Merge branch 'testing' into build/python3-migration

4 files changed, 142 insertions, 23 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 07704e4c..295f5c48 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -152,7 +152,8 @@ Publish or ProbeSet. E.g.
 
         if t in ['pheno', 'other_pheno']:
             name = name.replace("Publish", "")
-        if bool(len(g.db.execute(sql_query_mapping[t].format(name)))):
+
+        if bool(len(g.db.execute(sql_query_mapping[t].format(name)).fetchone())):
             self.datasets[name] = dataset_name_mapping[t]
             self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
             return True
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 189c1985..78b1f7b0 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -37,6 +37,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
             opt_list.append("--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt")
         if control_marker != "" and do_control == "true":
             opt_list.append("-c " + control_marker)
+        if manhattan_plot != True:
+            opt_list.append("--interval 1")
 
         reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'),
                                                                                                                 genofile_name,
@@ -85,9 +87,17 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
     p_values = []
     marker_obs = []
 
+    only_cm = False
+    only_mb = False
+
     with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, gwa_filename)) as output_file:
         for line in output_file:
             if line.startswith("ID\t"):
+                if len(line.split("\t")) < 8:
+                    if 'cM' in line.split("\t"):
+                        only_cm = True
+                    else:
+                        only_mb = True
                 continue
             else:
                 marker = {}
@@ -96,16 +106,30 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
                     marker['chr'] = int(line.split("\t")[2])
                 except:
                     marker['chr'] = line.split("\t")[2]
-                marker['cM'] = float(line.split("\t")[3])
-                if float(line.split("\t")[4]) > 1000:
-                    marker['Mb'] = float(line.split("\t")[4])/1000000
+                if only_cm or only_mb:
+                    if only_cm:
+                        marker['cM'] = float(line.split("\t")[3])
+                    else:
+                        if float(line.split("\t")[3]) > 1000:
+                            marker['Mb'] = float(line.split("\t")[3])/1000000
+                        else:
+                            marker['Mb'] = float(line.split("\t")[3])
+                    if float(line.split("\t")[6]) != 1:
+                        marker['p_value'] = float(line.split("\t")[6])
+                    marker['lrs_value'] = float(line.split("\t")[4])
+                    marker['lod_score'] = marker['lrs_value'] / 4.61
+                    marker['additive'] = float(line.split("\t")[5])
                 else:
-                    marker['Mb'] = float(line.split("\t")[4])
-                if float(line.split("\t")[7]) != 1:
-                    marker['p_value'] = float(line.split("\t")[7])
-                marker['lrs_value'] = float(line.split("\t")[5])
-                marker['lod_score'] = marker['lrs_value'] / 4.61
-                marker['additive'] = float(line.split("\t")[6])
+                    marker['cM'] = float(line.split("\t")[3])
+                    if float(line.split("\t")[4]) > 1000:
+                        marker['Mb'] = float(line.split("\t")[4])/1000000
+                    else:
+                        marker['Mb'] = float(line.split("\t")[4])
+                    if float(line.split("\t")[7]) != 1:
+                        marker['p_value'] = float(line.split("\t")[7])
+                    marker['lrs_value'] = float(line.split("\t")[5])
+                    marker['lod_score'] = marker['lrs_value'] / 4.61
+                    marker['additive'] = float(line.split("\t")[6])
                 marker_obs.append(marker)
 
     #ZS: Results have to be reordered because the new reaper returns results sorted alphabetically by chr for some reason, resulting in chr 1 being followed by 10, etc
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 7ae84b16..c606cf53 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -372,10 +372,15 @@ class RunMapping(object):
               self.annotations_for_browser = []
               highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
               for marker in results:
+                  if 'Mb' in marker:
+                      this_ps = marker['Mb']*1000000
+                  else:
+                      this_ps = marker['cM']*1000000
+
                   browser_marker = dict(
                       chr = str(marker['chr']),
                       rs  = marker['name'],
-                      ps  = marker['Mb']*1000000,
+                      ps  = this_ps,
                       url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno"
                   )
 
