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Installation for mac users
From Bibus
Contents |
Mac OS < 10.5
This this the procedure to install bibus under macOS. This procedure is not complete and should be updated
- Install:
- python >=3D 2.3 (the same version that the version in OOo. Normally 2.3)
- wxpython with unicode support for the correct python version
- pysqlite version 1.0; 1.1 or 2.0. The best is 2.0
- Download bibus.tar.gz and unpack
- Open a terminal:
- cd "bibus installation directory"
- python bibus.py
- Now we have to setup OOo communication
- Start OOo
- open in OOo: "bibus_installation_directory"/Setup/UnoConnectionListener.odg (In OOo2.3 you first have to change in the option the macro rights to "Ask for macro from non-certified source")
- Starting bibus with OOo communication: Under linux you must set the LD_LIBRARY_PATH variable. I have no idea of what is the equivalent under MacOS. This variable add library to the path when the libs are not in the standard places. What are the standard places for libs under macOSX ?
Installing Bibus on a Mac OS10.5 (Leopard) and MySQL
It seems that with Mac OS 10.5 things have become a bit easier. Python, SQLite and pySQLite are already shipping with the system (They might be on the developer tools only which come on the DVD and which I have installed. I don't use SQLite, however, but need MySQL connection to work with remote servers).
I managed to get at least to start the application, it is not functional yet. Maybe somebody can correct this and help Mac Users to get Bibus running.
Here is what I did:
MySQL
I did not install a "native" MySQL server but used the MAMP system as a backend: http://www.mamp.info/en/index.php
Here is Apple's Info on how to load the mysql client binaries: http://docs.info.apple.com/article.html?artnum=306782
- Download the file at http://www.opensource.apple.com/darwinsource/other/MySQL-43.binaries.tar.gz and unpack it
- In a terminal, go into the folder
- execute " sudo tar -xzvf MySQL-43.root.tar.gz -C /"
Python MySQL bindings
There are some problems with the MySQLdb bindings of the Python version shipped with the Mac, see http://www.arnebrodowski.de/blog/472-MySQLdb-unter-Mac-OS-10.5-installieren.html
- Get mysql-python from https://sourceforge.net/projects/mysql-python
- Unzip and open the folder. In the file "site.cfg", you need to configure the "mysql_config" variable like so: "mysql_config = /usr/bin/mysql_config". Or course, uncomment the ligns that you modified.
- There is a problem with Python's default enconding (ascii). In python >= 2.5, sitecustomize no longer exists. To turn python's default encoding into 'UTF-8', you have to change (as root)
/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site.pyFind the ligne "def setencoding():". For lignes after, turn , turn encoding ='ascii' into encoding = "UTF-8". - In the file "_mysql.c", you need to delete the three following lines:
#ifndef uint #define uint unsigned int #endif
- Contrary to the how-to mentioned above, creating a symlink seems not necessary
- execute "sudo python setup.py install"
Creating Databases
Somehow Bibus did not create the databases for me, so I did it manually:
- In your MySQL installation, manually create database "Biblio"
- Create tables by executing the sql in db_models/mysql.sql
Configuring Bibus
Create a file Makefile.MacOSX in the Setup folder with a text editor (vim or Emacs). Insert the following text:
