class openSBML(SpyderPluginWidget):
"Open sbml files and translate into antimony string"
CONF_SECTION = 'openSBML'
CONFIGWIDGET_CLASS = None
def __init__(self, main):
super(openSBML, self).__init__(main)
self.dockwidget = SpyderDockWidget(self.get_plugin_title(), main)
self.dockwidget.hide()
# --- SpyderPluginWidget API ----------------------------------------------
def get_plugin_title(self):
"""Return widget title"""
return _("Open SBML")
def register_plugin(self):
"""Register plugin in Spyder's main window"""
opensbml_act = create_action(self.main,
_("Open SBML file"),
triggered=self.run_opensbml)
self.main.file_menu_actions.insert(5, opensbml_act)
def closing_plugin(self, cancelable=False):
"""Perform actions before parent main window is closed"""
return True
def apply_plugin_settings(self, options):
"""Apply configuration file's plugin settings"""
pass
# --- Public API ----------------------------------------------------------
def run_opensbml(self,
filenames=None,
goto=None,
word='',
editorwindow=None,
processevents=True):
"""Prompt the user to load a SBML file, translate to antimony, and
display in a new window"""
editor = self.main.editor
editor0 = editor.get_current_editor()
if editor0 is not None:
position0 = editor0.get_position('cursor')
filename0 = editor.get_current_filename()
else:
position0, filename0 = None, None
if not filenames:
# Recent files action
action = editor.sender()
if isinstance(action, QAction):
filenames = from_qvariant(action.data(), to_text_string)
if not filenames:
basedir = getcwd()
if editor.edit_filetypes is None:
editor.edit_filetypes = get_edit_filetypes()
if editor.edit_filters is None:
editor.edit_filters = get_edit_filters()
c_fname = editor.get_current_filename()
if c_fname is not None and c_fname != editor.TEMPFILE_PATH:
basedir = os.path.dirname(c_fname)
editor.redirect_stdio.emit(False)
parent_widget = editor.get_current_editorstack()
if filename0 is not None:
selectedfilter = get_filter(editor.edit_filetypes,
os.path.splitext(filename0)[1])
else:
selectedfilter = ''
if not running_under_pytest():
customfilters = 'SBML files (*.sbml *.xml);;All files (*.*)'
filenames, _sf = getopenfilenames(
parent_widget,
_("Open SBML file"),
basedir,
customfilters,
selectedfilter=selectedfilter,
options=QFileDialog.HideNameFilterDetails)
else:
# Use a Qt (i.e. scriptable) dialog for pytest
dialog = QFileDialog(parent_widget,
_("Open SBML file"),
options=QFileDialog.DontUseNativeDialog)
if dialog.exec_():
filenames = dialog.selectedFiles()
editor.redirect_stdio.emit(True)
if filenames:
filenames = [os.path.normpath(fname) for fname in filenames]
else:
return
focus_widget = QApplication.focusWidget()
if editor.dockwidget and\
(not editor.dockwidget.isAncestorOf(focus_widget)\
and not isinstance(focus_widget, CodeEditor)):
editor.dockwidget.setVisible(True)
editor.dockwidget.setFocus()
editor.dockwidget.raise_()
def _convert(fname):
fname = os.path.abspath(encoding.to_unicode_from_fs(fname))
if os.name == 'nt' and len(fname) >= 2 and fname[1] == ':':
fname = fname[0].upper() + fname[1:]
return fname
if hasattr(filenames, 'replaceInStrings'):
# This is a QStringList instance (PyQt API #1), converting to list:
filenames = list(filenames)
if not isinstance(filenames, list):
filenames = [_convert(filenames)]
else:
filenames = [_convert(fname) for fname in list(filenames)]
if isinstance(goto, int):
goto = [goto]
elif goto is not None and len(goto) != len(filenames):
goto = None
for index, filename in enumerate(filenames):
p = re.compile('(.xml$|.sbml$)')
pythonfile = p.sub('_antimony.py', filename)
if (pythonfile == filename):
pythonfile = filename + "_antimony.py"
# -- Do not open an already opened file
current_editor = editor.set_current_filename(
pythonfile, editorwindow)
if current_editor is None:
# -- Not a valid filename:
if not os.path.isfile(filename):
continue
