def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = "# -*- coding: utf-8 -*-\n\n" + '"Generated by Import Combine with PhrasedML plugin ' + time.strftime(
"%m/%d/%Y"
) + '"\n"Extracted from ' + filename + '"\n\n# Translated SBML\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(zipextloc + sedmlloclist[j])
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(outputstr + "AntimonyModel = '''\n" +
sbmlstrlist[0] +
"'''\n\nPhrasedMLstr = '''\n" +
sedmlstrlist[k] + "'''")
delseq(zipextloc)
return outputstrlist
def load_and_translate(self, sedmlfile, pythonfile, editor, set_current=True):
"""
Read filename as SED-ML file, translate it to PhrasedML, and
create an editor instance and return it
*Warning* This is loading file, creating editor but not executing
the source code analysis -- the analysis must be done by the editor
plugin (in case multiple editorstack instances are handled)
"""
#sedmlfile = to_text_string(sedmlfile)
sedmlfile = str(sedmlfile)
self.emit(SIGNAL('starting_long_process(QString)'),
_("Loading %s...") % sedmlfile)
text, enc = encoding.read(sedmlfile)
fname = os.path.basename(sedmlfile)
temp = '# -*- coding: utf-8 -*-\n\n' + "'Generated by Import SED-ML with PhrasedML plugin " + time.strftime('%m/%d/%Y') + "'\n'Extracted from " + fname + "'\n\n'''"
text = temp + pl.convertFile(sedmlfile) + "'''"
widgeteditor = editor.editorstacks[0]
finfo = widgeteditor.create_new_editor(pythonfile, enc, text, set_current, new=True)
index = widgeteditor.data.index(finfo)
widgeteditor._refresh_outlineexplorer(index, update=True)
self.emit(SIGNAL('ending_long_process(QString)'), "")
if widgeteditor.isVisible() and widgeteditor.checkeolchars_enabled \
and sourcecode.has_mixed_eol_chars(text):
name = os.path.basename(pythonfile)
QMessageBox.warning(self, widgeteditor.title,
_("<b>%s</b> contains mixed end-of-line "
"characters.<br>Spyder will fix this "
"automatically.") % name,
QMessageBox.Ok)
widgeteditor.set_os_eol_chars(index)
widgeteditor.is_analysis_done = False
finfo.editor.set_cursor_position('eof')
finfo.editor.insert_text(os.linesep)
return finfo, sedmlfile
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = '"End of code generated by Import Combine as PhrasedML plugin ' + time.strftime(
"%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(os.path.join(zipextloc, sbmlloclist[i]))
try:
transtext = te.sbmlToAntimony(sbml)
except Exception as e:
transtext = """*********************WARNING*********************
Failed to translate the SBML model to Antimony string.
Please check that the SBML file is valid.
*********************WARNING*********************"""
transtext = transtext + "\n\n" + str(e)
sbmlstrlist.append(transtext)
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(os.path.join(zipextloc, sedmlloclist[j]))
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(
"AntimonyModel = '''\n" + sbmlstrlist[0] +
"'''\n\nPhrasedMLstr = '''\n" + sedmlstrlist[k] +
"'''\n\nimport tellurium as te\n\nexp = te.experiment([AntimonyModel], [PhrasedMLstr])\nexp.execute(PhrasedMLstr)\n\n"
+ outputstr)
delseq(zipextloc)
return outputstrlist
def toPhrasedml(self):
if self.sedml_str:
result = phrasedml.convertString(self.sedml_str)
if result is None:
raise RuntimeError(phrasedml.getLastError())
return self.fixModelRefs(phrasedml.getLastPhraSEDML())
elif self.sedml_path:
result = phrasedml.convertFile(self.sedml_str)
if result is None:
raise RuntimeError(phrasedml.getLastError())
return self.fixModelRefs(phrasedml.getLastPhraSEDML())
def load_and_translate(self,
sedmlfile,
pythonfile,
editor,
set_current=True):
"""
Read filename as SED-ML file, translate it to PhrasedML, and
create an editor instance and return it
