class FileUploadHelper(QDialog):
# settings
kegg_domain = 'KEGG'
supported_domains = OrderedDict({
'Gene Ontology': gene_ontology_domain,
'Gene Sets': gene_sets_domain
})
supported_organisms = [
common_taxid_to_name(tax_id) for tax_id in common_taxids()
]
hierarchies = {
'GO - Biological Process': ('GO', 'biological_process'),
'GO - Molecular Function': ('GO', 'molecular_function'),
'GO - Cellular Component': ('GO', 'cellular_component'),
'KEGG - Pathways': ('KEGG', 'pathways'),
'KEGG - Orthologs': ('KEGG', 'orthologs')
}
def __init__(self, parent=None):
super(FileUploadHelper, self).__init__(
parent, Qt.Window | Qt.WindowTitleHint | Qt.CustomizeWindowHint
| Qt.WindowCloseButtonHint | Qt.WindowMaximizeButtonHint)
self.setAttribute(Qt.WA_DeleteOnClose)
self.setWindowTitle('Add new file')
self.info_state = INFO_FILE_SCHEMA
self.layout = QVBoxLayout(self)
# domain selection combobox
self.domain_selection = QComboBox()
self.domain_selection.addItems(self.supported_domains.keys())
self.domain_selection.currentIndexChanged.connect(
self.__on_domain_selection)
self.__create_selection_row('Domain: ', self.domain_selection)
# domain selection combobox
self.hierarchy_selection = QComboBox()
self.hierarchy_selection.addItems(self.hierarchies.keys())
self.layout.addWidget(self.hierarchy_selection,
alignment=Qt.AlignVCenter)
self.__on_domain_selection()
# select organism
self.organism_selection = QComboBox()
self.organism_selection.addItems(self.supported_organisms)
self.__create_selection_row('Organism: ', self.organism_selection)
# title
self.line_edit_title = QLineEdit()
self.__create_selection_row('Title: ', self.line_edit_title)
# tags
self.line_edit_tags = QLineEdit()
self.__create_selection_row('Tags (comma-separated): ',
self.line_edit_tags)
# file selector
self.file_info = QLabel()
self.file_select_btn = QPushButton('Select File', self)
self.file_select_btn.clicked.connect(self.__handle_file_selector)
self.__create_selection_row(' ', self.file_select_btn)
# add file info section
self.layout.addWidget(self.file_info, alignment=Qt.AlignCenter)
self.layout.addStretch(1)
# Ok and Cancel buttons
self.buttons = QDialogButtonBox(
QDialogButtonBox.Ok | QDialogButtonBox.Cancel, Qt.Horizontal, self)
self.layout.addWidget(self.buttons, alignment=Qt.AlignJustify)
self.buttons.accepted.connect(self.__accept)
self.buttons.rejected.connect(self.__close)
# path to a selected file
self.file_path = None
def __on_domain_selection(self):
selected = self.__get_selected_domain() == gene_sets_domain
self.hierarchy_selection.setVisible(selected)
def __get_selected_domain(self):
domain_label = list(self.supported_domains.keys())[
self.domain_selection.currentIndex()]
return self.supported_domains[domain_label]
def __get_selected_hier(self):
hier_label = list(
self.hierarchies.keys())[self.hierarchy_selection.currentIndex()]
return self.hierarchies[hier_label]
def __create_selection_row(self, label, widget):
self.layout.addWidget(QLabel(label), alignment=Qt.AlignLeft)
self.layout.addWidget(widget, alignment=Qt.AlignVCenter)
def __accept(self):
if self.file_path:
self.info_state = self.__parse_selection()
self.__move_to_serverfiles_folder(self.file_path)
self.parent().initialize_files_view()
self.close()
def __close(self):
self.close()
def closeEvent(self, event):
# clean-up
self.parent()._dialog = None
def __filename(self, domain, organism):
""" Create filename based od domain name and organism.
"""
if domain in self.supported_domains.values(
) and domain == gene_ontology_domain and organism:
return FILENAME_ANNOTATION.format(organism)
elif domain in self.supported_domains.values(
) and domain == gene_sets_domain and organism:
return filename((self.__get_selected_hier()), organism)
def __parse_selection(self):
try:
domain = self.__get_selected_domain()
organism = taxname_to_taxid(self.supported_organisms[
self.organism_selection.currentIndex()])
except KeyError as e:
raise e
return {
'domain': domain,
'organism': organism,
'filename': self.__filename(domain, organism),
'title': self.line_edit_title.text(),
'tags': self.line_edit_tags.text().split(','),
'source': SOURCE_USER
}
def __move_to_serverfiles_folder(self, selected_file_path):
domain_path = serverfiles.localpath(self.info_state['domain'])
file_path = os.path.join(domain_path, self.info_state['filename'])
create_folder(domain_path)
try:
copyfile(selected_file_path, file_path)
except IOError as e:
# TODO: handle error properly
raise e
# if copy successful create .info file
create_info_file(file_path, **self.info_state)
def __handle_file_selector(self):
self.file_path = QFileDialog.getOpenFileName(self, 'Open File')[0]
self.file_info.setText('Selected File: {}'.format(
os.path.basename(self.file_path)))
