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version 1.8, 2001/02/14 14:33:35 version 1.20, 2002/11/16 00:57:28
Line 8 Line 8
 Scott Harrison  Scott Harrison
 </P>  </P>
 <P>  <P>
 Last updated: 02/12/2001  Last updated: 02/15/2001
 </P>  </P>
 <P>  <P>
 This file describes issues associated with LON-CAPA  This file describes issues associated with LON-CAPA
Line 17  and a SQL database. Line 17  and a SQL database.
 <H2>Latest HOWTO</H2>  <H2>Latest HOWTO</H2>
 <P>  <P>
 <UL>  <UL>
   <LI>Important notes
 <LI>Current status of documentation</LI>  <LI>Current status of documentation</LI>
 <LI>Current status of implementation</LI>  <LI>Current status of implementation</LI>
 <LI>Purpose within LON-CAPA</LI>  <LI>Purpose within LON-CAPA</LI>
Line 29  and a SQL database. Line 30  and a SQL database.
 <LI>Example sections of code relevant to LON-CAPA</LI>  <LI>Example sections of code relevant to LON-CAPA</LI>
 </UL>  </UL>
 </P>  </P>
   <H2>Important notes</H2>
   <P>
   The current database is implemented assuming a non-adjustable
   architecture involving these data fields (specific to each version
   of a resource).
   <UL>
   <LI>title</LI>
   <LI>author</LI>
   <LI>subject</LI>
   <LI>notes</LI>
   <LI>abstract</LI>
   <LI>mime</LI>
   <LI>language</LI>
   <LI>creationdate</LI>
   <LI>lastrevisiondate</LI>
   <LI>owner</LI>
   <LI>copyright</LI>
   </UL>
   </P>
   <P>
   Security occurs as a function of the user 'www',
   and the permissions on the files in the /usr/local/mysql
   directory.  (These files and directories should
   be 700, 600, 500, 400, etc; not allow access to anyone
   but user 'www'.)
   </P>
   <P>
   These commands create the loncapameta database.
   <PRE>
   mysql> CREATE DATABASE IF NOT EXISTS loncapa;
   mysql> USE loncapa;
   mysql> CREATE TABLE IF NOT EXISTS metadata (title TEXT, author TEXT, subject TEXT, url TEXT, keywords TEXT, version TEXT, notes TEXT, abstract TEXT, mime TEXT, language TEXT, creationdate DATETIME, lastrevisiondate DATETIME, owner TEXT, copyright TEXT, FULLTEXT idx_title (title), FULLTEXT idx_author (author), FULLTEXT idx_subject (subject), FULLTEXT idx_url (url), FULLTEXT idx_keywords (keywords), FULLTEXT idx_version (version), FULLTEXT idx_notes (notes), FULLTEXT idx_abstract (abstract), FULLTEXT idx_mime (mime), FULLTEXT idx_language (language), FULLTEXT idx_owner (owner), FULLTEXT idx_copyright (copyright)) TYPE=MYISAM;
   mysql> INSERT INTO metadata VALUES ('The Structure of Scientific Revolutions','Thomas S. Kuhn','scientific philosophy','/res/msu/shh1/poobah2.html','aphorisms, theories, paradigm, revolution','current','still developing','This famous book stands out in contrast to the more rigid theories of Popper.','html','seniso','1999-03-03 12:34:56','1999-03-03 3:12:00','shh1@msu.edu','default');
   mysql> SELECT * FROM metadata WHERE title REGEXP "1";
   </PRE>
   </P>
   <P>
   Current time values for things.
   <PRE>
   fenchurch.lite.msu.edu
   Mem:    46812K av,   45632K used,    1180K free,   14756K shrd,    4292K buff
   Swap: 1148608K av,   11260K used, 1137348K free                   13244K cached
   
   Red Hat Linux release 6.2 (Zoot)
   Kernel 2.2.16-3 on an i586
   </PRE>
   <BR>Q: How big are data records in test database? A: on average, 1000 bytes each, medline records from PubMed.
   <BR>Q: How big is the biggest field? A: on average, 838 bytes each
   <BR>Q: How much time to insert 5284 medline records into database?
   A: 600 seconds
   <BR>Q: What about when using "speed-technique" on page 130? A: 689 seconds (weird, eh?)
   <BR>Q: What about REGEXP searching? A: about 1-2 seconds for small fields;
   10 to 20 seconds for REGEXP search on "abstract" field
   <BR>Q: What about FULLTEXT indexing? A: about 6 seconds for abstract field.
   
