From 9e6ca731467c1449873c85422ba6f88840326fe3 Mon Sep 17 00:00:00 2001 From: Martijn Vermaat <martijn@vermaat.name> Date: Thu, 20 Nov 2014 16:46:44 +0100 Subject: [PATCH] Fix form buttons and general language issues --- mutalyzer/website/templates/batch-jobs.html | 4 +- .../templates/description-extractor.html | 2 +- mutalyzer/website/templates/homepage.html | 196 +++++++++--------- mutalyzer/website/templates/name-checker.html | 10 +- .../website/templates/name-generator.html | 17 +- .../website/templates/position-converter.html | 11 +- .../website/templates/reference-loader.html | 2 +- .../website/templates/snp-converter.html | 7 +- .../website/templates/static/js/generator.js | 18 +- .../website/templates/syntax-checker.html | 11 +- tests/test_website.py | 4 +- 11 files changed, 144 insertions(+), 138 deletions(-) diff --git a/mutalyzer/website/templates/batch-jobs.html b/mutalyzer/website/templates/batch-jobs.html index f428b69c..fc09635f 100644 --- a/mutalyzer/website/templates/batch-jobs.html +++ b/mutalyzer/website/templates/batch-jobs.html @@ -38,7 +38,7 @@ <div class="form-group"> <label for="email">Email address</label> - <input name="email" type="email" class="form-control" placeholder="Email address" required value="{{ email }}"> + <input name="email" type="email" class="form-control" placeholder="Email address (notification will be sent here)" required value="{{ email }}"> </div> <div class="form-group"> @@ -48,7 +48,7 @@ </div> <div class="form-group"> - <input type="submit" class="btn btn-primary" value="Submit"> + <input type="submit" class="btn btn-primary" value="Submit batch job"> <a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/BatchCheckers" target="new" class="btn btn-default pull-right">Help</a> <a href="#" onclick="toggle_visibility('help');" class="btn btn-default pull-right">File format help <span class="caret"></span></a> </div> diff --git a/mutalyzer/website/templates/description-extractor.html b/mutalyzer/website/templates/description-extractor.html index 98efb347..4d965cdf 100644 --- a/mutalyzer/website/templates/description-extractor.html +++ b/mutalyzer/website/templates/description-extractor.html @@ -41,7 +41,7 @@ Please supply a reference sequence and an observed sequence. <p>Example: <code class="example-input-2">ATGATTTGATCAGATACATGTGATACCGGTAGTTAGGACAA</code></p> </div> <div class="form-group"> - <input type="submit" class="btn btn-primary" value="Submit"> + <input type="submit" class="btn btn-primary" value="Extract variant description"> <a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/DescriptionExtractor" target="new" class="btn btn-default pull-right">Help</a> </div> </form> diff --git a/mutalyzer/website/templates/homepage.html b/mutalyzer/website/templates/homepage.html index cf3caf33..36b869e7 100644 --- a/mutalyzer/website/templates/homepage.html +++ b/mutalyzer/website/templates/homepage.html @@ -18,106 +18,106 @@ for the checks: </p> <div class="row"> - <div class="col-md-12"> - <div class="thumbnail thumb-home thumb-large"> - <div class="caption"> - <h3>Name Checker</h3> - <p>The Name Checker takes the complete sequence variant description as input and checks whether it is correct.</p> - <p>Example: <code class="example-input">AB026906.1:c.274G>T</code></p> - - <!-- <a href="{{ url_for('.name_checker') }}" class="btn btn-default btn-small btn-primary">Try - this</a> --> - - <form class="form" action="{{ url_for('.name_checker') }}" method="get"> - <div class="input-group"> - <input class="form-control form-control-small form-pre example-target" type="text" name="description" value="{{ description }}" placeholder="Mutation name using HGVS format"> - <span class="input-group-btn"> - <input type="submit" class="btn btn-primary pull-right" value="Try the Name Checker"> - </span> - </div> - </form> - - </div> - </div> - </div> + <div class="col-md-12"> + <div class="thumbnail thumb-home thumb-large"> + <div class="caption"> + <h3>Name Checker</h3> + <p>The Name Checker takes the complete sequence variant description as input and checks whether it is correct.