aboutsummaryrefslogtreecommitdiff
path: root/uploader/templates
diff options
context:
space:
mode:
Diffstat (limited to 'uploader/templates')
-rw-r--r--uploader/templates/base.html120
-rw-r--r--uploader/templates/genotypes/index.html4
-rw-r--r--uploader/templates/genotypes/select-population.html16
-rw-r--r--uploader/templates/index.html134
-rw-r--r--uploader/templates/jobs/job-error.html17
-rw-r--r--uploader/templates/jobs/job-not-found.html11
-rw-r--r--uploader/templates/jobs/job-status.html24
-rw-r--r--uploader/templates/login.html7
-rw-r--r--uploader/templates/macro-step-indicator.html15
-rw-r--r--uploader/templates/phenotypes/add-phenotypes-base.html357
-rw-r--r--uploader/templates/phenotypes/add-phenotypes-raw-files.html375
-rw-r--r--uploader/templates/phenotypes/bulk-edit-upload.html62
-rw-r--r--uploader/templates/phenotypes/create-dataset.html12
-rw-r--r--uploader/templates/phenotypes/edit-phenotype.html126
-rw-r--r--uploader/templates/phenotypes/index.html15
-rw-r--r--uploader/templates/phenotypes/list-datasets.html9
-rw-r--r--uploader/templates/phenotypes/load-phenotypes-success.html42
-rw-r--r--uploader/templates/phenotypes/macro-display-preview-table.html8
-rw-r--r--uploader/templates/phenotypes/macro-display-resumable-elements.html12
-rw-r--r--uploader/templates/phenotypes/review-job-data.html30
-rw-r--r--uploader/templates/phenotypes/select-population.html12
-rw-r--r--uploader/templates/phenotypes/view-dataset.html97
-rw-r--r--uploader/templates/phenotypes/view-phenotype.html2
-rw-r--r--uploader/templates/platforms/index.html4
-rw-r--r--uploader/templates/platforms/list-platforms.html2
-rw-r--r--uploader/templates/populations/create-population.html14
-rw-r--r--uploader/templates/populations/index.html4
-rw-r--r--uploader/templates/populations/list-populations.html2
-rw-r--r--uploader/templates/populations/macro-display-population-card.html5
-rw-r--r--uploader/templates/populations/macro-select-population.html72
-rw-r--r--uploader/templates/publications/base.html12
-rw-r--r--uploader/templates/publications/create-publication.html191
-rw-r--r--uploader/templates/publications/index.html100
-rw-r--r--uploader/templates/publications/view-publication.html78
-rw-r--r--uploader/templates/samples/index.html4
-rw-r--r--uploader/templates/samples/list-samples.html2
-rw-r--r--uploader/templates/samples/select-population.html23
-rw-r--r--uploader/templates/samples/upload-failure.html2
-rw-r--r--uploader/templates/species/create-species.html112
-rw-r--r--uploader/templates/species/list-species.html2
-rw-r--r--uploader/templates/species/macro-select-species.html83
41 files changed, 1384 insertions, 835 deletions
diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index c124b13..3c0d0d4 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -8,14 +8,14 @@
<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',
filename='css/bootstrap.min.css')}}" />
<link rel="stylesheet" type="text/css"
- href="{{url_for('base.bootstrap',
- filename='css/bootstrap-theme.min.css')}}" />
+ href="{{url_for('base.datatables',
+ filename='css/dataTables.bootstrap5.min.css')}}" />
<link rel="stylesheet" type="text/css" href="/static/css/styles.css" />
{%block css%}{%endblock%}
@@ -23,28 +23,32 @@
</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()}} &mdash; 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>
+ {{user_email()}} 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>
+ <li {%if activemenu=="publications"%}class="activemenu"{%endif%}>
+ <a href="{{url_for('publications.index')}}"
+ title="View and manage publications.">Publications</a></li>
<li {%if activemenu=="species"%}class="activemenu"{%endif%}>
<a href="{{url_for('species.list_species')}}"
title="View and manage species information.">Species</a></li>
@@ -70,6 +74,7 @@
<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."
@@ -87,47 +92,70 @@
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>
+ <!--
+ Core dependencies
+ -->
<script src="{{url_for('base.jquery',
filename='jquery.min.js')}}"></script>
<script src="{{url_for('base.bootstrap',
filename='js/bootstrap.min.js')}}"></script>
- <script type="text/javascript" src="/static/js/misc.js"></script>
- {%block javascript%}{%endblock%}
- </body>
+ <!--
+ DataTables dependencies
+ -->
+ <script type="text/javascript"
+ src="{{url_for('base.datatables',
+ filename='js/dataTables.min.js')}}"></script>
+ <script type="text/javascript"
+ src="{{url_for('base.datatables_extensions',
+ filename='scroller/js/dataTables.scroller.min.js')}}"></script>
+ <script type="text/javascript"
+ src="{{url_for('base.datatables_extensions',
+ filename='buttons/js/dataTables.buttons.min.js')}}"></script>
+ <script type="text/javascript"
+ src="{{url_for('base.datatables_extensions',
+ filename='select/js/dataTables.select.min.js')}}"></script>
+ <!--
+ local dependencies
+ -->
+ <script type="text/javascript" src="/static/js/utils.js"></script>
+ <script type="text/javascript" src="/static/js/datatables.js"></script>
+ {%block javascript%}{%endblock%}
+ </body>
</html>
diff --git a/uploader/templates/genotypes/index.html b/uploader/templates/genotypes/index.html
index e749f5a..b50ebc5 100644
--- a/uploader/templates/genotypes/index.html
+++ b/uploader/templates/genotypes/index.html
@@ -26,3 +26,7 @@
species)}}
</div>
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
diff --git a/uploader/templates/genotypes/select-population.html b/uploader/templates/genotypes/select-population.html
index 7c81943..acdd063 100644
--- a/uploader/templates/genotypes/select-population.html
+++ b/uploader/templates/genotypes/select-population.html
@@ -12,20 +12,14 @@
{{flash_all_messages()}}
<div class="row">
- <p>
- You have indicated that you intend to upload the genotypes for species
- '{{species.FullName}}'. We now just require the population for your
- experiment/study, and you should be good to go.
- </p>
-</div>
-
-<div class="row">
- {{select_population_form(url_for("species.populations.genotypes.select_population",
- species_id=species.SpeciesId),
- populations)}}
+ {{select_population_form(url_for("species.populations.genotypes.select_population", species_id=species.SpeciesId), species, populations)}}
</div>
{%endblock%}
{%block sidebarcontents%}
{{display_species_card(species)}}
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/populations.js"></script>
+{%endblock%}
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 &mdash; 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. &hellip;</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 &ndash; 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 &ndash;
- 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 &hellip;</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 &hellip;</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 &hellip;</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 &hellip;</p>
</div>
+ -->
</div>
{%endblock%}
diff --git a/uploader/templates/jobs/job-error.html b/uploader/templates/jobs/job-error.html
new file mode 100644
index 0000000..b3015fc
--- /dev/null
+++ b/uploader/templates/jobs/job-error.html
@@ -0,0 +1,17 @@
+{%extends "base.html"%}
+
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Background Jobs: Error{%endblock%}
+
+{%block pagetitle%}Background Jobs: Error{%endblock%}
+
+{%block contents%}
+
+<h1>Background Jobs: Error</h1>
+<p>Job <strong>{{job["job_id"]}}</strong> failed!</p>
+<p>The error details are in the "STDERR" section below.</p>
+
+<h2>STDERR</h2>
+<pre>{{job["stderr"]}}</pre>
+{%endblock%}
diff --git a/uploader/templates/jobs/job-not-found.html b/uploader/templates/jobs/job-not-found.html
new file mode 100644
index 0000000..a71e66f
--- /dev/null
+++ b/uploader/templates/jobs/job-not-found.html
@@ -0,0 +1,11 @@
+{%extends "base.html"%}
+
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Background Jobs{%endblock%}
+
+{%block pagetitle%}Background Jobs{%endblock%}
+
+{%block contents%}
+<p>Could not find job with ID: {{job_id}}</p>
+{%endblock%}
diff --git a/uploader/templates/jobs/job-status.html b/uploader/templates/jobs/job-status.html
new file mode 100644
index 0000000..83c02fd
--- /dev/null
+++ b/uploader/templates/jobs/job-status.html
@@ -0,0 +1,24 @@
+{%extends "base.html"%}
+
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block extrameta%}
+<meta http-equiv="refresh" content="5" />
+{%endblock%}
+
+{%block title%}Background Jobs{%endblock%}
+
+{%block pagetitle%}Background Jobs{%endblock%}
+
+{%block contents%}
+
+<p>Status: {{job["metadata"]["status"]}}</p>
+<p>Job Type: {{job["metadata"]["job-type"]}}</p>
+
+<h2>STDOUT</h2>
+<pre>{{job["stdout"]}}</pre>
+
+<h2>STDERR</h2>
+<pre>{{job["stderr"]}}</pre>
+
+{%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/macro-step-indicator.html b/uploader/templates/macro-step-indicator.html
new file mode 100644
index 0000000..ac0be77
--- /dev/null
+++ b/uploader/templates/macro-step-indicator.html
@@ -0,0 +1,15 @@
+{%macro step_indicator(step, width=100)%}
+<svg width="{{width}}" height="{{width}}" xmlns="http://www.w3.org/2000/svg">
+ <circle cx="{{0.5*width}}"
+ cy="{{0.5*width}}"
+ r="{{0.5*width}}"
+ fill="#E5E5FF" />
+ <text x="{{0.5*width}}"
+ y="{{0.6*width}}"
+ font-size="{{0.2*width}}"
+ text-anchor="middle"
+ fill="#555555">
+ Step {{step}}
+ </text>
+</svg>
+{%endmacro%}
diff --git a/uploader/templates/phenotypes/add-phenotypes-base.html b/uploader/templates/phenotypes/add-phenotypes-base.html
index 97b55f2..9909c20 100644
--- a/uploader/templates/phenotypes/add-phenotypes-base.html
+++ b/uploader/templates/phenotypes/add-phenotypes-base.html
@@ -42,110 +42,30 @@
{%block frm_add_phenotypes_elements%}{%endblock%}
- <div class="checkbox">
- <label>
- <input id="chk-published" type="checkbox" name="published?" />
- These phenotypes are published</label>
- </div>
-
- <fieldset id="fldset-publication-info" class="hidden">
+ <fieldset id="fldset-publication-info">
<legend>Publication Information</legend>
- <div class="form-group">
- <label for="txt-pubmed-id" class="form-label">Pubmed ID</label>
- <div class="input-group">
- <input id="txt-pubmed-id" name="pubmed-id" type="text"
- class="form-control" />
- <span class="input-group-btn">
- <button id="btn-search-pubmed-id" class="btn btn-info">Search</button>
- </span>
- </div>
- <span id="search-pubmed-id-error"
- class="form-text text-muted text-danger hidden">
- </span><br />
- <span class="form-text text-muted">
- Enter your publication's PubMed ID above and click "Search" to search
- for some (or all) of the publication details requested below.