# you presumably will only have to change the three first lines below
DESTDIR = /Applications/Bibus.app/Contents
python = /usr/bin/python
oopath = /Applications/OpenOffice.org.app/Contents/MacOS,~/Applications/OpenOffice.org.app
/Contents/MacOS,/Applications/NeoOffice.app/Contents/MacOS,~/Applications/NeoOffice.app/Co
ntents/MacOS
#
prefix = $(DESTDIR)
exec_prefix = $(prefix)/MacOS
bindir = $(exec_prefix)
datadir = $(prefix)/Resources
sysconfdir = $(datadir)
mandir = $(datadir)/man
man1dir = $(mandir)/man1
define install-files
install -d $(bindir) $(datadir) $(sysconfdir) $(mandir) $(man1dir) $(datadir)/Bibu
s\ Help
install *.py MySQL_Bibus.ini $(bindir)
for dir in bibMSW Data db_models Export FirstStart Format Import MySQL_Setup Style
Editor FirstStart bibOOo db_models Pixmaps Setup StyleEditor wxg ; do \
find -d $$dir ! -path '*CVS*' -a -type d -exec install -d $(bindir)/'{}' '
;' ; \
done
for dir in bibMSW Data db_models Export FirstStart Format Import MySQL_Setup Style
Editor FirstStart bibOOo db_models Pixmaps Setup StyleEditor wxg ; do \
find -d $$dir ! -path '*CVS*' -a -type f -exec install '{}' $(bindir)/'{}'
';' ; \
done
# locale files. We look for all the directory in locale/
for dir in $(wildcard locale/*); do \
if [ $$dir ] && [ $$dir != "locale/CVS" ] && [ $$dir != "bibus.pot" ] ; th
en \
install -d -m664 $(datadir)/$$dir/LC_MESSAGES/ ; \
install -m664 $$dir/LC_MESSAGES/bibus.mo $(datadir)/$$dir/LC_MESSA
GES/ ; \
fi; \
done
ln -s $(datadir)/locale $(bindir)/
# bibus.config
install bibus.config $(sysconfdir)/
# Create PkgInfo file.
echo "APPL????" > $(DESTDIR)/PkgInfo
# Create information property list file (Info.plist).
touch $(DESTDIR)/Info.plist
chmod 755 $(DESTDIR)/Info.plist
echo '<?xml version="1.0" encoding="UTF-8"?>' >> $(DESTDIR)/Info.plist
echo '<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.ap
ple.com/DTDs/PropertyList-1.0.dtd">' >> $(DESTDIR)/Info.plist
echo '<plist version=\"1.0\">' >> $(DESTDIR)/Info.plist
echo '<dict>' >> $(DESTDIR)/Info.plist
echo ' <key>CFBundleDevelopmentRegion</key>' >> $(DESTDIR)/Info.plist
echo ' <string>English</string>' >> $(DESTDIR)/Info.plist
echo ' <key>CFBundleExecutable</key>' >> $(DESTDIR)/Info.plist
echo ' <string>'bibus.sh'</string>' >> $(DESTDIR)/Info.plist
echo ' <key>CFBundleInfoDictionaryVersion</key>' >> $(DESTDIR)/Info.plist
echo ' <string>6.0</string>' >> $(DESTDIR)/Info.plist
echo ' <key>CFBundlePackageType</key>' >> $(DESTDIR)/Info.plist
echo ' <string>APPL</string>' >> $(DESTDIR)/Info.plist
echo ' <key>CFBundleSignature</key>' >> $(DESTDIR)/Info.plist
echo ' <string>????</string>' >> $(DESTDIR)/Info.plist
echo ' <key>CFBundleVersion</key>' >> $(DESTDIR)/Info.plist
echo ' <string>1.0</string>' >> $(DESTDIR)/Info.plist
echo ' <key>CSResourcesFileMapped</key>' >> $(DESTDIR)/Info.plist
echo ' <true/>' >> $(DESTDIR)/Info.plist
echo ' <key>CFBundleGetInfoString</key>' >> $(DESTDIR)/Info.plist
echo ' <string>Bibus 1.2.11 GNU – GNU-FDL</string>' >> $(DESTDIR)/Info.plist
echo ' <key>CFBundleHelpBookFolder</key>' >> $(DESTDIR)/Info.plist
echo ' <string>Bibus Help</string>' >> $(DESTDIR)/Info.plist
echo ' <key>CFBundleName</key>' >> $(DESTDIR)/Info.plist
echo ' <string>Bibus</string>' >> $(DESTDIR)/Info.plist
echo ' <key>CFBundleShortVersionString</key>' >> $(DESTDIR)/Info.plist
echo ' <string>1.2.11</string>' >> $(DESTDIR)/Info.plist
echo '</dict>' >> $(DESTDIR)/Info.plist
