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Do not expose OMERO_HOME in the doc (see #10603) #310

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merged 6 commits into from
Apr 9, 2013
Merged

Do not expose OMERO_HOME in the doc (see #10603) #310

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1eb3b8a
Replace OMERO_HOME environment variable by OMERO_PREFIX
sbesson Mar 28, 2013
9565011
Replace OMERO_HOME by OMERO_SOURCE_PREFIX when pointing at source code
sbesson Mar 29, 2013
a6d2c1f
Add warning about setting the OMERO_HOME environment variable
sbesson Apr 1, 2013
94f3b41
Improve readability of paragraphs referring to OMERO_PREFIX
sbesson Apr 1, 2013
c655639
Restore usage of OMERO_HOME variable in OMERO.grid page
sbesson Apr 1, 2013
4c16c77
Expand exported variable and removed unclear paragraph
sbesson Apr 1, 2013
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8 changes: 4 additions & 4 deletions developers/GettingStarted.txt
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Expand Up @@ -74,22 +74,22 @@ the following variables:
::

# E.g. If you built the server yourself
export OMERO_HOME=~/Desktop/OMERO/dist
export OMERO_PREFIX=~/Desktop/OMERO/dist
# Or you downloaded a release package
export OMERO_HOME=~/Desktop/OMERO.server-Beta-4.2.2
export OMERO_PREFIX=~/Desktop/OMERO.server-Beta-4.2.2

- Add the /bin/ directory to your PATH - allows you to call the 'omero'
command from anywhere

::

export PATH=$PATH:$OMERO_HOME/bin/
export PATH=$PATH:$OMERO_PREFIX/bin/

- For Python developers, set your PYTHONPATH as follows

::

export PYTHONPATH=$PYTHONPATH:$OMERO_HOME/lib/python/
export PYTHONPATH=$PYTHONPATH:$OMERO_PREFIX/lib/python/

Now checkout the |CLI|.

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2 changes: 1 addition & 1 deletion developers/Modules/Search.txt
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Expand Up @@ -114,7 +114,7 @@ If you need to re-index your database, stop your server, and:

::

cd $OMERO_HOME
cd $OMERO_PREFIX
CLASSPATH=etc:`find lib/server | xargs | sed 's/ /:/g'`
java -Dlog4j.configuration=log4j-cli.properties -Xmx512M ome.services.fulltext.Main full

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4 changes: 2 additions & 2 deletions developers/Python.txt
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Expand Up @@ -24,8 +24,8 @@ the server package) and setup your PYTHONPATH to include them:

.. parsed-literal::

export OMERO_HOME=~/Desktop/|OMEROserver| # for example
export PYTHONPATH=$OMERO_HOME/lib/python
export OMERO_PREFIX=~/Desktop/|OMEROserver| # for example
export PYTHONPATH=$OMERO_PREFIX/lib/python

.. |OMEROserver| replace:: OMERO.server-|release|-ice3x-byy

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6 changes: 3 additions & 3 deletions developers/Web/CreateApp.txt
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Expand Up @@ -74,11 +74,11 @@ need to follow a few steps (commands are shown below):

::

$ export OMERO_HOME = ~/Desktop/OMERO/dist # Example server build path
$ export OMERO_PREFIX = ~/Desktop/OMERO/dist # Example server build path

# Make sure the Django code etc can be imported
$ export PYTHONPATH=$OMERO_HOME/lib/python/:$PYTHONPATH
$ cd $OMERO_HOME
$ export PYTHONPATH=$OMERO_PREFIX/lib/python/:$PYTHONPATH
$ cd $OMERO_PREFIX
# need to remove the built omeroweb code so it doesn't get imported
$ rm -rf lib/python/omeroweb/

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6 changes: 3 additions & 3 deletions developers/build-system.txt
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Expand Up @@ -20,8 +20,8 @@ it is put, and what role it plays in the distribution.
.. list-table::
:header-rows: 1

* - OMERO_HOME
- OMERO\_HOME/dist
* - OMERO_SOURCE_PREFIX
- OMERO_SOURCE_PREFIX/dist
- Comments
* - components/blitz/target/blitz.jar
- lib/server
Expand Down Expand Up @@ -91,7 +91,7 @@ OMERO:

::

OMERO_HOME
OMERO_SOURCE_PREFIX
|
|-- build.xml .......................... Top-level build driver
|
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2 changes: 1 addition & 1 deletion developers/testing.txt
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Expand Up @@ -33,7 +33,7 @@ which will be missing from any Eclipse project you open before building
the source.

Secondly, Ivy is used to copy all the jar dependencies from
``OMERO_HOME/lib/repository`` to ``COMPONENT/target/libs``, which is
``OMERO_SOURCE_PREFIX/lib/repository`` to ``COMPONENT/target/libs``, which is
then used in the Eclipse :file:`.classpath` files.

If Eclipse ever gets out of sync after the first build,
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12 changes: 6 additions & 6 deletions sysadmins/grid.txt
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Expand Up @@ -374,8 +374,8 @@ Logging
^^^^^^^

Currently all output from OMERO.grid is
stored in ``$OMERO_HOME/var/log/master.out`` with error messages going
to ``$OMERO_HOME/var/log/master.err``. Individual services may also create their
stored in ``$OMERO_PREFIX/var/log/master.out`` with error messages going
to ``$OMERO_PREFIX/var/log/master.err``. Individual services may also create their
own log files.

