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added validation: reject leaf nodes named 'root' #11

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Oct 30, 2019
Merged

added validation: reject leaf nodes named 'root' #11

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26 changes: 15 additions & 11 deletions Docker/validate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,16 +10,21 @@

def valid_leaf_names(tree, gs_tree):
"""Check that prediction tree uses correct leaf labels."""
root_taxon_exists = tree.find_node_with_taxon_label('root')

valid_names = set([t.label for t in gs_tree.taxon_namespace])
valid = False
valid_names = [t.label for t in gs_tree.taxon_namespace]
unique_names = set(valid_names)

root_taxon_exists = tree.find_node_with_taxon_label('root')
if root_taxon_exists:
valid_names.add('root')
submission_names = set([t.label for t in tree.taxon_namespace])
intersect = valid_names.intersection(submission_names)
all_exist = len(intersect) == len(valid_names)
unique_names.add('root')

if len(valid_names) == len(unique_names):
submission_names = set([t.label for t in tree.taxon_namespace])
intersect = unique_names.intersection(submission_names)
valid = len(intersect) == len(unique_names)

return all_exist
return valid


def validate_tree(pred_tree, gs_tree):
Expand All @@ -39,9 +44,9 @@ def validate_tree(pred_tree, gs_tree):
invalid_errors.append("Prediction tree must contain 'root' node")

if not valid_leaf_names(pred_tree, gs_tree):
invalid_errors.append("Prediction tree must contain all the cell "
"identifiers, a 'root' node and must have "
f"{len(gs_tree.taxon_namespace)} cell lines")
invalid_errors.append("Prediction tree must have a single 'root' node, "
f"use the correct identifier names, and contain "
f"{len(gs_tree.taxon_namespace):,} cell lines.")
return invalid_errors


Expand All @@ -55,7 +60,6 @@ def main(submission, entity_type, goldstandard, results):
"""

invalid_reasons = []
root_exists = False
gs_tree = dendropy.Tree.get(file=open(goldstandard, 'r'),
schema="newick",
tree_offset=0)
Expand Down