echo '</plist>' >> $(DESTDIR)/Info.plist
# man page
install -m644 Setup/bibus.1 $(mandir)/
# freedesktop icon and shortcut
install -m664 Pixmaps/bibus.png Setup/bibus.desktop $(datadir)/
echo 'Exec=$(bindir)/bibus' >> $(datadir)/bibus.desktop
echo 'Icon=$(datadir)/bibus.png' >> $(datadir)/bibus.desktop
# bibus command
install Setup/UnoConnectionListener.odg *.py MySQL_Bibus.ini $(bindir)/
ln -sf $(datadir)/bibusStart.py $(bindir)/bibus
chmod 755 $(bindir)/bibus
touch $(bindir)/bibus.sh
echo '#!/bin/sh' > $(bindir)/bibus.sh
echo 'export DYLD_LIBRARY_PATH="/Applications/OpenOffice.org.app/Contents/MacOS:/u
sr/lib:$DYLD_LIBRARY_PATH"'
echo 'exec /usr/bin/python /Applications/Bibus.app/Contents/MacOS/bibus.py' >> $(b
indir)/bibus.sh
chmod 775 $(bindir)/bibus.sh
# copying doc files
install -d $(datadir)/Bibus\ Help
cp -R Docs/html/* $(datadir)/Bibus\ Help/
ln -s $(datadir)/Bibus\ Help $(bindir)/Docs
# generating bibus.cfg file
echo '[PATH]' > $(datadir)/bibus.cfg
echo 'python = $(python)' >> $(datadir)/bibus.cfg
echo 'oopath = $(oopath)' >> $(datadir)/bibus.cfg
echo 'docdir = $(datadir)/Bibus\ Help' >> $(datadir)/bibus.cfg
echo 'licence = $(datadir)/Bibus\ Help/copying' >> $(datadir)/bibus.cfg
echo 'localedir = $(datadir)/locale' >> $(datadir)/bibus.cfg
echo 'systemconf = $(sysconfdir)/bibus.config' >> $(datadir)/bibus.cfg
ln -s $(datadir)/bibus.cfg $(bindir)
endef
define compile
# compile recursively all the python files located in $(bindir)/
$(python) -c "import compileall ; compileall.compile_dir('$(bindir)/')"
$(python) -O -c "import compileall ; compileall.compile_dir('$(bindir)/')"
endef
install-files:
$(install-files)
install:
$(install-files)
$(compile)
# write uninstaller in $(datadir)/Setup/uninstall.sh
echo "#!/bin/sh" > $(bindir)/uninstall.sh
echo "rm -rf $(DESTDIR)" >> $(bindir)/uninstall.sh
chmod 744 $(bindir)/uninstall.sh
# end uninstaller
You can change the bibus settings in bibus.cfg:
oopath = /Applications/OpenOffice.org.app/Contents/MacOS</tt> or /Applications/NeoOffice.app/Contents/MacOS/ BIBbase.DB_STARTUP = 1 # 0 = last used db used at startup. 1 = default db BIBbase.DB_TYPE ='MySQL' # type of database used 'MySQL','SQlite', etc... => modules dbBibMySQL,dbBibSQLite, etc...
Since I use a MAMP MySQL server, the socket entry is
BIBbase.SOCKET = '/Applications/MAMP/tmp/mysql/mysql.sock'
See http://sfbloggr.blogspot.com/2007/10/nachtrag-vorbereitungen-fr-os-x-105.html for other cases.
I created a user bibus with password bibus who had access to the "Biblio" database and entered the following configuration values:
BIBbase.PORT = 3306 BIBbase.HOST = 'localhost' BIBbase.USER = u'bibus' BIBbase.PASSWORD = u'bibus'
However, it would still connect with my system user name and ask the password, so I had to create a user in the database that corresponded with my system user name.
If you have OpenOffice3.org Aqua installed, this path becomes : /Applications/OpenOffice.org.app/Contents/MacOS/ In order to configure bibus to interact with Neo/ OpenOffice3.org Aqua, you will need later to acces his program directory. Make a symlink as root in the console, e.g. by typing $: ln -s /Applications/OpenOffice.org.app/Contents/MacOS /Volumes/Your-HD-Name/program
Go to the bibus folder and run as root: make -f Setup/Makefile.MacOSX. A MacOS-like application will be created in the Applications folder. So now, you may remove the bibus source folder. Double-click on the Bibus Application and Bibus starts.
