def test_open_external_link_externally(self):
model = HTMLModel(content="""
<html>
<a
href='test://testing'
target='_blank'
style='display:block; width: 100%; height: 100%'>
External Link
</a>
</html>
""")
view = View(
Item("content", editor=HTMLEditor(open_externally=True))
)
with self.tester.create_ui(model, dict(view=view)) as ui:
html_view = self.tester.find_by_name(ui, "content")
with mock.patch("webbrowser.open_new") as mocked_browser:
html_view.perform(MouseClick())
self.assertIn(
"External Link",
html_view.inspect(HTMLContent()),
)
is_webkit = _is_webkit_page(html_view._target.control.page())
if is_webkit:
# This is the expected behavior.
mocked_browser.assert_called_once_with("test://testing")
else:
# Expected failure:
# See enthought/traitsui#1464
# This is the current unexpected behavior if QtWebEngine is used.
mocked_browser.assert_not_called()
def get_view(base_url_name):
return View(
Item("content",
editor=HTMLEditor(
format_text=True,
base_url_name=base_url_name,
)))
def test_open_internal_link_externally(self):
# this test requires Qt because it relies on the link filling up
# the entire page through the use of CSS, which isn't supported
# by Wx.
model = HTMLModel(content="""
<html>
<a
href='test://testing'
target='_self'
style='display:block; width: 100%; height: 100%'>
Internal Link
</a>
</html>
""")
view = View(
Item("content", editor=HTMLEditor(open_externally=True))
)
with self.tester.create_ui(model, dict(view=view)) as ui:
html_view = self.tester.find_by_name(ui, "content")
with mock.patch("webbrowser.open_new") as mocked_browser:
html_view.perform(MouseClick())
self.assertIn(
"Internal Link",
html_view.inspect(HTMLContent()),
)
mocked_browser.assert_called_once_with("test://testing")
def test_open_external_link(self):
# this test requires Qt because it relies on the link filling up
# the entire page through the use of CSS, which isn't supported
# by Wx.
model = HTMLModel(content="""
<html>
<a
href='test://testing'
target='_blank'
style='display:block; width: 100%; height: 100%'>
External Link
</a>
</html>
""")
view = View(
Item("content", editor=HTMLEditor())
)
with self.tester.create_ui(model, dict(view=view)) as ui:
html_view = self.tester.find_by_name(ui, "content")
with mock.patch("webbrowser.open_new") as mocked_browser:
html_view.perform(MouseClick())
self.assertIn(
"External Link",
html_view.inspect(HTMLContent()),
)
# See enthought/traitsui#1464
# This is the expected behaviour:
# mocked_browser.assert_called_once_with("test://testing")
# However, this is the current unexpected behaviour
mocked_browser.assert_not_called()
class TestHTML(HasPrivateTraits):
# -------------------------------------------------------------------------
# Trait definitions:
# -------------------------------------------------------------------------
# Text string to display as HTML:
html = Code(sample)
# -------------------------------------------------------------------------
# Traits view definitions:
# -------------------------------------------------------------------------
view = View(
Group(
[Item('html#@', editor=HTMLEditor(format_text=True)), '|<>'],
['{Enter formatted text and/or HTML below:}@', 'html#@', '|<>'],
'|<>',
layout='split',
),
title='HTML Editor Test',
resizable=True,
width=0.4,
height=0.6,
)
class InfoViewer(HasTraits):
text = Str()
view = View(Item('text', editor=HTMLEditor(format_text=True), style='readonly', show_label=False),
resizable=True,
width=0.3,
height=0.3)
class HelpDockPane(TraitsDockPane):
"""
A DockPane to view help for the current module
"""
#### TaskPane interface ###############################################
id = 'edu.mit.synbio.cytoflowgui.help_pane'
name = 'Help'
# the Task that serves as the controller
task = Instance(Task)
view_plugins = List(IViewPlugin)
op_plugins = List(IOperationPlugin)
help_id = Str
html = HTML("<b>Welcome to Cytoflow!</b>")
traits_view = View(
Item('html',
editor=HTMLEditor(base_url=pathlib.Path(__file__).parent.joinpath(
'help').as_posix()),
show_label=False))
def create_contents(self, parent):
self.ui = self.edit_traits(kind='subpanel', parent=parent)
layout = QtGui.QHBoxLayout()
control = HintedWidget()
layout.addWidget(self.ui.control)
control.setLayout(layout)
control.setParent(parent)
parent.setWidget(control)
return control
@on_trait_change('help_id', post_init=True)
def _on_help_id_changed(self):
for plugin in self.view_plugins:
if self.help_id == plugin.view_id:
try:
self.html = plugin.get_help()
except AttributeError:
pass
finally:
return
for plugin in self.op_plugins:
if self.help_id == plugin.operation_id:
try:
self.html = plugin.get_help()
except AttributeError:
pass
finally:
return
def html_editor():
""" Factory function for an "editor" that displays a multi-line string as
interpreted HTML.