   </P>
   <P>
   An important quote from the manual:
   <BLOCKQUOTE>
   In MySQL Version 3.23.23 or later, you can also create special FULLTEXT indexes. They are used for full-text search. Only the MyISAM table type supports FULLTEXT indexes. They can be created only from
   VARCHAR and TEXT columns. Indexing always happens over the entire column and partial indexing is not supported. See section 25.2 MySQL Full-text Search for details. 
   </BLOCKQUOTE>
   </P>
   <P>
   I plan on using a MyISAM table type with 11 metadata fields of column 
   type=TEXT.
   </P>
   <P>
   It might be worthwhile to look at /usr/local/mysql/manual.html.
   It is quite in depth.
   </P>
 <H2>Current status of documentation</H2>  <H2>Current status of documentation</H2>
 <P>  <P>
 I am going to begin documentation by inserting what notes  I am going to begin documentation by inserting what notes
Line 157  core, minimal RPM set.) Line 229  core, minimal RPM set.)
 <LI>egcs-1.1.2-30</LI>  <LI>egcs-1.1.2-30</LI>
 <LI>cpp-1.1.2-30</LI>  <LI>cpp-1.1.2-30</LI>
 <LI>glibc-devel-2.1.3-15</LI>  <LI>glibc-devel-2.1.3-15</LI>
 <LI>glibc-devel-2.1.3-15</LI>  
 <LI>zlib-devel-1.1.3-6</LI>  <LI>zlib-devel-1.1.3-6</LI>
 </UL>  </UL>
   
 </P>  </P>
 <H2>Installation</H2>  <H2>Installation</H2>
 <P>  <P>
Line 212  and LON-CAPA-mysql since we, in fact, ma Line 282  and LON-CAPA-mysql since we, in fact, ma
 <BR>This tarball Last changed 2000-11-11  <BR>This tarball Last changed 2000-11-11
 <BR>This is actually a binary tarball (as opposed to source code  <BR>This is actually a binary tarball (as opposed to source code
 that is subsequently compiled).  that is subsequently compiled).
 <LI>  <LI>http://www.cpan.org/authors/id/TIMB/DBI-1.14.tar.gz
 <BR>  <BR>This tarball Released 14th June 2000
 </UL>  </UL>
 </P>  </P>
   <P>So, here is exactly how I installed MySQL-3.23. (Note that all files
   wind up in /usr/local/mysql-3.23.33-pc-linux-gnu-i686 except for
   a link from /usr/local/mysql to /usr/local/mysql-3.23.33-pc-linux-gnu-i686
   and some files involved in system process handling (/etc/rc.d/*/*mysql).
   <PRE>
   (As user=root)
   cd /usr/local/;
   tar xzvf mysql-3.23.33-pc-linux-gnu-i686.tar.gz
   ln -s /usr/local/mysql-3.23.33-pc-linux-gnu-i686 mysql
   cd /usr/local/mysql
   chown -R www /usr/local/mysql/.
   chgrp -R users /usr/local/mysql/.
   chmod -R g-w,g-r,g-x /usr/local/mysql/.
   (probably also want chmod -R a-w,a-r,a-x /usr/local/mysql/.)
   
   Alter <TT>safe_mysqld</TT>
   and <TT>support-files/mysql.server</TT> to use 'localhosts' instead
   of `bin/hostname`.  Also, to use user 'www' instead of 'mysql'.
   
   (These changes could be done with /etc/my.cnf, but
   I think this approach makes sure the database NEVER
   gets screwed up due to somebody forgetting to install /etc/my.cnf).
   
