(x-cmin)/float(cmax-cmin)))-10)
- return prime
-
-def setupItem(modelPath,cntDict):
- '''This function collects information of what is connected to what. \
- eg. substrate and product connectivity to reaction's and enzyme's \
- sumtotal connectivity to its pool are collected '''
- #print " setupItem"
- sublist = []
- prdlist = []
- zombieType = ['ReacBase','EnzBase','Function','StimulusTable']
- for baseObj in zombieType:
- path = '/##[ISA='+baseObj+']'
- if modelPath != '/':
- path = modelPath+path
- if ( (baseObj == 'ReacBase') or (baseObj == 'EnzBase')):
- for items in moose.wildcardFind(path):
- sublist = []
- prdlist = []
- uniqItem,countuniqItem = countitems(items,'subOut')
- subNo = uniqItem
- for sub in uniqItem:
- sublist.append((moose.element(sub),'s',countuniqItem[sub]))
-
- uniqItem,countuniqItem = countitems(items,'prd')
- prdNo = uniqItem
- if (len(subNo) == 0 or len(prdNo) == 0):
- print("Substrate Product is empty ",path, " ",items)
-
- for prd in uniqItem:
- prdlist.append((moose.element(prd),'p',countuniqItem[prd]))
-
- if (baseObj == 'CplxEnzBase') :
- uniqItem,countuniqItem = countitems(items,'toEnz')
- for enzpar in uniqItem:
- sublist.append((moose.element(enzpar),'t',countuniqItem[enzpar]))
-
- uniqItem,countuniqItem = countitems(items,'cplxDest')
- for cplx in uniqItem:
- prdlist.append((moose.element(cplx),'cplx',countuniqItem[cplx]))
-
- if (baseObj == 'EnzBase'):
- uniqItem,countuniqItem = countitems(items,'enzDest')
- for enzpar in uniqItem:
- sublist.append((moose.element(enzpar),'t',countuniqItem[enzpar]))
- cntDict[items] = sublist,prdlist
- elif baseObj == 'Function':
- for items in moose.wildcardFind(path):
- sublist = []
- prdlist = []
- item = items.path+'/x[0]'
- uniqItem,countuniqItem = countitems(item,'input')
- for funcpar in uniqItem:
- sublist.append((moose.element(funcpar),'sts',countuniqItem[funcpar]))
-
- uniqItem,countuniqItem = countitems(items,'valueOut')
- for funcpar in uniqItem:
- prdlist.append((moose.element(funcpar),'stp',countuniqItem[funcpar]))
- cntDict[items] = sublist,prdlist
- else:
- for tab in moose.wildcardFind(path):
- tablist = []
- uniqItem,countuniqItem = countitems(tab,'output')
- for tabconnect in uniqItem:
- tablist.append((moose.element(tabconnect),'tab',countuniqItem[tabconnect]))
- cntDict[tab] = tablist
-def countitems(mitems,objtype):
- items = []
- items = moose.element(mitems).neighbors[objtype]
- uniqItems = set(items)
- countuniqItems = Counter(items)
- return(uniqItems,countuniqItems)
-
-def setupMeshObj(modelRoot):
- ''' Setup compartment and its members pool,reaction,enz cplx under self.meshEntry dictionaries \
- self.meshEntry with "key" as compartment,
- value is key2:list where key2 represents moose object type,list of objects of a perticular type
