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Merge pull request #1 from UUDeCART/master #4

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23566ad
Merge pull request #1 from UUDeCART/master
UU00180764 Jun 28, 2019
b3838c7
initial changes
UU00180764 Jun 28, 2019
58e4ddc
updated notebooks
UU00180764 Jun 28, 2019
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3 changes: 3 additions & 0 deletions .gitattributes
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@@ -0,0 +1,3 @@
*.ipynb filter=nbstripout

*.ipynb diff=ipynb
2 changes: 1 addition & 1 deletion .gitignore
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@@ -1,4 +1,4 @@
.ipynb_checkpoints
.gitattributes
__pycache__
*.swp
*.ziggy
2 changes: 1 addition & 1 deletion modules/module1/InClass/Index.ipynb
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Expand Up @@ -54,7 +54,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.2"
"version": "3.7.3"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,
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47 changes: 47 additions & 0 deletions modules/module1/InClass/Untitled.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
"\n",
"cd /home/uu00180764/DATA/Numerics/mimic2/hr/subjects\n",
"grep -lrP \"\\b(?<!\\.)[23]\\d{2,2}\\b\" . > ~/hr200.txt\n",
"cd /home/uu01080764/DATA/Numerics/mimic2/bp/subjects\n",
"grep -lrP \"\\b(?<!\\.)[23]\\d{2,2}\\b\" . > ~/bp200.txt\n",
"grep -Fx -f ~/bp200.txt ~/hr200.txt"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
27 changes: 17 additions & 10 deletions modules/module1/InClass/environment_variables.ipynb
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Expand Up @@ -239,10 +239,10 @@
"outputs": [],
"source": [
"%%bash\n",
"rm -r /home/jovyan/bin\n",
"mkdir /home/jovyan/bin\n",
"cp ./ls /home/jovyan/bin/.\n",
"chmod +x /home/jovyan/bin/ls"
"rm -r /home/uu00180764/bin\n",
"mkdir /home/uu00180764/bin\n",
"cp ./ls /home/uu00180764/bin/.\n",
"chmod +x /home/uu00180764/bin/ls"
]
},
{
Expand All @@ -252,7 +252,7 @@
"outputs": [],
"source": [
"%%bash\n",
"/home/jovyan/bin/ls"
"/home/uu00180764/bin/ls"
]
},
{
Expand Down Expand Up @@ -280,9 +280,9 @@
"source": [
"%%bash\n",
"\n",
"PATH=/home/jovyan/bin:$PATH\n",
"PATH=/home/uu00180764/bin:$PATH\n",
"which ls\n",
"ls /home/jovyan/DATA/Misc"
"ls /home/uu00180764/DATA/Misc"
]
},
{
Expand All @@ -293,9 +293,9 @@
"source": [
"%%bash\n",
"echo $PATH\n",
"export PATH=$PATH:/home/jovyan/bin\n",
"export PATH=$PATH:/home/uu00180764/bin\n",
"which ls\n",
"ls /home/jovyan/DATA/Misc\n"
"ls /home/uu00180764/DATA/Misc\n"
]
},
{
Expand All @@ -307,6 +307,13 @@
"%%bash\n",
"echo $PATH"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand All @@ -325,7 +332,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.5.2"
"version": "3.7.3"
}
},
"nbformat": 4,
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41 changes: 23 additions & 18 deletions modules/module1/InClass/finding_files.ipynb
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Expand Up @@ -128,7 +128,7 @@
"outputs": [],
"source": [
"%%bash\n",
"find /home/jovyan -name 'README'"
"find /home/uu00180764 -name 'README'"
]
},
{
Expand Down Expand Up @@ -172,7 +172,7 @@
"outputs": [],
"source": [
"%%bash\n",
"find /home/jovyan/work/decart_bootcamp_part1 -name '*.ipynb'\n"
"find /home/uu00180764/work -name '*.ipynb'\n"
]
},
{
Expand All @@ -199,7 +199,8 @@
"metadata": {},
"outputs": [],
"source": [
"%%bash\n"
"%%bash\n",
"find /home/uu00180764/DATA -name '*.wav'\n"
]
},
{
Expand All @@ -208,7 +209,7 @@
"metadata": {},
"outputs": [],
"source": [
"mitral_files()"
"mitral_files(2)"
]
},
{
Expand All @@ -217,7 +218,7 @@
"metadata": {},
"outputs": [],
"source": [
"wave_files()"
"wave_files(11)"
]
},
{
Expand Down Expand Up @@ -258,7 +259,8 @@
"metadata": {},
"outputs": [],
"source": [
"%%bash"
"%%bash\n",
"find /home/uu00180764/DATA -name '*.txt' -size 10k | wc -1\n"
]
},
{
Expand All @@ -267,7 +269,7 @@
"metadata": {},
"outputs": [],
"source": [
"find_10k_files()"
"find_10k_files(71)"
]
},
{
Expand All @@ -293,7 +295,7 @@
