Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

1 files changed, 352 insertions, 0 deletions

diff --git a/gn2/wqflask/templates/oauth2/view-resource.html b/gn2/wqflask/templates/oauth2/view-resource.html
new file mode 100644
index 00000000..275fcb24
--- /dev/null
+++ b/gn2/wqflask/templates/oauth2/view-resource.html
@@ -0,0 +1,352 @@
+{%extends "base.html"%}
+{%from "oauth2/profile_nav.html" import profile_nav%}
+{%from "oauth2/display_error.html" import display_error%}
+{%block title%}View User{%endblock%}
+{%block content%}
+<div class="container" style="min-width: 1250px;">
+  {{profile_nav("resources", user_privileges)}}
+  <h3>Resources</h3>
+
+  {{flash_me()}}
+
+  <div class="container-fluid">
+
+    {%if resource_error is defined %}
+    {{display_error("Resource", resource_error)}}
+    {%else%}
+    <div class="row">
+      <h3>Resource Details</h3>
+      <table class="table">
+	<caption>Resource: {{resource.resource_name}}</caption>
+	<thead>
+	  <tr>
+	    <th>Name</th>
+	    <th>Category</th>
+	    <th colspan="3" style="text-align: center;">Actions</th>
+	  </tr>
+	</thead>
+
+	<tbody>
+	  <tr>
+	    <td>{{resource.resource_name}}</td>
+	    <td>{{resource.resource_category.resource_category_description}}</td>
+	    <td>
+	      <form method="POST"
+		    action="{{url_for(
+			    'oauth2.resource.toggle_public',
+			    resource_id=resource.resource_id)}}">
+
+		<div class="input-group">
+		  {%if resource.public%}
+		  <input type="submit" value="Make Private"
+			 class="btn btn-success" />
+		  {%else%}
+		  <input type="submit" value="Make Public"
+			 class="btn btn-danger" />
+		  {%endif%}
+		</div>
+	      </form>
+	    </td>
+	    <td>
+	      <a href="{{url_for(
+		       'oauth2.resource.edit_resource',
+		       resource_id=resource.resource_id)}}"
+		 title="Edit resource"
+		 class="btn btn-warning">Edit</a>
+	    </td>
+	    <td>
+	      <a href="{{url_for(
+		       'oauth2.resource.delete_resource',
+		       resource_id=resource.resource_id)}}"
+		 title="Edit resource"
+		 class="btn btn-danger">Delete</a>
+	    </td>
+	  </tr>
+	</tbody>
+      </table>
+    </div>
+
+    <div class="row">
+      <h3>Resource Data</h3>
+      <table class="table">
+	<caption>Resource Data</caption>
+	<thead>
+	  <tr>
+	    {%if resource.resource_category.resource_category_key == "phenotype"%}
+	    <th>Trait</th>
+	    <th>Description</th>
+	    <th>Year</th>
+	    {%endif%}
+	    <th>Dataset Name</th>
+	    <th>Full Name</th>
+	    <th>Actions</th>
+	  </tr>
+	</thead>
+
+	<tbody>
+	  {%for data_item in resource.resource_data:%}
+	  <tr>
+	    {%if resource.resource_category.resource_category_key == "phenotype"%}
+	    <td>
+	      <a href="/show_trait?trait_id={{data_item.PublishXRefId}}&dataset={{data_item.dataset_name}}"
+		 title="Trait Data and Analysis for {{data_item.PublishXRefId}}"
+		 target="_blank">
+		{{data_item.PublishXRefId}}
+	      </a>
+	    </td>
+	    <td>{{data_item.description}}</td>
+	    <td>
+	      {%if data_item.PubMed_ID%}
+	      <a href="https://pubmed.ncbi.nlm.nih.gov/{{data_item.PubMed_ID}}/"
+		 title="{{data_item.Title}}" target="_blank">
+		{{data_item.Year}}
+	      </a>
+	      {%else%}
+	      {{data_item.Year}}
+	      {%endif%}
+	    </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>
+	      <form action="{{url_for('oauth2.resource.unlink_data_from_resource')}}"
+		    method="POST">
+		<input type="hidden" name="resource_id"
+		       value="{{resource.resource_id}}" />
+		<input type="hidden" name="data_link_id"
+		       value="{{data_item.data_link_id}}" />
+		<input type="submit" value="Unlink" class="btn btn-danger" />
+	      </form>
+	    </td>
+	  </tr>
+	  {%else%}
+	  <tr>
+	    <td colspan="2">
+	      <span class="glyphicon glyphicon-info-sign text-danger">
+	      </span>
+	      &nbsp;
+	      <strong class="text-info">No linked data.</strong>
+	    </td>
+	  </tr>
+	  {%endfor%}
+	</tbody>
+      </table>
+      <form action="{{url_for('oauth2.resource.view_resource', resource_id=resource.resource_id)}}"
+	    method="GET"
+	    style="width:100%;text-align:center;">
+	<input type="hidden" name="page" value="{{page}}" />
+	<input type="hidden" name="count_per_page" value="{{count_per_page}}" />
+
+	<input type="submit" name="submit" value="prev" class="btn btn-info"
+	       {%if page == 1 %}disabled="disabled"{%endif%} />
+	<input type="submit" name="submit" value="next" class="btn btn-info"
+	       {%if resource.resource_data | length < count_per_page %}