"""
global HTMLTextEditor
if HTMLTextEditor is None:
from traitsui.api import HTMLEditor
HTMLTextEditor = HTMLEditor()
return HTMLTextEditor
class ShowUsage(HasTraits):
usage_str = Str()
traits_view = View(
Item("usage_str", style='readonly', show_label=False,
editor=HTMLEditor(), resizable=True),
width=680, resizable=True, icon=icon,
title='Swift Console Usage')
def __init__(self, usage, error_str):
if error_str != "":
self.usage_str = "<pre>" + error_str + '<br><br><br>' + usage + "</pre>"
else:
self.usage_str = "<pre>" + usage + "</pre>"
class EK60Dialog(HasTraits):
"""
This class implements a dialog box that displays bandwidth averaged sphere
TS estimates.
"""
html_text = Str()
view = View(Item('html_text',
editor=HTMLEditor(format_text=False),
show_label=False),
title='EK60',
buttons=[OKButton],
resizable=True)
class ModelHelpPane(TraitsDockPane):
""" A dock pane for viewing any help associated with a model.
"""
#### 'ITaskPane' interface ################################################
id = "example.attractors.model_help_pane"
name = "Model Information"
#### 'ModelConfigPane' interface ##########################################
model = Instance(HasTraits)
html = Property(Str, observe="model")
view = View(
Item(
"pane.html",
editor=HTMLEditor(base_url=HELP_PATH, open_externally=True),
show_label=False,
),
width=300,
resizable=True,
)
###########################################################################
# Protected interface.
###########################################################################
@cached_property
def _get_html(self):
""" Fetch the help HTML for the current model.
"""
if self.model is None:
return "No model selected."
# Determine the name of the model.
model = self.model
while hasattr(model, "adaptee"):
model = model.adaptee
name = model.__class__.__name__.lower()
# Load HTML file, if possible.
path = os.path.join(HELP_PATH, name + ".html")
if os.path.isfile(path):
with codecs.open(path, "r", "utf-8") as f:
return f.read()
else:
return "No information available for model."
def traits_view(self):
v = View(
Item('message',
style='custom',
editor=HTMLEditor(),
show_label=False),
HGroup(spring, Item('dismiss_notification')),
kind='modal',
handler=VersionInfoHandler,
buttons=['OK'],
width=300,
height=300,
title='Version Info',
)
return v
class HTMLEditorDemo(HasTraits):
""" Defines the main HTMLEditor demo class. """
# Define a HTML trait to view
my_html_trait = HTML(sample_text)
# Demo view
traits_view = View(
UItem(
'my_html_trait',
# we specify the editor explicitly in order to set format_text:
editor=HTMLEditor(format_text=True)),
title='HTMLEditor',
buttons=['OK'],
width=800,
height=600,
resizable=True)
class HTMLItem(ADescriptionItem):
""" Defines a class used for displaying a single HTML page within the tutor
using the default Traits HTML editor.
"""
url = Str
view = View(
Item('content',
style='readonly',
show_label=False,
editor=HTMLEditor()))
def _url_changed(self, url):
""" Sets the item title when the 'url' is changed.
"""
match = url_pat1.match(url)
if match is not None:
title = match.group(2).strip()
else:
title = url.strip()
col = title.rfind('/')
if col >= 0:
title = os.path.splitext(title[col + 1:])[0]
self.title = title
@cached_property
def _get_content(self):
""" Returns the item content.
"""
url = self.url
if url != '':
match = url_pat1.match(url)
if match is not None:
url = match.group(1) + match.group(3)
return url
return read_file(self.path)
def _set_content(self, content):
""" Sets the item content.
