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Enable URL BIOM file import and fix bugs. #54

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a8b2441
Fix variable name
bgruening Jul 10, 2015
c2d145d
Add an alert when BIOM file is missing metadata.
blankenberg Mar 31, 2016
f829061
Allow loading biom by url query parameter named biomURL.
blankenberg Mar 31, 2016
b0ab071
Fix for preparsed JSON when loading from URLs.
blankenberg Mar 31, 2016
1d6747e
provide loading url message
blankenberg Mar 31, 2016
3bc240e
Add alert when taxonomy metadata is missing in taxonomyViz
blankenberg Mar 31, 2016
4d847c2
Fixes for BIOM files that don't have column metadata.
blankenberg Apr 1, 2016
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29 changes: 18 additions & 11 deletions src/filter.coffee
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Original file line number Diff line number Diff line change
Expand Up @@ -95,12 +95,17 @@ class filter

generateColumns: () ->

if !biom.columns[0].metadata?
for i in [0..attr_length]
if !biom.columns[i].metadata?
biom.columns[i].metadata = {}

for key of biom.columns[0].metadata
if key.toLowerCase().indexOf("date") != -1
date_array.push(key)

else if key == 'phinchID'
console.log 'PhinchID does exsit!'
console.log 'PhinchID does exist!'

else if (key.toLowerCase().indexOf("barcode") != -1) || (key.toLowerCase().indexOf("sequence") != -1) || (key.toLowerCase().indexOf("reverse") != -1) || (key.toLowerCase() == "internalcode") || (key.toLowerCase() == "description") || (key.toLowerCase().indexOf("adapter") !=-1)
no_data_attributes_array.push(key)
Expand Down Expand Up @@ -362,7 +367,7 @@ class filter
toprocess = []

content = ""
content += "<span class = 'biom_valid_attr'>" + groupable_array[_i] + "</span><br/>"
content += "<span class = 'biom_valid_attr'>" + groupable_array[i] + "</span><br/>"

if groupable_array_content.length > 0
for j in [pointer_left..groupable_array_content.length-1]
Expand All @@ -379,7 +384,7 @@ class filter

if toprocess.length > 0
for k in [0..toprocess.length-1]
content += "<input type='checkbox' name='groupable_check_group' id='groupable_check_" + check_count + "' checked='checked' /><label for='groupable_check_" + check_count + "'></label><span class = 'biom_valid_attr_grp'>" + toprocess[_k] + "</span><br/>"
content += "<input type='checkbox' name='groupable_check_group' id='groupable_check_" + check_count + "' checked='checked' /><label for='groupable_check_" + check_count + "'></label><span class = 'biom_valid_attr_grp'>" + toprocess[k] + "</span><br/>"
check_count++

$('#groupable_att').append("<div class='overflowControl'>" + content + "</div>")
Expand Down Expand Up @@ -601,16 +606,18 @@ class filter
for i in [0..biom.shape[1]-1]

# If this is a not selected descriptive attribute, delete it
for j in [0..no_data_attributes_array.length-1]
if @selected_no_data_attributes_array.indexOf(no_data_attributes_array[j]) == -1
@removeFromObjectByKey(phinch.columns[i].metadata, no_data_attributes_array[j])

if no_data_attributes_array.length > 0
for j in [0..no_data_attributes_array.length-1]
if @selected_no_data_attributes_array.indexOf(no_data_attributes_array[j]) == -1
@removeFromObjectByKey(phinch.columns[i].metadata, no_data_attributes_array[j])
# If this is not a selected attributes, delete it
for k in [0..attributes_array.length-1]
if @selected_attributes_array.indexOf(attributes_array[k]) == -1
@removeFromObjectByKey(phinch.columns[i].metadata, attributes_array[k])

if attributes_array.length > 0
for k in [0..attributes_array.length-1]
if @selected_attributes_array.indexOf(attributes_array[k]) == -1
@removeFromObjectByKey(phinch.columns[i].metadata, attributes_array[k])
# Add the new phinch Id column back in the file
if !phinch.columns[i].metadata?
phinch.columns[i].metadata = {}
phinch.columns[i].metadata['phinchID'] = phinchID_array[i]


Expand Down
31 changes: 30 additions & 1 deletion src/readFile.coffee
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Expand Up @@ -18,15 +18,44 @@ class readFile
@checkFile(files)
false)

# Load by URL, requires CORS at remote server
query = window.location.search.substring(1)
raw_vars = query.split("&")
params = {}
for v in raw_vars
[key, val] = v.split("=")
params[key] = decodeURIComponent(val)
if params['biomURL']?
$('#loadTestFile').hide()
$('#fileDrag').hide()
$('#progress_bar').hide()
$('#frmUpload').hide()
$('#parse').html('loading URL...&nbsp;&nbsp;<i class="icon-spinner icon-spin icon-large"></i>');
$.get(params['biomURL'], (urlData) =>
if urlData.constructor != String
urlData = JSON.stringify( urlData )
biomToStore = {}
biomToStore.name = params['biomURL']
biomToStore.size = urlData.length
biomToStore.data = urlData
d = new Date();
biomToStore.date = d.getUTCFullYear() + "-" + (d.getUTCMonth() + 1) + "-" + d.getUTCDate() + "T" + d.getUTCHours() + ":" + d.getUTCMinutes() + ":" + d.getUTCSeconds() + " UTC"
@server.biom.add(biomToStore).done () ->
setTimeout( "window.location.href = 'preview.html'", 1)
)


# load test file
document.getElementById('loadTestFile').addEventListener('click', (evt) =>
$('#loadTestFile').html('loading...&nbsp;&nbsp;<i class="icon-spinner icon-spin icon-large"></i>');
hostURL = 'http://' + window.location.host + window.location.pathname.substr(0, window.location.pathname.lastIndexOf('/'))
testfile = hostURL + '/data/testdata.biom' ## Dev TODO http://phinch.org/data/testdata.biom
$.get(testfile, (testdata) =>
if testdata.constructor != String
testdata = JSON.stringify( testdata )
biomToStore = {}
biomToStore.name = 'testdata.biom'
biomToStore.size = 15427024
biomToStore.size = testdata.length
biomToStore.data = testdata
d = new Date();
biomToStore.date = d.getUTCFullYear() + "-" + (d.getUTCMonth() + 1) + "-" + d.getUTCDate() + "T" + d.getUTCHours() + ":" + d.getUTCMinutes() + ":" + d.getUTCSeconds() + " UTC"
Expand Down
3 changes: 3 additions & 0 deletions src/taxonomyViz.coffee
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Expand Up @@ -242,6 +242,9 @@ class taxonomyViz
comp_i = new Array(7)
comb_len = unique_taxonomy_comb.length

if !biom.rows[i].metadata? or !biom.rows[i].metadata.taxonomy?
alert '"taxonomy" metadata needs to be provided in BIOM file'

if biom.rows[i].metadata.taxonomy.indexOf(';') != -1
comp_i = biom.rows[i].metadata.taxonomy.replace(/\s+/g, '').replace(/;/g,',').split(',')
else
Expand Down