</p> + <p>Example: <code class="example-input">AB026906.1:c.274G>T</code></p> + + <!-- <a href="{{ url_for('.name_checker') }}" class="btn btn-default btn-small btn-primary">Try + this</a> --> + + <form class="form" action="{{ url_for('.name_checker') }}" method="get"> + <div class="input-group"> + <input class="form-control form-control-small form-pre example-target" type="text" name="description" value="{{ description }}" placeholder="Variant description using HGVS format"> + <span class="input-group-btn"> + <input type="submit" class="btn btn-primary pull-right" value="Try the Name Checker"> + </span> + </div> + </form> + + </div> + </div> + </div> </div> <div class="row"> - <div class="col-md-3"> - <div class="thumbnail thumb-home clickbox color-1"> - <div class="caption"> - <h3>Syntax Checker</h3> - <p>The Syntax Checker takes the complete sequence variant description as input and checks whether the syntax is correct.</p> - <a href="{{ url_for('.syntax_checker') }}" class="btn btn-default btn-small btn-home-down">Try this</a> - </div> - </div> - </div> - <div class="col-md-3"> - <div class="thumbnail thumb-home clickbox color-2"> - <div class="caption"> - <h3>Position Converter</h3> - <p>The Position Converter can convert chromosomal positions to transcript orientated positions and vice versa.</p> - <a href="{{ url_for('.position_converter') }}" class="btn btn-default btn-small btn-home-down">Try this</a> - </div> - </div> - </div> - <div class="col-md-3"> - <div class="thumbnail thumb-home clickbox color-3"> - <div class="caption"> - <h3>SNP Converter</h3> - <p>The SNP Converter allows you to convert a dbSNP rsId to HGVS notation.</p> - <a href="{{ url_for('.snp_converter') }}" class="btn btn-default btn-small btn-home-down">Try this</a> - </div> - </div> - </div> - <div class="col-md-3"> - <div class="thumbnail thumb-home clickbox color-4"> - <div class="caption"> - <h3>Name Generator</h3> - <p>The Name Generator is a user friendly interface that helps to make a valid HGVS variant description.</p> - <a href="{{ url_for('.name_generator') }}" class="btn btn-default btn-small btn-home-down">Try this</a> - </div> - </div> - </div> + <div class="col-md-3"> + <div class="thumbnail thumb-home clickbox color-1"> + <div class="caption"> + <h3>Syntax Checker</h3> + <p>The Syntax Checker takes the complete sequence variant description as input and checks whether the syntax is correct.</p> + <a href="{{ url_for('.syntax_checker') }}" class="btn btn-default btn-small btn-home-down">Try this</a> + </div> + </div> + </div> + <div class="col-md-3"> + <div class="thumbnail thumb-home clickbox color-2"> + <div class="caption"> + <h3>Position Converter</h3> + <p>The Position Converter can convert chromosomal positions to transcript orientated positions and vice versa.</p> + <a href="{{ url_for('.position_converter') }}" class="btn btn-default btn-small btn-home-down">Try this</a> + </div> + </div> + </div> + <div class="col-md-3"> + <div class="thumbnail thumb-home clickbox color-3"> + <div class="caption"> + <h3>SNP Converter</h3> + <p>The SNP Converter allows you to convert a dbSNP rsId to HGVS notation.</p> + <a href="{{ url_for('.snp_converter') }}" class="btn btn-default btn-small btn-home-down">Try this</a> + </div> + </div> + </div> + <div class="col-md-3"> + <div class="thumbnail thumb-home clickbox color-4"> + <div class="caption"> + <h3>Name Generator</h3> + <p>The Name Generator is a user friendly interface that helps to make a valid HGVS variant description.</p> + <a href="{{ url_for('.name_generator') }}" class="btn btn-default btn-small btn-home-down">Try this</a> + </div> + </div> + </div> </div> <div class="row"> - <div class="col-md-3"> - <div class="thumbnail thumb-home clickbox color-5"> - <div class="caption"> - <h3>Description Extractor</h3> - <p>The Description Extractor allows you to generate the HGVS variant description from a reference sequence and an observed sequence.