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Support lineNameInfo in SmartSource header imports.

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Closes #305.
This commit is contained in:
D. Berge
2024-05-04 17:35:41 +02:00
parent e48c734ea9
commit 524420d945
1 changed files with 43 additions and 13 deletions
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56
bin/import_smsrc.py
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@@ -15,6 +15,7 @@ import re
import time
import configuration
import smsrc
import fwr
from datastore import Datastore
if __name__ == '__main__':
@@ -33,17 +34,21 @@ if __name__ == '__main__':
db.set_survey(survey["schema"])
try:
raw_smsrc = survey["raw"]["smsrc"]
raw_smsrc = survey["raw"]["source"]["smsrc"]["header"]
except KeyError:
print("No SmartSource data configuration")
continue
flags = 0
if "flags" in raw_smsrc:
configuration.rxflags(raw_smsrc["flags"])
# NOTE I've no idea what this is 🤔
# flags = 0
# if "flags" in raw_smsrc:
# configuration.rxflags(raw_smsrc["flags"])
pattern = raw_smsrc["pattern"]
rx = re.compile(pattern["regex"], flags)
lineNameInfo = raw_smsrc.get("lineNameInfo")
pattern = raw_smsrc.get("pattern")
rx = None
if pattern and pattern.get("regex"):
rx = re.compile(pattern["regex"])
for fileprefix in raw_smsrc["paths"]:
realprefix = configuration.translate_path(fileprefix)
@@ -64,14 +69,39 @@ if __name__ == '__main__':
print("Importing")
match = rx.match(os.path.basename(logical_filepath))
if not match:
error_message = f"File path not matching the expected format! ({logical_filepath} ~ {pattern['regex']})"
print(error_message, file=sys.stderr)
print("This file will be ignored!")
continue
if rx:
match = rx.match(os.path.basename(logical_filepath))
if not match:
error_message = f"File path not matching the expected format! ({logical_filepath} ~ {pattern['regex']})"
print(error_message, file=sys.stderr)
print("This file will be ignored!")
continue
file_info = dict(zip(pattern["captures"], match.groups()))
file_info = dict(zip(pattern["captures"], match.groups()))
file_info["meta"] = {}
if lineNameInfo:
basename = os.path.basename(physical_filepath)
fields = lineNameInfo.get("fields", {})
fixed = lineNameInfo.get("fixed")
try:
parsed_line = fwr.parse_line(basename, fields, fixed)
except ValueError as err:
parsed_line = "Line format error: " + str(err)
if type(parsed_line) == str:
print(parsed_line, file=sys.stderr)
print("This file will be ignored!")
continue
file_info = {}
file_info["sequence"] = parsed_line["sequence"]
file_info["line"] = parsed_line["line"]
del(parsed_line["sequence"])
del(parsed_line["line"])
file_info["meta"] = {
"fileInfo": parsed_line
}
smsrc_records = smsrc.from_file(physical_filepath)