self-test and prerequisites

Makefile

 .PHONY: slides
 
-all: slides rush
+all: slides rush self-test.pdf
 
 slides:
 	$(MAKE) -C ./slides
@@ -16,5 +16,9 @@ exam_questions.pdf: exam_questions.md Makefile
 	--highlight-style zenburn \
 	--resource-path images $< -o $@ 
 
+self-test.pdf: self-test.md
+	pandoc --standalone --metadata-file ~/.mdpdf.yaml --to=latex \
+	--filter pandoc-crossref --citeproc --output $@ $<
+
 mrproper: 
 	$(RM) shell-scripting_beamer.pdf exam_questions.pdf

prerequisites.md

@@ -22,8 +22,9 @@ Shells in General
 -----------------
 
 * What a shell is
-* What kind of work is typically done in shells
 * How to launch a shell on your machine
+* How one works in the shell, especially as compared with working in a graphical
+  environment
 
 Commands
 --------
@@ -42,13 +43,38 @@ The Filesystem
 * How to list files in the current directory (and, for that matter, in any
   directory)
 * How to move around the filesystem
+* How to rename and move files
 
+Text Files
+----------
 
-Participants are expected to know how to use a Unix shell interactively, i.e.,
-moving around the filesystem, understanding pathnames, lauching programs that
-work on data, redirecting output to files or other programs, etc.
-They are also expected to have some familiarity with basic shell
-utilities like grep, cut, tr, etc (although no expert skills are required).
-Notions of programming (in any language) will be useful, but not essential.
-Finally, some proficiency with a text editor is a must.
+* What a text file is, how it differs from, say, a Word document, and how this
+  relates to shell commands
 
+Redirection and Pipelines
+-------------------------
+
+* How to redirect commands' input and output to/from files
+* How to pass the output of one command to another command's input
+* What a pipeline is
+
+Familiar Shell Tools
+====================
+
+You should know the purpose of the following tools, and be able to understand
+what they do (though in-depth knowledge is not required):
+
+* `cut`
+* `find`
+* `grep`
+* `head`
+* `man`
+* `sort`
+* `tail`
+* `tr`
+* `wc`
+
+Text Editor
+===========
+
+We'll be writing code, so you need to be comfortable with a text editor/IDE. 

self-test.md

+---
+title: Self-Test Questions
+subtitle: for the SIB Shell Programming Course
+author: Thomas Junier
+date: \today{}
+classoption:
+  -onecolumn
+number-sections: false
+---
+
+
+**NOTE** All questions have between 0 and 5 (included) correct answers.
+
+### Question 1
+
+Which part the following command is an _option_?
+
+```bash
+$ ls -l
+```
+
+* [ ] none
+* [x] `-l`
+* [ ] Unix commands do not have options
+* [ ] `ls`
+* [ ] both
+
+### Question 2
+
+How can I obtain help about the `mv` command?
+
+* [ ] `manual mv`
+* [x] `man mv`
+* [ ] `mv help`
+* [ ] `describe mv`
+* [ ] `help mv`
+
+### Question 3
+
+Suppose you are logged in as `myself`, and currently working in
+`/home/myself/project/`. Which of the following commands will
+bring you to your home directory?
+
+* [ ] `cd .`
+* [x] `cd /home/myself`
+* [x] `cd`
+* [x] `cd $HOME`
+* [x] `cd ..`
+
+### Question 4
+
+Which of the following terms best describes any document that is _not_ text in
+the sense of a Unix text file?
+
+* [ ] CSS
+* [ ] graphics
+* [x] binary
+* [ ] HTML
+* [ ] PDF 
+
+### Question 5
+
+What operator(s) redirect(s) a command's output into a file (possibly, but not
+necessarily, creating or deleting it beforehand)?
+
+* [ ] `%`
+* [x] `>`
+* [ ] `|`
+* [x] `>>`
+* [ ] `&`
+
+### Question 6
+
+Why does this not replace `myfile` with a sorted version of itself?
+
+```bash
+$ sort < myfile > myfile # bad!
+```
+
+* [ ] the file to be `sort`ed and the output file must both be passed as arguments
+* [x] redirections occur before execution, so `myfile` is empty when `sort` runs
+* [ ] `myfile` has the wrong permissions
+* [ ] sort always deletes its argument
+* [ ] the file to be `sort`ed must be passed as an argument
+
+### Question 7
+
+These two commands work without problems and produce the same output:
+
+```bash
+$ grep tiffany /etc/passwd
+$ grep tiffany < /etc/passwd
+```
+
+So why does this work...
+
+```bash
+$ tr ':' ';' < /etc/passwd
+```
+
+...but not this:
+
+```bash
+$ tr ':' ';' /etc/passwd
+```
+
+* [ ] `tr` is not allowed to read `/etc/passwd` for security reasons
+* [ ] `tr` expects its input in a file named by its first argument
+* [ ] `tr` expects its input in a file named by its third argument
+* [ ] `tr` expects its input in a file named by its second argument
+* [x] `tr` expects its input on standard input
+
+### Question 8
+
+What would be the most straightforward way of displaying the first ten lines of
+file `myfile` that contain the string `GAATTC`?
+
+* [ ] `grep GAATTC > tmp; head < tmp`
+* [ ] `find GAATTC < myfile -n 10`
+* [ ] `grep GAATTC > tmp; head < tmp; rm tmp`
+* [x] `grep GAATTC < myfile | head`
+* [ ] `head < myfile | grep GAATTC`
+
+### Question 9
+
+What is wrong with this?
+
+```bash
+$ cat myfile | grep '^[a-z]\+' >> output.txt
+```
+
+* [ ] The regular expression is wrong
+* [ ] There will be a bottleneck because `cat` is much slower than `grep`
+* [ ] There must be a '`<`' before `myfile`
+* [ ] There is nothing wrong with this command
+* [x] `cat` is unnecessary and wastes resources
+
+### Question 10
+
+You are given a file named `sci_names.txt` with scientific names, one per line, as follows:
+
+```
+Panthera leo
+Balaena mysticetus
+Panthera tigris
+Panthera pardus
+Corvus monedula
+Corvus corax
+Solanum tuberosum
+Bacillus subtilis
+...
+```
+
+Your task is to find the genus with the most species (in the snippet above, that
+would be _Panthera_, with three species). The expected output is just the genus
+name, nothing else. Which command does the job? 
+
+* [ ] `cut -d' ' -f1 < sci_names.txt | sort | uniq -c | sort -k1,1rn | head -1 | tr -d ' 0-9' | wc -c`
+* [ ] `cut -d' ' -f1 < sci_names.txt | uniq -c | sort -k1,1rn | head -1 | tr -d ' 0-9' | wc -c`
+* [ ] A 100-line Python script
+* [ ] `cut -d ' ' -f1 < sci_names.txt | sort | uniq -c | sort -k1,1rn`
+* [x] `cut -d' ' -f1 < sci_names.txt | sort | uniq -c | sort -k1,1rn | head -1 | tr -d ' 0-9'`
+
+**Note** there are plenty of solutions to this problem. The choices above avoid
+some of the more powerful shell tools (like `sed` and `awk`) not because they're
+not suitable (they are!) but because they may be less familiar.