def perform_xml_lookup(oai_record, **kwargs):
"""Parse additions/updates & add boundwiths."""
if len(cache) == 0:
logging.info("*** Fetching CSV lookup file from s3 ***")
access_id = kwargs.get("access_id")
access_secret = kwargs.get("access_secret")
bucket = kwargs.get("bucket_name")
lookup_key = kwargs.get("lookup_key")
csv_data = process.get_s3_content(bucket, lookup_key, access_id,
access_secret)
cache["value"] = pandas.read_csv(io.BytesIO(csv_data), header=0)
lookup_csv = cache["value"]
for record in oai_record.xpath(".//marc21:record", namespaces=NS):
record_id = process.get_record_001(record)
logging.info("Reading in Record %s", record_id)
parent_txt = lookup_csv.loc[lookup_csv.child_id == int(record_id),
"parent_xml"].values
if len(set(parent_txt)) >= 1:
logging.info("Child XML record found %s", record_id)
for parent_node in parent_txt[0].split("||"):
try:
record.append(etree.fromstring(parent_node))
except etree.XMLSyntaxError as error:
logging.error("Problem with string syntax:")
logging.error(error)
logging.error(parent_node)
return oai_record
def prepare_oai_boundwiths(**kwargs):
"""Grab Boundwith Files and Generate Child Lookup."""
access_id = kwargs.get("AWS_ACCESS_KEY_ID")
access_secret = kwargs.get("AWS_SECRET_ACCESS_KEY")
bucket = kwargs.get("BUCKET")
bw_prefix = kwargs.get("SOURCE_FOLDER")
lookup_prefix = kwargs.get("DEST_FOLDER")
bw_keys = [key for key in ast.literal_eval(kwargs.get("S3_KEYS")) if key.startswith(bw_prefix)]
csv_in_mem = io.StringIO()
lookup_csv = csv.DictWriter(csv_in_mem, fieldnames=["child_id", "parent_id", "parent_xml"])
lookup_csv.writeheader()
logging.info("Starting to iterate over S3 Boundwith objects")
for key in bw_keys:
logging.info("Loading s3 key %s", key)
source_obj = process.get_s3_content(bucket, key, access_id, access_secret)
source_xml = process.add_marc21xml_root_ns(source_obj)
for record in source_xml.xpath("oai:record/oai:metadata/marc21:record", namespaces=NS):
boundwith_record_process(record, lookup_csv)
process.generate_s3_object(
csv_in_mem.getvalue(),
bucket,
lookup_prefix,
access_id,
access_secret
)
def prepare_alma_data(**kwargs):
"""Update XML records by injecting parent xml when record 001 is in lookup child_id column."""
access_id = kwargs.get("AWS_ACCESS_KEY_ID")
access_secret = kwargs.get("AWS_SECRET_ACCESS_KEY")
bucket = kwargs.get("BUCKET")
dest_prefix = kwargs.get("DEST_PREFIX")
lookup_key = kwargs.get("LOOKUP_KEY")
src_prefix = kwargs.get("SOURCE_PREFIX")
src_suffix = kwargs.get("SOURCE_SUFFIX")
s3_keys = ast.literal_eval(kwargs.get("S3_KEYS"))
# Generate list of S3 keys we want to index
alma_keys = [key for key in s3_keys if key.startswith(src_prefix) and key.endswith(src_suffix)]
# Read Boundwith Lookup file into Memory, with child_id column as array
csv_data = process.get_s3_content(bucket, lookup_key, access_id, access_secret)
lookup_csv = pandas.read_csv(io.BytesIO(csv_data), header=0)
