diff options
Diffstat (limited to 'uploader/templates')
| -rw-r--r-- | uploader/templates/base.html | 87 | ||||
| -rw-r--r-- | uploader/templates/index.html | 134 | ||||
| -rw-r--r-- | uploader/templates/login.html | 7 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/add-phenotypes-raw-files.html | 2 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/edit-phenotype.html | 361 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/view-dataset.html | 69 | ||||
| -rw-r--r-- | uploader/templates/phenotypes/view-phenotype.html | 54 | ||||
| -rw-r--r-- | uploader/templates/platforms/list-platforms.html | 2 | ||||
| -rw-r--r-- | uploader/templates/populations/list-populations.html | 2 | ||||
| -rw-r--r-- | uploader/templates/populations/macro-display-population-card.html | 5 | ||||
| -rw-r--r-- | uploader/templates/populations/macro-select-population.html | 41 | ||||
| -rw-r--r-- | uploader/templates/samples/list-samples.html | 2 | ||||
| -rw-r--r-- | uploader/templates/species/list-species.html | 2 | ||||
| -rw-r--r-- | uploader/templates/species/macro-select-species.html | 42 |
14 files changed, 485 insertions, 325 deletions
diff --git a/uploader/templates/base.html b/uploader/templates/base.html index c124b13..90652bf 100644 --- a/uploader/templates/base.html +++ b/uploader/templates/base.html @@ -8,7 +8,7 @@ <meta name="viewport" content="width=device-width, initial-scale=1.0" /> {%block extrameta%}{%endblock%} - <title>GN Uploader: {%block title%}{%endblock%}</title> + <title>Data Upload and Quality Control: {%block title%}{%endblock%}</title> <link rel="stylesheet" type="text/css" href="{{url_for('base.bootstrap', @@ -23,25 +23,26 @@ </head> <body> - <header id="header" class="container-fluid"> - <div class="row"> - <span class="header col-lg-9">GeneNetwork Data Quality Control and Upload</span> - <nav class="header-nav col-lg-3"> - <ul class="nav justify-content-end"> - <li> - {%if user_logged_in()%} - <a href="{{url_for('oauth2.logout')}}" - title="Log out of the system">{{user_email()}} — Log Out</a> - {%else%} - <a href="{{authserver_authorise_uri()}}" - title="Log in to the system">Log In</a> - {%endif%} - </li> - </ul> - </nav> + <header id="header"> + <span id="header-text">GeneNetwork</span> + <nav id="header-nav"> + <ul class="nav justify-content-end"> + <li> + {%if user_logged_in()%} + <a href="{{url_for('oauth2.logout')}}" + title="Log out of the system"> + <span class="glyphicon glyphicon-user"></span> + Sign Out</a> + {%else%} + <a href="{{authserver_authorise_uri()}}" + title="Log in to the system">Sign In</a> + {%endif%} + </li> + </ul> + </nav> </header> - <aside id="nav-sidebar" class="container-fluid"> + <aside id="nav-sidebar"> <ul class="nav flex-column"> <li {%if activemenu=="home"%}class="activemenu"{%endif%}> <a href="/" >Home</a></li> @@ -70,6 +71,7 @@ <li {%if activemenu=="phenotypes"%}class="activemenu"{%endif%}> <a href="{{url_for('species.populations.phenotypes.index')}}" title="Upload phenotype data.">Phenotype Data</a></li> + <!-- <li {%if activemenu=="expression-data"%}class="activemenu"{%endif%}> <a href="{{url_for('species.populations.expression-data.index')}}" title="Upload expression data." @@ -87,35 +89,36 @@ class="not-implemented" title="View and manage the backgroud jobs you have running"> Background Jobs</a></li> + --> </ul> </aside> - <main id="main" class="main container-fluid"> + <main id="main" class="main"> - <div class="pagetitle row"> - <span class="title">GN Uploader: {%block pagetitle%}{%endblock%}</span> - <nav> - <ol class="breadcrumb"> - <li {%if activelink is not defined or activelink=="home"%} - class="breadcrumb-item active" - {%else%} - class="breadcrumb-item" - {%endif%}> - <a href="{{url_for('base.index')}}">Home</a> - </li> - {%block lvl1_breadcrumbs%}{%endblock%} - </ol> - </nav> + <div id="pagetitle" class="pagetitle"> + <span class="title">Data Upload and Quality Control: {%block pagetitle%}{%endblock%}</span> + <!