Commit e0f62afe authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Enable hamap integration into dbxref

parent 41069c00
......@@ -24,7 +24,7 @@ def main():
print(json.dumps(documents, sort_keys=True, indent=4))
def retrieve(dbxrefs, matrix, basics):
def retrieve(dbxrefs, matrix=False, basics=True):
"""Retrieve text document from expasy/hamap api and parse into json format."""
# example list input:
# [
......@@ -69,7 +69,7 @@ def retrieve(dbxrefs, matrix, basics):
r = requests.get(text_url)
logger.debug('Content: %s', r.text)
lines = r.text.strip().split('\n')
output = {}
output = {"id": entry["dbxref"]}
matrix_list = []
for line in lines:
if basics:
......@@ -85,18 +85,21 @@ def retrieve(dbxrefs, matrix, basics):
if line.startswith("DT"):
output.update({"dates": read_date(line)})
except RuntimeError:
print("Basic information were not or only partly available.")
logger.warning("Basic information were not or only partly available.")
raise
if matrix:
try:
if line.startswith("MA") and matrix:
matrix_list.append(line.replace("MA", "").strip())
except RuntimeError:
print("Matrix was not available.")
logger.warning("Matrix was not available.")
raise
if matrix and matrix_list:
try:
output.update({"matrix": matrix_list})
except RuntimeError:
print("An error occurred regarding the matrix.")
logger.warning("An error occurred regarding the matrix.")
raise
documents.append(output)
return documents
......
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