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Sep 18, 2017
Merged

redbiom now adds per sample studies to analysis #2288

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d4cc989
redbiom now adds per sample studies to analysis
antgonza Sep 15, 2017
46b174e
add prints to review errors
antgonza Sep 16, 2017
38e5cd7
rm prints
antgonza Sep 16, 2017
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32 changes: 18 additions & 14 deletions qiita_pet/handlers/qiita_redbiom.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
# -----------------------------------------------------------------------------

from requests import ConnectionError
from future.utils import viewitems
from collections import defaultdict
import redbiom.summarize
import redbiom.search
Expand Down Expand Up @@ -42,35 +43,38 @@ def _redbiom_metadata_search(self, query, contexts):
'Not a valid search: "%s", your query is too small '
'(too few letters), try a longer query' % query)
if not message:
sids = set([s.split('.', 1)[0] for s in samples])
for s in sids:
study_artifacts[s] = [a.id for a in Study(s).artifacts(
artifact_type='BIOM')]
study_samples = defaultdict(list)
for s in samples:
study_samples[s.split('.', 1)[0]].append(s)
for sid, samps in viewitems(study_samples):
study_artifacts[sid] = {
a.id: samps for a in Study(sid).artifacts(
artifact_type='BIOM')}

return message, study_artifacts

def _redbiom_feature_search(self, query, contexts):
study_artifacts = defaultdict(list)
study_artifacts = defaultdict(lambda: defaultdict(list))
query = [f for f in query.split(' ')]
for ctx in contexts:
for idx in redbiom.util.ids_from(query, True, 'feature', ctx):
aid, sid = idx.split('_', 1)
sid = sid.split('.', 1)[0]
study_artifacts[sid].append(aid)
aid, sample_id = idx.split('_', 1)
sid = sample_id.split('.', 1)[0]
study_artifacts[sid][aid].append(sample_id)

return '', study_artifacts

def _redbiom_taxon_search(self, query, contexts):
study_artifacts = defaultdict(list)
study_artifacts = defaultdict(lambda: defaultdict(list))
for ctx in contexts:
# find the features with those taxonomies and then search
# those features in the samples
features = redbiom.fetch.taxon_descendents(ctx, query)
for idx in redbiom.util.ids_from(features, True, 'feature',
ctx):
aid, sid = idx.split('_', 1)
sid = sid.split('.', 1)[0]
study_artifacts[sid].append(aid)
aid, sample_id = idx.split('_', 1)
sid = sample_id.split('.', 1)[0]
study_artifacts[sid][aid].append(sample_id)

return '', study_artifacts

Expand Down Expand Up @@ -98,8 +102,8 @@ def _redbiom_search(self, query, search_on, callback):
study_artifacts.keys(), True)
# inserting the artifact_biom_ids to the results
for i in range(len(results)):
results[i]['artifact_biom_ids'] = list(set(
study_artifacts[str(results[i]['study_id'])]))
results[i]['artifact_biom_ids'] = study_artifacts[
str(results[i]['study_id'])]
else:
message = "No samples where found! Try again ..."
else:
Expand Down
64 changes: 50 additions & 14 deletions qiita_pet/static/js/qiita.js
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Expand Up @@ -149,25 +149,35 @@ function show_hide_process_list() {
* Note that we have a list of artifact ids cause the user can select one single
* artifact to add or all study artifacts
*/
function send_samples_to_analysis(button, aids) {
function send_samples_to_analysis(button, aids, samples = null) {
button.value = 'Adding';
button.disabled = true;
$(button).addClass("btn-info");
bootstrapAlert('We are adding ' + aids.length + ' artifact(s) to the analysis. This ' +
'might take some time based on the number of samples on each artifact.', "warning", 10000);
$.get('/artifact/samples/', {ids:aids})
.done(function ( data ) {
if (data['status']=='success') {
qiita_websocket.send('sel', data['data']);
button.value = 'Added';
$(button).removeClass("btn-info");
} else {
bootstrapAlert('ERROR: ' + data['msg'], "danger");
button.value = 'There was an error, scroll up to see it';
button.disabled = false;
$(button).addClass("btn-danger");
}
if (samples === null) {
$.get('/artifact/samples/', {ids:aids})
.done(function ( data ) {
if (data['status']=='success') {
qiita_websocket.send('sel', data['data']);
button.value = 'Added';
$(button).removeClass("btn-info");
} else {
bootstrapAlert('ERROR: ' + data['msg'], "danger");
button.value = 'There was an error, scroll up to see it';
button.disabled = false;
$(button).addClass("btn-danger");
}
});
} else {
$.each(aids, function(i, aid) {
var to_send = {};
to_send[aid] = samples.split(',');
qiita_websocket.send('sel', to_send);
});
button.value = 'Added';
$(button).removeClass("btn-info");
}
}