@@ -384,7 +389,7 @@ class RunMapping(object):
                           name = str(marker['name']),
                           chr = str(marker['chr']),
                           rs  = marker['name'],
-                          pos  = marker['Mb']*1000000,
+                          pos  = this_ps,
                           url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno"
                       )
                   else:
@@ -392,7 +397,7 @@ class RunMapping(object):
                           name = str(marker['name']),
                           chr = str(marker['chr']),
                           rs  = marker['name'],
-                          pos  = marker['Mb']*1000000
+                          pos  = this_ps
                       )
                   #if 'p_value' in marker:
                   #    logger.debug("P EXISTS:", marker['p_value'])
@@ -531,10 +536,10 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
         output_file.write("\n")
         output_file.write("Name,Chr,")
         if score_type.lower() == "-log(p)":
-            score_type = "'-log(p)"
-        if mapping_scale == "physic":
+            score_type = "-log(p)"
+        if 'Mb' in markers[0]:
             output_file.write("Mb," + score_type)
-        else:
+        if 'cM' in markers[0]:
             output_file.write("Cm," + score_type)
         if "additive" in list(markers[0].keys()):
             output_file.write(",Additive")
@@ -542,8 +547,12 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
             output_file.write(",Dominance")
         output_file.write("\n")
         for i, marker in enumerate(markers):
-            output_file.write(marker['name'] + "," + str(marker['chr']) + "," + str(marker['Mb']) + ",")
-            if "lod_score" in list(marker.keys()):
+            output_file.write(marker['name'] + "," + str(marker['chr']) + ",")
+            if 'Mb' in marker:
+                output_file.write(str(marker['Mb']) + ",")
+            if 'cM' in marker:
+                output_file.write(str(marker['cM']) + ",")
+            if "lod_score" in marker.keys():
                 output_file.write(str(marker['lod_score']))
             else:
                 output_file.write(str(marker['lrs_value']))
@@ -667,16 +676,22 @@ def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results):
             except:
                 chr_as_num = 20
             if chr_as_num > this_chr or i == (len(qtl_results) - 1):
-                chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)})
-                this_chr = chr_as_num
-                highest_pos = 0
+                if i == (len(qtl_results) - 1):
+                    if mapping_method == "reaper":
+                        highest_pos = float(result['cM']) * 1000000
+                    else:
+                        highest_pos = float(result['Mb']) * 1000000
+                    chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)})
+                else:
+                    chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)})
+                    this_chr = chr_as_num
             else:
                 if mapping_method == "reaper":
                     if float(result['cM']) > highest_pos:
-                        highest_pos = float(result['cM'])
+                        highest_pos = float(result['cM']) * 1000000
                 else:
                     if float(result['Mb']) > highest_pos:
-                        highest_pos = float(result['Mb'])
+                        highest_pos = float(result['Mb']) * 1000000
 
     return chr_lengths
 
diff --git a/wqflask/wqflask/templates/admin/manage_user.html b/wqflask/wqflask/templates/admin/manage_user.html
new file mode 100644
index 00000000..7afe075f
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/manage_user.html
@@ -0,0 +1,79 @@
+{% extends "base.html" %}

+{% block title %}View and Edit Group{% endblock %}

+{% block css %}

+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />

+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">

+    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />

+{% endblock %}

+{% block content %}

+<!-- Start of body -->

+    <div class="container">

+        {% if 'full_name' in user_details %}

+        <div class="page-header">

+            <h1>User details for: {{ user_details.full_name }}</h1>

+        </div>

+        {% endif %}

+        <form id="user_form" action="/user/manage" method="POST">

+            <div class="row">

+                <div id="user_info_div" class="col-xs-8" style="margin-right: 30px; min-width: 800px; max-width: 1000px;">

+                    <div class="form-horizontal">

+                        <div class="form-group">

+                            <label for="email_address" style="text-align: left;" class="col-xs-2">Email Address:</label>

+                            <div style="margin-left: 20px; text-align: left;" class="col-xs-2 controls">

+                                <span id="email_address">{% if 'email_address' in user_details %}{{ user_details.email_address }}{% else %}N/A{% endif %}</span>

+                            </div>

+                        </div>

+                        <div class="form-group">

+                            <label for="full_name" style="text-align: left;" class="col-xs-2">User Name:</label>

+                            <div style="margin-left: 20px; text-align: left;" class="col-xs-2 controls">

+                                <span id="full_name" class="old_user_attribute">{% if 'full_name' in user_details %}{{ user_details.full_name }}{% else %}N/A{% endif %}</span>

+                                <input type="text" name="new_full_name" style="display: none; width: 500px;" class="form-control new_user_attribute" placeholder="{% if 'full_name' in user_details %}{{ user_details.full_name }}{% else %}N/A{% endif %}"> 

+                            </div>

+                        </div>

+                        <div class="form-group">

+                            <label for="organization" style="text-align: left;" class="col-xs-2">Organization:</label>

+                            <div style="margin-left: 20px; text-align: left;" class="col-xs-2 controls">

+                                <span id="organization" class="old_user_attribute">{% if 'organization' in user_details %}{{ user_details.organization }}{% else %}N/A{% endif %}</span>

+                                <input type="text" name="new_organization" style="display: none; width: 500px;" class="form-control new_user_attribute" placeholder="{% if 'organization' in user_details %}{{ user_details.organization }}{% else %}N/A{% endif %}"> 

+                            </div>

+                        </div>

+                        <div class="form-group">

+                            <label for="change_user_details" style="text-align: left;" class="col-xs-2"></label>

+                            <div style="margin-left: 20px; text-align: left;" class="col-xs-2 controls">

+                                <input type="button" id="change_user_details" value="Change Details">

+                                <input type="button" id="save_changes" value="Save Changes" style="display: none;">

+                            </div>

+                        </div>

+                    </div>

+                </div>

+            </div>

+        </form>

+    </div>

+

+<!-- End of body -->

+

+{% endblock %}

+

+{% block js %}

+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>

+

+    <script type="text/javascript" charset="utf-8">

+        $(document).ready( function () {

+            $('#change_user_details').click(function(){

+                $('.new_user_attribute').css("display", "inline-block");

+                $('.old_user_attribute').css("display", "none");

+                $('#change_user_details').css("display", "none");

+                $('#save_changes').css("display", "inline-block");

+            });

+

+            $('#save_changes').click(function(){

+                $('.new_user_attribute').each(function(){

+                    if ($(this).val() == ""){

+                        $(this).val($(this).attr("placeholder"))

+                    }

+                });

+                $('#user_form').submit();

+            });

+        });

+    </script>

+{% endblock %}