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Allow user sequence submission
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@etorres
etorres committed Dec 10, 2015
1 parent 8d1b4b1 commit fb7e861
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Showing 14 changed files with 708 additions and 148 deletions.
236 changes: 167 additions & 69 deletions lvl-project/lvl-bundle/src/main/ui/js/apps/collection/submit/collection_submit_view.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
* RequireJS module that defines the view: collection->submit.
*/

define([ 'app', 'tpl!apps/collection/submit/tpls/collection_submit', 'chance', 'pace', 'bootstrapvalidator', 'backbone.syphon' ], function(Lvl, SubmitTpl, Chance, pace) {
define([ 'app', 'tpl!apps/collection/submit/tpls/collection_submit', 'chance', 'pace', 'backbone.oauth2', 'bootstrapvalidator', 'backbone.syphon' ], function(Lvl, SubmitTpl, Chance, pace) {
Lvl.module('CollectionApp.Submit.View', function(View, Lvl, Backbone, Marionette, $, _) {
'use strict';
var lvlService = Lvl.config.get('service.url');
Expand All @@ -11,15 +11,48 @@ define([ 'app', 'tpl!apps/collection/submit/tpls/collection_submit', 'chance', '
template : SubmitTpl,
templateHelpers : function() {
return {
pendingId : function() {
return 'user-' + new Chance().string({
submissionId : function() {
return 'user-seq-' + new Chance().string({
length : 8,
pool : 'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789'
});
}
}
}
},
events : {
'change [name="inputLongitude"]' : 'geocodeFn',
'change [name="inputLatitude"]' : 'geocodeFn',
'change [name="inputOrganism"]' : function(e) {
var self = this;
var organism = $(e.target).val();
var form = $('#lvlSubmitSequenceForm');
if (organism === 'Leishmania') {
self.$('#inputPhylum').val('Euglenozoa');
self.$('#inputClass').val('Kinetoplastea');
self.$('#inputOrder').val('Trypanosomatida');
self.$('#inputFamily').val('Trypanosomatidae');
self.$('#inputGenus').val('Leishmania');
form.bootstrapValidator('resetField', 'inputEpithet', true);
self.$('#inputScientificName').val('');
} else if (organism === 'Sandflies') {
self.$('#inputPhylum').val('Arthropoda');
self.$('#inputClass').val('Insecta');
self.$('#inputOrder').val('Diptera');
self.$('#inputFamily').val('Psychodidae');
form.bootstrapValidator('resetField', 'inputGenus', true);
form.bootstrapValidator('resetField', 'inputEpithet', true);
self.$('#inputScientificName').val('');
}
form.bootstrapValidator('validateField', 'inputGenus');
},
'change #inputGenus' : function(e) {
var self = this;
self.$('#inputScientificName').val(self.$('#inputGenus').val() + ' ' + self.$('#inputEpithet').val());
},
'change #inputEpithet' : function(e) {
var self = this;
self.$('#inputScientificName').val(self.$('#inputGenus').val() + ' ' + self.$('#inputEpithet').val());
},
'focus #lvlSubmitSequenceForm input.form-control' : function(e) {
var form = $('#lvlSubmitSequenceForm');
if (Boolean(form.attr('data-pristine') === 'true')) {
Expand All @@ -42,6 +75,19 @@ define([ 'app', 'tpl!apps/collection/submit/tpls/collection_submit', 'chance', '
}
}
},
'inputGenus' : {
verbose : false,
validators : {
notEmpty : {
message : 'The genus is required and cannot be empty'
},
stringLength : {
min : 3,
max : 128,
message : 'The genus is required to be of 3-128 characters in length'
}
}
},
'inputEpithet' : {
verbose : false,
validators : {
Expand Down Expand Up @@ -112,6 +158,19 @@ define([ 'app', 'tpl!apps/collection/submit/tpls/collection_submit', 'chance', '
regexp: {
regexp: /^[ACTG]+$/i,
message: 'The origin can consist of A, C, T and G only'
}
}
},
'inputIndividualCount' : {
verbose : false,
validators : {
integer : {
message : 'The value is not an integer'
},
between : {
min : 0,
max : 1000,
message : 'The individual count must be between 0 and 1000'
}
}
},
Expand All @@ -134,81 +193,120 @@ define([ 'app', 'tpl!apps/collection/submit/tpls/collection_submit', 'chance', '
data.bv.disableSubmitButtons(!isValid);
});
}
}, 'click #lvlResetSequenceBtn' : function(e) {
e.preventDefault();
var form = $('#lvlSubmitSequenceForm');
form[0].reset();
form.bootstrapValidator('resetForm', true);
form.bootstrapValidator('disableSubmitButtons', true);
}, 'click #lvlSubmitSequenceBtn' : function(e) {
e.preventDefault();
pace.restart();
$('#lvlSubmitSequenceForm button[type="submit"]').attr('disabled', 'disabled');
var formData = Backbone.Syphon.serialize(this);
var request = new FormData();
var issueBlob = new Blob([ JSON.stringify({
'sample' : {
'institutionCode' : formData.inputInstitution,
'collectionCode' : formData.inputInstitution + '-collection',
'continent' : 'Europe', // TODO
'country' : 'Spain', // TODO
'stateProvince' : 'Madrid', // TODO
'county' : 'Madrid', // TODO
'locality' : 'Fuenlabrada', // TODO
'decimalLatitude' : formData.inputLatitude,
'decimalLongitude' : formData.inputLongitude,
'scientificName' : 'Leishmania infantum',
'phylum' : 'Euglenozoa', // TODO
'clazz' : 'Kinetoplastea', // TODO
'order' : 'Trypanosomatida', // TODO
'family' : 'Trypanosomatidae', // TODO
'genus' : 'Leishmania', // TODO
'specificEpithet' : 'infantum' // TODO
},
'sequence' : formData.inputOrigin
}) ], {
type : 'application/json'
});
request.append('issue', issueBlob);

