def load_and_translate(self, sedmlfile, pythonfile, editor, set_current=True):
"""
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)
"""
#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 plugin ' + time.strftime("%m/%d/%Y") + '"\n"Extracted from ' + fname + '"\n\n'
text = te.sedmlToPython(sedmlfile) + 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 translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
rePath = r"loadSBMLModel\((.*)\)"
reFig = r"savefig\((.*)\)"
outputstr = '"End of code generated by Import Combine 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 = te.sedmlToPython(
os.path.join(zipextloc, sedmlloclist[j]))
lines = sedmlstr.splitlines()
for i, s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
s = s.replace("loadSBMLModel", "loada")
s = s.replace(reSearchPath[1], "AntimonyModel")
lines[i] = s
lines.insert(
i - 1,
"AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n")
for i, s in enumerate(lines):
reSearchFig = re.split(reFig, s)
if len(reSearchFig) > 1:
del lines[i]
sedmlstr = '\n'.join(lines)
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(sedmlstrlist[k] + '\n\n' + outputstr)
delseq(zipextloc)
return outputstrlist
def load_and_translate(self,
sedmlfile,
pythonfile,
editor,
set_current=True):
"""
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)
"""
#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 plugin ' + time.strftime(
"%m/%d/%Y") + '"\n"Extracted from ' + fname + '"\n\n'
text = te.sedmlToPython(sedmlfile) + 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 translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
rePath = r"loadSBMLModel\((.*)\)"
reFig = r"savefig\((.*)\)"
outputstr = '"End of code generated by Import Combine 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 = te.sedmlToPython(zipextloc + sedmlloclist[j])
lines = sedmlstr.splitlines()
for i,s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
s = s.replace("loadSBMLModel", "loada")
s = s.replace(reSearchPath[1],"AntimonyModel")
lines[i] = s
lines.insert(i - 1, "AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n")
for i,s in enumerate(lines):
reSearchFig = re.split(reFig, s)
if len(reSearchFig) > 1:
del lines[i]
sedmlstr = '\n'.join(lines)
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(sedmlstrlist[k] + '\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