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-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py43
-rw-r--r--wqflask/wqflask/do_search.py1
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js176
-rw-r--r--wqflask/wqflask/views.py66
4 files changed, 180 insertions, 106 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 9b048346..12f76b7d 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -236,28 +236,29 @@ class CorrelationResults(object):
self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
elif self.corr_type == "sample":
- if self.dataset.type == "ProbeSet" and cache_available:
- dataset_file = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r')
-
- #XZ, 01/08/2009: read the first line
- line = dataset_file.readline()
- dataset_strains = webqtlUtil.readLineCSV(line)[1:]
-
- self.this_trait_vals = []
- for item in dataset_strains:
- if item in self.sample_data:
- self.this_trait_vals.append(self.sample_data[item])
- else:
- self.this_trait_vals.append("None")
- num_overlap = len(self.this_trait_vals)
- logger.debug("DOING PARALLEL")
- self.do_parallel_correlation(db_filename, num_overlap)
- else:
- for trait, values in self.target_dataset.trait_data.iteritems():
- self.get_sample_r_and_p_values(trait, values)
+ #ZS: Commented out since parallel correlation has issues with gunicorn
+ # if self.dataset.type == "ProbeSet" and cache_available:
+ # dataset_file = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r')
+
+ ##XZ, 01/08/2009: read the first line
+ # line = dataset_file.readline()
+ # dataset_strains = webqtlUtil.readLineCSV(line)[1:]
+
+ # self.this_trait_vals = []
+ # for item in dataset_strains:
+ # if item in self.sample_data:
+ # self.this_trait_vals.append(self.sample_data[item])
+ # else:
+ # self.this_trait_vals.append("None")
+ # num_overlap = len(self.this_trait_vals)
+ # logger.debug("DOING PARALLEL")
+ # self.do_parallel_correlation(db_filename, num_overlap)
+ # else:
+ for trait, values in self.target_dataset.trait_data.iteritems():
+ self.get_sample_r_and_p_values(trait, values)
- self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(),
- key=lambda t: -abs(t[1][0])))
+ self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(),
+ key=lambda t: -abs(t[1][0])))
if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index e1df1e63..17625474 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -989,3 +989,4 @@ if __name__ == "__main__":
#results = GoSearch("0045202", dataset, cursor, db_conn).run()
logger.debug("results are:", pf(results))
+ db_conn.close()
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index df10c060..117d8f12 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -250,15 +250,29 @@
};
redraw_box_plot = function() {
- var x;
- var _i, _len, _ref, data;
- _ref = _.values(root.selected_samples[root.stats_group]);
- trait_vals = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- x = _ref[_i];
- trait_vals.push(x.value);
+ var y_value_list = []
+ for (var sample_group in root.selected_samples){
+ var trait_sample_data = _.values(root.selected_samples[sample_group])
+ var trait_vals = [];
+ for (i = 0, len = trait_sample_data.length; i < len; i++) {
+ this_sample_data = trait_sample_data[i];
+ trait_vals.push(this_sample_data.value);
+ }
+ y_value_list.push(trait_vals)
+ }
+
+ if (Object.keys(js_data.sample_group_types).length > 1) {
+ var update = {
+ y: y_value_list
+ }
+ console.log("REDRAW UPDATE:", update)
+ Plotly.restyle('box_plot', update, [0, 1, 2])
+ } else {
+ var update = {
+ y: y_value_list
+ }
+ Plotly.restyle('box_plot', update)
}
- Plotly.restyle('box_plot', 'y', [trait_vals])
}
redraw_prob_plot = function() {
@@ -640,6 +654,108 @@
};
root.stats_group = 'samples_primary';
+
+ if (Object.keys(js_data.sample_group_types).length > 1) {
+ full_sample_lists = [sample_lists[0], sample_lists[1], sample_lists[0].concat(sample_lists[1])]
+ sample_group_list = [js_data.sample_group_types['samples_primary'], js_data.sample_group_types['samples_other'], js_data.sample_group_types['samples_all']]
+ } else {
+ full_sample_lists = [sample_lists[0]]
+ sample_group_list = [js_data.sample_group_types['samples_primary']]
+ }
+
+ if (full_sample_lists.length > 1) {
+ var box_layout = {
+ width: 1200,
+ height: 500,
+ margin: {
+ l: 50,
+ r: 30,
+ t: 30,
+ b: 80
+ }
+ };
+ var trace1 = {
+ y: get_sample_vals(full_sample_lists[0]),
