ChemWiki - User contributions [en]

It:seminars

2007-05-15T15:02:09Z

Tjohns:

= Seminar System =

== Functionality (current system) ==

=== Users ===

Three levels of user
* Admin
* Logged in "editor"
* All others (not logged in)

=== Privileges ===

==== Admin ====
* add new editor privileges to user
* add/edit/delete any record in database
* View all info

==== Editors ====
* add/edit/delete seminar records & addition of other related records
* View all records

==== All others ====
* View all records

=== Data held for seminars ===
* ID
* Name of speaker (can be IC speaker - chosen from list - or external speaker)
* Address of speaker (if non-IC, auto fill for IC speaker?)
* email of speaker (if non-IC, auto fill for IC speaker?)
* URL of speaker
* Date of seminar
* Title of seminar
* Venue of seminar (chosen from list)
* Group (seminar stream e.g. research group/department)
(descriptive info)
* Keywords
* Description (used for abstract)
* PRISM (Henry expand here, please)
* XML
(admin info stored about system users)
* Date record entered
* Date last updated
* Creator
* Last edited by

'''Comment:''' there is a dateUpdated field and a lastUpdated field. How do these differ?

== v2.0 system functionality ==

=== RSS ===

* RSS 1.0/2.0/Atom based outputs, RSS output to be customisable, including RSS type (1.0, 2.0 and Atom) and transclusion of namespaced XML, multiple group selection, recent changes and additions. RSS 1.0 to include RDF serialisation.

=== Push/Pull ===

* Automatic push/pull of seminars into departmental/group websites based on category that they are given on creation

=== Video/Audio functions ===

* Flag for live broadcast of seminar
** When seminar is live "watch live" link to appear on web pages
* Field for archive documents inlcuding handouts, other text documents as well as multiple video files. This should not be done from the content area

=== Calendar ===

* Calendar view for current month/week with highlighted, clickable days when seminars are happening
* Same view available for seminar archive

=== Search ===

* ability to search by title, speaker, location, keywords

=== Browser compliance ===

* Tested compliance with range of Browsers (ie not just Windows/IE)

== Provisional Specification for V 2.0 of system ==

#Active Directory/LDAP based authentication, with resolution of user ID to real name.
#Permission/ACL-based hierarchical adminstrative interface, including who can edit what on both group and global levels and including input of new groups, venues and URLs to venues
#Enumerated and XML based inputs, including XML validation, character escaping and namespace checking
# Input fields to include:
##Title
##controlled date and start/end time
##controlled venue
##Speaker name, email, URL and FOAF,
##address
##keywords
##abstract
##DOI/Handle including resolution check
##namespaced XML entry
##Podcast/Blog/Video URL and resolution check and readily extensible for future fields
#Fielded entry Search, with full boolean support
#Detection of seminar conflicts (ie same time in same venue, or same group, different venue, or same speaker invited by different groups)
# RSS 1.0/2.0/Atom based outputs, RSS output to be customisable, including RSS type (1.0, 2.0 and Atom) and transclusion of namespaced XML, multiple group selection, recent changes and additions. RSS 1.0 to include RDF serialisation.
# Export to Web page environments of pre-determined, customisable, packaging of group and departmental events.
# Options to bundle grouped seminars into
## an e-mail digest, and for users to subscribe to this digest, including when the digest is sent (or via an RSS re-direct of same)
## a calendar entry
# Suggestion/bug fix entry facility
# Web presentation to be controlled by (administrator-enabled) editable templates
# Backups to be controlled by e.g. crontab/regular export of entire seminar database
# Minimise dependence on commercial software, ie OpenSource wherever possible.
# Tested compliance with range of Browsers (ie not just Windows/IE)
# Product will conform to Opensource distribution requirements.

----
--[[User:Rzepa|Rzepa]] 17:35, 17 April 2007 (BST)

It:seminars

2007-05-02T09:48:36Z

Tjohns:

= Seminar System =

== Functionality (current system) ==

=== Users ===

Three levels of user
* Admin
* Logged in "editor"
* All others (not logged in)

=== Privileges ===

==== Admin ====
* add new editor privileges to user
* add/edit/delete any record in database
* View all info

==== Editors ====
* add/edit/delete seminar records & addition of other related records
* View all records

==== All others ====
* View all records

=== Data held for seminars ===
* ID
* Name of speaker
* Address of speaker
* email of speaker
* URL of speaker
* Date of seminar
* Title of seminar
* Venue of seminar
* Group (seminar stream e.g. research group/department)
(descriptive info)
* Keywords
* Description (can be used for abstract)
* PRISM (Henry expand here, please)
* XML
(admin info stored about system users)
* Date record entered
* Date last updated
* Creator
* Last edited by

'''Comment:''' there is a dateUpdated field and a lastUpdated field. How do these differ?