-- + <nav> + <ol class="breadcrumb"> + <li {%if activelink is not defined or activelink=="home"%} + class="breadcrumb-item active" + {%else%} + class="breadcrumb-item" + {%endif%}> + <a href="{{url_for('base.index')}}">Home</a> + </li> + {%block lvl1_breadcrumbs%}{%endblock%} + </ol> + </nav> + --> </div> - <div class="row"> - <div class="container-fluid"> - <div class="col-md-8 main-content"> - {%block contents%}{%endblock%} - </div> - <div class="sidebar-content col-md-4"> - {%block sidebarcontents%}{%endblock%} - </div> + <div id="all-content"> + <div id="main-content"> + {%block contents%}{%endblock%} + </div> + <div id="sidebar-content"> + {%block sidebarcontents%}{%endblock%} </div> </div> </main> @@ -127,7 +130,5 @@ filename='js/bootstrap.min.js')}}"></script> <script type="text/javascript" src="/static/js/misc.js"></script> {%block javascript%}{%endblock%} - </body> - </html> diff --git a/uploader/templates/index.html b/uploader/templates/index.html index d6f57eb..aa1414e 100644 --- a/uploader/templates/index.html +++ b/uploader/templates/index.html @@ -10,90 +10,98 @@ <div class="row"> {{flash_all_messages()}} <div class="explainer"> - <p>Welcome to the <strong>GeneNetwork Data Quality Control and Upload System</strong>. This system is provided to help in uploading your data onto GeneNetwork where you can do analysis on it.</p> + <p>Welcome to the <strong>GeneNetwork Data Upload and Quality Control + System</strong>.</p> + <p>This tool helps you prepare and upload research data to GeneNetwork for + analysis.</p> - <p>The sections below provide an overview of what features the menu items on - the left provide to you. Please peruse the information to get a good - big-picture understanding of what the system provides you and how to get - the most out of it.</p> + <h2 class="heading">Getting Started</h2> + <p>The sections below explain the features of the system. Review this guide + to learn how to use the system.</p> {%block extrapageinfo%}{%endblock%} - <h2>Species</h2> - - <p>The GeneNetwork service provides datasets and tools for doing genetic - studies — from - <a href="{{gn2server_intro}}" - target="_blank" - title="GeneNetwork introduction — opens in a new tab."> - its introduction</a>: - - <blockquote class="blockquote"> - <p>GeneNetwork is a group of linked data sets and tools used to study - complex networks of genes, molecules, and higher order gene function - and phenotypes. …</p> - </blockquote> - </p> - - <p>With this in mind, it follows that the data in the system is centered - aroud a variety of species. The <strong>species section</strong> will - list the currently available species in the system, and give you the - ability to add new ones, if the one you want to work on does not currently - exist on GeneNetwork</p> - - <h2>Populations</h2> - - <p>Your studies will probably focus on a particular subset of the entire - species you are interested in – your population.</p> - <p>Populations are a way to organise the species data so as to link data to - specific know populations for a particular species, e.g. The BXD - population of mice (Mus musculus)</p> - <p>In older GeneNetwork documentation, you might run into the term - <em>InbredSet</em>. Should you run into it, it is a term that we've - deprecated that essentially just means the population.</p> - - <h2>Samples</h2> - - <p>These are the samples or individuals (sometimes cases) that were involved - in the experiment, and from whom the data was derived.</p> - - <h2>Genotype Data</h2> - - <p>This section will allow you to view and upload the genetic markers for - your species, and the genotype encodings used for your particular - population.</p> - <p>While, technically, genetic markers relate to the species in general, and - not to a particular population, the data (allele information) itself - relates to the particular population it was generated from – - specifically, to the actual individuals used in the experiment.</p> - <p>This is the reason why the genotype data information comes under the - population, and will check for the prior existence of the related - samples/individuals before attempting an upload of your data.</p> - - <h2>Expression Data</h2> + <h3 class="subheading">Species</h3> - <p class="text-danger"> - <span class="glyphicon glyphicon-exclamation-sign"></span> - <strong>TODO</strong>: Document this …</p> + <p>GeneNetwork supports genetic studies across multiple species (e.g. mice + [Mus musculus], human [homo sapiens], rats [Rattus norvegicus], etc.) . + Here you can:</p> + <ul> + <li>View all species that are currently supported</li> + <li>Add new species not yet in the system</li> + </ul> + + <h3 class="subheading">Populations</h3> + + <p>A "population" refers to a specific subgroup within a species that you’re + studying (e.g., BXD mice). Here you can:</p> + <ul> + <li>View the populations that exist for a selected species</li> + <li>Add