From 105934ca5cf253c0f002a007ee57460a7632e2b8 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 22 Jan 2024 13:37:12 +0300
Subject: UI: Fix some UI bugs.

---
 qc_app/templates/index.html                        |  4 +--
 qc_app/templates/rqtl2/select-geno-dataset.html    | 28 +++++++++++++++--
 .../templates/rqtl2/select-probeset-dataset.html   | 35 ++++++++++++++++++++++
 .../templates/rqtl2/select-probeset-study-id.html  | 25 ++++++++++++++--
 4 files changed, 84 insertions(+), 8 deletions(-)

(limited to 'qc_app/templates')

diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html
index 358b521..00714f0 100644
--- a/qc_app/templates/index.html
+++ b/qc_app/templates/index.html
@@ -21,7 +21,7 @@
     <button class="btn btn-main">upload R/qtl2 bundle</button></a>
 </div>
 
-<h2>Expression Data</h2>
+<h2 class="heading">Expression Data</h2>
 
 <div class="explainer">
   <p>This application assumes that you are familiar with the basics of data
@@ -112,7 +112,7 @@
   </form>
 </div>
 
-<h2>samples/cases</h2>
+<h2 class="heading">samples/cases</h2>
 
 <div class="explainer">
   <p>For the expression data above, you need the samples/cases in your file to
diff --git a/qc_app/templates/rqtl2/select-geno-dataset.html b/qc_app/templates/rqtl2/select-geno-dataset.html
index 64f886e..1964a79 100644
--- a/qc_app/templates/rqtl2/select-geno-dataset.html
+++ b/qc_app/templates/rqtl2/select-geno-dataset.html
@@ -43,6 +43,10 @@
       <option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option>
       {%endfor%}
     </select>
+    <span class="form-col-2">
+      Select from the existing genotype datasets for species
+      {{species.SpeciesName}} ({{species.FullName}}).
+    </span>
   </fieldset>
 
   <fieldset>
@@ -76,6 +80,9 @@
 	   id="txt:dataset-name"
 	   name="dataset-name"
 	   required="required" />
+    <span class="form-col-2">
+      Provide the new name for the genotype dataset, e.g. "BXDGeno"
+    </span>
   </fieldset>
 
   <fieldset>
@@ -84,21 +91,36 @@
 	   id="txt:dataset-fullname"
 	   name="dataset-fullname"
 	   required="required" />
+
+    <span class="form-col-2">
+      Provide a longer name that better describes the genotype dataset, e.g.
+      "BXD Genotypes"
+    </span>
   </fieldset>
 
   <fieldset>
     <label for="txt:dataset-shortname">Short Name</label>
     <input type="text"
 	   id="txt:dataset-shortname"
-	   name="dataset-shortname"
-	   required="required" />
+	   name="dataset-shortname" />
+
+    <span class="form-col-2">
+      Provide a short name for the genotype dataset. This is optional. If not
+      provided, we'll default to the same value as the "Name" above.
+    </span>
   </fieldset>
 
   <fieldset>
     <input type="checkbox"
 	   id="chk:dataset-public"
-	   name="dataset-public" />
+	   name="dataset-public"
+	   checked="checked" />
     <label for="chk:dataset-public">Public?</label>
+
+    <span class="form-col-2">
+      Specify whether the dataset will be available publicly. Check to make the
+      dataset publicly available and uncheck to limit who can access the dataset.
+    </span>
   </fieldset>
 
   <fieldset>
diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html
index 3e160fd..ebd715e 100644
--- a/qc_app/templates/rqtl2/select-probeset-dataset.html
+++ b/qc_app/templates/rqtl2/select-probeset-dataset.html
@@ -45,6 +45,8 @@
       </option>
       {%endfor%}
     </select>
+
+    <span class="form-col-2">Select from existing ProbeSet datasets.</span>
   </fieldset>
 
   <fieldset>
@@ -57,6 +59,10 @@
 <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
 {%endif%}
 
+<div class="explainer">
+  <p>Create an entirely new ProbeSet dataset for your data.</p>
+</div>
+
 <form method="POST"
       action="{{url_for('upload.rqtl2.create_probeset_dataset',
 	      species_id=species.SpeciesId, population_id=population.Id)}}"
@@ -86,6 +92,10 @@
       </option>
       {%endfor%}
     </select>
+
+    <span class="form-col-2">
+      Select the averaging method used for your data.
+    </span>
   </fieldset>
 