# --
current_es = editor.get_current_editorstack(editorwindow)
# Creating the editor widget in the first editorstack (the one
# that can't be destroyed), then cloning this editor widget in
# all other editorstacks:
finfo, newname = self.load_and_translate(
filename, pythonfile, editor)
finfo.path = editor.main.get_spyder_pythonpath()
editor._clone_file_everywhere(finfo)
current_editor = current_es.set_current_filename(newname)
current_es.analyze_script()
if goto is not None: # 'word' is assumed to be None as well
current_editor.go_to_line(goto[index], word=word)
position = current_editor.get_position('cursor')
editor.cursor_moved(filename0, position0, filename, position)
if (current_editor is not None):
current_editor.clearFocus()
current_editor.setFocus()
current_editor.window().raise_()
if processevents:
QApplication.processEvents()
def load_and_translate(self,
sbmlfile,
pythonfile,
editor,
set_current=True):
"""
Read filename as combine archive, unzip, translate, reconstitute in
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)
"""
widgeteditor = editor.editorstacks[0]
sbmlfile = str(sbmlfile)
widgeteditor.starting_long_process.emit(_("Loading %s...") % sbmlfile)
text, enc = encoding.read(sbmlfile)
sbmlstr = te.readFromFile(sbmlfile)
try:
transtext = str(te.sbmlToAntimony(sbmlstr))
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)
text = "import tellurium as te\n\nr = te.loada('''\n" + transtext + "''')"
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, sbmlfile
class teImport(SpyderPluginWidget):
"""teImport script"""
CONF_SECTION = 'teImport'
CONFIGWIDGET_CLASS = None
def __init__(self, main):
super(teImport, self).__init__(main)
self.dockwidget = SpyderDockWidget(self.get_plugin_title(), main)
self.dockwidget.hide()
#------ SpyderPluginWidget API --------------------------------------------
def get_plugin_title(self):
"""Return widget title"""
return _("Import COMBINE and SED-ML")
def register_plugin(self):
"""Register plugin in Spyder's main window"""
c2p_act = create_action(self.main,
_("Import COMBINE as Python"),
triggered=self.run_Import)
c2p_act.triggered.connect(functools.partial(self.run_Import, 'c2p'))
c2pwp_act = create_action(self.main,
_("Import COMBINE as PhrasedML"),
triggered=self.run_Import)
c2pwp_act.triggered.connect(functools.partial(self.run_Import,
'c2pwp'))
s2p_act = create_action(self.main,
_("Import SED-ML as Python"),
triggered=self.run_Import)
s2p_act.triggered.connect(functools.partial(self.run_Import, 's2p'))
s2pwp_act = create_action(self.main,
_("Import SED-ML as PhrasedML"),
triggered=self.run_Import)
s2pwp_act.triggered.connect(functools.partial(self.run_Import,
's2pwp'))
for item in self.main.file_menu_actions:
try:
menu_title = item.title()
except AttributeError:
pass
else:
if not is_text_string(menu_title): # string is a QString
menu_title = to_text_string(menu_title.toUtf8)
if item.title() == str("Import"):
item.addAction(c2p_act, c2pwp_act, s2p_act, s2pwp_act)
all_actions = (None, c2p_act, c2pwp_act, s2p_act, s2pwp_act)
import_menu = QMenu(_("Import"))
add_actions(import_menu, all_actions)
self.main.file_menu_actions.insert(6, import_menu)
def on_first_registration(self):
"""Action to be performed on first plugin registration"""
self.main.tabify_plugins(self.main.help, self)
self.dockwidget.hide()
def closing_plugin(self, cancelable=False):
"""Perform actions before parent main window is closed"""
return True
def apply_plugin_settings(self, options):
"""Apply configuration file's plugin settings"""
pass
# --- Public API ----------------------------------------------------------
def run_Import(self, action):
"""Prompt user to load a COMBINE archive or SED-ML file and translates it"""
if action == 'c2p' or action == 'c2pwp' or action == 's2p' or action == 's2pwp':
editorwindow = None #Used in editor.load
processevents = True #Used in editor.load