- e.g self.meshEntry[meshEnt] = { 'reaction': reaction_list,'enzyme':enzyme_list,'pool':poollist,'cplx': cplxlist }
- '''
- meshEntry = {}
- if meshEntry:
- meshEntry.clear()
else:
- meshEntry = {}
- meshEntryWildcard = '/##[ISA=ChemCompt]'
- if modelRoot != '/':
- meshEntryWildcard = modelRoot+meshEntryWildcard
- for meshEnt in moose.wildcardFind(meshEntryWildcard):
- mollist = []
- cplxlist = []
- mol_cpl = moose.wildcardFind(meshEnt.path+'/##[ISA=PoolBase]')
- funclist = moose.wildcardFind(meshEnt.path+'/##[ISA=Function]')
- enzlist = moose.wildcardFind(meshEnt.path+'/##[ISA=EnzBase]')
- realist = moose.wildcardFind(meshEnt.path+'/##[ISA=ReacBase]')
- tablist = moose.wildcardFind(meshEnt.path+'/##[ISA=StimulusTable]')
- if mol_cpl or funclist or enzlist or realist or tablist:
- for m in mol_cpl:
- if isinstance(moose.element(m.parent),moose.CplxEnzBase):
- cplxlist.append(m)
- elif isinstance(moose.element(m),moose.PoolBase):
- mollist.append(m)
-
- meshEntry[meshEnt] = {'enzyme':enzlist,
- 'reaction':realist,
- 'pool':mollist,
- 'cplx':cplxlist,
- 'table':tablist,
- 'function':funclist
- }
- return(meshEntry)
-def autoCoordinates(meshEntry,srcdesConnection):
- G = nx.Graph()
- for cmpt,memb in list(meshEntry.items()):
- for enzObj in find_index(memb,'enzyme'):
- #G.add_node(enzObj.path)
- G.add_node(enzObj.path,label=enzObj.name,shape='ellipse',color='',style='filled',fontname='Helvetica',fontsize=12,fontcolor='blue')
- for cmpt,memb in list(meshEntry.items()):
- for poolObj in find_index(memb,'pool'):
- #G.add_node(poolObj.path)
- G.add_node(poolObj.path,label = poolObj.name,shape = 'box',color = '',style = 'filled',fontname = 'Helvetica',fontsize = 12,fontcolor = 'blue')
- for cplxObj in find_index(memb,'cplx'):
- pass
- #G.add_node(cplxObj.path)
- #G.add_edge((cplxObj.parent).path,cplxObj.path)
- for reaObj in find_index(memb,'reaction'):
- #G.add_node(reaObj.path)
- G.add_node(reaObj.path,label=reaObj.name,shape='',color='')
- for funcObj in find_index(memb,'function'):
- G.add_node(poolObj.path,label = funcObj.name,shape = 'box',color = 'red',style = 'filled',fontname = 'Helvetica',fontsize = 12,fontcolor = 'blue')
+
+ ignoreColor= ["mistyrose","antiquewhite","aliceblue","azure","bisque","black","blanchedalmond","blue","cornsilk","darkolivegreen","darkslategray","dimgray","floralwhite","gainsboro","ghostwhite","honeydew","ivory","lavender","lavenderblush","lemonchiffon","lightcyan","lightgoldenrodyellow","lightgray","lightyellow","linen","mediumblue","mintcream","navy","oldlace","papayawhip","saddlebrown","seashell","snow","wheat","white","whitesmoke","aquamarine","lightsalmon","moccasin","limegreen","snow","sienna","beige","dimgrey","lightsage"]
+ matplotcolor = {}
+ for name,hexno in matplotlib.colors.cnames.items():
+ matplotcolor[name]=hexno
+ if filename.rfind('.') != -1:
+ filename = filename[:filename.rfind('.')]