new populations of study for a selected species</li> + </ul> + + <h3 class="subheading">Samples</h3> + + <p>Manage individual specimens or cases used in your experiments. These + include:</p> + + <ul> + <li>Experimental subjects</li> + <li>Data sources (e.g., tissue samples, clinical cases)</li> + <li>Strain means (instead of entering multiple BXD1 individuals, for + example, the mean would be entered for a single BXD1 strain)</li> + </ul> + + + <h3 class="subheading">Genotype Data</h3> + + <p>Upload and review genetic markers and allele encodings for your + population. Key details:</p> + + <ul> + <li>Markers are species-level (e.g., mouse SNP databases).</li> + <li>Allele data is population-specific (tied to your experimental + samples).</li> + </ul> + + <p><strong>Requirement</strong>: Samples must already have been registered + in the system before uploading genotype data.</p> + + <h3 class="subheading">Phenotype Data</h3> + + <p>Phenotypes are the visible traits or features of a living thing. For + example, phenotypes include:</p> + + <ul> + <li>Weight</li> + <li>Height</li> + <li>Color (such as the color of fur or eyes)</li> + </ul> + + <p>This part of the system will allow you to upload and manage the values + for different phenotypes from various samples in your studies.</p> + + <!-- - <h2>Phenotype Data</h2> + <h3 class="subheading">Expression Data</h3> <p class="text-danger"> <span class="glyphicon glyphicon-exclamation-sign"></span> <strong>TODO</strong>: Document this …</p> - <h2>Individual Data</h2> + <h3 class="subheading">Individual Data</h3> <p class="text-danger"> <span class="glyphicon glyphicon-exclamation-sign"></span> <strong>TODO</strong>: Document this …</p> - <h2>RNA-Seq Data</h2> + <h3 class="subheading">RNA-Seq Data</h3> <p class="text-danger"> <span class="glyphicon glyphicon-exclamation-sign"></span> <strong>TODO</strong>: Document this …</p> </div> + --> </div> {%endblock%} diff --git a/uploader/templates/login.html b/uploader/templates/login.html index 1f71416..e76c644 100644 --- a/uploader/templates/login.html +++ b/uploader/templates/login.html @@ -5,7 +5,8 @@ {%block pagetitle%}log in{%endblock%} {%block extrapageinfo%} -<p class="text-dark text-primary"> - You <strong>do need to be logged in</strong> to upload data onto this system. - Please do that by clicking the "Log In" button at the top of the page.</p> +<p class="text-dark"> + You <strong>need to + <a href="{{authserver_authorise_uri()}}" + title="Sign in to the system">sign in</a></strong> to use this system.</p> {%endblock%} diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html index d9a8424..7f8d8b0 100644 --- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html +++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html @@ -600,10 +600,12 @@ console.log("SUCCESS DATA: ", data); console.log("SUCCESS STATUS: ", textstatus); console.log("SUCCESS jqXHR: ", jqxhr); + window.location.assign(window.location.origin + data["redirect-to"]); }, }); return false; } + return false; }; var uploadSuccess = (file_input_name) => { diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html index 8b1642c..32c903f 100644 --- a/uploader/templates/phenotypes/edit-phenotype.html +++ b/uploader/templates/phenotypes/edit-phenotype.html @@ -25,165 +25,302 @@ <div class="row"> <h2 class="heading">edit phenotype data</h2> - <p>The two (2) forms provided in this page help you update the data for the + <p>The forms provided in this page help you update the data for the phenotypes, and the publication information for the phenotype, respectively.</p> </div> <div class="row"> + <h3 class="subheading">Basic metadata</h3> + <form name="frm-phenotype-basic-metadata" + class="form-horizontal" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}"> + <input type="hidden" name="phenotype-id" value="{{phenotype.Id}}" /> + <div class="form-group"> + <label for="txt-pre-publication-description" + class="control-label col-sm-2">Pre-Publication Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-pre-publication-description" + name="pre-publication-description" + class="form-control" + value="{{phenotype['Pre_publication_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-pre-publication-abbreviation" + class="control-label col-sm-2">Pre-Publication Abbreviation</label> + <div class="col-sm-10"> + <input