   Change this line in mysql.server from
     pid_file=$datadir/`@HOSTNAME@`.pid
   to
     pid_file=$datadir/localhost.pid
   
   Change this line in safe_mysqld from
   user=root
   to
   user=www
   
   Change this line in safe_mysqld from
     pid_file=$DATADIR/`/bin/hostname`.pid
   to
     pid_file=$DATADIR/localhost.pid
   
   Change this line in safe_mysqld from
   test -z "$err_log"  && err_log=$DATADIR/`/bin/hostname`.err
   to
   test -z "$err_log"  && err_log=$DATADIR/localhost.err
   
   cp -p support-files/mysql.server /etc/rc.d/init.d/mysql
   chmod 755 /etc/rc.d/init.d/mysql
   /sbin/chkconfig --add mysql
   /etc/rc.d/init.d/mysql start
   
   </PRE>
   </P>
   <P>This is how I installed the Msql-Mysql-modules perl modules.
   <PRE>
   [root@fenchurch Msql-Mysql-modules-1.2215]# perl Makefile.PL 
   Which drivers do you want to install?
   
       1) MySQL only
       2) mSQL only (either of mSQL 1 or mSQL 2)
       3)  MySQL and mSQL (either of mSQL 1 or mSQL 2)
   
       4)  mSQL 1 and mSQL 2
       5)  MySQL, mSQL 1 and mSQL 2
   
   Enter the appropriate number:  [3] 1
   
   
   Do you want to install the MysqlPerl emulation? You might keep your old
   Mysql module (to be distinguished from DBD::mysql!) if you are concerned
   about compatibility to existing applications! [y] n
   Where is your MySQL installed? Please tell me the directory that
   contains the subdir 'include'. [/usr/local/mysql] 
   Which database should I use for testing the MySQL drivers? [test] 
   On which host is database test running (hostname, ip address
   or host:port) [localhost] 
   User name for connecting to database test? [undef]
   Password for connecting to database test? [undef]
   [root@fenchurch Msql-Mysql-modules-1.2215]# make
   [root@fenchurch Msql-Mysql-modules-1.2215]# make test
   make[1]: Entering directory `/home/user/Msql-Mysql-modules-1.2215/mysql'
   make[1]: Leaving directory `/home/user/Msql-Mysql-modules-1.2215/mysql'
   make[1]: Entering directory `/home/user/Msql-Mysql-modules-1.2215/mysql'
   PERL_DL_NONLAZY=1 /usr/bin/perl -I../blib/arch -I../blib/lib -I/usr/lib/perl5/5.00503/i386-linux -I/usr/lib/perl5/5.00503 -e 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
   t/00base............ok
   t/10dsnlist.........ok
   t/20createdrop......ok
   t/30insertfetch.....ok
   t/40bindparam.......ok
   t/40blobs...........ok
   t/40listfields......ok
   t/40nulls...........ok
   t/40numrows.........ok
   t/50chopblanks......ok
   t/50commit..........ok
   t/60leaks...........skipping test on this platform
   t/ak-dbd............ok
   t/akmisc............ok
   t/dbdadmin..........ok
   t/mysql.............ok
   t/mysql2............ok
   All tests successful, 1 test skipped.
   Files=17,  Tests=732, 40 wallclock secs (15.38 cusr +  1.30 csys = 16.68 CPU)
   [root@fenchurch Msql-Mysql-modules-1.2215]# make install
   
   These files are installed.
   /usr/bin/dbimon
   /usr/lib/perl5/man/man3/Bundle::DBD::mysql.3
   /usr/lib/perl5/man/man3/DBD::mysql.3
   /usr/lib/perl5/man/man3/Mysql.3
   /usr/lib/perl5/site_perl/5.005/i386-linux/Bundle/DBD/mysql.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBD/mysql.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/Mysql.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/Mysql/Statement.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/auto/DBD/mysql/mysql.bs
   /usr/lib/perl5/site_perl/5.005/i386-linux/auto/DBD/mysql/mysql.so
   /usr/man/man1/dbimon.1
   /usr/lib/perl5/site_perl/5.005/i386-linux/auto/Msql-Mysql-modules/.packlist
   </PRE>
   </P>
   <P>
   This is how I installed the DBI perl modules.
   <PRE>$dbh
   [root@fenchurch DBI-1.14]# perl Makefile.PL
   *** Note:
       The optional PlRPC-modules (RPC::PlServer etc) are not installed.
       If you want to use the DBD::Proxy driver and DBI::ProxyServer
       modules, then you'll need to install the RPC::PlServer, RPC::PlClient,
       Storable and Net::Daemon modules. The CPAN Bundle::DBI may help you.
       You can install them any time after installing the DBI.
       You do *not* need these modules for typical DBI usage.
   
