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-rw-r--r--wqflask/wqflask/api/router.py116
-rw-r--r--wqflask/wqflask/static/new/javascript/plotly_probability_plot.js11
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js23
-rw-r--r--wqflask/wqflask/templates/show_trait.html19
-rw-r--r--wqflask/wqflask/templates/show_trait_calculate_correlations.html2
-rw-r--r--wqflask/wqflask/templates/show_trait_edit_data.html2
-rw-r--r--wqflask/wqflask/templates/show_trait_transform_and_filter.html8
7 files changed, 156 insertions, 25 deletions
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 845873a0..4ecd6699 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -290,6 +290,106 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+@app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=('GET',))
+@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=('GET',))
+def fetch_traits(dataset_name, file_format = "csv"):
+ trait_ids, _trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name)
+ if ('ids_only' in request.args) and (len(trait_ids) > 0):
+ if file_format == "json":
+ filename = dataset_name + "_trait_ids.json"
+ return flask.jsonify(trait_ids)
+ else:
+ filename = dataset_name + "_trait_ids.csv"
+
+ si = StringIO.StringIO()
+ csv_writer = csv.writer(si)
+ csv_writer.writerows([[trait_id] for trait_id in trait_ids])
+ output = make_response(si.getvalue())
+ output.headers["Content-Disposition"] = "attachment; filename=" + filename
+ output.headers["Content-type"] = "text/csv"
+ return output
+ else:
+ if len(trait_ids) > 0:
+ if data_type == "ProbeSet":
+ query = """
+ SELECT
+ ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias,
+ ProbeSetXRef.mean, ProbeSetXRef.se, ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive, ProbeSetXRef.h2
+ FROM
+ ProbeSet, ProbeSetXRef
+ WHERE
+ ProbeSetXRef.ProbeSetFreezeId = '{0}' AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id
+ ORDER BY
+ ProbeSet.Id
+ """
+
+ field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"]
+ elif data_type == "Geno":
+ query = """
+ SELECT
+ Geno.Id, Geno.Name, Geno.Marker_Name, Geno.Chr, Geno.Mb, Geno.Sequence, Geno.Source
+ FROM
+ Geno, GenoXRef
+ WHERE
+ GenoXRef.GenoFreezeId = '{0}' AND
+ GenoXRef.GenoId = Geno.Id
+ ORDER BY
+ Geno.Id
+ """
+
+ field_list = ["Id", "Name", "Marker_Name", "Chr", "Mb", "Sequence", "Source"]
+ else:
+ query = """
+ SELECT
+ PublishXRef.Id, PublishXRef.PhenotypeId, PublishXRef.PublicationId, PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive, PublishXRef.Sequence
+ FROM
+ PublishXRef
+ WHERE
+ PublishXRef.InbredSetId = {0}
+ ORDER BY
+ PublishXRef.Id
+ """
+
+ field_list = ["Id", "PhenotypeId", "PublicationId", "Locus", "LRS", "Additive", "Sequence"]
+
+ if file_format == "json":
+ filename = dataset_name + "_traits.json"
+
+ final_query = query.format(dataset_id)
+
+ result_list = []
+ for result in g.db.execute(final_query).fetchall():
+ trait_dict = {}
+ for i, field in enumerate(field_list):
+ if result[i]:
+ trait_dict[field] = result[i]
+ result_list.append(trait_dict)
+
+ return flask.jsonify(result_list)
+ elif file_format == "csv":
+ filename = dataset_name + "_traits.csv"
+
+ results_list = []
+ header_list = []
+ header_list += field_list
+ results_list.append(header_list)
+
+ final_query = query.format(dataset_id)
+ for result in g.db.execute(final_query).fetchall():
+ results_list.append(result)
+
+ si = StringIO.StringIO()
+ csv_writer = csv.writer(si)
+ csv_writer.writerows(results_list)
+ output = make_response(si.getvalue())
+ output.headers["Content-Disposition"] = "attachment; filename=" + filename
+ output.headers["Content-type"] = "text/csv"
+ return output
+ else:
+ return return_error(code=400, source=request.url_rule.rule, title="Invalid Output Format", details="Current formats available are JSON and CSV, with CSV as default")
+ else:
+ return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
