This is used in conjunction with Endnote (my university supplies me a free licence) to manage my references and bibliography in the actual chapters I write (so far, one down, two to go!). Endnote must be used to manage the referencing and bibliography separately: most of the databases export the relevant reference import data for Endnote. You can also search the Library of Congress to get complete information for books that you need in your bibliography. Better than typing it all in by hand! Endnote will also handle reformatting the referencing method used (if you find the guidelines are different) and its creates a bibliography automatically out of everything you reference.

Back in Evernote, I drag all the PDFs of journal articles that I download from the various scholarly databases I search into Evernote, then I tag them with relevant information.  This gives me s searchable database of relevant articles. Then for each article, and for each book or other non-PDF source, I write up a set of notes into my word processor, and export that note as a PDF file. These finished notes are then imported into Evernote and I tag them with relevant information which helps me find related ideas among notes.

There are a few features that I think Evernote needs to have to be a fully successful scholarly research tool. I’d love to be able to directly cross-reference two notes directly, rather than indirectly via tags. Maybe even an ability to attach a note to the cross-reference, that would be super-cool, that way I could describe the nature of the linkage of ideas.  Fully notated cross-referencing is necessary for me because scholarly research doesn’t occur in a flat, one or two dimensional ‘tagged’ space. Tagging only gets you so far.

Speaking of tags, its tagging needs to be properly hierarchical. You can give tags sub-tags, true enough. However if you add the leaf tag to an article, the parent tag is not automatically also available. So you might have a tag Rome, which has a sub-tag, Republic, but if you add a note to the Republic tag, it doesn’t appear when you select the Rome tag. Which is a bit silly.

Another great feature would be an ability to do the tasks of Endnote. Failing that (it is pretty specialised), a way for it to co-operate with Endnote, e.g by linking notes in Evernote to bibliography entries in Endnote, would be totally awesome, but quite unexpected.

Also there is a small bug which means while reading a PDF in Evernote it doesn’t seem to obey the page up / page down or arrow keys which is a little annoying – you have to use the mouse, or double click to open the PDF in Apple Preview.

But overall a relatively satisfying experience so far.

UPDATE 28 June 2010: Via Google Buzz, my friend Shannon O’Neill put me onto the Mac program Papers – http://mekentosj.com/papers/ … I just had a quick look at it tonight. it certainly has some potential. With a bit of coaxing I had it authenticate against my university’s EZproxy and thence searching and downloading journal articles straight from JSTOR (online database).

There is no way to make synthetic notes that link different journal papers, though, which is a pity. Also the notes window is a little cramped, which is a pity.

I also imported my Endnote database and it could then retrieve at least some of the article PDFs so-referenced from JSTOR and other sources. However it did think that the couple of anthology articles I had in Endnote were in ‘journals’ but worse than that it also lists the anthology editor(s) as one of the paper’s editors. Oops. But all in all it turns out it might be useful tip. Anything to keep me from writing – I can now spend days if not weeks fiddling with bibliographic databases instead!

I was off the client site so I couldn’t rely on a fast connection to their development databases. I just wrote a dummy function that was called the same as the real function with the same input and output parameters and instead of the complex function body it just wrapped a simple mock table of test data. Problem solved, Oracle XE to the rescue. But first you have get Oracle XE running on your Mac, this is what the rest of this article is about, because you can’t just download an Oracle XE edition for the Macintosh.

Virtualisation is great – use a Linux VM

However modern Virtualisation is your saviour. Put simply, you can use a virtualisation tool like Parallels, or my choice, VMWare Fusion, to run a virtualised version of Linux that contains the Oracle XE instance.

Because VMs can waste a bit of your local resources, luckily there is a specialised version of Ubuntu designed for running as a virtualised machine of this type. Its called JeOS (pron. Juice, apparently). It doesn’t have an X-window environment, just the shell, so it’s pretty lightweight and can run, with Oracle XE, in less than 512MB of memory. Perfect for getting a copy of Oracle XE onto your Macbook Pro.

It will however, eat up a couple of gigabytes of disk space, up to the maximum limit you choose for your disk size in the VMWare configuration. However it will only use the current amount of disk needed, as VMWare will expand the size of the image as needed (I’ll just assume that Parallels does something similar).

Setting it up – basic instructions

This page here – has a great set of instructions for getting JeOS installed and configured with Oracle XE on it. Follow the instructions there exactly – but only to the point where you install and configure Oracle XE – don’t go further than that.

Make sure you configure plenty of swap space as outlined in the instructions.

Setting it up on standard Ubuntu/Debian

If you are running a full Ubuntu or other Debian based instance, the instructions are somewhat simpler. Install it as per normal in your VM. But make sure your swap space is twice the memory you have assigned to the VM! Oracle XE demands things to be like that.

Add

deb http://oss.oracle.com/debian unstable main non-free

to /etc/apt/sources.list and then:

$ wget http://oss.oracle.com/el4/RPM-GPG-KEY-oracle  -O- | sudo apt-key add -
$ sudo apt-get update
$ sudo apt-get install oracle-xe

These instructions were cribbed from here.