"""
self._content = content
class HelpDockPane(TraitsDockPane):
"""
A DockPane to view help for the current module
"""
#### TaskPane interface ###############################################
id = 'edu.mit.synbio.help_pane'
name = 'Help'
# the Task that serves as the controller
task = Instance(Task)
view_plugins = List(IViewPlugin)
op_plugins = List(IOperationPlugin)
help_id = Str
html = HTML("<b>Welcome to Cytoflow!</b>")
traits_view = View(
Item('html',
editor=HTMLEditor(base_url=pathlib.Path(__file__).parent.joinpath(
'help').as_posix()),
show_label=False))
@on_trait_change('help_id', post_init=True)
def _on_help_id_changed(self):
for plugin in self.view_plugins:
if self.help_id == plugin.view_id:
try:
self.html = plugin.get_help()
except AttributeError:
pass
finally:
return
for plugin in self.op_plugins:
if self.help_id == plugin.operation_id:
try:
self.html = plugin.get_help()
except AttributeError:
pass
finally:
return
class AboutDialog(HasTraits):
"""
This class implements an About dialog box using the TraitsUI user interface
framework. The text displayed in the dialog is read from a file containing
html-formatted text.
"""
helpFile = 'about.html'
about_text = Str()
view = View(Item('about_text', editor=HTMLEditor(), show_label=False),
resizable=True,
title='About',
buttons=[OKButton])
def load_help_text(self):
"""
Loads the help text from the file.
"""
f = open(self.helpFile, 'r')
self.about_text = f.read()
def traits_view(self):
""" Default view to show for this class. """
args = []
kw_args = {
"title": "Preferences Page Help",
"buttons": ["OK"],
"width": 800,
"height": 800,
"resizable": True,
"id": "apptools.preferences.ui.preferences_manager.help",
}
to_show = {}
for name, trait_obj in self.traits().items():
if name != "trait_added" and name != "trait_modified":
to_show[name] = trait_obj.help
for name in to_show:
args.append(Item(name, style="readonly", editor=HTMLEditor()))
view = View(*args, **kw_args)
return view
def traits_view(self):
""" Default view to show for this class. """
args = []
kw_args = {
'title': 'Preferences Page Help',
'buttons': ['OK'],
'width': 800,
'height': 800,
'resizable': True,
'id': 'apptools.preferences.ui.preferences_manager.help'
}
to_show = {}
for name, trait_obj in self.traits().items():
if name != 'trait_added' and name != 'trait_modified':
to_show[name] = trait_obj.help
for name in to_show:
args.append(Item(name, style='readonly', editor=HTMLEditor()))
view = View(*args, **kw_args)
return view
def trait_view(self, name='default'):
rest_editor = CodeEditor(lexer='rest',
selected_line='selected_line',
auto_scroll=True,
squiggle_lines='warning_lines',
selected_text='selected_text',
selected_start_pos='selected_start_pos',
selected_end_pos='selected_end_pos')
warning_editor = TabularEditor(editable=False,
adapter=DocUtilsWarningAdapter(),
dclicked='dclicked_warning')
html_editor = HTMLEditor(open_externally=True,
base_url_name='base_url')
return View(Group(Group(Item('object.model.rest',
style='custom',
editor=rest_editor),
Item('html', editor=html_editor),
id='rest_editor_view.PairView.HorzGroup',
show_labels=False,
orientation='horizontal',
layout='split'),
Item('object.model.warnings',
height=0.2,
editor=warning_editor),
id='rest_editor_view.PairView.VertGroup',
show_labels=False,
orientation='vertical',
layout='split'),
id='rest_editor_view.PairView',
handler=ReSTHTMLPairHandler(),
width=800,
height=600,
resizable=True)
_, ext = splitext(filename)
file_factory = self._file_factory[ext]
demo_file = file_factory(parent=self, name=filename)
return demo_file
# -------------------------------------------------------------------------
# Defines the demo tree editor:
# -------------------------------------------------------------------------
demo_path_view = View(
UItem(
"description",
style="readonly",
editor=HTMLEditor(
format_text=True,
base_url_name='base_url',
),
),
id="demo_path_view",
kind='subpanel',
)
demo_file_view = View(
HSplit(
UItem(
"description",
style="readonly",
editor=HTMLEditor(
format_text=True,
base_url_name='base_url',
),
class CiteOverlapGUI(HasTraits):
"""GUI for Citation Overlap."""
#: str: Default extractor option to prompt user to select an extractor.