Shortcuts
Expand Down Expand Up @@ -405,24 +405,24 @@ Symbolic linking
Shortcuts allow the :file:`bin/omero` script to function as a init.d script
when named "**omero-admin**\ ", and need only be copied to
``/etc/init.d/`` to function properly. It will resolve its installation
directory, and execute from there unless ``OMERO_HOME`` is set.
directory, and execute from there unless :envvar:`OMERO_HOME` is set.

For example,

::

ln -s $OMERO_HOME/bin/omero /usr/local/bin/omero
ln -s $OMERO_PREFIX/bin/omero /usr/local/bin/omero
omero-admin start

The same works for putting :file:`bin/omero` on your path:

::

PATH=$OMERO_HOME/bin:$PATH
PATH=$OMERO_PREFIX/bin:$PATH

This means that OMERO.grid can be unpacked
anywhere, and as long as the user invoking the commands has the proper
permissions on the ``$OMERO_HOME`` directory, it will function normally.
permissions on the ``$OMERO_PREFIX`` directory, it will function normally.


Running as root
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4 changes: 2 additions & 2 deletions sysadmins/server-backup-and-restore.txt
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Expand Up @@ -22,8 +22,8 @@ This can be performed daily using cron with a script such as:
USERNAME="root"
PASSWORD="root_password"
BINARY_REPOSITORY="/OMERO"
OMERO_HOME=/home/omero/OMERO-CURRENT
$OMERO_HOME/bin/omero -s localhost -u $USERNAME -w $PASSWORD admin cleanse $BINARY_REPOSITORY
OMERO_PREFIX=/home/omero/OMERO-CURRENT
$OMERO_PREFIX/bin/omero -s localhost -u $USERNAME -w $PASSWORD admin cleanse $BINARY_REPOSITORY

Managing OMERO.server log files
-------------------------------
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33 changes: 18 additions & 15 deletions sysadmins/unix/server-install-linux.txt
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Expand Up @@ -134,12 +134,6 @@ moved into. For example, to install OMERO locally into a directory called
$ mkdir OMERO
$ cd OMERO

.. note::
Recall that earlier you set the :envvar:`OMERO_HOME` environment variable
to :file:`~/apps/OMERO/OMERO.server`. If you change the location that you
wish to install OMERO to then you will also have to alter your
:envvar:`OMERO_HOME` environment variable to reflect this.

OMERO |release|
^^^^^^^^^^^^^^^

Expand All @@ -151,9 +145,10 @@ a release version of OMERO.server, extract it from the zip archive:

$ unzip OMERO.server-|release|-ice33-byy.zip

Give your OMERO software install a nice local name to save some typing
later, to reflect what you set :envvar:`OMERO_HOME` to, and to make it easy to
manage the installation of newer versions of the server at a later date:
Give your OMERO software install a nice local name to save some typing later,
to reflect what you set :envvar:`OMERO_PREFIX` to in the
:ref:`linux_configuration` section, and to make it easy to manage the
installation of newer versions of the server at a later date:

.. parsed-literal::

Expand All @@ -164,20 +159,27 @@ Development server

.. include:: development-server

.. _linux_configuration:

Configuration
-------------

Environment variables
^^^^^^^^^^^^^^^^^^^^^

.. warning::
The :envvar:`OMERO_HOME` environment variable is used internally by OMERO.
Unless you really know what you are doing, it is strongly recommended not
to set this variable.

Edit your :file:`.bashrc` file, e.g. **$ vim ~/.bashrc** and add the
following::

export JAVA_HOME=/usr/lib/jvm/java-6-sun
export ICE_HOME=/usr/share/Ice-3.3.1
export POSTGRES_HOME=/usr/lib/postgresql/8.4
export OMERO_HOME=~/apps/OMERO/OMERO.server
export PATH=$PATH:$JAVA_HOME/bin:$ICE_HOME:$POSTGRES_HOME/bin:$OMERO_HOME/bin
export OMERO_PREFIX=~/apps/OMERO/OMERO.server
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Do we need a warning not to call this OMERO_HOME? It would be so natural to do so given the other _HOMEs.

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That probably brings us back to the question of whether the use of OMERO_HOME internally should be modified.

export PATH=$PATH:$JAVA_HOME/bin:$ICE_HOME:$POSTGRES_HOME/bin:$OMERO_PREFIX/bin
export PYTHONPATH=/usr/lib/pymodules/python2.6:$PYTHONPATH
export LD_LIBRARY_PATH=/usr/share/java:/usr/lib:$LD_LIBRARY_PATH

Expand All @@ -196,12 +198,13 @@ apply them using the **source** built in command::
You can check that the new environment variables have taken by printing
their values to the shell, e.g.::

$ echo $OMERO_HOME

should give output similar to the following::

$ echo $OMERO_PREFIX
~/apps/OMERO/OMERO.server
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I'd be surprised if the tilde got this far, won't it have been expanded in the processing of a previous export statement?


If you change the location that you wish to install OMERO to, then you will
also have to alter your :envvar:`OMERO_PREFIX` environment variable to reflect
this.
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Why? Surely it only has any effect if one also sets the variables that depend upon it in the other export statements?


Database creation
^^^^^^^^^^^^^^^^^

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