From 6e45510c3ee685a960db594aef70661220bebe60 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 20 Mar 2023 16:01:45 +0300
Subject: oauth2: Load menu and populate dropdown

In order to enable searching through the existing datasets for linking
with the auth system, we need a way to filter the data.

In this commit, I load the menu and load it onto a dropdown box as a
proof of concept to give an idea of some of the filters I can use down
the road to fetch the data.

This commit breaks the data-linking code. I will need to rework the
data-linking code entirely to get it working again.
---
 wqflask/wqflask/oauth2/data.py                  |  36 ++++-
 wqflask/wqflask/templates/oauth2/data-list.html | 200 ++++++++++++++----------
 2 files changed, 149 insertions(+), 87 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/oauth2/data.py b/wqflask/wqflask/oauth2/data.py
index 8005a2a0..0cd110f6 100644
--- a/wqflask/wqflask/oauth2/data.py
+++ b/wqflask/wqflask/oauth2/data.py
@@ -23,15 +23,47 @@ def list_data():
             **{key:val for key,val in kwargs.items()
                if key not in ("groups", "data_items", "user_privileges")})
 
+    def __process_menus__(mns):
+        return {
+            species_id: {
+                "display_name": display_name,
+                "family": family,
+                "groups": {
+                    group_id: {
+                        "group_name": group_name,
+                        "family": family,
+                        "types": {
+                            type_id: {
+                                "menu_value": type_menu_value,
+                                "menu_heading": type_menu_heading,
+                                "datasets": tuple(
+                                    dict(zip(("accession_id", "dataset_id",
+                                              "dataset_fullname"),
+                                             dataset_row))
+                                    for dataset_row in mns["datasets"][
+                                            species_id][group_id][type_id])
+                            }
+                            for type_id, type_menu_value, type_menu_heading
+                            in mns["types"][species_id][group_id]
+                        }
+                    }
+                    for group_id, group_name, family in mns["groups"][species_id]
+                }
+            }
+            for species_id, display_name, family in mns["species"]}
+
     groups = oauth2_get("oauth2/group/list").either(
         lambda err: {"groups_error": process_error(err)},
         lambda grp: {"groups": grp})
     roles = oauth2_get("oauth2/user/roles").either(
         lambda err: {"roles_error": process_error(err)},
         lambda roles: {"roles": roles})
+    menus = oauth2_get("menu/generate/json").either(
+        lambda err: {"menus_error": process_error(err)},
+        lambda mns: {"menus": __process_menus__(mns)})
 
     if request.method == "GET":
-        return __render__(**{**groups, **roles})
+        return __render__(**{**groups, **roles, **menus})
 
     dataset_type = request.form["dataset_type"]
     offset = int(request.form.get("offset", 0)) + (
@@ -47,7 +79,7 @@ def list_data():
             lambda err: {"data_items_error": process_error(err)},
             lambda data: {"data_items": data})
     return __render__(**{
-        **groups, **roles, **data_items, "dataset_type": dataset_type,
+        **groups, **roles, **menus, **data_items, "dataset_type": dataset_type,
             "offset": offset
     })
 