== Provisional Specification for V 2.0 of system ==

#Active Directory/LDAP based authentication, with resolution of user ID to real name.
#Permission/ACL-based hierarchical adminstrative interface, including who can edit what on both group and global levels and including input of new groups, venues and URLs to venues
#Enumerated and XML based inputs, including XML validation, character escaping and namespace checking
# Input fields to include:
##Title
##controlled date and start/end time
##controlled venue
##Speaker name, email, URL and FOAF,
##address
##keywords
##abstract
##DOI/Handle including resolution check
##namespaced XML entry
##Podcast/Blog/Video URL and resolution check and readily extensible for future fields
#Fielded entry Search, with full boolean support
#Detection of seminar conflicts (ie same time in same venue, or same group, different venue, or same speaker invited by different groups)
# RSS 1.0/2.0/Atom based outputs, RSS output to be customisable, including RSS type (1.0, 2.0 and Atom) and transclusion of namespaced XML, multiple group selection, recent changes and additions. RSS 1.0 to include RDF serialisation.
# Export to Web page environments of pre-determined, customisable, packaging of group and departmental events.
# Options to bundle grouped seminars into
## an e-mail digest, and for users to subscribe to this digest, including when the digest is sent (or via an RSS re-direct of same)
## a calendar entry
# Suggestion/bug fix entry facility
# Web presentation to be controlled by (administrator-enabled) editable templates
# Backups to be controlled by e.g. crontab/regular export of entire seminar database
# Minimise dependence on commercial software, ie OpenSource wherever possible.
# Tested compliance with range of Browsers (ie not just Windows/IE)
# Product will conform to Opensource distribution requirements.

----
--[[User:Rzepa|Rzepa]] 17:35, 17 April 2007 (BST)

IT:servers

2006-07-17T09:18:30Z

Tjohns: /* MySQL */

== Configuring Servers ==

The following is specified for the SGI-based argon server. The location of various library and include paths will vary from machine to machine. The current base for the SGI is argon.ch.ic.ac.uk and /var/www/ This contains Apache, php, MySQL, htDig and various other utilities. Contact Henry Rzepa (rzepa@ic.ac.uk) for further information about these systems.

The new system is to be migrated to neon.ch.ic.ac.uk. Current paths are /var/www/ for installations etc and /mpt/web/ for
htdocs. No decision on log files yet made.

==Apache==

Currently 2.055, but might be upgradable to 2.2
<pre> ./configure --prefix=/var/www/apache2055 \
--enable-dav --enable-ssl --enable-rewrite --enable-ldap \
--enable-auth-ldap --with-ldap --with-speling --libdir=/usr/lib \
--with-ldap-include=/usr/include \
--with-ldap-lib=/usr/lib/ \
--with-ssl-include=/usr/include/openssl/ \
--with-ssl-lib=/usr/lib/ \
--with-ssl \
CPPFLAGS=-I/usr/kerberos/include</pre>

#Configuration files for apache: [http://www.ch.ic.ac.uk/rzepa/config/httpd.conf httpd.conf], [http://www.ch.ic.ac.uk/rzepa/config/mime.types mime.types], [http://www.ch.ic.ac.uk/rzepa/config/ssl.conf ssl.conf],
# A SSL server certificate needs to be installed for the system.
# Authentication uses SSL and LDAP, as specified in the configuration files.
# Server started using <pre>./apachectl startssl</pre>
#Path to htdocs on new server <pre>/mpt/web/htdocs/</pre>

==MySQL==

Currently 4.0.13. Not tested at 4.1.18. The existing databases will have to be backed up using e.g.
<pre>mysqldump –u root –psecret --all-databases > all.sql</pre> and reloaded into the new MySQL.

Mysql server installed by Sam Sharpe at <pre>/usr/bin/nysql</pre>

Please contact HSR for MySQL root password.

GRANT ALL PRIVILEGES ON PSS.* TO pss@unixweb1.cc.ic.ac.uk IDENTIFIED BY '*****'

GRANT ALL PRIVILEGES ON PSS.* TO pss@unixweb2.cc.ic.ac.uk IDENTIFIED BY '*****'

The password needed is stored in config.inc.php. Take care; the above line is case sensitive throughout.

==PHP ==

Currently 4.4.2, but will need to move to 5 at some stage.

<pre>./configure --with-mysql=/usr/bin/mysql --with-apxs2=/var/www/apache2055/bin/apxs\
--with-ldap --with-config-file-path=/mpt/web/htdocs/php/</pre>

#Configuration files for php: [http://www.ch.ic.ac.uk/php/php.ini php.ini]
#Admin utility for php: [http://www.ch.ic.ac.uk/php/phpMyAdmin-2.5.3/ phpMyAdmin]
# The current system configuration is summarised [http://www.ch.ic.ac.uk/php/ here]

==Wiki==

[http://meta.wikimedia.org/wiki/MediaWiki Mediawiki] is the current flavour.

#The local settings file is [http://www.ch.ic.ac.uk/wiki/LocalSettings.php here]
#A [http://wiki.jmol.org/index.php/MediaWiki Jmol extension] is loaded to enable molecule display within the wiki
#A local authentication module [http://www.ch.ic.ac.uk/wiki/LdapAuthentication.php has been added]

==[http://www.muquit.com/muquit/software/Count/Count.html Web page counter]==

Can be replaced by any suitable alternative.

