Configuration Options
This section describes the options in the configuration file. To make your own
configuration file:
-
Copy and rename either
./doc/sample_files/SampleDataModel.xml or
./doc/sample_files/SampleDataModelWithPlugins.xml.
-
Put your copy in the
./models folder of your installation directory
-
Edit your configuration file as needed. For now we expect you to edit your own file
by example.
The following sections describe configuration options in more detail
Properties of general_information tag
General information properties are pieces of information which appear in the
automatically generated "Help" page which appears in the Help menu of the Logging Tool.
| XML Tag Property |
Description |
Example |
Default |
project_title
|
The name of the application. This is used in the title of the Administration and Logging tools.
|
-
Clinical Trials of ABC Strain Knock-out Mice
-
University of XYZ Jaundice Study
-
Malaria Treatment using Permathrine Nets
|
Clinical Study Tracker
|
main_contact_name
|
Person who is mainly responsible for the project.
|
|
|
email
|
Main contact users should e-mail if they encounter problems or have questions about the
study.
|
|
|
phone
|
Phone number of main contact
|
|
|
project_description
|
|
|
|
project_title
|
The name of the application. This is used in the title of the Administration and Logging tools.
|
-
Clinical Trials of ABC Strain Knock-out Mice
-
University of XYZ Jaundice Study
-
Malaria Treatment using Permathrine Nets
|
Clinical Study Tracker
|
application_name
|
The name of the application for use by other programs. The name should have all lower case
letters and have no spaces.
|
knockout_mice_study_app
|
cst_app
|
application_version
|
The version of the application.
|
knockout_mice_study_app
|
cst_app
|
Properties of database_properties tag
| XML Tag Property |
Description |
Example |
Default |
database_name
|
The name of the MySQL database.
|
clinicalDB
|
clinicalTrials
|
database_server
|
The name of the server which hosts the MySQL installation
|
-
neptune.uabc.ac.uk
-
localhost
|
localhost
|
database_port
|
the communication port used by CST to communicate with the database.
|
Usually 8080
|
null
|
user_table_name
|
the name of the table used to hold information about userIDs.
|
data_curators, registered_users.
|
users
|
subject_table_name
|
The table which holds the primary key identifier (eg: serial number), as well as subject attribute data
(eg: Location="Manchester", Gender="Female")
|
|
case_study_members
|
activity_changes_table_name
|
name of the table that will record the changes users make to data.
|
|
trial_activity_changes
|
primary_key_length
|
the number of characters in a primary key. Typically less than 15. Note that
long primary keys may lead to inefficient database processing.
|
20
|
40
|
subject_attribute_length
|
the number of characters allowed in a value for a subject attribute. For example
if the value of a subject attribute "Location" is "Manchester", the length would
have to be at least 10 characters.
|
25
|
50
|
comments_length
|
the number of characters allocated to store comments a user makes about one activity
for one case study member.
|
|
255
|
start_date
|
The start date of the study. The date is used to provide the lower bound value for
date field values.
|
|
2007
|
end_date
|
The end date of the study. The date is used to provide the upper bound value for
date field values.
|
|
2010
|
Properties of tracked_object_properties tag
These are properties for the tag
tracked_object_properties. This tag also contains
these nested tags:
| XML Tag Property |
Description |
Example |
Default |
singular name
|
singular case of the word that describes the subjects of the study
|
|
case study member
|
singular name
|
plural case of the word that describes the subjects of the study
|
|
case study members
|
primary_key_attribute
|
See properties of primary_key_attribute
|
|
|
subject_attribute
|
See properties of subject_attribute
|
|
|
Properties of primary_key_attribute tag
The primary key field describes the primary key used in the subject
table and all of the activity tables as well. This key relates all the
other tables together.
| XML Tag Property |
Description |
Example |
Default |
display_name
|
The display name of the primary key as it would appear in the forms of the
Logging Tool.
|
|
-
|
data storage name
|
The name of the primary key as it would appear as a field name in the
MySQL database. The field should have no spaces and have letters all in
lower case. Words in the name should be separated by underscore characters.
|
|
-
|
Properties of subject_attribute tag
| XML Tag Property |
Description |
Example |
Default |
display_name
|
The name of the subject attribute which is displayed to end-users of the Logging
Tool. The names appear in parts of the Filter and Reports menu.
|
Site Location
|
-
|
data_storage_name |
The name of the subject attribute which appears as a field in the MySQL database.