/**
Expand Down Expand Up @@ -388,25 +398,51 @@ function show_alert(data) {
$('#dflt-sel-info').css('color', 'rgb(0, 160, 0)');
}

function format_biom_rows(data, row) {
function format_biom_rows(data, row, for_study_list = true, samples = null) {
var proc_data_table = '<table class="table" cellpadding="0" cellspacing="0" border="0" style="padding-left:0px;width:95%">';
proc_data_table += '<tr>';
if (for_study_list) {
proc_data_table += '<th></th>';
}
proc_data_table += '<th>Name</th>';
if (for_study_list) {
proc_data_table += '<th>Data type</th>';
}
proc_data_table += '<th>Processing method</th>';
proc_data_table += '<th>Parameters</th>';
if (for_study_list) {
proc_data_table += '<th>Samples in Prep Info</th>';
}
proc_data_table += '<th>Files</th>';
proc_data_table += '</tr>';

$.each(data, function (idx, info) {
if (typeof info !== 'string' && !(info instanceof String)) {
proc_data_table += '<tr>';
if (for_study_list) {
if (samples === null) {
proc_data_table += '<td><input type="button" class="btn btn-sm" value="Add" onclick="send_samples_to_analysis(this, [' + info.artifact_id + '])"></td>';
} else {
proc_data_table += '<td><input type="button" class="btn btn-sm" value="Add" onclick="send_samples_to_analysis(this, [' + info.artifact_id + "], '" + samples[info.artifact_id].join(',') + "'" + ')"></td>';
}
}
proc_data_table += '<td>' + info.name + ' (' + info.artifact_id + ' - ' + info.timestamp.split('.')[0] + ')</td>';

if (for_study_list) {
proc_data_table += '<td>' + info.data_type + ' (' + info.target_subfragment.join(', ') + ')</td>';
}
proc_data_table += '<td>' + info.algorithm + '</td>';

var params = '';
for (var key in info.parameters) {
params += '<i>' + key + '</i>: ' + info.parameters[key] + '<br/>';
}
proc_data_table += '<td><small>' + params + '</small></td>';
if (for_study_list) {
proc_data_table += '<td>' + info.prep_samples + '</td>';
}
proc_data_table += '<td><small>' + info.files.join('<br/>') + '</small></td>';

