diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/__init__.py | 1 | ||||
| -rw-r--r-- | wqflask/run_gunicorn.py | 19 | ||||
| -rw-r--r-- | wqflask/runserver.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 17 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/dataset_menu_structure.json | 24 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/loading.html | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 22 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_details.html | 31 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_mapping_tools.html | 174 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 3 | ||||
| -rw-r--r-- | wqflask/wsgi.py | 4 |
14 files changed, 210 insertions, 118 deletions
diff --git a/wqflask/__init__.py b/wqflask/__init__.py index 315b709e..e69de29b 100644 --- a/wqflask/__init__.py +++ b/wqflask/__init__.py @@ -1 +0,0 @@ -from wqflask import app diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py new file mode 100644 index 00000000..14a2d689 --- /dev/null +++ b/wqflask/run_gunicorn.py @@ -0,0 +1,19 @@ +# Run with gunicorn, see ./bin/genenetwork2 for an example +# +# Run standalone with +# +# ./bin/genenetwork2 ./etc/default_settings.py -c run_gunicorn.py + +# from flask import Flask +# application = Flask(__name__) + +print "Starting up Gunicorn process" + +from wqflask import app + +@app.route("/gunicorn") +def hello(): + return "<h1 style='color:blue'>Hello There!</h1>" + +if __name__ == "__main__": + app.run(host='0.0.0.0') diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 50f134db..a0c76e51 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -1,5 +1,7 @@ # Starts the webserver with the ./bin/genenetwork2 command # +# This uses Werkzeug WSGI, see ./run_gunicorn.py for the alternative +# # Please note, running with host set externally below combined with # debug mode is a security risk unless you have a firewall setup, e.g. # diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index bcb14451..087b95b4 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -79,6 +79,16 @@ class MarkerRegression(object): self.samples.append(sample) self.vals.append(value) + #ZS: Check if genotypes exist in the DB in order to create links for markers + if "geno_db_exists" in start_vars: + self.geno_db_exists = start_vars['geno_db_exists'] + else: + try: + geno_dataset = data_set.create_dataset(self.dataset.group.name + "Geno") + self.geno_db_exists = "True" + except: + self.geno_db_exists = "False" + self.mapping_method = start_vars['method'] if "results_path" in start_vars: self.mapping_results_path = start_vars['results_path'] diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py index 93bd9d42..211cf187 100644 --- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py +++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py @@ -174,6 +174,8 @@ class MarkerRegression(object): if 'genofile_string' in start_vars: self.genofile_string = start_vars['genofile_string'] + self.geno_db_exists = start_vars['geno_db_exists'] + #Needing for form submission when doing single chr mapping or remapping after changing options self.samples = start_vars['samples'] self.vals = start_vars['vals'] @@ -576,7 +578,7 @@ class MarkerRegression(object): self.gifmap = gifmap.__str__() self.filename= webqtlUtil.genRandStr("Itvl_") - intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='jpeg') + intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='png') intImg=HT.Image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap') #Scales plot differently for high resolution @@ -616,7 +618,7 @@ class MarkerRegression(object): else: showLocusForm = intImg - if self.permChecked and self.nperm > 0 and not self.multipleInterval and 0 < self.nperm: + if (self.permChecked and self.nperm > 0) and not (self.multipleInterval and 0 < self.nperm): self.perm_filename = self.drawPermutationHistogram() #perm_text_file = self.permutationTextFile() @@ -1200,8 +1202,10 @@ class MarkerRegression(object): if self.controlLocus and self.doControl != "false": string2 = 'Using %s as control' % self.controlLocus else: - if self.mapping_method == "gemma": + if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam": string2 = 'Using GEMMA mapping method with no control for other QTLs.' + elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno": + string2 = 'Using