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rewrite of UI; additional apache security
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@jweile
jweile committed May 3, 2018
1 parent bed8d91 commit 0a0d8dc
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10 changes: 7 additions & 3 deletions docker/Dockerfile
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Expand Up @@ -15,7 +15,7 @@ ENV DEBIAN_FRONTEND noninteractive
RUN apt update && \
apt -y dist-upgrade && \
apt install -y apache2 && \
a2enmod cgi
a2enmod cgi headers

# Apache ports for HTTP and HTTPS
EXPOSE 80
Expand Down Expand Up @@ -44,7 +44,7 @@ RUN wget https://github.com/mittinatten/freesasa/releases/download/2.0.2/freesas
#install R packages
#The UPDATE_RPKG argument doens't actually do anything in the script
#it just allows forcing docker to override the cache for this instruction
#by running $docker build --build-arg UPDATE_RPKG=`date +%s` -t jweile/mavevis
#by running $docker build --build-arg UPDATE_RPKG=`date +%s` -t jweile/mavevis .
COPY installDependencies.R /setup/
RUN Rscript installDependencies.R ${UPDATE_RPKG}

Expand All @@ -59,16 +59,20 @@ RUN mkdir -p /var/www/mavevis/httpdocs &&\
#set environment variables so the app knows were to write/read data
ENV MAVEVIS_CACHE /var/www/mavevis/cache/
ENV MAVEVIS_LOGS /var/www/mavevis/logs/
#Note: the apache user cannot see these variables, so they must also be set in the
# apache config file (mavevis.conf)!!!
RUN printf "export MAVEVIS_CACHE=/var/www/mavevis/cache/\n">>/etc/apache2/envvars &&\
printf "export MAVEVIS_LOGS=/var/www/mavevis/logs/\n">>/etc/apache2/envvars

#Move CGI scripts to staging location and grant access to apache
ADD cgi/ /var/www/html/mavevis/httpdocs/
COPY mavevis_launcher.R /var/www/html/mavevis/
COPY searchIndex.csv /var/www/mavevis/cache/
RUN chmod a+rx /var/www/html/mavevis/httpdocs/*.R &&\
chmod a+rx /var/www/html/mavevis/*.R &&\
mkdir /var/www/html/mavevis/httpdocs/results/ &&\
chmod 777 /var/www/html/mavevis/httpdocs/results/
chmod 777 /var/www/html/mavevis/httpdocs/results/ &&\
chmod 666 /var/www/mavevis/cache/searchIndex.csv

#Introduce apache configuration files for app and enable it
COPY security.conf /etc/apache2/conf-available/
Expand Down
48 changes: 48 additions & 0 deletions docker/cgi/findPDBs.R
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@@ -0,0 +1,48 @@
#!/usr/bin/Rscript

options(stringsAsFactors=FALSE)

suppressMessages({
library(cgir)
library(RJSONIO)
library(mavevis)
})
log.dir <- Sys.getenv("MAVEVIS_LOGS",unset="/var/www/mavevis/logs/")
setMessageSink(paste0(log.dir,"exec.log"))

#Caching directory
cache.dir <- Sys.getenv("MAVEVIS_CACHE",unset="/var/www/mavevis/cache/")

#read data from HTTP POST request
postdata <- readPOST()

#check if uniprot acc was supplied
if (!("uniprot" %in% names(postdata))) {
#otherwise respond with error message
respond400("No uniprot accession provided!")
quit(save="no",status=0)
}

#check if uniprot accession was valid
uniprotRegex <- "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$"
if (!grepl(uniprotRegex,postdata$uniprot)) {
#otherwise respond with error message
respond400("Invalid uniprot accession provided!")
quit(save="no",status=0)
}

#helper function to turn data.frame into list of lists
lol <- function(df) lapply(1:nrow(df),function(i) as.list(df[i,]))

tryCatch({
messages <- capture.output({
results <- find.pdbs(postdata$uniprot)
})
if (!is.null(results) && nrow(results) > 0) {
respondJSON(lol(results))
} else {
respondJSON(list())
}
},error=function(e) {
respond500(e)
})
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130 changes: 63 additions & 67 deletions docker/cgi/index.html
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@@ -1,5 +1,6 @@
<!DOCTYPE html>
<html>

<head>
<title>Atlas of Variant Effects</title>
<link rel="stylesheet" href="style.css" type="text/css"/>
Expand All @@ -8,99 +9,94 @@
<script src="jquery-ui.min.js"></script>
<script src="mavevis.js"></script>
</head>

<body>
<!-- <h1>MaveDB visualizer</h1> -->
<div id="dialog" title="Error"></div>

<p class="header">
<img src="logo2.png" alt="Atlas of Variant Effects" width="300px">
</p>

