From 6326357250711650bc8b4c0b90f8c0b94d72c39e Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 29 Mar 2024 13:14:14 +0300
Subject: Add UI to select/create tissue.

---
 qc_app/templates/rqtl2/create-tissue-success.html  | 104 +++++++++++++++++++
 .../templates/rqtl2/select-probeset-study-id.html  |  20 +---
 qc_app/templates/rqtl2/select-tissue.html          | 112 +++++++++++++++++++++
 3 files changed, 218 insertions(+), 18 deletions(-)
 create mode 100644 qc_app/templates/rqtl2/create-tissue-success.html
 create mode 100644 qc_app/templates/rqtl2/select-tissue.html

(limited to 'qc_app/templates')

diff --git a/qc_app/templates/rqtl2/create-tissue-success.html b/qc_app/templates/rqtl2/create-tissue-success.html
new file mode 100644
index 0000000..ea05624
--- /dev/null
+++ b/qc_app/templates/rqtl2/create-tissue-success.html
@@ -0,0 +1,104 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_all_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Select Tissue</h2>
+
+<div class="explainer">
+  <p>You have successfully added a new tissue, organ or biological material with
+    the following details:</p>
+</div>
+
+{{flash_all_messages()}}
+
+<form id="frm-create-tissue-display"
+      method="POST"
+      action="#">
+  <legend class="heading">Create Tissue</legend>
+
+  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+  <input type="hidden" name="population_id"
+	 value="{{population.InbredSetId}}" />
+  <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
+  <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+  <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
+
+  <fieldset>
+    <label>Name</label>
+    <label>{{tissue.TissueName}}</label>
+  </fieldset>
+
+  <fieldset>
+    <label>Short Name</label>
+    <label>{{tissue.Short_Name}}</label>
+  </fieldset>
+
+  {%if tissue.BIRN_lex_ID%}
+  <fieldset>
+    <label>BIRN Lex ID</label>
+    <label>{{tissue.BIRN_lex_ID}}</label>
+  </fieldset>
+  {%endif%}
+
+  {%if tissue.BIRN_lex_Name%}
+  <fieldset>
+    <label>BIRN Lex Name</label>
+    <label>{{tissue.BIRN_lex_Name}}</label>
+  </fieldset>
+  {%endif%}
+</form>
+
+<div id="action-buttons"
+     style="width:65ch;display:inline-grid;column-gap:5px;">
+
+  <form id="frm-create-tissue-success-continue"
+        method="POST"
+        action="{{url_for('upload.rqtl2.select_dataset_info',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        style="display: inline; width: 100%; grid-column: 1 / 2;
+               padding-top: 0.5em; text-align: center; border: none;
+               background-color: inherit;">
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+    <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
+
+    <input type="submit"
+	   value="continue"
+	   class="btn btn-main form-col-2" />
+  </form>
+
+  <p style="display:inline;width:100%;grid-column:2/3;text-align:center;
+            color:#336699;font-weight:bold;">
+    OR
+  </p>
+
+  <form id="frm-create-tissue-success-select-existing"
+        method="POST"
+        action="{{url_for('upload.rqtl2.select_tissue',
+	        species_id=species.SpeciesId,
+	        population_id=population.InbredSetId)}}"
+        style="display: inline; width: 100%; grid-column: 3 / 4;
+               padding-top: 0.5em; text-align: center; border: none;
+               background-color: inherit;">
+
+    <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+    <input type="hidden" name="population_id"
+	   value="{{population.InbredSetId}}" />
+    <input type="hidden" name="rqtl2_bundle_file" value="{{rqtl2_bundle_file}}" />
+    <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+
+    <input type="submit"
+	   value="select from existing tissues"
+	   class="btn btn-main form-col-2" />
+  </form>
+
+</div>
+
+{%endblock%}
diff --git a/qc_app/templates/rqtl2/select-probeset-study-id.html b/qc_app/templates/rqtl2/select-probeset-study-id.html
index 3bbb94a..23bbbf0 100644
--- a/qc_app/templates/rqtl2/select-probeset-study-id.html
+++ b/qc_app/templates/rqtl2/select-probeset-study-id.html
@@ -26,6 +26,7 @@
   <input type="hidden" name="rqtl2_bundle_file"
 	 value="{{rqtl2_bundle_file}}" />
   <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+  <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
 
   <fieldset>
     <label for="select:probe-study">Study</label>
@@ -71,6 +72,7 @@
   <input type="hidden" name="rqtl2_bundle_file"
 	 value="{{rqtl2_bundle_file}}" />
   <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+  <input type="hidden" name="tissueid" value="{{tissue.Id}}" />
 
   <fieldset>
     <label for="select:platform">Platform</label>
@@ -89,24 +91,6 @@
     </span>
   </fieldset>
 
