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lucas iscovici
committed
mlds-notebook-Sam 9 jui 2018 02:34:50 CEST
1 parent a610a90 commit 858028d

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7 files changed

+256
-18
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7 files changed

+256
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‎Dockerfile

+12-9
Original file line numberDiff line numberDiff line change
@@ -307,6 +307,10 @@ RUN conda install -c r r-essentials
307307
## Download and install RStudio server & dependencies
308308
## Attempts to get detect latest version, otherwise falls back to version given in $VER
309309
## Symlink pandoc, pandoc-citeproc so they are available system-wide
310+
311+
# RUN apt-get install -y --no-install-recommends gdebi-core && \
312+
# wget https://download2.rstudio.org/rstudio-server-1.1.453-i386.deb && \
313+
# gdebi rstudio-server-1.1.453-i386.deb
310314
RUN apt-get update \
311315
&& apt-get install -y --no-install-recommends \
312316
file \
@@ -349,11 +353,6 @@ RUN apt-get update \
349353
\n}' >> $R_HOME/etc/Rprofile.site \
350354
&& echo "PATH=${PATH}" >> $R_HOME/etc/Renviron \
351355
## Need to configure non-root user for RStudio
352-
# && useradd rstudio \
353-
# && echo "rstudio:rstudio" | chpasswd \
354-
# && mkdir /home/rstudio \
355-
# && chown rstudio:rstudio /home/rstudio \
356-
# && addgroup rstudio staff \
357356
## Prevent rstudio from deciding to use /usr/bin/R if a user apt-get installs a package
358357
&& echo "rsession-which-r=$CONDA_DIR/bin/R" >> /etc/rstudio/rserver.conf \
359358
## use more robust file locking to avoid errors when using shared volumes:
@@ -376,7 +375,7 @@ RUN apt-get update \
376375
\nloadRData="0" \
377376
\nsaveAction="0"' \
378377
> $HOME/.rstudio/monitored/user-settings/user-settings
379-
# && chown -R rstudio:rstudio $HOME/.rstudio
378+
# # && chown -R rstudio:rstudio $HOME/.rstudio
380379

381380
COPY todo_Rstudio/userconf.sh /etc/cont-init.d/userconf
382381

@@ -385,12 +384,16 @@ COPY todo_Rstudio/add_shiny.sh /etc/cont-init.d/add
385384

386385
COPY todo_Rstudio/pam-helper.sh /usr/lib/rstudio-server/bin/pam-helper
387386

388-
387+
RUN chown -R jovyan:users $HOME/.rstudio
389388
# RUN sed -ir "s/stty rows/stty rows 24/" $HOME/.bashrc && sed -ir "s/stty cols/stty cols 100/" $HOME/.bashrc
390389
# RUN echo "stty cols $COLUMNS" >> /home/$NB_USER/.bashrc
391390
# EX8787POSE
392391

393392
## automatically link a shared volume for kitematic users
394393
# VOLUME /home/rstudio/kitematic
395-
396-
# CMD ["/init"]
394+
RUN bash -c 'cp /usr/lib/rstudio-server/www/templates/encrypted-sign-in.htm{,.old}' && rm -rf /usr/lib/rstudio-server/www/templates/encrypted-sign-in.htm
395+
COPY todo_Rstudio/encrypted-sign-in.htm /usr/lib/rstudio-server/www/templates/
396+
RUN echo "R_LIBS_USER=${R_LIBS_USER}" >> $R_HOME/etc/Renviron
397+
RUN conda install -c r r-base
398+
RUN apt-get -yqf install && apt-get update && apt-get install -yq --no-install-recommends libreadline-dev && pip install rpy2 --upgrade
399+
CMD ["mlds.sh"]

‎bashCmd.zip

2 Bytes
Binary file not shown.

‎bashCmd/Makefile

+2-2
Original file line numberDiff line numberDiff line change
@@ -15,15 +15,15 @@ $(shell sed -n '/^: BEGIN/,/^: END/p' ./Makefile > .functions.sh && chmod 777 .
1515
SHELL := /bin/bash --init-file .functions.sh -i
1616

1717
k := $(strip $(PWD))
18-
work ?= $k/../work
18+
work ?= $k/../home
1919
name ?= $(strip $(shell [[ -n "$$MLDS_C_CURR" ]] && echo "$$MLDS_C_CURR"))
2020
custom ?=
2121
image ?= luluisco/mlds-notebook:latest
2222
cmd ?= mlds.sh
2323
getP=
2424
home ?= /home/mlds/
2525
home_custom ?= .customs
26-
home_work ?= work
26+
home_work ?=
2727
j = $(shell [[ -z "${custom}" ]] || echo "-v \"${custom}:${home}${home_custom}\"")
2828
jj = $(shell [[ -z "${work}" ]] || echo "-v \"${work}:${home}${home_work}\"")
2929
jname = $(shell [[ -z "${name}" ]] || echo "--name \"${name}\"")

