Mysql installation with macports (macOS 10.6.3), Json libs in HVP pilot

Mysql installation problem in MacOS using macports (10.6.3)

• Mysql socket problem @ macports installation problem solved :
  • ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/opt/local/var/run/mysql5/mysqld.sock' (2)
    • solved by ".set the mysqld_safe socket path in a new MySQL configuration file. Create /opt/local/etc/mysql5/my.cnf, add the following to it, save, the try again.[mysqld_safe] socket = /tmp/mysql.sock

NOTE: If you've installed MacPort's PHP 5 you will probably need to tell PHP where the MySQL socket is. Edit your php.ini file located at /opt/local/etc/php.ini.

mysql.default_socket = /tmp/mysql.sock" DONE

related links

• ​http://2tbsp.com/content/install_and_configure_mysql_5_macports
• It is weird though , although the mysql.sock supposed to be in /tmp (​http://dev.mysql.com/doc/refman/5.0/en/mac-os-x-installation.html) , it is not there , but works.:
  • ​http://forums.mysql.com/read.php?35,64808,228369#msg-228369!
  • ​http://forums.mysql.com/read.php?35,64808,254785#msg-254785
• Now pma problem , although mysql is running : Phpmyadmin problem : #2002 Cannot log in to the MySQL server
• same problem @ ​http://127.0.0.1/~despoina/pma/index.php
  • ​http://forums.mysql.com/read.php?35,64808,75300#msg-75300
  • Setup Missing : ​http://www.phpmyadmin.net/documentation/Documentation.html#setup_script This worked for phpmyadmin problem!
    • DONE , pma working.
  • ...and last but not least ..​http://www.comentum.com/mysql-administration.html
  • Mysql tables location : /opt/local/var/db/mysql5/
• Table database_test.gene (mark's database dump) successfully imported in hvp_pilot.gene table
  • DONE
• Lucene :
  • path problems ... *
    • TODO
• D2RQ : path problem : TODO

Install graphviz using Macports

• GraphViz?: :macports despoina$ sudo port install graphviz : /opt/local/var/macports/software/graphviz/2.26.3_1+macosx
• ​http://code.google.com/p/macvim/ , ​http://macvim.org/ DONE

JSON libs in HVP pilot

• TODO : include json libs in hvp_pilot
  • retrieve from ontocat (pilot : ​http://localhost:8080/ontocat/version0.3/test.html)
  • ​http://www.json.org/JSONRequest.html
  • ​http://www.hunlock.com/blogs/Mastering_JSON_(_JavaScript_Object_Notation_)
  • ​http://www.restlet.org/
• Molgenis distro rdf test :
  • Added a function for Http connection . Test if working. Error:
    • This seems familiar : SEVERE: Error configuring application listener of class MolgenisCompatibleD2RWebappInitListener

How to retrieve json data

Use json native available in several javascript libs