The intent of the procedure described below is to find new bugs or unexpected side effects in the code after a release lifecycle is completed.
Goal: Compare two files obtained from RedCAP after two separate
imports are performed using the production and the candidate versions of
Note: The login credentials for the RedCAP web application on the
testing VM at http://localhost:8998/redcap/index.php are:
Obtain the candidate version (redi_B) of the software
$ git clone git@repo_redi redi_new $ cd redi_new && git checkout develop
Clone the config repository at ./config and checkout the tag that matched the REDI version
git clone git@repo_config config cd config && git checkout develop
If needed, revise the settings.ini lines that identify the host and authorize access. For this VM, the lines are
"redcap_uri": "http://localhost:8998/redcap/api/", "token": "121212", $ sed -i 's/^\s\+"redcap_uri.*/\t"redcap_uri" : "http:\/\/localhost:8998\/redcap\/api\/",/' settings.ini $ sed -i 's/^\s\+"token.*/\t"token" : "121212",/' settings.ini
Go to the vagrant folder and remove the old virtual machine (VM) instance if necessary:
$ cd vagrant && vagrant destroy
Start a fresh VM:
$ vagrant up
The expected output from this command should look like:
redcap.zip content indicates Redcap version: 5.7.4 Setting the connection variables in: /var/www/redcap/database.php Checking if redcap application is running... <b>Welcome to REDCap!</b>
If you need to preserve the database state then you can create a backup of the REDCap database before we insert any data by running the redcapdbm.php script on the VM:
$ vagrant ssh -c ‘cd /vagrant/scripts && php redcapdbm.php -b’
Note: The commands above create a file like
backup-redcap-YYYYmmdd-HHMM.sql on the VM
Erase the data in the REDCap instance using redcapdbm.php. First, enumerate the REDCap projects
$ vagrant ssh -c ‘cd /vagrant/scripts && php redcapdbm.php -l’
The following projects are currently available in the redcap database:
project_id: 1, project_name: redcap_demo_cda700 project_id: 2, project_name: redcap_demo_f3746b project_id: 3, project_name: redcap_demo_117155 ... project_id: 12, project_name: hcvtarget_20_development ...
Erase the data in the correct project if necessary:
$ cd ../vagrant && vagrant ssh -c 'cd /vagrant/scripts && php redcapdbm.php -d 12' Deleting data for project: 12, name: hcvtarget_20_development Rows deleted from `redcap_surveys_response`:0 Rows deleted from `redcap_surveys_participants`:0 Rows deleted from `redcap_surveys_emails`:0
If needed, load a minimal set of data to get research identifiers into REDCap. Use the redcap_records utility to load this data.
$ ../redi/utils/redcap_records.py --token=121212 --url=http://localhost:8998/redcap/api/ -i demographic_test_data.csv
On success the following text is returned:
Upload raw.txt file to REDCap using redi_B
Note: You may want to increase the number of requests allowed for processing before proceeding with data upload.
Open the address "localhost:8998" using your browser Login to REDCap and then click on "Control Center" tab Click on the "Security & Authentication Configuration" link on the left menu Find and adjust the "Rate Limiter" field to something like 60000 $ python ../redi/redi.py
If the output from the command above produces an exception then check if
your IP was not banned due to numerous requests sent (@see related code
checkBannedIp() and storeHashedIp())
select * from redcap_ip_banned where ip = '10.0.2.2'; +----------+---------------------+ | ip | time_of_ban | +----------+---------------------+ | 10.0.2.2 | 2014-06-06 18:59:25 | +----------+---------------------+
To fix this, use these SQL commands:
update redcap_config set value = 600000 where field_name = 'page_hit_threshold_per_minute'; delete from redcap_ip_banned;
If the token is invalid the following error is returned:
Cannot connect to project at http://localhost:8998/redcap/api/ with token 121212
Download relevant forms from REDCap using a command like:
$ ../redi/utils/redcap_records.py --token=121212 --url=http://localhost:8998/redcap/api/ -f "demgraphics chemistry" > output_B.csv
If you have a lot of forms, the output comparison is easier if you export the forms separately like this:
#!/bin/bash batch=$1 forms="demographics chemistry cbc inr hcv_rna_results" if [ ! -e $batch ]; then mkdir $batch fi for form in $forms do ../redi/utils/redcap_records.py --token=121212 --url=http://localhost:8998/redcap/api/ --forms=$form > $batch/$form.csv done
Later do the diff like this:
diff -ur a/ b/
At this point we have gathered the output from the release candidate software redi_B. If we there is reference output file available than we can just compare the outputs:
$ diff -u output_A.csv output_B.csv
If there is no reference output file available than we have to get a previous version redi_A and generate it.
Erase the REDCap data first:
cd ../vagrant && vagrant ssh -c 'cd /vagrant/scripts && php redcapdbm.php -d 12'
Obtain the reference version (redi_A) of redi software.
$ git clone git@repo_redi redi_old $ cd redi_old && git checkout TAG_ID_OLD $ git clone git@repo_config config $ cd ../config && git checkout TAG_ID_OLD_CONFIG
Repeat steps 8-10 with redi_A software with the only difference being that the output file is changed to
output_A.csvon step 10.
Compare the files
output_B.csvto insure there are no differences or expected differences are present:
$ diff -u output_A.csv output_B.csv
If no new behavior was introduced the output from the command above should be an empty string.