def clear_taxonomic_coverage(package_name):
# When user selects Clear Taxonomic Coverage to get rid of coverage imported from XML, we delete it and
# set the flag that says its OK for ezEML to handle even though the package was imported from XML.
eml_node = load_eml(filename=package_name)
coverage_node = eml_node.find_single_node_by_path([names.DATASET, names.COVERAGE])
if coverage_node:
taxonomic_coverage_nodes = coverage_node.find_all_children(names.TAXONOMICCOVERAGE)
for taxonomic_coverage_node in taxonomic_coverage_nodes:
coverage_node.remove_child(taxonomic_coverage_node)
Node.delete_node_instance(taxonomic_coverage_node.id)
clear_taxonomy_imported_from_xml(eml_node, package_name)
def expand(node: Node):
references = list()
node.find_all_descendants(names.REFERENCES, references)
ids = _register_ids(node)
for reference in references:
if reference.content not in ids:
msg = f"ID not found for REFERENCE '{reference}'"
raise ValueError(msg)
source_node = ids[reference.content]
destination_node = reference.parent
destination_node.remove_child(reference)
Node.delete_node_instance(reference.id)
for source_child in source_node.children:
source_child_copy = source_child.copy()
destination_node.add_child(source_child_copy)
def test_delete_node_no_children(self):
eml = Node(names.EML)
eml.add_attribute('packageId', 'edi.23.1')
eml.add_attribute('system', 'metapype')
access = Node(names.ACCESS, parent=eml)
access.add_attribute('authSystem', 'pasta')
access.add_attribute('order', 'allowFirst')
eml.add_child(access)
allow = Node(names.ALLOW, parent=access)
access.add_child(allow)
principal = Node(names.PRINCIPAL, parent=allow)
principal.content = 'uid=gaucho,o=EDI,dc=edirepository,dc=org'
allow.add_child(principal)
permission = Node(names.PERMISSION, parent=allow)
permission.content = 'all'
allow.add_child(permission)
node = Node.get_node_instance(principal.id)
self.assertIs(principal, node)
Node.delete_node_instance(eml.id, children=False)
self.assertIn(principal.id, Node.store)
def test_delete_node_no_children():
eml = Node(names.EML)
eml.add_attribute("packageId", "edi.23.1")
eml.add_attribute("system", "metapype")
access = Node(names.ACCESS, parent=eml)
access.add_attribute("authSystem", "pasta")
access.add_attribute("order", "allowFirst")
eml.add_child(access)
allow = Node(names.ALLOW, parent=access)
access.add_child(allow)
principal = Node(names.PRINCIPAL, parent=allow)
principal.content = "uid=gaucho,o=EDI,dc=edirepository,dc=org"
allow.add_child(principal)
permission = Node(names.PERMISSION, parent=allow)
permission.content = "all"
allow.add_child(permission)
node = Node.get_node_instance(principal.id)
assert principal is node
Node.delete_node_instance(eml.id, children=False)
assert principal.id in Node.store
def prune(n: Node, strict: bool = False) -> list:
"""
Prune in place all non-valid nodes from the tree
Args:
n: Node
strict:
Returns: List of pruned nodes
Side-effects: Non-valid nodes are pruned from the tree
"""
pruned = list()
if n.name != "metadata":
try:
node(n)
except UnknownNodeError as ex:
logger.debug(f"Pruning: {n.name}")
pruned.append((n, str(ex)))
if n.parent is not None:
n.parent.remove_child(n)
Node.delete_node_instance(n.id)
return pruned
except ChildNotAllowedError as ex:
r = rule.get_rule(n.name)
children = n.children.copy()
for child in children:
if not r.is_allowed_child(child.name):
logger.debug(f"Pruning: {child.name}")
pruned.append((child, str(ex)))
n.remove_child(child)
Node.delete_node_instance(child.id)
except MetapypeRuleError as ex:
logger.info(ex)
children = n.children.copy()
for child in children:
pruned += prune(child, strict)
if strict and child not in pruned:
try:
node(child)
except MetapypeRuleError as ex:
logger.debug(f"Pruning: {child.name}")
pruned.append((child, str(ex)))
n.remove_child(child)
Node.delete_node_instance(child.id)
return pruned