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-rw-r--r--uploader/templates/base.html56
-rw-r--r--uploader/templates/genotypes/index.html4
-rw-r--r--uploader/templates/genotypes/select-population.html16
-rw-r--r--uploader/templates/index.html133
-rw-r--r--uploader/templates/login.html7
-rw-r--r--uploader/templates/macro-step-indicator.html15
-rw-r--r--uploader/templates/phenotypes/create-dataset.html6
-rw-r--r--uploader/templates/phenotypes/index.html15
-rw-r--r--uploader/templates/phenotypes/list-datasets.html9
-rw-r--r--uploader/templates/phenotypes/select-population.html12
-rw-r--r--uploader/templates/phenotypes/view-dataset.html74
-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-select-population.html73
-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/species/create-species.html112
-rw-r--r--uploader/templates/species/list-species.html2
-rw-r--r--uploader/templates/species/macro-select-species.html83
23 files changed, 404 insertions, 268 deletions
diff --git a/uploader/templates/base.html b/uploader/templates/base.html
index 2229b3d..873b9e8 100644
--- a/uploader/templates/base.html
+++ b/uploader/templates/base.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
{%block extrameta%}{%endblock%}
- <title>GN Uploader: {%block title%}{%endblock%}</title>
+ <title>Data Upload and Quality Control: {%block title%}{%endblock%}</title>
<link rel="stylesheet" type="text/css"
href="{{url_for('base.bootstrap',
@@ -24,7 +24,7 @@
<body>
<header id="header">
- <span id="header-text">GeneNetwork: Data Upload and Quality Control</span>
+ <span id="header-text">GeneNetwork</span>
<nav id="header-nav">
<ul class="nav justify-content-end">
<li>
@@ -96,19 +96,21 @@
<main id="main" class="main">
<div id="pagetitle" class="pagetitle">
- <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>
+ <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 id="all-content">
@@ -122,11 +124,35 @@
</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>
+
+ <!--
+ 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/misc.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 e954a1c..aa1414e 100644
--- a/uploader/templates/index.html
+++ b/uploader/templates/index.html
@@ -10,87 +10,92 @@
<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>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>
- <p class="text-danger">
- <span class="glyphicon glyphicon-exclamation-sign"></span>
- <strong>TODO</strong>: Document this &hellip;</p>
+ <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>
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/create-dataset.html b/uploader/templates/phenotypes/create-dataset.html
index 93de92f..8e45491 100644
--- a/uploader/templates/phenotypes/create-dataset.html
+++ b/uploader/templates/phenotypes/create-dataset.html
@@ -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">
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/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 4e1be6b..6b35f6a 100644
--- a/uploader/templates/phenotypes/view-dataset.html
+++ b/uploader/templates/phenotypes/view-dataset.html
@@ -5,11 +5,6 @@
{%block title%}Phenotypes{%endblock%}
-{%block css%}
-<link rel="stylesheet"
- href="{{url_for('base.datatables', filename='css/jquery.dataTables.css')}}" />
-{%endblock%}
-
{%block pagetitle%}Phenotypes{%endblock%}
{%block lvl4_breadcrumbs%}
@@ -61,10 +56,21 @@
<div class="row">
<h2>Phenotype Data</h2>
- <table id="tbl-phenotypes-list" class="table">
+
+ <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>
+
+
+<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>
@@ -81,17 +87,24 @@
{%block javascript%}
-<script src="{{url_for('base.datatables',
- filename='js/jquery.dataTables.js')}}"></script>
<script type="text/javascript">
$(function() {
- $("#tbl-phenotypes-list").DataTable({
- responsive: true,
- data: {{phenotypes | tojson}},
- columns: [
- {data: "sequence_number"},
+ var data = {{phenotypes | tojson}};
+ var dtPhenotypesList = buildDataTable(
+ "#tbl-phenotypes-list",
+ data,
+ [
{
data: function(pheno) {
+ return `<input type="checkbox" name="selected-phenotypes" `
+ + `id="chk-selected-phenotypes-${pheno.InbredSetCode}_${pheno.xref_id}" `
+ + `value="${pheno.InbredSetCode}_${pheno.xref_id}" `
+ + `class="chk-row-select" />`
+ }
+ },
+ {data: "sequence_number"},
+ {
+ data: function(pheno, type, set, meta) {
var spcs_id = {{species.SpeciesId}};
var pop_id = {{population.Id}};
var dtst_id = {{dataset.Id}};
@@ -104,13 +117,32 @@
`</a>`;
}
},
- {data: function(pheno) {
- return (pheno.Post_publication_description ||
- pheno.Original_description ||
- pheno.Pre_publication_description);
- }}
- ]
- });
+ {
+ data: function(pheno) {
+ return (pheno.Post_publication_description ||
+ pheno.Original_description ||
+ pheno.Pre_publication_description);
+ }
+ }
+ ],
+ {
+ select: "multi+shift",
+ scrollY: "1000px",
+ layout: {
+ top1: "search",
+ topStart: {
+ buttons: [
+ {extend: "selectAll", className: "btn btn-info"},
+ {extend: "selectNone", className: "btn btn-info"}
+ ]
+ },
+ topEnd: "info",
+ bottomEnd: null
+ },
+ rowId: function(pheno) {
+ return `${pheno.InbredSetCode}_${pheno.xref_id}`;
+ }
+ });
});
</script>
{%endblock%}
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-select-population.html b/uploader/templates/populations/macro-select-population.html
index ef74ac3..14b0510 100644
--- a/uploader/templates/populations/macro-select-population.html
+++ b/uploader/templates/populations/macro-select-population.html
@@ -1,33 +1,52 @@
-{%macro select_population_form(form_action, populations)%}
+{%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">
- <legend>Select Population</legend>
-
- <div class="form-group">
- <label for="select-population" class="control-label col-sm-2">
- Population</label>
- <div class="col-sm-10">
- <select id="select-population"
- name="population_id"
- class="form-control"
- required="required">
- <option value="">Select Population</option>
- {%for family in populations%}
- <optgroup {%if family[0][1] is not none%}
- label="{{family[0][1]}}"
- {%else%}
- label="Undefined"
- {%endif%}>
- {%for population in family[1]%}
- <option value="{{population.Id}}">{{population.FullName}}</option>
- {%endfor%}
- </optgroup>
- {%endfor%}
- </select>
- </div>
+
+ <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="col-sm-offset-2 col-sm-10">
- <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/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/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 36ed102..3714ae4 100644
--- a/uploader/templates/species/macro-select-species.html
+++ b/uploader/templates/species/macro-select-species.html
@@ -1,38 +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}}" class="form-horizontal">
- <div class="form-group">
- <label for="select-species" class="control-label col-sm-2">Species</label>
- <div class="col-sm-10">
- <select id="select-species"
- name="species_id"
- class="form-control"
- required="required">
- <option value="">Select Species</option>
- {%for group in species%}
- {{group}}
- <optgroup {%if group[0][1] is not none%}
- label="{{group[0][1].capitalize()}}"
- {%else%}
- label="Undefined"
- {%endif%}>
- {%for aspecies in group[1]%}
- <option value="{{aspecies.SpeciesId}}">{{aspecies.MenuName}}</option>
- {%endfor%}
- </optgroup>
- {%endfor%}
- </select>
- </div>
+
+ <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="col-sm-offset-2 col-sm-10">
- <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%}