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How to Update from v16 (Microscope Windows Computer) » History » Revision 2

Revision 1 (Anchi Cheng, 05/18/2010 09:43 PM) → Revision 2/21 (Anchi Cheng, 05/18/2010 10:15 PM)

h1. How to Update from v16 (Window) 

 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 By switching to svn package check out, you now need to also update the packages install svn on Windows to get the microscope-controlling computer 
 since the pyScope update need to be synchronized. updated packages. Because numextension and libCV requires extra compiler, we have created 
 window installer for them for python 2.5 and made them available through "http://www.leginon.org/":http://www.leginon.org/ 

 See [[Installation Troubleshooting]] <link linkend="InstT_install">Installation Troubleshooting</link> and    "Leginon Bulletin Board":http://emg.nysbc.org/bb/viewforum.php?f=2    searching 
 for "install" if you run into problems. 

 h2. Packages required from NRAMM 

 All Leginon (and Appion) packages distributed from NRAMM are now 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 Package Name|_.Installed Python Package Name|_.Reason for update:| 
 |numextension|package import method change| |leginon|Leginon|new features| 
 |libcv|package import method change| |pyami|pyami|clean up| 
 |leginon|new features| |sinedon|sinedon|new stuff| 
 |pyami|new features| |pyScope|pyScope|new instrument configuration| 
 |sinedon|required |ImageViewer|ImageViewer|updated and required for updating database| 
 |pyscope|new method for creating pythoncom modules| 
 |imageviewer|debug| tomography| 

 Because numextension and libcv libCV requires extra compiler, we have created 
 window installer 
 for them for python 2.5 and made them available through "http://www.leginon.org/":http://www.leginon.org/ 

 h2. Check out SVN Source Files from the depository 

 Assuming that you have installed some kind of svn client such as TortoiseSVN "http://tortoisesvn.tigris.org/", you can use your mouse to do the following |_.Downloadfile Name|_.Installed Python Package File|_.Reason for update:| 
 *Create Leginon2.0 directory somewhere at your convenience |NumExtension-1.2.0.win32-py2.5.exe|numextension.pyd|clean up| 
 *Change directory into Leginon2.0 
 *Right-click the mouse botton in this directory window and select Tortoise svn 
 Checkout in the menu:!http://emg.nysbc.org/software/leginon/images/images/svnmenu.png! 
 *Set up svn checkout window like this, but check out from http://emg.nysbc.org/svn/myami/trunk and save it to Leginon2.0 folder !http://emg.nysbc.org/software/leginon/images/images/svnco.png! 


 h2. Perform system check if you can't remember where you have installed your Leginon before. |libCV-0.2.win32-py2.5.exe|libCV.pyd|bug fixes| 

 *Go to ~/Leginon2.0/leginon 
 *Double click on 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". 

 h2. Uninstall your existing packages: 

 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 before new installation. 

 Use "Add or Remove Programs" application in "Control Panel" to do this. Leginon related 
 packages are shown with prefix "Python 2.5" 

 If you didn't use Installer to install previously, the packages may not show up in the 
 Programs list. Simply remove or rename the folder containing the old packages in this case. 

 h2. Move your existing packages to a backup directory: Download and install SVN client program: 

 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 By switching to remove svn package check out, you now need to install svn client on Windows to 
 get the old files updated packages. We recommand TortoiseSVN "http://tortoisesvn.tigris.org/":http://www.leginon.org/ . 

 h2. Check out SVN Source Files from the path before new installation.    Better yet, copy into a backup folder because we need some configuration files from them. depository 

 For example, Use your Leginon folder is at C:\\python25\Lib\site-packages\Leginon 

 <pre>Go mouse to C\\python25\site-packages do the following 
 Create Leginon1_6_backup folder *Create Leginon-1.6-ALL directory somewhere at your convenience 
 Move Leginon fold *Change directory into Leginon1_6_backup folder</pre> 

 Be aware that Leginon-1.6-ALL 
 *Right-click the mouse botton in some cases the installed package name is different (capitalized) from your this directory window and select Tortoise svn package name and that numextension amd libCV are not 
 Checkout in its own subdirectory in the python library but just menu:!http://emg.nysbc.org/software/leginon/images/images/svnmenu.png! 
 *Set up svn checkout window like this for each of the compiled .so files leginon package!http://emg.nysbc.org/software/leginon/images/images/svnco.png! 

 h2. Install the subpackages packages you downloaded from NRAMM svn depository 

 * Start a command line Window from Start Menu 

 * Reinstall the package in each folder with commands such as 
 <pre>cd Your_Download_Place\Leginon 2.0\leginon Your_Download_Place\Leginon-1.6-ALL\leginon 
 c:\\python25\python.exe setup.py install</pre> 
 * run syscheck.py again to make sure you have everything. 

 h2. Copy your Leginon1.6 sinedon.cfg to Download the new installation two Window Installer Files from Leginon website 

 * Find your sinedon.cfg. Depending on your previous setting, look in "http://www.leginon.org/":http://www.leginon.org/ 

 h2. Install individual packages 

 Excute 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 installer files and type these follow the instruction. 

 h2. Transfer Drift adjustment preference to find out: 
 <pre>python> import sinedon 
 python> sinedon</pre> use Transform Manager 

 *    If sinedon.cfg reside in the installed sinedon subpackage, you should copy it from your Leginon1.6 backup This procedure copies all most recent user settings to that required by the new installation. 
 <pre>go to    C:\\python25\Lib\site-packages\ transform 
 copy Leginon_1_6_backup\sinedon\sinedon.cfg    into the new sinedon folder manager.<pre>cd leginon 
 </pre> python update16.py</pre> 

 h2. 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 Import the update new (1.6) applications included with Leginon 

 * 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 Follow the same to any of your processing databases if you have installed and used Appion 1.0 

 h2. Install updated Web viewers and tools 

 See [[Install the Web Interface]] section instructions in Complete Installation Administrator Chapter to put the new web tools (Now under subpackage myamiweb) to document root for the web server.    The Setup Wizard will take you through the steps to create config.php and to create and initialize values for the new tables. 

 h2. Run database update scripts 

 <pre>cd ~/Leginon2.0/dbschema on <link linkend="admin_app_import" 
 python schema-r12857.py 
 python schema-r13713.py 
 </pre> 

 The first one update 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, and some on projectdata and leginondata. 

 >Import applications</link>