https://github.com/tfrayner/clinstudyweb
Flexible database system supporting clinical studies
https://github.com/tfrayner/clinstudyweb
Last synced: 29 days ago
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Flexible database system supporting clinical studies
- Host: GitHub
- URL: https://github.com/tfrayner/clinstudyweb
- Owner: tfrayner
- License: gpl-2.0
- Created: 2019-10-26T11:21:44.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-10-26T11:23:34.000Z (over 6 years ago)
- Last Synced: 2023-10-20T23:23:03.577Z (over 2 years ago)
- Language: JavaScript
- Homepage: https://sourceforge.net/projects/clinstudyweb/
- Size: 2.95 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README
- Changelog: Changes
- License: LICENSE
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README
ClinStudyWeb
============
Installation
------------
The ClinStudyWeb software has many prerequisite Perl modules, which
should be installed (ideally using CPAN, CPANPLUS or a similar
dependencies management system) before doing anything else. To get a
list of required packages, run
perl Makefile.PL
which will also set up a makefile for you to use during the build phase.
Copy the "clinstudy_web.yml-example" file to "clinstudy_web.yml" and
edit it to point to your newly installed database, giving a username
and password if necessary (this is recommended!).
Once you have edited the config file, install the server scripts:
make
make test
make install
The next step is to install the database schema. Instructions given
here are for MySQL; it should however be relatively simple to switch
between database backends if desired; the only changes that are needed
are to the SQL syntax in the initial database table creation
statements. First, deploy the core tables and triggers. If your target
database is named "clinstudy":
mysql clinstudy < schema/clindb_mysql.sql
Since we are using triggers, note that you will most likely need the
SUPER privilege on the target database.
Next, deploy the audit history tables:
perl -Ilib -MClinStudy::ORM -e '$s=ClinStudy::ORM->connect("dbi:mysql:clinstudy"); $s->bootstrap_journal()'
Finally, you will want to load in some initial database users and a
semantic framework:
clinstudy_import.pl -d schema/clindb_admin.xsd -c clinstudy_web.yml -x schema/default_user_accounts.xml
clinstudy_import.pl -d schema/clindb_admin.xsd -c clinstudy_web.yml -x schema/default_semantic_framework.xml
Note that the semantic framework document will almost certainly need
tailoring to your own particular circumstances. It defines the
controlled vocabularies and clinical test behaviours used in the
database. The example distributed with this package is from the
original installation which handled data from a series of studies on
autoimmune diseases. Please see the ClinStudyWeb Trac wiki for more
information on semantic frameworks:
http://trac2.xp-dev.com/clinstudyweb/wiki
You should now be ready to start up a test server (running by default
at http://localhost:3000):
clinstudy_web_server.pl
Check the web page is up and running; you should be able to log in to
the default admin account (username: admin, password: admin). Don't
forget to change the default user accounts!