Connecting Bibus to your database
If your settings doesn't allow you to access to your database from Bibus, you can change these into Bibus. Edition > Preferences. Click on "Préférences avancées" below left. Choose "Base" to change your database settings. Menu File > Connect ("Fichier > Se connecter"). You can now insert new references.
Import worked with the Medline format (Sqlite -> medline. Menu File > Import > Medline) but the Identifier Field was corrupted.
Connecting to your database with NeoOffice or OpenOffice
You have two ways to do it : ODBC or JDBC. The mysql-connector-odbc doesn't work very well yet. You can better choose the mysql-connector-jdbc.
Connecting to your data base with ODBC
You have to install an ODBC driver for your database.
- For MySQL databases, install mysql-connector-mysql or his latest version.
- For SQLite, install SQLite ODBC. You can choose the installer package (ppc) or compile yourself the latest package. ODBC Driver works, but access to SQLite databases from OpenOffice not tested.
Before to open the ODBC administrator (/Applications/Utlities/ODBC Administrator), a few steps are needed.
- $: chmod 664 /Library/ODBC/odbc*) in order to make possible to create a system DSN. You can revert it by typing $: chmod 644 /Library/ODBC/odbc*. Don't worry, ODBC Administrator fails very often. If you changed the permissions, it will still fail but after saving your modifications.
Open the ODBC Administrator application. You have first to declare what driver are available. If you have mysql-connector-odbc, you can skip to the next step. For SQLite, click on Driver > Add… In the driver file field, type /usr/local/lib/libsqlite3odbc.so. In the configuration file field, type the same (/usr/local/lib/libsqlite3odbc.so). Define it as "system" (available for the entier system).
Declare your datasources in DSN users or DNS system, e.g. DSN system > Add… Choose the driver for your database type (in my case "MySQL ODBC 5.1 Driver" becaus MySQL ODBC 3 fails). Configure the acces to your database. If your using MAMP :
Data Source Name : Biblio Server : localhost #default User : Biblio Password : •••• Database : Biblio
In the Connect options,
Port : 8889 #(depending on MAMP. MySQL default port : 3306) Socket : /Applications/MAMP/tmp/mysql/mysql.sock Character Set : utf8
You can test the connection. If it works, the your database will be available for OpenOffice.org or NeoOffice.
For SQLite : you just have to give a name of your DNS. DNS Users/System > Add… Type any name (you will chose your database file later).
Connecting to your database with JDBC
- For SQLite, install javasqlite or sqlitejdbc. Javasqlite fails on compilation (see [1]). A OSX package is available for SQLite JDBC (not tested).
- For MySQL, install MySQL connector/J.
Unpack it and remember the location of the driver file (e.g. mysql-connector-java-<version>-bin.jar or sqlitejdbc-v43-native.jar).
Connecting NeoOffice/OpenOffice.org to your database
ODBC users, skip this step. JDBC Users choose in OpenOffice or NeoOffice in the menu Tools > Options… > OpenOffice.org/NeoOffice > Java > Class path… and select your JDBC driver.
In OpenOffice.org/NeoOffice, create a new database. Choose to connect to an existing database. Select MySQL, ODBC or JDBC.
- JDBC
| URL of the database | Driver class |
|---|---|
| mysql://localhost/Biblio | org.gjt.mm.mysql.Driver |
| mysql://localhost/Biblio | com.sun.star.sdbc.JDBCDriver (doesn't work) |
| sqlite:///Path-to-your-database | org.sqlite.JDBC |
- MySQL
- JDBC: Type the informations about the server of your database as in the DSN declaration
- ODBC : Type the DSN name
- ODBC : type the DSN name
Current Status
- The application starts, and new references can be inserted with Bibus. These references can be inserted in Neo/OpenOffice.org but not with Bibus.
- Importing fails, message is "Table tmp_import does not exist
- OpenOffice in Bibus menu doesn't work yet
Please edit this how-to if you know what has do be done differently.