+ type: 'box',
+ name: sample_group_list[0],
+ boxpoints: 'all',
+ jitter: 0.5,
+ whiskerwidth: 0.2,
+ fillcolor: 'cls',
+ marker: {
+ size: 2
+ },
+ line: {
+ width: 1
+ }
+ }
+ var trace2 = {
+ y: get_sample_vals(full_sample_lists[1]),
+ type: 'box',
+ name: sample_group_list[1],
+ boxpoints: 'all',
+ jitter: 0.5,
+ whiskerwidth: 0.2,
+ fillcolor: 'cls',
+ marker: {
+ size: 2
+ },
+ line: {
+ width: 1
+ }
+ }
+ var trace3 = {
+ y: get_sample_vals(full_sample_lists[2]),
+ type: 'box',
+ name: sample_group_list[2],
+ boxpoints: 'all',
+ jitter: 0.5,
+ whiskerwidth: 0.2,
+ fillcolor: 'cls',
+ marker: {
+ size: 2
+ },
+ line: {
+ width: 1
+ }
+ }
+ box_data = [trace1, trace2, trace3]
+ } else {
+ var box_layout = {
+ width: 500,
+ height: 500,
+ margin: {
+ l: 50,
+ r: 30,
+ t: 30,
+ b: 80
+ }
+ };
+ box_data = [
+ {
+ type: 'box',
+ y: get_sample_vals(full_sample_lists[0]),
+ name: sample_group_list[0],
+ boxpoints: 'all',
+ jitter: 0.5,
+ whiskerwidth: 0.2,
+ fillcolor: 'cls',
+ marker: {
+ size: 2
+ },
+ line: {
+ width: 1
+ }
+ }
+ ]
+ }
+
+ obj = {
+ data: box_data,
+ layout: box_layout
+ }
+ Plotly.newPlot('box_plot', obj);
+
// Histogram
var hist_trace = {
x: get_sample_vals(sample_lists[0]),
@@ -686,50 +802,6 @@
root.bar_layout = layout
Plotly.newPlot('bar_chart', root.bar_data, layout)
- if (Object.keys(js_data.sample_group_types).length > 1) {
- full_sample_lists = [sample_lists[0], sample_lists[1], sample_lists[0].concat(sample_lists[1])]
- sample_group_list = [js_data.sample_group_types['samples_primary'], js_data.sample_group_types['samples_other'], js_data.sample_group_types['samples_all']]
- } else {
- full_sample_lists = [sample_lists[0]]
- sample_group_list = [js_data.sample_group_types['samples_primary']]
- }
-
- data = []
- for ( var i = 0; i < full_sample_lists.length; i ++ ) {
- var box_trace = {
- type: 'box',
- y: get_sample_vals(full_sample_lists[i]),
- name: sample_group_list[i],
- boxpoints: 'all',
- jitter: 0.5,
- whiskerwidth: 0.2,
- fillcolor: 'cls',
- marker: {
- size: 2
- },
- line: {
- width: 1
- }
- };
- data.push(box_trace)
- };
- layout = {
- title: 'Box Plot',
- yaxis: {
- autorange: true,
- showgrid: true,
- zeroline: true
- },
- margin: {
- l: 50,
- r: 30,
- t: 80,
- b: 80
- }
- };
-
- Plotly.newPlot('box_plot', data, layout);
-
$('.histogram_samples_group').val(root.stats_group);
$('.histogram_samples_group').change(function() {
root.stats_group = $(this).val();
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 17a2d762..998e5302 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -123,7 +123,7 @@ def handle_bad_request(e):
@app.route("/")
def index_page():
logger.info("Sending index_page")
- logger.error(request.url)
+ logger.debug(request.url)
params = request.args
if 'import_collections' in params:
import_collections = params['import_collections']
@@ -141,7 +141,7 @@ def index_page():
def tmp_page(img_path):
logger.info("In tmp_page")
logger.info("img_path:", img_path)
- logger.error(request.url)
+ logger.debug(request.url)
initial_start_vars = request.form
logger.info("initial_start_vars:", initial_start_vars)
imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb')
@@ -174,7 +174,7 @@ def twitter(filename):
@app.route("/search", methods=('GET',))
def search_page():
logger.info("in search_page")
- logger.error(request.url)
+ logger.debug(request.url)
if 'info_database' in request.args:
logger.info("Going to sharing_info_page")
template_vars = sharing_info_page()
@@ -213,7 +213,7 @@ def search_page():
@app.route("/gsearch", methods=('GET',))
def gsearchact():
- logger.error(request.url)
+ logger.debug(request.url)
result = gsearch.GSearch(request.args).__dict__
type = request.args['type']
if type == "gene":
@@ -224,7 +224,7 @@ def gsearchact():
@app.route("/gsearch_updating", methods=('POST',))
def gsearch_updating():
logger.info("REQUEST ARGS:", request.values)
- logger.error(request.url)
+ logger.debug(request.url)
result = update_search_results.GSearch(request.args).__dict__
return result['results']
# type = request.args['type']
@@ -235,31 +235,31 @@ def gsearch_updating():
@app.route("/docedit")
def docedit():
- logger.error(request.url)
+ logger.debug(request.url)
doc = docs.Docs(request.args['entry'])
return render_template("docedit.html", **doc.__dict__)
@app.route('/generated/<filename>')
def generated_file(filename):