- </span>
- </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 in the following format &hellip;</span>
- </div>
-
- <div class="form-group">
- <label for="txt-publication-title" class="form-label">
- 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>
-
- <div class="form-group">
- <label for="txt-publication-abstract" class="form-label">
- 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>
-
- <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>
- </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 &hellip;</span>
- </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>
- </div>
-
- <div class="form-group">
- <label for="select-publication-month" class="form-label">
- 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>
+ <input type="hidden" name="publication-id" id="txt-publication-id" />
+ <span class="form-text text-muted">
+ Select a publication for your data. <br />
+ Can't find a publication you can use? Go ahead and
+ <a href="{{url_for(
+ 'publications.create_publication',
+ return_to='species.populations.phenotypes.add_phenotypes',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}">create a new publication</a>.</span>
+ <table id="tbl-select-publication" class="table compact stripe">
+ <thead>
+ <tr>
+ <th>#</th>
+ <th>PubMed ID</th>
+ <th>Title</th>
+ <th>Authors</th>
+ </tr>
+ </thead>
+
+ <tbody></tbody>
+ </table>
</fieldset>
<div class="form-group">
@@ -165,165 +85,80 @@
{%block javascript%}
<script type="text/javascript">
- var remove_class = (element, classvalue) => {
- new_classes = (element.attr("class") || "").split(" ").map((val) => {
- return val.trim();
- }).filter((val) => {
- return ((val !== classvalue) &&
- (val !== ""))
- }).join(" ");
-
- if(new_classes === "") {
- element.removeAttr("class");
- } else {
- element.attr("class", new_classes);
- }
- };
-
- var add_class = (element, classvalue) => {
- remove_class(element, classvalue);
- element.attr("class", (element.attr("class") || "") + " " + classvalue);
- };
-
- $("#chk-published").on("click", (event) => {
- pub_details = $("#fldset-publication-info")
- if(event.target.checked) {
- // display the publication details
- remove_class(pub_details, "hidden");
- } else {
- // hide the publication details
- add_class(pub_details, "hidden");
- }
- });
-
- var extract_details = (pubmed_id, details) => {
- var months = {
- "jan": "January",
- "feb": "February",
- "mar": "March",
- "apr": "April",
- "may": "May",
- "jun": "June",
- "jul": "July",
- "aug": "August",
- "sep": "September",
- "oct": "October",
- "nov": "November",
- "dec": "December"
- };
- var _date = details[pubmed_id].pubdate.split(" ");
- return {
- "authors": details[pubmed_id].authors.map((authobj) => {
- return authobj.name;
- }),
- "title": details[pubmed_id].title,
- "journal": details[pubmed_id].fulljournalname,
- "volume": details[pubmed_id].volume,
- "pages": details[pubmed_id].pages,
- "month": _date.length > 1 ? months[_date[1].toLowerCase()] : "jan",
- "year": _date[0],
- };
- };
-
- var update_publication_details = (details) => {
- Object.entries(details).forEach((entry) => {;
- switch(entry[0]) {
- case "authors":
- $("#txt-publication-authors").val(entry[1].join(", "));
- break;
- case "month":
- $("#select-publication-month")
- .children("option")
- .each((index, child) => {
- child.selected = child.value == entry[1].toLowerCase();
- });
- default:
- $("#txt-publication-" + entry[0]).val(entry[1]);
- break;
- }
+ $(function() {
+ var publicationsDataTable = buildDataTable(
+ "#tbl-select-publication",
+ [],
+ [
+ {data: "index"},
+ {
+ searchable: true,
+ data: (pub) => {
+ if(pub.PubMed_ID) {
+ return `<a href="https://pubmed.ncbi.nlm.nih.gov/` +
+ `${pub.PubMed_ID}/" target="_blank" ` +
+ `title="Link to publication on NCBI.">` +
+ `${pub.PubMed_ID}</a>`;
+ }
+ return "";
+ }
+ },
+ {
+ searchable: true,
+ data: (pub) => {
+ var title = "⸻";
+ if(pub.Title) {
+ title = pub.Title
+ }
+ return `<a href="/publications/view/${pub.Id}" ` +
+ `target="_blank" ` +
+ `title="Link to view publication details">` +
+ `${title}</a>`;
+ }
+ },
+ {
+ searchable: true,
+ data: (pub) => {
+ authors = pub.Authors.split(",").map(
+ (item) => {return item.trim();});
+ if(authors.length > 1) {
+ return authors[0] + ", et. al.";
+ }
+ return authors[0];
+ }
+ }
+ ],
+ {
+ serverSide: true,
+ ajax: {
+ url: "/publications/list",
+ dataSrc: "publications"
+ },
+ select: "single",
+ paging: true,
+ scrollY: 700,
+ deferRender: true,
+ scroller: true,
+ scrollCollapse: true,
+ layout: {
+ topStart: "info",
+ topEnd: "search"
+ }
+ });
+ publicationsDataTable.on("select", (event, datatable, type, indexes) => {
+ indexes.forEach((element, index, thearray) => {
+ let row = datatable.row(element).node();
+ console.debug(datatable.row(element).data());
+ $("#frm-add-phenotypes #txt-publication-id").val(
+ datatable.row(element).data().Id);
+ });
+ });
+ publicationsDataTable.on("deselect", (event, datatable, type, indexes) => {
+ indexes.forEach((element, index, thearray) => {
+ let row = datatable.row(element).node();
+ $("#frm-add-phenotypes #txt-publication-id").val(null);
+ });
});
- };
-
- var fetch_publication_abstract = (pubmed_id, pub_details) => {
- $.ajax("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi",
- {
- "method": "GET",
- "data": {
- "db": "pubmed",
- "id": pubmed_id,
- "rettype": "abstract",
- "retmode": "xml"
- },
- "success": (data, textStatus, jqXHR) => {
- update_publication_details({
- ...pub_details,
- ...{
- "abstract": Array.from(data
- .getElementsByTagName(
- "Abstract")[0]
- .children)
- .map((elt) => {return elt.textContent.trim();})
- .join("\r\n")
- }});
- },
- "error": (jqXHR, textStatus, errorThrown) => {},
- "complete": (jqXHR, textStatus) => {},
- "dataType": "xml"
- });
- };
-
- var fetch_publication_details = (pubmed_id, complete_thunks) => {
- error_display = $("#search-pubmed-id-error");
- error_display.text("");
- add_class(error_display, "hidden");
- $.ajax("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi",
- {
- "method": "GET",
- "data": {"db": "pubmed", "id": pubmed_id, "format": "json"},
- "success": (data, textStatus, jqXHR) => {
- // process and update publication details
- hasError = (
- Object.hasOwn(data, "error") ||
- Object.hasOwn(data.result[pubmed_id], "error"));
- if(hasError) {
- error_display.text(
- "There was an error fetching a publication with " +
- "the given PubMed ID! The error received " +
- "was: '" + (
- data.error ||
- data.result[pubmed_id].error) +
- "'. Please check ID you provided and try " +
- "again.");
- remove_class(error_display, "hidden");
- } else {
- fetch_publication_abstract(
- pubmed_id,
- extract_details(pubmed_id, data.result));
- }
- },
- "error": (jqXHR, textStatus, errorThrown) => {},
- "complete": () => {
- complete_thunks.forEach((thunk) => {thunk()});
- },
- "dataType": "json"
- });
- };
-
- $("#btn-search-pubmed-id").on("click", (event) => {
- event.preventDefault();
- var search_button = event.target;
- var pubmed_id = $("#txt-pubmed-id").val().trim();
- remove_class($("#txt-pubmed-id").parent(), "has-error");
- if(pubmed_id == "") {
- add_class($("#txt-pubmed-id").parent(), "has-error");
- return false;
- }
-
- search_button.disabled = true;
- // Fetch publication details
- fetch_publication_details(pubmed_id,
- [() => {search_button.disabled = false;}]);
- return false;
});
</script>
diff --git a/uploader/templates/phenotypes/add-phenotypes-raw-files.html b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
index d9a8424..67b56e3 100644
--- a/uploader/templates/phenotypes/add-phenotypes-raw-files.html
+++ b/uploader/templates/phenotypes/add-phenotypes-raw-files.html
@@ -105,111 +105,213 @@
</div>
</fieldset>
-<fieldset id="fldset-data-files">
+<fieldset id="fldset-files">
<legend>Data File(s)</legend>