   Optional modules are available from any CPAN mirror, in particular
       http://www.perl.com/CPAN/modules/by-module
       http://www.perl.org/CPAN/modules/by-module
       ftp://ftp.funet.fi/pub/languages/perl/CPAN/modules/by-module
   
   Checking if your kit is complete...
   Looks good
   Writing Makefile for DBI
   
       Remember to actually *read* the README file!
       Use  'make' to build the software (dmake or nmake on Windows).
       Then 'make test' to execute self tests.
       Then 'make install' to install the DBI and then delete this working
       directory before unpacking and building any DBD::* drivers.
   
   [root@fenchurch DBI-1.14]# make
   [root@fenchurch DBI-1.14]# make test
   PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib/perl5/5.00503/i386-linux -I/usr/lib/perl5/5.00503 -e 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
   t/basics............ok
   t/dbidrv............ok
   t/examp.............ok
   t/meta..............ok
   t/proxy.............skipping test on this platform
   t/shell.............ok
   t/subclass..........ok
   All tests successful, 1 test skipped.
   Files=7,  Tests=179,  7 wallclock secs ( 6.46 cusr +  0.49 csys =  6.95 CPU)
   PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib/perl5/5.00503/i386-linux -I/usr/lib/perl5/5.00503 test.pl
   test.pl 
   DBI test application $Revision$
   Using /home/user/DBI-1.14/blib
   Switch: DBI 1.14 by Tim Bunce, 1.14
   Available Drivers: ADO, ExampleP, Multiplex, Proxy, mysql
   dbi:ExampleP:: testing 5 sets of 20 connections:
   Connecting... 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 
   Disconnecting...
   Connecting... 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 
   Disconnecting...
   Connecting... 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 
   Disconnecting...
   Connecting... 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 
   Disconnecting...
   Connecting... 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 
   Disconnecting...
   Made 100 connections in  0 wallclock secs ( 0.22 usr +  0.03 sys =  0.25 CPU)
   
   Testing handle creation speed...
   5000 NullP statement handles cycled in 6.6 cpu+sys seconds (762 per sec)
   
   test.pl done
   
   [root@fenchurch DBI-1.14]# make install
   These files are installed.
   /usr/lib/perl5/site_perl/5.005/i386-linux/auto/DBI/.packlist
   /usr/bin/dbiproxy
   /usr/bin/dbish
   /usr/lib/perl5/man/man3/Bundle::DBI.3
   /usr/lib/perl5/man/man3/DBD::ADO.3
   /usr/lib/perl5/man/man3/DBD::Multiplex.3
   /usr/lib/perl5/man/man3/DBD::Proxy.3
   /usr/lib/perl5/man/man3/DBI.3
   /usr/lib/perl5/man/man3/DBI::DBD.3
   /usr/lib/perl5/man/man3/DBI::FAQ.3
   /usr/lib/perl5/man/man3/DBI::Format.3
   /usr/lib/perl5/man/man3/DBI::ProxyServer.3
   /usr/lib/perl5/man/man3/DBI::Shell.3
   /usr/lib/perl5/man/man3/DBI::W32ODBC.3
   /usr/lib/perl5/man/man3/Win32::DBIODBC.3
   /usr/lib/perl5/site_perl/5.005/i386-linux/Bundle/DBI.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBD/ADO.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBD/ExampleP.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBD/Multiplex.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBD/NullP.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBD/Proxy.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBD/Sponge.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBI.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBI/DBD.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBI/FAQ.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBI/Format.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBI/ProxyServer.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBI/Shell.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/DBI/W32ODBC.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/Win32/DBIODBC.pm
   /usr/lib/perl5/site_perl/5.005/i386-linux/auto/DBI/DBI.bs
   /usr/lib/perl5/site_perl/5.005/i386-linux/auto/DBI/DBI.so
   /usr/lib/perl5/site_perl/5.005/i386-linux/auto/DBI/DBIXS.h
   /usr/lib/perl5/site_perl/5.005/i386-linux/auto/DBI/Driver.xst
   /usr/lib/perl5/site_perl/5.005/i386-linux/auto/DBI/dbd_xsh.h
   /usr/lib/perl5/site_perl/5.005/i386-linux/auto/DBI/dbi_sql.h
   /usr/lib/perl5/site_perl/5.005/i386-linux/auto/DBI/dbipport.h
   /usr/man/man1/dbiproxy.1
   /usr/man/man1/dbish.1
   </PRE>
   </P>
 <FONT COLOR="green"> old notes in green  <FONT COLOR="green"> old notes in green
 <P>  <P>
 The following set of tarballs was found to work together  The following set of tarballs was found to work together
Line 233  and typing the several "make" commands f Line 526  and typing the several "make" commands f
 </FONT>  </FONT>
 <H2>Configuration (automated)</H2>  <H2>Configuration (automated)</H2>
 <P>  <P>
 Not yet developed.  This will be part of an interface  Not yet stabilized.  We are looking at webmin
 present on LON-CAPA systems that can be launched by  and/or a text-UI tool with less software dependencies
 entering the command <TT>/usr/sbin/loncapaconfig</TT>.  than the python-anaconda hunk represented by
   the prior loncapaconfig.
 </P>  </P>
 <H2>Manual configuration</H2>  <H2>Manual configuration</H2>
 <P>  <P>
Line 263  VALUES ('localhost','www',password('newm Line 557  VALUES ('localhost','www',password('newm
 <P>  <P>
 <STRONG>Granting privileges to user 'www'</STRONG>:  <STRONG>Granting privileges to user 'www'</STRONG>:
 <PRE>  <PRE>
 GRANT ALL PRIVILEGES ON *.* TO www@localhost;  INSERT INTO db VALUES ('localhost','loncapa','www',
   'Y','Y','Y','Y','Y','Y','N'\,'Y','Y','Y');
 FLUSH PRIVILEGES;  FLUSH PRIVILEGES;
 </PRE>  </PRE>
 </P>  </P>
Line 324  As user www, run this command Line 619  As user www, run this command
 enter the password as SOMEPASSWORD  enter the password as SOMEPASSWORD
   