type="text" + id="txt-pre-publication-abbreviation" + name="pre-publication-abbreviation" + class="form-control" + value="{{phenotype['Pre_publication_abbreviation'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-post-publication-description" + class="control-label col-sm-2">Post-Publication Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-post-publication-description" + name="post-publication-description" + class="form-control" + value="{{phenotype['Post_publication_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-post-publication-abbreviation" + class="control-label col-sm-2">Post-Publication Abbreviation</label> + <div class="col-sm-10"> + <input type="text" + id="txt-post-publication-abbreviation" + name="post-publication-abbreviation" + class="form-control" + value="{{phenotype['Post_publication_abbreviation'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-original-description" + class="control-label col-sm-2">Original Description</label> + <div class="col-sm-10"> + <input type="text" + id="txt-original-description" + name="original-description" + class="form-control" + value="{{phenotype['Original_description'] or ''}}" /> + </div> + </div> + + <div class="form-group"> + <label for="txt-units" + class="control-label col-sm-2">units</label> + <div class="col-sm-10"> + <input type="text" + id="txt-units" + name="units" + class="form-control" + required="required" + value="{{phenotype['Units']}}" /> + </div> + </div> + + <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + name="submit" + class="btn btn-primary" + value="update basic metadata"> + </div> + </div> + </form> +</div> + + +<div class="row"> <h3 class="subheading">phenotype data</h3> - <form id="frm-edit-phenotype-data"> + <form id="frm-edit-phenotype-data" + class="form-horizontal" + method="POST" + action="{{url_for( + 'species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}"> <div style="max-height: 23.37em;overflow-y: scroll;"> - <table class="table table-striped table-responsive table-form-table"> - <thead style="position: sticky; top: 0;"> - <tr> - <th>#</th> - <th>Sample</th> - <th>Value</th> - {%if population.Family in families_with_se_and_n%} - <th>Standard-Error</th> - <th>Number of Samples</th> - {%endif%} - </tr> - </thead> - - <tbody> - {%for item in phenotype.data%} - <tr> - <td>{{loop.index}}</td> - <td>{{item.StrainName}}</td> - <td> - <input type="text" - name="value::{{item.DataId}}::{{item.StrainId}}" - value="{{item.value}}" - data-original-value="{{item.value}}" - class="form-control" /></td> - {%if population.Family in families_with_se_and_n%} - <td> - <input type="text" - name="se::{{item.DataId}}::{{item.StrainId}}" - value="{{item.error or ''}}" - data-original-value="{{item.error or ''}}" - class="form-control" /></td> - <td><input type="text" - name="n::{{item.DataId}}::{{item.StrainId}}" + <table class="table table-striped table-responsive table-form-table"> + <thead style="position: sticky; top: 0;"> + <tr> + <th>#</th> + <th>Sample</th> + <th>Value</th> + {%if population.Family in families_with_se_and_n%} + <th>Standard-Error</th> + <th>Number of Samples</th> + {%endif%} + </tr> + </thead> + + <tbody> + {%for item in phenotype.data%} + <tr> + <td>{{loop.index}}</td> + <td>{{item.StrainName}}</td> + <td> + <input type="text" + name="value-new::{{item.DataId}}::{{item.StrainId}}" + value="{{item.value}}" + class="form-control" /> + <input type="hidden" + name="value-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.value}}" /></td> + {%if population.Family in families_with_se_and_n%} + <td> + <input type="text" + name="se-new::{{item.DataId}}::{{item.StrainId}}" + value="{{item.error or ''}}" + data-original-value="{{item.error or ''}}" + class="form-control" /> + <input type="hidden" + name="se-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.error or ''}}" /></td> + <td> + <input type="text" + name="n-new::{{item.DataId}}::{{item.StrainId}}" value="{{item.count or ''}}" data-original-value="{{item.count or "-"}}" - class="form-control" /></td> - {%endif%} - </tr> - {%endfor%} - </tbody> - </table> + class="form-control" /> + <input type="hidden" + name="n-original::{{item.DataId}}::{{item.StrainId}}" + value="{{item.count or ''}}" /></td> + {%endif%} + </tr> + {%endfor%} + </tbody> + </table> </div> <div class="form-group"> - <input type="submit" - name="submit" - class="btn btn-primary not-implemented" - value="update data" /> + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + name="submit" + class="btn btn-primary" + value="update data" /> + </div> </div> </form> </div> + <div class="row"> <h3 class="subheading">publication information</h3> <p>Use the form below to update the publication information for this phenotype.