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-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py188
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py2
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js4
-rw-r--r--wqflask/wqflask/templates/correlation_page.html29
-rw-r--r--wqflask/wqflask/templates/loading_correlation.html24
-rw-r--r--wqflask/wqflask/templates/mapping_error.html14
-rw-r--r--wqflask/wqflask/templates/search_result_page.html4
-rw-r--r--wqflask/wqflask/templates/show_trait.html50
-rw-r--r--wqflask/wqflask/views.py95
9 files changed, 252 insertions, 158 deletions
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 73d985b8..7ee3ac01 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -242,99 +242,103 @@ class RunMapping(object):
else:
logger.debug("RUNNING NOTHING")
- if self.pair_scan == True:
- self.qtl_results = []
- highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
- for marker in results:
- if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
- if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
- highest_chr = marker['chr1']
- if 'lod_score' in marker.keys():
- self.qtl_results.append(marker)
-
- self.trimmed_markers = results
-
- for qtl in enumerate(self.qtl_results):
- self.json_data['chr1'].append(str(qtl['chr1']))
- self.json_data['chr2'].append(str(qtl['chr2']))
- self.json_data['Mb'].append(qtl['Mb'])
- self.json_data['markernames'].append(qtl['name'])
-
- self.js_data = dict(
- json_data = self.json_data,
- this_trait = self.this_trait.name,
- data_set = self.dataset.name,
- maf = self.maf,
- manhattan_plot = self.manhattan_plot,
- mapping_scale = self.mapping_scale,
- qtl_results = self.qtl_results
- )
-
+ self.no_results = False
+ if len(results) == 0:
+ self.no_results = True
else:
- self.qtl_results = []
- highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
- for marker in results:
- if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
- if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
- highest_chr = marker['chr']
- if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
- self.qtl_results.append(marker)
-
- with Bench("Exporting Results"):
- export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
-
- with Bench("Trimming Markers for Figure"):
- if len(self.qtl_results) > 30000:
- self.qtl_results = trim_markers_for_figure(self.qtl_results)
-
- with Bench("Trimming Markers for Table"):
- self.trimmed_markers = trim_markers_for_table(results)
-
- if self.mapping_method != "gemma":
- self.json_data['chr'] = []
- self.json_data['pos'] = []
- self.json_data['lod.hk'] = []
- self.json_data['markernames'] = []
-
- self.json_data['suggestive'] = self.suggestive
- self.json_data['significant'] = self.significant
-
- #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
- for index, qtl in enumerate(self.qtl_results):
- #if index<40:
- # logger.debug("lod score is:", qtl['lod_score'])
- if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
- #logger.debug("changing to X")
- self.json_data['chr'].append("X")
- else:
- self.json_data['chr'].append(str(qtl['chr']))
- self.json_data['pos'].append(qtl['Mb'])
- if 'lrs_value' in qtl.keys():
- self.json_data['lod.hk'].append(str(qtl['lrs_value']))
- else:
- self.json_data['lod.hk'].append(str(qtl['lod_score']))
- self.json_data['markernames'].append(qtl['name'])
-
- #Get chromosome lengths for drawing the interval map plot
- chromosome_mb_lengths = {}
- self.json_data['chrnames'] = []
- for key in self.species.chromosomes.chromosomes.keys():
- self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
- chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
-
- self.js_data = dict(
- result_score_type = self.score_type,
- json_data = self.json_data,
- this_trait = self.this_trait.name,
- data_set = self.dataset.name,
- maf = self.maf,
- manhattan_plot = self.manhattan_plot,
- mapping_scale = self.mapping_scale,
- chromosomes = chromosome_mb_lengths,
- qtl_results = self.qtl_results,
- num_perm = self.num_perm,
- perm_results = self.perm_output,
- )
+ if self.pair_scan == True:
+ self.qtl_results = []
+ highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
+ for marker in results:
+ if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
+ if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
+ highest_chr = marker['chr1']
+ if 'lod_score' in marker.keys():
+ self.qtl_results.append(marker)
+
+ self.trimmed_markers = results
+
+ for qtl in enumerate(self.qtl_results):
+ self.json_data['chr1'].append(str(qtl['chr1']))
+ self.json_data['chr2'].append(str(qtl['chr2']))
+ self.json_data['Mb'].append(qtl['Mb'])
+ self.json_data['markernames'].append(qtl['name'])
+
+ self.js_data = dict(
+ json_data = self.json_data,
+ this_trait = self.this_trait.name,
+ data_set = self.dataset.name,
+ maf = self.maf,
+ manhattan_plot = self.manhattan_plot,
+ mapping_scale = self.mapping_scale,
+ qtl_results = self.qtl_results
+ )
+
+ else:
+ self.qtl_results = []
+ highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
+ for marker in results:
+ if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
+ if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
+ highest_chr = marker['chr']
+ if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
+ self.qtl_results.append(marker)
+
+ with Bench("Exporting Results"):
+ export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
+
+ with Bench("Trimming Markers for Figure"):
+ if len(self.qtl_results) > 30000:
+ self.qtl_results = trim_markers_for_figure(self.qtl_results)
+
+ with Bench("Trimming Markers for Table"):
+ self.trimmed_markers = trim_markers_for_table(results)
+
+ if self.mapping_method != "gemma":
+ self.json_data['chr'] = []
+ self.json_data['pos'] = []
+ self.json_data['lod.hk'] = []
+ self.json_data['markernames'] = []
+
+ self.json_data['suggestive'] = self.suggestive
+ self.json_data['significant'] = self.significant
+
+ #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
+ for index, qtl in enumerate(self.qtl_results):
+ #if index<40:
+ # logger.debug("lod score is:", qtl['lod_score'])
+ if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y":
+ #logger.debug("changing to X")
+ self.json_data['chr'].append("X")
+ else:
+ self.json_data['chr'].append(str(qtl['chr']))
+ self.json_data['pos'].append(qtl['Mb'])
+ if 'lrs_value' in qtl.keys():
+ self.json_data['lod.hk'].append(str(qtl['lrs_value']))
+ else:
+ self.json_data['lod.hk'].append(str(qtl['lod_score']))
+ self.json_data['markernames'].append(qtl['name'])
+
+ #Get chromosome lengths for drawing the interval map plot
+ chromosome_mb_lengths = {}
+ self.json_data['chrnames'] = []
+ for key in self.species.chromosomes.chromosomes.keys():
+ self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
+ chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
+
+ self.js_data = dict(
+ result_score_type = self.score_type,
+ json_data = self.json_data,
+ this_trait = self.this_trait.name,
+ data_set = self.dataset.name,
+ maf = self.maf,
+ manhattan_plot = self.manhattan_plot,
+ mapping_scale = self.mapping_scale,
+ chromosomes = chromosome_mb_lengths,
+ qtl_results = self.qtl_results,
+ num_perm = self.num_perm,
+ perm_results = self.perm_output,
+ )
def run_rqtl_plink(self):
