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Protégé Server Build Procedures
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Objective
This procedural guide is meant for use in performing a new Protégé server build for both the NCI Thesaurus and BiomedGT instances. Protégé server builds can be performed either manually, or via automated run scripts. Generally, using the automated scripts would be less time-consuming. However, it is recommended that going through the manual process (at least once) be performed to understand the concepts and the workflow of a Protege build. Doing so will facilitate troubleshooting any future problems during a build.
Server builds can include items such as bug fixes, software updates, and updates to the database schema. Build procedures will differ depending upon the aforementioned scenarios.
Background
Protégé is a free, open-source editor, specific for working with ontologies.
Component Overview
- MySQL - All Protégé data resides in a MySQL database.
- Protégé Server - The Protégé Server itself is an open-source application developed by Stanford University. It pulls data from a MySQL database and serves it up through RMI. The Protégé Server is compiled and run with Java 5.0. We currently have it running on a Linux OS.
- Explanation Server - The Explanation server is also an open-source application developed by the Clark & Parsia group in the Washington D.C. area. The server makes a connection to a specified Protege database, and classifies all concepts. The server will then allow users to pull up and view any concept's super-concepts as well as sub-concepts.
- Protégé Client (Editor) - The Protégé Client is the editing tool which the editors utilize to create, update, or view the various concept and concept property data. Data can be accessed from the database via the Protégé Server. The editors have the client running on their Windows workstations.
Steps for Jenkins build
There are 2 parts to the Jenkins build, the compilation and the deployment. Navigate to https://evs-jenkins.nci.nih.gov and find "default >> lower >> protege". Select "protege-build" and select the tag given to you by the developers. The build will take 10-15 minutes. At the conclusion, go to "protege_deploy_dev" and deploy the tag you just built.
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Steps to complete a Manual Protégé Server Build Process for Dev, QA, and Stage Tiers
You will need tier-specific info for Dev, QA, Stage before commencing the build. Production-tier information is separated, since the information is a bit different than the other tiers.
Backup Current Database Project
If there is an existing database project file which the Protege server is referencing, it would be a good idea to save a backup copy, in case the project ever needs to be rolled back to due to new build complications. Please follow the steps below to export a copy of the database to a file. If this is the very first build from scratch, scroll down to the 'Protege Updated File Checkout and Build' section.
- Open Reflection X to connect to your server instance (obtain username and password info from the system administrator).
- Before shutting down the server, we will need to create a backup of the project before updating. From the terminal, go to
...
- /usr/local/protégé/Protégé_x.x/<PROTÉGÉ
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- INSTANCE>/Protégé.Client-x.x.x
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- and
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- run
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- sh
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- run_protege.bat.
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Protege_x.x
...
- represents
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- the
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- current
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- Protégé
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- release
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- version
...
- number.
...
PROTÉGÉ
...
- INSTANCE
...
- represents
...
- either
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- BiomedGT
...
- or
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- NCIThesaurus
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- ontology.
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Protégé.Client-x.x.x
...
- represents
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- the
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- current
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- build
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- version
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- number.
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- Connect
...
- with
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- the
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- database
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- project
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- on
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- the
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- server.
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- The
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- database
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- project
...
- should
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- have
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- the
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- following
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- naming
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- convention:
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- <PROTEGE
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- INSTANCE>-YYMMDD-DB.pprj.
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- Click
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- File,
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- Convert
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- Project
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- to
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- Format,
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- Select
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- OWL
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- /
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- RDF
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- File,
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- Enter
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- location
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- and
...
- name
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- of
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- new
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- file
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- (Use
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- '<PROTÉGÉ
...
- INSTANCE>-YYMMDD-File.owl'
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- as
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- the
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- filename
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- convention),
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- Click
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- OK.
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- This
...
- file
...
- can
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- be
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- saved
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- at
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- app/protégé/data/Protégé_x.x/<PROTÉGÉ
...
- INSTANCE>.
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- Depending
...
- on
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- the
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- size
...
- of
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- the
...
- database,
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- conversion
...
- can
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- usually
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- take
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- up
...
- to
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- 30
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- minutes.
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- Exit
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- the
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- Protégé
...
- client
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- WITHOUT
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- saving.
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Protégé
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Updated
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File
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Checkout
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and
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Build
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- Checkout
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- can
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- be
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- performed
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- from
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- a
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- Windows
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- GUI
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- (if
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- the
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- Tortoise
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- SVN
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- client
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- tool
...
