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sheenamt/gist:97286ea893dfbc5e7cc8

Created August 26, 2014 20:55
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gistfile1.txt
{
"metadata": {
"name": ""
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"Code Review:\n",
"\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"<img src=\"files/sally-code-review.png\">"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Many options about who/when/how that we should discuss as a group"
]
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"unittesting:"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Here's an example function that reformats the tumor types entered into the LIS. "
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"TUMOR_TYPES = {'liver', 'lung', 'all', 'aml', 'bladder', 'brain', 'unknown primary', 'unknown'}\n",
"\n",
"def fix_tumor_type(tumor_type, tumors=TUMOR_TYPES):\n",
" \"\"\"Normalize `tumor_type`, discarding entries not in `tumors`.\n",
" \"\"\"\n",
" tumor_type = tumor_type.lower().strip()\n",
" return tumor_type if tumor_type in tumors else None"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 12
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Here's how many of us would test our function:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"lis_tumors = {'liver', 'Lung', 'ALL', 'AML', 'bladder', 'armesis'}\n",
"\n",
"for tumor in lis_tumors:\n",
" print \"{} becomes {}\" .format(tumor, fix_tumor_type(tumor))"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"ALL becomes all\n",
"AML becomes aml\n",
"bladder becomes bladder\n",
"Lung becomes lung\n",
"liver becomes liver\n",
"armesis becomes None\n"
]
}
],
"prompt_number": 21
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"A class is created to test the function instead. This scripts is part of the genetics_db package, in the annotation.py script. "
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"import unittest\n",
"import sys\n",
"\n",
"class TestAnnotation(unittest.TestCase):\n",
" def testFixTumorType(self):\n",
" self.assertEqual(fix_tumor_type('Aml'), 'aml')\n",
" self.assertEqual(fix_tumor_type('Lung'), 'lung')\n",
" self.assertEqual(fix_tumor_type('Cancel, see detail'), None)"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 59
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"suite = unittest.TestLoader().loadTestsFromTestCase( TestAnnotation )\n",
"unittest.TextTestRunner(verbosity=2,stream=sys.stderr).run( suite )"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stderr",
"text": [
"testFixTumorType (__main__.TestAnnotation) ... "
]
},
{
"output_type": "stream",
"stream": "stderr",
"text": [
"ok\n",
"\n",
"----------------------------------------------------------------------\n",
"Ran 1 test in 0.001s\n",
"\n",
"OK\n"
]
},
{
"metadata": {},
"output_type": "pyout",
"prompt_number": 67,
"text": [
"<unittest.runner.TextTestResult run=1 errors=0 failures=0>"
]
}
],
"prompt_number": 67
},
{
"cell_type": "heading",
"level": 1,
"metadata": {},
"source": [
"virtualenv:"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"You can create a virtualenv for development easily:"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"virtualenv new_project"
],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"To begin using the virtual environment, it needs to be activated:\n",
"You can then begin installing any new modules without affecting the system default Python or other virtual environments.\n",
"\n"
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"source new_project/bin/activate"
],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If you are done working in the virtual environment for the moment, you can deactivate it:\n",
"This puts you back to the system's default Python interpreter with all its installed libraries."
]
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"deactivate"
],
"language": "python",
"metadata": {},
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"To delete a virtual environment, just delete its folder."
]
}
],
"metadata": {}
}
]
}
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