_DEFAULT_EXTRACTOR = "Select..."
#: int: Default number of import views.
_DEFAULT_NUM_IMPORTS = 3
#: OrderedDict[str, str]: Dictionary of separator descriptions to
# separator characters.
_EXPORT_SEPS = OrderedDict((
('Tabs (.tsv)', '\t'),
('Comma (.csv)', ','),
('Bar (.csv)', '|'),
('Semi-colon (.csv)', ';'),
))
# handler triggers
selectSheetTab = Int(-1) # tab index to select
renameSheetTab = Int(-1) # tab index to rename
renameSheetName = Str # new tab name
# CONTROL PANEL TRAITS
# citation list import views
importMedline = Instance(CiteImport)
importEmbase = Instance(CiteImport)
importScopus = Instance(CiteImport)
importOther1 = Instance(CiteImport)
importOther2 = Instance(CiteImport)
importOther3 = Instance(CiteImport)
importOther4 = Instance(CiteImport)
_importAddBtn = Button('Add Sheet')
# extractor drop-downs
_extractorNames = Instance(TraitsList)
_extractorAddBtn = Button('Add Extractor')
# button to find overlaps and progress bar
_overlapBtn = Button('Find Overlaps')
_progBarPct = Int(0)
_progBarMsg = Str('Awaiting overlaps')
# table export
_exportBtn = Button('Export Tables')
_exportSep = Str
_exportSepNames = Instance(TraitsList)
_statusBarMsg = Str
# HELP PANEL TRAITS
pkgDir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
docsDir = os.path.join(pkgDir, "docs")
if getattr(sys, "frozen", False) and hasattr(sys, "_MEIPASS"):
# detect frozen env using the PyInstaller-specific attributes
# (currently works even without this setting through symlinks)
docsDir = os.path.realpath(os.path.join(sys._MEIPASS, "docs"))
with open(os.path.join(docsDir, "sidebar.html"), mode="r") as help_file:
helpMsg = "".join(help_file.readlines())
_helpHtml = HTML(helpMsg)
# SHEETS TRAITS
# counter for number of "other citation" sheets
_numCitOther = Int(0)
_tabularArgs = {
'editable': True,
'auto_resize_rows': True,
'stretch_last_section': False
}
# Import view groups, which need an adapter set here to avoid sharing
# the adapter across view instances
# MEDLINE table
_medlineAdapter = TableArrayAdapter()
_medlineTable = TabularEditor(adapter=_medlineAdapter, **_tabularArgs)
_medline = CiteSheet(adapter=_medlineAdapter)
# Embase table
_embaseAdapter = TableArrayAdapter()
_embaseTable = TabularEditor(adapter=_embaseAdapter, **_tabularArgs)
_embase = CiteSheet(adapter=_embaseAdapter)
# Scopus table
_scopusAdapter = TableArrayAdapter()
_scopusTable = TabularEditor(adapter=_scopusAdapter, **_tabularArgs)
_scopus = CiteSheet(adapter=_scopusAdapter)
# Other 1 table
_citOther1Adapter = TableArrayAdapter()
_citOther1Table = TabularEditor(adapter=_citOther1Adapter, **_tabularArgs)
_citOther1 = CiteSheet(adapter=_citOther1Adapter)
# Other 2 table
_citOther2Adapter = TableArrayAdapter()
_citOther2Table = TabularEditor(adapter=_citOther2Adapter, **_tabularArgs)
_citOther2 = CiteSheet(adapter=_citOther2Adapter)
# Other 3 table
_citOther3Adapter = TableArrayAdapter()
_citOther3Table = TabularEditor(adapter=_citOther3Adapter, **_tabularArgs)
_citOther3 = CiteSheet(adapter=_citOther3Adapter)
# Other 4 table
_citOther4Adapter = TableArrayAdapter()
_citOther4Table = TabularEditor(adapter=_citOther4Adapter, **_tabularArgs)
_citOther4 = CiteSheet(adapter=_citOther4Adapter)
# Overlaps output table
_overlapsAdapter = TableArrayAdapter()
_outputTable = TabularEditor(adapter=_overlapsAdapter, **_tabularArgs)
_overlaps = CiteSheet(adapter=_overlapsAdapter)
# TRAITUI WIDGETS
# controls panel
_controlsPanel = VGroup(
VGroup(
Item('importMedline', show_label=False, style='custom'),
Item('importEmbase', show_label=False, style='custom'),
Item('importScopus', show_label=False, style='custom'),
Item('importOther1',
show_label=False,
style='custom',
visible_when='_numCitOther >= 1'),
Item('importOther2',
show_label=False,
style='custom',
visible_when='_numCitOther >= 2'),
Item('importOther3',
show_label=False,
style='custom',
visible_when='_numCitOther >= 3'),
Item('importOther4',
show_label=False,
style='custom',
visible_when='_numCitOther >= 4'),
HGroup(
Item('_importAddBtn',
show_label=False,
springy=True,
enabled_when='_numCitOther <= object._DEFAULT_NUM_IMPORTS'