- <div class="form-group non-resumable-elements">
- <label for="finput-phenotype-descriptions" class="form-label">
- Phenotype Descriptions</label>
- <input id="finput-phenotype-descriptions"
- name="phenotype-descriptions"
- class="form-control"
- type="file"
- data-preview-table="tbl-preview-pheno-desc"
- required="required" />
- <span class="form-text text-muted">
- Provide a file that contains only the phenotype descriptions,
- <a href="#docs-file-phenotype-description"
- title="Documentation of the phenotype data file format.">
- the documentation for the expected format of the file</a>.</span>
- </div>
-
- {{display_resumable_elements(
- "resumable-phenotype-descriptions",
- "phenotype descriptions",
- '<p>You can drop a CSV file that contains the phenotype descriptions here,
- or you can click the "Browse" button (below and to the right) to select it
- from your computer.</p>
- <p>The CSV file must conform to some standards, as documented in the
- <a href="#docs-file-phenotype-description"
- title="Documentation of the phenotype data file format.">
- "Phenotypes Descriptions" documentation</a> section below.</p>')}}
-
-
- <div class="form-group non-resumable-elements">
- <label for="finput-phenotype-data" class="form-label">Phenotype Data</label>
- <input id="finput-phenotype-data"
- name="phenotype-data"
- class="form-control"
- type="file"
- data-preview-table="tbl-preview-pheno-data"
- required="required" />
- <span class="form-text text-muted">
- Provide a file that contains only the phenotype data. See
- <a href="#docs-file-phenotype-data"
- title="Documentation of the phenotype data file format.">
- the documentation for the expected format of the file</a>.</span>
- </div>
-
- {{display_resumable_elements(
- "resumable-phenotype-data",
- "phenotype data",
- '<p>You can drop a CSV file that contains the phenotype data here,
- or you can click the "Browse" button (below and to the right) to select it
- from your computer.</p>
- <p>The CSV file must conform to some standards, as documented in the
- <a href="#docs-file-phenotype-data"
- title="Documentation of the phenotype data file format.">
- "Phenotypes Data" documentation</a> section below.</p>')}}
-
- {%if population.Family in families_with_se_and_n%}
- <div class="form-group non-resumable-elements">
- <label for="finput-phenotype-se" class="form-label">Phenotype: Standard Errors</label>
- <input id="finput-phenotype-se"
- name="phenotype-se"
- class="form-control"
- type="file"
- data-preview-table="tbl-preview-pheno-se"
- required="required" />
- <span class="form-text text-muted">
- Provide a file that contains only the standard errors for the phenotypes,
- computed from the data above.</span>
- </div>
- {{display_resumable_elements(
- "resumable-phenotype-se",
- "standard errors",
- '<p>You can drop a CSV file that contains the computed standard-errors data
- here, or you can click the "Browse" button (below and to the right) to
- select it from your computer.</p>
- <p>The CSV file must conform to some standards, as documented in the
- <a href="#docs-file-phenotype-se"
- title="Documentation of the phenotype data file format.">
- "Phenotypes Data" documentation</a> section below.</p>')}}
+ <fieldset id="fldset-descriptions-file">
+ <div class="form-group">
+ <div class="form-check">
+ <input id="chk-phenotype-descriptions-transposed"
+ name="phenotype-descriptions-transposed"
+ type="checkbox"
+ class="form-check-input"
+ style="border: solid #8EABF0" />
+ <label for="chk-phenotype-descriptions-transposed"
+ class="form-check-label">
+ Description file transposed?</label>
+ </div>
+
+ <div class="non-resumable-elements">
+ <label for="finput-phenotype-descriptions" class="form-label">
+ Phenotype Descriptions</label>
+ <input id="finput-phenotype-descriptions"
+ name="phenotype-descriptions"
+ class="form-control"
+ type="file"
+ data-preview-table="tbl-preview-pheno-desc"
+ required="required" />
+ <span class="form-text text-muted">
+ Provide a file that contains only the phenotype descriptions,
+ <a href="#docs-file-phenotype-description"
+ title="Documentation of the phenotype data file format.">
+ the documentation for the expected format of the file</a>.</span>
+ </div>
+ {{display_resumable_elements(
+ "resumable-phenotype-descriptions",
+ "phenotype descriptions",
+ '<p>Drag and drop the CSV file that contains the descriptions of your
+ phenotypes here.</p>
+
+ <p>The CSV file should be a matrix of
+ <strong>phenotypes × descriptions</strong> i.e. The first column
+ contains the phenotype names/identifiers whereas the first row is a list
+ of metadata fields like, "description", "units", etc.</p>
+
+ <p>If the format is transposed (i.e.
+ <strong>descriptions × phenotypes</strong>) select the checkbox above.
+ </p>
+
+ <p>Please see the
+ <a href="#docs-file-phenotype-description"
+ title="Documentation of the phenotype data file format.">
+ "Phenotypes Descriptions" documentation</a> section below for more
+ information on the expected format of the file provided here.</p>')}}
+ {{display_preview_table(
+ "tbl-preview-pheno-desc", "phenotype descriptions")}}
+ </div>
+ </fieldset>
+
+
+ <fieldset id="fldset-data-file">
+ <div class="form-group">
+ <div class="form-check">
+ <input id="chk-phenotype-data-transposed"
+ name="phenotype-data-transposed"
+ type="checkbox"
+ class="form-check-input"
+ style="border: solid #8EABF0" />
+ <label for="chk-phenotype-data-transposed" class="form-check-label">
+ Data file transposed?</label>
+ </div>
+
+ <div class="non-resumable-elements">
+ <label for="finput-phenotype-data" class="form-label">Phenotype Data</label>
+ <input id="finput-phenotype-data"
+ name="phenotype-data"
+ class="form-control"
+ type="file"
+ data-preview-table="tbl-preview-pheno-data"
+ required="required" />
+ <span class="form-text text-muted">
+ Provide a file that contains only the phenotype data. See
+ <a href="#docs-file-phenotype-data"
+ title="Documentation of the phenotype data file format.">
+ the documentation for the expected format of the file</a>.</span>
+ </div>
+
+ {{display_resumable_elements(
+ "resumable-phenotype-data",
+ "phenotype data",
+ '<p>Drag and drop a CSV file that contains the phenotypes numerical data
+ here. You can click the "Browse" button (below and to the right) to
+ select the file from your computer.</p>
+
+ <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>,
+ i.e. The first column contains the samples identifiers while the first
+ row is the list of phenotypes identifiers occurring in the phenotypes
+ descriptions file.</p>
+
+ <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>)
+ select the checkbox above.</p>
+ <p>Please see the
+ <a href="#docs-file-phenotype-data"
+ title="Documentation of the phenotype data file format.">
+ "Phenotypes Data" documentation</a> section below for more information
+ on the expected format for the file provided here.</p>')}}
+ {{display_preview_table("tbl-preview-pheno-data", "phenotype data")}}
+ </div>
+ </fieldset>
- <div class="form-group non-resumable-elements">
- <label for="finput-phenotype-n" class="form-label">Phenotype: Number of Samples/Individuals</label>
- <input id="finput-phenotype-n"
- name="phenotype-n"
- class="form-control"
- type="file"
- data-preview-table="tbl-preview-pheno-n"
- required="required" />
- <span class="form-text text-muted">
- Provide a file that contains only the number of samples/individuals used in
- the computation of the standard errors above.</span>
- </div>
- {{display_resumable_elements(
- "resumable-phenotype-n",
- "number of samples/individuals",
- '<p>You can drop a CSV file that contains the number of samples/individuals
- used in computation of the standard-errors here, or you can click the
- "Browse" button (below and to the right) to select it from your computer.