<pre><nowiki><img src="http://origin.ch.ic.ac.uk/cgi-bin/Count.cgi?df=pericyclic.dat&dd=B" alt="counter" /></nowiki></pre>

== [http://www.htdig.org/install.html htDig 3.1.6] Index and Search Engine.==

It employs external parsers for chemical files. UltraSeek might be useable, but would need to be configured for these external file types. The output templates are also special, invoking the Jmol applet to display certain types of file found by the search. For an example of the latter, see [http://www.ch.ic.ac.uk/local/symmetry/ the symmetry site]. Invoke the default search, and select load molecule.

#Configuration file for building htdig [http://www.ch.ic.ac.uk/rzepa/config/CONFIG CONFIG]
#Configuration files for indexing entire server: [http://www.ch.ic.ac.uk/rzepa/config/origin.conf origin.conf] [http://www.ch.ic.ac.uk/rzepa/config/motm.conf motm.conf] [http://www.ch.ic.ac.uk/rzepa/config/sym.conf sym.conf] [http://www.ch.ic.ac.uk/rzepa/config/it.conf it.conf] [http://www.ch.ic.ac.uk/rzepa/config/pericyclic.conf pericyclic.conf]
#External parsers for htdig: [http://www.ch.ic.ac.uk/rzepa/config/runchemdig.sh runchemdig.sh] doc2html
#Output templates for htdig: [http://www.ch.ic.ac.uk/rzepa/config/header.html header.html] [http://www.ch.ic.ac.uk/rzepa/config/long.html long.html] [http://www.ch.ic.ac.uk/rzepa/config/nomatch.html nomatch.html] [http://www.ch.ic.ac.uk/rzepa/config/footer.html footer.html]

==[http://www.analog.cx/ Analog log file analyzer]==

Currently set up as a crontab job, to run weekly. Used in conjuction with ReportMagic to generate
reports.

==[http://tomcat.apache.org/ Tomcat]==

Currently not installed, but should be.

==[http://www.openrdf.org/ Sesame]==

Currently not installed, but should be.

--[[User:Rzepa|Rzepa]] 08:42, 19 April 2006 (bst)

== [http://www.openafs.org openAFS for OS X] ==

*Install the openafs package
*sudo edit /private/var/db/openAFS/etc/CellServDB and add the ic.ac.uk domain
<pre>>ic.ac.uk #Imperial College London
155.198.63.149 #icafs1.cc.ic.ac.uk
155.198.63.148 #icafs2.cc.ic.ac.uk</pre>
*sudo edit /private/var/db/openAFS/etc/ThisCell and replace entry with
<pre>ic.ac.uk</pre>
*sudo edit /etc/krb5.conf and add the following:
<pre>[logging]
default = FILE:/var/log/krb5libs.log
kdc = FILE:/var/log/krb5kdc.log
admin_server = FILE:/var/log/kadmind.log

[libdefaults]
ticket_lifetime = 24000
default_realm = IC.AC.UK
dns_lookup_realm = false
dns_lookup_kdc = false
#supported_enctypes = des3-cbc-sha1:normal des-cbc-md5:normal des-cbc-crc:afs3

# default_tkt_enctypes = des-cbc-md5
# default_tgs_enctypes =des-cbc-md5
# default_etypes = des-cbc-md5
# default_etypes_des = des-cbc-md5

[realms]
IC.AC.UK = {
kdc = icads11.ic.ac.uk:88
kdc = icads1.ic.ac.uk:88
kdc = icads2.ic.ac.uk:88
kdc = icads4.ic.ac.uk:88
# kdc = icafs2.cc.ic.ac.uk:88
}

[domain_realm]
.ic.ac.uk = IC.AC.UK
ic.ac.uk = IC.AC.UK

[kdc]
profile = /var/kerberos/krb5kdc/kdc.conf

[appdefaults]
pam = {
debug = false
ticket_lifetime = 3600000
renew_lifetime = 3600000
forwardable = true
krb4_convert = false
}</pre>
*to login do
<pre>kinit username</pre> followed by
<pre>aklog</pre>
*to logout do
<pre>kdestroy</pre> to destroy your kerberos ticket and unlog to drop your afs token

==== Brief list of useful commands.====
<pre>
login
------
kinit <USERNAME> ## get kerberos tickets
kdestroy ## drop kerberos tickets
aklog ## get AFS token
unlog ## drop afs token
------------------------------------------------------
Setting up a group
---------------------
pts creategroup <groupname> ## create a group (will be a negative number)
pts chown <groupname> <username> ## change the owner of the group (you will be the owner by default)
pts listowned <username> ## list groups you own
pts adduser -user <name> -group <groupname> ## add another user to a group
-------------------------------------------------------
ACLS
-----
fs listacl /afs/ic.ac.uk/software ## list acls on a directory
fs setacl /afs/ic.ac.uk/software <user> none. ## remove user access to a folder
fs setacl /afs/ic.ac.uk/software <user> rl ## grant read and list permissions
fs setacl /afs/ic.ac.uk/software <user> all ## grant all permissions to a user.</pre>

IT:servers

2006-07-13T13:54:21Z

Tjohns: /* MySQL */

== Configuring Servers ==

The following is specified for the SGI-based argon server. The location of various library and include paths will vary from machine to machine. The current base for the SGI is argon.ch.ic.ac.uk and /var/www/ This contains Apache, php, MySQL, htDig and various other utilities. Contact Henry Rzepa (rzepa@ic.ac.uk) for further information about these systems.