The data storage name will not have spaces. A good convention to use is to
use all lower case letters, with words separated by underscore characters.
|
site_location
|
-
|
Properties of the tag form
| XML Tag Property |
Description |
Example |
Default |
order
|
The order in which the form will appear in the list of tabbed panes of the Logging Tool.
|
1,2,3 etc.
|
Configuration manager counts forms it parses and assigns 1 for the first, 2 for the second...
|
display_name
|
The name of the activity which will be displayed to the end-user. The names will appear as titles
of the tabbed pane items of the Logging Tool and will appear in other places such as in the
Filter and Reports menus. Often the display names will have spaces. |
Diabetes Test
|
-
|
data_storage_name
|
The name of the activity which will be used to name an activity table in the MySQL database.
The names will appear in SQL queries found in the classes of the
cst.loggingTool.persistenceLayer package. The names should not have spaces.
You should use the naming convention of having all lower case letters with words separated
by underscores.
|
diabetes_test
|
-
|
tool_tip
|
Help text displayed to users when their mouse pointers hover over the titles of tabbed panes.
A useful convention is to put the initials of a person responsible for the activity in brackets.
|
This activity tracks the activity of testing for diabetes from blood samples to archiving the
test results. (KG)
|
-
|
enforce_chronology
|
If "true" then CST will detect an error if the sequence of dates in an activity records appear
in descending chronological order. If "false", then the validation check is not done. It is useful
to set this flag to "false" if delays happen in activities which violate the order in which steps
are assumed to occur.
|
|
true |
form_fields
|
See form_field properties
|
|
true |
Properties of form_field tag
| XML Tag Property |
Description |
Example |
Default |
order
|
The order in which the field appears in the sequence of activity steps.
|
1,2,3 etc.
|
If no order tag is specified, CST assigns 1 to the first field it parses, 2 to the
second field it parses, etc.
|
display_name
|
The name of the field which is displayed in the Logging Tool forms. The field names
will appear in the tabbed panes and in options in the Filters and Reports menu.
|
Results Archived
|
If no order tag is specified, CST assigns 1 to the first field it parses, 2 to the
second field it parses, etc.
|
data_storage_name
|
The name of the field as it would appear in a table of the MySQL database.
|
results_archived
|
-
|
tool_tip
|
Help text that appears when users hover their mice pointers on the field label
of date fields in the tabbed panes. It is good practice to put the initials of
the person who manages the activity step.
|
Results archived on CDs and placed in filing cabinet (KG).
|
-
|
Properties of plugins tag
| XML Tag Property |
Description |
Example |
Default |
import_export_plugin
|
See
plugin properties.
This kind of plugin is advertised in the Database menu of the Logging Tool.
|
-
|
-
|
report_plugin
|
See plugin properties.
This kind of plugin is advertised in the Reports menu of the Logging Tool.
|
-
|
-
|
subject_information_plugin
|
See plugin properties.
This kind of plugin is advertised in the Options menu of the Logging Tool.
|
-
|
-
|
Properties of the plugins
Tags for
import_export_plugin,
report_plugin
and
subject_information_plugin all have the same attributes
listed below. Fields such as title, description, author and email are used
by CST to describe future plugins to end-users. These values are displayed
in a pop-up dialog which tells the users what the plugin does and that the
feature is not yet completed.
| XML Tag Property |
Description |
Example |
Default |
menu_display_name
|
The name of the menu item which will advertise and activate this plugin.
|
Export to XML...
|
-
|
title
|
The title of the plugin. This may be longer than the menu display name.
|
Exporting Activity Data to XML files.
|
-
|
description
|
Describes what the plugin does.
|
Exports activity data to an XML file format.
|
-
|
author
|
Person who manages the code for the plugin.
|
John Smith
|
-
|
email
|
Email address end-users should use if they want to know more about the plugin.
|
jsmith@abc.edu
|
-
|
parameters
|
See properties of the
parameter. tag
|
-
|
-
|
Properties of the parameter tag
| XML Tag Property |
Description |
Example |
Default |
name
|
name of the property
|
enable_remote_access
|
-
|
value
|
value of the property
|
true
|
-
|
Author: Kevin Garwood
(c)2010 Medical Research Council. Licensed under
Apache 2.0.
/div>