</p> - <a href="{{ url_for('.description_extractor') }}" class="btn btn-default btn-small btn-home-down">Try this</a> - </div> - </div> - </div> - <div class="col-md-3"> - <div class="thumbnail thumb-home clickbox color-6"> - <div class="caption"> - <h3>Reference File Loader</h3> - <p>The Reference File Loader allows you to load and use your own reference sequence.</p> - <a href="{{ url_for('.reference_loader') }}" class="btn btn-default btn-small btn-home-down">Try this</a> - </div> - </div> - </div> - <div class="col-md-3"> - <div class="thumbnail thumb-home clickbox color-7"> - <div class="caption"> - <h3>Batch Checkers</h3> - <p>The Batch Checkers are interfaces that accept a list of inputs. These interfaces can be used for large quantities of checks is correct.</p> - <a href="{{ url_for('.batch_jobs') }}" class="btn btn-default btn-small btn-home-down">Try this</a> - </div> - </div> - </div> - <div class="col-md-3"> - <div class="thumbnail thumb-home clickbox color-8"> - <div class="caption"> - <h3>Web services</h3> - <p>The Web services page provides instructions for the web services.</p> - <a href="{{ url_for('.webservices') }}" class="btn btn-default btn-small btn-home-down">Try this</a> - </div> - </div> - </div> + <div class="col-md-3"> + <div class="thumbnail thumb-home clickbox color-5"> + <div class="caption"> + <h3>Description Extractor</h3> + <p>The Description Extractor allows you to generate the HGVS variant description from a reference sequence and an observed sequence.</p> + <a href="{{ url_for('.description_extractor') }}" class="btn btn-default btn-small btn-home-down">Try this</a> + </div> + </div> + </div> + <div class="col-md-3"> + <div class="thumbnail thumb-home clickbox color-6"> + <div class="caption"> + <h3>Reference File Loader</h3> + <p>The Reference File Loader allows you to load and use your own reference sequence.</p> + <a href="{{ url_for('.reference_loader') }}" class="btn btn-default btn-small btn-home-down">Try this</a> + </div> + </div> + </div> + <div class="col-md-3"> + <div class="thumbnail thumb-home clickbox color-7"> + <div class="caption"> + <h3>Batch Checkers</h3> + <p>The Batch Checkers are interfaces that accept a list of inputs. These interfaces can be used for large quantities of checks is correct.</p> + <a href="{{ url_for('.batch_jobs') }}" class="btn btn-default btn-small btn-home-down">Try this</a> + </div> + </div> + </div> + <div class="col-md-3"> + <div class="thumbnail thumb-home clickbox color-8"> + <div class="caption"> + <h3>Web Services</h3> + <p>The Web services page provides instructions for the web services.</p> + <a href="{{ url_for('.webservices') }}" class="btn btn-default btn-small btn-home-down">Try this</a> + </div> + </div> + </div> </div> @@ -136,10 +136,10 @@ This project is sponsored by <a href = "http://www.sun.com">SUN Microsystems</a> </p> <script> - $(".clickbox").click(function(){ - window.location=$(this).find("a").attr("href"); - return false; - }); + $(".clickbox").click(function(){ + window.location=$(this).find("a").attr("href"); + return false; + }); </script> {% endblock content %} diff --git a/mutalyzer/website/templates/name-checker.html b/mutalyzer/website/templates/name-checker.html index a568c9f9..72ebc317 100644 --- a/mutalyzer/website/templates/name-checker.html +++ b/mutalyzer/website/templates/name-checker.html @@ -40,7 +40,7 @@ {% if not standalone %} <p> - Please insert the mutation name using + Please insert the variant description using the <a href="http://www.hgvs.org/mutnomen" title="Human Genome Variation Society standard variant nomenclature" alt="Human Genome Variation Society standard variant nomenclature">HGVS</a> format: @@ -50,13 +50,15 @@ <form class="form" action="{{ url_for('.name_checker') }}" method="get"> <div class="form-group"> - <label for="description">HGVS Description</label> - <input class="form-control form-pre example-target" type="text" name="description" id="hgvs" value="{{ description }}" placeholder="Mutation