),
Item('_extractorAddBtn', show_label=False, springy=True),
),
label='Load Citation Files',
),
VGroup(
HGroup(Item('_overlapBtn', show_label=False, springy=True), ),
Item('_progBarPct',
show_label=False,
editor=ProgressEditor(min=0,
max=100,
message_name='_progBarMsg')),
HGroup(
Item('_exportBtn', show_label=False, springy=True),
Item("_exportSep",
label="Separator",
editor=CheckListEditor(
name="object._exportSepNames.selections")),
),
label='Detect Overlapping Citations',
),
label="Import",
)
# help panel
_helpPanel = VGroup(
Item("_helpHtml",
editor=HTMLEditor(format_text=True),
show_label=False),
label="Help",
)
# tabbed panel for sidebar
_sidebarTabs = Tabbed(
_controlsPanel,
_helpPanel,
)
# Tabbed viewers of tables
# WORKAROUND: Because of an apparent limitation in adding tabs dynamically
# in TraitsUI (https://github.com/enthought/traitsui/pull/1456), separate
# views are created and toggled depending on the number of "other" sheets,
# toggled by the "visible_when" flag
# default tabbed viewer
_tableView1 = Tabbed(
Item('object._medline.data',
editor=_medlineTable,
show_label=False,
width=1000),
Item('object._embase.data', editor=_embaseTable, show_label=False),
Item('object._scopus.data', editor=_scopusTable, show_label=False),
Item('object._overlaps.data', editor=_outputTable, show_label=False),
visible_when='_numCitOther == 0',
)
# tabbed viewer of tables with one "other" sheet
_tableView2 = Tabbed(
Item('object._medline.data',
editor=_medlineTable,
show_label=False,
width=1000),
Item('object._embase.data', editor=_embaseTable, show_label=False),
Item('object._scopus.data', editor=_scopusTable, show_label=False),
Item('object._citOther1.data',
editor=_citOther1Table,
show_label=False),
Item('object._overlaps.data', editor=_outputTable, show_label=False),
visible_when='_numCitOther == 1',
)
# tabbed viewer of tables with two "other" sheets
_tableView3 = Tabbed(
Item('object._medline.data',
editor=_medlineTable,
show_label=False,
width=1000),
Item('object._embase.data', editor=_embaseTable, show_label=False),
Item('object._scopus.data', editor=_scopusTable, show_label=False),
Item('object._citOther1.data',
editor=_citOther1Table,
show_label=False),
Item('object._citOther2.data',
editor=_citOther2Table,
show_label=False),
Item('object._overlaps.data', editor=_outputTable, show_label=False),
visible_when='_numCitOther == 2',
)
# tabbed viewer of tables with three "other" sheets
_tableView4 = Tabbed(
Item('object._medline.data',
editor=_medlineTable,
show_label=False,
width=1000),
Item('object._embase.data', editor=_embaseTable, show_label=False),
Item('object._scopus.data', editor=_scopusTable, show_label=False),
Item('object._citOther1.data',
editor=_citOther1Table,
show_label=False),
Item('object._citOther2.data',
editor=_citOther2Table,
show_label=False),
Item('object._citOther3.data',
editor=_citOther2Table,
show_label=False),
Item('object._overlaps.data', editor=_outputTable, show_label=False),
visible_when='_numCitOther == 3',
)
# tabbed viewer of tables with four "other" sheets
_tableView5 = Tabbed(
Item('object._medline.data',
editor=_medlineTable,
show_label=False,
width=1000),
Item('object._embase.data', editor=_embaseTable, show_label=False),
Item('object._scopus.data', editor=_scopusTable, show_label=False),
Item('object._citOther1.data',
editor=_citOther1Table,
show_label=False),
Item('object._citOther2.data',
editor=_citOther2Table,
show_label=False),
Item('object._citOther3.data',
editor=_citOther2Table,
show_label=False),
Item('object._citOther4.data',
editor=_citOther2Table,
show_label=False),
Item('object._overlaps.data', editor=_outputTable, show_label=False),
visible_when='_numCitOther == 4',
)
# main view
view = View(
HSplit(
_sidebarTabs,
# only one table view should be displayed at a time
Group(
_tableView1,
_tableView2,
_tableView3,
_tableView4,
_tableView5,
),
),
width=1300, # also influenced by _tableView width
height=800,
title='Citation Overlap',
resizable=True,
handler=CiteOverlapHandler(),
statusbar="_statusBarMsg")
def __init__(self):
"""Initialize the GUI."""
