What I find most fascinating about this topic is that I can do a lot of theoretical pure computer science research, but then can directly apply it to world class systems that we develop and implement here at Bodleian Libraries, University of Oxford. This will not only feed my passion for pure computer science research, it will also provide me with opportunities of doing hands on research, actually resulting in some benefit to the vendors of the product.

So my personal targets now are:

1. Make a comprehensive bibliography of existing research
2. Read one paper a week
3. Write my notes – preparation for a literature survey
4. Find a real problem and possibly think of a solution
5. Write the theoretical portion of problem/solution
6. Generate the dataset against which problem can be proven
7. Implement/Code the solution
8. Generate results against the original dataset with (hopefully) better results this time
9. Write up the whole thing
10. Submit the paper

The overall target for achieving all these 10 steps is by the end of this year. That is the only realistic possibility (considering I am fairly out of touch from research). I am also thinking Irum’s input here might be very beneficial as she is already doing her research on a very similar topic.

Coming back to the topic of this post, I needed to install Oracle’s SQL Developer. As I did a clean install of Ubuntu, I first needed to install JDK. I decided to go with Oracle’s JDK 1.7. Here is how I installed it.

For Ubuntu 11.10 64 bit OS, download and extract the right version of JDK for your platform.

http://www.oracle.com/technetwork/java/javase/downloads/jdk-7u1-download-513651.html

Copy the extracted directory to /usr/lib and follow the steps as shown below:

masud@masud:/opt$ sudo mv jdk1.7.0_01/ jdk1.7.0
masud@masud:/opt$ ls
jdk1.7.0
masud@masud:/opt$ sudo mv jdk1.7.0/ /usr/lib
masud@masud:/opt$ ls
masud@masud:/opt$ sudo update-alternatives --install "/usr/bin/java" "java" "/usr/lib/jdk1.7.0/bin/java" 1
masud@masud:/opt$ sudo update-alternatives --install "/usr/bin/javac" "javac" "/usr/lib/jdk1.7.0/bin/javac" 1
update-alternatives: using /usr/lib/jdk1.7.0/bin/javac to provide /usr/bin/javac (javac) in auto mode.
masud@masud:/opt$ sudo update-alternatives --install "/usr/bin/javaws" "javaws" "/usr/lib/jdk1.7.0/bin/javaws" 1
masud@masud:/opt$ sudo update-alternatives --config java
There are 2 choices for the alternative java (providing /usr/bin/java).

Selection Path Priority Status
------------------------------------------------------------
* 0 /usr/lib/jvm/java-6-openjdk/jre/bin/java 1061 auto mode
 1 /usr/lib/jdk1.7.0/bin/java 1 manual mode
 2 /usr/lib/jvm/java-6-openjdk/jre/bin/java 1061 manual mode

Press enter to keep the current choice[*], or type selection number: 1
update-alternatives: using /usr/lib/jdk1.7.0/bin/java to provide /usr/bin/java (java) in manual mode.
masud@masud:/opt$ java -version
java version "1.7.0_01"
Java(TM) SE Runtime Environment (build 1.7.0_01-b08)
Java HotSpot(TM) 64-Bit Server VM (build 21.1-b02, mixed mode)
masud@masud:/opt$ sudo update-alternatives --config javac
There is only one alternative in link group javac: /usr/lib/jdk1.7.0/bin/javac
Nothing to configure.
masud@masud:/opt$ sudo update-alternatives --config javaws
There are 2 choices for the alternative javaws (providing /usr/bin/javaws).

Selection Path Priority Status
------------------------------------------------------------
* 0 /usr/lib/jvm/java-6-openjdk/jre/bin/javaws 1061 auto mode
 1 /usr/lib/jdk1.7.0/bin/javaws 1 manual mode
 2 /usr/lib/jvm/java-6-openjdk/jre/bin/javaws 1061 manual mode

Press enter to keep the current choice[*], or type selection number: 1
update-alternatives: using /usr/lib/jdk1.7.0/bin/javaws to provide /usr/bin/javaws (javaws) in manual mode.
masud@masud:/opt$

Now download the Oracle’s SQL Developer package for your system from the following address.
http://www.oracle.com/technetwork/developer-tools/sql-developer/downloads/index.html
Now go through the following steps:

masud@masud:~/Downloads$ sudo mv sqldeveloper /usr/lib
masud@masud:~/Downloads$ cd /usr/lib
masud@masud:/usr/lib$ cd sqldeveloper/
masud@masud:/usr/lib/sqldeveloper$ ls
dataminer ide jdbc jdev.label jviews modules readme.html sqldeveloper sqldeveloper.sh timingframework
icon.png j2ee jdev jlib lib rdbms sleepycat sqldeveloper.exe sqlj view-source-paths.lis
masud@masud:/usr/lib/sqldeveloper$ ls -lrt sqldeveloper.sh
-rw-r--r-- 1 masud masud 71 2011-03-25 14:59 sqldeveloper.sh
masud@masud:/usr/lib/sqldeveloper$ chmod +x sqldeveloper.sh
masud@masud:/usr/lib/sqldeveloper$ ./sqldeveloper.sh

Oracle SQL Developer
 Copyright (c) 1997, 2011, Oracle and/or its affiliates. All rights reserved.

masud@masud:/usr/lib/sqldeveloper$

You may get a message by SQL Developer that version 1.7 of Java is not supported at this time.