name using HGVS format"> + <label for="description">Variant description</label> + <input class="form-control form-pre example-target" type="text" + name="description" id="hgvs" value="{{ description }}" + placeholder="Variant description using HGVS format"> <p>Example: <code class="example-input">AB026906.1:c.274G>T</code></p> </div> <div class="form-group button-group"> - <input type="submit" class="btn btn-primary" value="Check name"> + <input type="submit" class="btn btn-primary" value="Check variant description"> <a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/NameChecker" target="new" class="btn btn-default pull-right">Help</a> </div> </form> diff --git a/mutalyzer/website/templates/name-generator.html b/mutalyzer/website/templates/name-generator.html index fcf152e3..3e948b6c 100644 --- a/mutalyzer/website/templates/name-generator.html +++ b/mutalyzer/website/templates/name-generator.html @@ -7,7 +7,8 @@ <div class="form"> - <p>Construct the mutation from a reference by adding variants to it. The HGVS name is constructed instantly <a href="#constructed_name">below</a>. + <p>Construct the variant from a reference by adding variants to + it. The HGVS variant description is constructed instantly <a href="#constructed_name">below</a>. <hr/> @@ -22,7 +23,7 @@ </div> <div class="form-group"> - <label for="seqT" class="col-sm-2 control-label">Sequence Type</label> + <label for="seqT" class="col-sm-2 control-label">Sequence type</label> <div class="col-sm-10"> <select name="seqT" class="form-control"> <option value="g">Genomic</option> @@ -84,7 +85,7 @@ <div id="varianttemplate" style="display: none"> <div class="row form-horizontal-inline"> <div class="form-group col-md-6" id="V{NMBR}mutTrow"> - <label for="V{NMBR}mutT" id="V{NMBR}mutTname">Mutation Type</label> + <label for="V{NMBR}mutT" id="V{NMBR}mutTname">Variant type</label> <select name="V{NMBR}mutT" onchange="update();"class="form-control input-sm" > <option value="1">Substitution</option> <option value="2">Deletion</option> @@ -97,13 +98,13 @@ </div> <div class="form-group col-md-6" id="V{NMBR}P1row"> - <label id="V{NMBR}P1name">Start Position</label> + <label id="V{NMBR}P1name">Start position</label> <input type="text" name="V{NMBR}P1" value="" class="form-control input-sm"> <div class="text-danger small" id="V{NMBR}P1error"></div> </div> <div class="form-group col-md-6" id="V{NMBR}P2row"> - <label id="V{NMBR}P2name">End Position</label> + <label id="V{NMBR}P2name">End position</label> <input type="text" name="V{NMBR}P2" size="20" value="" class="form-control input-sm" > <div class="text-danger small" id="V{NMBR}P2error"></div> </div> @@ -111,7 +112,7 @@ <div class="row form-horizontal-inline"> <div class="col-md-6" id="V{NMBR}S1row"> <div class="form-group" name="S1"> - <label id="V{NMBR}S1name">Old Sequence</label> + <label id="V{NMBR}S1name">Old sequence</label> <input type="text" name="V{NMBR}S1" size="20" value=""class="form-control input-sm"> <div class="text-danger small" id="V{NMBR}S1error"></div> </div> @@ -119,7 +120,7 @@ <div class="col-md-6" id="V{NMBR}S2row"> <div class="form-group" name="S2"> - <label id="V{NMBR}S2name">New Sequence</label> + <label id="V{NMBR}S2name">New sequence</label> <input type="text" name="V{NMBR}S2" size="20" value=""class="form-control input-sm"> <div class="text-danger small" id="V{NMBR}S2error"></div> </div> @@ -144,7 +145,7 @@ <hr/> - <a id="constructed_name"></a><h4>Constructed HGVS Name</h4> + <a id="constructed_name"></a><h4>Constructed HGVS variant description</h4> <p><code id="output" > <!