source: extensions/net.sf.basedb.reggie/trunk/README @ 1546

Last change on this file since 1546 was 1527, checked in by Nicklas Nordborg, 10 years ago

Preparing release Reggie 2.2

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[1282]1== Requirements ==
2
[1463]3 1. BASE 3.0 or later.
[1282]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
[1463]13== Installation and updating ==
[1282]14
15 1. Download the reggie-*.tar.gz file.
16 2. Unpack the downloaded file to a directory of your choice.
[1463]17 3. Copy the 'reggie.jar' file to your BASE plug-ins directory.
18    Eg. the directory specified by the 'plugins.dir' setting in 'base.config'.
19 4. Log in to BASE as a user with Administrator priviliges.
20 5. Go to 'Administrate->Plug-ins & Extensions->Overview' page.
21    Run the installation wizard and select to install/update 'reggie.jar'.
[1310]22 6. Create a project and set it as the active project. This step is
23    optional but is recommended. Running Reggie without an active project
24    will generate warning messages later on.
[1334]25 7. Go to the Extensions->Reggie menu. Select the 'Installation wizard'
26    If the 'Reggie' menu is not visible try BASE->Reload permissions menu.
[1310]27 8. It should display a list with several error message about missing items.
28    Click on the "Create missing items" button to create them. If no project
29    was created in step 6, all annotatation types will be shared with the
30    'PatientCurator' group, otherwise only some will be shared to the
31    group and some will be shared to the active project.
32 9. Done.
[1301]33
34== Using ==
35 
[1282]36Reggie appears as a menu entry in the Extensions menu. All operations
[1301]37are available on that page.
[1282]38
[1334]39 * Installation wizard:
[1301]40   This entry is available if the logged in user is an 'Administrator' and
41   will perform some basic checks that items that are needed by Reggie
42   exists and have been properly configured. Items that doesn't exists can
43   be created automatically.
44   
[1334]45 * Personal information registration wizard:
[1301]46   This entry is available for 'Administrators' and members of the
47   'PatientCurator' group. It is used to register new patients and
48   cases and connect this information to (already existing)
[1334]49   specimen tubes. It can also be used to update missing information
50   on existing cases and specimen tubes.
[1527]51 
52 * Blood referral form registration wizard
53   This entry is available for 'Administrators' and members of the
54   'PatientCurator' group. It is used to register blood samples
55   and connect them with patients. The patient doesn't have to exists.
56   If the blood sample already exists, the wizard can be used to update
57   missing information.
58
[1337]59 * Referral form registration wizard:
60   This entry is available for 'Administrators' and members of the
61   'PatientCurator' group. It is used to connect scanned referral
62   forms (eg. pdf files) to already existing cases.
[1301]63
[1355]64 * Consent form registration wizard:
65    This entry is available for 'Administrators' and members of the
66   'PatientCurator' group. It is used to connect register consent
[1461]67   for participating in the study.
68   
69 * Specimen tube registration wizard:
70   This entry is available for those with permission to create samples.
71   It is used to register new specimen tubes for cases that are not yet
72   in BASE.
73 
74 * Partition registration wizard:
75   This entry is available for those with permission to create samples
76   and extracts. It is used to register new partitions of existing
77   specimen tubes.
[1301]78
[1282]79== Compiling ==
80
81To compile this package you also need:
82 
83 1. Ant 1.6
84 2. Java 1.6
85
86Follow these instructions:
87
88 1. Download the source code from the subversion repository. See
89    http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie for instructions.
90 
91 2. Type `ant download-lib` to automatically download the BASE core JAR files that
92    are neeed for compilation. You can also do this manually by copying the
[1463]93    base-*.jar files from the BASE installation directory
94    (<basedir>/www/WEB-INF/lib/) to the ./lib/compile directory.
[1282]95
96 3. Type 'ant' to compile the code and generate the 'reggie.jar' file
97    in the project directory.
98
99 4. Use 'ant package' to create a downloadable tar.gz package.
100 
101Tip: If you need different values for any of the properties defined in
102the 'build.xml' file, create a file named 'build.properties' and set
103the values there.
104
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