1. To get PRINCE2 certified.
2. To get a driving license.
3. To get my ILR.
4. To publish, either in the field of library and information sciences or mobile/multi -agent systems or model based testing.
5. To be a better photographer and learn more about using my Nikon D3100.
6. To blog more often.

Now these are in no particular order and they may not sound S.M.A.R.T to you at all, but I have done my calculations on what, why, time scales, etc. and I will slowly share my experiences through this blog (goal number 6).

Let the good times begin

Following is the code for that. If you want to see it live in action, click here.

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
    "http://www.w3.org/TR/html4/strict.dtd"
    >
<html lang="en">
<head>
    <title>jQuery Textbox Colour Demo</title>
    <script src="//ajax.googleapis.com/ajax/libs/jquery/1.4.3/jquery.min.js"></script>
    <style type="text/css">
        #textbox.green {background-color:green;}
        #textbox.red {background-color:red;}
    </style>

    <script type="text/javascript">

    $(document).ready(function() {

        $("#textbox").keyup(function() {
            if(($("#textbox").val() == "")) {
                $("#textbox").removeClass("red");
                $("#textbox").removeClass("green");
            }
            else {
                if(isPalindrome($("#textbox").val())) {
                    $("#textbox").removeClass("red");
                    $("#textbox").addClass("green");
                }
                else {
                    $("#textbox").removeClass("green");
                    $("#textbox").addClass("red");
                }
            }
        });
    });

    function reverseString(strval){
        var  reversestrval = "";
        var  len = strval.length;
        for (var i = len ; i > 0 ; i--){
            reversestrval += strval.charAt(i-1)
        }
        return reversestrval;
    }

    function isPalindrome(strval)
    {
        if(strval == reverseString(strval)) {
                return true;
            }
            else {
                return false;
            }
    }
    </script>
</head>
<body>
    Enter string: <input type="text" name="query" id="textbox"/>
</body>
</html>

log4perl.logger=INFO, LOGFILE
log4perl.logger.Loggers.MailLogger=ERROR, Mailer

log4perl.appender.LOGFILE = Log::Log4perl::Appender::File
log4perl.appender.LOGFILE.filename = ../logs/plif.log
log4perl.appender.LOGFILE.mode=append
log4perl.appender.LOGFILE.layout = Log::Log4perl::Layout::PatternLayout
log4perl.appender.LOGFILE.layout.ConversionPattern = %d{dd MMM yyyy HH:mm:ss} - [%p] Line %L - %m%n

log4perl.appender.Mailer = Log::Dispatch::Email::MailSender
log4perl.appender.Mailer.to = masud.khokhar@bodleian.ox.ac.uk
log4perl.appender.Mailer.from = Masud Khokhar masud.khokhar@gmail.com
log4perl.appender.Mailer.subject = Fatal Error!
log4perl.appender.Mailer.smtp = smtp.ox.ac.uk
log4perl.appender.Mailer.layout = Log::Log4perl::Layout::PatternLayout
log4perl.appender.Mailer.layout.ConversionPattern = %d{dd MMM yyyy HH:mm:ss} - [%p] Line %L - %m%n
log4perl.appender.Mailer.buffer = 0

and initialise it in the code (I use Readonly but that’s not the important part here):

#### For logging
use Log::Log4perl;
use Log::Dispatch;

#### Global logger initialisations
Readonly::Scalar my $LOG_PATH => '../config/log4perl.conf';
Log::Log4perl->init($LOG_PATH);

#### Set up a file logger for logging
Readonly::Scalar my $FILE_LOGGER => Log::Log4perl->get_logger('logger');

#### Set up a mail logger
Readonly::Scalar my $MAIL_LOGGER =>  Log::Log4perl->get_logger('Loggers::MailLogger');

and then you can log to file by using

$FILE_LOGGER->info( 'Processing record:' . $row_ref->{record_id} );

and send an email by using

$MAIL_LOGGER->fatal( 'Error processing record:' . $row_ref->{record_id} );

Tip: If the mail part of your logging is not working, try installing Mail::Sender through CPAN or through other source (e.g. apt-cache search mail sender)

I am going to write down some important points from the presentations for people who were unable to attend but are interested in knowing what happened.