</p> <form id="frm-edit-phenotype-pub-data" + class="form-horizontal" method="POST" action="#"> <div class="form-group"> - <label for="txt-pubmed-id" class="form-label">Pubmed ID</label> - <input id="txt-pubmed-id" name="pubmed-id" type="text" - class="form-control" /> - <span class="form-text text-muted"> - Enter your publication's PubMed ID. - </span> + <label for="txt-pubmed-id" class="control-label col-sm-2">Pubmed ID</label> + <div class="col-sm-10"> + <input id="txt-pubmed-id" name="pubmed-id" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter your publication's PubMed ID.</span> + </div> </div> <div class="form-group"> - <label for="txt-publication-authors" class="form-label">Authors</label> - <input id="txt-publication-authors" name="publication-authors" - type="text" class="form-control" /> - <span class="form-text text-muted"> - Enter the authors.</span> + <label for="txt-publication-authors" class="control-label col-sm-2">Authors</label> + <div class="col-sm-10"> + <input id="txt-publication-authors" name="publication-authors" + type="text" class="form-control" /> + <span class="form-text text-muted"> + Enter the authors.</span> + </div> </div> <div class="form-group"> - <label for="txt-publication-title" class="form-label"> + <label for="txt-publication-title" class="control-label col-sm-2"> Publication Title</label> - <input id="txt-publication-title" name="publication-title" type="text" - class="form-control" /> - <span class="form-text text-muted"> - Enter your publication's title.</span> + <div class="col-sm-10"> + <input id="txt-publication-title" name="publication-title" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter your publication's title.</span> + </div> </div> <div class="form-group"> - <label for="txt-publication-abstract" class="form-label"> + <label for="txt-publication-abstract" class="control-label col-sm-2"> Publication Abstract</label> - <textarea id="txt-publication-abstract" name="publication-abstract" - class="form-control" rows="10"></textarea> - <span class="form-text text-muted"> - Enter the abstract for your publication.</span> + <div class="col-sm-10"> + <textarea id="txt-publication-abstract" name="publication-abstract" + class="form-control" rows="10"></textarea> + <span class="form-text text-muted"> + Enter the abstract for your publication.</span> + </div> </div> <div class="form-group"> - <label for="txt-publication-journal" class="form-label">Journal</label> - <input id="txt-publication-journal" name="journal" type="text" - class="form-control" /> - <span class="form-text text-muted"> - Enter the name of the journal where your work was published.</span> + <label for="txt-publication-journal" class="control-label col-sm-2">Journal</label> + <div class="col-sm-10"> + <input id="txt-publication-journal" name="journal" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the name of the journal where your work was published.</span> + </div> </div> <div class="form-group"> - <label for="txt-publication-volume" class="form-label">Volume</label> - <input id="txt-publication-volume" name="publication-volume" type="text" - class="form-control" /> - <span class="form-text text-muted"> - Enter the volume in the following format …</span> + <label for="txt-publication-volume" class="control-label col-sm-2">Volume</label> + <div class="col-sm-10"> + <input id="txt-publication-volume" name="publication-volume" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the volume in the following format …</span> + </div> </div> <div class="form-group"> - <label for="txt-publication-pages" class="form-label">Pages</label> - <input id="txt-publication-pages" name="publication-pages" type="text" - class="form-control" /> - <span class="form-text text-muted"> - Enter the journal volume where your work was published.</span> + <label for="txt-publication-pages" class="control-label col-sm-2">Pages</label> + <div class="col-sm-10"> + <input id="txt-publication-pages" name="publication-pages" type="text" + class="form-control" /> + <span class="form-text text-muted"> + Enter the journal volume where your work was published.