The new system is to be migrated to neon.ch.ic.ac.uk. Current paths are /var/www/ for installations etc and /mpt/web/ for
htdocs. No decision on log files yet made.

==Apache==

Currently 2.055, but might be upgradable to 2.2
<pre> ./configure --prefix=/var/www/apache2055 \
--enable-dav --enable-ssl --enable-rewrite --enable-ldap \
--enable-auth-ldap --with-ldap --with-speling --libdir=/usr/lib \
--with-ldap-include=/usr/include \
--with-ldap-lib=/usr/lib/ \
--with-ssl-include=/usr/include/openssl/ \
--with-ssl-lib=/usr/lib/ \
--with-ssl \
CPPFLAGS=-I/usr/kerberos/include</pre>

#Configuration files for apache: [http://www.ch.ic.ac.uk/rzepa/config/httpd.conf httpd.conf], [http://www.ch.ic.ac.uk/rzepa/config/mime.types mime.types], [http://www.ch.ic.ac.uk/rzepa/config/ssl.conf ssl.conf],
# A SSL server certificate needs to be installed for the system.
# Authentication uses SSL and LDAP, as specified in the configuration files.
# Server started using <pre>./apachectl startssl</pre>
#Path to htdocs on new server <pre>/mpt/web/htdocs/</pre>

==MySQL==

Currently 4.0.13. Not tested at 4.1.18. The existing databases will have to be backed up using e.g.
<pre>mysqldump –u root –psecret --all-databases > all.sql</pre> and reloaded into the new MySQL.

Mysql server installed by Sam Sharpe at <pre>/usr/bin/nysql</pre>

Please contact HSR for MySQL root password.

GRANT ALL PRIVILEGES ON PSS.* TO pss@unixdevweb1.cc.ic.ac.uk IDENTIFIED BY '*****'

GRANT ALL PRIVILEGES ON PSS.* TO pss@unixdevweb2.cc.ic.ac.uk IDENTIFIED BY '*****'

The password needed is stored in config.inc.php. Take care; the above line is case sensitive throughout.

==PHP ==

Currently 4.4.2, but will need to move to 5 at some stage.

<pre>./configure --with-mysql=/usr/bin/mysql --with-apxs2=/var/www/apache2055/bin/apxs\
--with-ldap --with-config-file-path=/mpt/web/htdocs/php/</pre>

#Configuration files for php: [http://www.ch.ic.ac.uk/php/php.ini php.ini]
#Admin utility for php: [http://www.ch.ic.ac.uk/php/phpMyAdmin-2.5.3/ phpMyAdmin]
# The current system configuration is summarised [http://www.ch.ic.ac.uk/php/ here]

==Wiki==

[http://meta.wikimedia.org/wiki/MediaWiki Mediawiki] is the current flavour.

#The local settings file is [http://www.ch.ic.ac.uk/wiki/LocalSettings.php here]
#A [http://wiki.jmol.org/index.php/MediaWiki Jmol extension] is loaded to enable molecule display within the wiki
#A local authentication module [http://www.ch.ic.ac.uk/wiki/LdapAuthentication.php has been added]

==[http://www.muquit.com/muquit/software/Count/Count.html Web page counter]==

Can be replaced by any suitable alternative.

<pre><nowiki><img src="http://origin.ch.ic.ac.uk/cgi-bin/Count.cgi?df=pericyclic.dat&dd=B" alt="counter" /></nowiki></pre>

== [http://www.htdig.org/install.html htDig 3.1.6] Index and Search Engine.==

It employs external parsers for chemical files. UltraSeek might be useable, but would need to be configured for these external file types. The output templates are also special, invoking the Jmol applet to display certain types of file found by the search. For an example of the latter, see [http://www.ch.ic.ac.uk/local/symmetry/ the symmetry site]. Invoke the default search, and select load molecule.

#Configuration file for building htdig [http://www.ch.ic.ac.uk/rzepa/config/CONFIG CONFIG]
#Configuration files for indexing entire server: [http://www.ch.ic.ac.uk/rzepa/config/origin.conf origin.conf] [http://www.ch.ic.ac.uk/rzepa/config/motm.conf motm.conf] [http://www.ch.ic.ac.uk/rzepa/config/sym.conf sym.conf] [http://www.ch.ic.ac.uk/rzepa/config/it.conf it.conf] [http://www.ch.ic.ac.uk/rzepa/config/pericyclic.conf pericyclic.conf]
#External parsers for htdig: [http://www.ch.ic.ac.uk/rzepa/config/runchemdig.sh runchemdig.sh] doc2html
#Output templates for htdig: [http://www.ch.ic.ac.uk/rzepa/config/header.html header.html] [http://www.ch.ic.ac.uk/rzepa/config/long.html long.html] [http://www.ch.ic.ac.uk/rzepa/config/nomatch.html nomatch.html] [http://www.ch.ic.ac.uk/rzepa/config/footer.html footer.html]

==[http://www.analog.cx/ Analog log file analyzer]==

Currently set up as a crontab job, to run weekly. Used in conjuction with ReportMagic to generate
reports.

