Trying something new . . . again (part 1)

Since I just had to reinstall Leopard and lost all my custom PHP and MySQL installations (and the MySQL databases, unfortunately), I tried to remedy that yesterday and today.

I’m still pissed off that OS X doesn’t come with working PHP and MySQL out of the box, including the PHP libraries. With a simple way to know where the data are being stored, and a way to back it up (in one’s Home folder, perhaps). But I digress–I’m sick of spending hours getting things to work when they ought to work.

So I decided to try out XAMPP for Mac (I tried it a few years back for Windows and enjoyed it), and it worked. Here are a few notes.

1. Everything is installed in the Applications folder. I’m not sure I like this, since I hate having stupid little folders (and DATA) in the Applications folder. I’m not sure if this can be easily changed, perhaps with a symbolic link to somewhere else (such as my Home folder, so it will get backed up).

2. Leopard MySQL was running when I installed, so I had to kill it with ‘sudo killall mysql’ and it will hopefully not start up again when I restart. The main reason I was having issues was that Leopard AGAIN lost mysql.sock.

3. I turned off Web Sharing in System Preferences. This is probably a good thing, and it will at least keep my computer from trying to run two Apache servers at once.

4. I wanted to keep the Sites folder as my web root for localhost, so I opened /Applications/xampp/etc/httpd.conf and changed DocumentRoot to point toward my Sites directory (e.g., “/Users/Matt/Sites”). I then copied everything in /Applications/xampp/xamppfiles/htdocs into /Users/Matt/Sites, and things seem to still work fine.

5. The MySQL databases, in case you want them backed up with the rest of the file structure rather than using phpMyAdmin, are stored in /Applications/xampp/xamppfiles/var/mysql. I may try to move them (with a symbolik link) to be stored in my Home folder since I won’t be keeping a lot of data in them but it’s annoying when I lose settings for various PHP applications (Simple Machines Forum, OpenX, Drupal, Serendipity, etc.).

6. I cannot get MySQL to work if I set a password for it, which means no logging into phpMyAdmin and no access to the MySQL databases. I get “Access denied for user ‘root’@’localhost’ (using password: NO)” instead, until I reset the password to blank. (Note to self, to do this, the command is [sudo ./bin/mysqladmin -u root -p password ”] (no brackets). The -p is important, because it will them ask you for your current password rather than assuming that you just didn’t want to supply it. Idiotic.)

7. Overall, aside from having to install all my databases again (not the fault of XAMPP), it seems to be working well so far. It just miffs me that I have a non-functioning version of MySQL on my laptop as well as an unused (although missing certain useful libraries) version of PHP 5 floating around. At this point I’ll take what I can get.

Specify 5.2 and my quest to import lots of data

I’ve been unable to figure out how to get a username and password to login to the Specify forum; I’ve requested help with that but until I get a response, I’m going to shout my questions out to the ether and hope I get some echos of answers back.

UPDATE: Apparently you have to email specify@ku.edu to get a login (source).

1. When is Specify 6 coming out? Originally it was early 2008, then it was mid 2008, and I haven’t seen any updates recently. I hope it comes out soon.

2. Is there a Specify mailing list? If there isn’t, there should be, especially since it seems like nobody is able to log into the official forum. I might be interested in getting one going depending on interest, since there are supposedly lots of people using the software. There is a mailing list here.

3. The big question: is it possible to add more than the default offering of a few new fields to each form? I’m on the cusp of moving over a great deal of data, and I’d like to be able to include everything and add fields as necessary, but that doesn’t seem to be an option.

I’ve tried adding fields to the database itself (through Server Management Studio Express), but I think the number and name of each field is hard-coded into the Specify program rather than being stored as an expandable list in the database, because the new field doesn’t show up when I go to edit forms. For example, each field has both a name and a set of properties–the properties (such as what kind of data is allowed, how long it is allowed to be, etc.) are described in the database tables, but I have not been able to determine where the name of each field is stored. Hold up. It has to be stored somewhere, because it can be changed by the user. I may have to dig deeper. Sometimes talking through things does lead to answers. We’ll see what I can dig up.

In any case, I’m very comfortable with messing with the database tables themselves in order to get the data in, which is what I’m going to have to do anyway, because the data will be coming out of a tab-delimited file when I’m done with it and should be easy to get into SQL. It’s just a question of making sure those columns exist in the tables first…

Anyway, that’s where I stand. I’ll update when I know more.