# os.chdir("") never do this inside a webserver!!
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 9b4470fe..4e4c7705 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -414,7 +414,7 @@ def get_table_widths(sample_groups, has_num_cases=False):
trait_table_width += 70
if has_num_cases:
trait_table_width += 30
- trait_table_width += len(sample_groups[0].attributes)*40
+ trait_table_width += len(sample_groups[0].attributes)*70
trait_table_width = str(trait_table_width) + "px"
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index bcb67527..f278b840 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -447,14 +447,14 @@ submit_special = function(url) {
submit_corr = function(){
var url;
- url = "/corr_compute";
+ url = "/corr_loading";
return submit_special(url);
};
$(".corr_compute").on("click", (function(_this) {
return function() {
var url;
- url = "/corr_compute";
+ url = "/corr_loading";
return submit_special(url);
};
})(this));
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 76aa8d2d..76513c82 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -229,22 +229,6 @@
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script type="text/javascript" charset="utf-8">
- function getValue(x) {
- if (x.indexOf('input') >= 0) {
- if ($(x).val() == 'x') {
- return 0;
- }
- else {
- return parseFloat($(x).val());
- }
- }
- else if (isNaN(x)) {
- return x;
- }
- return parseFloat(x);
- }
-
-
jQuery.fn.dataTableExt.oSort['numeric-html-asc'] = function(a,b) {
a = Math.abs(parseFloat($(a).text()));
b = Math.abs(parseFloat($(b).text()));
@@ -258,24 +242,19 @@
};
jQuery.fn.dataTableExt.oSort['cust-txt-asc'] = function (a, b) {
- var x = getValue(a);
- var y = getValue(b);
-
- if (x == 'N/A' || x == '') {
+ if (a == 'N/A' || a == '') {
return 1;
}
- else if (y == 'N/A' || y == '') {
+ else if (b == 'N/A' || b == '') {
return -1;
}
else {
- return ((x < y) ? -1 : ((x > y) ? 1 : 0));
+ return ((a < b) ? -1 : ((a > b) ? 1 : 0));
}
};
jQuery.fn.dataTableExt.oSort['cust-txt-desc'] = function (a, b) {
- var x = getValue(a);
- var y = getValue(b);
- return ((x < y) ? 1 : ((x > y) ? -1 : 0));
+ return ((a < b) ? 1 : ((a > b) ? -1 : 0));
};
diff --git a/wqflask/wqflask/templates/loading_correlation.html b/wqflask/wqflask/templates/loading_correlation.html
new file mode 100644
index 00000000..2017c3de
--- /dev/null
+++ b/wqflask/wqflask/templates/loading_correlation.html
@@ -0,0 +1,24 @@
+<title>Loading Correlation Results</title>
+<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
+<form method="post" action="/corr_compute" name="loading_form" id="loading_form" class="form-horizontal">
+ {% for key, value in start_vars.iteritems() %}
+ <input type="hidden" name="{{ key }}" value="{{ value }}">
+ {% endfor %}
+ <div class="container">
+ <div>
+ <div style="min-height: 80vh; display: flex; align-items: center;">
+ <div style="margin-bottom: 10px; left: 50%; margin-right: -50%; transform: translate(-50%, -50%); position: absolute;">
+ <h1>Loading&nbsp;Correlation&nbsp;Results...</h1>
+ </div>
+ <div class="progress center-block" style="margin-top: 5px; margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;">
+ <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div>
+ </div>
+ </div>
+ </div>
+ </div>
+</form>
+<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
+<script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
+<script type="text/javascript">
+$("#loading_form").submit();
+</script> \ No newline at end of file
diff --git a/wqflask/wqflask/templates/mapping_error.html b/wqflask/wqflask/templates/mapping_error.html
new file mode 100644
index 00000000..b73a2c31
--- /dev/null
+++ b/wqflask/wqflask/templates/mapping_error.html
@@ -0,0 +1,14 @@
+{% extends "base.html" %}
+{% block title %}Error{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ {{ header("An error occurred during mapping") }}
+
+ <div class="container">
+ <p>There is likely an issue with the genotype file associated with this group/RISet. Please contact Zach Sloan (zachary.a.sloan@gmail.com) or Arthur Centeno (acenteno@gmail.com) about the data set in question.</p>