==[http://tomcat.apache.org/ Tomcat]==

Currently not installed, but should be.

==[http://www.openrdf.org/ Sesame]==

Currently not installed, but should be.

--[[User:Rzepa|Rzepa]] 08:42, 19 April 2006 (bst)

== [http://www.openafs.org openAFS for OS X] ==

*Install the openafs package
*sudo edit /private/var/db/openAFS/etc/CellServDB and add the ic.ac.uk domain
<pre>>ic.ac.uk #Imperial College London
155.198.63.149 #icafs1.cc.ic.ac.uk
155.198.63.148 #icafs2.cc.ic.ac.uk</pre>
*sudo edit /private/var/db/openAFS/etc/ThisCell and replace entry with
<pre>ic.ac.uk</pre>
*sudo edit /etc/krb5.conf and add the following:
<pre>[logging]
default = FILE:/var/log/krb5libs.log
kdc = FILE:/var/log/krb5kdc.log
admin_server = FILE:/var/log/kadmind.log

[libdefaults]
ticket_lifetime = 24000
default_realm = IC.AC.UK
dns_lookup_realm = false
dns_lookup_kdc = false
#supported_enctypes = des3-cbc-sha1:normal des-cbc-md5:normal des-cbc-crc:afs3

# default_tkt_enctypes = des-cbc-md5
# default_tgs_enctypes =des-cbc-md5
# default_etypes = des-cbc-md5
# default_etypes_des = des-cbc-md5

[realms]
IC.AC.UK = {
kdc = icads11.ic.ac.uk:88
kdc = icads1.ic.ac.uk:88
kdc = icads2.ic.ac.uk:88
kdc = icads4.ic.ac.uk:88
# kdc = icafs2.cc.ic.ac.uk:88
}

[domain_realm]
.ic.ac.uk = IC.AC.UK
ic.ac.uk = IC.AC.UK

[kdc]
profile = /var/kerberos/krb5kdc/kdc.conf

[appdefaults]
pam = {
debug = false
ticket_lifetime = 3600000
renew_lifetime = 3600000
forwardable = true
krb4_convert = false
}</pre>
*to login do
<pre>kinit username</pre> followed by
<pre>aklog</pre>
*to logout do
<pre>kdestroy</pre> to destroy your kerberos ticket and unlog to drop your afs token

==== Brief list of useful commands.====
<pre>
login
------
kinit <USERNAME> ## get kerberos tickets
kdestroy ## drop kerberos tickets
aklog ## get AFS token
unlog ## drop afs token
------------------------------------------------------
Setting up a group
---------------------
pts creategroup <groupname> ## create a group (will be a negative number)
pts chown <groupname> <username> ## change the owner of the group (you will be the owner by default)
pts listowned <username> ## list groups you own
pts adduser -user <name> -group <groupname> ## add another user to a group
-------------------------------------------------------
ACLS
-----
fs listacl /afs/ic.ac.uk/software ## list acls on a directory
fs setacl /afs/ic.ac.uk/software <user> none. ## remove user access to a folder
fs setacl /afs/ic.ac.uk/software <user> rl ## grant read and list permissions
fs setacl /afs/ic.ac.uk/software <user> all ## grant all permissions to a user.</pre>

IT:servers

2006-07-13T13:54:00Z

Tjohns: /* MySQL */

== Configuring Servers ==

The following is specified for the SGI-based argon server. The location of various library and include paths will vary from machine to machine. The current base for the SGI is argon.ch.ic.ac.uk and /var/www/ This contains Apache, php, MySQL, htDig and various other utilities. Contact Henry Rzepa (rzepa@ic.ac.uk) for further information about these systems.

The new system is to be migrated to neon.ch.ic.ac.uk. Current paths are /var/www/ for installations etc and /mpt/web/ for
htdocs. No decision on log files yet made.

==Apache==

Currently 2.055, but might be upgradable to 2.2
<pre> ./configure --prefix=/var/www/apache2055 \
--enable-dav --enable-ssl --enable-rewrite --enable-ldap \
--enable-auth-ldap --with-ldap --with-speling --libdir=/usr/lib \
--with-ldap-include=/usr/include \
--with-ldap-lib=/usr/lib/ \
--with-ssl-include=/usr/include/openssl/ \
--with-ssl-lib=/usr/lib/ \
--with-ssl \
CPPFLAGS=-I/usr/kerberos/include</pre>

#Configuration files for apache: [http://www.ch.ic.ac.uk/rzepa/config/httpd.conf httpd.conf], [http://www.ch.ic.ac.uk/rzepa/config/mime.types mime.types], [http://www.ch.ic.ac.uk/rzepa/config/ssl.conf ssl.conf],
# A SSL server certificate needs to be installed for the system.
# Authentication uses SSL and LDAP, as specified in the configuration files.
# Server started using <pre>./apachectl startssl</pre>
#Path to htdocs on new server <pre>/mpt/web/htdocs/</pre>

==MySQL==

Currently 4.0.13. Not tested at 4.1.18. The existing databases will have to be backed up using e.g.
<pre>mysqldump –u root –psecret --all-databases > all.sql</pre> and reloaded into the new MySQL.