proc_data_table += '</tr>';
}
});
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/templates/artifact_ajax/artifact_summary.html
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Expand Up @@ -108,7 +108,7 @@ <h4>
{% if editable %}
<a class="btn btn-default btn-sm" data-toggle="modal" data-target="#update-artifact-name"><span class="glyphicon glyphicon-pencil"></span> Edit</a>
{% if artifact_type == 'BIOM' %}
<a class="btn btn-default btn-sm" onclick="send_samples_to_analysis(this, [{{artifact_id}}]);"> Add to analysis</a>
<input type="button" class="btn btn-default btn-sm" value="Add to Analysis" onclick="send_samples_to_analysis(this, [{{artifact_id}}]);">
{% else %}
<a class="btn btn-default btn-sm" onclick="load_process_artifact_ui({{artifact_id}});"><span class="glyphicon glyphicon-play"></span> Process</a>
{% end %}
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/templates/list_analyses.html
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@
$.get('/artifact/info/', {ids: JSON.parse(row.data()[0]), only_biom: 'False' })
.done(function ( data ) {
if (data['status']=='success') {
$('td', row.child()).html(format_biom_rows(data.data, row.index())).show();
$('td', row.child()).html(format_biom_rows(data.data, row.index(), for_study_list=false)).show();
} else {
bootstrapAlert('ERROR: ' + data['msg'], "danger", 10000);
}
Expand Down
35 changes: 0 additions & 35 deletions qiita_pet/templates/list_studies.html
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Original file line number Diff line number Diff line change
Expand Up @@ -54,41 +54,6 @@
$("#search-waiting").hide();
qiita_websocket.init(window.location.host + '{% raw qiita_config.portal_dir %}/study/list/socket/', error, error);
qiita_websocket.add_callback('sel', show_alert);
function format_biom_rows(data, row) {
var proc_data_table = '<table class="table" cellpadding="0" cellspacing="0" border="0" style="padding-left:0px;width:95%">';
proc_data_table += '<tr>';
proc_data_table += '<th></th>';
proc_data_table += '<th>Name</th>';
proc_data_table += '<th>Data type</th>';
proc_data_table += '<th>Processing method</th>';
proc_data_table += '<th>Parameters</th>';
proc_data_table += '<th>Samples in Prep Info</th>';
proc_data_table += '<th>Files</th>';
proc_data_table += '</tr>';

$.each(data, function (idx, info) {
if (typeof info !== 'string' && !(info instanceof String)) {
proc_data_table += '<tr>';
proc_data_table += '<td><input type="button" class="btn btn-sm" value="Add" onclick="send_samples_to_analysis(this, [' + info.artifact_id + '])"></td>';
proc_data_table += '<td>' + info.name + ' (' + info.artifact_id + ' - ' + info.timestamp.split('.')[0] + ')</td>';
proc_data_table += '<td>' + info.data_type + ' (' + info.target_subfragment.join(', ') + ')</td>';
proc_data_table += '<td>' + info.algorithm + '</td>';

var params = '';
for (var key in info.parameters) {
params += '<i>' + key + '</i>: ' + info.parameters[key] + '<br/>';
}
proc_data_table += '<td><small>' + params + '</small></td>';
proc_data_table += '<td>' + info.prep_samples + '</td>';
proc_data_table += '<td><small>' + info.files.join('<br/>') + '</small></td>';

proc_data_table += '</tr>';
}
});

proc_data_table += '</table>';
return proc_data_table;
}

$('#user-studies-table').dataTable({
"lengthMenu": [[5, 10, 50, -1], [5, 10, 50, "All"]],
Expand Down
57 changes: 37 additions & 20 deletions qiita_pet/templates/redbiom.html
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Original file line number Diff line number Diff line change
Expand Up @@ -15,42 +15,55 @@
// adding total features found

var api = this.api(), data;
var total_features = api
var artifacts_samples = api
.column(0)
.data()
.reduce( function (a, b) {return a + b.length}, 0);

