Changes between Version 1 and Version 2 of net.sf.basedb.meludi.notes1_5_0

Oct 21, 2016, 3:43:09 PM (7 years ago)

Added more information on MeLuDI 1.5.0


  • net.sf.basedb.meludi.notes1_5_0

    v1 v2  
    1313 ii. MeLuDI v1.5.0 should be used with Tomcat 8.
     15=== b. Create BASE projects to be used with MeLuDI ===
     17 i. 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.
     18 ii. Make a note if the project names, since they are needed for the MeLuDI configuration and case label files.
     20=== c. Install MeLuDI configuration file `meludi-config.xml` ===
     22 i. 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:
     25<?xml version="1.0" encoding="UTF-8"?>
     27        <projects>
     28                <project>
     29                        <name>...</name>
     30                        <sample-item-prefix>...</sample-item-prefix
     31                        <start-list-item-prefix>...</start-list-item-prefix>
     32                        <start-plate-item-prefix>...</start-plate-item-prefix>
     33                        <patient-item-prefix>...</patient-item-prefix>
     34                        <project-focus-default>...</project-focus-default>
     35                        <specimen-type-default>...</specimen-type-default>
     36                </project>
     37                ...
     38        </projects>
     42Add a `<project></project>` XML block for each project. Configuration values for each project:
     44|| '''XML tag name''' || '''Description''' || '''Value for original MeLuDI project''' ||
     45|| `name` || Name of the project item in BASE. || `MeLuDi` ||
     46|| `sample-item-prefix` || Prefix for sample items in project. || `ML` ||
     47|| `start-list-item-prefix` || Prefix for start list items in project. || `SL` ||
     48|| `start-plate-item-prefix` || Prefix for start plate items in project. || `LP` ||
     49|| `patient-item-prefix` || Prefix for patient items in project. || `MLP` ||
     50|| `project-focus-default` || Cancer type studied in the project. || <empty string> (unknown) ||
     51|| `specimen-type-default` || Primary tumor or metastasis. || <empty string> (unknown)
     52Note: 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.
     54The menu option values for project focus default and specimen type default are:
     56|| '''Project focus''' ||
     57|| '''Menu option value''' || '''Menu option text''' ||
     58|| `` || unknown ||
     59|| `melanoma` || Melanoma ||
     60|| `lungcancer` || Lung cancer ||
     61|| `coloncancer` || Colon cancer ||
     62|| `GIST` || GIST (Gastrointestinal stromal tumour) ||
     64|| '''Specimen type''' ||
     65|| '''Menu option value''' || '''Menu option text''' ||
     66|| `` || unknown ||
     67|| `Primary` || Primary tumour ||
     68|| `MetastasisDistant` || Metastasis ||
     70` `ii. Place configuration file `meludi-config.xml` on the BASE server in same directory as `base.config`.
     72=== d. Update MeLuDI case label info file `Case_Label_Info.csv`, if existing ===
     74 i. 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.
     75 ii. If no case label info file `Case_Label_Info.csv` exists, no action is needed, since MeLuDI 1.5.0 will create it automatically.
    1577== 2. Update to MeLuDI v1.5.0