- </p>
- <p>The CSV file must conform to some standards, as documented in the
- <a href="#docs-file-phenotype-n"
- title="Documentation of the phenotype data file format.">
- "Phenotypes Data" documentation</a> section below.</p>')}}
+ {%if population.Family in families_with_se_and_n%}
+ <fieldset id="fldset-se-file">
+ <div class="form-group">
+ <div class="form-check">
+ <input id="chk-phenotype-se-transposed"
+ name="phenotype-se-transposed"
+ type="checkbox"
+ class="form-check-input"
+ style="border: solid #8EABF0" />
+ <label for="chk-phenotype-se-transposed" class="form-check-label">
+ Standard-Errors file transposed?</label>
+ </div>
+ <div class="group non-resumable-elements">
+ <label for="finput-phenotype-se" class="form-label">Phenotype: Standard Errors</label>
+ <input id="finput-phenotype-se"
+ name="phenotype-se"
+ class="form-control"
+ type="file"
+ data-preview-table="tbl-preview-pheno-se"
+ required="required" />
+ <span class="form-text text-muted">
+ Provide a file that contains only the standard errors for the phenotypes,
+ computed from the data above.</span>
+ </div>
+
+ {{display_resumable_elements(
+ "resumable-phenotype-se",
+ "standard errors",
+ '<p>Drag and drop a CSV file that contains the phenotypes standard-errors
+ data here. You can click the "Browse" button (below and to the right) to
+ select the file from your computer.</p>
+
+ <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>,
+ i.e. The first column contains the samples identifiers while the first
+ row is the list of phenotypes identifiers occurring in the phenotypes
+ descriptions file.</p>
+
+ <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>)
+ select the checkbox above.</p>
+
+ <p>Please see the
+ <a href="#docs-file-phenotype-se"
+ title="Documentation of the phenotype data file format.">
+ "Phenotypes Data" documentation</a> section below for more information
+ on the expected format of the file provided here.</p>')}}
+
+ {{display_preview_table("tbl-preview-pheno-se", "standard errors")}}
+ </div>
+ </fieldset>
+
+
+ <fieldset id="fldset-n-file">
+ <div class="form-group">
+ <div class="form-check">
+ <input id="chk-phenotype-n-transposed"
+ name="phenotype-n-transposed"
+ type="checkbox"
+ class="form-check-input"
+ style="border: solid #8EABF0" />
+ <label for="chk-phenotype-n-transposed" class="form-check-label">
+ Counts file transposed?</label>
+ </div>
+ <div class="non-resumable-elements">
+ <label for="finput-phenotype-n" class="form-label">Phenotype: Number of Samples/Individuals</label>
+ <input id="finput-phenotype-n"
+ name="phenotype-n"
+ class="form-control"
+ type="file"
+ data-preview-table="tbl-preview-pheno-n"
+ required="required" />
+ <span class="form-text text-muted">
+ Provide a file that contains only the number of samples/individuals used in
+ the computation of the standard errors above.</span>
+ </div>
+
+ {{display_resumable_elements(
+ "resumable-phenotype-n",
+ "number of samples/individuals",
+ '<p>Drag and drop a CSV file that contains the samples\' phenotypes counts
+ data here. You can click the "Browse" button (below and to the right) to
+ select the file from your computer.</p>
+
+ <p>The CSV should be a matrix of <strong>samples × phenotypes</strong>,
+ i.e. The first column contains the samples identifiers while the first
+ row is the list of phenotypes identifiers occurring in the phenotypes
+ descriptions file.</p>
+
+ <p>If the format is transposed (i.e <strong>phenotypes × samples</strong>)
+ select the checkbox above.</p>
+
+ <p>Please see the
+ <a href="#docs-file-phenotype-se"
+ title="Documentation of the phenotype data file format.">
+ "Phenotypes Data" documentation</a> section below for more information
+ on the expected format of the file provided here.</p>')}}
+
+ {{display_preview_table("tbl-preview-pheno-n", "number of samples/individuals")}}
+ </div>
+ </fieldset>
</fieldset>
{%endif%}
{%endblock%}
@@ -322,15 +424,15 @@
<span id="docs-file-phenotype-data"></span>
<span id="docs-file-phenotype-se"></span>
<span id="docs-file-phenotype-n"></span>
- <p>The data is a matrix of <em>phenotypes × individuals</em>, e.g.</p>
+ <p>The data is a matrix of <em>samples(or individuals) × phenotypes</em>, e.g.</p>
<code>
# num-cases: 2549
# num-phenos: 13
- id,IND001,IND002,IND003,IND004,…<br />
- pheno10001,61.400002,54.099998,483,49.799999,…<br />
- pheno10002,49,50.099998,403,45.5,…<br />
- pheno10003,62.5,53.299999,501,62.900002,…<br />
- pheno10004,53.099998,55.099998,403,NA,…<br />
+ id,pheno10001,pheno10002,pheno10003,pheno10004,53.099998,…<br />
+ IND001,61.400002,49,62.5,55.099998,…<br />
+ IND002,54.099998,50.099998,53.299999,55.099998,…<br />
+ IND003,483,403,501,403,…<br />
+ IND004,49.799999,45.5,62.900002,NA,…<br />
⋮<br /></code>
<p>where <code>IND001,IND002,IND003,IND004,…</code> are the
@@ -346,12 +448,6 @@
{%endblock%}
{%block sidebarcontents%}
-{{display_preview_table("tbl-preview-pheno-desc", "descriptions")}}
-{{display_preview_table("tbl-preview-pheno-data", "data")}}
-{%if population.Family in families_with_se_and_n%}
-{{display_preview_table("tbl-preview-pheno-se", "standard errors")}}
-{{display_preview_table("tbl-preview-pheno-n", "number of samples")}}
-{%endif%}
{{display_pheno_dataset_card(species, population, dataset)}}
{%endblock%}
@@ -429,9 +525,9 @@
});
if(table.find("tbody tr.data-row").length > 0) {
- add_class(table.find(".data-row-template"), "hidden");
+ add_class(table.find(".data-row-template"), "visually-hidden");
} else {
- remove_class(table.find(".data-row-template"), "hidden");
+ remove_class(table.find(".data-row-template"), "visually-hidden");
}
};
@@ -467,13 +563,24 @@
Object.entries(preview_tables_to_elements_map).forEach((mapentry) => {
var preview_table = $(mapentry[0]);
var file_input = $(mapentry[1]);
- if(file_input.length === 1) {
+ if(file_input[0].files.length > 0) {
readFirstNLines(
file_input[0].files[0],
10,
[makePreviewUpdater(preview_table)]);
}
});
+
+ if(typeof(resumables) !== "undefined") {
+ resumables.forEach((resumable) => {
+ if(resumable.files.length > 0) {
+ readFirstNLines(
+ resumable.files[0].file,
+ 10,
+ [makePreviewUpdater(resumable.preview_table)]);
+ }
+ });
+ }
};
[
@@ -506,7 +613,7 @@
var display_element = display_area
.find(".file-display-template")
.clone();
- remove_class(display_element, "hidden");
+ remove_class(display_element, "visually-hidden");
remove_class(display_element, "file-display-template");
add_class(display_element, "file-display");
display_element.find(".filename").text(file.name
@@ -526,7 +633,7 @@
return () => {/*Has no event!*/
var progress = (resumable.progress() * 100).toFixed(2);
var pbar = progress_bar.find(".progress-bar");
- remove_class(progress_bar, "hidden");
+ remove_class(progress_bar, "visually-hidden");
pbar.css("width", progress+"%");
pbar.attr("aria-valuenow", progress);
pbar.text("Uploading: " + progress + "%");
@@ -536,9 +643,9 @@
var retryUpload = (retry_button, cancel_button) => {
retry_button.on("click", (event) => {
resumable.files.forEach((file) => {file.retry();});
- add_class(retry_button, "hidden");
- remove_class(cancel_button, "hidden");
- add_class(browse_button, "hidden");
+ add_class(retry_button, "visually-hidden");
+ remove_class(cancel_button, "visually-hidden");
+ add_class(browse_button, "visually-hidden");
});
};
@@ -549,18 +656,18 @@
file.abort();
}
});
- add_class(cancel_button, "hidden");
- remove_class(retry_button, "hidden");
- remove_class(browse_button, "hidden");
+ add_class(cancel_button, "visually-hidden");
+ remove_class(retry_button, "visually-hidden");
+ remove_class(browse_button, "visually-hidden");
});
};
var startUpload = (browse_button, retry_button, cancel_button) => {
return (event) => {
- remove_class(cancel_button, "hidden");
- add_class(retry_button, "hidden");
- add_class(browse_button, "hidden");
+ remove_class(cancel_button, "visually-hidden");
+ add_class(retry_button, "visually-hidden");
+ add_class(browse_button, "visually-hidden");
};
};
@@ -574,6 +681,7 @@
}));
});
formdata.append("resumable-upload", "true");
+ formdata.append("publication-id", $("#txt-publication-id").val());
return formdata;
}
@@ -600,10 +708,12 @@
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) => {
@@ -640,7 +750,7 @@
file_input.parent(),
$("#" + resumable_element_id),
submit_button,
- ["csv", "tsv"]),
+ ["csv", "tsv", "txt"]),
file_input.parent(),
$("#" + resumable_element_id),
$("#" + resumable_element_id + "-browse-button")),
@@ -676,13 +786,20 @@
["frm-add-phenotypes", "finput-phenotype-se", "resumable-phenotype-se", "tbl-preview-pheno-se"],
["frm-add-phenotypes", "finput-phenotype-n", "resumable-phenotype-n", "tbl-preview-pheno-n"],
].map((row) => {
- return makeResumableObject(row[0], row[1], row[2], row[3]);
+ r = makeResumableObject(row[0], row[1], row[2], row[3]);
+ r.preview_table = $("#" + row[3]);
+ return r;
}).filter((val) => {
return Boolean(val);
});
$("#frm-add-phenotypes input[type=submit]").on("click", (event) => {
event.preventDefault();
+ console.debug();
+ if ($("#txt-publication-id").val() == "") {
+ alert("You MUST provide a publication for the phenotypes.");
+ return false;
+ }
// TODO: Check all the relevant files exist
// TODO: Verify that files are not duplicated
var filenames = [];
diff --git a/uploader/templates/phenotypes/bulk-edit-upload.html b/uploader/templates/phenotypes/bulk-edit-upload.html
new file mode 100644
index 0000000..d0f38f5
--- /dev/null
+++ b/uploader/templates/phenotypes/bulk-edit-upload.html
@@ -0,0 +1,62 @@
+{%extends "phenotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "macro-table-pagination.html" import table_pagination%}
+{%from "populations/macro-display-population-card.html" import display_population_card%}
+
+{%block title%}Phenotypes{%endblock%}
+
+{%block pagetitle%}Phenotypes{%endblock%}
+
+{%block lvl4_breadcrumbs%}
+<li {%if activelink=="view-dataset"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.phenotypes.view_dataset',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}">View</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+<div class="row">
+ <p>Upload the edited file you downloaded and edited.</p>
+</div>
+
+<div class="row">
+ <form id="frm-bulk-edit-upload"
+ class="form-horizontal"
+ method="POST"
+ action="{{url_for(
+ 'species.populations.phenotypes.edit_upload_phenotype_data',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}"
+ enctype="multipart/form-data">
+
+ <div class="form-group row">
+ <label for="file-upload-bulk-edit-upload"
+ class="form-label col-form-label col-sm-2">
+ Edited File</label>
+ <div class="col-sm-10">
+ <input id="file-upload-bulk-edit-upload"
+ name="file-upload-bulk-edit-upload"
+ class="form-control"
+ type="file"
+ accept="text/tab-separated-values"
+ required="required" />
+ </div>
+ </div>
+
+ <input type="submit" class="btn btn-primary"
+ value="upload to edit" />
+
+ </form>
+</div>
+{%endblock%}
+
+
+{%block javascript%}
+{%endblock%}
diff --git a/uploader/templates/phenotypes/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html
index 93de92f..19a2b34 100644
--- a/uploader/templates/phenotypes/create-dataset.html
+++ b/uploader/templates/phenotypes/create-dataset.html
@@ -42,7 +42,7 @@
<input type="text"
name="dataset-name"
id="txt-dataset-name"
- value="{{original_formdata.get('dataset-name') or (population.InbredSetCode + 'Publish')}}"
+ value="{{original_formdata.get('dataset-name') or (population.Name + 'Publish')}}"
{%if errors["dataset-name"] is defined%}
class="form-control danger"
{%else%}
@@ -51,7 +51,7 @@
required="required" />
<small class="form-text text-muted">
<p>A short representative name for the dataset.</p>
- <p>Recommended: Use the population code and append "Publish" at the end.