After installing and configuring Oracle XE

After you run the XE configuration (‘$’ represents the Unix shell prompt and should not be typed);

$ sudo /etc/init.d/oracle-xe configure

If you’re running on JeOS don’t yet make the machine “headless”! Or you might find there are issues with the “Apex” application. The problem is that the Apex application, which is a useful web-based administration program for Oracle XE (especially for developers who don’t want to be forced to use sqlplus for all their database administration), will only allow connections from localhost – and you don’t have X-window, or a browser, to access it (I don’t know if lynx will work with Apex and I wasn’t going to try).

Get SSH installed

First get SSH installed in JeOS so you can get to the command prompt remotely:

$ sudo apt-get install ssh

Find out the VM’s IP address

Now, if you type ifconfig (/sbin/ifconfig if that’s not found on your path) you will be able to determine the IP address of your VM running on your Macintosh. At this point you can connect to the VM using ssh from a Macintosh terminal window:

$ ssh username@ip_address

Actually, at this point you can go ahead and make the machine headless, if you want. I would recommend not to do that until you’re sure of everything you’ve configured.

Configure environment to run sqlplus

After you’ve logged back into the running Linux VM using ssh from the Mac Terminal, the next thing is you’ve got to get sqlplus access working to the XE instance you installed. Funnily enough, although the .deb file that is installed off the Oracle site creates an oracle user, it doesn’t in any way set that user up so you can use the command line tools. SO you can’t just su – oracle and get a functional environment.

Anyway, you will need to do two things to your environment; add the ORACLE_HOME environment variable and set up your PATH so it can find sqlplus.

$ export ORACLE_HOME=/usr/lib/oracle/xe/app/oracle/product/10.2.0/server
$ export PATH=${PATH}:${ORACLE_HOME}/bin

You should add these two lines to your .profile or .bash_profile file – probably best for the ‘oracle’ user that the installation will have created. But you can actually set this up for any regular user that you configure in this VM. You can also just type them at the command line to get them in your current environment, if you have to.

Configure Apex to accept non-localhost connections

The web-based administration software for XE, called “APEX”, only binds to localhost. This is a big hassle if your VM copy of Linux (like JeOS) doesn’t have a GUI, because you don’t have a browser (lynx/links excluded, I did not try those!).  However, you can make Apex bind to the “external” IP address for your VM, but you’ll need to use sqlplus.

To run sqlplus, do the following:

$ sqlplus system@XE
  Enter password:

Enter the password you specified at the ‘oracle-xe configure’ step above.

At the SQL prompt, enter the following command:

SQL> EXEC DBMS_XDB.SETLISTENERLOCALACCESS(FALSE);

Now you’ll have to stop and start Oracle to make the configuration active:

$ sudo /etc/init.d/oracle-xe restart

After which, if you type

$ netstat -tna

You should find a line

tcp        0      0 0.0.0.0:8080            0.0.0.0:*               LISTEN

This indicates a process is listening to the port 8080 on all IP addresses for connections coming from any other IP address. Assuming you specified port 8080 at the ‘oracle-xe configure’ step. Sometimes I use 8888 especially if I have a Tomcat instance in the same VM, as Tomcat will also like to run on 8080 and I’d prefer it if it did.

Test and use Apex

Test this connection in your browser, in my case, the address was 10.1.2.17, but you will have to substitute your own VM’s IP address – http://10.1.2.17:8080/apex. I like to make an /etc/hosts entry that points to this address as ‘oracleXE’. That way I can use a symbolic name in my jdbc connection strings and actually switch which instance of XE I am using depending which VM I’ve fired up without editing the jdbc configuration of the application under development – I just change the /etc/hosts entry instead.

Anyway once you connect to apex you can login using the user name and password you set up during your XE install and configuration process (same as you used for sqlplus). The users will be sys and system, you can use them to create new users to contain your databases for development.

The same IP address as above will be used to connect to your Oracle database from the programs you are developing. The default port should be 1521 and the SID should be XE.

Enjoy!

Thunderbird 2 doesn’t integrate with the Macintosh Address Book, so that rules it out straight away, had to go straight to Thunderbird 3 beta. I got the latest, beta 3, released in July.

After about 5 minutes with Thunderbird 3 beta I was telling it to go fsck itself. Here’s why:

