From 800ef54d2b53d34f8120c8e7da29450d560cd391 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 10 Apr 2023 12:58:21 +0300
Subject: Add UI for searching and linking mRNA Assay datasets.

---
 wqflask/wqflask/oauth2/data.py                     |  46 +++++-
 .../templates/oauth2/data-list-genotype.html       |   2 +-
 .../wqflask/templates/oauth2/data-list-mrna.html   | 166 +++++++++++++++++++++
 3 files changed, 207 insertions(+), 7 deletions(-)
 create mode 100644 wqflask/wqflask/templates/oauth2/data-list-mrna.html

(limited to 'wqflask')

diff --git a/wqflask/wqflask/oauth2/data.py b/wqflask/wqflask/oauth2/data.py
index 03fde15f..6804dafa 100644
--- a/wqflask/wqflask/oauth2/data.py
+++ b/wqflask/wqflask/oauth2/data.py
@@ -20,7 +20,20 @@ def __render_template__(templatepath, **kwargs):
         templatepath, **kwargs, user_privileges=user_privileges)
 
 def __search_mrna__(query, template, **kwargs):
-    return __render_template__(template, **kwargs)
+    species_name = kwargs["species_name"]
+    search_uri = urljoin(app.config["GN_SERVER_URL"], "oauth2/data/search")
+    print(f"SEARCHING FOR mrna")
+    datasets = oauth2_get(
+        "oauth2/data/search",
+        json = {
+            "query": query,
+            "dataset_type": "mrna",
+            "species_name": species_name,
+            "selected": __selected_datasets__()
+        }).either(
+            lambda err: {"datasets_error": process_error(err)},
+            lambda datasets: {"datasets": datasets})
+    return __render_template__(template, search_uri=search_uri, **datasets, **kwargs)
 
 def __selected_datasets__():
     if bool(request.json):
@@ -70,12 +83,7 @@ def __search_phenotypes__(query, template, **kwargs):
 def json_search_genotypes() -> Response:
     def __handle_error__(err):
         error = process_error(err)
-        print(f"THE ERROR: {error}")
         return jsonify(error), error["status_code"]
-
-    print(f"===============================================")
-    print(request.json)
-    print(f"===============================================")
     
     return oauth2_get(
         "oauth2/data/search",
@@ -213,3 +221,29 @@ def link_genotype_data():
         "selected": tuple(json.loads(dataset) for dataset
                                    in form.getlist("selected"))
     }).either(lambda err: __link_error__(process_error(err)), __link_success__)
+
+
+@data.route("/link/mrna", methods=["POST"])
+def link_mrna_data():
+    """Link mrna data to a group."""
+    form = request.form
+    link_source_url = redirect(url_for("oauth2.data.list_data"))
+    if bool(form.get("species_name")):
+        link_source_url = redirect(url_for(
+            "oauth2.data.list_data_by_species_and_dataset",
+            species_name=form["species_name"], dataset_type="mrna"))
+
+    def __link_error__(err):
+        flash(f"{err['error']}: {err['error_description']}", "alert-danger")
+        return link_source_url
+
+    def __link_success__(success):
+        flash(success["description"], "alert-success")
+        return link_source_url
+
+    return oauth2_post("oauth2/data/link/mrna", json={
+        "species_name": form.get("species_name"),
+        "group_id": form.get("group_id"),
+        "selected": tuple(json.loads(dataset) for dataset
+                                   in form.getlist("selected"))
+    }).either(lambda err: __link_error__(process_error(err)), __link_success__)
diff --git a/wqflask/wqflask/templates/oauth2/data-list-genotype.html b/wqflask/wqflask/templates/oauth2/data-list-genotype.html
index 47c21079..30ee0d27 100644
--- a/wqflask/wqflask/templates/oauth2/data-list-genotype.html
+++ b/wqflask/wqflask/templates/oauth2/data-list-genotype.html
@@ -25,7 +25,7 @@
   <div class="row">
     <form id="frm-link-genotypes" method="POST"
 	  action="{{url_for('oauth2.data.link_genotype_data')}}">
-      <legend>Link Genotype Traits to Group</legend>
+      <legend>Link Genotype Datasets to Group</legend>
 