<div class="main">
<div class="box" id="controlpanel">
<form onsubmit="return false;">
<p><a title="The MaveDB score-set identifier">
<label class="left" for="ssid">Score-set ID</label>
<input id="ssid" type="text" name="scoresetID" placeholder="SCS000002A.1"/>
</a></p>
<p><a title="The Uniprot accession for the wild-type protein">
<label class="left" for="uniprot">Uniprot Acc.</label>
<input type="text" name="uniprot" id="uniprot" placeholder="P63279"/>
</a></p>
<p><a title="Multiple comma-separated values allowed!">
<label class="left" for="pdb">PDB Acc.</label>
<input type="text" name="pdb" id="pdb" placeholder="3UIP"/>
</a></p>
<p><a title="Multiple comma-separated values allowed!">
<label class="left" for="mc">PDB chain</label>
<input type="text" name="mainChain" id="mc" placeholder="A"/>
</a></p>
<details>
<summary>Advanced options</summary>
<p>
<textarea cols=70 rows=10 name="WT" id="wt" placeholder="Custom wildtype sequence"></textarea>
</p>
<p><a title="Offset of the mapped area from the sequence start">
<label class="left" for="seqOffset">Sequence offset</label>
<input id="seqOffset" type="number" name="seqOffset" value="0" step="1"/>
</a></p>
<p><a title="Auto: Use median of synonymous variant scores">
<label class="left" for="synMed">WT-like score</label>
<input id="synMed" type="number" name="synMed" value="1" step="0.01" disabled/>
<input type="checkbox" id="synAuto" value="TRUE" checked/>
<label for="synAuto">auto</label>
</a></p>
<p><a title="Auto: Use median of nonsense variant scores">
<label class="left" for="stopMed">Null-like score</label>
<input id="stopMed" type="number" name="stopMed" value="0" step="0.01" disabled/>
<input type="checkbox" id="stopAuto" value="TRUE" checked/>
<label for="stopAuto">auto</label>
</a></p>
<p>
<label class="left" for="pngRes">Image resolution</label>
<input id="pngRes" type="number" name="pngRes" min="50" max="800" step="10" value="100"/>
<label for="pngRes">DPI</label>
</p>
<p><a title="Recalculate all assets instead of using cached data">
<label class="left" for="overrideCache">Override cache</label>
<input id="overrideCache" type="checkbox" name="overrideCache" value="TRUE"/>
</a></p>
</details>
<p></p>
<input id="submit" type="submit" value="Apply"/>
</form>
<h3>Create Genophenogram</h3>
<p><a title="Search for a Protein or other molecule by name">
<label class="left" for="molecule">Score set</label>
<input id="molecule" type="text" name="molecule"/>
</a></p>
<p id="uniprotOptions"><a title="The Uniprot accession for the selected protein">
<label class="left" for="uniprot">Uniprot Acc</label>
<input id="uniprot" type="text" name="uniprot"/>
</a></p>
<p id="pdbOptions"><a title="PDB structure accessions and chain IDs">
<label class="left" for="pdb">PDB structures</label>
<input type="text" name="pdb" id="pdb" style="width:110px;" disabled/>
<button id="pdbButton">Browse</button>
</a></p>
<p id="synOptions"><a title="Typical score of a synonymous or WT-like variant">
<label class="left" for="synMed">WT-like score</label>
<input id="synMed" type="number" name="synMed" value="1" step="0.01"/>
</a></p>
<p id="stopOptions"><a title="Typical score of a nonsense/stop variant">
<label class="left" for="stopMed">Null-like score</label>
<input id="stopMed" type="number" name="stopMed" value="0" step="0.01"/>
</a></p>
<div class="buttonbar">
<button id="resetButton">Reset</button>
<button id="submitButton">Submit</button>
</div>
</div>

<div id="right">
<div class="box" id="outputpanel">
<div id="mainProgressbar">
<div class="progress-label">Submitting...</div>
</div>
<div class="passepartoutImg" id="imagepanel">

</div>
<div>
<div id="downloadpanel">
<form method="POST" action="fetch.R" target="_blank">
<input type="hidden" id="jobIDHolder" name="jobID" value="">
Download:
<input type="submit" id="pdfbutton" name="format" value="pdf" disabled/>
<input type="submit" id="pngbutton" name="format" value="png" disabled/>
<input type="submit" id="pdfbutton" name="format" value="pdf"/>
<input type="submit" id="pngbutton" name="format" value="png"/>
</form>
</div>
</div>
<div class="box" id="consolepanel">
<div class="passepartoutCons" style="">
<pre id="console">Connection established...
Ready.</pre><span class="blink" style="color: white;">&#9646;</span>
<pre id="console"></pre><span class="blink" style="color: white;">&#9646;</span>
</div>
</div>
</div>
</div>
<br/>
</div>

<div class="footer">
Copyright &copy; 2018 Jochen Weile, <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPLv3.0</a> &nbsp; This project is Free and Open Source. Check it out <a href="https://github.com/jweile/mavevis">Github</a> and <a href="https://hub.docker.com/r/jweile/mavevis/">Docker Hub</a>.
</div>
<!--<script type="text/javascript">
document.getElementById('synAuto').onchange = function() {
document.getElementById('synMed').disabled = this.checked;
};
document.getElementById('stopAuto').onchange = function() {
document.getElementById('stopMed').disabled = this.checked;
};
</script>-->

<div id="pdbDialog" title="PDB data selection">
<div id="pdbProgressbar">
<div class="progress-label">Searching for PDB entries...</div>
</div>
<table id="pdbtable">
<tbody></tbody>
<!-- <tr>
<th>PDB</th>
<th>Method</th>
<th>Resolution</th>
<th>Main chains</th>
<th>Start</th>
<th>End</th>
<th>Interactors</th>
</tr> -->
</table>
</div>

<div id="errordialog" title="Error">
<p><span class="ui-icon ui-icon-alert" style="float:left; margin:0 7px 20px 0;"></span><div id="errormessage"></div></p>
</div>

</body>
</html>
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