- is
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- installed)
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- or,
...
- if
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- via
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- command
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- prompt
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- on
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- the
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- Linux
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- server.
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- To
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- run
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- from
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- the
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- Windows
...
- GUI:
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- Create
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- the
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- following
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- folder
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- structure:
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- nciscn<YYMMDD><VERSION>/protegegui/.
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- From
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- this
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- location,
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- right
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- click,
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- select
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- 'SVN
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- Checkout'.
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- A
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- window
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- will
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- appear
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- asking
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- for
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- the
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- source
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- and
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- target
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- of
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- files.
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- Protégé
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- files
...
- are
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- located
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- in
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- NCI
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- SVN,
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- and
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- can
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- be
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- checked
...
- out
...
- from:
...
...
To
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run
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from
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command
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prompt
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on
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the
...
server,
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navigate
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to
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/app/protégé/repo,
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and
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create
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the
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following
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directory
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ncisvn<YYMMDD><VERSION>/protegegui/
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and
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run the svn checkout:
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To checkout the Protege source code, you can use the following target:
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There may be instances where you will need to modify a few targets within the branches tag to reflect changes in other projects. In this case, you must verify that the proper 'svn-url.properties
...
file
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is
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being
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referenced
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in
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the
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build.xml
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file.
...
Each
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build
...
will
...
hold
...
2
...
separate
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svn-url.properties
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files.
...
One
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is
...
usually
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the
...
default,
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which
...
builds
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from
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the
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trunk
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folder.
...
There
...
is
...
also
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a
...
customized
...
file
...
that
...
will
...
build
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from
...
the
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branches
...
folders.
...
Example
...
code
...
snippets
...
are
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below
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for
...
each
...
file:
...
Code Block
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svn-url-trunk.properties (default) 'ncitab.url=$nci.base.url/protegegui/*trunk*' ncitab.project=$projects/ncitab nciconcepthistory.url=$nci.base.url/protegehistory/NCIConceptHistory/*trunk* nciconcepthistory.project=$projects/nciprojecthistory ncievshistory.url=$nci.base.url/protegehistory/NCIEVSHistory/*trunk* ncievshistory.project=$projects/ncievshistory classification.url=$nci.base.url/classification/*trunk* classification.project=$projects/classification *svn-url-1.4.properties (customized)* ncitab.url=$nci.base.url/*nci-branches/1.4*/protegegui ncitab.project=$projects/ncitab nciconcepthistory.url=$nci.base.url/*nci-branches/1.4*/NCIConceptHistory nciconcepthistory.project=$projects/nciconcepthistory ncievshistory.url=$nci.base.url*/nci-branches/1.4*/NCIEVSHistory ncievshistory.project=$projects/ncievshistory classification.url=$nci.base.url/*nci-branches/1.4*/classification classification.project=$projects/classification
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- You can either keep the newly created build folder in your local directory and build from there (assuming ant is installed locally), or transfer it to the server machine under app/protégé/repo.
...
- Utilize
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- secure
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- ssh
...
- client
...
- to
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- transfer
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- the
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- svn
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- checkout
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- files
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- over
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- to
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- the
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- server.
...
- Navigate
...
- to
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- <PATH>/trunk
...
- and
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- open
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- the
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- '
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- build.properties'
...
- file
...
- and
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- modify
...
- the
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- 'PromptNCIPlugins.properties
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- settings'
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- section
...
- within
...
- the
...
- file.
...
- This
...
- info
...
- represents
...
- the
...
...
...
...
...
- ,
...
- and
...
- will
...
- need
...
- to
...
- be
...
- set
...
- before
...
- running
...
- the
...
- ant
...
- build
...
- commands.
...
- To
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- edit
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- the
...
- file
...
- using
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- a
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- Unix
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- VI
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- editor
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- within
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- the
...
- server
...
- console,
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- type
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- 'vi
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- local.properties'.
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- The
...
- file
...
- should
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- now
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- be
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- displayed
...
- in
...
- the
...
- console.
...
- ype
...
- 'Shift
...
- +
...
- I
...
- (eye)'
...
- to
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- enable
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- editing,
...
- and
...
- utilize
...
- the
...
- arrow
...
- keys
...
- to
...
- navigate
...
- to
...
- the
...
- PromptNCIPlugins.properties
...
- section,
...
- and
...
- fill
...
- in
...
- the
...
- default
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- database
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- connection
...
- values
...
