def update_hierarchy(self):
"""
TODO!!! requires the logging methods!!!
this method accepts only the final taxon list
where all we need to check if the consecutive
taxa has a child-parent relationship. if not
set the relationshp.
"""
if sorted([tax.level for tax in self.lineage.taxon_list]) != sorted(self.lineage.default_levels):
raise Exception("Required taxonomic levels are not satisfied yet.")
for i in range(len(self.lineage.taxon_list)-1):
child_tax= self.lineage.taxon_list[i]
parent_tax= self.lineage.taxon_list[i+1]
#try:
hier= self.lineage.biodb_selector.store.find(Hierarchy, Hierarchy.childID == child_tax.taxon.id ).one()
#except:
# continue
if hier.parent.id != parent_tax.taxon.id:
new_hier= Hierarchy()
new_hier.parentID= parent_tax.taxon.id
new_hier.childID= child_tax.taxon.id
self.lineage.biodb_selector.store.remove(hier)
self.lineage.biodb_selector.store.add(new_hier)
child_id= child_tax.taxon.id
old_parent_id= hier.parentID
new_parent_id= parent_tax.taxon.id
#self.logger.error("child id: %d, old parent id: %d, new parent id: %d" %(child_id, old_parent_id, new_parent_id))
#self.logger.error("child name: %s, old parent name: %s, new parent name: %s" %(child_tax.taxon.name, hier.parent.name, parent_tax.taxon.name))
### DONT FORGET TO COMMIT
self.lineage.biodb_selector.store.commit()