def set_dataset(self, data=None):
self.closeContext()
self.clear()
self.Error.clear()
# print(data)
if data:
self.input_data = data
self.tax_id = data.attributes[TableAnnotation.tax_id]
self.use_attr_names = data.attributes[
TableAnnotation.gene_as_attr_name]
if self.use_attr_names:
self.gene_id_attribute = data.attributes[
TableAnnotation.gene_id_attribute]
else:
self.gene_id_column = data.attributes[
TableAnnotation.gene_id_column]
self.annotation_index = None
_c2i = {
a.taxid: i
for i, a in enumerate(self.available_annotations)
}
try:
self.annotation_index = _c2i[self.tax_id]
except KeyError:
self.Error.serverfiles_unavailable()
# raise ValueError('Taxonomy {} not supported.'.format(self.tax_id))
return
self.gene_info = gene.GeneInfo(self.tax_id)
self.__invalidate()
def test_gene_info(self):
ncbi_id = 6331
organism = '9606'
gene_info_obj = gene.GeneInfo(organism)
gene_info = gene_info_obj.get_gene_by_id(ncbi_id)
self.assertIsNone(gene_info.input_name)
for tag in gene.GENE_INFO_TAGS:
self.assertIsNotNone(getattr(gene_info, tag))
def handle_genes_input(self, data):
self.Error.clear()
self.__reset_widget_state()
# clear output
self.Outputs.matched_genes.send(None)
# clear input values
self.input_genes = []
self.input_data = None
self.tax_id = None
self.use_attr_names = None
self.gene_id_attribute = None
self.gs_widget.clear()
self.gs_widget.clear_gene_sets()
self.update_info_box()
if data:
self.input_data = data
self.tax_id = str(self.input_data.attributes.get(TAX_ID, None))
self.use_attr_names = self.input_data.attributes.get(
GENE_AS_ATTRIBUTE_NAME, None)
self.gene_id_attribute = self.input_data.attributes.get(
GENE_ID_ATTRIBUTE, None)
self.gene_id_column = self.input_data.attributes.get(
GENE_ID_COLUMN, None)
self.update_info_box()
if not (self.use_attr_names is not None and
((self.gene_id_attribute is None) ^
(self.gene_id_column is None))):
if self.tax_id is None:
self.Error.missing_annotation()
return
self.Error.missing_gene_id()
return
elif self.tax_id is None:
self.Error.missing_tax_id()
return
if self.__check_organism_mismatch():
self.Error.organism_mismatch()
return
self.gs_widget.load_gene_sets(self.tax_id)
self.gene_info = gene.GeneInfo(self.tax_id)
# if input data change, we need to refresh custom sets
if self.custom_data:
self.gs_widget.clear_custom_sets()
self.handle_custom_gene_sets()
self.invalidate()
def set_dataset(self, data=None):
self.closeContext()
self.clear()
self.Error.clear()
if data:
self.input_data = data
self.tax_id = str(self.input_data.attributes.get(TAX_ID, None))
self.use_attr_names = self.input_data.attributes.get(
GENE_AS_ATTRIBUTE_NAME, None)
self.gene_id_attribute = self.input_data.attributes.get(
GENE_ID_ATTRIBUTE, None)
self.gene_id_column = self.input_data.attributes.get(
GENE_ID_COLUMN, None)
self.annotation_index = None
if not (self.use_attr_names is not None and
((self.gene_id_attribute is None) ^
(self.gene_id_column is None))):
if self.tax_id is None:
self.Error.missing_annotation()
return
self.Error.missing_gene_id()
return
elif self.tax_id is None:
self.Error.missing_tax_id()
return
_c2i = {
a.taxid: i
for i, a in enumerate(self.available_annotations)
}
try:
self.annotation_index = _c2i[self.tax_id]
except KeyError:
self.Error.serverfiles_unavailable()
# raise ValueError('Taxonomy {} not supported.'.format(self.tax_id))
return
self.gene_info = gene.GeneInfo(self.tax_id)
self.__invalidate()
def get_ncbi_info(taxid):
return gene.GeneInfo(taxid)