Changes between Version 5 and Version 6 of net.sf.basedb.meludi.notes1_5_0


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Timestamp:
Nov 1, 2016, 10:36:48 AM (4 years ago)
Author:
olle
Comment:

Added information on new options in MeLuDI 1.5.0

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  • net.sf.basedb.meludi.notes1_5_0

    v5 v6  
    1818 ii. Make a note of the project names, since they are needed for the MeLuDI configuration file.
    1919
    20 === c. Install MeLuDI configuration file `meludi-config.xml` ===
     20=== c. Information and recommendations regarding new MeLuDI configuration file `meludi-config.xml` ===
     21
     22MeLuDI 1.5.0 relies on a data in configuration file `meludi-config.xml` to obtain project-specific settings.
     23
     24 i. Backward compatibility with original MeLuDI project.[[BR]]If MeLuDI 1.5.0 is to be installed on a BASE server used to store data for the original MeLuDI project (named "!MeLuDi" in BASE), settings for the latter must be added in the configuration file, to enable MeLuDI to be used as previously with this project (see next section for what settings to use). Even if no new samples will be registered in the original MeLuDI project, the configuration of prefixes is needed to ensure that "Case summary", "Sample source report", "Sample processing statistics", and other inspection wizards can be used to inspect the data.
     25 ii. Recommendations for choice of project-specific prefixes for item names.[[BR]]For each item type, it is strongly recommended that unique prefixes are chosen for all projects to be used with MeLuDI.
     26 iii. Use with non-configured projects.[[BR]]MeLuDI 1.5.0 allows a non-configured BASE project to be used as active project, but all item name prefixes will then be empty strings, and item names will consist of a pure serial number with optional suffix (e.g. for storage boxes). If more than one non-configured project is used, the same name might be used for items in different projects, which may cause confusion. This is therefore not recommended.
     27
     28=== d. Create MeLuDI configuration file `meludi-config.xml` ===
    2129
    2230 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:
     
    2836                <project>
    2937                        <name>...</name>
    30                         <sample-item-prefix>...</sample-item-prefix
     38                        <sample-item-prefix>...</sample-item-prefix>
     39                        <storage-box-prefix>...</storage-box-prefix>
    3140                        <start-list-item-prefix>...</start-list-item-prefix>
    3241                        <start-plate-item-prefix>...</start-plate-item-prefix>
    3342                        <patient-item-prefix>...</patient-item-prefix>
     43                        <libprep-kit-item-prefix>...</libprep-kit-item-prefix>
    3444                        <project-focus-default>...</project-focus-default>
    3545                        <specimen-type-default>...</specimen-type-default>
     46                        <specimen-input-type-default>...</specimen-input-type-default>
    3647                </project>
    3748                ...
     
    4556|| `name` || Name of the project item in BASE. || `MeLuDi` ||
    4657|| `sample-item-prefix` || Prefix for sample items in project. || `ML` ||
     58|| `storage-box-prefix` || Prefix for storage boxes in project. || `ML_` ||
    4759|| `start-list-item-prefix` || Prefix for start list items in project. || `SL` ||
    4860|| `start-plate-item-prefix` || Prefix for start plate items in project. || `LP` ||
    4961|| `patient-item-prefix` || Prefix for patient items in project. || `MLP` ||
     62|| `libprep-kit-item-prefix` || Prefix for library preparation kit items in project. || `LP_kit_` ||
    5063|| `project-focus-default` || Cancer type studied in the project. || <empty string> (unknown) ||
    51 || `specimen-type-default` || Primary tumor or metastasis. || <empty string> (unknown)
     64|| `specimen-type-default` || Primary tumor or metastasis. || <empty string> (unknown) ||
     65|| `specimen-input-type-default` || The form in which a specimen is delivered. || <empty string> (unknown) ||
    5266Note: 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.
    5367
    54 The menu option values for project focus default and specimen type default are:
     68The menu option values for project focus, specimen type, and specimen input type to use for default choices are:
    5569
    5670|| '''Project focus''' ||
     
    6175|| `coloncancer` || Colon cancer ||
    6276|| `GIST` || GIST (Gastrointestinal stromal tumour) ||
     77|| `breastcancer` || Breast cancer ||
    6378[[BR]]
    6479|| '''Specimen type''' ||
     
    6782|| `Primary` || Primary tumour ||
    6883|| `MetastasisDistant` || Metastasis ||
     84[[BR]]
     85|| '''Specimen input type''' ||
     86|| '''Menu option value''' || '''Menu option text''' ||
     87|| `` || unknown ||
     88|| `fresh_frozen` || Fresh frozen ||
     89|| `ffpe_section` || FFPE section ||
     90|| `ffpe_punch` || FFPE punch ||
     91|| `ffpe_slide` || FFPE slide ||
     92|| `cell_line` || Cell line ||
    6993
    70 ` `ii. Place configuration file `meludi-config.xml` on the BASE server in same directory as `base.config`.
     94=== e. Install MeLuDI configuration file `meludi-config.xml` ===
    7195
    72 === d. Update MeLuDI case label info file `Case_Label_Info.csv`, if existing ===
     96 i. Place configuration file `meludi-config.xml` on the BASE server in same directory as `base.config`.
     97
     98=== f. Update MeLuDI case label info file `Case_Label_Info.csv`, if existing ===
    7399
    74100 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.
     
    77103== 2. Update to MeLuDI v1.5.0
    78104
    79  i. After installation of MeLuDI v1.5.0, run the installation wizard, ''for each of the configured projects as active project''.
     105 i. After installation of MeLuDI v1.5.0, run the installation wizard, ''for each of the configured projects as active project''. This assumes that a BASE project exists for all the projects configured in `meludi-config.xml`. However, it is allowed to configure projects in advance, and then create BASE projects when needed. In that case, run the installation wizard after a configured project has been created in BASE.
     106
     107== 3. Check/modify roles of users
     108
     109 i. MeLuDI v1.5.0 allows a PAD/CL number (Patho-Anatomical Diagnosis/cytology number) to be registered with a case, even if no other patient data is known (e.g. personal number). However, the PAD/CL input field will be disabled if the logged-in user does not have `PatientCurator` or `Administrator` roles. If registration of a PAD/CL number is essential, make sure that all users, that should perform the registration, have `PatientCurator` or `Administrator` roles.