super().__init__()
# set up import views
self.importMedline = CiteImport(sheet=self._medline)
self.importEmbase = CiteImport(sheet=self._embase)
self.importScopus = CiteImport(sheet=self._scopus)
self.importOther1 = CiteImport(sheet=self._citOther1)
self.importOther2 = CiteImport(sheet=self._citOther2)
self.importOther3 = CiteImport(sheet=self._citOther3)
self.importOther4 = CiteImport(sheet=self._citOther4)
self.importViews = (
self.importMedline,
self.importEmbase,
self.importScopus,
self.importOther1,
self.importOther2,
self.importOther3,
self.importOther4,
)
# populate drop-down of available extractors from directory of
# extractors, displaying only basename but keeping dict with full path
extractor_paths = []
for extractor_dir in config.extractor_dirs:
extractor_paths.extend(glob.glob(str(extractor_dir / "*")))
self._extractor_paths = {
os.path.basename(f): f
for f in extractor_paths
}
self._updateExtractorNames(True)
for importer in self.importViews:
importer.observe(self.renameTabEvent, "extractor")
importer.observe(self.importFile, "path")
importer.observe(self.clearSheet, "clearBtn")
# populate drop-down of separators/delimiters
self._exportSepNames = TraitsList()
self._exportSepNames.selections = list(self._EXPORT_SEPS.keys())
self._exportSep = self._exportSepNames.selections[0]
# extractor and overlaps thread instances
self.dbExtractor = extractor.DbExtractor()
self._overlapsThread = None
# last opened directory
self._save_dir = None
def _updateExtractorNames(self, reset=False):
"""Update the list of extractor names shown in the combo boxes.
Args:
reset (bool): True to reset to default selections; defaults to
False.
"""
if reset:
# pick default selections for each extractor
selections = [e.value for e in extractor.DefaultExtractors]
numExtra = len(self.importViews) - len(selections)
if numExtra > 0:
selections.extend([self._DEFAULT_EXTRACTOR] * numExtra)
else:
# keep current selections
selections = [v.extractor for v in self.importViews]
# update combo box from extractor path keys
self._extractorNames = TraitsList()
extractorNames = [self._DEFAULT_EXTRACTOR]
extractorNames.extend(self._extractor_paths.keys())
self._extractorNames.selections = extractorNames
# assign default extractor selections
for view, selection in zip(self.importViews, selections):
view.extractorNames = self._extractorNames
view.extractor = selection
def renameTabEvent(self, event):
"""Handler to rename a spreadsheet tab.
Args:
event (:class:`traits.observation.events.TraitChangeEvent`): Event.
"""
self.renameSheetTab = self.importViews.index(event.object)
self.renameSheetName = _displayExtractor(event.object.extractor)
def clearSheet(self, event):
"""Clear the sheet associated with an import view.
Args:
event (:class:`traits.observation.events.TraitChangeEvent`): Event.
"""
event.object.sheet.data = np.empty((0, 0))
del self.dbExtractor.dbsParsed[event.object.dbName]
event.object.path = ''
@staticmethod
def _df_to_cols(df):
"""Convert a data frame to table columns with widths adjusted to
fit the column width up to a given max amount.
Args:
df (:obj:`pd.DataFrame`): Data frame to enter into table.
Returns:
dict[int, int], list[(str, Any)], :obj:`np.ndarray`: Dictionary of
column indices to width, list of column tuples given as
``(col_name, col_ID)``, and data frame as a Numpy arry.
