From 717677b0c09f6ba08268db12d4889503cc2606d9 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 2 Nov 2016 20:00:04 +0000 Subject: Added Scroller functionality to regular (but not global) search, which increases table load speed In order to implement Scroller (and make table look nicer), all rows are the same height and excess description/authors text is shown in a tooltip Increased table width for non-Geno DBs Fixed issue where Genotype traits did not fetch their location_repr (text for displaying location), causing that column to be blank in searches Fixed issue causing Correlation Matrix cells to not be colored corresponding with their correlation and also increased cell font a little Fixed issue where dataset link in the Correlation Page did not correctly point to corresponding GN1 page --- wqflask/base/data_set.py | 17 ++- wqflask/base/trait.py | 103 +++++++++++++++-- wqflask/wqflask/search_results.py | 6 +- .../static/new/javascript/create_corr_matrix.js | 79 +++++++------ .../packages/bootstrap/css/non-responsive.css | 2 +- wqflask/wqflask/templates/correlation_matrix.html | 4 +- wqflask/wqflask/templates/correlation_page.html | 4 +- wqflask/wqflask/templates/search_result_page.html | 126 ++++++++++++--------- 8 files changed, 229 insertions(+), 112 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index fddfce58..04436a2e 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -271,7 +271,8 @@ class DatasetGroup(object): self.f1list = None self.parlist = None self.get_f1_parent_strains() - #logger.debug("parents/f1s: {}:{}".format(self.parlist, self.f1list)) + + self.accession_id = self.get_accession_id() self.species = webqtlDatabaseFunction.retrieve_species(self.name) @@ -279,6 +280,20 @@ class DatasetGroup(object): self.allsamples = None self._datasets = None + def get_accession_id(self): + results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where + InbredSet.Name = %s and + PublishFreeze.InbredSetId = InbredSet.Id and + InfoFiles.InfoPageName = PublishFreeze.Name and + PublishFreeze.public > 0 and + PublishFreeze.confidentiality < 1 order by + PublishFreeze.CreateTime desc""", (self.name)).fetchone() + + if results != None: + return str(results[0]) + else: + return "None" + def get_specified_markers(self, markers = []): self.markers = HumanMarkers(self.name, markers) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 276c624a..8788d983 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -91,16 +91,27 @@ class GeneralTrait(object): additive=self.additive ) elif self.dataset.type == "Publish": - return dict(name=self.name, - dataset=self.dataset.name, - description=self.description_display, - authors=self.authors, - pubmed_text=self.pubmed_text, - pubmed_link=self.pubmed_link, - lrs_score=self.LRS_score_repr, - lrs_location=self.LRS_location_repr, - additive=self.additive - ) + if self.pubmed_id: + return dict(name=self.name, + dataset=self.dataset.name, + description=self.description_display, + authors=self.authors, + pubmed_text=self.pubmed_text, + pubmed_link=self.pubmed_link, + lrs_score=self.LRS_score_repr, + lrs_location=self.LRS_location_repr, + additive=self.additive + ) + else: + return dict(name=self.name, + dataset=self.dataset.name, + description=self.description_display, + authors=self.authors, + pubmed_text=self.pubmed_text, + lrs_score=self.LRS_score_repr, + lrs_location=self.LRS_location_repr, + additive=self.additive + ) elif self.dataset.type == "Geno": return dict(name=self.name, dataset=self.dataset.name, @@ -109,6 +120,62 @@ class GeneralTrait(object): else: return dict() + def jsonable_table_row(self, index, search_type): + """Return a list suitable for json and intended to be displayed in a table + + Actual turning into json doesn't happen here though""" + + if self.dataset.type == "ProbeSet": + if self.mean == "": + mean = "N/A" + else: + mean = "%.3f" % round(float(self.additive), 2) + if self.additive == "": + additive = "N/A" + else: + additive = "%.3f" % round(float(self.additive), 2) + return ['', + index, + ''+str(self.name)+'', + self.symbol, + self.description_display, + self.location_repr, + mean, + self.LRS_score_repr, + self.LRS_location_repr, + additive] + elif self.dataset.type == "Publish": + if self.additive == "": + additive = "N/A" + else: + additive = "%.2f" % round(float(self.additive), 2) + if self.pubmed_id: + return ['', + index, + ''+str(self.name)+'', + self.description_display, + self.authors, + '' + self.pubmed_text + '', + self.LRS_score_repr, + self.LRS_location_repr, + additive] + else: + return ['', + index, + ''+str(self.name)+'', + self.description_display, + self.authors, + self.pubmed_text, + self.LRS_score_repr, + self.LRS_location_repr, + additive] + elif self.dataset.type == "Geno": + return ['', + index, + ''+str(self.name)+'', + self.location_repr] + else: + return dict() def get_name(self): stringy = "" @@ -418,7 +485,7 @@ class GeneralTrait(object): self.description_display = description_display #XZ: trait_location_value is used for sorting - trait_location_repr = 'N/A' + self.location_repr = 'N/A' trait_location_value = 1000000 if self.chr and self.mb: @@ -438,6 +505,18 @@ class GeneralTrait(object): self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb)) self.location_value = trait_location_value + elif self.dataset.type == "Geno": + self.location_repr = 'N/A' + trait_location_value = 1000000 + + if self.chr and self.mb: + #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") + #This is so we can convert the location to a number used for sorting + trait_location_value = convert_location_to_value(self.chr, self.mb) + + #ZS: Put this in function currently called "convert_location_to_value" + self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb)) + self.location_value = trait_location_value if get_qtl_info: #LRS and its location @@ -459,7 +538,7 @@ class GeneralTrait(object): logger.sql(query) trait_qtl = g.db.execute(query).fetchone() if trait_qtl: - self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl + self.locus, self.lrs, self.pvalue, self.mean, self.additive = trait_qtl if self.locus: query = """ select Geno.Chr, Geno.Mb from Geno, Species diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py index a924c7c9..cae6868e 100644 --- a/wqflask/wqflask/search_results.py +++ b/wqflask/wqflask/search_results.py @@ -86,12 +86,13 @@ views.py). """ self.trait_list = [] + json_trait_list = [] species = webqtlDatabaseFunction.retrieve_species(self.dataset.group.name) # result_set represents the results for each search term; a search of # "shh grin2b" would have two sets of results, one for each term logger.debug("self.results is:", pf(self.results)) - for result in self.results: + for index, result in enumerate(self.results): if not result: continue @@ -101,6 +102,9 @@ views.py). trait_id = result[0] this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False) self.trait_list.append(this_trait) + json_trait_list.append(this_trait.jsonable_table_row(index + 1)) + + self.json_trait_list = json.dumps(json_trait_list) #def get_group_species_tree(self): # self.species_groups = collections.default_dict(list) diff --git a/wqflask/wqflask/static/new/javascript/create_corr_matrix.js b/wqflask/wqflask/static/new/javascript/create_corr_matrix.js index adb91295..a34fc408 100644 --- a/wqflask/wqflask/static/new/javascript/create_corr_matrix.js +++ b/wqflask/wqflask/static/new/javascript/create_corr_matrix.js @@ -1,48 +1,47 @@ // Generated by CoffeeScript 1.8.0 -var get_data, get_options, root; +// var get_data, get_options, root; -root = typeof exports !== "undefined" && exports !== null ? exports : this; +// root = typeof exports !== "undefined" && exports !== null ? exports : this; -$(function() { - var chartOpts, data, mychart; - console.log("js_data:", js_data); - chartOpts = get_options(); - data = get_data(); - console.log(data); - return mychart = corr_matrix(data, chartOpts); -}); +// $(function() { + // var chartOpts, data, mychart; + // console.log("js_data:", js_data); + // chartOpts = get_options(); + // data = get_data(); + // console.log(data); + // return mychart = corr_matrix(data, chartOpts); +// }); -get_options = function() { - var chartOpts; - chartOpts = { - cortitle: "Correlation Matrix", - scattitle: "Scatterplot", - h: 450, - w: 450, - margin: { - left: 100, - top: 40, - right: 5, - bottom: 70, - inner: 5 - } - }; - return chartOpts; -}; - -get_data = function() { - var data; - data = {}; - data["var"] = js_data.traits; - data.group = js_data.groups; - data.indID = js_data.samples; - data.dat = js_data.sample_data; - data.corr = js_data.corr_results; - data.cols = js_data.cols; - data.rows = js_data.rows; - return data; -}; +// get_options = function() { + // var chartOpts; + // chartOpts = { + // cortitle: "Correlation Matrix", + // scattitle: "Scatterplot", + // h: 450, + // w: 450, + // margin: { + // left: 100, + // top: 40, + // right: 5, + // bottom: 70, + // inner: 5 + // } + // }; + // return chartOpts; +// }; +// get_data = function() { + // var data; + // data = {}; + // data["var"] = js_data.traits; + // data.group = js_data.groups; + // data.indID = js_data.samples; + // data.dat = js_data.sample_data; + // data.corr = js_data.corr_results; + // data.cols = js_data.cols; + // data.rows = js_data.rows; + // return data; +// }; var neg_color_scale = chroma.scale(['#FF0000', 'white']).domain([-1, -0.4]); var pos_color_scale = chroma.scale(['white', 'aqua']).domain([0.4, 1]) diff --git a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css index 076b6dae..9da73a8f 100644 --- a/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css +++ b/wqflask/wqflask/static/packages/bootstrap/css/non-responsive.css @@ -28,7 +28,7 @@ body { /* Reset the container */ .container { - width: 1200px; + width: 1400px; max-width: none !important; } diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html index 593c7bea..d847614a 100644 --- a/wqflask/wqflask/templates/correlation_matrix.html +++ b/wqflask/wqflask/templates/correlation_matrix.html @@ -36,7 +36,7 @@ {% if result[0].name == trait.name %} n
{{ result[2] }} {% else %} - {{ '%0.3f' % result[1] }}
{{ result[2] }} + {{ '%0.3f' % result[1] }}
{{ result[2] }} {% endif %} {% endfor %} @@ -85,6 +85,7 @@ {% block js %} @@ -98,5 +99,6 @@ + {% endblock %} diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html index c5b4477b..dab196cb 100644 --- a/wqflask/wqflask/templates/correlation_page.html +++ b/wqflask/wqflask/templates/correlation_page.html @@ -14,8 +14,8 @@