</span> + </div> </div> <div class="form-group"> - <label for="select-publication-month" class="form-label"> + <label for="select-publication-month" class="control-label col-sm-2"> Publication Month</label> - <select id="select-publication-month" name="publication-month" - class="form-control"> - {%for month in monthnames%} - <option value="{{month | lower}}" - {%if current_month | lower == month | lower%} - selected="selected" - {%endif%}>{{month | capitalize}}</option> - {%endfor%} - </select> - <span class="form-text text-muted"> - Select the month when the work was published. - <span class="text-danger"> - This cannot be before, say 1600 and cannot be in the future!</span></span> - </div> - - <div class="form-group"> - <label for="txt-publication-year" class="form-label">Publication Year</label> - <input id="txt-publication-year" name="publication-year" type="text" - class="form-control" value="{{current_year}}" /> - <span class="form-text text-muted"> - Enter the year your work was published. - <span class="text-danger"> - This cannot be before, say 1600 and cannot be in the future!</span> - </span> - </div> - <div class="form-group"> - <input type="submit" - name="submit" - class="btn btn-primary not-implemented" - value="update publication" /> + <div class="col-sm-10"> + <select id="select-publication-month" name="publication-month" + class="form-control"> + {%for month in monthnames%} + <option value="{{month | lower}}" + {%if current_month | lower == month | lower%} + selected="selected" + {%endif%}>{{month | capitalize}}</option> + {%endfor%} + </select> + <span class="form-text text-muted"> + Select the month when the work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span></span> + </div> + </div> + + <div class="form-group"> + <label for="txt-publication-year" class="control-label col-sm-2">Publication Year</label> + <div class="col-sm-10"> + <input id="txt-publication-year" name="publication-year" type="text" + class="form-control" value="{{current_year}}" /> + <span class="form-text text-muted"> + Enter the year your work was published. + <span class="text-danger"> + This cannot be before, say 1600 and cannot be in the future!</span> + </span> + </div> + </div> + <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> + <input type="submit" + name="submit" + class="btn btn-primary not-implemented" + value="update publication" /> + </div> </div> </form> </div> diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html index 011f8f6..4f2b79b 100644 --- a/uploader/templates/phenotypes/view-dataset.html +++ b/uploader/templates/phenotypes/view-dataset.html @@ -5,6 +5,11 @@ {%block title%}Phenotypes{%endblock%} +{%block css%} +<link rel="stylesheet" + href="{{url_for('base.datatables', filename='css/jquery.dataTables.css')}}" /> +{%endblock%} + {%block pagetitle%}Phenotypes{%endblock%} {%block lvl4_breadcrumbs%} @@ -56,38 +61,16 @@ <div class="row"> <h2>Phenotype Data</h2> - - <p>This dataset has a total of {{phenotype_count}} phenotypes.</p> - - {{table_pagination(start_from, count, phenotype_count, url_for('species.populations.phenotypes.view_dataset', species_id=species.SpeciesId, population_id=population.Id, dataset_id=dataset.Id), "phenotypes")}} - - <table class="table"> + <table id="tbl-phenotypes-list" class="table"> <thead> <tr> - <th>#</th> + <th></th> <th>Record</th> <th>Description</th> </tr> </thead> - <tbody> - {%for pheno in phenotypes%} - <tr> - <td>{{pheno.sequence_number}}</td> - <td><a href="{{url_for('species.populations.phenotypes.view_phenotype', - species_id=species.SpeciesId, - population_id=population.Id, - dataset_id=dataset.Id, - xref_id=pheno['pxr.Id'])}}" - title="View phenotype details" - target="_blank"> - {{pheno.InbredSetCode}}_{{pheno["pxr.Id"]}}</a></td> - <td>{{pheno.Post_publication_description or pheno.Pre_publication_abbreviation or pheno.Original_description}}</td> - </tr> - {%else%} - <tr><td colspan="5"></td></tr> - {%endfor%} - </tbody> + <tbody></tbody> </table> </div> {%endblock%} @@ -95,3 +78,39 @@ {%block sidebarcontents%} {{display_population_card(species, population)}} {%endblock%} + + +{%block javascript%} +<script src="{{url_for('base.datatables', + filename='js/jquery.dataTables.js')}}"></script> +<script type="text/javascript"> + $(function() { + $("#tbl-phenotypes-list").DataTable({ + responsive: true, + data: {{phenotypes | tojson}}, + columns: [ + {data: "sequence_number"}, + { + data: function(pheno) { + var spcs_id = {{species.SpeciesId}}; + var pop_id = {{population.Id}}; + var dtst_id = {{dataset.Id}}; + return `<a href="/species/${spcs_id}` + + `/populations/${pop_id}` + + `/phenotypes/datasets/${dtst_id}` + + `/phenotype/${pheno.xref_id}` + + `" target="_blank">` + + `${pheno.InbredSetCode}_${pheno.xref_id}` + + `</a>`; + } + }, + {data: function(pheno) { + return (pheno.Post_publication_description || + pheno.Original_description || + pheno.Pre_publication_description); + }} + ] + }); + }); +</script> +{%endblock%} diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html index 18ac202..21ac501 100644 --- a/uploader/templates/phenotypes/view-phenotype.html +++ b/uploader/templates/phenotypes/view-phenotype.html @@ -16,7 +16,7 @@ species_id=species.SpeciesId, population_id=population.Id, dataset_id=dataset.Id, - xref_id=xref_id)}}">View Datasets</a> + xref_id=xref_id)}}">View Phenotype</a> </li> {%endblock%} @@ -62,36 +62,28 @@ {%if "group:resource:edit-resource" in privileges or "group:resource:delete-resource" in privileges%} <div class="row"> - <form action="#edit-delete-phenotype" - method="POST" - id="frm-delete-phenotype"> - - <input type="hidden" name="species_id" value="{{species.SpeciesId}}" /> - <input type="hidden" name="population_id" value="{{population.Id}}" /> - <input type="hidden" name="dataset_id" value="{{dataset.Id}}" /> - <input type="hidden" name="phenotype_id" value="{{phenotype.Id}}" /> - - <div class="btn-group btn-group-justified"> - <div class="btn-group"> - {%if "group:resource:edit-resource" in privileges%} - <input type="submit" - title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values." - class="btn btn-primary not-implemented" - value="edit" /> - {%endif%} - </div> - <div class="btn-group"></div> - <div class="btn-group"> - {%if "group:resource:delete-resource" in privileges%} - <input type="submit" - title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype." - class="btn btn-danger not-implemented" - disabled="disabled" - value="delete" /> - {%endif%} - </div> + <div class="btn-group btn-group-justified"> + <div class="btn-group"> + {%if "group:resource:edit-resource" in privileges%} + <a href="{{url_for('species.populations.phenotypes.edit_phenotype_data', + species_id=species.SpeciesId, + population_id=population.Id, + dataset_id=dataset.Id, + xref_id=xref_id)}}" + title="Edit the values for the phenotype. This is meant to be used when you need to update only a few values." + class="btn btn-primary">Edit</a> + {%endif%} </div> - </form> + <div class="btn-group"></div> + <div class="btn-group"> + {%if "group:resource:delete-resource" in privileges%} + <a href="#" + title="Delete the entire phenotype. This is useful when you need to change data for most or all of the fields for this phenotype." + class="btn btn-danger not-implemented" + disabled="disabled">delete</a> + {%endif%} + </div> + </div> </div> {%endif%} @@ -106,7 +98,7 @@ or "group:resource:delete-resource" in privileges%} <th>Sample</th> <th>Value</th> {%if has_se%} - <th>SE: {{has_se}}</th> + <th>SE</th> <th>N</th> {%endif%} </tr> diff --git a/uploader/templates/platforms/list-platforms.html b/uploader/templates/platforms/list-platforms.html index 718dd1d..a6bcfdc 100644 --- a/uploader/templates/platforms/list-platforms.html +++ b/uploader/templates/platforms/list-platforms.html @@ -58,7 +58,7 @@ <table class="table"> <thead> <tr> - <th>#</th> + <th></th> <th>Platform Name</th> <th><a href="https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms&tax={{species.TaxonomyId}}" title="Gene Expression Omnibus: Platforms section" diff --git a/uploader/templates/populations/list-populations.html b/uploader/templates/populations/list-populations.html index 7c7145f..f780e94 100644 --- a/uploader/templates/populations/list-populations.html +++ b/uploader/templates/populations/list-populations.html @@ -51,7 +51,7 @@ <caption>Populations for {{species.FullName}}</caption> <thead> <tr> - <th>#</th> + <th></th> <th>Name</th> <th>Full Name</th> <th>Description</th> diff --git a/uploader/templates/populations/macro-display-population-card.html b/uploader/templates/populations/macro-display-population-card.html index 79f7925..16b477f 100644 --- a/uploader/templates/populations/macro-display-population-card.html +++ b/uploader/templates/populations/macro-display-population-card.html @@ -33,11 +33,6 @@ <td>Family</td> <td>{{population.Family}}</td> </tr> - - <tr> - <td>Description</td> - <td>{{(population.Description