@app.route("/api/v_{}/sample_data/<path:dataset_name>".format(version))
@app.route("/api/v_{}/sample_data/<path:dataset_name>.<path:file_format>".format(version))
@@ -528,8 +628,6 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"):
PublishXRef.Id = '{0}' AND
PublishXRef.InbredSetId = '{1}'
""".format(trait_name, group_id)
-
- logger.debug("QUERY:", pheno_query)
pheno_results = g.db.execute(pheno_query)
@@ -612,13 +710,6 @@ def get_genotypes(group_name, file_format="csv"):
return output
-@app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=('GET',))
-@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=('GET',))
-def get_traits(dataset_name, file_format = "json"):
- #ZS: Need to check about the "start" and "stop" stuff since it seems to just limit the number of results to stop - start + 1 in Pjotr's elixir code
-
- NotImplemented
-
def return_error(code, source, title, details):
json_ob = {"errors": [
{
@@ -652,7 +743,7 @@ def get_dataset_trait_ids(dataset_name):
dataset_id = results[0][2]
return trait_ids, trait_names, data_type, dataset_id
- elif "Publish" in dataset_name:
+ elif "Publish" in dataset_name or get_group_id(dataset_name):
data_type = "Publish"
dataset_name = dataset_name.replace("Publish", "")
dataset_id = get_group_id(dataset_name)
@@ -743,7 +834,10 @@ def get_group_id_from_dataset(dataset_name):
result = g.db.execute(query).fetchone()
- return result[0]
+ if len(result) > 0:
+ return result[0]
+ else:
+ return None
def get_group_id(group_name):
query = """
diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
index 14b0e056..d52cb100 100644
--- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
@@ -161,8 +161,14 @@
intercept_line['samples_all'] = [[first_x, last_x], [first_value, last_value]]
}
+ if (Math.max(y_values['samples_all']) - Math.min(y_values['samples_all']) < 6){
+ tick_digits = '.1f'
+ } else {
+ tick_digits = 'f'
+ }
+
var layout = {
- title: 'Quantile-Quantile Plot<a href="https://en.wikipedia.org/wiki/Q-Q_plot"><sup>?</sup></a>',
+ title: js_data.trait_id,
margin: {
l: 65,
r: 30,
@@ -196,7 +202,8 @@
ticklen: 4,
tickfont: {
size: 16
- }
+ },
+ tickformat: tick_digits
},
hovermode: "closest"
}
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 31f59a13..167fafcb 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -922,6 +922,11 @@ get_bar_range = function(sample_list){
}
root.chart_range = get_bar_range(sample_lists[0])
+if (root.chart_range[1] - root.chart_range[0] < 4){
+ tick_digits = '.1f'
+} else {
+ tick_digits = 'f'
+}
if (js_data.num_values < 256) {
bar_chart_width = 25 * get_sample_vals(sample_lists[0]).length
@@ -930,6 +935,7 @@ if (js_data.num_values < 256) {
bottom_margin = get_bar_bottom_margin(sample_lists[0])
root.bar_layout = {
+ title: js_data.trait_id,
xaxis: {
titlefont: {
size: 16
@@ -941,6 +947,7 @@ if (js_data.num_values < 256) {
}
},
yaxis: {
+ title: js_data.unit_type,
range: root.chart_range,
titlefont: {
size: 16
@@ -949,12 +956,13 @@ if (js_data.num_values < 256) {
ticklen: 4,
tickfont: {
size: 16
- }
+ },
+ tickformat: tick_digits
},
width: bar_chart_width,
height: 600,
margin: {
- l: 50,
+ l: 55,
r: 30,
t: 30,
b: bottom_margin
@@ -979,7 +987,7 @@ var hist_trace = {
root.histogram_data = [hist_trace];
root.histogram_layout = {
bargap: 0.05,
- title: "Sample Values",
+ title: js_data.trait_id,
xaxis: {
autorange: true,
title: "Value",
@@ -1025,6 +1033,7 @@ $('.histogram_samples_group').change(function() {
});
root.box_layout = {
+ title: js_data.trait_id,
xaxis: {
showline: true,
tickfont: {
@@ -1032,12 +1041,14 @@ root.box_layout = {
},
},
yaxis: {
+ title: js_data.unit_type,
autorange: true,
showline: true,
ticklen: 4,
tickfont: {
size: 16
- }
+ },
+ tickformat: tick_digits
},
margin: {
l: 50,
@@ -1136,7 +1147,7 @@ $('.box_plot_tab').click(function() {
// Violin Plot
root.violin_layout = {
- title: "Violin Plot",