+ else:
+ filename = filename[:len(filename)]
+ filename = filename+'.g'
+ global NA
+ NA = 6.0221415e23
+ global cmin,cmax,xmin,xmax,ymin,ymax
+ cmin, xmin, ymin = 0, 0, 0
+ cmax, xmax, ymax = 1, 1, 1
- for inn,out in list(srcdesConnection.items()):
- if (inn.className =='ZombieReac'): arrowcolor = 'green'
- elif(inn.className =='ZombieEnz'): arrowcolor = 'red'
- else: arrowcolor = 'blue'
- if isinstance(out,tuple):
- if len(out[0])== 0:
- print(inn.className + ':' +inn.name + " doesn't have input message")
- else:
- for items in (items for items in out[0] ):
- G.add_edge(moose.element(items[0]).path,inn.path)
- if len(out[1]) == 0:
- print(inn.className + ':' + inn.name + "doesn't have output mssg")
- else:
- for items in (items for items in out[1] ):
- G.add_edge(inn.path,moose.element(items[0]).path)
- elif isinstance(out,list):
- if len(out) == 0:
- print("Func pool doesn't have sumtotal")
- else:
- for items in (items for items in out ):
- G.add_edge(moose.element(items[0]).path,inn.path)
-
- position = nx.graphviz_layout(G, prog = 'dot')
- if int( nx.__version__.split( '.' )[-1] ) >= 11:
- position = nx.spring_layout( G )
+ compt = moose.wildcardFind(modelpath+'/##[ISA=ChemCompt]')
+ maxVol = estimateDefaultVol(compt)
+ positionInfoExist = True
+ if compt:
+ if bool(sceneitems):
+ cmin,cmax,xmin1,xmax1,ymin1,ymax1 = findMinMax(sceneitems)
+ elif not bool(sceneitems):
+ srcdesConnection = {}
+ setupItem(modelpath,srcdesConnection)
+ meshEntry,xmin,xmax,ymin,ymax,positionInfoExist,sceneitems = setupMeshObj(modelpath)
+ if not positionInfoExist:
+ #cmin,cmax,sceneitems = autoCoordinates(meshEntry,srcdesConnection)
+ sceneitems = autoCoordinates(meshEntry,srcdesConnection)
+
+ if not positionInfoExist:
+ # if position are not from kkit, then zoom factor is applied while
+ # writing to genesis. Like if position is from pyqtSceneItem or auto-coordinates
+ cmin,cmax,xmin1,xmax1,ymin1,ymax1 = findMinMax(sceneitems)
+ for k,v in list(sceneitems.items()):
+ anno = moose.element(k.path+'/info')
+ x1 = calPrime(v['x'])
+ y1 = calPrime(v['y'])
+ sceneitems[k]['x'] = x1
+ sceneitems[k]['y'] = y1
+
+ f = open(filename, 'w')
+ writeHeader (f,maxVol)
+
+ gtId_vol = writeCompartment(modelpath,compt,f)
+ writePool(modelpath,f,gtId_vol,sceneitems)
+ reacList = writeReac(modelpath,f,sceneitems)
+ enzList = writeEnz(modelpath,f,sceneitems)
+ writeSumtotal(modelpath,f)
+ f.write("simundump xgraph /graphs/conc1 0 0 99 0.001 0.999 0\n"
+ "simundump xgraph /graphs/conc2 0 0 100 0 1 0\n")
+ tgraphs = moose.wildcardFind(modelpath+'/##[ISA=Table2]')
+ first, second = " ", " "
+ if tgraphs:
+ first,second = writeplot(tgraphs,f)
+ if first:
+ f.write(first)
+ f.write("simundump xgraph /moregraphs/conc3 0 0 100 0 1 0\n"
+ "simundump xgraph /moregraphs/conc4 0 0 100 0 1 0\n")
+ if second:
+ f.write(second)
+ f.write("simundump xcoredraw /edit/draw 0 -6 4 -2 6\n"
+ "simundump xtree /edit/draw/tree 0 \\\n"
+ " /kinetics/#[],/kinetics/#[]/#[],/kinetics/#[]/#[]/#[][TYPE!=proto],/kinetics/#[]/#[]/#[][TYPE!=linkinfo]/##[] \"edit_elm.D <v>; drag_from_edit.w <d> <S> <x> <y> <z>\" auto 0.6\n"
+ "simundump xtext /file/notes 0 1\n")
+ storeReacMsg(reacList,f)
+ storeEnzMsg(enzList,f)
+ if tgraphs:
+ storePlotMsgs(tgraphs,f)
+ writeFooter1(f)
+ writeNotes(modelpath,f)
+ writeFooter2(f)
+ print('Written to file '+filename)
+ return True
+ else:
+ print(("Warning: writeKkit:: No model found on " , modelpath))
+ return False
- #agraph = nx.to_agraph(G)
- #agraph.draw("writetogenesis.png", format = 'png', prog = 'dot')
- sceneitems = {}
