source: extensions/net.sf.basedb.reggie/branches/ticket-422/README @ 1757

Last change on this file since 1757 was 1757, checked in by Nicklas Nordborg, 11 years ago

Catching up on trunk revisions 1734 to 1756.

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[1282]1== Requirements ==
[1757]3 1. BASE 3.2 or later.
5== Introduction ==
7This package is an extension package to BASE that can be used to
8simplify biosource and sample registration.
10 * The homepage for this extension:
[1463]13== Installation and updating ==
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.
[1630]32 9. Manual fixes. Check the release information if any manual changes are
33    needed to items that already exists in BASE.
3410. Done.
36== Using ==
[1282]38Reggie appears as a menu entry in the Extensions menu. All operations
[1301]39are available on that page.
[1334]41 * Installation wizard:
[1301]42   This entry is available if the logged in user is an 'Administrator' and
43   will perform some basic checks that items that are needed by Reggie
44   exists and have been properly configured. Items that doesn't exists can
45   be created automatically.
[1334]47 * Personal information registration wizard:
[1301]48   This entry is available for 'Administrators' and members of the
49   'PatientCurator' group. It is used to register new patients and
50   cases and connect this information to (already existing)
[1334]51   specimen tubes. It can also be used to update missing information
52   on existing cases and specimen tubes.
54 * Blood referral form registration wizard
55   This entry is available for 'Administrators' and members of the
56   'PatientCurator' group. It is used to register blood samples
57   and connect them with patients. The patient doesn't have to exists.
58   If the blood sample already exists, the wizard can be used to update
59   missing information.
[1337]61 * Referral form registration wizard:
62   This entry is available for 'Administrators' and members of the
63   'PatientCurator' group. It is used to connect scanned referral
64   forms (eg. pdf files) to already existing cases.
[1355]66 * Consent form registration wizard:
67    This entry is available for 'Administrators' and members of the
68   'PatientCurator' group. It is used to connect register consent
[1461]69   for participating in the study.
71 * Specimen tube registration wizard:
72   This entry is available for those with permission to create samples.
73   It is used to register new specimen tubes for cases that are not yet
74   in BASE.
76 * Partition registration wizard:
77   This entry is available for those with permission to create samples
78   and extracts. It is used to register new partitions of existing
79   specimen tubes.
81 * DNA/RNA extraction wizards
82   Wizards for registering the extraction of DNA and RNA from the
83   sample material.
[1606]85 * Histology wizards
86   TODO
[1557]88 * RNA quality control wizards
89   Three wizards that are used in the RNA quality control workflow. The
90   first wizard is used for placing the RNA aliquots on a Caliper or
91   Bioanalyzer plate. The second wizard generates a sample name file that
92   can be used by the Caliper software. The third wizard import the results
93   from Caliper back into BASE.
[1282]95== Compiling ==
97To compile this package you also need:
99 1. Ant 1.6
100 2. Java 1.6
102Follow these instructions:
104 1. Download the source code from the subversion repository. See
105 for instructions.
107 2. Type `ant download-lib` to automatically download the BASE core JAR files that
108    are neeed for compilation. You can also do this manually by copying the
[1463]109    base-*.jar files from the BASE installation directory
110    (<basedir>/www/WEB-INF/lib/) to the ./lib/compile directory.
112 3. Type 'ant' to compile the code and generate the 'reggie.jar' file
113    in the project directory.
115 4. Use 'ant package' to create a downloadable tar.gz package.
117Tip: If you need different values for any of the properties defined in
118the 'build.xml' file, create a file named '' and set
119the values there.
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