+ title: js_data.trait_id,
xaxis: {
showline: true,
tickfont: {
@@ -1144,12 +1155,14 @@ root.violin_layout = {
}
},
yaxis: {
+ title: js_data.unit_type,
autorange: true,
showline: true,
ticklen: 4,
tickfont: {
size: 16
},
+ tickformat: tick_digits,
zeroline: false
},
margin: {
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 6ab7d635..378f91b1 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -271,7 +271,7 @@
'data': null,
'orderDataType': "dom-checkbox",
'render': function(data, type, row, meta) {
- return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="" checked="checked">'
+ return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="">'
}
},
{
@@ -403,7 +403,7 @@
'data': null,
'orderDataType': "dom-checkbox",
'render': function(data, type, row, meta) {
- return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="" checked="checked">'
+ return '<input type="checkbox" name="searchResult" style="min-height: 20px;" class="checkbox edit_sample_checkbox" value="">'
}
},
{
@@ -491,7 +491,20 @@
} );
{% endif %}
- $('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'yellow')
+ $('#samples_primary, #samples_other').find("tr.outlier").css('background-color', 'orange')
+
+ $('.edit_sample_checkbox:checkbox').change(function() {
+ if ($(this).is(":checked")) {
+ if (!$(this).closest('tr').hasClass('selected')) {
+ $(this).closest('tr').addClass('selected')
+ }
+ }
+ else {
+ if ($(this).closest('tr').hasClass('selected')) {
+ $(this).closest('tr').removeClass('selected')
+ }
+ }
+ });
var slider = document.getElementById('p_range_slider');
noUiSlider.create(slider, {
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index ef233333..8ceec4fa 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -73,6 +73,7 @@
</select>
</div>
</div>
+ {% if dataset.type != "Publish" %}
<div class="form-group">
<label class="col-xs-2 control-label">Min Expr</label>
<div class="col-xs-3 controls">
@@ -89,6 +90,7 @@
<br>
</div>
</div>
+ {% endif %}
<div class="form-group">
<label class="col-xs-2 control-label">Range</label>
<div class="col-xs-5 controls">
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 667d557c..fec141dc 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -1,6 +1,6 @@
<div>
<div style="padding-bottom: 10px;">
- <input type="button" class="btn btn-primary reset" value="Reset">
+ <input type="button" class="btn btn-success reset" value="Reset">
<span class="input-append">
<input type="button" class="btn btn-default export" value="Export">
<select class="select optional span2 export_format">
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 94b3fda3..fbdebcd0 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -16,7 +16,7 @@
{{ sample_group_types['samples_other'] }}
</option>
</select>
- <input type="button" id="block_by_index" class="btn" value="Block">
+ <input type="button" id="block_by_index" class="btn btn-danger" value="Block">
</div>
<div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
@@ -38,7 +38,7 @@
<div>
<input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
<input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
- <input type="button" class="btn btn-primary reset" value="Reset">
+ <input type="button" class="btn btn-success reset" value="Reset">
<span class="input-append">
<input type="button" class="btn btn-default export" value="Export">
<select class="select optional span2 export_format">
@@ -48,9 +48,11 @@
</span>
<br>
<div style="margin-top:10px;">
- <input type="button" id="normalize" class="btn btn-default" value="Normalize">
+ <input type="button" id="normalize" class="btn btn-success" value="Normalize">
<select id="norm_method" class="select optional span2">
+ {% if negative_vals_exist == "false" %}
<option value="log2">Log2</option>
+ {% endif %}
<option value="zscore">Z-score</option>
<option value="qnorm">Quantile</option>
<option value="sqrt">Square Root</option>