Mysql server installed by Sam Sharpe at <pre>/usr/bin/nysql</pre>

Please contact HSR for MySQL root password.

GRANT ALL PRIVILEGES ON PSS.* TO pss@unixdevweb1.cc.ic.ac.uk IDENTIFIED BY '*****'

GRANT ALL PRIVILEGES ON PSS.* TO pss@unixdevweb2.cc.ic.ac.uk IDENTIFIED BY '*****'

The password needed is stored in config.inc.php. Take care; the above line is case sensitive throughout.

==PHP ==

Currently 4.4.2, but will need to move to 5 at some stage.

<pre>./configure --with-mysql=/usr/bin/mysql --with-apxs2=/var/www/apache2055/bin/apxs\
--with-ldap --with-config-file-path=/mpt/web/htdocs/php/</pre>

#Configuration files for php: [http://www.ch.ic.ac.uk/php/php.ini php.ini]
#Admin utility for php: [http://www.ch.ic.ac.uk/php/phpMyAdmin-2.5.3/ phpMyAdmin]
# The current system configuration is summarised [http://www.ch.ic.ac.uk/php/ here]

==Wiki==

[http://meta.wikimedia.org/wiki/MediaWiki Mediawiki] is the current flavour.

#The local settings file is [http://www.ch.ic.ac.uk/wiki/LocalSettings.php here]
#A [http://wiki.jmol.org/index.php/MediaWiki Jmol extension] is loaded to enable molecule display within the wiki
#A local authentication module [http://www.ch.ic.ac.uk/wiki/LdapAuthentication.php has been added]

==[http://www.muquit.com/muquit/software/Count/Count.html Web page counter]==

Can be replaced by any suitable alternative.

<pre><nowiki><img src="http://origin.ch.ic.ac.uk/cgi-bin/Count.cgi?df=pericyclic.dat&dd=B" alt="counter" /></nowiki></pre>

== [http://www.htdig.org/install.html htDig 3.1.6] Index and Search Engine.==

It employs external parsers for chemical files. UltraSeek might be useable, but would need to be configured for these external file types. The output templates are also special, invoking the Jmol applet to display certain types of file found by the search. For an example of the latter, see [http://www.ch.ic.ac.uk/local/symmetry/ the symmetry site]. Invoke the default search, and select load molecule.

#Configuration file for building htdig [http://www.ch.ic.ac.uk/rzepa/config/CONFIG CONFIG]
#Configuration files for indexing entire server: [http://www.ch.ic.ac.uk/rzepa/config/origin.conf origin.conf] [http://www.ch.ic.ac.uk/rzepa/config/motm.conf motm.conf] [http://www.ch.ic.ac.uk/rzepa/config/sym.conf sym.conf] [http://www.ch.ic.ac.uk/rzepa/config/it.conf it.conf] [http://www.ch.ic.ac.uk/rzepa/config/pericyclic.conf pericyclic.conf]
#External parsers for htdig: [http://www.ch.ic.ac.uk/rzepa/config/runchemdig.sh runchemdig.sh] doc2html
#Output templates for htdig: [http://www.ch.ic.ac.uk/rzepa/config/header.html header.html] [http://www.ch.ic.ac.uk/rzepa/config/long.html long.html] [http://www.ch.ic.ac.uk/rzepa/config/nomatch.html nomatch.html] [http://www.ch.ic.ac.uk/rzepa/config/footer.html footer.html]

==[http://www.analog.cx/ Analog log file analyzer]==

Currently set up as a crontab job, to run weekly. Used in conjuction with ReportMagic to generate
reports.

==[http://tomcat.apache.org/ Tomcat]==

Currently not installed, but should be.

==[http://www.openrdf.org/ Sesame]==

Currently not installed, but should be.

--[[User:Rzepa|Rzepa]] 08:42, 19 April 2006 (bst)

== [http://www.openafs.org openAFS for OS X] ==

*Install the openafs package
*sudo edit /private/var/db/openAFS/etc/CellServDB and add the ic.ac.uk domain
<pre>>ic.ac.uk #Imperial College London
155.198.63.149 #icafs1.cc.ic.ac.uk
155.198.63.148 #icafs2.cc.ic.ac.uk</pre>
*sudo edit /private/var/db/openAFS/etc/ThisCell and replace entry with
<pre>ic.ac.uk</pre>
*sudo edit /etc/krb5.conf and add the following:
<pre>[logging]
default = FILE:/var/log/krb5libs.log
kdc = FILE:/var/log/krb5kdc.log
admin_server = FILE:/var/log/kadmind.log

[libdefaults]
ticket_lifetime = 24000
default_realm = IC.AC.UK
dns_lookup_realm = false
dns_lookup_kdc = false
#supported_enctypes = des3-cbc-sha1:normal des-cbc-md5:normal des-cbc-crc:afs3

# default_tkt_enctypes = des-cbc-md5
# default_tgs_enctypes =des-cbc-md5
# default_etypes = des-cbc-md5
# default_etypes_des = des-cbc-md5