   <fieldset>
@@ -93,6 +103,11 @@
     <input type="text" id="txt:datasetname" name="datasetname"
 	   required="required"
 	   title="Name of the dataset, e.g 'BXDMicroArray_ProbeSet_June03'. (Required)" />
+
+    <span class="form-col-2">
+      Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This
+      is mandatory <strong>MUST</strong> be provided.
+    </span>
   </fieldset>
 
   <fieldset>
@@ -100,12 +115,23 @@
     <input type="text" id="txt:datasetfullname" name="datasetfullname"
 	   required="required"
 	   title="A longer name for the dataset, e.g. 'UTHSC Brain mRNA U74Av2 (Jun03) MAS5'. (Required)" />
+
+    <span class="form-col-2">
+      Provide a longer, more descriptive name for the dataset e.g.
+      "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and
+      <strong>MUST</strong> be provided.
+    </span>
   </fieldset>
 
   <fieldset>
     <label for="txt:datasetshortname">Short Name</label>
     <input type="text" id="txt:datasetshortname" name="datasetshortname"
 	   title="An abbreviated name for the dataset, e.g 'Br_U_0603_M'. (Optional)" />
+
+    <span class="form-col-2">
+      Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M".
+      This is optional.
+    </span>
   </fieldset>
 
   <fieldset>
@@ -113,6 +139,11 @@
 	   checked="checked"
 	   title="Whether or not the dataset is accessible by the general public." />
     <label for="chk:datasetpublic">Public?</label>
+
+    <span class="form-col-2">
+      Check to specify that the dataset will be publicly available. Uncheck to
+      limit access to the dataset.
+    </span>
   </fieldset>
 
   <fieldset>
@@ -126,6 +157,10 @@
       <option value="linear">linear</option>
       <option value="linear_positive">linear_positive</option>
     </select>
+
+    <span class="form-col-2">
+      Select from a list of scaling methods.
+    </span>
   </fieldset>
 
   <fieldset>
diff --git a/qc_app/templates/rqtl2/select-probeset-study-id.html b/qc_app/templates/rqtl2/select-probeset-study-id.html
index 34aa54e..35fe655 100644
--- a/qc_app/templates/rqtl2/select-probeset-study-id.html
+++ b/qc_app/templates/rqtl2/select-probeset-study-id.html
@@ -9,7 +9,7 @@
 <div class="explainer">
   <p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
     file(s). This data needs to be organised under a study.</p>
-  <p>This page gives you the ability to do that.</p>
+  <p>In this page, you can either select from a existing dataset:</p>
 </div>
 
 {{flash_all_messages()}}
@@ -43,6 +43,7 @@
       </option>
       {%endfor%}
     </select>
+    <span class="form-col-2">Select from existing ProbeSet studies.</span>
   </fieldset>
 
   <fieldset>
@@ -54,6 +55,10 @@
 
 <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
 
+<div class="explainer">
+  <p>Create a new ProbeSet dataset below:</p>
+</div>
+
 <form method="POST"
       action="{{url_for('upload.rqtl2.create_probeset_study',
 	      species_id=species.SpeciesId, population_id=population.Id)}}"
@@ -80,6 +85,8 @@
       </option>
       {%endfor%}
     </select>
+    <span class="form-col-2">Select from a list of known genomics platforms.
+    </span>
   </fieldset>
 
   <fieldset>
@@ -95,6 +102,9 @@
       </option>
       {%endfor%}
     </select>
+    <span class="form-col-2">
+      Select the Tissue to which the data is concerned.
+    </span>
   </fieldset>
 
   <fieldset>
@@ -102,18 +112,27 @@
     <input type="text" id="txt:studyname" name="studyname"
 	   placeholder="Name of the study. (Required)"
 	   required="required" />
+    <span class="form-col-2">Provide a name for the study.</span>
   </fieldset>
 
   <fieldset>
-    <label for="txt:studyfullname">Study name</label>
+    <label for="txt:studyfullname">Full Study Name</label>
     <input type="text" id="txt:studyfullname" name="studyfullname"
 	   placeholder="Longer name of the study. (Optional)" />
+    <span class="form-col-2">
+      Provide a longer, more descriptive name for the study. This is optional
+      and you can leave it blank.
+    </span>
   </fieldset>
 
   <fieldset>
-    <label for="txt:studyshortname">Study name</label>
+    <label for="txt:studyshortname">Short Study Name</label>
     <input type="text" id="txt:studyshortname" name="studyshortname"
 	   placeholder="Shorter name of the study. (Optional)" />
+    <span class="form-col-2">
+      Provide a shorter name for the study. This is optional and you can leave
+      it blank.
+    </span>
   </fieldset>
 
     <fieldset>
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