diff --git a/wqflask/wqflask/templates/oauth2/data-list.html b/wqflask/wqflask/templates/oauth2/data-list.html
index 6d0ae427..019e2346 100644
--- a/wqflask/wqflask/templates/oauth2/data-list.html
+++ b/wqflask/wqflask/templates/oauth2/data-list.html
@@ -12,23 +12,46 @@
       <div class="row">
 	<form method="POST" action="{{url_for('oauth2.data.list_data')}}">
 	  <legend>Dataset Type</legend>
+	  <input type="hidden" name="offset" value="0" />
+	  <input type="hidden" name="menus" value="{{menus | tojson}}" />
+	  <div class="form-group">
+	    <label for="select-menu">Dataset</label>
+	    <select id="select-menu" name="dataset">
+	      {%for species_id, species_data in menus.items()%}
+	      <optgroup label="{{species_data.display_name}}">
+		{%for group_id, group_data in species_data["groups"].items()%}
+		<optgroup label=" {{group_data.group_name}}">
+		  {%for type_id, type_data in group_data["types"].items()%}
+		  <optgroup label="{{type_data.menu_heading}}">
+		    {%for dataset in type_data["datasets"]%}
+		    <option value="{{dataset.dataset_id}}">
+		      {{dataset.dataset_fullname}}
+		    </option>
+		    {%endfor%}
+		  </optgroup>
+		  {%endfor%}
+		</optgroup>
+		{%endfor%}
+	      </optgroup>
+	      {%endfor%}
+	    </select>
+	  </div>
 	  <div class="form-group">
-	    <input type="hidden" name="offset" value="0" />
 	    <label for="dataset_type" class="form-label">Dataset Type</label>
 	    <select name="dataset_type" required="required">
 	      <option value="">Select dataset type</option>
 	      <option value="mrna"
 		      {%if dataset_type=="mrna"%}
-			selected="selected"
+		      selected="selected"
 		      {%endif%}>mRNA Assay Datasets</option>
-		      <option value="genotype"
-			      {%if dataset_type=="genotype"%}
-				selected="selected"
-			      {%endif%}>Genotype Datasets</option>
-			      <option value="phenotype"
-				      {%if dataset_type=="phenotype"%}
-					selected="selected"
-				      {%endif%}>Phenotype/Publish Datasets</option>
+	      <option value="genotype"
+		      {%if dataset_type=="genotype"%}
+		      selected="selected"
+		      {%endif%}>Genotype Datasets</option>
+	      <option value="phenotype"
+		      {%if dataset_type=="phenotype"%}
+		      selected="selected"
+		      {%endif%}>Phenotype/Publish Datasets</option>
 	    </select>
 	  </div>
 	  <input type="submit" value="Fetch Unlinked Data" class="btn btn-primary" />
@@ -39,87 +62,94 @@
 	{%if data_items_error is defined%}
 	  {{display_error("Data Error", data_items_error)}}
 	{%else%}
-	  <div class="row">
-	    <table class="table">
-	      <caption>Link Data to Group</caption>
+      <div class="row">
+	<form method="POST" action="{{url_for('oauth2.data.link_data')}}">
+	  <legend>Link Data to Group</legend>
+	  <input type="hidden" name="offset" value="{{offset or 0}}" />
+	  <input type="hidden" name="dataset_type" value="{{dataset_type}}" />
 
-	      <thead>
-		<tr>
-		  {%if dataset_type == "phenotype"%}
-		  <th>Trait ID</th>
-		  <th>Data Group</th>
-		  {%endif%}
-		  <th>Dataset Name</th>
-		  <th>Dataset Full Name</th>
-		  <th>Group</th>
-		  <th>Link</th>
-		</tr>
-	      </thead>
+	  <div class="form-group">
+	    <label for="select-group-id">Group</label>
+	    <select name="group_id" required="required">
+	      <option value="">Select group</option>
+	      {%for group in groups%}
+	      <option value="{{group.group_id}}">{{group.group_name}}</option>
+	      {%endfor%}
+	    </select>
+	  </div>
 
-	      <tbody>
-		{%for data_item in data_items%}
-		  <tr>
-		    <form method="POST" action="{{url_for('oauth2.data.link_data')}}">
-		      <input type="hidden" name="offset" value="{{offset or 0}}" />
-		      <input type="hidden" name="dataset_id" value="{{data_item.Id}}" />
-		      <input type="hidden" name="dataset_type" value="{{dataset_type}}" />
-		      {%if dataset_type == "phenotype"%}
-		      <td>
-			<a href="/show_trait?trait_id={{data_item.Id}}&dataset={{data_item.dataset_name}}"
-			   title="Trait Page">
-			  {{data_item.Id}}
-			</a>
-		      </td>
-		      <td>{{data_item.InbredSetName}}</td>
-		      {%endif%}
-		      <td>
-			<a href="https://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId={{data_item.accession_id}}&InfoPageName={{data_item.dataset_name}}"
-			   title="Link to information on dataset '{{data_item.dataset_fullname}}'"
-			   target="_blank">
-			   {{data_item.dataset_name}}
-			</a>
-		      </td>
-		      <td>{{data_item.dataset_fullname}}</td>
-		      <td>
-			<select name="group_id" required="required">
-			  <option value="">Select group</option>
-			  {%for group in groups%}
-			    <option value="{{group.group_id}}">{{group.group_name}}</option>
-			  {%endfor%}
-			</select>
-		      </td>
-		      <td>
-			<input type="submit" value="Link" class="btn btn-info" />
-		      </td>
-		    </form>
-		  </tr>
-		{%else%}
-		  <tr>
-		    <td colspan="4">
-		      <span class="glyphicon glyphicon-info-sign text-danger">
-		      </span>
-		      &nbsp;
-		      <strong class="text-info">No available data to link</strong>
-		    </td>
-		  </tr>
-		{%endfor%}
-	      </tbody>
-	    </table>
+	  <table class="table">
+	    <caption>Link Data to Group</caption>
 