+ </div>
+
+
+<!-- End of body -->
+
+{% endblock %}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 31a5b94e..5f529edb 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -224,7 +224,7 @@
}
$('td', row).eq(4).attr('title', $('td', row).eq(4).text());
$('td', row).eq(4).attr('data-export', $('td', row).eq(4).text());
- $('td', row).slice(6,10).attr("align", "right");
+ $('td', row).slice(5,10).attr("align", "right");
$('td', row).eq(5).attr('data-export', $('td', row).eq(5).text());
$('td', row).eq(6).attr('data-export', $('td', row).eq(6).text());
$('td', row).eq(7).attr('data-export', $('td', row).eq(7).text());
@@ -282,6 +282,7 @@
{
'title': "Location",
'type': "natural",
+ 'width': "140px",
'data': "location"
},
{
@@ -299,6 +300,7 @@
{
'title': "Max LRS Location",
'type': "natural",
+ 'width': "140px",
'data': "lrs_location"
},
{
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 9d2cb7ed..d7d85741 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -161,12 +161,42 @@
} );
};
+ function getValue(x) {
+ if (x == 'x') {
+ return "x";
+ }
+ else {
+ return parseFloat(x);
+ }
+ }
+
$.fn.dataTable.ext.order['dom-input'] = function (settings, col) {
return this.api().column(col, { order: 'index' }).nodes().map(function (td, i) {
return $('input', td).val();
});
}
+ $.fn.dataTableExt.oSort['cust-txt-asc'] = function (a, b) {
+ var x = getValue(a);
+ var y = getValue(b);
+
+ if (x == 'x' || x == '') {
+ return 1;
+ }
+ else if (y == 'x' || y == '') {
+ return -1;
+ }
+ else {
+ return ((x < y) ? -1 : ((x > y) ? 1 : 0));
+ }
+ };
+
+ $.fn.dataTableExt.oSort['cust-txt-desc'] = function (a, b) {
+ var x = getValue(a);
+ var y = getValue(b);
+ return ((x < y) ? 1 : ((x > y) ? -1 : 0));
+ };
+
$(document).ready( function () {
$('.panel-heading').click(function () {
if ($(this).hasClass('collapsed')){
@@ -257,12 +287,13 @@
{
'title': "Value",
'orderDataType': "dom-input",
+ 'type': "cust-txt",
'data': null,
'render': function(data, type, row, meta) {
if (data.value == null) {
return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
} else {
- return '<input type="text" data-value="' + data.value + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value + '" size=6 maxlength=6>'
+ return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
}
}
}{% if sample_groups[0].se_exists() %},
@@ -277,20 +308,21 @@
{
'title': "SE",
'orderDataType': "dom-input",
+ 'type': "cust-txt",
'data': null,
'render': function(data, type, row, meta) {
if (data.variance == null) {
return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
} else {
- return '<input type="text" data-value="' + data.variance + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance + '" size=6 maxlength=6>'
+ return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
}
}
}{% endif %}{% if has_num_cases %},
{
'title': "N",
- 'type': "natural",
+ 'orderDataType': "dom-input",
+ 'type': "cust-txt",
'data': null,
- 'orderDataType': "cust-txt",
'render': function(data, type, row, meta) {
if (data.num_cases == null) {
return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
@@ -387,12 +419,13 @@
{
'title': "Value",
'orderDataType': "dom-input",
+ 'type': "cust-txt",
'data': null,
'render': function(data, type, row, meta) {
if (data.value == null) {
return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
} else {
- return '<input type="text" data-value="' + data.value + '" data-qnorm="' + js_data['qnorm_values'][1][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value + '" size=6 maxlength=6>'
+ return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][1][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
}
}
}{% if sample_groups[1].se_exists() %},
@@ -407,20 +440,21 @@
{
'title': "SE",
'orderDataType': "dom-input",
+ 'type': "cust-txt",
'data': null,
'render': function(data, type, row, meta) {
if (data.variance == null) {
return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
} else {
- return '<input type="text" data-value="' + data.variance + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance + '" size=6 maxlength=6>'