+ <p>Recommended: Use the population name and append "Publish" at the end.
<br />This field will only accept names composed of
letters ('A-Za-z'), numbers (0-9), hyphens and underscores.</p>
</small>
@@ -74,8 +74,10 @@
{%endif%}
required="required" />
<small class="form-text text-muted">
- <p>A longer, descriptive name for the dataset &mdash; useful for humans.
- </p></small>
+ <p>A longer, descriptive name for the dataset. The name is meant for use
+ by humans, and therefore, it should be clear what the dataset contains
+ from the name.</p>
+ </small>
</div>
<div class="form-group">
@@ -84,7 +86,7 @@
name="dataset-shortname"
type="text"
class="form-control"
- value="{{original_formdata.get('dataset-shortname') or (population.InbredSetCode + ' Publish')}}" />
+ value="{{original_formdata.get('dataset-shortname') or (population.Name + 'Publish')}}" />
<small class="form-text text-muted">
<p>An optional, short name for the dataset. <br />
If this is not provided, it will default to the value provided for the
diff --git a/uploader/templates/phenotypes/edit-phenotype.html b/uploader/templates/phenotypes/edit-phenotype.html
index 260d032..115d6af 100644
--- a/uploader/templates/phenotypes/edit-phenotype.html
+++ b/uploader/templates/phenotypes/edit-phenotype.html
@@ -25,7 +25,7 @@
<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>
@@ -201,130 +201,6 @@
</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="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="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="control-label col-sm-2">
- Publication Title</label>
- <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="control-label col-sm-2">
- Publication Abstract</label>
- <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="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="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 &hellip;</span>
- </div>
- </div>
-
- <div class="form-group">
- <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="control-label col-sm-2">
- Publication Month</label>
- <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>
-
{%endblock%}
{%block sidebarcontents%}
diff --git a/uploader/templates/phenotypes/index.html b/uploader/templates/phenotypes/index.html
index 0c691e6..689c28e 100644
--- a/uploader/templates/phenotypes/index.html
+++ b/uploader/templates/phenotypes/index.html
@@ -11,16 +11,11 @@
{{flash_all_messages()}}
<div class="row">
- <p>This section deals with phenotypes that
- <span class="text-warning">
- <span class="glyphicon glyphicon-exclamation-sign"></span>
- … what are the characteristics of these phenotypes? …</span></p>
- <p>Select the species to begin the process of viewing/uploading data about
- your phenotypes</p>
+ {{select_species_form(url_for("species.populations.phenotypes.index"), species)}}
</div>
+{%endblock%}
-<div class="row">
- {{select_species_form(url_for("species.populations.phenotypes.index"),
- species)}}
-</div>
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
{%endblock%}
diff --git a/uploader/templates/phenotypes/list-datasets.html b/uploader/templates/phenotypes/list-datasets.html
index 2eaf43a..2cf2c7f 100644
--- a/uploader/templates/phenotypes/list-datasets.html
+++ b/uploader/templates/phenotypes/list-datasets.html
@@ -48,9 +48,12 @@
</tbody>
</table>
{%else%}
- <p class="text-warning">
- <span class="glyphicon glyphicon-exclamation-sign"></span>
- There is no dataset for this population!</p>
+ <p>Phenotypes need to go into a dataset. We do not currently have a dataset
+ for species <strong>'{{species["FullName"]}} ({{species["Name"]}})'</strong>
+ phenotypes.</p>
+
+ <p>Do, please, create a new dataset by clicking on the "Create Dataset" button
+ below and following the prompts/instructions.</p>
<p><a href="{{url_for('species.populations.phenotypes.create_dataset',
species_id=species.SpeciesId,
population_id=population.Id)}}"
diff --git a/uploader/templates/phenotypes/load-phenotypes-success.html b/uploader/templates/phenotypes/load-phenotypes-success.html
new file mode 100644
index 0000000..645be16
--- /dev/null
+++ b/uploader/templates/phenotypes/load-phenotypes-success.html
@@ -0,0 +1,42 @@
+{%extends "phenotypes/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+{%from "macro-table-pagination.html" import table_pagination%}
+{%from "phenotypes/macro-display-pheno-dataset-card.html" import display_pheno_dataset_card%}
+
+{%block title%}Phenotypes{%endblock%}
+
+{%block pagetitle%}Phenotypes{%endblock%}
+
+{%block lvl4_breadcrumbs%}
+<li {%if activelink=="load-phenotypes-success"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('species.populations.phenotypes.add_phenotypes',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}">Add Phenotypes</a>
+</li>
+{%endblock%}
+
+{%block contents%}
+<div class="row">
+ <p>You have successfully loaded
+ <!-- maybe indicate the number of phenotypes here? -->your
+ new phenotypes into the database.</p>
+ <!-- TODO: Maybe notify user that they have sole access. -->
+ <!-- TODO: Maybe provide a link to go to GeneNetwork to view the data. -->
+ <p>View your data
+ <a href="{{search_page_uri}}"
+ target="_blank">on GeneNetwork2</a>.
+ You might need to login to GeneNetwork2 to view specific traits.</p>
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_pheno_dataset_card(species, population, dataset)}}
+{%endblock%}
+
+
+{%block more_javascript%}{%endblock%}
diff --git a/uploader/templates/phenotypes/macro-display-preview-table.html b/uploader/templates/phenotypes/macro-display-preview-table.html
index f54c53e..5a4c422 100644
--- a/uploader/templates/phenotypes/macro-display-preview-table.html
+++ b/uploader/templates/phenotypes/macro-display-preview-table.html
@@ -1,7 +1,7 @@
{%macro display_preview_table(tableid, filetype)%}
-<div class="card" style="max-width: 676px;">
+<div class="card">
<div class="card-body">
- <h5 class="card-title">Phenotypes '{{filetype | title}}' File Preview</h5>
+ <h5 class="card-title">{{filetype | title}}: File Preview</h5>
<div class="card-text" style="overflow: scroll;">
<table id="{{tableid}}" class="table table-condensed table-responsive">
<thead>
@@ -9,9 +9,7 @@
</tr>
<tbody>
<tr>
- <td class="data-row-template text-info">
- Provide a phenotype '{{filetype | lower}}' file to preview.
- </td>
+ <td class="data-row-template text-info"></td>
</tr>
</tbody>
</table>
diff --git a/uploader/templates/phenotypes/macro-display-resumable-elements.html b/uploader/templates/phenotypes/macro-display-resumable-elements.html
index b0bf1b5..ed14ea5 100644
--- a/uploader/templates/phenotypes/macro-display-resumable-elements.html
+++ b/uploader/templates/phenotypes/macro-display-resumable-elements.html
@@ -1,6 +1,6 @@
{%macro display_resumable_elements(id, title, help)%}
<div id="{{id}}"
- class="resumable-elements hidden"
+ class="resumable-elements visually-hidden"
style="background:#D4D4EE;border-radius: 5px;;padding: 1em;border-left: solid #B2B2CC 1px;border-bottom: solid #B2B2CC 2px;margin-top:0.3em;">
<strong style="line-height: 1.2em;">{{title | title}}</strong>
@@ -9,7 +9,7 @@
<div id="{{id}}-selected-files"
class="resumable-selected-files"
style="display:flex;flex-direction:row;flex-wrap: wrap;justify-content:space-around;gap:10px 20px;">
- <div class="panel panel-info file-display-template hidden">
+ <div class="panel panel-info file-display-template visually-hidden">
<div class="panel-heading filename">The Filename Goes Here!</div>
<div class="panel-body">
<ul>
@@ -33,10 +33,10 @@
<a id="{{id}}-browse-button"
class="resumable-browse-button btn btn-info"
- href="#"
+ href="#{{id}}"
style="margin-left: 80%;">Browse</a>
- <div id="{{id}}-progress-bar" class="progress hidden">
+ <div id="{{id}}-progress-bar" class="progress visually-hidden">
<div class="progress-bar"
role="progress-bar"
aria-valuenow="60"
@@ -49,11 +49,11 @@
<div id="{{id}}-cancel-resume-buttons">
<a id="{{id}}-resume-button"
- class="resumable-resume-button btn btn-info hidden"
+ class="resumable-resume-button btn btn-info visually-hidden"
href="#">resume upload</a>
<a id="{{id}}-cancel-button"
- class="resumable-cancel-button btn btn-danger hidden"
+ class="resumable-cancel-button btn btn-danger visually-hidden"
href="#">cancel upload</a>
</div>
</div>
diff --git a/uploader/templates/phenotypes/review-job-data.html b/uploader/templates/phenotypes/review-job-data.html
index 7bc8c62..859df74 100644
--- a/uploader/templates/phenotypes/review-job-data.html
+++ b/uploader/templates/phenotypes/review-job-data.html
@@ -35,14 +35,28 @@
{%if job%}
<div class="row">
<h3 class="heading">Data Review</h3>
+ <p class="text-info"><strong>
+ The data has <em>NOT</em> been added/saved yet. Review the details below
+ and click "Continue" to save the data.</strong></p>
<p>The &#x201C;<strong>{{dataset.FullName}}</strong>&#x201D; dataset from the
&#x201C;<strong>{{population.FullName}}</strong>&#x201D; population of the
species &#x201C;<strong>{{species.SpeciesName}} ({{species.FullName}})</strong>&#x201D;
will be updated as follows:</p>
+ <ul>
+ {%if publication%}
+ <li>All {{summary.get("pheno", {}).get("total-data-rows", "0")}} phenotypes
+ are linked to the following publication:
+ <ul>
+ <li><strong>Publication Title:</strong>
+ {{publication.Title or "—"}}</li>
+ <li><strong>Author(s):</strong>
+ {{publication.Authors or "—"}}</li>
+ </ul>
+ </li>
+ {%endif%}
{%for ftype in ("phenocovar", "pheno", "phenose", "phenonum")%}
{%if summary.get(ftype, False)%}
- <ul>
<li>A total of {{summary[ftype]["number-of-files"]}} files will be processed
adding {%if ftype == "phenocovar"%}(possibly){%endif%}
{{summary[ftype]["total-data-rows"]}} new
@@ -53,11 +67,21 @@
{%endif%}
to the database.