- logger.error(request.url)
+ logger.debug(request.url)
return send_from_directory(GENERATED_IMAGE_DIR,filename)
@app.route("/help")
def help():
- logger.error(request.url)
+ logger.debug(request.url)
doc = docs.Docs("help")
return render_template("docs.html", **doc.__dict__)
@app.route("/wgcna_setup", methods=('POST',))
def wcgna_setup():
logger.info("In wgcna, request.form is:", request.form) # We are going to get additional user input for the analysis
- logger.error(request.url)
+ logger.debug(request.url)
return render_template("wgcna_setup.html", **request.form) # Display them using the template
@app.route("/wgcna_results", methods=('POST',))
def wcgna_results():
logger.info("In wgcna, request.form is:", request.form)
- logger.error(request.url)
+ logger.debug(request.url)
wgcna = wgcna_analysis.WGCNA() # Start R, load the package and pointers and create the analysis
wgcnaA = wgcna.run_analysis(request.form) # Start the analysis, a wgcnaA object should be a separate long running thread
result = wgcna.process_results(wgcnaA) # After the analysis is finished store the result
@@ -268,13 +268,13 @@ def wcgna_results():
@app.route("/ctl_setup", methods=('POST',))
def ctl_setup():
logger.info("In ctl, request.form is:", request.form) # We are going to get additional user input for the analysis
- logger.error(request.url)
+ logger.debug(request.url)
return render_template("ctl_setup.html", **request.form) # Display them using the template
@app.route("/ctl_results", methods=('POST',))
def ctl_results():
logger.info("In ctl, request.form is:", request.form)
- logger.error(request.url)
+ logger.debug(request.url)
ctl = ctl_analysis.CTL() # Start R, load the package and pointers and create the analysis
ctlA = ctl.run_analysis(request.form) # Start the analysis, a ctlA object should be a separate long running thread
result = ctl.process_results(ctlA) # After the analysis is finished store the result
@@ -313,13 +313,13 @@ def environments():
@app.route("/submit_trait")
def submit_trait_form():
- logger.error(request.url)
+ logger.debug(request.url)
species_and_groups = get_species_groups()
return render_template("submit_trait.html", **{'species_and_groups' : species_and_groups, 'gn_server_url' : GN_SERVER_URL, 'version' : GN_VERSION})
@app.route("/create_temp_trait", methods=('POST',))
def create_temp_trait():
- logger.error(request.url)
+ logger.debug(request.url)
print("REQUEST.FORM:", request.form)
#template_vars = submit_trait.SubmitTrait(request.form)
@@ -332,7 +332,7 @@ def export_trait_excel():
"""Excel file consisting of the sample data from the trait data and analysis page"""
logger.info("In export_trait_excel")
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.debug(request.url)
sample_data = export_trait_data.export_sample_table(request.form)
logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
@@ -358,7 +358,7 @@ def export_trait_csv():
"""CSV file consisting of the sample data from the trait data and analysis page"""
logger.info("In export_trait_csv")
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.debug(request.url)
sample_data = export_trait_data.export_sample_table(request.form)
logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
@@ -379,7 +379,7 @@ def export_traits_csv():
"""CSV file consisting of the traits from the search result page"""
logger.info("In export_traits_csv")
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.debug(request.url)
csv_data = export_traits.export_search_results_csv(request.form)
return Response(csv_data,
@@ -389,7 +389,7 @@ def export_traits_csv():
@app.route('/export_perm_data', methods=('POST',))
def export_perm_data():
"""CSV file consisting of the permutation data for the mapping results"""
- logger.error(request.url)
+ logger.debug(request.url)
num_perm = float(request.form['num_perm'])
perm_data = json.loads(request.form['perm_results'])
@@ -412,7 +412,7 @@ def export_perm_data():
@app.route("/show_temp_trait", methods=('POST',))
def show_temp_trait_page():
- logger.error(request.url)
+ logger.debug(request.url)
template_vars = show_trait.ShowTrait(request.form)
#logger.info("js_data before dump:", template_vars.js_data)
template_vars.js_data = json.dumps(template_vars.js_data,
@@ -427,7 +427,7 @@ def show_temp_trait_page():
@app.route("/show_trait")
def show_trait_page():
- logger.error(request.url)
+ logger.debug(request.url)