-  <fieldset>
-    <label for="select:tissue">Tissue</label>
-    <select id="select:tissue"
-	    name="tissueid"
-	    required="required"
-	    {%if tissues | length == 0%}disabled="disabled"{%endif%}>
-      <option value="">Select tissue</option>
-      {%for tissue in tissues%}
-      <option value="{{tissue.Id}}">
-	{{tissue.TissueName}} ({{tissue.Short_Name}})
-      </option>
-      {%endfor%}
-    </select>
-    <span class="form-col-2">
-      Select the Tissue to which the data is concerned.
-    </span>
-  </fieldset>
-
   <fieldset>
     <label for="txt:studyname">Study name</label>
     <input type="text" id="txt:studyname" name="studyname"
diff --git a/qc_app/templates/rqtl2/select-tissue.html b/qc_app/templates/rqtl2/select-tissue.html
new file mode 100644
index 0000000..6f7d134
--- /dev/null
+++ b/qc_app/templates/rqtl2/select-tissue.html
@@ -0,0 +1,112 @@
+{%extends "base.html"%}
+{%from "flash_messages.html" import flash_messages%}
+
+{%block title%}Upload R/qtl2 Bundle{%endblock%}
+
+{%block contents%}
+<h2 class="heading">Tissue</h2>
+
+<div class="explainer">
+  <p>The data you are uploading concerns a tissue, cell, organ, or other
+    biological material used in an experiment.</p>
+  <p>Select the appropriate biological material below</p>
+</div>
+
+{%if tissues | length > 0%}
+<form method="POST"
+      action="{{url_for('upload.rqtl2.select_tissue',
+	      species_id=species.SpeciesId, population_id=population.Id)}}"
+      id="frm:select-probeset-dataset">
+  <legend class="heading">Select from existing ProbeSet datasets</legend>
+  {{flash_messages("error-select-tissue")}}
+
+  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+  <input type="hidden" name="population_id"
+	 value="{{population.InbredSetId}}" />
+  <input type="hidden" name="rqtl2_bundle_file"
+	 value="{{rqtl2_bundle_file}}" />
+  <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+
+  <fieldset>
+    <label for="select-tissue">Tissue</label>
+    <select id="select-tissue"
+	    name="tissueid"
+	    required="required"
+	    {%if tissues | length == 0%}disabled="disabled"{%endif%}>
+      <option value="">Select a tissue</option>
+      {%for tissue in tissues%}
+      <option value={{tissue.Id}}>
+	{{tissue.Name}}
+	{%if tissue.Short_Name%}
+	 -- ({{tissue.Short_Name}})
+	{%endif%}
+      </option>
+      {%endfor%}
+    </select>
+
+    <span class="form-col-2">Select from existing biological material.</span>
+  </fieldset>
+
+  <fieldset>
+    <input type="submit"
+	   value="use selected"
+	   class="btn btn-main form-col-2" />
+  </fieldset>
+</form>
+
+<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+{%endif%}
+
+<div class="explainer">
+  <p>If you cannot find the biological material in the drop-down above, add it
+    to the system below.</p>
+</div>
+
+<form method="POST"
+      action="{{url_for('upload.rqtl2.create_tissue',
+	      species_id=species.SpeciesId, population_id=population.Id)}}"
+      id="frm:create-probeset-dataset">
+  <legend class="heading">Add new tissue, organ or biological material</legend>
+  {{flash_messages("error-create-tissue")}}
+
+  <input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
+  <input type="hidden" name="population_id"
+	 value="{{population.InbredSetId}}" />
+  <input type="hidden" name="rqtl2_bundle_file"
+	 value="{{rqtl2_bundle_file}}" />
+  <input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
+
+  <fieldset>
+    <label for="tissue-name">name</label>
+    <input type="text"
+           id="txt-tissuename"
+           name="tissuename"
+           required="required"
+           title = "A name to identify the tissue, organ or biological material." />
+
+    <span class="form-col-2">
+      A name to identify the tissue, organ or biological material.
+    </span>
+  </fieldset>
+
+  <fieldset>
+    <label for="txt-shortname">short name</label>
+    <input type="text" id="txt-tissueshortname" name="tissueshortname"
+	   required="required"
+	   maxlength="7"
+	   title="A short name (e.g. 'Mam') for the biological material." />
+
+    <span class="form-col-2">
+      Provide a short name for the tissue, organ or biological material used in
+      the experiment.
+    </span>
+  </fieldset>
+
+  <fieldset>
+    <input type="submit"
+	   value="add new material"
+	   class="btn btn-main form-col-2" />
+  </fieldset>
+</form>
+
+{%endblock%}
-- 
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