diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 63 | ||||
| -rw-r--r-- | wqflask/wqflask/static/dbdoc/TODO.md | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/correlation_page.html | 65 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/empty_collection.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 2 |
5 files changed, 115 insertions, 18 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 4d7fea61..9b048346 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -32,6 +32,7 @@ import pp import math import collections import resource +import json import scipy @@ -51,6 +52,7 @@ import utility.webqtlUtil #this is for parallel computing only. from wqflask.correlation import correlation_functions from utility.benchmark import Bench import utility.webqtlUtil +from wqflask import user_manager from MySQLdb import escape_string as escape @@ -248,7 +250,7 @@ class CorrelationResults(object): 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(): @@ -335,6 +337,7 @@ class CorrelationResults(object): #print("self.correlation_results: ", pf(self.correlation_results)) + self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset) #XZ, 09/18/2008: get all information about the user selected database. #target_db_name = fd.corr_dataset @@ -1431,3 +1434,61 @@ class CorrelationResults(object): # for one_result in results: # for one_traitinfo in one_result: # allcorrelations.append( one_traitinfo ) + +def generate_corr_json(corr_results, this_trait, dataset, target_dataset): + results_list = [] + for i, trait in enumerate(corr_results): + results_dict = {} + results_dict['checkbox'] = "<INPUT TYPE='checkbox' NAME='searchResult' class='checkbox trait_checkbox' style='padding-right: 0px;' VALUE='" + user_manager.data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) + "'>" + results_dict['index'] = i + 1 + results_dict['trait_id'] = "<a href='/show_trait?trait_id="+str(trait.name)+"&dataset="+str(dataset.name)+"'>"+str(trait.name)+"</a>" + if target_dataset.type == "ProbeSet": + results_dict['symbol'] = trait.symbol + results_dict['description'] = trait.description_display + results_dict['location'] = trait.location_repr + results_dict['mean'] = float(trait.mean) + if trait.LRS_score_repr != "N/A": + results_dict['lrs_score'] = "%.1f" % float(trait.LRS_score_repr) + else: + results_dict['lrs_score'] = "N/A" + results_dict['lrs_location'] = trait.LRS_location_repr + if trait.additive != "": + results_dict['additive'] = "%0.3f" % float(trait.additive) + else: + results_dict['additive'] = "N/A" + results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % float(trait.sample_r) + "</a>" + results_dict['num_overlap'] = trait.num_overlap + results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + if trait.lit_corr == "" or trait.lit_corr == 0: + results_dict['lit_corr'] = "--" + else: + results_dict['lit_corr'] = "%0.3f" % float(trait.lit_corr) + if trait.tissue_corr == "" or trait.tissue_corr == 0: + results_dict['tissue_corr'] = "--" + else: + results_dict['tissue_corr'] = "%0.3f" % float(trait.tissue_corr) + elif target_dataset.type == "Publish": + results_dict['description'] = trait.description_display + results_dict['authors'] = trait.authors + if trait.pubmed_id: + results_dict['pubmed'] = "<a href='" + trait.pubmed_link + "'> " + trait.pubmed_text + "</a>" + else: + results_dict['pubmed'] = "N/A" + results_dict['lrs_score'] = trait.LRS_score_repr + results_dict['lrs_location'] = trait.LRS_location_repr + if trait.additive != "": + results_dict['additive'] = "%0.3f" % float(trait.additive) + else: + results_dict['additive'] = "N/A" + results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % trait.sample_r + "</a>" + results_dict['num_overlap'] = trait.num_overlap + results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + else: + results_dict['lrs_location'] = trait.LRS_location_repr + results_dict['sample_r'] = "<a target='_blank' href='corr_scatter_plot?dataset_1=" + str(dataset.name) + "&dataset_2=" + str(trait.dataset.name) + "&trait_1=" + str(this_trait.name) + "&trait_2=" + str(trait.name) + "'>" + "%0.3f" % float(trait.sample_r) + "</a>" + results_dict['num_overlap'] = trait.num_overlap + results_dict['sample_p'] = "%0.3e" % float(trait.sample_p) + + results_list.append(results_dict) + + return json.dumps(results_list) diff --git a/wqflask/wqflask/static/dbdoc/TODO.md b/wqflask/wqflask/static/dbdoc/TODO.md new file mode 100644 index 00000000..c0a8bab7 --- /dev/null +++ b/wqflask/wqflask/static/dbdoc/TODO.md @@ -0,0 +1 @@ +TODO: Add all database documentation into this folder diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index 629724c0..1254ea6a 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -65,8 +65,10 @@ <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1400px{% else %}800px{% endif %};"> <table id="trait_table" class="display dataTable nowrap" style="font-size: 12px; float: left;"> +<!