+def findMinMax(sceneitems):
+ cmin = 0.0
+ cmax = 1.0
+ xmin,xymin = 0.0,0.0
+ xmax,xymax = 1.0,1.0
xycord = []
-
- for key,value in list(position.items()):
- xycord.append(value[0])
- xycord.append(value[1])
- sceneitems[moose.element(key)] = {'x':value[0],'y':value[1]}
+ xcord = []
+ ycord = []
+ for k,v in list(sceneitems.items()):
+ xycord.append(v['x'])
+ xycord.append(v['y'])
+ xcord.append(v['x'])
+ ycord.append(v['y'])
+ xmin = min(xcord)
+ xmax = max(xcord)
+ ymin = min(ycord)
+ ymax = max(ycord)
cmin = min(xycord)
cmax = max(xycord)
- return cmin,cmax,sceneitems
+ return cmin,cmax,xmin,xmax,ymin,ymax
-def find_index(value, key):
- """ Value.get(key) to avoid expection which would raise if empty value in dictionary for a given key """
- if value.get(key) != None:
- return value.get(key)
- else:
- raise ValueError('no dict with the key found')
+def calPrime(x):
+ prime = int((20*(float(x-cmin)/float(cmax-cmin)))-10)
+ return prime
def storeCplxEnzMsgs( enz, f ):
for sub in enz.neighbors["subOut"]:
@@ -409,9 +267,7 @@ def nearestColorIndex(color, color_sequence):
#Trying to find the index to closest color map from the rainbow pickle file for matching the Genesis color map
distance = [ (color[0] - temp[0]) ** 2 + (color[1] - temp[1]) ** 2 + (color[2] - temp[2]) ** 2
for temp in color_sequence]
-
minindex = 0
-
for i in range(1, len(distance)):
if distance[minindex] > distance[i] : minindex = i
@@ -500,11 +356,23 @@ def storePlotMsgs( tgraphs,f):
for graph in tgraphs:
slash = graph.path.find('graphs')
if not slash > -1:
- slash = graph.path.find('graph_0')
+ slash = graph.path.find('graph')
if slash > -1:
- conc = graph.path.find('conc')
- if conc > -1 :
- tabPath = graph.path[slash:len(graph.path)]
+ foundConc = True
+ if not ( (graph.path.find('conc1') > -1 ) or
+ (graph.path.find('conc2') > -1 ) or
+ (graph.path.find('conc3') > -1 ) or
+ (graph.path.find('conc4') > -1) ):
+ foundConc = False
+
+ #conc = graph.path.find('conc')
+ # if conc > -1 :
+ # tabPath = graph.path[slash:len(graph.path)]
+ # else:
+ # slash1 = graph.path.find('/',slash)
+ # tabPath = "/graphs/conc1" +graph.path[slash1:len(graph.path)]
+ if foundConc == True:
+ tabPath = "/"+graph.path[slash:len(graph.path)]
else:
slash1 = graph.path.find('/',slash)
tabPath = "/graphs/conc1" +graph.path[slash1:len(graph.path)]
@@ -527,14 +395,21 @@ def writeplot( tgraphs,f ):
for graphs in tgraphs:
slash = graphs.path.find('graphs')
if not slash > -1:
- slash = graphs.path.find('graph_0')
+ slash = graphs.path.find('graph')
if slash > -1:
- conc = graphs.path.find('conc')
- if conc > -1 :
+ foundConc = True
+ if not ( (graphs.path.find('conc1') > -1 ) or
+ (graphs.path.find('conc2') > -1 ) or
+ (graphs.path.find('conc3') > -1 ) or
+ (graphs.path.find('conc4') > -1) ):
+ foundConc = False
+ if foundConc == True:
tabPath = "/"+graphs.path[slash:len(graphs.path)]
else:
slash1 = graphs.path.find('/',slash)
tabPath = "/graphs/conc1" +graphs.path[slash1:len(graphs.path)]
+
+
if len(moose.element(graphs).msgOut):
poolPath = (moose.element(graphs).msgOut)[0].e2.path
poolEle = moose.element(poolPath)
@@ -586,7 +461,7 @@ def writePool(modelpath,f,volIndex,sceneitems):
color = getRandColor()
if textcolor == "" or textcolor == " ":
textcolor = getRandColor()
- #print " trimPath",trimPath(p)
+ #print " trimPath",trimPath(p)
f.write("simundump kpool /kinetics/" + trimPath(p) + " 0 " +
str(p.diffConst) + " " +
str(0) + " " +
@@ -628,11 +503,6 @@ def getColorCheck(color,GENESIS_COLOR_SEQUENCE):
else:
raise Exception("Invalid Color Value!")