# Process filtered set of keys to untar, ungzip, add MARC21 XML namespaces,
# & inject parent XML if the record is an identified (via lookup) child record.
logging.info("Starting to iterate over S3 objects")
for key in alma_keys:
logging.info("Loading s3 key %s", key)
src_obj = process.get_s3_content(bucket, key, access_id, access_secret)
src_data = process.expand_alma_sftp_tarball(key, src_obj)
src_xml = process.add_marc21xml_root_ns(src_data)
for record in src_xml.findall("{http://www.loc.gov/MARC21/slim}record"):
record_id = process.get_record_001(record)
parent_txt = lookup_csv.loc[lookup_csv.child_id == int(record_id), 'parent_xml'].values
if len(set(parent_txt)) >= 1:
logging.info("Child XML record found %s", record_id)
for parent_node in parent_txt[0].split("||"):
try:
record.append(etree.fromstring(parent_node))
except etree.XMLSyntaxError as error:
logging.error("Problem with string syntax:")
logging.error(error)
logging.error(parent_node)
dest_key = key.replace(src_suffix, "").replace(src_prefix, dest_prefix + "/alma_bibs__")
process.generate_s3_object(
etree.tostring(src_xml),
bucket,
dest_key,
access_id,
access_secret
)
def report_s3_schematron(**kwargs):
"""Wrapper function for using S3 Retrieval, Schematron Reporting, and S3 Writer."""
source_prefix = kwargs.get("source_prefix")
dest_prefix = kwargs.get("destination_prefix")
bucket = kwargs.get("bucket")
schematron_file = kwargs.get("schematron_filename")
access_id = kwargs.get("access_id")
access_secret = kwargs.get("access_secret")
# create reporting csv
csv_in_mem = io.StringIO()
report_csv = csv.DictWriter(
csv_in_mem, fieldnames=["id", "report", "record", "source_file"])
report_csv.writeheader()
# get schematron doc & return lxml.etree.Schematron validator
schematron_doc = process.get_github_content("tulibraries/aggregator_mdx",
schematron_file)
schematron = isoschematron.Schematron(etree.fromstring(schematron_doc),
store_report=True)
# Iterate through S3 Files, Validate, & Save Report to CSV
total_transform_count = 0
for s3_key in process.list_s3_content(bucket, access_id, access_secret,
source_prefix):
logging.info("Validating & Reporting On File: %s", s3_key)
s3_content = process.get_s3_content(bucket, s3_key, access_id,
access_secret)
s3_xml = etree.fromstring(s3_content)
for record in s3_xml.iterchildren():
total_transform_count += 1
record_id = record.get("airflow-record-id")
logging.info("Ran report on record: %s", record_id)
schematron.validate(record)
report_csv.writerow({
"id":
record_id,
"report":
schematron_failed_validation_text(
schematron.validation_report),
"record":
identifier_or_full_record(record),
"source_file":
f"https://s3.console.aws.amazon.com/s3/object/{bucket}/{s3_key}"
})
report_filename = dest_prefix + "-report.csv"
logging.info("Records report: https://%s.s3.amazonaws.com/%s", bucket,
report_filename)
logging.info("Total Transform Count: %s", total_transform_count)
process.generate_s3_object(csv_in_mem.getvalue(), bucket, report_filename,
access_id, access_secret)
return {"transformed": total_transform_count}
def test_get_s3_content(self):
bucket = "test_bucket"
key = "test_key_2"
access_id = "test_access_id"
access_secret = "test_access_secret"
conn = boto3.client("s3",
aws_access_key_id=access_id,
aws_secret_access_key=access_secret)
conn.create_bucket(Bucket=bucket)
conn.put_object(Bucket=bucket, Key=key, Body="test more content")
test_content_exists = conn.get_object(Bucket=bucket, Key=key)
test_object_exists = conn.list_objects(Bucket=bucket)
self.assertEqual(test_content_exists["Body"].read(),
b"test more content")
self.assertEqual(
test_content_exists["ResponseMetadata"]["HTTPStatusCode"], 200)
self.assertEqual(test_object_exists["Contents"][0]["Key"], key)
test_run = process.get_s3_content(bucket, key, access_id,
access_secret)
self.assertEqual(test_run, b"test more content")
def transform_s3_xsl(**kwargs):
"""Transform & Write XML data to S3 using Saxon XSLT Engine."""