[realms]
IC.AC.UK = {
kdc = icads11.ic.ac.uk:88
kdc = icads1.ic.ac.uk:88
kdc = icads2.ic.ac.uk:88
kdc = icads4.ic.ac.uk:88
# kdc = icafs2.cc.ic.ac.uk:88
}

[domain_realm]
.ic.ac.uk = IC.AC.UK
ic.ac.uk = IC.AC.UK

[kdc]
profile = /var/kerberos/krb5kdc/kdc.conf

[appdefaults]
pam = {
debug = false
ticket_lifetime = 3600000
renew_lifetime = 3600000
forwardable = true
krb4_convert = false
}</pre>
*to login do
<pre>kinit username</pre> followed by
<pre>aklog</pre>
*to logout do
<pre>kdestroy</pre> to destroy your kerberos ticket and unlog to drop your afs token

==== Brief list of useful commands.====
<pre>
login
------
kinit <USERNAME> ## get kerberos tickets
kdestroy ## drop kerberos tickets
aklog ## get AFS token
unlog ## drop afs token
------------------------------------------------------
Setting up a group
---------------------
pts creategroup <groupname> ## create a group (will be a negative number)
pts chown <groupname> <username> ## change the owner of the group (you will be the owner by default)
pts listowned <username> ## list groups you own
pts adduser -user <name> -group <groupname> ## add another user to a group
-------------------------------------------------------
ACLS
-----
fs listacl /afs/ic.ac.uk/software ## list acls on a directory
fs setacl /afs/ic.ac.uk/software <user> none. ## remove user access to a folder
fs setacl /afs/ic.ac.uk/software <user> rl ## grant read and list permissions
fs setacl /afs/ic.ac.uk/software <user> all ## grant all permissions to a user.</pre>

IT:servers

2006-07-13T13:53:29Z

Tjohns:

== Configuring Servers ==

The following is specified for the SGI-based argon server. The location of various library and include paths will vary from machine to machine. The current base for the SGI is argon.ch.ic.ac.uk and /var/www/ This contains Apache, php, MySQL, htDig and various other utilities. Contact Henry Rzepa (rzepa@ic.ac.uk) for further information about these systems.

The new system is to be migrated to neon.ch.ic.ac.uk. Current paths are /var/www/ for installations etc and /mpt/web/ for
htdocs. No decision on log files yet made.

==Apache==

Currently 2.055, but might be upgradable to 2.2
<pre> ./configure --prefix=/var/www/apache2055 \
--enable-dav --enable-ssl --enable-rewrite --enable-ldap \
--enable-auth-ldap --with-ldap --with-speling --libdir=/usr/lib \
--with-ldap-include=/usr/include \
--with-ldap-lib=/usr/lib/ \
--with-ssl-include=/usr/include/openssl/ \
--with-ssl-lib=/usr/lib/ \
--with-ssl \
CPPFLAGS=-I/usr/kerberos/include</pre>

#Configuration files for apache: [http://www.ch.ic.ac.uk/rzepa/config/httpd.conf httpd.conf], [http://www.ch.ic.ac.uk/rzepa/config/mime.types mime.types], [http://www.ch.ic.ac.uk/rzepa/config/ssl.conf ssl.conf],
# A SSL server certificate needs to be installed for the system.
# Authentication uses SSL and LDAP, as specified in the configuration files.
# Server started using <pre>./apachectl startssl</pre>
#Path to htdocs on new server <pre>/mpt/web/htdocs/</pre>

==MySQL==

Currently 4.0.13. Not tested at 4.1.18. The existing databases will have to be backed up using e.g.
<pre>mysqldump –u root –psecret --all-databases > all.sql</pre> and reloaded into the new MySQL.

Mysql server installed by Sam Sharpe at <pre>/usr/bin/nysql</pre>

Please contact HSR for MySQL root password.

GRANT ALL PRIVILEGES ON PSS.* TO pss@unixdevweb1.cc.ic.ac.uk IDENTIFIED BY '*****'
GRANT ALL PRIVILEGES ON PSS.* TO pss@unixdevweb2.cc.ic.ac.uk IDENTIFIED BY '*****'

The password needed is stored in config.inc.php. Take care; the above line is case sensitive throughout.

==PHP ==

Currently 4.4.2, but will need to move to 5 at some stage.

<pre>./configure --with-mysql=/usr/bin/mysql --with-apxs2=/var/www/apache2055/bin/apxs\
--with-ldap --with-config-file-path=/mpt/web/htdocs/php/</pre>

#Configuration files for php: [http://www.ch.ic.ac.uk/php/php.ini php.ini]
#Admin utility for php: [http://www.ch.ic.ac.uk/php/phpMyAdmin-2.5.3/ phpMyAdmin]
# The current system configuration is summarised [http://www.ch.ic.ac.uk/php/ here]

==Wiki==

[http://meta.wikimedia.org/wiki/MediaWiki Mediawiki] is the current flavour.

#The local settings file is [http://www.ch.ic.ac.uk/wiki/LocalSettings.php here]
#A [http://wiki.jmol.org/index.php/MediaWiki Jmol extension] is loaded to enable molecule display within the wiki
#A local authentication module [http://www.ch.ic.ac.uk/wiki/LdapAuthentication.php has been added]

==[http://www.muquit.com/muquit/software/Count/Count.html Web page counter]==

Can be replaced by any suitable alternative.

