wiki:net.sf.basedb.meludi.notes1_5_0

Version 2 (modified by olle, 4 years ago) (diff)

Added more information on MeLuDI 1.5.0

Updating to MeLuDI 1.5.0

MeLuDI 1.5.0 contains added functionality to simplify using it with multiple BASE projects. Updating to MeLuDI 1.5.0 therefore requires some extra steps, in addition to the standard update procedure.

Follow this procedure:

1. Preparations before update to MeLuDI v1.5.0

a. Update BASE to at least version 3.7.0, if needed

  1. MeLuDI v1.5.0 requires at least version 3.7.0 of BASE. If needed, update BASE before installing MeLuDI v1.5.0. If the current BASE version is 3.5.0 (minimum version for use with MeLuDI version 1.3.3), perform a two-step upgrade, first 3.5.0 -> 3.6.0, then 3.6.0 -> 3.7.0.
  2. MeLuDI v1.5.0 should be used with Tomcat 8.

b. Create BASE projects to be used with MeLuDI

  1. Select BASE menu View -> Projects. Add all projects, that are intended to be used with MeLuDI. It is recommended to use complete and descriptive names, since the projects are to be selected from their names in BASE "Recently used projects" menu and the project names will be included in headers of generated protocols and reports (names may include spaces). Abbreviations that are commonly used, are of course eligible.
  2. Make a note if the project names, since they are needed for the MeLuDI configuration and case label files.

c. Install MeLuDI configuration file meludi-config.xml

  1. Create a MeLuDI configuration file meludi-config.xml with information on each project to be used with MeLuDI. The first version of the configuration file has the following structure:
<?xml version="1.0" encoding="UTF-8"?>
<meludi>
	<projects>
		<project>
			<name>...</name>
			<sample-item-prefix>...</sample-item-prefix
			<start-list-item-prefix>...</start-list-item-prefix>
			<start-plate-item-prefix>...</start-plate-item-prefix>
			<patient-item-prefix>...</patient-item-prefix>
			<project-focus-default>...</project-focus-default>
			<specimen-type-default>...</specimen-type-default>
		</project>
		...
	</projects>
</meludi>

Add a <project></project> XML block for each project. Configuration values for each project:

XML tag name Description Value for original MeLuDI project
name Name of the project item in BASE. MeLuDi
sample-item-prefix Prefix for sample items in project. ML
start-list-item-prefix Prefix for start list items in project. SL
start-plate-item-prefix Prefix for start plate items in project. LP
patient-item-prefix Prefix for patient items in project. MLP
project-focus-default Cancer type studied in the project. <empty string> (unknown)
specimen-type-default Primary tumor or metastasis. <empty string> (unknown)

Note: The "name" tag value is used by MeLuDI to identify the project item in BASE, so it is essential that it corresponds exactly to the project item name in BASE.

The menu option values for project focus default and specimen type default are:

Project focus
Menu option value Menu option text
unknown
melanoma Melanoma
lungcancer Lung cancer
coloncancer Colon cancer
GIST GIST (Gastrointestinal stromal tumour)


Specimen type
Menu option value Menu option text
unknown
Primary Primary tumour
MetastasisDistant Metastasis

ii. Place configuration file meludi-config.xml on the BASE server in same directory as base.config.

d. Update MeLuDI case label info file Case_Label_Info.csv, if existing

  1. Check on the BASE server if a MeLuDI case label info file Case_Label_Info.csv exists in BASE user files directory. If it does, MeLuDI versions prior to 1.5.0 stored information in a single line about the highest case number, for which a label file had been created. The line consisted of the string "Highest case number;" followed by the case number. MeLuDI 1.5.0 will store information in one line per project, for which a label file has been created, where each line consists of the project name, followed by a tab character and the case number. In order to make sure that information for the original MeLuDI project is retained, replace the string "Highest case number;" with "MeLuDi" followed by a tab character (Note that for historical reasons, the original MeLuDI project was named "MeLuDi" with a lowercase i at the end). As an example, if the original contents of file Case_Label_Info.csv was "Highest case number;1272", it should be changed to "MeLuDi 1272", with a tab character separating the project name and the highest label case number.
  2. If no case label info file Case_Label_Info.csv exists, no action is needed, since MeLuDI 1.5.0 will create it automatically.

2. Update to MeLuDI v1.5.0

  1. After installation of MeLuDI v1.5.0, run the installation wizard.