R/qtl mapping method with no control for other QTLs.' elif self.mapping_method == "plink": string2 = 'Using PLINK mapping method with no control for other QTLs.' else: @@ -1963,6 +1967,8 @@ class MarkerRegression(object): if self.permChecked and self.nperm > 0 and not self.multipleInterval: LRS_LOD_Max = max(self.significant, LRS_LOD_Max) + else: + LRS_LOD_Max = 1.15*LRS_LOD_Max #genotype trait will give infinite LRS LRS_LOD_Max = min(LRS_LOD_Max, webqtlConfig.MAXLRS) @@ -2164,10 +2170,7 @@ class MarkerRegression(object): # Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max if self.manhattan_plot == True: - if previous_chr_as_int % 2 == 1: - point_color = pid.grey - else: - point_color = pid.black + point_color = pid.black canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=point_color, font=symbolFont) else: LRSCoordXY.append((Xc, Yc)) diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json index 8de85a86..b7ebb9ed 100644 --- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json +++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json @@ -2974,6 +2974,20 @@ ] ] }, + "BXD-Harvested": { + "Liver mRNA": [ + [ + "843", + "UTHSC-BXD-Harv_Liv-0118", + "UTHSC BXD Harvested Liver RNA-Seq (Jan18) Log2 **" + ], + [ + "842", + "UTHSC-BXD-Liv-0917", + "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA **" + ] + ] + }, "BXD300": { "Genotypes": [ [ @@ -3864,6 +3878,10 @@ "BXD Bone" ], [ + "BXD-Harvested", + "BXD NIA Longevity Study" + ], + [ "BXD300", "BXD300" ], @@ -5007,6 +5025,12 @@ "Phenotypes" ] ], + "BXD-Harvested": [ + [ + "Liver mRNA", + "Liver mRNA" + ] + ], "BXD300": [ [ "Phenotypes", diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index 2f1d836a..4d98f5d8 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -245,6 +245,7 @@ //$("#static_progress_bar_container").modal(); url = "/loading"; $('input[name=method]').val("gemma_bimbam"); + $('input[name=num_perm]').val(0); $('input[name=genofile]').val($('#genofile_gemma').val()); $('input[name=maf]').val($('input[name=maf_gemma]').val()); form_data = $('#trait_data_form').serialize(); diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html index cede0e86..46136ddb 100644 --- a/wqflask/wqflask/templates/loading.html +++ b/wqflask/wqflask/templates/loading.html @@ -1,20 +1,20 @@ <title>Loading Mapping Results</title> <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" /> -<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/non-responsive.css" /> -<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" /> -<link rel="stylesheet" type="text/css" href="/static/packages/colorbox/example4/colorbox.css" /> -<link rel="stylesheet" type="text/css" href="/static/new/css/main.css" /> <form method="post" action="/marker_regression" 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 class="row"> - <div style="margin-left: 46%; margin-right: 50%; min-height: 100vh; display: flex; align-items: center;"> - <h1>Loading Mapping Results...</h1> + <div> + <div style="min-height: 80vh; display: flex; align-items: center;"> + <div class="center-block" style="margin-left: 38%; margin-right: 38%; position: absolute; height:50px; width:24%; top:40%;"> + <h1>Loading Mapping Results...</h1> + </div> </div> - <div class="progress center-block" style="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 style="min-height: 80vh; display: flex; align-items: center;"> + <div class="progress center-block" style="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> diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index d13c68cd..08a934a6 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -15,6 +15,7 @@ <input type="hidden" name="trait_id" value="{{ this_trait.name }}"> <input type="hidden" name="dataset" value="{{ dataset.name }}"> <input type="hidden" name="genofile" value="{{ genofile_string }}"> + <input type="hidden" name="geno_db_exists" value="{{ geno_db_exists }}"> <input type="hidden" name="results_path" value="{{ mapping_results_path }}"> <input type="hidden" name="method" value="{{ mapping_method }}"> {% for sample in samples %} @@ -154,7 +155,7 @@ <div class="tab-pane active" id="gn1_map"> <div class="qtlcharts"> {{ gifmap|safe }} - <img src="/generated/{{ filename }}.jpeg" usemap="#WebQTLImageMap"> + <img src="/generated/{{ filename }}.png" usemap="#WebQTLImageMap"> {% if additiveChecked|upper == "ON" %} <br> <span style="white-space: nowrap;">A positive additive coefficient (green line) indicates that {{ dataset.group.parlist[1] }} alleles increase trait values. In contrast, a negative additive coefficient (orange line) indicates that {{ dataset.group.parlist[0] }} alleles increase trait values.