A Journey Through England and Scotland to the Hebrides in 1784 by B. Faujas De Saint Fond

A Journey Through England and Scotland to the Hebrides in 1784

By

B. Faujas De Saint Fond

A revised edition of the English translation
edited, with notes
and a memoir of the author

by

Sir Archibald Geikie, D.C.L., Sec.R.S.
Correspondent of the Institute of France

Volume Two

Glasgow: High Hopkins
1907

Complete volume II (.pdf, 10 MB)

Front matter and table of contents (.pdf, 268 KB)

CONTENTS

CHAPTER I (.pdf, 276 KB)
Departure from Oban for the Island of Mull.–Passage of the Sound of Mull.–Small isle of Fiart.–Druidical Monuments.–Arrival at Aros

CHAPTER II (.pdf, 400 KB)
Journey from Aros to Torliosk.–Stay at Mr Maclean’s.–Tale of what happened to my fellow-travellers during their passage to, and continuance on, the Isle of Staffa

CHAPTER III (.pdf, 276 KB)
Voyage to Staffa

CHAPTER IV (.pdf, 1008 KB)
Description and Natural History of the Isle of Staffa.–General Views

CHAPTER V (.pdf, 700 KB)
Star at Mr Maclean’s.–Customs and Manners of the Inhabitants of the Isle of Mull

CHAPTER VI (.pdf, 548 KB)
Departure from Torliosk.–Stay at Aros.–Visit to two worthy Farmers, the Brothers Stuart of Aros.–Excursion to the Mountain of Ben More, the highest in the Isle of Mull.–Stop at Mr Campbell’s, of Knock.–His agricultural Operations.–The curious Lavas which his clearings have brought to light.–Departure from Aros for Auchnacraig

CHAPTER VII (.pdf, 1.2 MB)
Natural History of the Island of Mull

CHAPTER VIII (.pdf, 64 KB)
The Isle of Kerrera

CHAPTER IX (.pdf, 660 KB)
Departure from Oban.–Dalmally.–Tyndrum.–Leaa Ore.–Killin.–River-mussels containing Pearls.–Description of these Pearls and their origin

CHAPTER X (.pdf, 328 KB)
Kenmore.–Extraordinary Flux and Reflux of Loch Tay

CHAPTER XI (.pdf, 384 KB)
Perth, its Harbour and Manufactures.–Mr McComie, Teacher of Mathematics; Mr McGregor, Teacher of the French Language at the Academy.–Volcanic mountain of Kinnoul.–The Agates found there

CHAPTER XII (.pdf, 608 KB)
St Andrews.–University.–Library.–Old Churches.–Natural History

CHAPTER XIII (.pdf, 416 KB)
Departure from St Andrews.–Largo.–Leven.–Dysart.–Kirkcaldy.–Kinghorn.–Leith.–Return to Edinburgh

CHAPTER XIV (.pdf, 1.1 MB)
Edinburgh.–The University.–Learned Societies.–College of Physicians.–College of Surgeons.–Cabinets of Natural History.–Robertson.–Smith.–Black.–Cullen, &c.

CHAPTER XV (.pdf, 144 KB)
Departure from Edinburgh.–Itinerary to Manchester.–Natural History

CHAPTER XVI (.pdf, 104 KB)
Manchester.–Doctor Henry; his Cabinet.–Cotton Manufactures.–Messrs Thomas and Benjamin Potter.–Charles Taylor

CHAPTER XVII (.pdf, 1.1 MB)
Departure from Manchester.–Buxton; its Mineral Waters; fine Baths, constructed on a Plan of Carr, at the Expense of the Duke of Devonshire, the Proprietor of the Waters.–Dr Pearson.–Manufacture of Vases and other Articles in Fluor Spar of different Colours.–Cave of Poole’s Hole.–Toadstone composed of a basis of Trap, interspersed with grains of Calcareous Spar, presenting prismatic contraction as in basalt, though not the work of fire as the latter is

CHAPTER XVIII (.pdf, 596 KB)
Castleton.–Description of a fine Cavern.–Mines of Lead and Calamine, Veins of Fluor Spar.–Lead found in Channel or Cat-dirt

CHAPTER XIX (.pdf, 120 KB)
Derby.–Richard Brownn, dealer of objects of Natural History.–A Manufacture of Vases, and other works of Fluor Spar

CHAPTER XX (.pdf, 303 KB)
Departure from Derby.–Arrival at Birmingham; its numerous Manufactures.–Doctor Withering.–James Watt.–Doctor Priestley; his House; his Library; his chemical Laboratory

CHAPTER XXI (.pdf, 84 KB)
Departure from Birmingham.–Coventry.–Warwick.–Oxford.–Saint Albans.–Barnet.–London.–Return to France

Back matter and index (.pdf, 344 KB)

Scanned November 2008.

Newness

[EDIT: This applied when hosted by Blogger.  2014-02-10]

I’m experimenting with new colors and layout, having finally taken the leap away from hard-coding every aspect of this blog. This may be because it’s late in the evening and I’m not wondering what clothes to wear.

