Attention sites participating in the obesity survey,
Today we posted some updates to the obesity survey
tracker<https://bitbucket.org/bos_uthscsa/survey_tracker/overview>.
Specifically these changes will make handling surveys by email invitation
easier and clearer. "Instructions" have also been updated to with better
documentation about the format and required fields for the contact info input
file. The contact info input file is optional, and should be used by sites that
do not have Clarity/identified DW/Oracle databases. Additionally, we added a
sample survey_tracker output file in the format used to upload the initial
project data into REDCap.
Below is an example with more detailed info for a couple steps in the
"Instructions" based on the specific needs of CMH. Because they are a non-Epic
(Cerner) site, and also because a pediatric/email-only site, they must use the
contact input file method.
Step 5) Configure the survey_tracker
- Create a copy of tracker.ini.example file to start, name it tracker.ini
- Set site specific settings
[site]
site_abbr=CM
adult_only=false
use_email=true
- Set your data builder SQLite and contact info file names
[input_files]
deid_db= databuilder_obesity_pediatric.db
contact_info=contact_info.csv
- delete everything below this line (or add your own known patterns to be match
in bad address strings)
[invalid_patterns]
- leave everything else default; none of it will be used
Step 6) OPTIONAL: create preloaded contact info file in format of
id_data_DEMO.csv
At minimum the following fields must be populated: patient_ide, patient_number,
guardian_name, guardian_email
Step 7) Run the survey_tracker, using the -f option
$ python tracker_load.py -f
2015.07.14 19:39:21: Creating dir: output
2015.07.14 19:39:21: contacts info file: contact_info.csv
2015.07.14 19:39:21: deid_db: databuilder_obesity_pediatric.db
2015.07.14 19:39:21: tracker_db: tracker.db
...
2015.07.14 19:39:21: adult_only: False
2015.07.14 19:39:21: email_only: True
...
Step 8) Validate your i2b2 data builder and survey_tracker SQLite files
$ python validate_databuilder.py databuilder_obesity_pediatric.db
output/tracker.db
Please copy-n-paste the output of this command in an email to me, or at
least confirm that you see "no errors".
Questions, comments, and feedback are welcome!
-Angela | UTHSCSA
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