- with
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- tier-specific
...
- values.
...
- Upon
...
- completion,
...
- type
...
- 'esc'
...
- to
...
- move
...
- out
...
- of
...
- editing
...
- mode,
...
- and
...
- type
...
- ':wq'
...
- to
...
- overwrite,
...
- save
...
- changes,
...
- and
...
- exit
...
- the
...
- file
...
- back
...
- to
...
- the
...
- console
...
- prompt.
...
- Within
...
- the
...
- same
...
- directory,
...
- open
...
- the
...
- 'version.info'
...
- file
...
- and
...
- modify
...
- the
...
- current
...
- version
...
- to
...
- the
...
- latest
...
- version
...
- (if
...
- necessary)
...
- following
...
- the
...
- same
...
- steps
...
- as
...
- above.
...
- By
...
- default,
...
- the
...
- version
...
- number
...
- will
...
- display
...
- as
...
- 1.1.0.
...
- Save
...
- changes
...
- following
...
- the
...
- instructions
...
- above.
...
Protege
...
Server
...
Build
...
Ant
...
Commands
...
Run
...
the
...
following
...
ant
...
commands
...
within
...
the
...
same
...
directory
...
as
...
the
...
build.xml
...
file.
...
The
...
build.xml
...
is
...
usually
...
stored
...
in
...
the
...
same
...
directory
...
as
...
the
...
'local.properties'
...
and
...
'version.info'
...
file.
...
Once
...
the
...
build.xml
...
file
...
is
...
found,
...
the
...
ant
...
build
...
targets
...
are
...
now
...
ready
...
to
...
be
...
run:
...
- Run
...
- '
...
- ant
...
- checkout'
...
- .
...
- This
...
- command
...
- will
...
- check
...
- out
...
- all
...
- files
...
- from
...
- Stanford
...
- University
...
- that
...
- were
...
- not
...
- included,
...
- but
...
- are
...
- essential
...
- to
...
- the
...
- Protégé
...
- Build.
...
- Upon
...
- successful
...
- checkout,
...
- run
...
- '
...
- ant
...
- install
...
- .'
...
- This
...
- process
...
- will
...
- compile
...
- all
...
- checked
...
- out
...
- files
...
- and
...
- will
...
- create
...
- a
...
- build/dist
...
- and
...
- build/archive
...
- subdirectory.
...
- The
...
- build/dist
...
- folder
...
- will
...
- contains
...
- updated
...
- Protégé
...
- client,
...
- server,
...
- admin,
...
- and
...
- explanation
...
- folders.
...
- Run 'ant
...
- archive
...
- '
...
- to
...
- create
...
- zip
...
- files
...
- for
...
- each
...
- of
...
- the
...
- Protégé
...
- packages.
...
- The
...
- process
...
- will
...
- also
...
- create
...
- an
...
- ncibuilder.zip
...
- file.
...
- This
...
- file
...
- contains
...
- all
...
- files
...
- for
...
- the
...
- entire
...
- project.
...
- The
...
- file
...
- will
...
- be
...
- created
...
- at
...
- <PATH>
...
- /trunk/build/archive.
...
- Transfer
...
- the
...
- folders
...
- to
...
- usr/local/protégé/Protégé_x.x/<PROTÉGÉ
...
- INSTANCE>
...
- on
...
- the
...
- server
...
- machine.
...
- A
...
- copy
...
- of
...
- the
...
- client
...
- folder
...
- should
...
- also
...
- be
...
- saved
...
- on
...
- your
...
- local
...
- machine,
...
- to
...
- test
...
- a
...
- successful
...
- connection
...
- to
...
- the
...
- server
...
- after
...
- the
...
- build.
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| } When copying the client to any server tier from Windows, DO NOT copy the JRE folder. A copy of the JRE should already installed on the server box, and copying over an existing JRE will take too long. {note} h3. Configuring New Protege Build If the build involves software updates that include any database code or schema changes, skip to the '[Protege Software Updates & Configuring New Database Project|Protege Software Updates and Configuring New Database Project]' section. For builds that will only require software updates connecting to an existing database project, please follow the '[Protege Software Updates|Protege Software Updates]' section. {scrollbar:icons=false} |
Configuring New Protege Build
If the build involves software updates that include any database code or schema changes, skip to the 'Protege Software Updates & Configuring New Database Project' section. For builds that will only require software updates connecting to an existing database project, please follow the 'Protege Software Updates' section.
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