"outputs": [],
"source": [
"%%bash\n",
"find /home/jovyan \\( -name '*.db' -o -name '*.sqlite' \\)"
"find /home/uu00180764 \\( -name '*.db' -o -name '*.sqlite' \\)"
]
},
{
Expand All @@ -317,7 +319,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep chapel /home/jovyan/DATA/Misc/obits.txt"
"grep chapel /home/uu00180764/DATA/Misc/obits.txt"
]
},
{
Expand All @@ -334,7 +336,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i chapel /home/jovyan/DATA/Misc/obits.txt"
"grep -i chapel /home/uu00180764/DATA/Misc/obits.txt"
]
},
{
Expand All @@ -351,7 +353,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i -c chapel /home/jovyan/DATA/Misc/obits.txt"
"grep -i -c chapel /home/uu00180764/DATA/Misc/obits.txt"
]
},
{
Expand All @@ -368,7 +370,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i -c -r chapel /home/jovyan/DATA/Misc"
"grep -i -c -r chapel /home/uu00180764/DATA/Misc"
]
},
{
Expand All @@ -385,7 +387,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i -l -r chapel /home/jovyan/DATA/Misc"
"grep -i -l -r chapel /home/uu00180764/DATA/Misc"
]
},
{
Expand All @@ -402,8 +404,8 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i chapel /home/jovyan/DATA/Misc/obits.txt \\\n",
"/home/jovyan/DATA/Misc/icd9-short.txt"
"grep -i chapel /home/uu00180764/DATA/Misc/obits.txt \\\n",
"/home/uu00180764/DATA/Misc/icd9-short.txt"
]
},
{
Expand All @@ -413,7 +415,7 @@
"outputs": [],
"source": [
"%%bash\n",
"grep -i chapel /home/jovyan/DATA/Misc/*.txt"
"grep -i chapel /home/uu00180764/DATA/Numerics/mimic2/hr/subjects/*.txt"
]
},
{
Expand All @@ -434,7 +436,10 @@
"outputs": [],
"source": [
"%%bash\n",
"grep '7.-year-old' /home/jovyan/DATA/Misc/*.txt"
"grep -i '2..' /home/uu00180764/DATA/Numerics/mimic2/hr/subjects/*.txt > /home/uu00180764/work/hr_200.txt\n",
"cat /home/uu00180764/work/hr_200.txt\n",
"grep -i '2..' /home/uu00180764/DATA/Numerics/mimic2/bp/subjects/*.txt > /home/uu00180764/work/bp_200.txt\n",
"cat /home/uu00180764/work/bp_200.txt"
]
},
{
Expand Down Expand Up @@ -485,7 +490,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.5"
"version": "3.7.3"
}
},
"nbformat": 4,
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2 changes: 1 addition & 1 deletion modules/module1/InClass/introducing_shells.ipynb
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Expand Up @@ -86,7 +86,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.2"
"version": "3.7.3"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,
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23 changes: 15 additions & 8 deletions modules/module1/InClass/navigating_file_system.ipynb
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Expand Up @@ -287,9 +287,9 @@
"metadata": {},
"outputs": [],
"source": [
"number_of_files = -1\n",
"largest_file = \"None\"\n",
"most_recent_file = \"None\""
"number_of_files = 8\n",
"largest_file = \"Accidents7904.csv\"\n",
"most_recent_file = \"seinfeldFood.sqlite\""
]
},
{
Expand Down Expand Up @@ -340,7 +340,7 @@
"source": [
"%%bash\n",
"cd\n",
"mkdir Test1/test1_a"
"mkdir -p Test1/test1_a"
]
},
{
Expand Down Expand Up @@ -469,7 +469,13 @@
"outputs": [],
"source": [
"%%bash\n",
"ls -ltr /home/jovyan/DATA/Misc"
"ls -ltr /home/uu00180764/DATA/Misc\n",
"\n",
"mkdir -p OutbreakDetection/ChiefComplaints\n",
"cd OutbreakDetection\n",
"mkdir Obituaries\n",
"mkdir Sales\n",
"mkdir -p SocialMedia/Twitter\n"
]
},
{
Expand Down Expand Up @@ -649,7 +655,7 @@
"metadata": {},
"outputs": [],
"source": [
"navigating_quizzes.file_creator_quiz()"
"navigating_quizzes.file_creator_quiz()\n"
]
},
{
Expand Down Expand Up @@ -762,7 +768,8 @@
"outputs": [],
"source": [
"%%bash\n",
"# Write the correct command below\n"
"# Write the correct command below\n",
"mv /home/uu00180764/DATA/Misc/obits.txt ~/work/OutbreakDetection/Obituaries/obits.txt\n"
]
},
{
Expand Down Expand Up @@ -894,7 +901,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.2"
"version": "3.7.3"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,
Expand Down
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