</li>
- </ul>
{%endif%}
{%endfor%}
+ </ul>
- <a href="#" class="not-implemented btn btn-primary">continue</a>
+ <form id="frm-review-phenotype-data"
+ method="POST"
+ action="{{url_for('species.populations.phenotypes.load_data_to_database',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ dataset_id=dataset.Id)}}">
+ <input type="hidden" name="data-qc-job-id" value="{{job.jobid}}" />
+ <input type="submit"
+ value="continue"
+ class="btn btn-primary" />
+ </form>
</div>
{%else%}
<div class="row">
diff --git a/uploader/templates/phenotypes/select-population.html b/uploader/templates/phenotypes/select-population.html
index eafd4a7..48c19b1 100644
--- a/uploader/templates/phenotypes/select-population.html
+++ b/uploader/templates/phenotypes/select-population.html
@@ -11,18 +11,16 @@
{%block contents%}
{{flash_all_messages()}}
-<div class="row">
- <p>Select the population for your phenotypes to view and manage the phenotype
- datasets that relate to it.</p>
-</div>
<div class="row">
- {{select_population_form(url_for("species.populations.phenotypes.select_population",
- species_id=species.SpeciesId),
- populations)}}
+ {{select_population_form(url_for("species.populations.phenotypes.select_population", species_id=species.SpeciesId), species, populations)}}
</div>
{%endblock%}
{%block sidebarcontents%}
{{display_species_card(species)}}
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/populations.js"></script>
+{%endblock%}
diff --git a/uploader/templates/phenotypes/view-dataset.html b/uploader/templates/phenotypes/view-dataset.html
index 011f8f6..306dcce 100644
--- a/uploader/templates/phenotypes/view-dataset.html
+++ b/uploader/templates/phenotypes/view-dataset.html
@@ -57,37 +57,26 @@
<div class="row">
<h2>Phenotype Data</h2>
- <p>This dataset has a total of {{phenotype_count}} phenotypes.</p>
+ <p>Click on any of the phenotypes in the table below to view and edit that
+ phenotype's data.</p>
+ <p>Use the search to filter through all the phenotypes and find specific
+ phenotypes of interest.</p>
+</div>
- {{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">
+<div class="row">
+
+ <table id="tbl-phenotypes-list" class="table compact stripe cell-border">
<thead>
<tr>
- <th>#</th>
+ <th></th>
+ <th>Index</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 +84,67 @@
{%block sidebarcontents%}
{{display_population_card(species, population)}}
{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript">
+ $(function() {
+ var species_id = {{species.SpeciesId}};
+ var population_id = {{population.Id}};
+ var dataset_id = {{dataset.Id}};
+ var dataset_name = "{{dataset.Name}}";
+ var data = {{phenotypes | tojson}};
+
+ var dtPhenotypesList = buildDataTable(
+ "#tbl-phenotypes-list",
+ data,
+ [
+ {
+ data: function(pheno) {
+ return `<input type="checkbox" name="selected-phenotypes" `
+ + `id="chk-selected-phenotypes-${pheno.InbredSetCode}_${pheno.xref_id}" `
+ + `value="${pheno.InbredSetCode}_${pheno.xref_id}" `
+ + `class="chk-row-select" />`
+ }
+ },
+ {data: "sequence_number"},
+ {
+ data: function(pheno, type, set, meta) {
+ var spcs_id = {{species.SpeciesId}};
+ var pop_id = {{population.Id}};
+ var dtst_id = {{dataset.Id}};
+ return `<a href="/species/${spcs_id}` +
+ `/populations/${pop_id}` +
+ `/phenotypes/datasets/${dtst_id}` +
+ `/phenotype/${pheno.xref_id}` +
+ `" target="_blank">` +
+ `${pheno.InbredSetCode}_${pheno.xref_id}` +
+ `</a>`;
+ }
+ },
+ {
+ data: function(pheno) {
+ return (pheno.Post_publication_description ||
+ pheno.Original_description ||
+ pheno.Pre_publication_description);
+ }
+ }
+ ],
+ {
+ select: "multi+shift",
+ layout: {
+ top1Start: {
+ pageLength: {
+ text: "Show _MENU_ of _TOTAL_"
+ }
+ },
+ topStart: "info",
+ top1End: null
+ },
+ rowId: function(pheno) {
+ return `${pheno.InbredSetCode}_${pheno.xref_id}`;
+ }
+ });
+ });
+</script>
+{%endblock%}
diff --git a/uploader/templates/phenotypes/view-phenotype.html b/uploader/templates/phenotypes/view-phenotype.html
index b42f680..21ac501 100644
--- a/uploader/templates/phenotypes/view-phenotype.html
+++ b/uploader/templates/phenotypes/view-phenotype.html
@@ -98,7 +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/index.html b/uploader/templates/platforms/index.html
index 35b6464..555b444 100644
--- a/uploader/templates/platforms/index.html
+++ b/uploader/templates/platforms/index.html
@@ -19,3 +19,7 @@
{{select_species_form(url_for("species.platforms.index"), species)}}
</div>
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
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/create-population.html b/uploader/templates/populations/create-population.html
index b05ce37..c0c4f45 100644
--- a/uploader/templates/populations/create-population.html
+++ b/uploader/templates/populations/create-population.html
@@ -37,12 +37,15 @@
<div class="row">
<form method="POST"
action="{{url_for('species.populations.create_population',
- species_id=species.SpeciesId)}}">
+ species_id=species.SpeciesId,
+ return_to=return_to)}}">
<legend>Create Population</legend>
{{flash_all_messages()}}
+ <input type="hidden" name="return_to" value="{{return_to}}">
+
<div {%if errors.population_fullname%}
class="form-group has-error"
{%else%}
@@ -107,9 +110,12 @@
value="{{error_values.population_code or ''}}"
class="form-control" />
<small class="form-text text-muted">
- <p class="text-danger">
- <span class="glyphicon glyphicon-exclamation-sign"></span>
- What is this field is for? Confirm with Arthur and the rest.
+ <p class="form-text text-muted">
+ This is a 3-character code for your population, that is prepended to
+ the phenotype identifiers. e.g. For the "BXD Family" population, the
+ code is "BXD" and therefore, the phenotype identifiers for the
+ population look like the following examples: <em>BXD_10148</em>,
+ <em>BXD_10180</em>, <em>BXD_10197</em>, etc.
</p>
</small>
</div>
diff --git a/uploader/templates/populations/index.html b/uploader/templates/populations/index.html
index 4354e02..d2bee77 100644
--- a/uploader/templates/populations/index.html
+++ b/uploader/templates/populations/index.html
@@ -22,3 +22,7 @@
{{select_species_form(url_for("species.populations.index"), species)}}
</div>
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
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]}}&hellip;</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..14b0510 100644
--- a/uploader/templates/populations/macro-select-population.html
+++ b/uploader/templates/populations/macro-select-population.html
@@ -1,30 +1,52 @@
-{%macro select_population_form(form_action, populations)%}
-<form method="GET" action="{{form_action}}">
- <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>
- {%endfor%}
- </optgroup>
- {%endfor%}
- </select>
+{%from "macro-step-indicator.html" import step_indicator%}
+
+{%macro select_population_form(form_action, species, populations)%}
+<form method="GET" action="{{form_action}}" class="form-horizontal">
+
+ <h2>{{step_indicator("2")}} What population do you want to work with?</h2>
+
+ {%if populations | length != 0%}
+
+ <p class="form-text">Search for, and select the population from the table
+ below and click "Continue"</p>
+
+ <div class="radio">
+ <label class="control-label" for="rdo-cant-find-population">
+ <input type="radio" id="rdo-cant-find-population"
+ name="population_id" value="CREATE-POPULATION" />
+ I cannot find the population I want &mdash; create it!