goto = None
word = ''
editor = self.main.editor
editor0 = editor.get_current_editor()
if editor0 is not None:
position0 = editor0.get_position('cursor')
filename0 = editor.get_current_filename()
else:
position0, filename0 = None, None
# Recent files action
raction = editor.sender()
if isinstance(raction, QAction):
filenames = from_qvariant(raction.data(), to_text_string)
if not filenames:
basedir = getcwd()
if editor.edit_filetypes is None:
editor.edit_filetypes = get_edit_filetypes()
if editor.edit_filters is None:
editor.edit_filters = get_edit_filters()
c_fname = editor.get_current_filename()
if c_fname is not None and c_fname != editor.TEMPFILE_PATH:
basedir = os.path.dirname(c_fname)
editor.redirect_stdio.emit(False)
parent_widget = editor.get_current_editorstack()
if filename0 is not None:
selectedfilter = get_filter(editor.edit_filetypes,
os.path.splitext(filename0)[1])
else:
selectedfilter = ''
if action == 'c2p' or action == 'c2pwp':
filters = 'Combine archives (*.zip *.omex);;All files (*.*)'
filenames, _selfilter = getopenfilenames(
parent_widget,
_("Open combine archive"),
basedir,
filters,
selectedfilter=selectedfilter)
else:
filters = 'SED-ML files (*.sedml *.xml);;All files (*.*)'
filenames, _selfilter = getopenfilenames(
parent_widget,
_("Open SED-ML file"),
basedir,
filters,
selectedfilter=selectedfilter)
editor.redirect_stdio.emit(True)
if filenames:
filenames = [
os.path.normpath(fname) for fname in filenames
]
else:
return
focus_widget = QApplication.focusWidget()
if editor.dockwidget and\
(not editor.dockwidget.isAncestorOf(focus_widget)\
and not isinstance(focus_widget, CodeEditor)):
editor.dockwidget.setVisible(True)
editor.dockwidget.setFocus()
editor.dockwidget.raise_()
def _convert(fname):
fname = os.path.abspath(encoding.to_unicode_from_fs(fname))
if os.name == 'nt' and len(fname) >= 2 and fname[1] == ':':
fname = fname[0].upper() + fname[1:]
return fname
if hasattr(filenames, 'replaceInStrings'):
# This is a QStringList instance (PyQt API #1), converting to list:
filenames = list(filenames)
if not isinstance(filenames, list):
filenames = [_convert(filenames)]
else:
filenames = [_convert(fname) for fname in list(filenames)]
if isinstance(goto, int):
goto = [goto]
elif goto is not None and len(goto) != len(filenames):
goto = None
for index, filename in enumerate(filenames):
if action == 'c2p' or action == 'c2pwp':
p = re.compile('(.zip$|.omex$)')
pythonfile = p.sub('.py', filename)
if (pythonfile == filename):
pythonfile = filename + ".py"
else:
p = re.compile('(.xml$|.sedml$)')
if action == 's2p':
pythonfile = p.sub('_sedml.py', filename)
if (pythonfile == filename):
pythonfile = filename + "_sedml.py"
else:
pythonfile = p.sub('_phrasedml.py', filename)
if (pythonfile == filename):
pythonfile = filename + "_phrasedml.py"
current_editor = editor.set_current_filename(
pythonfile, editorwindow)
if current_editor is None:
# -- Not a valid filename:
if not os.path.isfile(filename):
continue
# --
current_es = editor.get_current_editorstack(editorwindow)
# Creating the editor widget in the first editorstack (the one
# that can't be destroyed), then cloning this editor widget in
# all other editorstacks:
finfo, newname = self.load_and_translate(
filename, pythonfile, editor, action)
finfo.path = editor.main.get_spyder_pythonpath()
editor._clone_file_everywhere(finfo)
current_editor = current_es.set_current_filename(newname)
current_es.analyze_script()
if goto is not None: # 'word' is assumed to be None as well
current_editor.go_to_line(goto[index], word=word)
position = current_editor.get_position('cursor')
editor.cursor_moved(filename0, position0, filename,
position)
if (current_editor is not None):
current_editor.clearFocus()
current_editor.setFocus()
current_editor.window().raise_()
if processevents:
QApplication.processEvents()
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