-ignoreColor= ["mistyrose","antiquewhite","aliceblue","azure","bisque","black","blanchedalmond","blue","cornsilk","darkolivegreen","darkslategray","dimgray","floralwhite","gainsboro","ghostwhite","honeydew","ivory","lavender","lavenderblush","lemonchiffon","lightcyan","lightgoldenrodyellow","lightgray","lightyellow","linen","mediumblue","mintcream","navy","oldlace","papayawhip","saddlebrown","seashell","snow","wheat","white","whitesmoke","aquamarine","lightsalmon","moccasin","limegreen","snow","sienna","beige","dimgrey","lightsage"]
-matplotcolor = {}
-for name,hexno in matplotlib.colors.cnames.items():
- matplotcolor[name]=hexno
-
def getRandColor():
k = random.choice(list(matplotcolor.keys()))
if k in ignoreColor:
@@ -761,13 +631,19 @@ def writeFooter2(f):
if __name__ == "__main__":
import sys
-
+ import os
filename = sys.argv[1]
- modelpath = filename[0:filename.find('.')]
+ filepath, filenameWithext = os.path.split(filename)
+ if filenameWithext.find('.') != -1:
+ modelpath = filenameWithext[:filenameWithext.find('.')]
+ else:
+ modelpath = filenameWithext
+
moose.loadModel(filename,'/'+modelpath,"gsl")
- output = modelpath+"_4mmoose.g"
- written = write('/'+modelpath,output)
+ output = modelpath+"_.g"
+ written = mooseWriteKkit('/'+modelpath,output)
+
if written:
print((" file written to ",output))
else:
- print(" could be written to kkit format")
+ print(" could be written to kkit format")
\ No newline at end of file
diff --git a/python/moose/moose.py b/python/moose/moose.py
index edc9954ede60f22beac919c43c91e22210dd60b6..1309c68fc838d4b225e75cad82c3347232c932fe 100644
--- a/python/moose/moose.py
+++ b/python/moose/moose.py
@@ -17,24 +17,9 @@ from collections import defaultdict
from . import _moose
from ._moose import *
import __main__ as main
-
-sbmlSupport_, genesisSupport_ = True, True
-try:
- import SBML.readSBML
- import SBML.writeSBML
-except Exception as e:
- print( 'MOOSE could not load SBML support due to %s' % e )
- sbmlSupport_ = False
-
-try:
- import genesis.writeKkit
-except Exception as e:
- print('MOOSE could not load GENESIS support')
- print('\tError was %s' % e)
- genesisSupport_ = False
-
-from . import add_Delete_ChemicalSolver
-
+import genesis.writeKkit
+import SBML.readSBML
+import SBML.writeSBML
sequence_types = ['vector<double>',
'vector<int>',
'vector<long>',
@@ -71,17 +56,10 @@ def mooseReadSBML(filepath, loadpath, solver='ee'):
solver -- Solver to use (default 'ee' ) \n
"""
- global sbmlSupport_
- if not sbmlSupport_:
- print('SBML support was not loaded')
- return None
- if not os.path.isfile(filepath):
- raise UserWarning('File %s not found' % filepath)
-
return SBML.readSBML.mooseReadSBML( filepath, loadpath, solver )
-def mooseWriteSBML(modelpath, filenpath, sceneitems={}):
+def mooseWriteSBML(modelpath, filepath, sceneitems={}):
"""Writes loaded model under modelpath to a file in SBML format.