+ </label>
+ </div>
+
+ <div class="col-sm-offset-10 col-sm-2">
+ <input type="submit" value="continue" class="btn btn-primary" />
+ </div>
+
+ <div style="margin-top:3em;">
+ <table id="tbl-select-population" class="table compact stripe"
+ data-populations-list='{{populations | tojson}}'>
+ <thead>
+ <tr>
+ <th></th>
+ <th>Population</th>
+ </tr>
+ </thead>
+
+ <tbody></tbody>
+ </table>
</div>
- <div class="form-group">
- <input type="submit" value="Select" class="btn btn-primary" />
+ {%else%}
+ <p class="form-text">
+ There are no populations currently defined for {{species['FullName']}}
+ ({{species['SpeciesName']}}).<br />
+ Click "Continue" to create the first!</p>
+ <input type="hidden" name="population_id" value="CREATE-POPULATION" />
+
+ <div class="col-sm-offset-10 col-sm-2">
+ <input type="submit" value="continue" class="btn btn-primary" />
</div>
+ {%endif%}
+
</form>
{%endmacro%}
diff --git a/uploader/templates/publications/base.html b/uploader/templates/publications/base.html
new file mode 100644
index 0000000..db80bfa
--- /dev/null
+++ b/uploader/templates/publications/base.html
@@ -0,0 +1,12 @@
+{%extends "base.html"%}
+
+{%block lvl1_breadcrumbs%}
+<li {%if activelink=="publications"%}
+ class="breadcrumb-item active"
+ {%else%}
+ class="breadcrumb-item"
+ {%endif%}>
+ <a href="{{url_for('publications.index')}}">Publications</a>
+</li>
+{%block lvl2_breadcrumbs%}{%endblock%}
+{%endblock%}
diff --git a/uploader/templates/publications/create-publication.html b/uploader/templates/publications/create-publication.html
new file mode 100644
index 0000000..3f828a9
--- /dev/null
+++ b/uploader/templates/publications/create-publication.html
@@ -0,0 +1,191 @@
+{%extends "publications/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}View Publication{%endblock%}
+
+{%block pagetitle%}View Publication{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <form id="frm-create-publication"
+ method="POST"
+ action="{{url_for('publications.create_publication', **request.args)}}"
+ class="form-horizontal">
+
+ <div class="row mb-3">
+ <label for="txt-pubmed-id" class="col-sm-2 col-form-label">
+ PubMed ID</label>
+ <div class="col-sm-10">
+ <div class="input-group">
+ <input type="text"
+ id="txt-pubmed-id"
+ name="pubmed-id"
+ class="form-control"/>
+ <div class="input-group-text">
+ <button class="btn btn-outline-primary"
+ id="btn-search-pubmed-id">search</button>
+ </div>
+ </div>
+ <span id="search-pubmed-id-error"
+ class="form-text text-muted text-danger visually-hidden">
+ </span>
+ <span class="form-text text-muted">This is the publication's ID on
+ <a href="https://pubmed.ncbi.nlm.nih.gov/"
+ title="Link to NCBI's PubMed service">NCBI's Pubmed Service</a>
+ </span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-title" class="col-sm-2 col-form-label">
+ Title</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-publication-title"
+ name="publication-title"
+ class="form-control" />
+ <span class="form-text text-muted">Provide the publication's title here.</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-authors" class="col-sm-2 col-form-label">
+ Authors</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-publication-authors"
+ name="publication-authors"
+ required="required"
+ class="form-control" />
+ <span class="form-text text-muted">
+ A publication <strong>MUST</strong> have an author. You <em>must</em>
+ provide a value for the authors field.
+ </span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-journal" class="col-sm-2 col-form-label">
+ Journal</label>
+ <div class="col-sm-10">
+ <input type="text"
+ id="txt-publication-journal"
+ name="publication-journal"
+ class="form-control" />
+ <span class="form-text text-muted">Provide the name journal where the
+ publication was done, here.</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="select-publication-month"
+ class="col-sm-2 col-form-label">
+ Month</label>
+ <div class="col-sm-4">
+ <select class="form-control"
+ id="select-publication-month"
+ name="publication-month">
+ <option value="">Select a month</option>
+ <option value="january">January</option>
+ <option value="february">February</option>
+ <option value="march">March</option>
+ <option value="april">April</option>
+ <option value="may">May</option>
+ <option value="june">June</option>
+ <option value="july">July</option>
+ <option value="august">August</option>
+ <option value="september">September</option>
+ <option value="october">October</option>
+ <option value="november">November</option>
+ <option value="december">December</option>
+ </select>
+ <span class="form-text text-muted">Month of publication</span>
+ </div>
+
+ <label for="txt-publication-year"
+ class="col-sm-2 col-form-label">
+ Year</label>
+ <div class="col-sm-4">
+ <input type="number"
+ id="txt-publication-year"
+ name="publication-year"
+ class="form-control"
+ min="1960" />
+ <span class="form-text text-muted">Year of publication</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-publication-volume"
+ class="col-sm-2 col-form-label">
+ Volume</label>
+ <div class="col-sm-4">
+ <input type="text"
+ id="txt-publication-volume"
+ name="publication-volume"
+ class="form-control">
+ <span class="form-text text-muted">Journal volume</span>
+ </div>
+
+ <label for="txt-publication-pages"
+ class="col-sm-2 col-form-label">
+ Pages</label>
+ <div class="col-sm-4">
+ <input type="text"
+ id="txt-publication-pages"
+ name="publication-pages"
+ class="form-control" />
+ <span class="form-text text-muted">Journal pages for the publication</span>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <label for="txt-abstract" class="col-sm-2 col-form-label">Abstract</label>
+ <div class="col-sm-10">
+ <textarea id="txt-publication-abstract"
+ name="publication-abstract"
+ class="form-control"
+ rows="7"></textarea>
+ </div>
+ </div>
+
+ <div class="row mb-3">
+ <div class="col-sm-2"></div>
+ <div class="col-sm-8">
+ <input type="submit" class="btn btn-primary" value="Add" />
+ <input type="reset" class="btn btn-danger" />
+ </div>
+ </div>
+
+</form>
+</div>
+
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/pubmed.js"></script>
+<script type="text/javascript">
+ $(function() {
+ $("#btn-search-pubmed-id").on("click", (event) => {
+ event.preventDefault();
+ var search_button = event.target;
+ var pubmed_id = $("#txt-pubmed-id").val().trim();
+ remove_class($("#txt-pubmed-id").parent(), "has-error");
+ if(pubmed_id == "") {
+ add_class($("#txt-pubmed-id").parent(), "has-error");
+ return false;
+ }
+
+ search_button.disabled = true;
+ // Fetch publication details
+ fetch_publication_details(pubmed_id,
+ [() => {search_button.disabled = false;}]);
+ return false;
+ });
+ });
+</script>
+{%endblock%}
diff --git a/uploader/templates/publications/index.html b/uploader/templates/publications/index.html
new file mode 100644
index 0000000..369812b
--- /dev/null
+++ b/uploader/templates/publications/index.html
@@ -0,0 +1,100 @@
+{%extends "publications/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Publications{%endblock%}
+
+{%block pagetitle%}Publications{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row" style="padding-bottom: 1em;">
+ <a href="{{url_for('publications.create_publication')}}"
+ class="btn btn-primary">
+ add new publication</a>
+</div>
+
+<div class="row">
+ <table id="tbl-list-publications" class="table compact stripe">
+ <thead>
+ <tr>
+ <th>#</th>
+ <th>PubMed ID</th>
+ <th>Title</th>
+ <th>Authors</th>
+ </tr>
+ </thead>
+
+ <tbody></tbody>
+ </table>
+</div>
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript">
+ $(function() {
+ var publicationsDataTable = buildDataTable(
+ "#tbl-list-publications",
+ [],
+ [
+ {data: "index"},
+ {
+ searchable: true,
+ data: (pub) => {
+ if(pub.PubMed_ID) {
+ return `<a href="https://pubmed.ncbi.nlm.nih.gov/` +
+ `${pub.PubMed_ID}/" target="_blank" ` +
+ `title="Link to publication on NCBI.">` +
+ `${pub.PubMed_ID}</a>`;
+ }
+ return "";
+ }
+ },
+ {
+ searchable: true,
+ data: (pub) => {
+ var title = "⸻";
+ if(pub.Title) {
+ title = pub.Title
+ }
+ return `<a href="/publications/view/${pub.Id}" ` +
+ `target="_blank" ` +
+ `title="Link to view publication details">` +
+ `${title}</a>`;
+ }
+ },
+ {
+ searchable: true,
+ data: (pub) => {
+ authors = pub.Authors.split(",").map(
+ (item) => {return item.trim();});
+ if(authors.length > 1) {
+ return authors[0] + ", et. al.";
+ }
+ return authors[0];
+ }
+ }
+ ],
+ {
+ serverSide: true,
+ ajax: {
+ url: "/publications/list",
+ dataSrc: "publications"
+ },
+ scrollY: 700,
+ scroller: true,
+ scrollCollapse: true,
+ paging: true,
+ deferRender: true,
+ layout: {
+ topStart: "info",
+ topEnd: "search",
+ bottomStart: "pageLength",
+ bottomEnd: false
+ }
+ });
+ });
+</script>
+{%endblock%}
diff --git a/uploader/templates/publications/view-publication.html b/uploader/templates/publications/view-publication.html
new file mode 100644
index 0000000..388547a
--- /dev/null
+++ b/uploader/templates/publications/view-publication.html
@@ -0,0 +1,78 @@
+{%extends "publications/base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}View Publication{%endblock%}
+
+{%block pagetitle%}View Publication{%endblock%}
+
+
+{%block contents%}
+{{flash_all_messages()}}
+
+<div class="row">
+ <table class="table">
+ <tr>
+ <th>PubMed</th>
+ <td>
+ {%if publication.PubMed_ID%}
+ <a href="https://pubmed.ncbi.nlm.nih.gov/{{publication.PubMed_ID}}/"
+ target="_blank">{{publication.PubMed_ID}}</a>
+ {%else%}
+ —
+ {%endif%}
+ </td>
+ </tr>
+ <tr>
+ <th>Title</th>
+ <td>{{publication.Title or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Authors</th>
+ <td>{{publication.Authors or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Journal</th>
+ <td>{{publication.Journal or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Published</th>
+ <td>{{publication.Month or ""}} {{publication.Year or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Volume</th>
+ <td>{{publication.Volume or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Pages</th>
+ <td>{{publication.Pages or "—"}}</td>
+ </tr>
+ <tr>
+ <th>Abstract</th>
+ <td>
+ {%for line in (publication.Abstract or "—").replace("\r\n", "<br />").replace("\n", "<br />").split("<br />")%}
+ <p>{{line}}</p>
+ {%endfor%}
+ </td>
+ </tr>
+ </table>
+</div>
+
+<div class="row">
+ <form id="frm-edit-delete-publication" method="POST" action="#">
+ <input type="hidden" name="publication_id" value="{{publication.Id}}" />
+ <div class="form-group">
+ <input type="submit" value="edit" class="btn btn-primary not-implemented" />
+ {%if linked_phenotypes | length == 0%}
+ <input type="submit" value="delete" class="btn btn-danger not-implemented" />
+ {%endif%}
+ </div>
+ </form>
+</div>
+{%endblock%}
+
+
+{%block javascript%}
+<script type="text/javascript">
+ $(function() {});
+</script>
+{%endblock%}
diff --git a/uploader/templates/samples/index.html b/uploader/templates/samples/index.html
index ee4a63e..ee98734 100644
--- a/uploader/templates/samples/index.html
+++ b/uploader/templates/samples/index.html
@@ -17,3 +17,7 @@
{{select_species_form(url_for("species.populations.samples.index"), species)}}
</div>
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/species.js"></script>
+{%endblock%}
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/samples/select-population.html b/uploader/templates/samples/select-population.html
index f437780..1cc7573 100644
--- a/uploader/templates/samples/select-population.html
+++ b/uploader/templates/samples/select-population.html
@@ -12,28 +12,15 @@
{{flash_all_messages()}}
<div class="row">
- <p>You have selected "{{species.FullName}}" as the species that your data relates to.</p>
- <p>Next, we need information regarding the population your data relates to. Do please select the population from the existing ones below</p>
-</div>
-
-<div class="row">
{{select_population_form(
- url_for("species.populations.samples.select_population", species_id=species.SpeciesId),
- populations)}}
-</div>
-
-<div class="row">
- <p>
- If you cannot find the population your data relates to in the drop-down
- above, you might want to
- <a href="{{url_for('species.populations.create_population',
- species_id=species.SpeciesId)}}"
- title="Create a new population for species '{{species.FullName}},">
- add a new population to GeneNetwork</a>
- instead.