"""
colWidths = []
colsIDs = []
for i, col in enumerate(df.columns.values.tolist()):
# get widths of all rows in column as well as header
colWidth = df[col].astype(str).str.len().tolist()
colWidth.append(len(col))
colWidths.append(colWidth)
# use index as ID except for group/sub-group, where using a string
# allows the col along with row to be accessed for individual cells
colID = col.lower() if col in ('Group', 'Subgrp') else i
colsIDs.append((col, colID))
# get max width for each col, taking log to slow the width increase
# for wider strings and capping at a max width
widths = {
i: min((math.log1p(max(c)) * 40, TableArrayAdapter.MAX_WIDTH))
for i, c in enumerate(colWidths)
}
return widths, colsIDs, df.to_numpy()
@on_trait_change('_importAddBtn')
def addImport(self):
"""Add import fields and a new sheet."""
if self._numCitOther < len(
self.importViews) - self._DEFAULT_NUM_IMPORTS:
# trigger additional import view and tab with new sheet
self._numCitOther += 1
@on_trait_change('_extractorAddBtn')
def addExtractor(self):
"""Add an extractor to the combo box."""
try:
# get path to extractor from file dialog
path = self._getFileDialogPath()
except FileNotFoundError:
return
# update combo box
pathName = os.path.basename(path)
self._extractor_paths[pathName] = path
self._updateExtractorNames()
def importFile(self, event):
"""Import a database file.
Args:
event (:class:`traits.observation.events.TraitChangeEvent`): Event.
Returns:
:obj:`pd.DataFrame`: Data frame of extracted file.
"""
path = event.object.path
if not os.path.exists(path):
if path:
# file inaccessible, or manually edited, non-accessible path
self._statusBarMsg = f'{path} could not be found, skipping'
return None
self._save_dir = os.path.dirname(path)
try:
# extract file
extractorPath = self._extractor_paths[event.object.extractor]
df, dbName = self.dbExtractor.extractDb(path, extractorPath)
event.object.dbName = dbName
try:
self.dbExtractor.checkExtraction(df)
self._statusBarMsg = f'Imported file from {path}'
except SyntaxWarning as e:
msg = \
f'WARNING: {str(e)}. Please check the selected file ' \
f'source and reload the citation file.'
self._statusBarMsg = msg
_logger.warning(msg)
sheet = event.object.sheet
if df is not None and sheet is not None:
# output data frame to associated table
sheet.adapter._widths, sheet.adapter.columns, sheet.data = \
self._df_to_cols(df)
self.selectSheetTab = self.importViews.index(event.object)
return df
except (FileNotFoundError, SyntaxError) as e:
self._statusBarMsg = str(e)
return None
def _updateProgBar(self, pct: int, msg: str):
""""Update progress bar.
Args:
pct: Percentage complete, from 0-100.
msg: Message to display.
"""
self._progBarPct = pct
self._progBarMsg = msg
def _overlapsHandler(self, result: Union[pd.DataFrame, str]):
"""Handle result from finding overlaps.
Args:
result: Data frame of overlaps or message.
"""
if isinstance(result, pd.DataFrame):
self._progBarPct = 100
if result is None:
# clear any existing data in sheet if no citation lists
self._overlaps.data = np.empty((0, 0))
self._statusBarMsg = 'No citation lists found'
return
# populate overlaps sheet
self._overlaps.adapter._widths, self._overlaps.adapter.columns, \
self._overlaps.data = self._df_to_cols(result)
self.selectSheetTab = self._DEFAULT_NUM_IMPORTS + self._numCitOther
self._statusBarMsg = 'Found overlaps across databases'
elif isinstance(result, str):
# show message
self._statusBarMsg = result
@on_trait_change('_overlapBtn')
def findOverlaps(self):
"""Find overlaps in a thread."""
self._progBarPct = 0
self._overlapsThread = overlaps_thread.OverlapsThread(
self.dbExtractor, self._overlapsHandler, self._updateProgBar)
self._overlapsThread.start()
def _getFileDialogPath(self, default_path='', mode='open'):
"""Get a path from the user through a file dialog.
Args:
default_path (str): Initial path to display in the dialog; defaults
to an emptry string. If :attr:`_save_dir` is set,
``default_path`` will be joined to the save directory.
mode (str): "open" for an open dialog, or "save as" for a save
dialog.
Returns:
str: Chosen path.
