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-rw-r--r--uploader/templates/samples/index.html6
-rw-r--r--uploader/templates/samples/list-samples.html91
-rw-r--r--uploader/templates/samples/select-population.html17
-rw-r--r--uploader/templates/samples/upload-samples.html7
4 files changed, 73 insertions, 48 deletions
diff --git a/uploader/templates/samples/index.html b/uploader/templates/samples/index.html
index 7c88c01..ee4a63e 100644
--- a/uploader/templates/samples/index.html
+++ b/uploader/templates/samples/index.html
@@ -11,10 +11,8 @@
{{flash_all_messages()}}
<div class="row">
- <p>Here, you can upload the samples/individuals that were used in your
- experiments.</p>
- <p>Since the samples are linked to specific species and populations, we will
- need to first select them in the next few steps.</p>
+ <p>GeneNetwork has a selection of different species of organisms to choose from. Within those species, there are the populations of interest for a variety of experiments, from which you, the researcher, picked your samples (or individuals or cases) from. Here you can provide some basic details about your samples.</p>
+ <p>To start off, we will need to know what species and population your samples belong to. Please provide that information in the next sections.</p>
{{select_species_form(url_for("species.populations.samples.index"), species)}}
</div>
diff --git a/uploader/templates/samples/list-samples.html b/uploader/templates/samples/list-samples.html
index 8f1bf16..13e5cec 100644
--- a/uploader/templates/samples/list-samples.html
+++ b/uploader/templates/samples/list-samples.html
@@ -24,45 +24,56 @@
<div class="row">
<p>
- Samples for population "{{population.FullName}}" from the
+ You selected the population "{{population.FullName}}" from the
"{{species.FullName}}" species.
</p>
+</div>
+
+{%if samples | length > 0%}
+<div class="row">
+ <p>
+ This population already has <strong>{{total_samples}}</strong>
+ samples/individuals entered. You can explore the list of samples in this
+ population in the table below.
+ </p>
+</div>
+
+<div class="row">
+ <div class="col-md-2">
+ {%if offset > 0:%}
+ <a href="{{url_for('species.populations.samples.list_samples',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ from=offset-count,
+ count=count)}}">
+ <span class="glyphicon glyphicon-backward"></span>
+ Previous
+ </a>
+ {%endif%}
+ </div>
- {%if samples | length > 0%}
- <div class="row">
- <div class="col-md-2">
- {%if offset > 0:%}
- <a href="{{url_for('species.populations.samples.list_samples',
- species_id=species.SpeciesId,
- population_id=population.Id,
- from=offset-count,
- count=count)}}">
- <span class="glyphicon glyphicon-backward"></span>
- Previous
- </a>
- {%endif%}
- </div>
-
- <div class="col-md-8" style="text-align: center;">
- Samples {{offset}} &mdash; {{offset+(count if offset + count < total_samples else total_samples - offset)}} / {{total_samples}}
- </div>
-
- <div class="col-md-2">
- {%if offset + count < total_samples:%}
- <a href="{{url_for('species.populations.samples.list_samples',
- species_id=species.SpeciesId,
- population_id=population.Id,
- from=offset+count,
- count=count)}}">
- Next
- <span class="glyphicon glyphicon-forward"></span>
- </a>
- {%endif%}
- </div>
+ <div class="col-md-8" style="text-align: center;">
+ Samples {{offset}} &mdash; {{offset+(count if offset + count < total_samples else total_samples - offset)}} / {{total_samples}}
+ </div>
+
+ <div class="col-md-2">
+ {%if offset + count < total_samples:%}
+ <a href="{{url_for('species.populations.samples.list_samples',
+ species_id=species.SpeciesId,
+ population_id=population.Id,
+ from=offset+count,
+ count=count)}}">
+ Next
+ <span class="glyphicon glyphicon-forward"></span>
+ </a>
+ {%endif%}
</div>
+</div>
+<div class="row">
<table class="table">
<thead>
<tr>
+ <th>#</th>
<th>Name</th>
<th>Auxilliary Name</th>
<th>Symbol</th>
@@ -73,6 +84,7 @@
<tbody>
{%for sample in samples%}
<tr>
+ <td>{{sample.sequence_number}}</td>
<td>{{sample.Name}}</td>
<td>{{sample.Name2}}</td>
<td>{{sample.Symbol or "-"}}</td>
@@ -90,10 +102,14 @@
delete all samples
</a>
</p>
- {%else%}
- <p class="text-danger">
- <span class="glyphicon glyphicon-exclamation-sign"></span>
- There are no samples for this population at this time.
+</div>
+
+{%else%}
+
+<div class="row">
+ <p>
+ There are no samples entered for this population. Do please go ahead and add
+ the samples for this population by clicking on the button below.
</p>
<p>
@@ -106,8 +122,9 @@
add samples
</a>
</p>
- {%endif%}
</div>
+{%endif%}
+
{%endblock%}
{%block sidebarcontents%}
diff --git a/uploader/templates/samples/select-population.html b/uploader/templates/samples/select-population.html
index 8e22ac1..f437780 100644
--- a/uploader/templates/samples/select-population.html
+++ b/uploader/templates/samples/select-population.html
@@ -12,20 +12,25 @@
{{flash_all_messages()}}
<div class="row">
- <p>Select the population to use with your samples:</p>
+ <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><strong>Cannot find your population in the list?</strong></p>
- <p>If you cannot find the population you want in the drop-down above, you can
- instead,
+<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}},">
- create a new population</a>.
+ add a new population to GeneNetwork</a>
+ instead.
</div>
{%endblock%}
diff --git a/uploader/templates/samples/upload-samples.html b/uploader/templates/samples/upload-samples.html
index b101b2e..25d3290 100644
--- a/uploader/templates/samples/upload-samples.html
+++ b/uploader/templates/samples/upload-samples.html
@@ -23,7 +23,12 @@
{{flash_all_messages()}}
<div class="row">
- <p>You can now upload a character-separated value (CSV) file that contains
+ <p>
+ You can now upload the samples for the "{{population.FullName}}" population
+ from the "{{species.FullName}}" species here.
+ </p>
+ <p>
+ Upload a <strong>character-separated value (CSV)</strong> file that contains
details about your samples. The CSV file should have the following fields:
<dl>
<dt>Name</dt>