</span> @@ -180,10 +181,10 @@ </form> {% if selectedChr == -1 %} - <div style="width:{% if 'additive' in trimmed_markers[0] %}45%{% else %}35%{% endif %};"> - <h2>Results</h2> - <div id="table_container"> - <table id="qtl_results" class="table table-hover table-striped nowrap"> + <div class="container" style="padding-left: 30px; width:{% if 'additive' in trimmed_markers[0] %}45%{% else %}35%{% endif %};"> + <h2>Mapping Statistics</h2> + <div id="table_container" style="border-style: solid; border-width: 1px; border-color: black;"> + <table id="trait_table" class="table table-hover table-striped nowrap"> <thead> <tr> <th></th> @@ -194,7 +195,7 @@ {% if plotScale != "physic" %} <th>cM</th> {% else %} - <th>Mb</th> + <th align="right">Mb</th> {% endif %} {% if 'additive' in trimmed_markers[0] %} <th>Add Eff</th> @@ -209,11 +210,11 @@ <tr> <td align="center" style="padding-right: 0px;"> <input type="checkbox" name="selectCheck" - class="checkbox edit_sample_checkbox" - value="{{ marker.name }}" checked="checked"> + class="checkbox trait_checkbox" + value="{{ marker.name }}"> </td> <td align="right">{{ loop.index }}</td> - <td>{{ marker.name }}</td> + <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td> {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %} {% if 'lod_score' in marker %} <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td> @@ -294,6 +295,7 @@ </script> {% endif %} + <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> {% if mapping_method != "gemma" and mapping_method != "plink" %} <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> @@ -304,7 +306,7 @@ <script type="text/javascript" charset="utf-8"> $(document).ready( function () { console.time("Creating table"); - $('#qtl_results').DataTable( { + $('#trait_table').DataTable( { {% if mapping_method != "reaper" %} "columns": [ { "type": "natural", "width": "5%" }, diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index a291baf3..dd4325e7 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -28,7 +28,9 @@ --> <div class="container"> <h2>Trait Data and Analysis for <b>{{ this_trait.name }}</b></h2> + {% if this_trait.dataset.type != 'Publish' %} <h3>{{ this_trait.description_fmt }}</h3> + {% endif %} </div> <form method="post" action="/corr_compute" target="_blank" name="trait_page" id="trait_data_form" diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index 2a62733e..1e6d41c2 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -8,6 +8,22 @@ <td>Tissue</td> <td>{{ this_trait.dataset.tissue }}</td> </tr> + <tr> + <td>Phenotype</td> + <td><div style="width:40%;">{{ this_trait.description_fmt }}</div></td> + </tr> + <tr> + <td>Authors</td> + <td><div style="width:40%;">{{ this_trait.authors }}</div></td> + </tr> + <tr> + <td>Title</td> + <td><div style="width:40%;">{{ this_trait.title }}</div></td> + </tr> + <tr> + <td>Journal</td> + <td>{{ this_trait.journal }} (<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" title="PubMed">{{ this_trait.year }}</a>)</td> + </tr> {% endif %} {% if this_trait.dataset.type == 'ProbeSet' %} {% if this_trait.symbol != None %} @@ -50,22 +66,29 @@ </td> </tr> {% endif %} + {% if this_trait.pubmed_id or this_trait.geneid or this_trait.omim or this_trait.symbol %} + {% if this_trait.dataset.type != 'Publish' %} <tr> <td>Resource Links</td> <td> - {% if this_trait.geneid != None %} + {% if this_trait.pubmed_id %} + <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" title="PubMed"> + PubMed + </a> + {% endif %} + {% if this_trait.geneid %} <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{ this_trait.geneid }}" title="Info from NCBI Entrez Gene"> NCBI </a> {% endif %} - {% if this_trait.omim != None %} + {% if this_trait.omim %} <a href="http://www.ncbi.nlm.nih.gov/omim/{{ this_trait.omim }}" title="Summary from On Mendelion Inheritance in Man"> OMIM </a> {% endif %} - {% if this_trait.symbol != None %} + {% if this_trait.symbol %} <a href="http://www.genotation.org/Getd2g.pl?gene_list={{ this_trait.symbol }}" title="Related