+ return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
}
}
}{% endif %}{% if has_num_cases %},
{
'title': "N",
- 'type': "natural",
+ 'orderDataType': "dom-input",
+ 'type': "cust-txt",
'data': null,
- 'orderDataType': "cust-txt",
'render': function(data, type, row, meta) {
if (data.num_cases == null) {
return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index cd2e047b..0b0871b1 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -684,36 +684,39 @@ def mapping_results_page():
with Bench("Total time in RunMapping"):
template_vars = run_mapping.RunMapping(start_vars, temp_uuid)
- if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
- template_vars.js_data = json.dumps(template_vars.js_data,
- default=json_default_handler,
- indent=" ")
-
- result = template_vars.__dict__
-
- if result['pair_scan']:
- with Bench("Rendering template"):
- img_path = result['pair_scan_filename']
- logger.info("img_path:", img_path)
- initial_start_vars = request.form
- logger.info("initial_start_vars:", initial_start_vars)
- imgfile = open(TEMPDIR + img_path, 'rb')
- imgdata = imgfile.read()
- imgB64 = imgdata.encode("base64")
- bytesarray = array.array('B', imgB64)
- result['pair_scan_array'] = bytesarray
- rendered_template = render_template("pair_scan_results.html", **result)
+ if template_vars.no_results:
+ rendered_template = render_template("mapping_error.html")
else:
- gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
- #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
- #logger.info("pickled result length:", len(pickled_result))
- #Redis.set(key, pickled_result)
- #Redis.expire(key, 1*60)
-
- with Bench("Rendering template"):
- if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
- gn1_template_vars.pop('qtlresults', None)
- rendered_template = render_template("mapping_results.html", **gn1_template_vars)
+ if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
+ template_vars.js_data = json.dumps(template_vars.js_data,
+ default=json_default_handler,
+ indent=" ")
+
+ result = template_vars.__dict__
+
+ if result['pair_scan']:
+ with Bench("Rendering template"):
+ img_path = result['pair_scan_filename']
+ logger.info("img_path:", img_path)
+ initial_start_vars = request.form
+ logger.info("initial_start_vars:", initial_start_vars)
+ imgfile = open(TEMPDIR + img_path, 'rb')
+ imgdata = imgfile.read()
+ imgB64 = imgdata.encode("base64")
+ bytesarray = array.array('B', imgB64)
+ result['pair_scan_array'] = bytesarray
+ rendered_template = render_template("pair_scan_results.html", **result)
+ else:
+ gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
+ #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
+ #logger.info("pickled result length:", len(pickled_result))
+ #Redis.set(key, pickled_result)
+ #Redis.expire(key, 1*60)
+
+ with Bench("Rendering template"):
+ if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
+ gn1_template_vars.pop('qtlresults', None)
+ rendered_template = render_template("mapping_results.html", **gn1_template_vars)
return rendered_template
@@ -769,6 +772,40 @@ def network_graph_page():
else:
return render_template("empty_collection.html", **{'tool':'Network Graph'})
+@app.route("/corr_loading", methods=('POST',))
+def corr_loading_page():
+ logger.info(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']
+ wanted = (
+ 'corr_type',
+ 'trait_id',
+ 'dataset',
+ 'group',
+ 'corr_sample_method',
+ 'corr_samples_group',
+ 'corr_dataset',
+ 'min_expr',
+ 'corr_return_results',
+ 'loc_chr',
+ 'min_loc_mb',
+ 'max_loc_mb',
+ 'p_range_lower',
+ 'p_range_upper'
+ )
+ start_vars_container = {}
+ start_vars = {}
+ for key, value in initial_start_vars.iteritems():
+ if key in wanted or key.startswith(('value:')):
+ start_vars[key] = value
+
+ start_vars_container['start_vars'] = start_vars
+ rendered_template = render_template("loading_correlation.html", **start_vars_container)
+
+ return rendered_template
+
+
@app.route("/corr_compute", methods=('POST',))
def corr_compute_page():
logger.info("In corr_compute, request.form is:", pf(request.form))
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 04:04:52 +0000