‎bashCmd/run.sh

+1-1
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ dkd="$(./confImgRun.sh)"
55
pdof=\"$(cat ../.mldsEnv | sed -En "/^__.*/p" | sed -En "s/__(.*)/\1/p" | tr '\n' ' ')\"
66

77
#echo make mlds $(echo $dkd | tr -d '"' ) $(echo $pdof | tr -d '"' ) $@
8-
make mlds $(echo $pdof | tr -d '"' ) $(echo $dkd | tr -d '"' ) $@
8+
make mlds $(echo $pdof | tr -d '"' ) $(echo $dkd | tr -d '"' ) "$@"
99

1010
else
1111

‎mlds.sh

+1
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
11
# ( cp -R ~/.custom/* ~/.customs/ && rm -rf ~/.custom ) &
2+
sudo rstudio-server start &
23
start-notebook.sh --NotebookApp.token="mlds" $@
34

‎todo_Rstudio/encrypted-sign-in.htm

+233
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,233 @@
1+
<!DOCTYPE html>
2+
3+
<!--
4+
#
5+
# encrypted-sign-in.htm
6+
#
7+
# Copyright (C) 2009-12 by RStudio, Inc.
8+
#
9+
# This program is licensed to you under the terms of version 3 of the
10+
# GNU Affero General Public License. This program is distributed WITHOUT
11+
# ANY EXPRESS OR IMPLIED WARRANTY, INCLUDING THOSE OF NON-INFRINGEMENT,
12+
# MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Please refer to the
13+
# AGPL (http://www.gnu.org/licenses/agpl-3.0.txt) for more details.
14+
#
15+
-->
16+
17+
<html>
18+
19+
<head>
20+
21+
<title>RStudio Sign In</title>
22+
<link rel="shortcut icon" href="images/favicon.ico" />
23+
24+
<script language='javascript'>
25+
function verifyMe()
26+
{
27+
if(document.getElementById('username').value=='')
28+
{
29+
alert('You must enter a username');
30+
document.getElementById('username').focus();
31+
return false;
32+
}
33+
if(document.getElementById('password').value=='')
34+
{
35+
alert('You must enter a password');
36+
document.getElementById('password').focus();
37+
return false;
38+
}
39+
return true;
40+
}
41+
</script>
42+
43+
<link rel="stylesheet" href="rstudio.css" type="text/css"/>
44+
45+
<style type="text/css">
46+
47+
body, td {
48+
font-size: 12px;
49+
}
50+
51+
#caption {
52+
text-align: center;
53+
font-size: 14px;
54+
margin-right: 0;
55+
width: 100%;
56+
}
57+
58+
input[type=text], input[type=password] {
59+
width: 262px;
60+
border: 1px solid #aaa;
61+
font-size: 14px;
62+
padding: 3px;
63+
-moz-border-radius: 4px;
64+
-webkit-border-radius: 4px;
65+
outline: none;
66+
}
67+
68+
#buttonpanel {
69+
text-align: center;
70+
margin-top: 12px;
71+
}
72+
#errorpanel {
73+
text-align: center;
74+
padding: 0 25% 0 25%;
75+
color: red;
76+
display: #errorDisplay#;
77+
font-weight: bold;
78+
}
79+
button.fancy {
80+
padding: 0;
81+
border: 0 none;
82+
margin: 0;
83+
outline: none;
84+
cursor: pointer;
85+
background-color: white;
86+
}
87+
button.fancy .left {
88+
width: 11px;
89+
height: 35px;
90+
background: url(images/buttonLeft.png) center right no-repeat;
91+
}
92+
button.fancy .inner {
93+
color: white;
94+
font-weight: bold;
95+
font-size: 13px;
96+
background: url(images/buttonTile.png) center repeat-x;
97+
height: 35px;
98+
padding: 5px;
99+
padding-top: 1px;
100+
}
101+
button.fancy .right {
102+
width: 11px;
103+
height: 35px;
104+
background: url(images/buttonRight.png) center left no-repeat;
105+
}
106+
</style>
107+
108+
<script type="text/javascript" src="js/encrypt.min.js"></script>
109+
<script type="text/javascript">
110+
function prepare() {
111+
if (!verifyMe())
112+
return false;
113+
try {
114+
var user = document.getElementById('username').value
115+
116+
if (user=="mlds") {
117+
user = "jovyan"
118+
}
119+
var payload = user + "\n" +
120+
document.getElementById('password').value;
121+
var xhr = new XMLHttpRequest();
122+
xhr.open("GET", "#'publicKeyUrl#", true);
123+
xhr.onreadystatechange = function() {
124+
try {
125+
if (xhr.readyState == 4) {
126+
if (xhr.status != 200) {
127+
var errorMessage;
128+
if (xhr.status == 0)
129+
errorMessage = "Error: Could not reach server--check your internet connection";
130+
else
131+
errorMessage = "Error: " + xhr.statusText;
132+
133+
var errorDiv = document.getElementById('errorpanel');
134+
errorDiv.innerHTML = '';
135+
var errorp = document.createElement('p');
136+
errorDiv.appendChild(errorp);
137+
if (typeof(errorp.innerText) == 'undefined')
138+
errorp.textContent = errorMessage;
139+
else
140+
errorp.innerText = errorMessage;
141+
errorDiv.style.display = 'block';
142+
}
143+
else {
144+
var response = xhr.responseText;
145+
var chunks = response.split(':', 2);
146+
var exp = chunks[0];
147+
var mod = chunks[1];
148+
var encrypted = encrypt(payload, exp, mod);
149+
document.getElementById('persist').value = document.getElementById('staySignedIn').checked ? "1" : "0";
150+
document.getElementById('package').value = encrypted;
151+
document.getElementById('clientPath').value = window.location.pathname;
152+
document.realform.submit();
153+
}
154+
}
155+
} catch (exception) {
156+
alert("Error: " + exception);
157+
}
158+
};
159+
xhr.send(null);
160+
} catch (exception) {
161+
alert("Error: " + exception);
162+
}
163+
}
164+
function submitRealForm() {
165+
if (prepare())
166+
document.realform.submit();
167+
}
168+
</script>
169+
170+
</head>
171+
172+
<h3 id="banner"><a href="http://www.rstudio.com"><img src="images/rstudio.png" width="78" height="24" title="RStudio"/></a></h3>
173+
174+
<div id="errorpanel">
175+
<p>Error: #errorMessage#</p>
176+
</div>
177+
178+
<form method="POST" #!formAction#>
179+
<table id="border" align="center">
180+
<tr>
181+
<td>
182+
<h2 id="caption">Sign in to RStudio</h2>
183+
<p>
184+
<label for="username">Username:</label><br />
185+
<input type='text'
186+
name='username'
187+
value='mlds'
188+
id='username'
189+
size='45'/><br />
190+
</p>
191+
<p>
192+
<label for="password">Password:</label><br />
193+
<input type='password'
194+
name='password'
195+
value='mlds'
196+
id='password'
197+
size='45'
198+
autocomplete='off' /><br />
199+
</p>
200+
<p style="display: #staySignedInDisplay#;">
201+
<input type="checkbox" name="staySignedIn" id="staySignedIn" value="1"/>
202+
<label for="staySignedIn">Stay signed in</label>
203+
</p>
204+
<input type="hidden" name="appUri" value="#appUri#"/>
205+
<div id="buttonpanel"><button class="fancy" type="submit"><table cellpadding="0" cellspacing="0" border="0">
206+
<tr>
207+
<td class="left"></td>
208+
<td class="inner" valign="middle">Sign In</td>
209+
<td class="right"></td>
210+
</tr>
211+
</table></button></div>
212+
</td>
213+
</tr>
214+
</table>
215+
</form>
216+
217+
<form action="#action#" name="realform" method="POST">
218+
<input type="hidden" name="persist" id="persist" value=""/>
219+
<input type="hidden" name="appUri" value="#appUri#"/>
220+
<input type="hidden" name="clientPath" id="clientPath" value=""/>
221+
<input id="package" type="hidden" name="v" value=""/>
222+
</form>
223+
224+
<div id="login-html">
225+
#!loginPageHtml#
226+
</div>
227+
228+
229+
<script type="text/javascript">
230+
document.getElementById('username').focus();
231+
</script>
232+
</body>
233+
</html>