*Warning* This is loading file, creating editor but not executing
the source code analysis -- the analysis must be done by the editor
plugin (in case multiple editorstack instances are handled)
"""
#sedmlfile = to_text_string(sedmlfile)
sedmlfile = str(sedmlfile)
self.emit(SIGNAL('starting_long_process(QString)'),
_("Loading %s...") % sedmlfile)
text, enc = encoding.read(sedmlfile)
fname = os.path.basename(sedmlfile)
temp = '"End of code generated by Import SED-ML with PhrasedML plugin ' + time.strftime(
'%m/%d/%Y') + '"\n"Extracted from ' + fname + '"'
text = "import tellurium as te\n\nphrasedmlStr = '''" + pl.convertFile(
sedmlfile
) + "'''\n\nte.executeSEDML(te.sedml.tephrasedml.phrasedml.convertString(phrasedmlStr))\n\n" + temp
widgeteditor = editor.editorstacks[0]
finfo = widgeteditor.create_new_editor(pythonfile,
enc,
text,
set_current,
new=True)
index = widgeteditor.data.index(finfo)
widgeteditor._refresh_outlineexplorer(index, update=True)
self.emit(SIGNAL('ending_long_process(QString)'), "")
if widgeteditor.isVisible() and widgeteditor.checkeolchars_enabled \
and sourcecode.has_mixed_eol_chars(text):
name = os.path.basename(pythonfile)
QMessageBox.warning(
self, widgeteditor.title,
_("<b>%s</b> contains mixed end-of-line "
"characters.<br>Spyder will fix this "
"automatically.") % name, QMessageBox.Ok)
widgeteditor.set_os_eol_chars(index)
widgeteditor.is_analysis_done = False
finfo.editor.set_cursor_position('eof')
finfo.editor.insert_text(os.linesep)
return finfo, sedmlfile
def toPhrasedml(self):
# assign sbml resources
# print('toPhrasedml sbml resources:')
phrasedml.clearReferencedSBML()
for sbml_resource in self.sbml_map:
# print(' {} -> {}'.format(sbml_resource, self.sbml_map[sbml_resource][:30]))
phrasedml.setReferencedSBML(sbml_resource, self.sbml_map[sbml_resource])
# convert to phrasedml
if self.sedml_str:
result = phrasedml.convertString(self.sedml_str)
if result is None:
raise RuntimeError(phrasedml.getLastError())
return self.fixModelRefs(phrasedml.getLastPhraSEDML())
elif self.sedml_path:
result = phrasedml.convertFile(self.sedml_str)
if result is None:
raise RuntimeError(phrasedml.getLastError())
return self.fixModelRefs(phrasedml.getLastPhraSEDML())
def toPhrasedml(self):
# assign sbml resources
# print('toPhrasedml sbml resources:')
phrasedml.clearReferencedSBML()
for sbml_resource in self.sbml_map:
# print(' {} -> {}'.format(sbml_resource, self.sbml_map[sbml_resource][:30]))
phrasedml.setReferencedSBML(sbml_resource, self.sbml_map[sbml_resource])
# convert to phrasedml
if self.sedml_str:
result = phrasedml.convertString(self.sedml_str)
if result is None:
raise RuntimeError(phrasedml.getLastError())
return self.fixModelRefs(phrasedml.getLastPhraSEDML())
elif self.sedml_path:
result = phrasedml.convertFile(self.sedml_str)
if result is None:
raise RuntimeError(phrasedml.getLastError())
return self.fixModelRefs(phrasedml.getLastPhraSEDML())
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = "# -*- coding: utf-8 -*-\n\n" + '"Generated by Import Combine with PhrasedML plugin ' + time.strftime("%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n\n# Translated SBML\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(zipextloc + sedmlloclist[j])
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(outputstr + "AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n\nPhrasedMLstr = '''\n" + sedmlstrlist[k] + "'''")
delseq(zipextloc)
return outputstrlist
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = '"End of code generated by Import Combine as PhrasedML plugin ' + time.strftime("%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(zipextloc + sedmlloclist[j])