-- Empty PlaceHolder --> </code></p> diff --git a/mutalyzer/website/templates/position-converter.html b/mutalyzer/website/templates/position-converter.html index 8099e3f1..e784e72b 100644 --- a/mutalyzer/website/templates/position-converter.html +++ b/mutalyzer/website/templates/position-converter.html @@ -26,12 +26,13 @@ normalize it to HGVS. Use the <a href="{{ url_for('.name_checker') }}">Name Chec </select> </div> <div class="form-group"> - <label for="description">Variant</label> - <input type="text" name="description" value="{{ description }}" class="form-control form-pre example-target" placeholder="Variant"> + <label for="description">Variant description</label> + <input type="text" name="description" value="{{ description }}" + class="form-control form-pre example-target" placeholder="Variant description using HGVS format"> <p>Examples: <code class="example-input">NM_003002.3:c.274G>T</code>, <code class="example-input">chr11:g.111959693G>T</code> and <code class="example-input">NC_000011.9:g.111959693G>T</code></p> </div> <div class="form-group button-group"> - <input type="submit" class="btn btn-primary" value="Submit"> + <input type="submit" class="btn btn-primary" value="Convert variant description"> <a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/PositionConverter" target="new" class="btn btn-default pull-right">Help</a> </div> </form> @@ -57,10 +58,10 @@ normalize it to HGVS. Use the <a href="{{ url_for('.name_checker') }}">Name Chec <p><code>{{ chromosomal_description }}</code></p> {% if transcript_descriptions %} - <h4>Found transcripts in mutation region</h4> + <h4>Found transcripts in variant region</h4> <pre>{% for d in transcript_descriptions %}{{ d }}<br>{% endfor %}</pre> {% else %} - <h4>No transcripts found in mutation region</h4> + <h4>No transcripts found in variant region</h4> {% endif %} {% endif %} {% endif %}{# description #} diff --git a/mutalyzer/website/templates/reference-loader.html b/mutalyzer/website/templates/reference-loader.html index 5f97e21c..1accdadd 100644 --- a/mutalyzer/website/templates/reference-loader.html +++ b/mutalyzer/website/templates/reference-loader.html @@ -153,7 +153,7 @@ sequence (maximum size is {{ max_file_size }} megabytes). </div> </div> <div class="form-group"> - <input type="submit" value="Submit"class="btn btn-primary"> + <input type="submit" value="Load reference file"class="btn btn-primary"> <a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/ReferenceLoader" target="_blank" class="btn btn-default pull-right">Help</a> </div> </form> diff --git a/mutalyzer/website/templates/snp-converter.html b/mutalyzer/website/templates/snp-converter.html index 69ea6c44..2b084818 100644 --- a/mutalyzer/website/templates/snp-converter.html +++ b/mutalyzer/website/templates/snp-converter.html @@ -14,13 +14,14 @@ the reference sequence(s) used by dbSNP. <form role="form" class="form" action="{{ url_for('.snp_converter') }}" method="get"> <div class="form-group"> - <label for="description">dbSNP rs number</label> - <input type="text" class="form-control form-pre example-target" name="rs_id" placeholder="" value="{{ rs_id }}" ></input> + <label for="description">SNP</label> + <input type="text" class="form-control form-pre example-target" + name="rs_id" placeholder="dbSNP rs number (including rs)" value="{{ rs_id }}" ></input> <p>Example: <code class="example-input">rs9919552</code></p> </div> <div class="form-group"> - <input type="submit" class="btn btn-primary" value="Submit"> + <input type="submit" class="btn btn-primary" value="Convert SNP"> <a href="https://humgenprojects.lumc.nl/trac/mutalyzer/wiki/SnpConverter" target="new" class="btn btn-default pull-right">Help</a> </div> </form> diff --git a/mutalyzer/website/templates/static/js/generator.js b/mutalyzer/website/templates/static/js/generator.js index 04ea449c..b330c141 100644 --- a/mutalyzer/website/templates/static/js/generator.js +++ b/mutalyzer/website/templates/static/js/generator.js @@ -101,18 +101,18 @@ var reference = { 'ok' : false, 'check' : isReference, 'errStr' : "should be of the format \"NM_002001.2\""}, - 'seqT': {'name' : "Sequence Type", + 'seqT': {'name' : "Sequence type", 'len' : "1", 'value' : "c", 'ok' : false, 'check' : isSequenceType, - 'errStr' : "You managed to select an impossible Sequence Type. Muppet!"}, - 'gSym': {'name' : "Gene Symbol", + 'errStr' : "You managed to select an impossible sequence type. Muppet!"