template_vars = show_trait.ShowTrait(request.args)
#logger.info("js_data before dump:", template_vars.js_data)
template_vars.js_data = json.dumps(template_vars.js_data,
@@ -443,7 +443,7 @@ def show_trait_page():
@app.route("/heatmap", methods=('POST',))
def heatmap_page():
logger.info("In heatmap, request.form is:", pf(request.form))
- logger.error(request.url)
+ logger.debug(request.url)
start_vars = request.form
temp_uuid = uuid.uuid4()
@@ -493,7 +493,7 @@ def mapping_results_container_page():
@app.route("/loading", methods=('POST',))
def loading_page():
- logger.error(request.url)
+ logger.debug(request.url)
initial_start_vars = request.form
logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items())
#temp_uuid = initial_start_vars['temp_uuid']
@@ -552,7 +552,7 @@ def loading_page():
def marker_regression_page():
initial_start_vars = request.form
logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items())
- logger.error(request.url)
+ logger.debug(request.url)
temp_uuid = initial_start_vars['temp_uuid']
wanted = (
'trait_id',
@@ -678,7 +678,7 @@ def marker_regression_page():
@app.route("/export_mapping_results", methods = ('POST',))
def export_mapping_results():
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.debug(request.url)
file_path = request.form.get("results_path")
results_csv = open(file_path, "r").read()
response = Response(results_csv,
@@ -691,7 +691,7 @@ def export_mapping_results():
@app.route("/export", methods = ('POST',))
def export():
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.debug(request.url)
svg_xml = request.form.get("data", "Invalid data")
filename = request.form.get("filename", "manhattan_plot_snp")
response = Response(svg_xml, mimetype="image/svg+xml")
@@ -702,7 +702,7 @@ def export():
def export_pdf():
import cairosvg
logger.info("request.form:", request.form)
- logger.error(request.url)
+ logger.debug(request.url)
svg_xml = request.form.get("data", "Invalid data")
logger.info("svg_xml:", svg_xml)
filename = request.form.get("filename", "interval_map_pdf")
@@ -715,7 +715,7 @@ def export_pdf():
@app.route("/network_graph", methods=('POST',))
def network_graph_page():
logger.info("In network_graph, request.form is:", pf(request.form))
- logger.error(request.url)
+ logger.debug(request.url)
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
if traits[0] != "":
@@ -731,7 +731,7 @@ def network_graph_page():
@app.route("/corr_compute", methods=('POST',))
def corr_compute_page():
logger.info("In corr_compute, request.form is:", pf(request.form))
- logger.error(request.url)
+ logger.debug(request.url)
#fd = webqtlFormData.webqtlFormData(request.form)
template_vars = show_corr_results.CorrelationResults(request.form)
return render_template("correlation_page.html", **template_vars.__dict__)
@@ -739,7 +739,7 @@ def corr_compute_page():
@app.route("/corr_matrix", methods=('POST',))
def corr_matrix_page():
logger.info("In corr_matrix, request.form is:", pf(request.form))
- logger.error(request.url)
+ logger.debug(request.url)
start_vars = request.form
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -755,7 +755,7 @@ def corr_matrix_page():
@app.route("/corr_scatter_plot")
def corr_scatter_plot_page():
- logger.error(request.url)
+ logger.debug(request.url)
template_vars = corr_scatter_plot.CorrScatterPlot(request.args)
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
@@ -764,7 +764,7 @@ def corr_scatter_plot_page():
@app.route("/submit_bnw", methods=('POST',))
def submit_bnw():
- logger.error(request.url)
+ logger.debug(request.url)
template_vars = get_bnw_input(request.form)
return render_template("empty_collection.html", **{'tool':'Correlation Matrix'})
@@ -772,7 +772,7 @@ def submit_bnw():
def sharing_info_page():
"""Info page displayed when the user clicks the "Info" button next to the dataset selection"""
logger.info("In sharing_info_page")
- logger.error(request.url)
+ logger.debug(request.url)
fd = webqtlFormData.webqtlFormData(request.args)
template_vars = SharingInfoPage.SharingInfoPage(fd)
return template_vars
@@ -780,7 +780,7 @@ def sharing_info_page():
# Take this out or secure it before putting into production
@app.route("/get_temp_data")
def get_temp_data():
- logger.error(request.url)
+ logger.debug(request.url)
temp_uuid = request.args['key']
return flask.jsonify(temp_data.TempData(temp_uuid).get_all())