/*
|| isBlank(trimToNull(pendingSeq.getSample().getCountry()))
|| isBlank(trimToNull(pendingSeq.getSample().getScientificName())))
*/

/* TODO
var inputScreenshot = $('#screenshot');
if (inputScreenshot.val()) {
request.append('file', inputScreenshot.get(0).files[0]);
}
// submit request to LVL server
var self = this;
$('#lvlSubmitSequenceBtn').tooltip('hide');
var self = this, formData = Backbone.Syphon.serialize(this), organism = formData.inputOrganism.toLowerCase();
require([ 'entities/pending_sequence' ], function(PendingSequenceModel) {
var pendingSeq = new PendingSequenceModel.PendingSequenceCreate();
pendingSeq.oauth2_token = Lvl.config.authorizationToken();
pendingSeq.save({
'sample' : {
'institutionCode' : formData.inputInstitution,
'collectionCode' : formData.inputInstitution + '-collection',
'country' : formData.inputCountry,
'stateProvince' : formData.inputStateProvince,
'county' : formData.inputCounty,
'locality' : formData.inputLocality,
'decimalLatitude' : formData.inputLatitude,
'decimalLongitude' : formData.inputLongitude,
'scientificName' : formData.inputScientificName,
'phylum' : formData.inputPhylum,
'clazz' : formData.inputClass,
'order' : formData.inputOrder,
'family' : formData.inputFamily,
'genus' : formData.inputGenus,
'specificEpithet' : formData.inputEpithet
},
'sequence' : formData.inputOrigin,
'preparation' : {
'sex' : formData.inputSex,
'individualCount' : formData.inputIndividualCount,
'collectingMethod' : formData.inputCollectingMethod,
'preparationType' : formData.inputPreparationType,
'materialType' : formData.inputMaterialType
}
}, {
success : function(model, resp, options) {
require([ 'common/growl' ], function(createGrowl) {
var anchor = $('<a>', {
href : options.xhr.getResponseHeader('Location')
})[0];
var id = anchor.pathname.substring(anchor.pathname.lastIndexOf('/') + 1);
createGrowl('New sequence created', id
+ ' <a href="/#collection/pending/' + organism + '"><i class="fa fa-arrow-circle-right fa-fw"></i> pending sequences</a>', false);
});
},
error : function(model, resp, options) {
require([ 'common/alert' ], function(alertDialog) {
alertDialog('Error', 'Failed to create sequence.');
});
}
}).always(function() {
pace.stop();
var form = self.$('#lvlSubmitSequenceForm');
form[0].reset();
form.bootstrapValidator('resetForm', true);
form.bootstrapValidator('disableSubmitButtons', true);
});
});
}
},
geocodeFn : function(e) {
var self = this;
var form = $('#lvlSubmitSequenceForm'), bootstrapValidator = form.data('bootstrapValidator');
if (bootstrapValidator.isValidField('inputLongitude') && bootstrapValidator.isValidField('inputLatitude')) {
var lng = this.$('#inputLongitude').val(), lat = this.$('#inputLatitude').val();
pace.restart();
var jqxhr = $.ajax({
type : 'POST',
processData : false,
contentType : false,
crossDomain : true,
url : lvlService + '/support/issues/with-attachment',
data : request
url : Lvl.config.googleGeocodeEndpoint(lat, lng)
}).always(function() {
pace.stop();
var form = $('#lvlIssueReportForm');
form.bootstrapValidator('resetForm', true);
form.bootstrapValidator('disableSubmitButtons', true);
}).done(
function(data, textStatus, request) {
require([ 'common/growl' ], function(createGrowl) {
createGrowl('New issue report created', 'Our team will investigate your report and will send you a '
+ 'follow-up e-mail at the address that you provided.', false);
});
}).fail(function(jqXHR, textStatus, errorThrown) {
if (jqXHR.status !== 404) {
pace.stop();
}).done(function(data, textStatus, request) {
if ('OK' === data.status) {
require([ 'common/geocode_parser' ], function(parseGeocode) {
var address = parseGeocode(data);
self.$('#inputCountry').val(address.country);
self.$('#inputStateProvince').val(address.stateProvince);
self.$('#inputCounty').val(address.county);
self.$('#inputLocality').val(address.locality);
});
} else {
require([ 'common/alert' ], function(alertDialog) {
alertDialog('Error', 'The issue report cannot be sent.');
alertDialog('Error', 'A location cannot be identified from the provided coordinates.');
});
self.resetAddress();
}
}); */

// TODO
console.log('FORM SUBMITTED!', JSON.stringify(issueBlob));
// TODO
}
}
}).fail(function(jqXHR, textStatus, errorThrown) {
require([ 'common/alert' ], function(alertDialog) {
alertDialog('Error', 'A location cannot be identified from the provided coordinates.');
});
});
} else self.resetAddress();
},
resetAddress : function() {
var self = this;
self.$('#inputCountry').val('Unknown');
self.$('#inputStateProvince').val('');
self.$('#inputCounty').val('');
self.$('#inputLocality').val('');
},
onRender : function() {
this.$el.find('[data-toggle="tooltip"]').tooltip();
},
onDestroy : function() {
pace.stop();
this.stopListening();
}
});
});
return Lvl.CollectionApp.Submit.View;
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