descriptive, genomic, clinical, functional and drug-therapy information"> Genotation </a> @@ -77,6 +100,8 @@ {% endif %} </td> </tr> + {% endif %} + {% endif %} </table> <div style="margin-bottom:15px;" class="btn-toolbar"> diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 77f78415..dcec2b9e 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -6,16 +6,16 @@ <ul class="nav nav-pills"> {% if dataset.group.mapping_id == "1" %} <li class="active"> - <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a> + <a href="#gemma" data-toggle="tab">GEMMA</a> </li> <li> - <a href="#pylmm" data-toggle="tab">pyLMM</a> + <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a> </li> <li> <a href="#rqtl_geno" data-toggle="tab">R/qtl</a> </li> <li> - <a href="#gemma" data-toggle="tab">GEMMA</a> + <a href="#pylmm" data-toggle="tab">pyLMM</a> </li> {% endif %} {% for mapping_method in dataset.group.mapping_names %} @@ -37,7 +37,60 @@ <div class="tab-content"> {# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #} {% if dataset.group.mapping_id == "1" %} - <div class="tab-pane active" id="interval_mapping"> + <div class="tab-pane active" id="gemma"> + <div style="padding-top: 10px;" class="form-horizontal"> + {% if genofiles and genofiles|length>0 %} + <div class="mapping_method_fields form-group"> + <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> + <div style="margin-left: 20px;" class="col-xs-8 controls"> + <select id="genofile_gemma" class="form-control"> + {% for item in genofiles %} + <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> + {% endfor %} + </select> + </div> + </div> + {% endif %} + <div class="mapping_method_fields form-group"> + <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label> + <div style="margin-left: 20px;" class="col-xs-3 controls"> + <input name="maf_gemma" value="0.01" type="text" class="form-control"> + </div> + </div> + <div class="mapping_method_fields form-group"> + <label class="col-xs-4 control-label">Use LOCO</label> + <div style="margin-left: 20px;" class="col-xs-4 controls"> + <label class="radio-inline"> + <input type="radio" name="use_loco" value="True"> + Yes + </label> + <label class="radio-inline"> + <input type="radio" name="use_loco" value="False" checked=""> + No + </label> + </div> + </div> + </div> + <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal"> + <div class="mapping_method_fields form-group"> + <button type="button" id="select_covariates" class="btn btn-default"> + Select Covariates + </button> + <button type="button" id="remove_covariates" class="btn btn-default"> + Remove Covariates + </button> + </div> + </div> + + <div class="form-group"> + <div class="col-xs-4 controls"> + <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression"> + Compute + </button> + </div> + </div> + </div> + <div class="tab-pane" id="interval_mapping"> <div style="margin-top: 20px" class="form-horizontal"> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> @@ -131,62 +184,6 @@ <!--<div id="alert_placeholder"></div>--> </div> </div> - <div class="tab-pane" id="pylmm"> - <div style="margin-top: 20px" class="form-horizontal"> - {% if genofiles and genofiles|length>0 %} - <div class="mapping_method_fields form-group"> - <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> - <div style="margin-left: 20px;" class="col-xs-8 controls"> - <select id="genofile_pylmm" class="form-control"> - {% for item in genofiles %} - <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> - {% endfor %} - </select> - </div> - </div> - {% endif %} -<!-- - <div class="mapping_method_fields form-group"> - <label for="control_for" class="col-xs-3 control-label">Control for</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> - {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} - <input name="control_pylmm" value="{{ nearest_marker }}" type="text" /> - {% else %} - <input name="control_pylmm" value="" type="text" /> - {% endif %} - <label class="radio-inline"> - <input type="radio" name="do_control_pylmm" value="true"> - Yes - </label> - <label class="radio-inline"> - <input type="radio" name="do_control_pylmm" value="false" checked=""> - No - </label> - </div> - </div> - <div class="mapping_method_fields form-group"> - <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label> - <div class="col-xs-12 controls"> - <label class="radio-inline"> - <input