• Revamp of documentation
• Looking for a new stable home for Shibboleth
• Enhance attribute resolver functionality in future, which means you can merge attributes at SP, drop scopes, or do some other things with an attribute on the SP side.
• The audit logs will be revamped, in Apache shortcode styles which you can use. E.g. %D, %u, etc. You can chose whichever detail you want to go in. You can therefore feed that into log analysers, e.g. AWStats.
• Embedded discovery service (1.0 beta) releasing very soon. Consumes data from SP 2.4+.
• The centralized discovery service will also have a major release soon. It will use the embedded DS as UI.
• The centralized DS will also package a Servlet container within itself, so it lowers the learning barrier for that.
• IdP 3.0 (major release) – separate credential extraction from validation. (As an example, to dig up things easily from a packaged message). This might be useful for sending credentials through software rather than a browser and then digging response from the returned packaged message.
• SPNEGO support (so you login to active directory means you login to your IdP).
• Conditional evaluation will be introduced, e.g. if the username is @student, it goes to one LDAP directory, and if the username is @staff, it goes to another.
• Out of the box attribute consent engine, similar to uApprove (Shib documentation has screenshots for IdP 3.0).
• Performance metrics will be introduced for IdP, e.g. that filter policy is taking a long time to run, e.g. that LDAP server is not responding in time, etc.
• IdP 3.0 shipped with installer configured container (again lowers learning barrier).
• Metadata Aggregator (to overcome the so called national boundaries).
• ETag and Last-Modified based conditional GETs for metadata. Already supported by UK metadata servers. Not gzip compression yet though.
• Metadata is now reloaded in a background thread. IdP 2.2 and SP 2.4 supports this.
• Dynamic metadata retrieval
• Just in time fetching of metadata by entity ID.
• As Sha1 becomes weak, rollout of new cryptographic algorithms is becoming an important question. However, rollout can cause problems. Does your relying party support the same, e.g. Sha512.
• In future, simple string attributes will be supported for release filter policy which is based on entity attributes (e.g. EU, so release the name attribute, US so don’t).
• For better UI purposes, the metadata has two new extensions.
  • UIInfo – display name, description, logo, keywords, information and privacy URLs
  • DiscoHints – IP Address ranges, domain names, geolocations. This is used for sorting purposes in the discovery services. Discovery service will not automatically pick or remove an IdP on this basis.
• Regarding SP UI, there should be a focus on Lazy Sessions and use of isPassive (do not disturb the user unless absolutely necessary). True SSO experience.
• SP UI should use errors that tell a user to contact the support team of the organization in question, not their home organization.
• Regarding IdP UI, it is recommended that you put your contact information on all pages, including error.jsp, login.jsp and consent pages which are *.jsp. Put your branding on all pages as well.
• Keep the login page as simple as possible. Keep each page focussed on one job.
• Detect and trap lack of LoginContext
  • Happens when people bookmark the authn page.
• Install uApprove
  • Even if consent isn’t required, informing the user is a good thing.

However, if you want to see performance related attributes in AWStats, you need to use the “Extra Sections” in AWStats. I was interested in the response time parameter for a query in Apache. As a result, my Apache LogFormat looks something like:

LogFormat “%h %u %l %t \”%r\” %>s %b \”%{Referer}i\” \”%{User-Agent}i\” %T %D” 443_combined

Where %T represents the response time in seconds (useless as most requests are performed in under a second) and %D represents the response time in microseconds.

Equivalent AWStats log format is:

LogFormat=”%host %other %logname %time1 %methodurl %code %bytesd %refererquot %uaquot %other %extra1″

And to show the %extra1 parameter in the graphical page, you use the EXTRA SECTIONS.

ExtraSectionName1="Response Time (in microseconds)"
ExtraSectionCodeFilter1="200 304"
ExtraSectionCondition1="URL,\/"
ExtraSectionFirstColumnTitle1="Response Time"
ExtraSectionFirstColumnValues1="extra1,([0-9]*)$"
ExtraSectionFirstColumnFormat1="%s"
ExtraSectionStatTypes1=P
ExtraSectionAddAverageRow1=0
ExtraSectionAddSumRow1=0
MaxNbOfExtra1=200
MinHitExtra1=1

Details of these parameters are in sample AWStats config file.

To configure AWStats to keep the data before Apache logs are rotated, you can write a pre-rotate routine in /etc/logrotate.d/apache2 just above postrotate, e.g.

prerotate
/usr/share/awstats/wwwroot/cgi-bin/awstats.pl -update -config=/etc/awstats/awstats.YOUR-CONFIG-FILE-NAME.conf

The most common problem that many people face is the installation of Oracle client on the system, especially if the system on which you will run your script is not the same as the Oracle database server (which is quite often the case).

