Merge pull request #82 from WHOIGit/dev

0.1.1-alpha

Author: joefutrelle

bin/update.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+SOURCE=$(dirname "${BASH_SOURCE[0]}")
+git pull && sh ${SOURCE}/assets.sh && sh ${SOURCE}/migrate.sh
+

ifcbdb/assets/css/site.css

@@ -169,4 +169,22 @@ div.scale-bar {
     background: black;
     width: 34px;
     height: 5px;
+}
+
+[data-toggle="collapse"] .fa:after {
+    content: "\f056";
+}
+
+[data-toggle="collapse"].collapsed .fa:after {
+    content: "\f055";
+}
+
+[data-toggle="collapse"] .fa:before {
+    content: "Hide Timeline ";
+    font-family: "Roboto";
+}
+
+[data-toggle="collapse"].collapsed .fa:before {
+    content: "Show Timeline ";
+    font-family: "Roboto";
 }

ifcbdb/assets/js/site.js

@@ -80,13 +80,39 @@ function getTimelineConfig() {
     return {
         responsive: true,
         displaylogo: false,
-        scrollZoom: true
+        scrollZoom: true,
+        modeBarButtonsToRemove: [
+            "sendDataToCloud",
+            "hoverCompareCartesian",
+            "hoverClosestCartesian",
+            "toImage",
+            "select2d",
+            "lasso2d",
+            "toggleSpikelines",
+            "resetScale2d"
+        ]
     };
 }
 
+function getTimelineTypeByMetric(metric) {
+    if (metric == "temperature" || metric == "humidity") {
+        return {
+            "type": "scatter",
+            "mode": "markers"
+        }
+    } else {
+        return {
+            "type": "bar",
+            "mode": "markers"
+        }
+    }
+}
 function getTimelineData(data, selectedDate) {
+    plotlyType = getTimelineTypeByMetric(currentMetric);
+
     var series = {
-        type: "bar",
+        type: plotlyType.type,
+        mode: plotlyType.mode,
         x: data["x"],
         y: data["y"],
         line: {

ifcbdb/dashboard/accession.py

@@ -74,7 +74,7 @@ def sync(self):
     def add_bin(self, bin, b): # IFCB bin, Bin instance
         print('{} checking and processing'.format(b.pid))
         # qaqc checks
-        qc_bad = qc_bad = check_bad(bin)
+        qc_bad = check_bad(bin)
         if qc_bad:
             b.qc_bad = True
             print('{} raw data is bad'.format(pid))

ifcbdb/dashboard/migrations/0019_auto_20190528_0647.py

@@ -0,0 +1,43 @@
+# Generated by Django 2.1.7 on 2019-05-28 06:47
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('dashboard', '0018_auto_20190508_1659'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='bin',
+            name='concentration',
+            field=models.FloatField(default=-9999999),
+        ),
+        migrations.AlterField(
+            model_name='bin',
+            name='humidity',
+            field=models.FloatField(default=-9999999),
+        ),
+        migrations.AlterField(
+            model_name='bin',
+            name='look_time',
+            field=models.FloatField(default=-9999999),
+        ),
+        migrations.AlterField(
+            model_name='bin',
+            name='ml_analyzed',
+            field=models.FloatField(default=-9999999),
+        ),
+        migrations.AlterField(
+            model_name='bin',
+            name='run_time',
+            field=models.FloatField(default=-9999999),
+        ),
+        migrations.AlterField(
+            model_name='bin',
+            name='temperature',
+            field=models.FloatField(default=-9999999),
+        ),
+    ]

ifcbdb/dashboard/models.py

@@ -23,6 +23,7 @@
 
 import ifcb
 
+from ifcb.data.adc import SCHEMA_VERSION_1
 from ifcb.data.stitching import InfilledImages
 from ifcb.viz.mosaic import Mosaic
 from ifcb.viz.blobs import blob_outline
@@ -47,7 +48,7 @@ class Timeline(object):
         "run_time": "Seconds",
         "look_time": "Seconds",
         "ml_analyzed": "Milliliters",
-        'concentration': 'Cells / ml',
+        'concentration': 'ROIs / ml',
         'n_triggers': 'Count',
         'n_images': 'Count',
     }
@@ -292,17 +293,20 @@ def roi_path(self):
 