type="radio" name="manhattan_plot_pylmm" value="True"> - Yes - </label> - <label class="radio-inline"> - <input type="radio" name="manhattan_plot_pylmm" value="False" checked=""> - No - </label> - </div> - </div> ---> - <div class="form-group"> - <div style="padding-left:15px;" class="controls"> - <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression"> - <i class="icon-ok-circle icon-white"></i> Compute - </button> - </div> - </div> - </div> - </div> <div class="tab-pane" id="rqtl_geno"> <div style="margin-top: 20px" class="form-horizontal"> @@ -294,13 +291,13 @@ </div> </div> </div> - <div class="tab-pane" id="gemma"> - <div style="padding-top: 10px;" class="form-horizontal"> + <div class="tab-pane" id="pylmm"> + <div style="margin-top: 20px" class="form-horizontal"> {% if genofiles and genofiles|length>0 %} <div class="mapping_method_fields form-group"> <label for="genofiles" class="col-xs-3 control-label">Genotypes</label> <div style="margin-left: 20px;" class="col-xs-8 controls"> - <select id="genofile_gemma" class="form-control"> + <select id="genofile_pylmm" class="form-control"> {% for item in genofiles %} <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option> {% endfor %} @@ -308,42 +305,45 @@ </div> </div> {% endif %} +<!-- <div class="mapping_method_fields form-group"> - <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label> - <div style="margin-left: 20px;" class="col-xs-3 controls"> - <input name="maf_gemma" value="0.01" type="text" class="form-control"> + <label for="control_for" class="col-xs-3 control-label">Control for</label> + <div style="margin-left: 20px;" class="col-xs-4 controls"> + {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %} + <input name="control_pylmm" value="{{ nearest_marker }}" type="text" /> + {% else %} + <input name="control_pylmm" value="" type="text" /> + {% endif %} + <label class="radio-inline"> + <input type="radio" name="do_control_pylmm" value="true"> + Yes + </label> + <label class="radio-inline"> + <input type="radio" name="do_control_pylmm" value="false" checked=""> + No + </label> </div> </div> <div class="mapping_method_fields form-group"> - <label class="col-xs-4 control-label">Use LOCO</label> - <div style="margin-left: 20px;" class="col-xs-4 controls"> + <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label> + <div class="col-xs-12 controls"> <label class="radio-inline"> - <input type="radio" name="use_loco" value="True"> + <input type="radio" name="manhattan_plot_pylmm" value="True"> Yes </label> <label class="radio-inline"> - <input type="radio" name="use_loco" value="False" checked=""> + <input type="radio" name="manhattan_plot_pylmm" value="False" checked=""> No </label> </div> </div> - </div> - <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal"> - <div class="mapping_method_fields form-group"> - <button type="button" id="select_covariates" class="btn btn-default"> - Select Covariates - </button> - <button type="button" id="remove_covariates" class="btn btn-default"> - Remove Covariates - </button> - </div> - </div> - - <div class="form-group"> - <div class="col-xs-4 controls"> - <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression"> - Compute - </button> +--> + <div class="form-group"> + <div style="padding-left:15px;" class="controls"> + <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression"> + <i class="icon-ok-circle icon-white"></i> Compute + </button> + </div> </div> </div> </div> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 68e779a1..4e81c29c 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -557,6 +557,7 @@ def marker_regression_page(): wanted = ( 'trait_id', 'dataset', + 'geno_db_exists', 'method', 'mapping_results_path', 'trimmed_markers', @@ -765,7 +766,7 @@ def corr_scatter_plot_page(): def submit_bnw(): logger.error(request.url) template_vars = get_bnw_input(request.form) - return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) + return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) # Todo: Can we simplify this? -Sam def sharing_info_page(): diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py new file mode 100644 index 00000000..be9c7b37 --- /dev/null +++ b/wqflask/wsgi.py @@ -0,0 +1,4 @@ +from run_gunicorn import app as application # expect application as a name + +if __name__ == "__main__": + application.run() |