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senrabc / honeyguide

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manual run following instructions won't complete #3

Open senrabc opened 6 years ago

senrabc commented 6 years ago

Error: generating the redcap data database Using quail.conf.yaml at /home/hcvprod/quailroot/quail.conf.yaml Loading metadata... Writing instruments tables... Traceback (most recent call last): File "/usr/local/bin/quail", line 11, in load_entry_point('quail', 'console_scripts', 'quail')() File "/home/hcvprod/QUAIL/quail/main.py", line 104, in cli_run main(args) File "/home/hcvprod/QUAIL/quail/main.py", line 92, in main redcap.gen_data(**conf) File "/home/hcvprod/QUAIL/quail/actions/redcap.py", line 175, in gen_data for instrument in instrumentor.get_all_instruments(): File "/home/hcvprod/QUAIL/quail/utils/redcap_util/redcap_sqlize.py", line 115, in get_all_instruments return [self.get_instrument_table(name) for name in self.instruments] File "/home/hcvprod/QUAIL/quail/utils/redcap_util/redcap_sqlize.py", line 115, in return [self.get_instrument_table(name) for name in self.instruments] File "/home/hcvprod/QUAIL/quail/utils/redcap_util/redcap_sqlize.py", line 110, in get_instrument_table in self.fields_for_instrument(instrument_name) File "/home/hcvprod/QUAIL/quail/utils/redcap_util/redcap_sqlize.py", line 111, in if self.is_lookup_field(field)] File "/home/hcvprod/QUAIL/quail/utils/redcap_util/redcap_sqlize.py", line 77, in is_lookup_field field = self.get_field(field_name) File "/home/hcvprod/QUAIL/quail/utils/redcap_util/redcap_sqlize.py", line 72, in get_field raise Exception('too many matching fields for %s' % field_name) Exception: too many matching fields for redcap_event_name NOTICE: database "latest" does not exist, skipping DROP DATABASE making a new postgres database CREATE DATABASE CREATE DATABASE CREATE ROLE GRANT GRANT loading the databases WARNING: Couldn't re-execute SBCL with proper personality flags (/proc isn't mounted? setuid?) Trying to continue anyway.

PFWhite commented 6 years ago

I think that this issue is actually a symptom rather than a cause, although the error is not the best. I have been able to replicate this bug but it is due to REDCap failing to deliver data. The exception that is being thrown is over specified.

senrabc commented 6 years ago

As you saw the data.db was 0 bytes.

PFWhite commented 6 years ago

If you pull QUAIL from my master branch this is fixed. I believe there is a pull request still out to update ctsit's quail

PFWhite commented 6 years ago

fixed pending code review