How to Update from v16 (Linux)¶

The changes from v1.6 requires update of all in-house components of Leginon, dbemtools (called myamiweb in the new version) and database
but not the php mrctools.

This processing package upgrade instruction includes that for installing Appion's processing scripts and executables. They have more supporting package requirement. Therefore, if you do not plan to use Appion on this computer, you may skip it.

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.

Check and correct the following before you start, because we did not put in the checks for you, and your upgrade will fail if it is incorrect.¶

You must have an administrator user in your database

1. Go to "http://your_host/dbem_1_5_1/adduser.php
2. Check to see that you do have a user with "name" ( as in username) as "administrator" (all lower-case). If you don't have one, make one and save it.

All users should be assigned to a group

1. Go to "http://your_host/dbem_1_5_1/addgroup.php
2. Create at least a group and save
3. Go to "http://your_host/dbem_1_5_1/adduser.php
4. If you did not have group created before, select each user and choose a group and then click save. If there is only one group that you just created, you will need to click save even though you can not make the group selection.

Packages required from NRAMM¶

All Leginon (and Appion) packages distributed from NRAMM are now under one svn control called myami.

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

Download Leginon 2.0 source code (substitute that of newer releases by 2.0 ones)¶

Download myami (contains Appion and Leginon) using one of the following options:

Option 1: 3.4 version (Current release)¶

• We have switched to git for version control.
  

  git clone -b myami-3.4 https://emg.nysbc.org/git/myami myami
  

  
  Note: If you are installing these files on a microscope Windows PC, you may use Git for Windows to clone the files. See notes on configuration note in Here Check compatibility as newer version does not support Windows XP.

Option 2: beta-release version (Used and updated at NRAMM daily with newest features that may not yet documented)¶

• We have switched to git for version control.
  

  git clone -b myami-beta https://emg.nysbc.org/git/myami myami
  

  
  Note: If you are installing these files on a microscope Windows PC, you may use Git for Windows to clone the files. See notes on configuration note in Here Check compatibility as newer version does not support Windows XP.

Option 3: Development version (For true developer to play with)¶

• We have switched to git for version control recently. trunk and future release branches will be available with git clone
• unstable with latest features

 
This contains features that may still be under development. It is not supported and may not be stable. Use at your own risk.

git clone -b trunk https://your_redmine_username@emg.nysbc.org/git/myami myami

• your_redmine_username is required if you intend and have permission to push changes to our repository. Please ask the development team if you would like to contribute.*

Note: If you are installing these files on a microscope Windows PC, you may use Git for Windows to clone the files. See notes on configuration note in Here Check compatibility as newer version does not support Windows XP.

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

cd /your_download_area/myami/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 python processing 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

cd /path/to/myami-VERSION/myami
sudo ./pysetup.sh install

That will install each package, and report any failures. To determine the cause of failure, see the generated log file "pysetup.log".

Packages installed by pysetup.sh¶

Package Path:
pyami
myami_test
sinedon
leginon
pyscope
imageviewer
modules/numextension
modules/radermacher
modules/libcv

alternatively, install a specific package in turn¶

If necessary, you can enter a specific package directory and run the python setup command manually. For example, if pyami failed to install, you can try again like this:

cd pyami
sudo python setup.py install

python-site-package-path: where the installed python packages went:¶

Python installer put the packages you installed into its site-packages directory. This enables all users on the same computer to access them. The easiest way to discover where your installed package is loaded from by python is to load a module from the package using interactive python command lines like this:

Start the python command line from shell:

python

Import a module from the package. Let's try pyami here. All packages installed through the above setup.py script should go to the same place.
At the python prompt (python>) type:

import pyami

If the module is loaded successfully, call the module attribute path (two underscrolls before "path" and two underscrolls after) will return the location of the module it is loaded from

pyami.__path__
['/usr/lib/python2.6/site-packages/pyami']

In this case, /usr/lib/python2.6/site-packages/ is your python-site-package-path. If you go to that directory, you will find all the packages you just installed.

Save this value as an environment variable for use later, for bash:

export PYTHONSITEPKG='/usr/lib/python2.6/site-packages'

or C shell

setenv PYTHONSITEPKG '/usr/lib/python2.6/site-packages'

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
  

Copy your Leginon1.6 leginon.cfg to the new installation similarly¶

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

  python> import leginon
  python> leginon

• If leginon.cfg reside in the installed leginon 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/Leginon/leginon.cfg leginon
  

Back up all your databases¶

Very Important: Fix the bad tables before backup with mysqldump or the backup would be corrrupted. Sorry, it was our fault a long time ago.

Check and Fix your database for bad tables¶

We've found this on two databases outside NRAMM that there are empty tables created that causes a bad database backup. Please check and correct your database first before your backup.

1. start mysql command line on your leginondb
   

   mysql -u usr_object your_leginon_database
   

2. display all tables
   

   mysql> show tables;
   

3. if you find both BindngSpecData and bindingspecdata, you have a problem. The former has data in there and the later does not. If you have data in both tables, please contact us. We will need to create a customized solution. You can check like this:
   

   mysql> select * from BindingSpecData;
   mysql> select * from bindingspecdata;
   

4. remove the empty lowercased table
   

   mysql> drop table bindingspecdata;
   

5. repeat 3-4 on launchedapplicationdata and nodespecdata

Backup¶

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 beta

Install updated Web viewers and tools¶

You will not need to upgrade php mrc tools.

See Install the Web Interface section in Complete Installation Chapter to put the new web tools (Now under subpackage myamiweb) to document root for the web server.

Step through setup wizard in the myamiweb on your server¶

The Setup Wizard will take you through the steps to create config.php and to create and initialize values for the new tables. For example, project database will contain a table called privileges when you finish. Your old config.php is not formatted correctly for the new viewers but the parameters for databases stands. You can enter them in the wizard.

You will be asked about whether you want to enable myamiweb user login feature that restricts individual user's access to projects and administrator features. Read about it here

Check and modify your sinedon.cfg to be compatible to the new version¶

All module names are now all in lower cass.

Run Database Update Script¶

Running the following script will indicate if you need to run any database update scripts.

cd /your_download_area/myami/dbschema
python schema_update.py

This will print out a list of commands to paste into a shell which will run database update scripts.
You can re-run schema_update.py at any time to update the list of which scripts still need to be run.

There should be a least scripts to run.
The first one updates UserData and GroupData so that new data viewing and processing privileges can be enforced
The second is a wide-scale change on database schema many on appion processing databases if you had one, and some on projectdata and leginondata.
The third fills in some appion data that was obtained with slow query in previous versions.
The rest are debug update after the release of 2.0.0.

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How to Update from v1.6 (Microscope Windows Computer) >

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