keyword arguments:\n
@@ -97,16 +75,10 @@ def mooseWriteSBML(modelpath, filenpath, sceneitems={}):
--- else, auto-coordinates is used for layout position and passed
"""
-
- global sbmlSupport_
- if not sbmlSupport_:
- print('SBML support was not loaded')
- return None
-
return SBML.writeSBML.mooseWriteSBML(modelpath, filepath, sceneitems)
-def mooseWriteKkit(modelpath, filepath):
+def mooseWriteKkit(modelpath, filepath,sceneitems={}):
"""Writes loded model under modelpath to a file in Kkit format.
keyword arguments:\n
@@ -114,12 +86,7 @@ def mooseWriteKkit(modelpath, filepath):
modelpath -- model path in moose \n
filepath -- Path of output file.
"""
- global genesisSupport_
- if not genesisSupport_:
- print('GENESIS(kkit) support was not loaded')
- return None
-
- return moose.genesis.writeKkit.mooseWiteKkit(modelpath, filepath)
+ return genesis.writeKkit.mooseWriteKkit(modelpath, filepath,sceneitems)
def moosedeleteChemSolver(modelpath):
@@ -128,7 +95,7 @@ def moosedeleteChemSolver(modelpath):
this should be followed by mooseaddChemSolver for add solvers on to compartment to simulate else
default is Exponential Euler (ee)
"""
- return add_Delete_ChemicalSolver.moosedeleteChemSolver(modelpath)
+ return chemUtil.add_Delete_ChemicalSolver.moosedeleteChemSolver(modelpath)
def mooseaddChemSolver(modelpath, solver):
@@ -142,7 +109,7 @@ def mooseaddChemSolver(modelpath, solver):
"Runge Kutta" ("gsl")
"""
- return add_Delete_ChemicalSolver.mooseaddChemSolver(modelpath, solver)
+ return chemUtil.add_Delete_ChemicalSolver.mooseaddChemSolver(modelpath, solver)
################################################################
# Wrappers for global functions
diff --git a/python/setup.py b/python/setup.py
index 47b5f3aa0d06da2ac630645b00ce7e9cc005e5c5..94d51ca14a0addf41ecb64901281d868b92956dd 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -12,34 +12,19 @@
# You should have received a copy of the GNU General Public License
# along with MOOSE. If not, see <http://www.gnu.org/licenses/>.
-
-"""setup.py:
-
- Script to install python targets.
-
-"""
-
__author__ = "Dilawar Singh"
-__copyright__ = "Copyright 2013, Dilawar Singh and NCBS Bangalore"
+__copyright__ = "Copyright 2013-17, Dilawar Singh"
__credits__ = ["NCBS Bangalore"]
-__license__ = "GNU GPL"
-__version__ = "1.0.0"
+__license__ = "GNU GPLv3"
__maintainer__ = "Dilawar Singh"
__email__ = "dilawars@ncbs.res.in"
-__status__ = "Development"
import os
from distutils.core import setup
script_dir = os.path.dirname( os.path.abspath( __file__ ) )
-version = '3.1'
-try:
- with open( os.path.join( script_dir, '..', 'VERSION'), 'r' ) as f:
- version = f.read( )
-except Exception as e:
- print( 'Failed to read VERSION %s' % e )
- print( 'Using default 3.1' )
+version = '3.1.2'
try:
import importlib.machinery
@@ -51,7 +36,7 @@ setup(
name='moose',
version=version,
description='MOOSE python scripting module.',
- author='MOOSERes',
+ author='See AUTHORS file',
author_email='bhalla@ncbs.res.in',
maintainer='Dilawar Singh',
maintainer_email='dilawars@ncbs.res.in',
@@ -62,6 +47,7 @@ setup(
, 'moose.SBML'
, 'moose.neuroml'
, 'moose.genesis'
+ , 'moose.chemUtil'
],
package_dir = {
'moose' : 'moose'