LIMS-1389 - Add upload to ccp4 cloud button

api/config_sample.php

@@ -379,4 +379,7 @@
     $dials_rest_url = "";
     $dials_rest_jwt = "";
     $dials_rest_url_rings = false;
+
+    # Add a button to upload file to CCP4 cloud
+    #$ccp4_cloud_upload_url = 'https://data.cloud.ccp4.ac.uk/api/data/<%=USERNAME%>/<%=FACILITYNAME%>/<%=IMAGEPREFIX%>_<%=DATACOLLECTIONNUMBER%>/upload';
 ?>

api/index.php

@@ -72,7 +72,7 @@ function setupApplication($mode): Slim
             $dhl_enable, $scale_grid, $scale_grid_end_date, $preset_proposal, $timezone,
             $valid_components, $enabled_container_types, $synchweb_version, $redirects,
             $shipping_service_app_url, $use_shipping_service_redirect, $use_shipping_service_redirect_incoming_shipments,
-            $dials_rest_url_rings, $closed_proposal_link;
+            $dials_rest_url_rings, $closed_proposal_link, $ccp4_cloud_upload_url;
         $app->contentType('application/json');
         $options = $app->container['options'];
         $app->response()->body(json_encode(array(
@@ -97,6 +97,7 @@ function setupApplication($mode): Slim
             'shipping_service_app_url_incoming' => $use_shipping_service_redirect_incoming_shipments ? $shipping_service_app_url : null,
             'closed_proposal_link' => $closed_proposal_link,
             'dials_rest_url_rings' => $dials_rest_url_rings,
+            'ccp4_cloud_upload_url' => $ccp4_cloud_upload_url,
             'redirects' => $redirects
         )));
     });

api/src/Page/Processing.php

@@ -16,16 +16,10 @@ class Processing extends Page {
 
         array('/downstream/:id', 'get', '_downstream'),
         array('/downstream/images/:aid(/n/:n)', 'get', '_downstream_images'),
-        array(
-            '/downstream/mapmodel/:aid(/n/:n)',
-            'get',
-            '_downstream_mapmodel',
-        ),
-        array(
-            '/multiplex_jobs/groups/:blSampleGroupId',
-            'get',
-            '_get_latest_multiplex_job_result'
-        ),
+        array('/downstream/mapmodel/:aid(/n/:n)', 'get', '_downstream_mapmodel'),
+        array('/multiplex_jobs/groups/:blSampleGroupId', 'get', '_get_latest_multiplex_job_result'),
+
+        array('/upload', 'post', '_upload_to_cloud'),
     );
 
     public static $arg_list = array(
@@ -44,6 +38,10 @@ class Processing extends Page {
         'rmeas' => '[\d\.]+',
         'cchalf' => '[\d\.]+',
         'ccanom' => '[\d\.]+',
+        'username' => '(\w|\s|\-|\.)+',
+        'cloudrunid' => '(\w|\-)+',
+        'AUTOPROCPROGRAMATTACHMENTID' => '\d+',
+        'DATACOLLECTIONFILEATTACHMENTID' => '\d+',
     );
 