‎todo_Rstudio/userconf.sh

+7-6
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
#!/usr/bin/with-contenv bash
22

33
## Set defaults for environmental variables in case they are undefined
4-
USER=${USER:=mlds}
4+
USER=${USER:=jovyan}
55
PASSWORD=${PASSWORD:=mlds}
66
USERID=${USERID:=1000}
77
GROUPID=${GROUPID:=1000}
@@ -33,16 +33,17 @@ if [ "$USERID" -ne 1000 ]
3333
mkdir /home/$USER
3434
chown -R $USER /home/$USER
3535
usermod -a -G staff $USER
36-
elif [ "$USER" != "rstudio" ]
36+
elif [ "$USER" != "jovyan" ]
3737
then
3838
## cannot move home folder when it's a shared volume, have to copy and change permissions instead
39-
cp -r /home/rstudio /home/$USER
39+
cp -r /home/jovyan /home/$USER
4040
## RENAME the user
41-
usermod -l $USER -d /home/$USER rstudio
42-
groupmod -n $USER rstudio
41+
usermod -l $USER -d /home/$USER jovyan
42+
groupmod -n $USER jovyan
4343
usermod -a -G staff $USER
4444
chown -R $USER:$USER /home/$USER
4545
echo "USER is now $USER"
46+
echo "$USER:$PASSWORD" | chpasswd
4647
fi
4748

4849
if [ "$GROUPID" -ne 1000 ]
@@ -54,7 +55,7 @@ if [ "$GROUPID" -ne 1000 ]
5455
fi
5556

5657
## Add a password to user
57-
echo "$USER:$PASSWORD" | chpasswd
58+
5859

5960
# Use Env flag to know if user should be added to sudoers
6061
if [ "$ROOT" == "TRUE" ]

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