diff options
| -rwxr-xr-x | wqflask/base/data_set.py | 32 | ||||
| -rw-r--r-- | wqflask/wqflask/do_search.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/search_results.py | 7 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.coffee | 86 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 10 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/stats.coffee | 31 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/stats.js | 18 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/search_result_page.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_details.html | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_edit_data.html | 2 |
12 files changed, 122 insertions, 84 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 9f0f3fac..2182fe9e 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -30,6 +30,7 @@ from htmlgen import HTMLgen2 as HT import reaper import webqtlConfig +from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil from MySQLdb import escape_string as escape @@ -72,10 +73,12 @@ class DatasetGroup(object): """ def __init__(self, dataset): """This sets self.group and self.group_id""" - self.name, self.group_id = g.db.execute(dataset.query).fetchone() + self.name, self.id = g.db.execute(dataset.query_for_group).fetchone() if self.name == 'BXD300': self.name = "BXD" + self.species = webqtlDatabaseFunction.retrieve_species(self.name) + self.incparentsf1 = False self.f1list = None self.parlist = None @@ -151,14 +154,25 @@ class DataSet(object): self.check_confidentiality() - self.retrieve_name() + self.retrieve_other_names() self.group = DatasetGroup(self) # sets self.group and self.group_id def get_desc(self): """Gets overridden later, at least for Temp...used by trait's get_given_name""" return None - + + #@staticmethod + #def get_by_trait_id(trait_id): + # """Gets the dataset object given the trait id""" + # + # + # + # name = g.db.execute(""" SELECT + # + # """) + # + # return DataSet(name) # Delete this eventually @property @@ -175,7 +189,7 @@ class DataSet(object): - def retrieve_name(self): + def retrieve_other_names(self): """ If the data set name parameter is not found in the 'Name' field of the data set table, check if it is actually the FullName or ShortName instead. @@ -326,7 +340,7 @@ class PhenotypeDataSet(DataSet): def retrieve_sample_data(self, trait): query = """ SELECT - Strain.Name, PublishData.value, PublishSE.error, NStrain.count, PublishData.Id + Strain.Name, PublishData.value, PublishSE.error, NStrain.count FROM (PublishData, Strain, PublishXRef, PublishFreeze) left join PublishSE on @@ -340,7 +354,7 @@ class PhenotypeDataSet(DataSet): PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id Order BY Strain.Name - """ % (self.trait.name, self.id) + """ % (trait.name, self.id) results = g.db.execute(query).fetchall() return results @@ -368,7 +382,7 @@ class GenotypeDataSet(DataSet): # Todo: Obsolete or rename this field self.type = 'Geno' - self.query = ''' + self.query_for_group = ''' SELECT InbredSet.Name, InbredSet.Id FROM @@ -418,7 +432,7 @@ class GenotypeDataSet(DataSet): GenoData.StrainId = Strain.Id Order BY Strain.Name - """ % (webqtlDatabaseFunction.retrieve_species_id(self.group), trait.name, self.name) + """ % (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait.name, self.name) results = g.db.execute(query).fetchall() return results @@ -476,7 +490,7 @@ class MrnaAssayDataSet(DataSet): # Todo: Obsolete or rename this field self.type = 'ProbeSet' - self.query = ''' + self.query_for_group = ''' SELECT InbredSet.Name, InbredSet.Id FROM diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index 69602748..403f1b5e 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -177,9 +177,6 @@ class PhenotypeSearch(DoSearch): from_clause = self.normalize_spaces(from_clause) - #Get group information for dataset - self.dataset.get_group() - query = (self.base_query + """%s WHERE %s @@ -189,7 +186,7 @@ class PhenotypeSearch(DoSearch): PublishFreeze.Id = %s""" % ( from_clause, where_clause, - escape(str(self.dataset.group_id)), + escape(str(self.dataset.group.id)), escape(str(self.dataset.id)))) print("query is:", pf(query)) diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index