Let me know if you have problems reading things.

Filling

One of my interests is building a PDF library for myself and fellow graduate and undergraduate students. Which means that it’s very hard to pass up PDFs when I come across them on the web. So right now I’m downloading anything I even look at during my research, to keep and to pass along.

This may well fill up my hard drive this semester.

Totally ignoring (skipping) a page in LaTeX

To include a dedication page in my thesis, I have to not number the page and not include the page in the numbering scheme. That is, if the dedication is on the 10th page of the thesis, the page before is numbered ix and the page after is numbered x.

To do this, use the \addtocounter command to add a negative value to the page counter when you start the page, and then don’t print the page number with \thispagestyle{empty}.

My dedication page:

%Dedication
\chapter*{} %blank chapter, no title, not included in table of contents
\thispagestyle{empty} %no page number
\addtocounter{page}{-1} %ignore this page when counting
\vspace{2.5in} %start the dedication halfway down
\begin{center} %center everything
\hl{Dedication} %the wonderful words
\end{center}

 

Source: Help On LaTeX \addtocounter: “\addtocounter{counter}{value}”

 

Posting with my real name

[I just wrote this over at The City Beat. I’m still working through some things.]

Ben T., Information Architects had some good things to say about posting comments with your real name.

http://informationarchitects.jp/use-your-real-name-when-you-comment/

I go back and forth on this, and I think it’s a really interesting topic. For one, I like knowing what I said, and now that Google has just about everything I’ve ever written on the Internet, if I always posted with my real name, I could go back and check up on it. So could other people, and this is what irks me about myself: do I want other people to be able to dredge up what I’ve said? A lot of it’s opinion, some of it’s having fun, and some of it reflects me having a bad day, or a bad year (I started blogging in high school, which means all sorts of “angry at the world” stuff.

What bothers me is that I have a problem with that. Shouldn’t I be able to stand behind everything I say, or everything I’ve ever said? I think I should, and yet I still post under a (normally transparent) pseudonym. I know that I want to be proud of everything I say, but it seems like things get blown way out of proportion online, compared to in person. If we met in person and I said “I’m just so pissed off, I’m never eating pickles again” (or something more serious), you could tell that I was momentarily pissed off, and that I probably would eat pickles again. Online, words have staying power, and no matter what you were thinking when you wrote them (“I hate you, I hope you die”), they can get dredged up by someone else and used against you.

This is possible to do in real life as well, but then when I say “I wasn’t serious, I was having a bad day,” how can you believe me, and how can I believe you when you say “I understand, we all have bad days sometimes”?

I’ve said some pretty stupid things in my life, online and off, and I’m trying to stop doing that (things like insulting people because they disagree with me). I’ve found that it’s immensely helpful to post under my real name, because it prevents me from going off half-cocked.

[Later]
Another question is whether or not I want to have an online presence at all. For someone as opinionated and communicative (sometimes) as I am, that’s a simple question to answer, but things are much more difficult online than they are in person, because you’re interacting with a much larger number of people.

I also forgot to mention that it seems weird to me that people use “throwaway” identities rather than a standard alter ego. If I did that, I’d forget what I wrote if I went back and read something again. Maybe that’s another issue: I go back and read things again, while others seem to do drive-by postings, where they drop their opinion, run, and never look back to see if anyone had something to say in reply. Why post if you don’t want to hear what the other person has to say?

How to edit a layer if you’ve never edited a layer before in QGIS

Remember, you have to set the snap tolerance of each layer individually for each layer you want to edit. To do this in 0.11.0 Metis, select Settings -> Project Properties and click “Snapping options…” under the “General” tab. Make sure the checkbox next to the layer you want to edit is selected. I have not needed to change the tolerance from “0” yet. This is set in map units (see Project Properties, General tab).

Really, this is an annoying step, and something that probably frustrates noobs like me (who jump in without reading the whole guide) a whole lot.

Source: QGIS User Guide for 0.9.1 Ganymede, Chapter 4.4 Editing (about page 47 of the PDF). This PDF should have come with your install.

QGIS Community

Fun extras with the OS X terminal

I’m writing some more R scripts today to make up for the discrepancy between different people’s interpretation of the concept of disparity and variance, and I felt the need to add a signal that the script was done running. I’ve used play() in the past, but it seems silly to use an extra library when I have other methods…

system("say All done!");

I was also playing with the system volume, but decided not to do too much, since I’m usually listening to music, and blowing my ears out is not my preferred method of learning that my function has completed running.

Change the system volume from the command line – OS X Daily Check out Kevin’s comment for some more tricky things.

Of course, you can always just play a sound without the play() function–just use Terminal! http://forums.macosxhints.com/showthread.php?t=33962