       <input type="hidden" name="species_name" value="{{species_name}}" />
 
diff --git a/wqflask/wqflask/templates/oauth2/data-list-mrna.html b/wqflask/wqflask/templates/oauth2/data-list-mrna.html
new file mode 100644
index 00000000..1c22f65c
--- /dev/null
+++ b/wqflask/wqflask/templates/oauth2/data-list-mrna.html
@@ -0,0 +1,166 @@
+{%extends "base.html"%}
+{%from "oauth2/profile_nav.html" import profile_nav%}
+{%from "oauth2/display_error.html" import display_error%}
+
+{%block title%}Link Data: Genotype{%endblock%}
+
+{%block css%}
+<link rel="stylesheet" type="text/css"
+      href="/css/DataTables/css/jquery.dataTables.css" />
+<link rel="stylesheet" type="text/css"
+      href="https://code.jquery.com/ui/1.12.1/themes/base/jquery-ui.css" />
+<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{%endblock%}
+
+{%block content%}
+<div class="container" style="width: 98%;">
+  {{profile_nav("data", user_privileges)}}
+
+  {{flash_me()}}
+
+  <div class="row">
+    <noscript>This page needs javascript to work correctly</noscript>
+  </div>
+
+  <div class="row">
+    <form id="frm-link-mrna" method="POST"
+	  action="{{url_for('oauth2.data.link_mrna_data')}}">
+      <legend>Link mRNA Assay Datasets to Group</legend>
+
+      <input type="hidden" name="species_name" value="{{species_name}}" />
+
+      <div class="form-group">
+	<label for="select-group">Group</label>
+	<select id="select-group" name="group_id" required="required"
+		class="form-control">
+	  <option value="">Select group</option>
+	  {%for group in groups%}
+	  <option value="{{group.group_id}}">{{group.group_name}}</option>
+	  {%endfor%}
+	</select>
+      </div>
+
+      <div class="form-group">
+      <table id="tbl-link-mrna"
+	     class="table-hover table-striped cell-border dataTable no-footer"
+	     data-selected-datasets='{{selected_datasets | list | tojson}}'>
+	<thead>
+	  <tr>
+	    <th>Deselect</th>
+	    <th>Group</th>
+	    <th>Dataset Name</th>
+	    <th>Dataset FullName</th>
+	    <th>Dataset ShortName</th>
+	  </tr>
+	</thead>
+	<tbody>
+	  {%for dataset in selected_datasets%}
+	  <tr>
+	    <td>
+	      <input type="checkbox" class="checkbox checkbox-selected"
+		     name="selected"
+		     value='{{dataset | tojson}}' />
+	    </td>
+	    <td>{{dataset.dataset_name}}</td>
+	    <td>{{dataset.dataset_fullname}}</td>
+	    <td>{{dataset.dataset_shortname}}</td>
+	  </tr>
+	  {%else%}
+	  <tr>
+	    <td colspan="100%" align="center">
+	      <span class="glyphicon glyphicon-info-sign text-info"></span>
+	      &nbsp
+	      No datasets selected for linking.
+	    </td>
+	  </tr>
+	  {%endfor%}
+	</tbody>
+      </table>
+      </div>
+
+      <div class="form-group text-center">
+	<input type="submit" value="Link Selected"
+	       class="btn btn-primary"
+	       style="border-top: 0.3em;"
+	       {%if groups | length <= 0 or selected_datasets | length <= 0%}
+	       disabled="disabled"
+	       {%endif%} />
+      </div>
+    </form>
+  </div>
+
+  <div class="row">
+    <span id="search-messages" class="alert-danger" style="display:none"></span>
+    <form id="frm-search"
+	  action="{{search_uri}}"
+	  method="POST">
+      <legend>Search: mRNA Assay</legend>
+      <input type="hidden" value="{{species_name}}" name="species"
+	     id="txt-species-name" />
+      <input type="hidden" value="{{dataset_type}}" name="dataset_type"
+	     id="txt-dataset-type"  />
+      <input type="hidden" value="{{per_page}}" name="per_page"
+	     id="txt-per-page"  />
+
+      <div class="form-group">
+	<label for="txt-query">Dataset Search String</label>
+	<input type="text" id="txt-query" name="query" class="form-control"
+	       value="{{query}}"/>
+      </div>
+    </form>
+  </div>
+
+  <div class="row">
+    <div id="search-error" class="text-danger" style="display: none;">
+      <span class="glyphicon glyphicon-exclamation-sign"></span>
+      &nbsp
+      <span id="search-error-text"></span>
+    </div>
+    <table id="tbl-search"
+	   class="table-hover table-striped cell-border dataTable no-footer"
+	   data-datasets='{{datasets | list | tojson}}'>
+      <thead>
+	<tr>
+	  <th>Select</th>
+	  <th>Group</th>
+	  <th>Study Name</th>
+	  <th>Dataset Name</th>
+	  <th>Dataset FullName</th>
+	  <th>Dataset ShortName</th>
+	</tr>
+      </thead>
+      <tbody>
+	{%for dataset in datasets:%}
+	<tr>
+	  <td>
+	    <input type="checkbox" class="checkbox checkbox-search"
+		   name="search_datasets"
+		   value='{{dataset | tojson}}' />
+	  </td>
+	  <td>{{dataset.InbredSetName}}</td>
+	  <td>{{dataset.StudyName}}</td>
+	  <td>{{dataset.dataset_name}}</td>
+	  <td>{{dataset.dataset_fullname}}</td>
+	  <td>{{dataset.dataset_shortname}}</td>
+	</tr>
+        {%else%}
+	<tr>
+	  <td colspan="100%" align="center">
+	      <span class="glyphicon glyphicon-info-sign text-info"></span>
+	      &nbsp
+	      No datasets available for selection.
+	  </td>
+	</tr>
+	{%endfor%}
+      </tbody>
+    </table>
+  </div>
+
+
+</div>
+{%endblock%}
+
+{%block js%}
+<script src="/static/new/javascript/auth/search_mrna.js"
+	language="javascript" type="text/javascript"></script>
+{%endblock%}
-- 
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