     # access to images
 
-    def images(self):
-        b = self._get_bin()
-        if b.schema == 1:
+    def images(self, bin=None):
+        if bin is None:
+            b = self._get_bin()
+        else:
+            b = bin
+        if b.schema == SCHEMA_VERSION_1:
             return InfilledImages(b)
         else:
             return b.images
 
     def image(self, target_number):
         b = self._get_bin()
         with b.as_single(target_number) as subset:
-            ii = InfilledImages(subset) # handle old-style data
+            ii = self.images(subset)
             try:
                 return ii[target_number]
             except IndexError as e:

ifcbdb/templates/base.html

@@ -119,12 +119,8 @@
         </div>
         <div class="footer-copyright text-center py-3 stylish-color-dark">
             <div>
-                Version 4.4 - 17 October 2018 -
-                <a href="#">About</a> |
-                <a href="https://beagle.whoi.edu/redmine/projects/ifcb-web/wiki" target="_blank">User guide</a> |
-                <a href="{% url 'secure:login' %}">Log in</a> |
-                <a href="#">Admin</a> |
-                <a href="#">API</a>
+                Version 0.1.1-alpha - 30 May 2019 -
+                <a href="{% url 'secure:login' %}">Log in</a>
             </div>
         </div>
     </footer>

ifcbdb/templates/dashboard/bin-details.html

@@ -10,7 +10,7 @@
         </span>
     </div>
     <div class="pl-3 align-self-center">
-        <a title="Share link"><span id="share-button" class="h5-responsive fa fa-share-square"></span></a>
+        <a id="share-button" title="Share This Bin"><span class="h5-responsive fa fa-share-square"></span>&nbsp;Share This Bin</a>
     </div>
 </div>
 <hr class="my-2">
@@ -205,7 +205,7 @@
     <div class="modal-dialog" role="document">
         <div class="modal-content">
             <div class="modal-header">
-                <h5 class="modal-title" id="exampleModalLabel">Share link</h5>
+                <h5 class="modal-title" id="exampleModalLabel">Share This Bin</h5>
                 <button type="button" class="close" data-dismiss="modal" aria-label="Close">
             <span aria-hidden="true">&times;</span>
           </button>
@@ -464,7 +464,9 @@ <h5 class="modal-title" id="exampleModalLabel">Share link</h5>
     });
 
 
-    $("#share-button").click(function () {
+    $("#share-button").click(function (e) {
+        e.preventDefault();
+        
         $("#share-modal").modal();
         $("#share-link").select();
     });

ifcbdb/templates/dashboard/dataset-details.html

@@ -3,17 +3,17 @@
 {% endblock %} {% block content %}
 <div class="row d-flex justify-content-between">
     <div class="pl-3">
-        <span class="h3-responsive">{{ dataset.title }}</span>
+        <span class="h3-responsive">{{ dataset.title }}</span><span><button class="btn btn-link" data-toggle="collapse" data-target=".ts-collapse" aria-expanded="true" aria-controls="ts-data"><i class="fa" aria-hidden="true"></i></button></span>
     </div>
     {% if user.is_authenticated %}
     <div>
         <a href="#" class="btn btn-sm btn-primary ml-3">Configure</a>
     </div>
     {% endif %}
-        <ul class="nav justify-content-end" id="ts-tabs" role="tablist">
+        <ul class="nav justify-content-end collapse show ts-collapse" id="ts-tabs" role="tablist">
             <li class="nav-item">
                 <a class="nav-link btn btn-mdb-color btn-sm" id="ts-size-tab" data-toggle="tab" data-metric="size" href="#ts-size"
-                   role="tab" data-target="ts-size" aria-selected="true">Data Size</a>
+                   role="tab" data-target="ts-size" aria-selected="false">Data Size</a>
             </li>
             <li class="nav-item">
                 <a class="nav-link btn btn-mdb-color btn-sm" id="ts-temperature-tab" data-toggle="tab" data-metric="temperature" href="#ts-temperature"
@@ -28,8 +28,8 @@
                    role="tab" data-target="ts-ml-analyzed" aria-selected="false">Volume Analyzed</a>
             </li>
             <li class="nav-item">
-                <a class="nav-link btn btn-mdb-color btn-sm" id="ts-concentration-tab" data-toggle="tab" data-metric="concentration" href="#ts-concentration"
-                   role="tab" data-target="ts-concentration" aria-selected="false">Concentration</a>
+                <a class="nav-link btn btn-mdb-color btn-sm active" id="ts-concentration-tab" data-toggle="tab" data-metric="concentration" href="#ts-concentration"
+                   role="tab" data-target="ts-concentration" aria-selected="true">ROIs / ml</a>
             </li>
             <li class="nav-item">
                 <a class="nav-link btn btn-mdb-color btn-sm" id="ts-triggers-tab" data-toggle="tab" data-metric="n-triggers" href="#ts-triggers"
@@ -44,8 +44,8 @@
 <hr class="my-2">
 <div class="row px-1">
     <div class="col-sm-12">
-        <div class="tab-content" id="ts-data">
-            <div class="tab-pane show active" id="ts-size" role="tabpanel" aria-labelledby="ts-size-tab">
+        <div class="tab-content collapse show ts-collapse" id="ts-data">
+            <div class="tab-pane" id="ts-size" role="tabpanel" aria-labelledby="ts-size-tab">
                 <div class="ts-plot-container"></div>
             </div>
             <div class="tab-pane" id="ts-temperature" role="tabpanel" aria-labelledby="ts-temperature-tab">
@@ -57,7 +57,7 @@
             <div class="tab-pane" id="ts-ml-analyzed" role="tabpanel" aria-labelledby="ts-ml-analyzed-tab">
                 <div class="ts-plot-container"></div>
             </div>
-            <div class="tab-pane" id="ts-concentration" role="tabpanel" aria-labelledby="ts-concentration-tab">
+            <div class="tab-pane show active" id="ts-concentration" role="tabpanel" aria-labelledby="ts-concentration-tab">
                 <div class="ts-plot-container"></div>
             </div>
             <div class="tab-pane" id="ts-triggers" role="tabpanel" aria-labelledby="ts-triggers-tab">
@@ -77,7 +77,7 @@
                 <div class="d-flex flex-row justify-content-between">
                     <div class="flex-column">
                         <form class="form-inline">
-                            <a href="#" id="previous-bin" data-bin="" class="btn btn-mdb-color btn-sm"><i class="fas fa-arrow-circle-left fa-1x"></i></a>
+                            <a href="#" id="previous-bin" data-bin="" class="btn btn-mdb-color btn-sm"><i class="fas fa-arrow-circle-left fa-1x"></i>&nbsp;&nbsp;Previous Bin</a>
                         </form>
                     </div>
                     <div class="flex-column align-self-center">
@@ -88,7 +88,7 @@
                     </div>
                     <div class="flex-column pt-1 pt-sm-0">
                         <form class="form-inline">
-                            <a href="#" id="next-bin" data-bin="" class="btn btn-mdb-color btn-sm"><i class="fas fa-arrow-circle-right fa-1x"></i></a>
+                            <a href="#" id="next-bin" data-bin="" class="btn btn-mdb-color btn-sm">Next Bin&nbsp;&nbsp;<i class="fas fa-arrow-circle-right fa-1x"></i></a>
                         </form>
                     </div>
                 </div>
@@ -235,7 +235,7 @@
 var currentBinTimestamp = null;
 var isBinLoading = false;
 var isMosaicLoading = false;
-var currentPlotId = "ts-size";
+var currentPlotId = "ts-concentration";
 