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append("AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n\nPhrasedMLstr = '''\n" + sedmlstrlist[k] +
"'''\n\nimport tellurium as te\n\nexp = te.experiment([AntimonyModel], [PhrasedMLstr])\nexp.execute(PhrasedMLstr)\n\n" + outputstr)
delseq(zipextloc)
return outputstrlist
def load_and_translate(self,
inputfile,
pythonfile,
editor,
action,
set_current=True):
"""
If the input is COMBINE archive, read filename as combine archive,
unzip, translate, reconstitute in Python or PhrasedML, and create an
editor instance and return it
If the input is SED-ML file, read filename as SED-ML file, translate
it to Python, and create an editor instance and return it
*Warning* This is loading file, creating editor but not executing
the source code analysis -- the analysis must be done by the editor
plugin (in case multiple editorstack instances are handled)
"""
inputfile = str(inputfile)
text, enc = encoding.read(inputfile)
if action == 'c2p':
fformat = '.py'
text = Translatecombine2P(inputfile)
zipextloctemp, sbmlloclisttemp, sedmlloclisttemp = manifestsearch(
inputfile)
elif action == 'c2pwp':
fformat = '_phrasedml.py'
text = Translatecombine2WP(inputfile)
zipextloctemp, sbmlloclisttemp, sedmlloclisttemp = manifestsearch(
inputfile)
elif action == 's2p':
fname = os.path.basename(inputfile)
temp = '"End of code generated by Import SED-ML plugin ' + time.strftime(
"%m/%d/%Y") + '"\n"Extracted from ' + fname + '"\n\n'
text = te.sedmlToPython(inputfile) + temp
else:
fname = os.path.basename(inputfile)
temp = '"End of code generated by Import SED-ML with PhrasedML plugin ' + time.strftime(
'%m/%d/%Y') + '"\n"Extracted from ' + fname + '"'
text = "import tellurium as te\n\nphrasedmlStr = '''" + pl.convertFile(
inputfile
) + "'''\n\nte.executeSEDML(te.sedml.tephrasedml.phrasedml.convertString(phrasedmlStr))\n\n" + temp
if action == 'c2p' or action == 'c2pwp':
for i in range(len(text)):
widgeteditor = editor.editorstacks[0]
widgeteditor.starting_long_process.emit(
_("Loading %s...") % inputfile)
sedmlfname = os.path.basename(sedmlloclisttemp[i])
finfo = widgeteditor.create_new_editor(
os.path.splitext(sedmlfname)[0] + fformat,
enc,
text[i],
set_current,
new=True)
index = widgeteditor.data.index(finfo)
widgeteditor._refresh_outlineexplorer(index, update=True)
widgeteditor.ending_long_process.emit("")
if widgeteditor.isVisible() and widgeteditor.checkeolchars_enabled \
and sourcecode.has_mixed_eol_chars(text[i]):
if action == 'c2p':
name = os.path.basename(
os.path.splitext(sedmlfname)[0] + fformat)
else:
name = os.path.basename(pythonfile[:-3] + fformat)
QMessageBox.warning(
self, widgeteditor.title,
_("<b>%s</b> contains mixed end-of-line "
"characters.<br>Spyder will fix this "
"automatically.") % name, QMessageBox.Ok)
widgeteditor.set_os_eol_chars(index)
widgeteditor.is_analysis_done = False
finfo.editor.set_cursor_position('eof')
finfo.editor.insert_text(os.linesep)
else:
widgeteditor = editor.editorstacks[0]
widgeteditor.starting_long_process.emit(
_("Loading %s...") % inputfile)
finfo = widgeteditor.create_new_editor(pythonfile,
enc,
text,
set_current,
new=True)
index = widgeteditor.data.index(finfo)
widgeteditor._refresh_outlineexplorer(index, update=True)
widgeteditor.ending_long_process.emit("")
if widgeteditor.isVisible() and widgeteditor.checkeolchars_enabled \
and sourcecode.has_mixed_eol_chars(text):
name = os.path.basename(pythonfile)
QMessageBox.warning(
self, widgeteditor.title,
_("<b>%s</b> contains mixed end-of-line "
"characters.<br>Spyder will fix this "
"automatically.") % name, QMessageBox.Ok)
widgeteditor.set_os_eol_chars(index)
widgeteditor.is_analysis_done = False
finfo.editor.set_cursor_position('eof')
finfo.editor.insert_text(os.linesep)
return finfo, inputfile