Querying MySQL from Stata

Step 0: Install the ODBC driver

  1. Download and install the iODBC driver manager. The next step will fail if this isn't installed first.
  2. Download and install the ODBC driver.

Step 1: Set up ODBC driver

See these instructions. My ODBC configuration (~/.odbc.ini) looks like:

[ODBC Data Sources]
mysql = MySQL ODBC 5.3 ANSI Driver

[ODBC]
Trace         = 0
TraceAutoStop = 0
TraceFile     = 
TraceLibrary  = 

[mysql]
Driver      = /usr/local/lib/libmyodbc5a.so
Description = desc here
SERVER      = localhost
PORT        = 3306
USER        = root
PASSWORD    = passwordhere
DATABASE    = databasehere

Make sure your driver location is correct. It could also be something like /usr/local/mysql-connector-odbc-5.3.7-macos10.12-x86-64bit/lib/libmyodbc5a.so.

Step 2: Make a ODBC call from Stata

For example:

clear
set odbcdriver ansi
odbc list
// Option 1
odbc load, table("tablename") dsn("mysql") clear noquote
// Option 2
odbc load, exec("select * from tablename") dsn("mysql") clear noquote

Using a plugin is another option, but I haven't tried this.

Update: Loading in SQL from an external file

This allows you to do something like:

cd "/path/to/your/folder"
clear
loadsql using your-sql.sql, dsn(mysql)

Literate Python setup with pweave and Atom

In the past I’ve used IPython/Jupyter notebooks for literate programming, but writing code in the browser is not a great experience and I was having terrible environment issues. I started looking at alternatives, and settled on trying out pweave. It’s the same idea as IPython, allowing me to intersperse code and output with prose, but rather than using the browser I can use a standard programming editor. (It also solves my environment problem.)

The setup for getting a pweave workflow that still has all the nice parts of an IPython notebook is a little involved, so here’s what I did:

  • Get the Atom editor (I generally use Sublime Text, but it can’t run Python inline)

  • Set up a virtualenv and pip install "ipython[notebook]" Pweave

  • Install the following Atom packages:
  • Make the following configuration changes:
    • Append to styles.less:

      // Hydrogen output - font size is too small  
      .hydrogen.output-bubble pre {  
        font-size: 16px !important;  
      }
      // Hydrogen - hack for 2x images  
      .hydrogen.output-bubble .bubble-result-container img {  
        width: 50% !important  
      }
      
    • Append to config.cson:

      ".md.pweave.source":  
        "expand-region":  
          commands: [  
            {
              command: "expand-region:select-inside-back-ticks"  
              recursive: true  
            }
          ]
      
    • Append to keymap.cson:

      '.platform-darwin atom-text-editor':  
        'cmd-enter': 'hydrogen:run',  
        'cmd-shift-space': 'expand-region:expand'
      
    • In the settings under Settings > Packages > Hydrogen:
      • Kernel Mappings (this enables support for .pmd files): {"pweave markdown": "Python 2"}

      • Startup Code:

        {"Python 2": "import matplotlib as matplotlib_import_only\nmatplotlib_import_only.use('Agg')\n%matplotlib inline\n%config InlineBackend.figure_format = 'retina'\npython=None"}
        

        This does a few hacky things:

        • import matplotlib as matplotlib_im ... rt_only.use('Agg'): fix for this issue with a bouncing rocketship dock icon
        • %matplotlib inline: display figures inside Atom rather than in a separate window
        • %config InlineBackend.figure_format = 'retina': turns on high-resolution figures, which are displayed by Atom as double-sized low-resolution figures without the hack in styles.less above
        • python=None: a hack to avoid an error when automatically selecting and running a block of Python code

Some of this configuration is necessary to just get hydrogen to run Python code.

The rest fixes a major problem with pweave: it’s easy to run one line of code, and it’s easy to run all the code in a file, but how do I run only one block of code? (This is equivalent to being able to running an entire cell in IPython with shift-enter.)

The solution is to use the expand-region plugin to select the current block of code, and the python=None hack to avoid an error when it selects the “python” in ```python.

Here’s what it looks like in action:


To convert the .pmd file to a .html that can be shared, simply run pweave -f md2html test.pmd. Here's what the output from the above example looks like.


Notes

  • Remember to open Atom from the command line after activating your virtualenv (see the "Usage" section here).
  • In order to get the pweave command to run with my virtualenv, I manually edited the shebang in /usr/local/bin/pweave to directly point to the Python binary in my virtualenv: #!/Users/max/.virtualenvs/data/bin/python

Keyboard Maestro: Convert Markdown to JIRA Markup

JIRA uses its own plain-text markup syntax, which I don't like as much as Markdown.

Fokke Zandbergen has a great online service for converting between JIRA markup and Markdown, but it's too cumbersome to use this when you are living in JIRA comments.

I re-appropriated Fokke's JavaScript into a Keyboard Maestro macro:

This will take the Markdown in the clipboard and paste it as JIRA markup whenever you type ";jira".

You can download the macro here.

Update – May 26, 2016: I have added support for multi-level unordered lists – the updated code is below.

Move newest file in Downloads folder to the frontmost Finder window

Here's what you do:

  1. Open the folder where you want to move your newest download in Finder.
  2. Trigger the shell script below.

The file will magically be moved! You'll even get a Notification Center notification.

The shell script

Triggering the shell script

I use an AppleScript saved as a .app and triggered with LaunchBar. Here's the AppleScript:

do shell script "bash /Users/YOUR_USERNAME/path/to/script.sh"