 function delayedMosaic(page) {
         $("#mosaic").hide();
@@ -319,8 +319,12 @@
             $("#next-bin").addClass("disabled");
 
             // workaround to prevent accepting clicks on the plotly controls
-            distanceFromTop = event.pageY - $(container[0]).offset().top;
-            if (distanceFromTop > 35) {
+            var offset = $(container[0]).offset();
+            var distanceFromTop = event.pageY - offset.top;
+            var margin = container[0]._fullLayout.margin.l;
+            var rightX = offset.left + $(container[0]).width();
+            var distanceFromRight = rightX - event.pageX - margin;
+            if (distanceFromTop > 35 || distanceFromRight > 75) {
                 changeToClosestBin($(container[0]).data("date"));
             }
         });
@@ -641,7 +645,7 @@
 });
 
 $(function() {
-    createTimeSeries($("#ts-size .ts-plot-container"), "size");
+    createTimeSeries($("#ts-concentration .ts-plot-container"), "concentration");
 
     changeBin("{{ bin.pid }}", false);
 });

ifcbdb/templates/dashboard/image-details.html

@@ -12,7 +12,7 @@
         <span class="h3-responsive">{{ bin.pid }}_{{ image_id|stringformat:"05d" }}</span>
     </div>
     <div class="pl-3 align-self-center">
-        <a title="Share link"><span id="share-button" class="h5-responsive fa fa-share-square"></span></a>
+        <a id="share-button" title="Share This Image"><span class="h5-responsive fa fa-share-square"></span>&nbsp;Share This Image</a>
     </div>
 </div>
 <hr class="my-2">
@@ -250,7 +250,7 @@ <h4 class="modal-title w-100 font-weight-bold">Add Tag</h4>
     <div class="modal-dialog" role="document">
         <div class="modal-content">
             <div class="modal-header">
-                <h5 class="modal-title" id="exampleModalLabel">Share link</h5>
+                <h5 class="modal-title" id="exampleModalLabel">Share This Image</h5>
                 <button type="button" class="close" data-dismiss="modal" aria-label="Close">
             <span aria-hidden="true">&times;</span>
           </button>
@@ -303,7 +303,9 @@ <h5 class="modal-title" id="exampleModalLabel">Share link</h5>
         $("#image-outline").height($("#image").height());
     });
 
-    $("#share-button").click(function () {
+    $("#share-button").click(function (e) {
+        e.preventDefault();
+
         $("#share-modal").modal();
         $("#share-link").select();
     });