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vsochvsoch
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quick fix for singularity hub
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5 files changed

+163
-11
lines changed

5 files changed

+163
-11
lines changed

‎examples/classify_image/estimate_os.py‎

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@@ -12,3 +12,6 @@
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# We can also get the whole list and values
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os_similarity = estimate_os(image_package=image_package,return_top=False)
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# If you want to sort
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os_similarity.sort_values(by=['SCORE'])

‎setup.py‎

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Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
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name="singularity",
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# Version number:
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version="0.82",
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version="0.83",
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# Application author details:
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author="Vanessa Sochat",

‎singularity/app.py‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -48,9 +48,11 @@ def __init__(self, *args, **kwargs):
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@app.route('/container/os')
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def app_plot_os_sims():
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if app.sims == None:
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app.sims = estimate_os(container=app.image,
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sims = estimate_os(container=app.image,
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sudopw=app.sudopw,
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return_top=False)['SCORE'].to_dict()
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return_top=False)
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sims = sims.sort_values(by=['SCORE'])
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app.sims = sims['SCORE'].to_dict()
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container_name = os.path.basename(app.image).split(".")[0]
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return render_template('similarity_scatter.html',sim_scores=app.sims,
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container_name=container_name)

‎singularity/templates/similarity_scatter.html‎

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@@ -0,0 +1,141 @@
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<meta charset="utf-8">
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<style> /* set the CSS */
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.bar { fill: steelblue; }
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body {
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font: 10px sans-serif;
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}
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.axis path,
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.axis line {
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fill: none;
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stroke: #000;
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shape-rendering: crispEdges;
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}
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.bar {
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fill: orange;
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}
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.bar:hover {
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fill: orangered ;
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}
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.x.axis path {
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display: none;
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}
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.d3-tip {
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line-height: 1;
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padding: 6px;
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background: rgba(0, 0, 0, 0.8);
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color: #fff;
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border-radius: 4px;
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font-size: 12px;
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}
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/* Creates a small triangle extender for the tooltip */
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.d3-tip:after {
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box-sizing: border-box;
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display: inline;
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font-size: 10px;
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width: 100%;
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line-height: 1;
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color: rgba(0, 0, 0, 0.8);
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content: "\25BC";
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position: absolute;
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text-align: center;
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}
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/* Style northward tooltips specifically */
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.d3-tip.n:after {
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margin: -2px 0 0 0;
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top: 100%;
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left: 0;
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}
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</style>
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<body>
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<h2>{{ container_name }} Similarity to Docker OS</h2>
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<!-- load the d3.js library -->
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<script src="//d3js.org/d3.v4.min.js"></script>
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<script src="https://rawgit.com/VACLab/d3-tip/master/d3-tip.js"></script>
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<script>
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// set the dimensions and margins of the graph
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var margin = {top: 20, right: 20, bottom: 30, left: 40},
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width = 960 - margin.left - margin.right,
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height = 500 - margin.top - margin.bottom,
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axis_height = height - 100;
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// set the ranges
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var x = d3.scaleBand()
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.range([0, width])
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.padding(0.1);
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var y = d3.scaleLinear()
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.range([height, 0]);
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// Setup the tool tip. Note that this is just one example, and that many styling options are available.
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// See original documentation for more details on styling: http://labratrevenge.com/d3-tip/
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var tool_tip = d3.tip()
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.attr("class", "d3-tip")
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.offset([-8, 0])
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.html(function(d) { return "Similarity Score: " + d.score; });
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// acppend the svg object to the body of the page
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// append a 'group' element to 'svg'
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// moves the 'group' element to the top left margin
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var svg = d3.select("body").append("svg")
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.attr("width", width + margin.left + margin.right)
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.attr("height", height + margin.top + margin.bottom + 200)
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.append("g")
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.attr("transform",
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"translate(" + margin.left + "," + margin.top + ")");
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svg.call(tool_tip);
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raw = {{ sim_scores | safe }};
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data = [];
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// Format the data
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for (var os in raw) {
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if (raw.hasOwnProperty(os)) {
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var new_os = {dist:os, score: parseFloat(raw[os]).toFixed(8)};
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data.push(new_os);
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}
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}
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// Scale the range of the data in the domains
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x.domain(data.map(function(d) { return d.dist; }));
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y.domain([0.0, 1.0]);
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// append the rectangles for the bar chart
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svg.selectAll(".bar")
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.data(data)
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.enter().append("rect")
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.attr("class", "bar")
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.attr("x", function(d) { return x(d.dist); })
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.attr("width", 15)
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.attr("y", function(d) { return y(d.score); })
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.attr("height", function(d) { return height - y(d.score); })
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.on('mouseover', tool_tip.show)
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.on('mouseout', tool_tip.hide)
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// add the x Axis
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svg.append("g")
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.classed('axis',true)
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.attr("transform", "translate(0," + height + ")")
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.call(d3.axisBottom(x))
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.selectAll("text")
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.style("text-anchor", "end")
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.attr("dx", "-.8em")
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.attr("dy", ".15em")
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.attr("transform", "rotate(-65)");
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// add the y Axis
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svg.append("g")
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.call(d3.axisLeft(y));
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</script>
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</body>

‎singularity/views/utils.py‎

Lines changed: 14 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -58,16 +58,22 @@ def get_container_contents(container=None,gets=None,split_delim=None,image_packa
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guts = load_package(image_package,get=gets)
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shutil.rmtree(tmpdir)
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return guts
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# Visualization deployed by singularity hub
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else:
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for sfile in container.files:
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for gut_key in gets:
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if os.path.basename(sfile['name']) == gut_key:
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if split_delim == None:
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guts[gut_key] = requests.get(sfile['mediaLink']).text
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else:
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guts[gut_key] = requests.get(sfile['mediaLink']).text.split(split_delim)
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# user has provided a package, but not a container
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if container == None:
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guts = load_package(image_package,get=gets)
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# user has provided a container, but not a package
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else:
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for sfile in container.files:
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for gut_key in gets:
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if os.path.basename(sfile['name']) == gut_key:
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if split_delim == None:
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guts[gut_key] = requests.get(sfile['mediaLink']).text
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else:
77+
guts[gut_key] = requests.get(sfile['mediaLink']).text.split(split_delim)
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return guts

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