<pre><nowiki><img src="http://origin.ch.ic.ac.uk/cgi-bin/Count.cgi?df=pericyclic.dat&dd=B" alt="counter" /></nowiki></pre>

== [http://www.htdig.org/install.html htDig 3.1.6] Index and Search Engine.==

It employs external parsers for chemical files. UltraSeek might be useable, but would need to be configured for these external file types. The output templates are also special, invoking the Jmol applet to display certain types of file found by the search. For an example of the latter, see [http://www.ch.ic.ac.uk/local/symmetry/ the symmetry site]. Invoke the default search, and select load molecule.

#Configuration file for building htdig [http://www.ch.ic.ac.uk/rzepa/config/CONFIG CONFIG]
#Configuration files for indexing entire server: [http://www.ch.ic.ac.uk/rzepa/config/origin.conf origin.conf] [http://www.ch.ic.ac.uk/rzepa/config/motm.conf motm.conf] [http://www.ch.ic.ac.uk/rzepa/config/sym.conf sym.conf] [http://www.ch.ic.ac.uk/rzepa/config/it.conf it.conf] [http://www.ch.ic.ac.uk/rzepa/config/pericyclic.conf pericyclic.conf]
#External parsers for htdig: [http://www.ch.ic.ac.uk/rzepa/config/runchemdig.sh runchemdig.sh] doc2html
#Output templates for htdig: [http://www.ch.ic.ac.uk/rzepa/config/header.html header.html] [http://www.ch.ic.ac.uk/rzepa/config/long.html long.html] [http://www.ch.ic.ac.uk/rzepa/config/nomatch.html nomatch.html] [http://www.ch.ic.ac.uk/rzepa/config/footer.html footer.html]

==[http://www.analog.cx/ Analog log file analyzer]==

Currently set up as a crontab job, to run weekly. Used in conjuction with ReportMagic to generate
reports.

==[http://tomcat.apache.org/ Tomcat]==

Currently not installed, but should be.

==[http://www.openrdf.org/ Sesame]==

Currently not installed, but should be.

--[[User:Rzepa|Rzepa]] 08:42, 19 April 2006 (bst)

== [http://www.openafs.org openAFS for OS X] ==

*Install the openafs package
*sudo edit /private/var/db/openAFS/etc/CellServDB and add the ic.ac.uk domain
<pre>>ic.ac.uk #Imperial College London
155.198.63.149 #icafs1.cc.ic.ac.uk
155.198.63.148 #icafs2.cc.ic.ac.uk</pre>
*sudo edit /private/var/db/openAFS/etc/ThisCell and replace entry with
<pre>ic.ac.uk</pre>
*sudo edit /etc/krb5.conf and add the following:
<pre>[logging]
default = FILE:/var/log/krb5libs.log
kdc = FILE:/var/log/krb5kdc.log
admin_server = FILE:/var/log/kadmind.log

[libdefaults]
ticket_lifetime = 24000
default_realm = IC.AC.UK
dns_lookup_realm = false
dns_lookup_kdc = false
#supported_enctypes = des3-cbc-sha1:normal des-cbc-md5:normal des-cbc-crc:afs3

# default_tkt_enctypes = des-cbc-md5
# default_tgs_enctypes =des-cbc-md5
# default_etypes = des-cbc-md5
# default_etypes_des = des-cbc-md5

[realms]
IC.AC.UK = {
kdc = icads11.ic.ac.uk:88
kdc = icads1.ic.ac.uk:88
kdc = icads2.ic.ac.uk:88
kdc = icads4.ic.ac.uk:88
# kdc = icafs2.cc.ic.ac.uk:88
}

[domain_realm]
.ic.ac.uk = IC.AC.UK
ic.ac.uk = IC.AC.UK

[kdc]
profile = /var/kerberos/krb5kdc/kdc.conf

[appdefaults]
pam = {
debug = false
ticket_lifetime = 3600000
renew_lifetime = 3600000
forwardable = true
krb4_convert = false
}</pre>
*to login do
<pre>kinit username</pre> followed by
<pre>aklog</pre>
*to logout do
<pre>kdestroy</pre> to destroy your kerberos ticket and unlog to drop your afs token

==== Brief list of useful commands.====
<pre>
login
------
kinit <USERNAME> ## get kerberos tickets
kdestroy ## drop kerberos tickets
aklog ## get AFS token
unlog ## drop afs token
------------------------------------------------------
Setting up a group
---------------------
pts creategroup <groupname> ## create a group (will be a negative number)
pts chown <groupname> <username> ## change the owner of the group (you will be the owner by default)
pts listowned <username> ## list groups you own
pts adduser -user <name> -group <groupname> ## add another user to a group
-------------------------------------------------------
ACLS
-----
fs listacl /afs/ic.ac.uk/software ## list acls on a directory
fs setacl /afs/ic.ac.uk/software <user> none. ## remove user access to a folder
fs setacl /afs/ic.ac.uk/software <user> rl ## grant read and list permissions
fs setacl /afs/ic.ac.uk/software <user> all ## grant all permissions to a user.</pre>