access_id = kwargs.get("access_id")
access_secret = kwargs.get("access_secret")
bucket = kwargs.get("bucket")
dest_prefix = kwargs.get("destination_prefix")
source_prefix = kwargs.get("source_prefix")
if kwargs.get("dag"):
run_id = kwargs.get("dag").dag_id
else:
run_id = "no-dag-provided"
saxon = prepare_saxon_engine()
transformed = etree.Element("collection")
transformed.attrib["dag-id"] = run_id
transformed.attrib["dag-timestamp"] = kwargs.get("timestamp",
"no-timestamp-provided")
xsl = "https://raw.github.com/{repo}/{branch}/{filename}".format(
repo=kwargs.get("xsl_repository", "tulibraries/aggregator_mdx"),
branch=kwargs.get("xsl_branch", "master"),
filename=kwargs.get("xsl_filename"))
for s3_key in process.list_s3_content(bucket, access_id, access_secret,
source_prefix):
logging.info("Transforming File %s", s3_key)
s3_content = process.get_s3_content(bucket, s3_key, access_id,
access_secret)
s3_xml = etree.fromstring(s3_content)
for record in s3_xml.iterchildren():
record_id = record.get("airflow-record-id")
logging.info("Transforming Record %s", record_id)
result_str = subprocess.check_output(
["java", "-jar", saxon, "-xsl:" + xsl, "-s:-"],
input=etree.tostring(record))
result = etree.fromstring(result_str)
result.attrib["airflow-record-id"] = record_id
transformed.append(result)
filename = s3_key.replace(source_prefix, dest_prefix)
transformed_xml = etree.tostring(transformed)
process.generate_s3_object(transformed_xml, bucket, filename,
access_id, access_secret)
def filter_s3_schematron(**kwargs):
"""Wrapper function for using S3 Retrieval, Schematron Filtering, and S3 Writer."""
source_prefix = kwargs.get("source_prefix")
dest_prefix = kwargs.get("destination_prefix")
report_prefix = kwargs.get("report_prefix")
bucket = kwargs.get("bucket")
schematron_file = kwargs.get("schematron_filename")
access_id = kwargs.get("access_id")
access_secret = kwargs.get("access_secret")
if kwargs.get("dag"):
run_id = kwargs.get("dag").dag_id
else:
run_id = "no-dag-provided"
if kwargs.get("timestamp"):
timestamp = kwargs.get("timestamp")
else:
timestamp = "no-timestamp-provided"
# create invalid records reporting csv
csv_in_mem = io.StringIO()
invalid_csv = csv.DictWriter(
csv_in_mem, fieldnames=["id", "report", "record", "source_file"])
invalid_csv.writeheader()
# get schematron doc & return lxml.etree.Schematron validator
schematron_doc = process.get_github_content("tulibraries/aggregator_mdx",
schematron_file)
schematron = isoschematron.Schematron(etree.fromstring(schematron_doc),
store_report=True)
total_filter_count = 0
total_record_count = 0
for s3_key in process.list_s3_content(bucket, access_id, access_secret,
source_prefix):
logging.info("Validating & Filtering File: %s", s3_key)
s3_content = process.get_s3_content(bucket, s3_key, access_id,
access_secret)
s3_xml = etree.fromstring(s3_content)
invalid_xml = etree.Element("collection")
invalid_xml.attrib["dag-id"] = run_id
invalid_xml.attrib["dag-timestamp"] = timestamp
filter_count = 0
record_count = 0
for record in s3_xml.iterchildren():
record_count += 1
total_record_count += 1
if not schematron.validate(record):
record_id = record.get("airflow-record-id")
logging.error("Invalid record found: %s", record_id)
s3_xml.remove(record)
filter_count += 1
invalid_csv.writerow({
"id":
record_id,
"report":
schematron_failed_validation_text(
schematron.validation_report),
"record":
identifier_or_full_record(record),
"source_file":
f"https://s3.console.aws.amazon.com/s3/object/{bucket}/{s3_key}"
})
total_filter_count += filter_count
filename = s3_key.replace(source_prefix, dest_prefix)
updated_s3_xml = etree.tostring(s3_xml)
process.generate_s3_object(updated_s3_xml, bucket, filename, access_id,
access_secret)
if filter_count == record_count and record_count != 0:
logging.warning(
f"All records filtered from {filename}. record_count: {record_count}"
)
invalid_filename = report_prefix + "-invalid.csv"
logging.info("Total Filter Count: %s", total_filter_count)
logging.info("Invalid Records report: https://%s.s3.amazonaws.com/%s",
bucket, invalid_filename)
process.generate_s3_object(csv_in_mem.getvalue(), bucket, invalid_filename,
access_id, access_secret)
if total_filter_count == total_record_count and total_record_count != 0:
raise AirflowException(
f"All records were filtered out: {total_record_count}")
return {"filtered": total_filter_count}