.reduce( function (a, b) {
var artifacts = 0, samples = 0;
$.each( b, function( key, value ) {
artifacts += 1;
samples += value.length;
});
return [artifacts, samples]}, [0, 0]);
var artifacts = artifacts_samples[0];
var samples = artifacts_samples[1];
$('.footer').addClass("col-md-12 text-right");
if (total_features == 0) {
if (artifacts == 0) {
text = '';
} else {
text = 'Found ' + total_features + ' artifacts.';
text = 'Found ' + artifacts + ' artifacts with ' + samples + ' samples.';
}
$('.footer').html(text)
},
"columns": [
{ "orderable": false, "width": "15%", "data": "artifact_biom_ids"},
{ "orderable": false, "width": "20%", "data": "artifact_biom_ids"},
{ "data": "study_title", "width": "70%" },
{ "data": "study_abstract", "width": "0%" },
{ "data": "study_id", "width": "15%" },
{ "data": "study_id", "width": "10%" },
{ "data": "study_alias", "width": "0%" }],
columnDefs: [
// {type:'natural', targets:[2,6,7]},
{"targets": [ 2, 4 ], "visible": false},
// render zero
{"render": function ( data, type, row, meta ) {
if (data !== null && data !== undefined && data.length != 0){
return '<div class="container" style="max-width: 5em;">'+
'<div class="row justify-content-md-center">' +
{% if current_user is not None %}
'<div class="col-md-1 text-center details-control">&nbsp;</div>' +
{% end %}
'<div class="col-md-1 text-center">' + data.length + '</div>' +
'</div>' +
'</div>';
} else {
return 'No BIOMs';
if (data !== null && data !== undefined){
var artifacts = 0, samples = 0;
for (var d in data) { if (data.hasOwnProperty(d)) { artifacts++; } }
if (artifacts != 0) {
return '<div class="container" style="max-width: 15em;">'+
'<div class="row justify-content-md-center">' +
{% if current_user is not None %}
'<div class="col-md-12 text-center details-control">&nbsp;</div>' +
{% end %}
'<div class="col-md-12 text-center">' +
'Artifacts: ' + artifacts + ' | ' +
'Samples: ' + artifacts +
'</div>' +
'</div>' +
'</div>';
}
}
return 'No BIOMs';
}, targets: [0]},
// render the title cell
{"render": function ( data, type, row, meta ) {
Expand Down Expand Up @@ -85,10 +98,14 @@
// modified from: https://jsfiddle.net/8rejaL88/2/
tr.addClass('shown');
row.child('<p><center><img src="{% raw qiita_config.portal_dir %}/static/img/waiting.gif" style="display:block;margin-left: auto;margin-right: auto"/></center></p>', 'no-padding' ).show();
$.get('/artifact/info/', {ids: row.data().artifact_biom_ids})

var artifact_biom_ids = row.data().artifact_biom_ids;
var artifact_biom_ids_keys = []
$.each(artifact_biom_ids, function(e){ artifact_biom_ids_keys.push(e) });
$.get('/artifact/info/', {ids: artifact_biom_ids_keys })
.done(function ( data ) {
if (data['status']=='success') {
$('td', row.child()).html(format_biom_rows(data.data, row.index())).show();
$('td', row.child()).html(format_biom_rows(data.data, row.index(), true, samples=artifact_biom_ids)).show();
} else {
bootstrapAlert('ERROR: ' + data['msg'], "danger", 10000);
}
Expand Down
12 changes: 9 additions & 3 deletions qiita_pet/test/test_qiita_redbiom.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,11 @@ def test_post_metadata(self):
response = self.post('/redbiom/', post_args)
self.assertEqual(response.code, 200)
data = DATA
data[0]['artifact_biom_ids'] = [4, 5, 6, 7]
samples = ['1.SKD6.640190', '1.SKD9.640182', '1.SKD8.640184',
'1.SKD5.640186', '1.SKD2.640178', '1.SKD4.640185',
'1.SKD1.640179', '1.SKD3.640198', '1.SKD7.640191']
data[0]['artifact_biom_ids'] = {
'5': samples, '4': samples, '7': samples, '6': samples}
exp = {'status': 'success', 'message': '', 'data': data}
self.assertEqual(loads(response.body), exp)

Expand Down Expand Up @@ -59,7 +63,8 @@ def test_post_features(self):
}
response = self.post('/redbiom/', post_args)
data = DATA
data[0]['artifact_biom_ids'] = ['5', '4']
data[0]['artifact_biom_ids'] = {
'5': ['1.SKM3.640197'], '4': ['1.SKM3.640197']}
exp = {'status': 'success', 'message': '', 'data': data}
self.assertEqual(response.code, 200)
self.assertEqual(loads(response.body), exp)
Expand All @@ -80,7 +85,8 @@ def test_post_taxon(self):
'search_on': 'taxon'
}
data = DATA
data[0]['artifact_biom_ids'] = ['5', '4']
data[0]['artifact_biom_ids'] = {
'5': ['1.SKM3.640197'], '4': ['1.SKM3.640197']}
response = self.post('/redbiom/', post_args)
exp = {'status': 'success', 'message': '', 'data': data}
self.assertEqual(response.code, 200)
Expand Down