1. Installing Thunderbird 3 – what’s with the “@googlemail.com’ for Gmail? I use ‘@gmail.com’ and always have and always will. That’s the option I want. Oh sweet lord, it will force me to use @googlemail.com – that’s a disaster right there. Can be edited later, however, I discover. But still.
2. Thunderbird 3  “integrates” with the Mac address book, which is to say it will pull addresses from it, but it does this through it’s own horrible, horrible, interface. Bad Mozilla! I want to use – at all times – the Apple ‘Calendar.app’ and ‘Address Book.app’, OK? Their user interfaces. Not yours.
3. I got some mail with pictures in it. I can view the pictures by selecting “view external content” button for this one email. If I select the “always view external content for xxxx” it wants to add the sender to the address book (it’s internal address book). No Mozilla, that’s not what I’m asking for. I just want the graphics for that newsletter I get sent to be shown without me pressing extra buttons every time I get this newsletter. I don’t want their address in my address book!
4. Arrrrgh! My eyes! Jesus it’s ugly. And clunky. It feels like Windows all over again. Good lord. I can’t find any way to change the list display fonts. It’s probably in there somewhere, I will admit, but I can’t find it.
5. Every single folder, I have to individually select “view by thread”, as far as I can tell.
6. Search is an entirely separate window/dialogue. I can’t search more than one account at once. “Search Subfolders” at the top level includes Spam folder. There doesn’t seem to be a way to add a criteria that “Message is not spam”.
7. The terrible search function is the only basis for “Smart Folders” that I can find so far, therefore it won’t work for what I need. In Mail.app, I use three smart folders:
   1. All unread mail in any account or sub-folder thereof
   2. All mail in the Inbox of any of my three “personal” accounts, that is, mail directly addressed to me personally.
   3. All mail in the Inbox of my work mail account.
8. On the plus side, it does have good support for keyboard commands. I’m an old mutt user (before that, elm) so I love keyboard commands in my mail program. Mail.app has rubbish support for this.
9. Also on the plus side, Thunderbird’s threading display is a little clearer. Mail.app just puts all messages in a thread under the one hierarchy, you don’t get any sense of what message is a reply to which.

OK  Apple Mail.app lost some sent mail  once in the middle of a godawful crash (but a crash nonetheless), and I’ve always hated its horrible keyboard support. However maybe I am willing to take those risks and annoyances if this is the alternative experience. I know that Mozilla is open source, and full of all that open sorcery goodness, but I live and die via my email program, right after my IDE, and I want a pretty nice experience with it. Thus, I’m now in a bind – use a program that just proved to me its data integrity is not 100%, or use a program that that just gives me a truly horrible user experience and wants to screw with my choice of Calendar and Address Book?

Mac email program suggestions in the comments if you like (and no, don’t suggest Entourage, it’s completely off the menu).

UPDATE: I should mention that, for me, the deal killers are points 2, 6, and 7.

Tip – I found where it was installed with this simple series of *nix commands that should work on most Unix variants such as Linux, for anything on your ${PATH}, using the ‘which’ command:

CrazyMcphee:systems smcphee$ which mvn
/usr/bin/mvn
CrazyMcphee:systems smcphee$ ls -lrta /usr/bin/mvn
lrwxr-xr-x  1 root  wheel  24  9 Mar 22:50 /usr/bin/mvn -> \
  /usr/share/maven/bin/mvn

Following the information on this page as a template, here’s the procedure I used to upgrade to the latest version at time of writing, Maven 2.1.0:

CrazyMcphee:~ smcphee$ sudo su -
Password:
CrazyMcphee:~ root# cd /usr/share/
CrazyMcphee:share root# mv maven maven-2.0.6
CrazyMcphee:share root# cp -R \
/Users/smcphee/Development/systems/apache-maven-2.1.0/ \
maven-2.1.0
CrazyMcphee:share root# ln -s maven-2.1.0/ maven
CrazyMcphee:share root# exit
logout
CrazyMcphee:~ smcphee$ mvn -version
Apache Maven 2.1.0 (r755702; 2009-03-19 05:10:27+1000)
Java version: 1.5.0_16
Java home: /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home
Default locale: en_AU, platform encoding: MacRoman
OS name: "mac os x" version: "10.5.6" arch: "i386" Family: "unix"

You’ll note I used a symlink for the ‘maven’ directory to the ‘maven-2.1.0′ directory (the command ‘ln -s maven-2.1.0/ maven’ …). This is to allow me to quickly switch back to version 2.0.6 if I find any incompatibilities in my old POM files with the new version of Maven, by simply changing which directory the symlink points to.

• Uploading photos in bulk does not preserve the order (any order) in the Flickr stream. So your photostream gets whack out of order.
• When you upload photos it assumes that whatever event, album, or smart album you’re currently viewing the photos in should be created as a Set on Flickr. Oh and if the event, album or smart album contains any ‘special’ character that Flickr won’t like in a set name, it won’t do the upload and doesn’t tell you why not.
• Deleting the spuriously created Flickr Album in iPhoto means the photos are removed from Flickr. After iPhoto tells you it won’t actually delete any photos! (it means from iPhoto, not Flickr).
• I tried moving the photos to another Set using Flickr’s interface, and removing the now-empty spurious set. IPhoto then asked me if this remotely-removed set should be removed, when I answered yes, somehow iPhoto still managed to delete the previously-moved photos from Flickr.
• Did I mention that iPhoto flakes the photostream order?

Most of this will also probably apply to the Facebook plugin integration too. This is seriously poor software from Apple. It effectively lies to you about what it’s doing. Yet again proving that Apple doesn’t like to play nice with others. Do not use the Apple-provided iPhoto to Flickr integration. It’s stuffed.

[UPDATE. More information from a iPhoto-Flickr plugin author here: http://speirs.org/2009/01/30/on-the-flickr-support-in-iphoto-09/ ... ]