| 1 | == Requirements == |
|---|
| 2 | |
|---|
| 3 | 1. BASE 2.16.0 or later. |
|---|
| 4 | |
|---|
| 5 | == Introduction == |
|---|
| 6 | |
|---|
| 7 | This package is an extension package to BASE that can be used to |
|---|
| 8 | simplify 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. Go to the Extensions->Reggie |
|---|
| 23 | menu. Select the 'Verify/install required annotation types and other items' |
|---|
| 24 | wizard and create the required items. If the 'Reggie' menu is not visible |
|---|
| 25 | try BASE->Reload permissions menu. |
|---|
| 26 | 6. Done. |
|---|
| 27 | |
|---|
| 28 | |
|---|
| 29 | == Using == |
|---|
| 30 | |
|---|
| 31 | Reggie appears as a menu entry in the Extensions menu. All operations |
|---|
| 32 | are available on that page. |
|---|
| 33 | |
|---|
| 34 | * Verify/install required annotation types and other items: |
|---|
| 35 | This entry is available if the logged in user is an 'Administrator' and |
|---|
| 36 | will perform some basic checks that items that are needed by Reggie |
|---|
| 37 | exists and have been properly configured. Items that doesn't exists can |
|---|
| 38 | be created automatically. |
|---|
| 39 | |
|---|
| 40 | * Personal information registration: |
|---|
| 41 | This entry is available for 'Administrators' and members of the |
|---|
| 42 | 'PatientCurator' group. It is used to register new patients and |
|---|
| 43 | cases and connect this information to (already existing) |
|---|
| 44 | specimen tubes. |
|---|
| 45 | |
|---|
| 46 | |
|---|
| 47 | == Compiling == |
|---|
| 48 | |
|---|
| 49 | To compile this package you also need: |
|---|
| 50 | |
|---|
| 51 | 1. Ant 1.6 |
|---|
| 52 | 2. Java 1.6 |
|---|
| 53 | |
|---|
| 54 | Follow these instructions: |
|---|
| 55 | |
|---|
| 56 | 1. Download the source code from the subversion repository. See |
|---|
| 57 | http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie for instructions. |
|---|
| 58 | |
|---|
| 59 | 2. Type `ant download-lib` to automatically download the BASE core JAR files that |
|---|
| 60 | are neeed for compilation. You can also do this manually by copying the |
|---|
| 61 | BASE2Core.jar, BASE2Webclient.jar and BASE2WSClient.jar |
|---|
| 62 | from the BASE installation directory (<basedir>/www/WEB-INF/lib/) to the |
|---|
| 63 | ./lib/compile directory. |
|---|
| 64 | |
|---|
| 65 | 3. Type 'ant' to compile the code and generate the 'reggie.jar' file |
|---|
| 66 | in the project directory. |
|---|
| 67 | |
|---|
| 68 | 4. Use 'ant package' to create a downloadable tar.gz package. |
|---|
| 69 | |
|---|
| 70 | Tip: If you need different values for any of the properties defined in |
|---|
| 71 | the 'build.xml' file, create a file named 'build.properties' and set |
|---|
| 72 | the values there. |
|---|
| 73 | |
|---|