b518ab99..5cb8e314 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -4,13 +4,6 @@ from wqflask import app from flask import render_template -################################################### -# # -# This file uses only spaces for indentation # -# # -################################################### - -#import string import os import cPickle import re diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index cd61d70c..d1c60877 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -32,13 +32,16 @@ from pprint import pformat as pf -class ShowTrait(templatePage): +class ShowTrait(object): def __init__(self, args): print("in ShowTrait, args are:", args) #self.group = args.group self.trait_id = args['trait_id'] + self.dataset = create_dataset(args['dataset']) + + #self.dataset = create_dataset(args['dataset']) self.cell_id = None #assert self.openMysql(), "No database!" @@ -817,7 +820,7 @@ class ShowTrait(templatePage): # )) pass - menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1") + #menuTable = HT.TableLite(cellpadding=2, Class="collap", width="150", id="target1") #menuTable.append(HT.TR(HT.TD(addSelectionButton, align="center"),HT.TD(updateButton, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) #menuTable.append(HT.TR(HT.TD(addSelectionText, align="center"),HT.TD(updateText, align="center"), colspan=3, height=50, style="vertical-align:bottom;")) diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index 6e22119f..3d9fcd5a 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -23,15 +23,15 @@ $ -> id = "#" + process_id(category, value_type) console.log("the_id:", id) in_box = $(id).html - + current_value = parseFloat($(in_box)).toFixed(decimal_places) - + console.log("urgh:", category, value_type) the_value = sample_sets[category][value_type]() console.log("After running sample_sets, the_value is:", the_value) if decimal_places > 0 the_value = the_value.toFixed(decimal_places) - + console.log("*-* the_value:", the_value) console.log("*-* current_value:", current_value) if the_value != current_value @@ -40,16 +40,16 @@ $ -> update_stat_values = (sample_sets)-> for category in ['samples_primary', 'samples_other', 'samples_all'] change_stats_value(sample_sets, category, "n_of_samples", 0) - for stat in ["mean", "median", "std_dev", "std_error"] + for stat in ["mean", "median", "std_dev", "std_error", "min", "max"] console.log("Calling change_stats_value") change_stats_value(sample_sets, category, stat, 2) - edit_data_change = -> + edit_data_change = -> sample_sets = samples_primary: new Stats([]) samples_other: new Stats([]) samples_all: new Stats([]) - + console.log("at beginning:", sample_sets) # ########## @@ -114,6 +114,14 @@ $ -> { vn: "std_dev" pretty: "Standard Deviation (SD)" + }, + { + vn: "min" + pretty: "Minimum" + }, + { + vn: "max" + pretty: "Maximum" } ] @@ -150,8 +158,8 @@ $ -> processed += "-" processed += value return processed - - + + show_hide_outliers = -> console.log("FOOBAR in beginning of show_hide_outliers") label = $('#show_hide_outliers').val() @@ -163,10 +171,10 @@ $ -> $('#show_hide_outliers').val("Hide Outliers") console.log("Should be now Hide Outliers") - + ##Calculate Correlations Code - - + + on_corr_method_change = -> console.log("in beginning of on_corr_method_change") corr_method = $('select[name=corr_method]').val() @@ -179,15 +187,15 @@ $ -> $("#corr_sample_method_options").show() $('select[name=corr_method]').change(on_corr_method_change) - - + + ##End Calculate Correlations Code - + ##Populate Samples Attribute Values Code - + create_value_dropdown = (value) -> return """<option val=#{value}>#{value}</option>""" - + populate_sample_attributes_values_dropdown = -> console.log("in beginning of psavd") $('#attribute_values').empty() @@ -205,14 +213,14 @@ $ -> if js_data.attribute_names.length > 0 populate_sample_attributes_values_dropdown() $('#exclude_menu').change(populate_sample_attributes_values_dropdown) - + ##End Populate Samples Attribute Values Codess ##Block Samples By Attribute Value Code block_by_attribute_value = -> attribute_name = $('#exclude_menu').val() exclude_by_value = $('#attribute_values').val() - + cell_class = ".column_name-#{attribute_name}" $(cell_class).each (index, element) => if $.trim($(element).text()) == exclude_by_value @@ -220,11 +228,11 @@ $ -> $(row).find(".trait_value_input").val("x") $('#exclude_group').click(block_by_attribute_value) - + ##End Block Samples By Attribute Value Code - + ##Block Samples By Index Code - + block_by_index = -> index_string = $('#remove_samples_field').val() index_list = [] @@ -241,7 +249,7 @@ $ -> index = parseInt(index_set) console.log("index:", index) index_list.push(index) - #catch(erro) + #catch(erro) # alert("Syntax error") console.log("index_list:", index_list) for index in index_list @@ -251,33 +259,33 @@ $ -> $('#Primary_'+index.toString()).find('.trait_value_input').val("x") else if $('#block_group').val() == "other" console.log("block_group:", $('#block_group').val()) - console.log("row:", $('#Other_'+index.toString())) + console.log("row:", $('#Other_'+index.toString())) $('#Other_'+index.toString()).find('.trait_value_input').val("x") - + $('#block_by_index').click(block_by_index) ##End Block Samples By Index Code - + ##Hide Sample Rows With No Value (value of 'x') Code - + hide_no_value = -> $('.value_se').each (_index, element) => if $(element).find('.trait_value_input').val() == 'x' $(element).hide() - + $('#hide_no_value').click(hide_no_value) ##End Hide Sample Rows With No Value Code - + ##Block Outliers Code block_outliers = -> $('.outlier').each (_index, element) => $(element).find('.trait_value_input').val('x') - + $('#block_outliers').click(block_outliers) - + ##End Block Outliers Code - + ##Reset Table Values Code reset_samples_table = -> $('.trait_value_input').each (_index, element) => @@ -289,9 +297,9 @@ $ -> $('#reset').click(reset_samples_table) ##End Reset Table Values Code - + ##Get Sample Data From Table Code - + get_sample_table_data = -> samples = {} primary_samples = [] @@ -315,27 +323,27 @@ $ -> ##End Get Sample Data from Table Code ##Export Sample Table Data Code - + export_sample_table_data = -> sample_data = get_sample_table_data() console.log("sample_data is:", sample_data) json_sample_data = JSON.stringify(sample_data) console.log("json_sample_data is:", json_sample_data) - + $('input[name=export_data]').val(json_sample_data) console.log("export_data is", $('input[name=export_data]').val()) - + format = $('#export_format').val() if format == "excel" $('#trait_data_form').attr('action', '/export_trait_excel') else $('#trait_data_form').attr('action', '/export_trait_csv') console.log("action is:", $('#trait_data_form').attr('action')) - + $('#trait_data_form').submit() $('#export').click(export_sample_table_data) - + ##End Export Sample Table Data Code @@ -344,7 +352,7 @@ $ -> console.log("after registering block_outliers") _.mixin(_.str.exports()); # Add string fuctions directly to underscore - $('#value_table').change(edit_data_change) + $('#edit_sample_lists').change(edit_data_change) console.log("loaded") #console.log("basic_table is:", basic_table) # Add back following two lines later diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 919bc766..84282aef 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -53,7 +53,7 @@ change_stats_value(sample_sets, category, "n_of_samples", 0); _results.push((function() { var _j, _len1, _ref1, _results1; - _ref1 = ["mean", "median", "std_dev", "std_error"]; + _ref1 = ["mean", "median", "std_dev", "std_error", "min", "max"]; _results1 = []; for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) { stat = _ref1[_j]; @@ -126,6 +126,12 @@ }, { vn: "std_dev", pretty: "Standard Deviation (SD)" + }, { + vn: "min", + pretty: "Minimum" + }, { + vn: "max", + pretty: "Maximum" } ]; console.log("rows are:", rows); @@ -362,7 +368,7 @@ $('#block_outliers').click(block_outliers); console.log("after registering block_outliers"); _.mixin(_.str.exports()); - $('#value_table').change(edit_data_change); + $('#edit_sample_lists').change(edit_data_change); console.log("loaded"); make_table(); edit_data_change(); diff --git a/wqflask/wqflask/static/new/javascript/stats.coffee b/wqflask/wqflask/static/new/javascript/stats.coffee index 677dc258..118ee7a8 100644 --- a/wqflask/wqflask/static/new/javascript/stats.coffee +++ b/wqflask/wqflask/static/new/javascript/stats.coffee @@ -1,20 +1,20 @@ class Stats constructor: (@the_values) -> - + add_value: (value) -> @the_values.push(value) - + n_of_samples: -> return @the_values.length - + sum: -> total = 0 total += value for value in @the_values return total - + mean: -> return @sum() / @n_of_samples() - + median: -> is_odd = @the_values.length % 2 median_position = Math.floor(@the_values.length / 2) @@ -24,7 +24,7 @@ class Stats else return (the_values_sorted[median_position] + the_values_sorted[median_position - 1]) / 2 - + std_dev: -> sum = 0 for value in @the_values @@ -32,15 +32,22 @@ class Stats sum += step_a step_b = sum / @the_values.length return Math.sqrt(step_b) - + std_error: -> return @std_dev() / Math.sqrt(@n_of_samples()) + min: -> + return Math.min(@the_values...) + + max: -> + return Math.max(@the_values...) + bxd_only = new Stats([3, 5, 7, 8]) -console.log("[red] bxd_only mean:", bxd_only.mean()) -console.log("[green] bxd_only median:", bxd_only.median()) -console.log("[purple] bxd_only std_dev:", bxd_only.std_dev()) -console.log("[magenta] bxd_only std_error:", bxd_only.std_error()) +console.log("[xred] bxd_only mean:", bxd_only.mean()) +console.log("[xgreen] bxd_only median:", bxd_only.median()) +console.log("[xpurple] bxd_only std_dev:", bxd_only.std_dev()) +console.log("[xmagenta] bxd_only std_error:", bxd_only.std_error()) +console.log("[xyellow] bxd_only min:", bxd_only.min()) -window.Stats = Stats \ No newline at end of file +window.Stats = Stats diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js index f95d03d4..620f7d5d 100644 --- a/wqflask/wqflask/static/new/javascript/stats.js +++ b/wqflask/wqflask/static/new/javascript/stats.js @@ -62,19 +62,29 @@ return this.std_dev() / Math.sqrt(this.n_of_samples()); }; + Stats.prototype.min = function() { + return Math.min.apply(Math, this.the_values); + }; + + Stats.prototype.max = function() { + return Math.max.apply(Math, this.the_values); + }; + return Stats; })(); bxd_only = new Stats([3, 5, 7, 8]); - console.log("[red] bxd_only mean:", bxd_only.mean()); + console.log("[xred] bxd_only mean:", bxd_only.mean()); + + console.log("[xgreen] bxd_only median:", bxd_only.median()); - console.log("[green] bxd_only median:", bxd_only.median()); + console.log("[xpurple] bxd_only std_dev:", bxd_only.std_dev()); - console.log("[purple] bxd_only std_dev:", bxd_only.std_dev()); + console.log("[xmagenta] bxd_only std_error:", bxd_only.std_error()); - console.log("[magenta] bxd_only std_error:", bxd_only.std_error()); + console.log("[xyellow] bxd_only min:", bxd_only.min()); window.Stats = Stats; diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 35ff4e8e..11f68bba 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -51,9 +51,9 @@ </TD> <TD> <a href="{{ url_for('show_trait_page', - dataset = dataset.name, trait_id = this_trait.name, - group = dataset.group)}}"> + dataset = dataset.name + )}}"> {{ this_trait.name }} </a> </TD> diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html index 163be69c..28341186 100644 --- a/wqflask/wqflask/templates/show_trait.html +++ b/wqflask/wqflask/templates/show_trait.html @@ -18,7 +18,7 @@ <div class="container"> <div class="page-header"> - <h1>{{ this_trait.species.capitalize() }} - + <h1>{{ dataset.group.species.capitalize() }} - {{ dataset.group.name }} - {{ this_trait.symbol }} </h1> diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html index e45886b4..e04fdd66 100644 --- a/wqflask/wqflask/templates/show_trait_details.html +++ b/wqflask/wqflask/templates/show_trait_details.html @@ -8,7 +8,7 @@ <dt>Database</dt> <dd> <a href="{{ this_trait.database.url }}" target="_blank"> - {{ this_trait.database.name }} + {{ dataset.name }} </a> </dd> diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html index 6c9b1073..9023b34d 100644 --- a/wqflask/wqflask/templates/show_trait_edit_data.html +++ b/wqflask/wqflask/templates/show_trait_edit_data.html @@ -77,7 +77,7 @@ <table id="stats_table" class="table table-hover"></table> </div> - <div> + <div id="edit_sample_lists"> {% for sample_type in sample_groups %} <div> <h3>{{ sample_type.header }}</h3> |