LIMS-1818: Add ability to download CSV of dispensing positions (#1001)

* LIMS-1818: Allow download of CSV of dispensing positions

* LIMS-1818: Always show CSV button

* LIMS-1818: Rename file, update drop names, add blank rows

* LIMS-1818: Print commas on empty lines

* Fix mime type

Co-authored-by: Guilherme Francisco <guilherme.de-freitas@diamond.ac.uk>

* LIMS-1818: Remove empty lines entirely

---------

Co-authored-by: Mark Williams <mark.williams@diamond.ac.uk>
Co-authored-by: Guilherme Francisco <guilherme.de-freitas@diamond.ac.uk>

Author: 3 people

api/src/Page/Download.php

@@ -35,6 +35,7 @@ class Download extends Page
 
         'ppl' => '\w+',
         'aid' => '\w+',
+        'cid' => '\d+',
 
         'filetype' => '\w+',
         'blsampleid' => '\d+',
@@ -49,6 +50,7 @@ class Download extends Page
     public static $dispatch = array(
         array('/plots', 'get', '_auto_processing_plots'),
         array('/csv/visit/:visit', 'get', '_csv_report'),
+        array('/csv/container/:cid', 'get', '_dispensing_csv'),
         array('/sign', 'post', '_sign_url'),
         array('/data/visit/:visit', 'get', '_download_visit'),
         array('/attachments', 'get', '_get_attachments'),
@@ -324,6 +326,52 @@ function _csv_report()
         }
     }
 
+    # ------------------------------------------------------------------------
+    # CSV Report of dispensing positions for a plate
+    function _dispensing_csv()
+    {
+        if (!$this->has_arg('cid'))
+            $this->_error('No container id specified');
+        $rows = $this->db->pq("SELECT c.code, s.location, ct.name, ct.capacity, ct.wellperrow,
+                bsp.posx, bsp.posy, si.imagefullpath, si.micronsperpixelx, si.micronsperpixely
+                FROM blsample s
+                INNER JOIN container c ON c.containerid = s.containerid
+                INNER JOIN blsampleimage si ON si.blsampleid = s.blsampleid
+                LEFT OUTER JOIN containertype ct ON (c.containertypeid IS NOT NULL AND c.containertypeid = ct.containertypeid) OR (c.containertypeid IS NULL AND c.containertype = ct.name)
+                LEFT OUTER JOIN
+                    (SELECT * FROM blsampleposition bsp1 WHERE bsp1.blsamplepositionid =
+                        (SELECT MAX(blsamplepositionid) FROM blsampleposition bsp2 WHERE bsp2.blsampleid = bsp1.blsampleid AND bsp2.positiontype='dispensing')
+                    ) bsp ON bsp.blsampleid = s.blsampleid
+                WHERE c.containerid=:1
+                ORDER BY s.location+0",
+                array($this->arg('cid')));
+        $plate = $rows[0];
+        $rowNames = range("A", "H");
+        $dropNames = range("a", "z");
+        // SWISSCI 3 Drop have drops a/c/d
+        if ($plate["NAME"] == "SWISSCI 3 Drop") {
+            $dropNames = array_merge(array("a"), range("c","z"));
+        }
+        $dropsPerWell = $plate["CAPACITY"] / (count($rowNames) * $plate["WELLPERROW"]);
+        $this->app->response->headers->set("Content-type", "text/csv");
+        $this->_set_disposition_attachment($this->app->response, $plate["CODE"] . "_targets.csv");
+        list($width, $height, $type, $attr) = getimagesize($plate['IMAGEFULLPATH']);
+        foreach ($rows as $r) {
+            if (!isset($r["POSX"]) || !isset($r["POSY"])) {
+                continue; # skip empty rows
+            }
+            $wellNumber = intval(($r["LOCATION"] - 1) / $dropsPerWell);  # 0 indexed
+            $rowNumber = intval($wellNumber / $plate["WELLPERROW"]);  # 0 indexed
+            $row = $rowNames[$rowNumber];
+            $column = str_pad($wellNumber - ($rowNumber * $plate["WELLPERROW"]) + 1, 2, 0, STR_PAD_LEFT);  # pad with a zero if needed
+            $dropNumber = intval($r["LOCATION"] - ($dropsPerWell * $wellNumber));  # 1 indexed
+            $drop = $dropNames[$dropNumber-1];
+            $xval = round(($r["POSX"] - $width/2) * $r["MICRONSPERPIXELX"]); # integers
+            $yval = round(($height/2 - $r["POSY"]) * $r["MICRONSPERPIXELY"]); # integers
+            print $row . $column . $drop . "," . $xval . "," . $yval . "\n";
+        }
+    }
+
 
     # ------------------------------------------------------------------------
     # Get dc attachmmnts

client/src/js/modules/shipment/views/containerplate.js

@@ -284,6 +284,7 @@ define(['marionette',
             'click @ui.adr': 'setAddSubsampleRegion',
             'click @ui.addis': 'setAddDispensing',
             'click @ui.deldis': 'deleteDispensing',
+            'click a.csv_dispensing': 'downloadDispensingCSV',
             'click a.add_inspection': 'showAddInspection',
             'click a.view_sched': 'showViewSchedule',
             'click @ui.play': 'playInspection',
@@ -313,6 +314,33 @@ define(['marionette',
             'change:QUEUED': 'updatedQueued',
         },
 
+        downloadDispensingCSV: function(e) {
+            e.preventDefault()
+            this.signHandler(app.apiurl+'/download/csv/container/'+this.model.get('CONTAINERID'));
+        },
+
+        signHandler(url) {
+            this.sign({
+                url: url,
+                callback: function(resp) {
+                    window.location = url+'?token='+resp.token
+                }
+            })
+        },
+
+        sign(options) {
+            Backbone.ajax({
+                url: app.apiurl+'/download/sign',
+                method: 'POST',
+                data: {
+                    validity: options.url.replace(app.apiurl, ''),
+                },
+                success: function(resp) {
+                    if (options && options.callback) options.callback(resp)
+                }
+            })
+        },
+
         setSampleStatusShown: function() {
 
             const showCurrentScore = this.ui.sampleStatusCurrent.is(':checked')            

client/src/js/templates/shipment/containerplateimage.html

@@ -176,21 +176,23 @@ <h1 class="no_mobile">Plate Details</h1>
         </li>
         <% } %>
 
-        <% if (IMAGERID) { %>
         <li class="clearfix">
             <span class="label">Actions</span>
-            
+
             <div class="text_table">
+                <% if (IMAGERID) { %>
                 <div class="queue"></div>
 
                 <div>
                     <select name="INSPECTIONTYPEID"></select> 
                     <span class="adhoc"></span>    
                 </div> 
-                <div class="return"></div>
+                <div class="return"></div><br />
+                <% } %>
+                <div><a href="#" class="button csv_dispensing"><i class="fa fa-file-o"></i> <span>Download Dispensing CSV</span></a></div>
             </div>
         </li>
-        <% } %>
+
 
         <li class="clearfix">
             <span class="label tw-align-top">Location History</span>