-	    <form method="POST" action="{{url_for('oauth2.data.list_data')}}">
-	      <input type="hidden" name="dataset_type" value="{{dataset_type}}" />
-	      <input type="hidden" name="offset" value="{{offset or 0}}" />
-	      <div class="form-group" style="margin: auto;width: 50%;">
-		{%if offset != 0%}
-		  <input type="submit" name="offset_submit" value="Previous" class="btn btn-warning" />
+	    <thead>
+	      <tr>
+		<th>Select</th>
+		{%if dataset_type == "phenotype"%}
+		<th>Trait ID</th>
+		<th>Data Group</th>
 		{%endif%}
-		{%if data_items | length == 100:%}
-		  <input type="submit" name="offset_submit" value="Next" class="btn btn-warning" />
+		<th>Dataset Name</th>
+		<th>Dataset Full Name</th>
+		<th>Link</th>
+	      </tr>
+	    </thead>
+
+	    <tbody>
+	      {%for data_item in data_items%}
+	      <tr>
+		<td>
+		  <input type="checkbox" value="{{data_item.Id}}"
+			 name="dataset_ids" />
+		</td>
+		{%if dataset_type == "phenotype"%}
+		<td>
+		  <a href="/show_trait?trait_id={{data_item.Id}}&dataset={{data_item.dataset_name}}"
+		     title="Trait Page">
+		    {{data_item.Id}}
+		  </a>
+		</td>
+		<td>{{data_item.InbredSetName}}</td>
 		{%endif%}
-	      </div>
-	    </form>
+		<td>
+		  <a href="https://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId={{data_item.accession_id}}&InfoPageName={{data_item.dataset_name}}"
+		     title="Link to information on dataset '{{data_item.dataset_fullname}}'"
+		     target="_blank">
+		    {{data_item.dataset_name}}
+		  </a>
+		</td>
+		<td>{{data_item.dataset_fullname}}</td>
+		<td>
+		  <input type="submit" value="Link" class="btn btn-info" />
+		</td>
+	      </tr>
+	      {%else%}
+	      <tr>
+		<td colspan="4">
+		  <span class="glyphicon glyphicon-info-sign text-danger">
+		  </span>
+		  &nbsp;
+		  <strong class="text-info">No available data to link</strong>
+		</td>
+	      </tr>
+	      {%endfor%}
+	    </tbody>
+	  </table>
+	</form>
+
+	<form method="POST" action="{{url_for('oauth2.data.list_data')}}">
+	  <input type="hidden" name="dataset_type" value="{{dataset_type}}" />
+	  <input type="hidden" name="offset" value="{{offset or 0}}" />
+	  <div class="form-group" style="margin: auto;width: 50%;">
+	    {%if offset != 0%}
+	    <input type="submit" name="offset_submit" value="Previous" class="btn btn-warning" />
+	    {%endif%}
+	    {%if data_items | length == 100:%}
+	    <input type="submit" name="offset_submit" value="Next" class="btn btn-warning" />
+	    {%endif%}
 	  </div>
-	{%endif%}
+	</form>
+      </div>
+      {%endif%}
       {%endif%}
 
     </div>
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