Let’s first download the important bits of software. At this time, the most recent version of instant client is 11.2, which can be downloaded from here (for Linux x86-64). Download the basic package, the SDK package, and the SQL Plus package. Extract all these files in the same folder (the sdk files should automatically extract in a sub folder called sdk in the main folder), the default folder created is called instant_client_11_2. Place this folder somewhere you would like to keep your instant client permanently, e.g. /usr/share/instant_client_11_2.

Now, as root, install the DBI module. The least problematic way to do this is to get the package and install it manually. To do this, use CPAN, e.g. as user masud,

masud@monkey:~$ sudo cpan
cpan[1]> get DBI
...
...
...
DBI-1.616/ex/corogofer.pl
DBI-1.616/ex/perl_dbi_nulls_test.pl
DBI-1.616/ex/profile.pl
CPAN: File::Temp loaded ok (v0.18)
Warning (usually harmless): 'YAML' not installed, will not store persistent state
cpan[2]>quit

Now as user root, install the module. To install the module properly, set your LD_LIBRARY_PATH to your instant client’s path. Also make sure you have cc or gcc installed.

masud@monkey:~$ sudo su -
monkey:~# export LD_LIBRARY_PATH=/usr/share/instant_client_11_2
monkey:~# cd /home/masud/.cpan/build/DBI-1.616-LWq6lO
monkey:~# perl Makefile.PL
monkey:~# make
monkey:~# make install
monkey:~# exit

Once DBI is successfully installed, it’s time for installation of DBD::Oracle. To do this, become root and use CPAN.

masud@monkey:~$ sudo su -
monkey:~# cpan install DBD::Oracle
monkey:~# exit
masud@monkey:~$

which should go fairly smoothly. The next thing to do is to install libaio1. This can be simply done by using apt-get. Don’t forget to export the LD_LIBRARY_PATH for the user running the script, in our case, ‘masud’.

masud@monkey:~$ sudo apt-get install libaio1
masud@monkey:~$ export LD_LIBRARY_PATH=/usr/share/instant_client_11_2

If you work with a tnsnames.ora file, you can place it in the instant client folder (in the sub folders network/admin). You need to create these folders yourself.

masud@monkey:~$ cd /usr/share/instant_client_11_2
masud@monkey:~$ mkdir network
masud@monkey:~$ cd network
masud@monkey:~$ mkdir admin

Important: Your connection with SQL Plus won’t work unless you have exported the LD_LIBRARY_PATH to the instant client folder for the user running the SQL Plus. A warning sign for this is when you get the following error when trying to run SQL plus (./sqlplus):

./sqlplus: error while loading shared libraries: libsqlplus.so: cannot open shared object file: No such file or directory

The Primo Central index is a mega-aggregation of hundreds of millions of scholarly e-resources of global and regional importance. These include journal articles, e-books, reviews, legal documents and more that are harvested from primary and secondary publishers and aggregators, and from open-access repositories. Ex Libris works with the world’s leading providers of global and regional information to benefit its customer community. The Primo Central index fully exploits the richness of the underlying data to facilitate fast and easy search.

Oxford went live with Primo Central in September 2010. We made Primo Central index part of our resource discovery platform SOLO based on Ex Libris’s Primo, and introduced it as a new tab called “Journal Articles (beta)“. We tagged it as beta, because we still believe that there are areas where Primo Central is not as comprehensive as it could be, e.g. Law resources. We also provided a brief description of the limitations and the advantages of Primo Central on SOLO’s home page so that people don’t think of it as comprehensive and the only place to look for resources. So far, we have received really good feedback from our users, excerpts of which follow:

This evening a reader successfully found the article he was looking for with just a couple of words in the title, rough year of publication and journal title. He (and me) were delighted.

the beta version of the solo journal search is truly great!

Solo Journal Articles (beta) – good stuff: User-friendly, and it’s made clear that this is not an exhaustive search of all subscribed databases.

I think Primo central is very promising. I started showing it to students and staff, mostly because I have observed that this years new students – grads and undergrads – tend to use SOLO.

Primo Central will often get good results even if you do a fairly rubbishy search, and compares well with google scholar. For Law researchers, I just give the usual advice that it’s not going to pick up westlaw articles etc, and that it won’t be comprehensive…

In my opinion, Primo Central as a resource is very valuable and promising. With more and more publishers providing their metadata to Ex Libris for addition to Primo Central, things are moving in the right direction. Please do share your experience if you subscribe to Primo Central or any other mega-aggregated index tool, such as Serial Solutions Summon, Encore Synergy, EBSCO Discovery Service, etc.

More details about the plug-in along with source code and installation instructions can be found here.

http://www.exlibrisgroup.org/display/PrimoCC/Nielsen+Enrichment+Plug-in+for+Primo