Correlation Table

-

Values of record {{ this_trait.name }} in the {{ dataset.fullname }} - dataset were compared to all records in the {{ target_dataset.fullname }} +

Values of record {{ this_trait.name }} in the {{ dataset.fullname }} + dataset were compared to all records in the {{ target_dataset.fullname }} dataset. The top {{ return_number }} correlations ranked by the {{ formatted_corr_type }} are displayed. You can resort this list by clicking the headers. Select the Record ID to open the trait data and analysis page. diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html index 0f5e68d7..f522564d 100644 --- a/wqflask/wqflask/templates/search_result_page.html +++ b/wqflask/wqflask/templates/search_result_page.html @@ -1,8 +1,8 @@ {% extends "base.html" %} {% block title %}Search Results{% endblock %} {% block css %} - - + + {% endblock %} @@ -11,7 +11,7 @@ {{ header("Search Results", 'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }} -

+
@@ -44,7 +44,7 @@ {% endfor %}

-

To study a record, click on its ID below. Check records below and click Add button to add to selection.

+

To study a record click on its ID below, and to view the whole description {% if dataset.type == "Publish" %}or list of authors {% endif %} hover over the table cell. Check records below and click Add button to add to selection.


@@ -79,7 +79,7 @@ -->
- +
@@ -94,46 +94,6 @@ {% endfor %} - - - {% for this_trait in trait_list %} - - - - - {% if dataset.type == 'ProbeSet' %} - - - - - - - - {% elif dataset.type == 'Publish' %} - - - - - - - {% elif dataset.type == 'Geno' %} - - {% endif %} - - {% endfor %} - {% if trait_list|length > 20 %} @@ -171,6 +131,10 @@ + +
- {{ loop.index }} - - {{ this_trait.name }} - - {{ this_trait.symbol }}{{ this_trait.description_display }}{{ this_trait.location_repr }}{{ '%0.3f' % this_trait.mean|float }}{{ '%0.3f' % this_trait.LRS_score_repr|float }}{{ this_trait.LRS_location_repr }}{{ '%0.3f' % this_trait.additive|float }}{{ this_trait.description_display }}{{ this_trait.authors }} - - {{ this_trait.pubmed_text }} - - {{ '%0.3f' % this_trait.LRS_score_repr|float }}{{ this_trait.LRS_location_repr }}{{ '%0.3f' % this_trait.additive|float }}{{ this_trait.location_repr }}