+ url_for("species.populations.samples.select_population", species_id=species.SpeciesId), species, populations)}}
</div>
{%endblock%}
{%block sidebarcontents%}
{{display_species_card(species)}}
{%endblock%}
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/populations.js"></script>
+{%endblock%}
diff --git a/uploader/templates/samples/upload-failure.html b/uploader/templates/samples/upload-failure.html
index 458ab55..2cf8053 100644
--- a/uploader/templates/samples/upload-failure.html
+++ b/uploader/templates/samples/upload-failure.html
@@ -15,7 +15,7 @@
<h3>Debugging Information</h3>
<ul>
- <li><strong>job id</strong>: {{job.job_id}}</li>
+ <li><strong>job id</strong>: {{job.jobid}}</li>
<li><strong>status</strong>: {{job.status}}</li>
<li><strong>job type</strong>: {{job["job-type"]}}</li>
</ul>
diff --git a/uploader/templates/species/create-species.html b/uploader/templates/species/create-species.html
index 0d0bedf..138dbaa 100644
--- a/uploader/templates/species/create-species.html
+++ b/uploader/templates/species/create-species.html
@@ -19,72 +19,88 @@
<div class="row">
<form id="frm-create-species"
method="POST"
- action="{{url_for('species.create_species')}}">
+ action="{{url_for('species.create_species', return_to=return_to)}}"
+ class="form-horizontal">
<legend>Create Species</legend>
{{flash_all_messages()}}
+ <input type="hidden" name="return_to" value="{{return_to}}">
+
<div class="form-group">
- <label for="txt-taxonomy-id" class="form-label">
+ <label for="txt-taxonomy-id" class="control-label col-sm-2">
Taxonomy ID</label>
- <div class="input-group">
- <input id="txt-taxonomy-id"
- name="species_taxonomy_id"
- type="text"
- class="form-control" />
- <span class="input-group-btn">
- <button id="btn-search-taxonid" class="btn btn-info">Search</button>
- </span>
+ <div class="col-sm-10">
+ <div class="input-group">
+ <input id="txt-taxonomy-id"
+ name="species_taxonomy_id"
+ type="text"
+ class="form-control" />
+ <span class="input-group-btn">
+ <button id="btn-search-taxonid" class="btn btn-info">Search</button>
+ </span>
+ </div>
+ <small class="form-text text-small text-muted">
+ Use
+ <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/"
+ title="NCBI's Taxonomy Browser homepage"
+ target="_blank">
+ NCBI's Taxonomy Browser homepage</a> to search for the species you
+ want. If the species exists on NCBI, they will have a Taxonomy ID. Copy
+ that Taxonomy ID to this field, and click "Search" to auto-fill the
+ details.<br />
+ This field is optional.</small>
</div>
- <small class="form-text text-small text-muted">Provide the taxonomy ID for
- your species that can be used to link to external sites like NCBI. Enter
- the taxonomy ID and click "Search" to auto-fill the form with data.
- <br />
- While it is recommended to provide a value for this field, doing so is
- optional.
- </small>
</div>
<div class="form-group">
- <label for="txt-species-name" class="form-label">Common Name</label>
- <input id="txt-species-name"
- name="common_name"
- type="text"
- class="form-control"
- required="required" />
- <small class="form-text text-muted">Provide the common, possibly
- non-scientific name for the species here, e.g. Human, Mouse, etc.</small>
+ <label for="txt-species-name" class="control-label col-sm-2">Common Name</label>
+ <div class="col-sm-10">
+ <input id="txt-species-name"
+ name="common_name"
+ type="text"
+ class="form-control"
+ required="required" />
+ <small class="form-text text-muted">This is the day-to-day term used by
+ laymen, e.g. Mouse (instead of Mus musculus), round worm (instead of
+ Ascaris lumbricoides), etc.<br />
+ For species without this, just enter the scientific name.
+ </small>
+ </div>
</div>
<div class="form-group">
- <label for="txt-species-scientific" class="form-label">
+ <label for="txt-species-scientific" class="control-label col-sm-2">
Scientific Name</label>
- <input id="txt-species-scientific"
- name="scientific_name"
- type="text"
- class="form-control"
- required="required" />
- <small class="form-text text-muted">Provide the scientific name for the
- species you are creating, e.g. Homo sapiens, Mus musculus, etc.</small>
+ <div class="col-sm-10">
+ <input id="txt-species-scientific"
+ name="scientific_name"
+ type="text"
+ class="form-control"
+ required="required" />
+ <small class="form-text text-muted">This is the scientific name for the
+ species e.g. Homo sapiens, Mus musculus, etc.</small>
+ </div>
</div>
<div class="form-group">
- <label for="select-species-family" class="form-label">Family</label>
- <select id="select-species-family"
- name="species_family"
- required="required"
- class="form-control">
- <option value="">Please select a grouping</option>
- {%for family in families%}
- <option value="{{family}}">{{family}}</option>
- {%endfor%}
- </select>
- <small class="form-text text-muted">
- This is a generic grouping for the species that determines under which
- grouping the species appears in the GeneNetwork menus</small>
+ <label for="select-species-family" class="control-label col-sm-2">Family</label>
+ <div class="col-sm-10">
+ <select id="select-species-family"
+ name="species_family"
+ required="required"
+ class="form-control">
+ <option value="ungrouped">I do not know what to pick</option>
+ {%for family in families%}
+ <option value="{{family}}">{{family}}</option>
+ {%endfor%}
+ </select>
+ <small class="form-text text-muted">
+ This is a rough grouping of the species.</small>
+ </div>
</div>
- <div class="form-group">
+ <div class="col-sm-offset-2 col-sm-10">
<input type="submit"
value="create new species"
class="btn btn-primary" />
@@ -113,7 +129,7 @@
}
msg = (
"Request to '${uri}' failed with message '${textStatus}'. "
- + "Please try again later, or fill the details manually.");
+ + "Please try again later, or fill the details manually.");
alert(msg);
console.error(msg, data, textStatus);
return false;
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..3714ae4 100644
--- a/uploader/templates/species/macro-select-species.html
+++ b/uploader/templates/species/macro-select-species.html
@@ -1,36 +1,59 @@
+{%from "macro-step-indicator.html" import step_indicator%}
+
{%macro select_species_form(form_action, species)%}
-{%if species | length > 0%}
-<form method="GET" action="{{form_action}}">
- <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>
- {%endfor%}
- </optgroup>
- {%endfor%}
- </select>
+<form method="GET" action="{{form_action}}" class="form-horizontal">
+
+ <h2>{{step_indicator("1")}} What species do you want to work with?</h2>
+
+ {%if species | length != 0%}
+
+ <p class="form-text">Search for, and select the species from the table below
+ and click "Continue"</p>
+
+ <div class="radio">
+ <label for="rdo-cant-find-species"
+ style="font-weight: 1;">
+ <input id="rdo-cant-find-species" type="radio" name="species_id"
+ value="CREATE-SPECIES" />
+ I could not find the species I want (create it).
+ </label>
</div>
- <div class="form-group">
- <input type="submit" value="Select" class="btn btn-primary" />
+ <div class="col-sm-offset-10 col-sm-2">
+ <input type="submit"
+ class="btn btn-primary"
+ value="continue" />
</div>
+
+ <div style="margin-top:3em;">
+ <table id="tbl-select-species" class="table compact stripe"
+ data-species-list='{{species | tojson}}'>
+ <div class="">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Species Name</th>
+ </tr>
+ </thead>
+
+ <tbody></tbody>
+ </table>
+ </div>
+
+ {%else%}
+
+ <label class="control-label" for="rdo-cant-find-species">
+ <input id="rdo-cant-find-species" type="radio" name="species_id"
+ value="CREATE-SPECIES" />
+ There are no species to select from. Create the first one.</label>
+
+ <div class="col-sm-offset-10 col-sm-2">
+ <input type="submit"
+ class="btn btn-primary col-sm-offset-1"
+ value="continue" />
+ </div>
+
+ {%endif%}
+
</form>
-{%else%}
-<p class="text-danger">
- <span class="glyphicon glyphicon-exclamation-mark"></span>
- We could not find species to select from!
-</p>
-{%endif%}
{%endmacro%}