 To add the user www to the MySQL server, and grant all  To add the user www to the MySQL server, and grant all
 privileges on *.* to www@localhost identified by 'SOMEPASSWORD'  privileges on loncapa.* to www@localhost identified by 'SOMEPASSWORD'
 with grant option;  with grant option;
   
 INSERT INTO user (Host, User, Password)  INSERT INTO user (Host, User, Password)
 VALUES ('localhost','www',password('SOMEPASSWORD'));  VALUES ('localhost','www',password('SOMEPASSWORD'));
   
 GRANT ALL PRIVILEGES ON *.* TO www@localhost;  GRANT ALL PRIVILEGES ON loncapa.* TO 'www@localhost';
   
 FLUSH PRIVILEGES;  FLUSH PRIVILEGES;
   
Line 342  An up-to-date lond and lonsql. Line 637  An up-to-date lond and lonsql.
 </P>  </P>
 <H2>Testing</H2>  <H2>Testing</H2>
 <P>  <P>
   To test the backend MySQL database, a number of commands should be
   run after installation.
   <UL>
   <LI><TT>cd /usr/local/mysql/sql-bench; ./run-all-tests --small-test</TT></LI>
   <BR>without the --small-test flag, this test can take more than 10 hours!
   <LI><TT>cd /usr/local/mysql; bin/mysqladmin version</TT></LI>
   <LI><TT>cd /usr/local/mysql; bin/mysqladmin variables</TT></LI>
   <LI><TT>cd /usr/local/mysql; bin/mysqlshow</TT></LI>
   <LI><TT>cd /usr/local/mysql; bin/mysqlshow mysql</TT></LI>
   <LI><TT>cd /usr/local/mysql; bin/mysql -e "select host,db,user from db" mysql</TT></LI>
   <LI><TT>cd /usr/local/mysql/mysql-test; ./test-run-all</TT></LI>
   
   </UL>
   <P>
   These are sections of perl code which helps test the LON-CAPA network.
 <PRE>  <PRE>
 <STRONG>** TEST the database connection with my current tester.pl code  <STRONG>** TEST the database connection with my current tester.pl code
 which mimics what command will eventually be sent through lonc.</STRONG>  which mimics what command will eventually be sent through lonc.</STRONG>
Removed from v.1.8  
changed lines
  Added in v.1.20

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