-- <thead> <tr> + <th></th> {% for header in target_dataset.header_fields %} {% if header == 'Year' %} <th>{{header}}</th> @@ -129,7 +131,8 @@ <tbody> {% for trait in correlation_results %} <tr> - <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center; display: inline;">{{ loop.index }}<INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td> + <td><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td> + <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center; display: inline;">{{ loop.index }}</td> <td> <a href="{{ url_for('show_trait_page', trait_id = trait.name, @@ -182,6 +185,7 @@ </tr> {% endfor %} </tbody> +--> </table> </div> </div> @@ -267,24 +271,55 @@ $(document).ready( function () { + var table_json = {{ json_results | safe }} + + + {% if target_dataset.type == "ProbeSet" %} + var json_array = new Array(); + + for (i=0; i < table_json.length; i++){ + json_array.push({ + checkbox: table_json[i]["checkbox"], + index: table_json[i]["index"], + trait_id: table_json[i]["trait_id"], + symbol: table_json[i]["symbol"], + description: table_json[i]["description"], + location: table_json[i]["location"], + mean: table_json[i]["mean"], + lrs_score: table_json[i]["lrs_score"], + lrs_location: table_json[i]["lrs_location"], + additive: table_json[i]["additive"], + sample_r: table_json[i]["sample_r"], + num_overlap: table_json[i]["num_overlap"], + sample_p: table_json[i]["sample_p"], + lit_corr: table_json[i]["lit_corr"], + tissue_corr: table_json[i]["tissue_corr"] + }); + console.log("JSON_DATA:", json_array); + } + //console.log("JSON_DATA:", json_array) + $("#trait_table").tabulator({ + data: json_array, columns:[ - {title:"Index", formatter:"html"}, - {title:"Record", formatter:"html"}, - {title:"Symbol", formatter:"plaintext"}, - {title:"Description", formatter:"textarea", width:"25%"}, - {title:"Location", formatter:"plaintext"}, - {title:"Mean", formatter:"plaintext"}, - {title:"Max LRS", formatter:"plaintext"}, - {title:"Max LRS Location", formatter:"plaintext"}, - {title:"Additive Effect", formatter:"plaintext"}, - {title:"Sample r", formatter:"html"}, - {title:"N", formatter:"plaintext"}, - {title:"Sample p(r)", formatter:"plaintext"}, - {title:"Lit r", formatter:"plaintext"}, - {title:"Tissue r", formatter:"plaintext"} + {title:"", field:"checkbox", formatter:"html"}, + {title:"Index", field:"index", formatter:"plaintext"}, + {title:"Record", field:"trait_id", formatter:"html"}, + {title:"Symbol", field:"symbol", formatter:"plaintext"}, + {title:"Description", field:"description", formatter:"textarea", width:"25%"}, + {title:"Location", field:"location", formatter:"plaintext"}, + {title:"Mean", field:"mean", formatter:"plaintext"}, + {title:"Max LRS", field:"lrs_score", formatter:"plaintext"}, + {title:"Max LRS Location", field:"lrs_location", formatter:"plaintext"}, + {title:"Additive Effect", field:"additive", formatter:"plaintext"}, + {title:"Sample r", field:"sample_r", formatter:"html"}, + {title:"N", field:"num_overlap", formatter:"plaintext"}, + {title:"Sample p(r)", field:"sample_p", formatter:"plaintext"}, + {title:"Lit r", field:"lit_corr", formatter:"plaintext"}, + {title:"Tissue r", field:"tissue_corr", formatter:"plaintext"} ] }); + {% endif %} $('#trait_table tr').click(function(event) { if (event.target.type !== 'checkbox') { diff --git a/wqflask/wqflask/templates/empty_collection.html b/wqflask/wqflask/templates/empty_collection.html index 3f2b3786..d1b779ef 100644 --- a/wqflask/wqflask/templates/empty_collection.html +++ b/wqflask/wqflask/templates/empty_collection.html @@ -6,7 +6,7 @@ <div class="container"> <input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}"> - <p>You must select at least one trait to use the {{ tool }}.</p> + <p>You must select at least two traits to use the {{ tool }}.</p> </div> diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 4e81c29c..187b60dc 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -743,7 +743,7 @@ def corr_matrix_page(): start_vars = request.form traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] - if traits[0] != "": + if len(traits) > 1: template_vars = show_corr_matrix.CorrelationMatrix(start_vars) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, |