Raises:
FileNotFoundError: User canceled file selection.
"""
if self._save_dir:
# use directory of last chosen import file
default_path = os.path.join(self._save_dir, default_path)
# open a PyFace file dialog in save mode
save_dialog = FileDialog(action=mode, default_path=default_path)
if save_dialog.open() == OK:
# get user selected path
return save_dialog.path
else:
# user canceled file selection
raise FileNotFoundError("User canceled file selection")
@on_trait_change('_exportBtn')
def exportTables(self):
"""Export tables to a files."""
self.dbExtractor.saveSep = self._EXPORT_SEPS[self._exportSep]
try:
# prompt user to select an output file path for the combined list;
# save along with filtered folders in a separate dir there
save_path = self._getFileDialogPath(
self.dbExtractor.DEFAULT_OVERLAPS_PATH, "save as")
self.dbExtractor.exportDataFrames(save_path)
self._statusBarMsg = (
f'Saved combined table to "{save_path}" and filtered tables '
f'alongside in "{self.dbExtractor.DEFAULT_CLEANED_DIR_PATH}"')
except FileNotFoundError:
print("Skipping file save")
return len(self.resources) > 0
def get_children(self):
return self.resources
# -------------------------------------------------------------------------
# Defines the demo tree editor:
# -------------------------------------------------------------------------
demo_path_view = View(
UItem(
"description",
style="readonly",
editor=HTMLEditor(
format_text=True,
base_url_name='base_url',
),
),
id="demo_path_view",
kind='subpanel',
)
demo_file_view = View(
HSplit(
UItem(
"description",
style="readonly",
editor=HTMLEditor(
format_text=True,
base_url_name='base_url',
open_externally=True,
class MainWindow(HasTraits):
title = String()
date = String()
category = Enum(['nus', 'travel', 'pics', 'food'])
dirpath = Directory()
codedir = Directory()
html_text = String('')
status = String('no connection')
ftp_url = String('files.000webhost.com')
ftp_user = String('maxinsingapore')
ftp_dir = String('public_html/pictures')
ftp_pw = String()
upload_btn = Button('Upload')
html_preview = HTML()
preview_btn = Button('HTML preview')
uploadthread = Instance(UploadThread)
notuploading = Bool(True)
html_intro_1 = '''<!DOCTYPE html><html><head><link href="main.css" rel="stylesheet"/>
<title>Max in Singapore</title>
</head>
<body>
<?php require("ground.php"); ?>
<div class = "title">
<a href="'''
html_intro_2 = '''.php"><figure><p>back</p</figure></a>
</div>
<div class="center">'''
html_end = ''' </div>
</div>
</div>
</body>
</html>'''
traits_view = View(
HGroup('ftp_url', 'ftp_user', 'ftp_pw', 'ftp_dir'),
HGroup('title', 'date', 'category'),
HGroup(Item('html_text', editor=CodeEditor()),
Item('html_preview', editor=HTMLEditor())), 'preview_btn',
Item('dirpath', label='Photo Directory'),
Item('codedir', label='Code Directory'),
Item('status', style='readonly'),
Item('upload_btn', enabled_when='notuploading'))
def _preview_btn_fired(self):
html_intro = self.html_intro_1 + self.category + self.html_intro_2
self.html_preview = html_intro + self.html_text + self.html_end
def _upload_btn_fired(self):
if self.dirpath != '' and self.codedir != '':
self.notuploading = False
self.uploadthread = UploadThread()
self.uploadthread.wants_abort = False
self.uploadthread.master = self
self.uploadthread.start()
else:
self.status = "choose directories"
if ext == '.py':
return True
return False
#-------------------------------------------------------------------------------
# Defines the demo tree editor:
#-------------------------------------------------------------------------------
path_view = View(
Tabbed(
Item( 'description',
label = 'Description',
show_label = False,
style = 'readonly',
editor=HTMLEditor(format_text=True)
),
Item( 'source',
label = 'Source',
show_label = False,
style = 'custom'
),
export = 'DockWindowShell',
id = 'tabbed'
),
id = 'traitsui.demos.demo.path_view',
#dock = 'horizontal'
)
demo_view = View(
#VSplit(
def html_editor():
""" Factory function for an "editor" that displays a multi-line string as
interpreted HTML.
"""
from traitsui.api import HTMLEditor
return HTMLEditor()