or "")[0:500]}}…</td> - </tr> </tbody> </table> </div> diff --git a/uploader/templates/populations/macro-select-population.html b/uploader/templates/populations/macro-select-population.html index af4fd3a..ef74ac3 100644 --- a/uploader/templates/populations/macro-select-population.html +++ b/uploader/templates/populations/macro-select-population.html @@ -1,29 +1,32 @@ {%macro select_population_form(form_action, populations)%} -<form method="GET" action="{{form_action}}"> +<form method="GET" action="{{form_action}}" class="form-horizontal"> <legend>Select Population</legend> <div class="form-group"> - <label for="select-population" class="form-label">Select Population</label> - <select id="select-population" - name="population_id" - class="form-control" - required="required"> - <option value="">Select Population</option> - {%for family in populations%} - <optgroup {%if family[0][1] is not none%} - label="{{family[0][1]}}" - {%else%} - label="Undefined" - {%endif%}> - {%for population in family[1]%} - <option value="{{population.Id}}">{{population.FullName}}</option> + <label for="select-population" class="control-label col-sm-2"> + Population</label> + <div class="col-sm-10"> + <select id="select-population" + name="population_id" + class="form-control" + required="required"> + <option value="">Select Population</option> + {%for family in populations%} + <optgroup {%if family[0][1] is not none%} + label="{{family[0][1]}}" + {%else%} + label="Undefined" + {%endif%}> + {%for population in family[1]%} + <option value="{{population.Id}}">{{population.FullName}}</option> + {%endfor%} + </optgroup> {%endfor%} - </optgroup> - {%endfor%} - </select> + </select> + </div> </div> - <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> <input type="submit" value="Select" class="btn btn-primary" /> </div> </form> diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html index 13e5cec..185e784 100644 --- a/uploader/templates/samples/list-samples.html +++ b/uploader/templates/samples/list-samples.html @@ -73,7 +73,7 @@ <table class="table"> <thead> <tr> - <th>#</th> + <th></th> <th>Name</th> <th>Auxilliary Name</th> <th>Symbol</th> diff --git a/uploader/templates/species/list-species.html b/uploader/templates/species/list-species.html index 85c9d40..64084b0 100644 --- a/uploader/templates/species/list-species.html +++ b/uploader/templates/species/list-species.html @@ -29,7 +29,7 @@ <caption>Available Species</caption> <thead> <tr> - <th>#</td> + <th></td> <th title="A common, layman's name for the species.">Common Name</th> <th title="The scientific name for the species">Organism Name</th> <th title="An identifier for the species in the NCBI taxonomy database"> diff --git a/uploader/templates/species/macro-select-species.html b/uploader/templates/species/macro-select-species.html index dd086c0..36ed102 100644 --- a/uploader/templates/species/macro-select-species.html +++ b/uploader/templates/species/macro-select-species.html @@ -1,29 +1,31 @@ {%macro select_species_form(form_action, species)%} {%if species | length > 0%} -<form method="GET" action="{{form_action}}"> +<form method="GET" action="{{form_action}}" class="form-horizontal"> <div class="form-group"> - <label for="select-species" class="form-label">Species</label> - <select id="select-species" - name="species_id" - class="form-control" - required="required"> - <option value="">Select Species</option> - {%for group in species%} - {{group}} - <optgroup {%if group[0][1] is not none%} - label="{{group[0][1].capitalize()}}" - {%else%} - label="Undefined" - {%endif%}> - {%for aspecies in group[1]%} - <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option> + <label for="select-species" class="control-label col-sm-2">Species</label> + <div class="col-sm-10"> + <select id="select-species" + name="species_id" + class="form-control" + required="required"> + <option value="">Select Species</option> + {%for group in species%} + {{group}} + <optgroup {%if group[0][1] is not none%} + label="{{group[0][1].capitalize()}}" + {%else%} + label="Undefined" + {%endif%}> + {%for aspecies in group[1]%} + <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option> + {%endfor%} + </optgroup> {%endfor%} - </optgroup> - {%endfor%} - </select> + </select> + </div> </div> - <div class="form-group"> + <div class="col-sm-offset-2 col-sm-10"> <input type="submit" value="Select" class="btn btn-primary" /> </div> </form> |