def upload_recordset_from_file(rsid, fname):
"""
Given a recordset uuid and a local dataset filename, upload the local
dataset file as the "current" file for that uuid.
Parameters
----------
rsid : uuid
An iDigBio recordset uuid
fname : string
Filename (full path or current directory only)
Returns
-------
bool
True if successful, False otherwise
"""
# convert rsid uuid to string here because of either:
# psycopg2.ProgrammingError: can't adapt type 'UUID'
# or
# TypeError: 'UUID' object does not support indexing
rsuuid = str(rsid)
logger.info("Manual upload of '{0}' from file '{1}' requested.".format(
rsuuid, fname))
# do some checks here
try:
f = open(fname)
f.close()
except:
logger.error(
"Cannot access file: '{0}'. Aborting upload.".format(fname))
raise
db = PostgresDB()
sql = ("""SELECT id FROM recordsets WHERE uuid=%s""", (rsuuid, ))
idcount = db.execute(*sql)
if idcount < 1:
logger.error(
"Cannot find uuid '{0}' in db. Aborting upload.".format(rsuuid))
db.rollback()
return False
# output the "before" state
results = db.fetchall(
"""SELECT id,file_harvest_date,file_harvest_etag FROM recordsets WHERE uuid=%s""",
(rsuuid, ))
for each in results:
logger.debug("{0}".format(each))
try:
etag = upload_recordset(rsuuid, fname, db)
assert etag
sql = ("""UPDATE recordsets
SET file_harvest_etag=%s, file_harvest_date=%s
WHERE uuid=%s""", (etag, datetime.datetime.now(), rsuuid))
update_count = db.execute(*sql)
db.commit()
logger.info("UPDATED {0} rows.".format(update_count))
logger.info(
"Finished manual upload of file '{0}', result etag = '{1}', saved to db."
.format(fname, etag))
except:
logger.error(
"An exception occurred during upload of file or db update for '{0}'"
.format(fname))
raise
# output the "after" state
results = db.fetchall(
"""SELECT id,file_harvest_date,file_harvest_etag FROM recordsets WHERE uuid=%s""",
(rsuuid, ))
for each in results:
logger.debug("{0}".format(each))
return True
def process_file(fname,
mime,
rsid,
existing_etags,
existing_ids,
ingest=False,
commit_force=False,
ispaused=False):
rlogger = getrslogger(rsid)
rlogger.info("Processing %s, type: %s", fname, mime)
counts = {}
t = datetime.datetime.now()
filehash = calcFileHash(fname)
db = PostgresDB()
commited = False
try:
if mime == "application/zip":
dwcaobj = Dwca(fname, skipeml=True, logname="idb")
for dwcrf in dwcaobj.extensions:
rlogger.debug("Processing %r", dwcrf.name)
counts[dwcrf.name] = process_subfile(dwcrf,
rsid,
existing_etags,
existing_ids,
ingest=ingest,
db=db)
dwcrf.close()
rlogger.debug("processing core %r", dwcaobj.core.name)
counts[dwcaobj.core.name] = process_subfile(dwcaobj.core,
rsid,
existing_etags,
existing_ids,
ingest=ingest,
db=db)
dwcaobj.core.close()
dwcaobj.close()
elif mime == "text/plain":
commas = False
with open(fname, "rb") as testf:
commas = "," in testf.readline()
if commas:
csvrf = DelimitedFile(fname, logname="idigbio")
counts[fname] = process_subfile(csvrf,
rsid,
existing_etags,
existing_ids,
ingest=ingest,
db=db)
else:
tsvrf = DelimitedFile(fname,
delimiter="\t",
fieldenc=None,
logname="idigbio")
counts[fname] = process_subfile(tsvrf,
rsid,
existing_etags,
existing_ids,
ingest=ingest,
db=db)
if ingest:
commit_ok = commit_force
type_commits = []
for k in counts:
if k not in ingestion_types:
continue
if (counts[k]["create"] /
float(counts[k]["processed_line_count"]) >= 0.5
and counts[k]["delete"] /
float(counts[k]["processed_line_count"]) >= 0.5):
type_commits.append(True)
else:
type_commits.append(False)
commit_ok = all(type_commits)
if commit_ok:
rlogger.info("Ready to Commit")
db.commit()
commited = True
else:
rlogger.error("Rollback")
db.rollback()
else:
db.rollback()
db.close()
except Exception:
logger.exception(
"Unhandled Exception when processing {0}".format(fname))
db.rollback()
db.close()
# Clear after processing an archive
unconsumed_extensions.clear()
core_siblings.clear()
return {
"name": fname,
"filemd5": filehash,
"recordset_id": rsid,
"counts": counts,
"processing_start_datetime": t.isoformat(),
"total_processing_time": (datetime.datetime.now() - t).total_seconds(),
"commited": commited,
"paused": ispaused
}