     /**
@@ -66,6 +64,80 @@ function _map_status($status) {
         }
     }
 
+    function _make_curl_file($file){
+        $mime = mime_content_type($file);
+        $info = pathinfo($file);
+        $name = $info['basename'];
+        $output = new \CURLFile($file, $mime, $name);
+        return $output;
+    }
+
+    function _upload_to_cloud() {
+        global $facility_name, $facility_short, $ccp4_cloud_upload_url;
+        if (!$this->has_arg('AUTOPROCPROGRAMATTACHMENTID') && !$this->has_arg('DATACOLLECTIONFILEATTACHMENTID')) {
+            $this->_error('No file specified');
+        }
+        if (!$this->has_arg('username')) {
+            $this->_error('No username specified');
+        }
+        if (!$this->has_arg('cloudrunid')) {
+            $this->_error('No cloudrun id specified');
+        }
+        if ($this->has_arg('AUTOPROCPROGRAMATTACHMENTID')) {
+            $select = ", concat(appa.filepath, '/', appa.filename) as filefullpath";
+            $join = "INNER JOIN processingjob pj ON dc.datacollectionid = pj.datacollectionid
+                INNER JOIN autoprocprogram app ON pj.processingjobid = app.processingjobid
+                INNER JOIN autoprocprogramattachment appa ON app.autoprocprogramid = appa.autoprocprogramid";
+            $where = "WHERE appa.autoprocprogramattachmentid=:1";
+            $args = array($this->arg('AUTOPROCPROGRAMATTACHMENTID'));
+        } else if ($this->has_arg('DATACOLLECTIONFILEATTACHMENTID')) {
+            $select = ", dcfa.filefullpath";
+            $join = "INNER JOIN datacollectionfileattachment dcfa ON dc.datacollectionid = dcfa.datacollectionid";
+            $where = "WHERE dcfa.datacollectionfileattachmentid=:1";
+            $args = array($this->arg('DATACOLLECTIONFILEATTACHMENTID'));
+        }
+        $dc = $this->db->pq(
+            "SELECT dc.imageprefix, dc.datacollectionnumber, concat(p.proposalcode, p.proposalnumber, '-', s.visit_number) as visit
+                $select
+                FROM datacollection dc
+                INNER JOIN blsession s ON dc.sessionid = s.sessionid
+                INNER JOIN proposal p ON s.proposalid = p.proposalid
+                $join
+                $where",
+            $args);
+        $dc = $dc[0];
+        $dc['USERNAME'] = $this->arg('username');
+        $dc['FACILITYNAME'] = strtolower(preg_replace( '/[\W]/', '', $facility_name));
+        $dc['FACILITYSHORT'] = strtolower(preg_replace( '/[\W]/', '', $facility_short));
+        $url = preg_replace_callback('/<%=(\w+)%>/',
+            function($mat) use ($dc) {
+                if (array_key_exists($mat[1], $dc)) {
+                    return $dc[$mat[1]];
+                }
+            },
+            $ccp4_cloud_upload_url);
+        $ch = curl_init($url);
+        $headers = array('cloudrun_id: '.$this->arg('cloudrunid'));
+        $data = array('file' => $this->_make_curl_file($dc['FILEFULLPATH']));
+        curl_setopt_array(
+            $ch,
+            array(
+                CURLOPT_RETURNTRANSFER => TRUE,
+                CURLOPT_HTTPHEADER => $headers,
+                CURLOPT_TIMEOUT => 10,
+                CURLOPT_POST => TRUE,
+                CURLOPT_POSTFIELDS => $data,
+            )
+        );
+        $result = json_decode(curl_exec($ch));
+        curl_close($ch);
+        if (isset($result->error)) {
+            $this->_error($result);
+        } else {
+            $this->_output($result);
+        }
+    }
+
     function _screening_status($where, $ids) {
         $screenings = $this->db->pq(
             "SELECT dc.datacollectionid, sc.programversion, so.indexingsuccess, so.strategysuccess, so.alignmentsuccess

client/src/css/partials/_utility.scss

@@ -97,6 +97,10 @@
     font-weight: bold;
 }
 
+.u {
+    text-decoration: underline;
+}
+
 .nowrap {
     white-space: nowrap;
 }

client/src/js/modules/dc/views/attachments.js

@@ -3,15 +3,17 @@ define(['marionette',
     'views/table', 
     'collections/attachments', 
     'views/log',
+    'views/cloudupload',
     'utils'], 
-    function(Marionette, Backgrid, TableView, attachments, LogView, utils) {
+    function(Marionette, Backgrid, TableView, attachments, LogView, CloudUploadView, utils) {
 
 
     var OptionsCell = Backgrid.Cell.extend({
         events: {
             'click a.dl': utils.signHandler,
             'click a.rsv': 'closeDialog',
             'click a.vatlog': 'showLog',
+            'click a.vatupload': 'showCloudUpload',
         },
 
         closeDialog: function() {
@@ -30,6 +32,11 @@ define(['marionette',
             })
         },
 
+        showCloudUpload: function(e) {
+            e.preventDefault()
+            app.dialog.show(new CloudUploadView({ model: this.model, collection: this.model.collection }))
+        },
+
         render: function() {
             // This was using an 'id' passed into the column as the dcid (getOption('id')).
             // However, this is not present when loading attachments from a data collection group
@@ -46,6 +53,10 @@ define(['marionette',
                 this.$el.append('<a href="/dc/rsv/id/'+dcid+'" class="button rsv"><i class="fa fa-search"></i> Reciprocal Space Viewer</a>')
             }
 
+            if (app.options.get('ccp4_cloud_upload_url') && this.model.get('FILETYPE') == 'params') {
+                this.$el.append('<a class="vatupload button" href="#"><i class="fa fa-cloud-upload"></i> CCP4 Cloud</a>')
+            }
+
             return this
         }
     })

client/src/js/modules/dc/views/autointegration.js

@@ -41,7 +41,7 @@ define(['marionette',
         },
 
         showAttachments: function(e) {
-            e.preventDefault()
+            if (e) e.preventDefault()
 
             this.attachments = new AutoProcAttachments()
             this.attachments.queryParams.AUTOPROCPROGRAMID = this.model.get('AID')
@@ -52,6 +52,8 @@ define(['marionette',
                 view: new AutoProcAttachmentsView({ collection: this.attachments }), 
                 autosize: true 
             }))
+
+            this.listenTo(this.attachments, 'file:uploaded', this.showAttachments, this)
         },
 
         showLog: function(e) {

client/src/js/modules/dc/views/autoprocattachments.js

@@ -4,17 +4,19 @@ define(['marionette',
     'modules/dc/views/aiplots',
     'modules/dc/views/vue-plotly',
     'views/log',
+    'views/cloudupload',
     'views/table', 'utils'], 
     function(Marionette, Backbone, Backgrid, 
-    AIPlotsView, PlotlyPlotView, LogView,
+    AIPlotsView, PlotlyPlotView, LogView, CloudUploadView,
     TableView, utils) {
 
