source: extensions/net.sf.basedb.reggie/trunk/README @ 1310

Last change on this file since 1310 was 1310, checked in by Nicklas Nordborg, 11 years ago

References #292: Check/create annotation types, etc. required by reggie

Smarter check for required permissions when a project is active. Only some of the annotation types (with personal information) need to be shared to the 'PatientCurator?' group. The other annotation types can be shared to the active project.

Important note! This code is affected by http://base.thep.lu.se/ticket/1583 if an item is already shared to a different project or group than the active project or 'PatientCurator?' group. This will result in a (almost) blank page that can't be used for validation or create missing items.

File size: 3.0 KB
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1== Requirements ==
2
3 1. BASE 2.16.0 or later.
4 
5== Introduction ==
6
7This package is an extension package to BASE that can be used to
8simplify biosource and sample registration.
9
10 * The homepage for this extension:
11   http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie
12
13== Installation ==
14
15 1. Download the reggie-*.tar.gz file.
16 2. Unpack the downloaded file to a directory of your choice.
17 3. Copy the 'reggie.jar' file and the 'lib' directory to your BASE extensions
18    directory: WEB-INF/extensions.
19 4. Run the 'Extensions->Manual scan' command if you have disabled automatic
20    installation. Otherwise, just wait a bit and the automatic installation will
21    find and install the new extension.
22 5. Log in as a user with Administrator priviliges.
23 6. Create a project and set it as the active project. This step is
24    optional but is recommended. Running Reggie without an active project
25    will generate warning messages later on.
26 7. Go to the Extensions->Reggie menu. Select the 'Verify/install required
27    annotation types and other items' wizard. If the 'Reggie' menu is not
28    visible try BASE->Reload permissions menu.
29 8. It should display a list with several error message about missing items.
30    Click on the "Create missing items" button to create them. If no project
31    was created in step 6, all annotatation types will be shared with the
32    'PatientCurator' group, otherwise only some will be shared to the
33    group and some will be shared to the active project.
34 9. Done.
35
36 
37== Using ==
38 
39Reggie appears as a menu entry in the Extensions menu. All operations
40are available on that page.
41
42 * Verify/install required annotation types and other items:
43   This entry is available if the logged in user is an 'Administrator' and
44   will perform some basic checks that items that are needed by Reggie
45   exists and have been properly configured. Items that doesn't exists can
46   be created automatically.
47   
48 * Personal information registration:
49   This entry is available for 'Administrators' and members of the
50   'PatientCurator' group. It is used to register new patients and
51   cases and connect this information to (already existing)
52   specimen tubes.
53
54
55== Compiling ==
56
57To compile this package you also need:
58 
59 1. Ant 1.6
60 2. Java 1.6
61
62Follow these instructions:
63
64 1. Download the source code from the subversion repository. See
65    http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie for instructions.
66 
67 2. Type `ant download-lib` to automatically download the BASE core JAR files that
68    are neeed for compilation. You can also do this manually by copying the
69    BASE2Core.jar, BASE2Webclient.jar and BASE2WSClient.jar
70    from the BASE installation directory (<basedir>/www/WEB-INF/lib/) to the
71    ./lib/compile directory.
72
73 3. Type 'ant' to compile the code and generate the 'reggie.jar' file
74    in the project directory.
75
76 4. Use 'ant package' to create a downloadable tar.gz package.
77 
78Tip: If you need different values for any of the properties defined in
79the 'build.xml' file, create a file named 'build.properties' and set
80the values there.
81
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