}, + 'gSym': {'name' : "Gene symbol", 'len' : "*", 'value' : "", 'ok' : false, 'check' : isGeneSymbol, - 'errStr' : "should only contain Letters and Numbers"}, + 'errStr' : "should only contain letters and numbers"}, 'tVar': {'name' : "Transcript", 'len' : "*", 'value' : "", @@ -193,11 +193,11 @@ var seqTypes = { 'pr1' : { 'pCheck' : isPosition, 'sCheck' : isProteinSequence1, - 'errorStr' : "must consist of the Single Letter AminoAcids Code"}, + 'errorStr' : "must consist of the single letter amino acids code"}, 'pr3' : { 'pCheck' : isPosition, 'sCheck' : isProteinSequence3, - 'errorStr' : "must consist of the Three Letter AminoAcids Code"} + 'errorStr' : "must consist of the three letter amino acids code"} } /* mutTypes Object @@ -319,9 +319,9 @@ var VariantField = { var i = this[name].index; return mutTypes[this["mType"]]["flags"].substring(i,i+1);}, getName : function(name){ - var S1Name = mutTypes[this["mType"]]["S1"]+" Sequence"; - var S2Name = mutTypes[this["mType"]]["S2"]+" Sequence"; - var defaultnames = ["Start Position", "End Position", S1Name, S2Name]; + var S1Name = mutTypes[this["mType"]]["S1"]+" sequence"; + var S2Name = mutTypes[this["mType"]]["S2"]+" sequence"; + var defaultnames = ["Start position", "End position", S1Name, S2Name]; return defaultnames[this[name].index];}, getErr : function(name){ if(name.substring(1,0)=="P") diff --git a/mutalyzer/website/templates/syntax-checker.html b/mutalyzer/website/templates/syntax-checker.html index 3854c8c1..118cc85c 100644 --- a/mutalyzer/website/templates/syntax-checker.html +++ b/mutalyzer/website/templates/syntax-checker.html @@ -1,12 +1,12 @@ {% extends "base.html" %} {% set active_page = "syntax-checker" %} -{% set page_title = "Syntax checker" %} +{% set page_title = "Syntax Checker" %} {% block content %} <p> -Please insert the mutation name using +Please insert the variant description using the <a href="http://www.hgvs.org/mutnomen" title="Human Genome Variation Society standard variant nomenclature" alt="Human Genome Variation Society standard variant nomenclature">HGVS</a> format: @@ -16,8 +16,9 @@ standard variant nomenclature">HGVS</a> format: <form class="form" action="{{ url_for('.syntax_checker') }}" method="get"> <div class="form-group"> - <label for="description">HGVS Description</label> - <input class="form-control form-pre example-target" type="text" name="description" value="{{ description }}" placeholder="Mutation name using HGVS format"> + <label for="description">Variant description</label> + <input class="form-control form-pre example-target" type="text" + name="description" value="{{ description }}" placeholder="Variant description using HGVS format"> <p>Example: <code class="example-input">AB026906.1:c.274G>T</code></p> </div> <div class="form-group button-group"> @@ -35,7 +36,7 @@ standard variant nomenclature">HGVS</a> format: <p>The "^" indicates the position where the error occurred.</p> </div> {% else %} - <p class="alert alert-success">The syntax of this variant is OK!</p> + <p class="alert alert-success">The syntax of this variant description is OK!</p> {% endif %} {% if messages %} diff --git a/tests/test_website.py b/tests/test_website.py index 06b19d9d..b299722d 100644 --- a/tests/test_website.py +++ b/tests/test_website.py @@ -115,7 +115,7 @@ class TestWebsite(MutalyzerTest): """ r = self.app.get('/syntax-checker', query_string={'description': 'AB026906.1:c.274G>T'}) - assert 'The syntax of this variant is OK!' in r.data + assert 'The syntax of this variant description is OK!' in r.data def test_checksyntax_invalid(self): """ @@ -137,7 +137,7 @@ class TestWebsite(MutalyzerTest): assert '0 Errors' in r.data assert '0 Warnings' in r.data assert 'Raw variant 1: deletion of 1' in r.data - assert '<input class="form-control form-pre example-target" type="text" name="description" id="hgvs" value="NM_002001.2:g.1del" placeholder="Mutation name using HGVS format">' in r.data + assert 'value="NM_002001.2:g.1del"' in r.data def test_check_invalid(self): """ -- GitLab