-    
+
     var OptionsCell = Backgrid.Cell.extend({
         events: {
             'click a.dl': utils.signHandler,
             'click a.vaplog': 'showLog',
             'click a.vapplot': 'showPlots',
+            'click a.vapupload': 'showCloudUpload',
         },
 
         render: function() {
@@ -28,9 +30,18 @@ define(['marionette',
                 this.$el.append('<a class="vapplot button" href="#"><i class="fa fa-line-chart"></i> View</a>')
             }
 
+            if (app.options.get('ccp4_cloud_upload_url') && this.model.get('FILETYPE') == 'Result') {
+                this.$el.append('<a class="vapupload button" href="#"><i class="fa fa-cloud-upload"></i> CCP4 Cloud</a>')
+            }
+
             return this
         },
 
+        showCloudUpload: function(e) {
+            e.preventDefault()
+            app.dialog.show(new CloudUploadView({ model: this.model, collection: this.model.collection }))
+        },
+
         showPlots: function(e) {
             e.preventDefault()
 

client/src/js/templates/dc/cloudupload.html

@@ -0,0 +1,25 @@
+
+<div>
+In order to upload to CCP4 cloud, we need your CCP4 Cloud username, and your CloudRun Id.<br />
+You can find your CloudRun Id on the 'My Account' page of CCP4 Cloud.
+</div>
+<br />
+<div>
+Once uploaded, create or select a CCP4 Cloud project and select the task 'Import from Cloud Storage'.<br />
+Click 'Select file(s)', then click 'My Cloud Storage'.
+</div>
+<br />
+<div>
+See <a class="u" href="https://cloud.ccp4.ac.uk/manuals/html-userguide/jscofe_synchweb.html">here</a> for more information.
+</div>
+<br />
+
+<div class="table">
+<table>
+<tr><td><span class="b">Filename: </span></td><td><%-FILENAME%></td></tr>
+<tr><td><span class="b">CCP4 Cloud Username: </span></td><td><input name="username"></input></td></tr>
+<tr><td><span class="b">CCP4 CloudRun Id: </span></td><td><input name="cloudrunid" placeholder="####-####-####-####"></input></td></tr>
+<tr><td><span class="b">Remember these: </span></td><td><input type="checkbox" name="remember"></input></td></tr>
+</table>
+</div>
+

client/src/js/views/cloudupload.js

@@ -0,0 +1,71 @@
+define([
+    'backbone',
+    'views/dialog',
+    'templates/dc/cloudupload.html',
+    'jquery.cookie'
+], function(
+    Backbone,
+    DialogView,
+    template
+) {
+
+    return DialogView.extend({
+        template: template,
+        title: 'Upload to CCP4 Cloud',
+
+        buttons: {
+            'Upload': 'upload',
+            'Cancel': 'closeDialog',
+        },
+
+        ui: {
+            username: 'input[name=username]',
+            cloudrunid: 'input[name=cloudrunid]',
+            remember: 'input[name=remember]',
+        },
+
+        upload: function() {
+            if (this.ui.remember.is(':checked')) {
+                let cookieOpts = { expires: 365, path: '/' }
+                $.cookie('ccp4_username', this.ui.username.val(), cookieOpts)
+                $.cookie('ccp4_cloudrunid', this.ui.cloudrunid.val(), cookieOpts)
+            }
+            let data = { cloudrunid: this.ui.cloudrunid.val(), username: this.ui.username.val() }
+            if (this.model.get('AUTOPROCPROGRAMATTACHMENTID')) {
+                data.AUTOPROCPROGRAMATTACHMENTID = this.model.get('AUTOPROCPROGRAMATTACHMENTID')
+            } else if (this.model.get('DATACOLLECTIONFILEATTACHMENTID')) {
+                data.DATACOLLECTIONFILEATTACHMENTID = this.model.get('DATACOLLECTIONFILEATTACHMENTID')
+            }
+            var self = this
+            Backbone.ajax({
+                url: app.apiurl+'/processing/upload',
+                type: 'POST',
+                data: data,
+                success: function() {
+                    app.alert({ className: 'message notify', message: 'File successfully uploaded' })
+                    self.closeDialog()
+                    self.collection.trigger('file:uploaded')
+
+                },
+                error: function(xhr, status, error) {
+                    app.alert({ message: 'Something went wrong uploading this file: '+xhr.responseText })
+                },
+            })
+        },
+
+        initialize: function(options) {
+            this.collection = options.collection
+        },
+
+        onRender: function() {
+            let ccp4_username = $.cookie('ccp4_username');
+            let ccp4_cloudrunid = $.cookie('ccp4_cloudrunid');
+            if (ccp4_username) this.ui.username.val(ccp4_username)
+            if (ccp4_cloudrunid) this.ui.cloudrunid.val(ccp4_cloudrunid)    
+            if (ccp4_username || ccp4_cloudrunid) this.ui.remember.prop('checked', true)
+        }
+
+
+    })
+
+})