How to Update from v16 (Linux)¶

The changes from v1.6 requires update of all in-house components of Leginon, dbemtools and database
but not the mrctools.
Don't forget that you need to also update the packages on the microscope-controlling computer
since the pyScope update need to be synchronized.

See Installation Troubleshooting and Leginon Bulletin Board searching
for "install" if you run into problems.

Packages required from NRAMM¶

All Leginon (and Appion) packages distributed from NRAMM are not under one svn control.

A few updates are needed for preparation of python 3.0 compatibility where the method for importing module is changed. They will still run under python 2.4 and up.
Here are the packages you need to install with python installer

SVN subPackage Name	Reason for update:
numextension	package import method change
libcv	package import method change
leginon	new features
pyami	new features
sinedon	required for updating database
pyscope	new method for creating pythoncom modules
imageviewer	debug

Check out SVN Source Files from the depository¶

From a text terminal:

cd ~
svn co http://emg.nysbc.org/svn/myami/trunk Leginon2.0

Perform system check if you can't remember where you have installed your Leginon before.¶

cd ~/Leginon2.0/leginon
python syscheck.py

You should have all the supporting packages installed for v1.6. If you see any lines like "*** Failed...", then you have something missing. Otherwise, everything should result in "OK".

Move your existing packages to a backup directory:¶

At the beginning of the syscheck.py output, the location of the exisiting Leginon folder is shown. Although new installation overwrite the old in most cases, problem has been observed in the past. Therefore, it is best to remove the old files from the path before new installation. Better yet, copy into a backup folder because we need some configuration files from them.

For example, your Leginon folder is at /usr/lib/python/site-packages/Leginon

cd /usr/lib/python/site-packages
mkdir Leginon1_6_backup
mv Leginon Leginon1_6_backup

Be aware that in some cases the installed package name is different (capitalized) from your svn package name and that numextension amd libCV are not in its own subdirectory in the python library but just the compiled .so files

Install the subpackages you downloaded from NRAMM svn depository¶

• run syscheck.py again to make sure you have everything.

• Reinstall the subpackage in each folder with commands such as
  

  cd ~/Leginon2.0/leginon
  python setup.py install

Copy your Leginon1.6 sinedon.cfg to the new installation¶

• Find your sinedon.cfg. Depending on your previous setting, look in the directories listed here in order:
  *your home directory as described in syscheck.py
  *The sinedon directory where it is called from. If unsure, start python command line and type these to find out:
  

  python> import sinedon
  python> sinedon

• If sinedon.cfg reside in the installed sinedon subpackage, you should copy it from your Leginon1,6 backup to the new installation.
  

  cd /your_default_python_installation_path
  cp Leginon_1_6_backup/sinedon/sinedon.cfg sinedon
  

Back up all your databases¶

We will be doing a database update that is not backward compatible, Make sure you back up all your current databases before performing the update

• mysqldump -u usr_object your_leginon_database > leginondb_1_6_backup_today's_date
• mysqldump -u usr_object your_project_database > projectdb_1_2_backup_today's_date
• .... do the same to any of your processing databases if you have installed and used Appion 1.0

Install updated Web viewers and tools¶

See Install the Web Interface section in Complete Installation Chapter before coming back to the next step.

Reset installation status in the project database¶

You can do this directly by mysql commands.

mysql projectdata

> mysql projectdata -u usr_object
mysql> drop table install;
mysql> exit

Alternatively, you can use phpMyAdmin to achieve this by visiting the database, find the table and click on drop.

Visit the updated tools for project management¶

See projecttools installation section in Complete Installation Chapter.

Run database update scripts¶

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