"""
Reproduction: vanilla BioCypher corrupts already-written part files when a later
batch of the same node type introduces a new property.

Run:
    pip install biocypher
    python reproduce_header_misalignment.py

Tested against BioCypher 0.15.1. Self-contained: writes its own config files
into a temp dir, needs no Neo4j (offline CSV writer only).

Background
----------
MeDaX ingests data in successive batches and extends the schema on the fly:
when a node/edge type or attribute first appears, it is added to the schema so
no information is dropped. BioCypher's Neo4j batch writer rewrites the *header*
file on every write_nodes() call, but leaves the *part files already on disk*
untouched. As soon as a new attribute widens/reorders the header, the rows in
earlier part files no longer line up with it -> silent column misalignment on
neo4j-admin import.

Exact location upstream:
    biocypher/output/write/graph/_neo4j.py
    _Neo4jBatchWriter._write_node_headers()   (and ._write_edge_headers())
    -> the `if os.path.exists(header_path): logger.warning("... Overwriting.")`
       branch rewrites the header but never reconciles existing -part*.csv files.
"""

import glob
import os
import sys
import tempfile

from biocypher import BioCypher

workdir = tempfile.mkdtemp(prefix="bc_repro_")
os.chdir(workdir)

with open("schema_config.yaml", "w") as fh:
    fh.write(
        "patient:\n"
        "  represented_as: node\n"
        "  input_label: patient\n"
        "  is_a: entity\n"  # no fixed `properties:` -> inferred from data per batch
    )

with open("biocypher_config.yaml", "w") as fh:
    fh.write(
        "biocypher:\n"
        "  dbms: neo4j\n"
        "  offline: true\n"
        "  strict_mode: false\n"
        "  schema_config_path: schema_config.yaml\n"
        "  head_ontology:\n"
        "    url: https://raw.githubusercontent.com/biolink/biolink-model/v3.2.1/biolink-model.owl.ttl\n"
        "    root_node: entity\n"
    )

bc = BioCypher(
    biocypher_config_path="biocypher_config.yaml",
    schema_config_path="schema_config.yaml",
    output_directory="out",
)

# Batch 1: patients described by {name, age}
bc.write_nodes(
    [
        ("p1", "patient", {"name": "Alice", "age": 30}),
        ("p2", "patient", {"name": "Bob", "age": 41}),
    ],
    force=True,
)

# Batch 2: same node type, now with an extra `diagnosis` attribute.
bc.write_nodes(
    [("p3", "patient", {"name": "Carol", "age": 52, "diagnosis": "E11"})],
    force=True,
)

# --- Inspect what ended up on disk -----------------------------------------
header_path = "out/Patient-header.csv"
header_cols = open(header_path).read().strip().split(";")
n_header = len(header_cols)

print("HEADER :", header_cols, f"({n_header} columns)")
ok = True
for part in sorted(glob.glob("out/Patient-part*.csv")):
    for row in open(part).read().splitlines():
        n_row = len(row.split(";"))
        flag = "" if n_row == n_header else "  <-- MISALIGNED"
        if n_row != n_header:
            ok = False
        print(f"{os.path.basename(part)}: {n_row} columns{flag}  {row}")

print()
if ok:
    print("PASS: every part file matches the header.")
    sys.exit(0)
else:
    print(
        "FAIL: a part file written before the schema grew no longer matches the\n"
        "      header. On import, its values land under the wrong columns\n"
        "      (e.g. the node id ends up under `diagnosis`, :LABEL ends up empty)."
    )
    sys.exit(1)