+	       disabled="disabled"
+	       {%endif%} />
+      </form>
+    </div>
+
+    <div class="row">
+      <h3>Unlinked Data</h3>
+      <table class="table">
+	<caption>Link Data</caption>
+	<thead>
+	  <tr>
+	    {%if resource.resource_category.resource_category_key == "phenotype"%}
+	    <th>Trait</th>
+	    <th>Description</th>
+	    <th>Year</th>
+	    {%endif%}
+	    <th>Dataset Name</th>
+	    <th>Dataset FullName</th>
+	    <th>Actions</th>
+	  </tr>
+	</thead>
+	<tbody>
+	  {%if unlinked_error is defined%}
+	  {{display_error("Unlinked Data Error", unlinked_error)}}
+	  {%else%}
+	  {%for data_item in unlinked_data:%}
+	  <tr>
+	    {%if resource.resource_category.resource_category_key == "phenotype"%}
+	    <td>
+	      <a href="/show_trait?trait_id={{data_item.PublishXRefId}}&dataset={{data_item.dataset_name}}"
+		 title="Trait Data and Analysis for {{data_item.PublishXRefId}}"
+		 target="_blank">
+		{{data_item.PublishXRefId}}
+	      </a>
+	    </td>
+	    <td>{{data_item.description}}</td>
+	    <td>
+	      {%if data_item.PubMed_ID%}
+	      <a href="https://pubmed.ncbi.nlm.nih.gov/{{data_item.PubMed_ID}}/"
+		 title="{{data_item.Title}}" target="_blank">
+		{{data_item.Year}}
+	      </a>
+	      {%else%}
+	      {{data_item.Year}}
+	      {%endif%}
+	    </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="Dataset Group: {{data_item.dataset_name}}"
+		 target="_blank">
+		{{data_item.dataset_name}}
+	      </a>
+	    </td>
+	    <td>{{data_item.dataset_fullname}}</td>
+	    <td>
+	      <form method="POST"
+		    action="{{url_for('oauth2.resource.link_data_to_resource')}}">
+		<input type="hidden" name="resource_id"
+		       value="{{resource.resource_id}}" />
+		<input type="hidden" name="data_link_id"
+		       value="{{data_item.data_link_id}}" />
+		<input type="hidden" name="dataset_type"
+		       value="{{resource.resource_category.resource_category_key | lower}}" />
+		<input type="submit" value="Link" class="btn btn-info"
+		       {%if resource.resource_category.resource_category_description == "mRNA Dataset" and resource.resource_data | count != 0%}
+		       disabled="disabled"
+		       {%endif%} />
+	      </form>
+	    </td>
+	  </tr>
+	  {%else%}
+	  <span class="glyphicon glyphicon-info-sign text-info">
+	  </span>
+	  &nbsp;
+	  <strong class="text-info">No data to link.</strong>
+	  {%endfor%}
+	  {%endif%}
+	</tbody>
+      </table>
+    </div>
+
+    <div class="row">
+      <h3>User Roles</h3>
+      {%if users_n_roles_error is defined%}
+      {{display_error("Users and Roles", users_n_roles_error)}}
+      {%else%}
+      <table class="table">
+	<caption>User Roles</caption>
+	<thead>
+	  <tr>
+	    <th>User Email</th>
+	    <th>User Name</th>
+	    <th>User Group</th>
+	    <th colspan="2">Assigned Roles</th>
+	  </tr>
+	</thead>
+	<tbody>
+	  {%for user_row in users_n_roles%}
+	  <tr>
+	    <td rowspan="{{user_row.roles | length + 1}}">{{user_row.user.email}}</td>
+	    <td rowspan="{{user_row.roles | length + 1}}">{{user_row.user.name}}</td>
+	    <td rowspan="{{user_row.roles | length + 1}}">
+	      {{user_row.user_group.group_name}}</td>
+	    <th>Role</th>
+	    <th>Action</th>
+	  </tr>
+	  {%for grole in user_row.roles%}
+	  <tr>
+	    <td>
+	      <a href="{{url_for(
+		       'oauth2.role.role',
+		       role_id=grole.role_id)}}"
+		 title="Details for '{{grole.role_name}}' role">
+		{{grole.role_name}}
+	      </a>
+	    </td>
+	    <td>
+	      <form action="{{url_for('oauth2.resource.unassign_role',
+			    resource_id=resource.resource_id)}}"
+		    method="POST">
+		<input type="hidden" name="user_id"
+		       value="{{user_row.user.user_id}}" />
+		<input type="hidden" name="group_role_id"
+		       value="{{grole.group_role_id}}">
+		<input type="submit"
+		       value="Unassign"
+		       class="btn btn-danger"
+		       {%if user_row.user.user_id==this_user.user_id%}
+		       disabled="disabled"
+		       {%endif%}>
+	      </form>
+	    </td>
+	  </tr>
+	  {%endfor%}
+	  {%else%}
+	  <tr>
+	    <td colspan="5">
+	      <span class="glyphicon glyphicon-info-sign text-info">
+	      </span>
+	      &nbsp;
+	      <span class="text-info">
+		There are no users assigned any role for this resource.
+	      </span>
+	    </td>
+	  </tr>
+	  {%endfor%}
+	</tbody>
+      </table>
+      {%endif%}
+    </div>
+
+    <div class="row">
+      <h3>Assign</h3>
+      {%if group_roles_error is defined%}
+      {{display_error("Group Roles", group_roles_error)}}
+      {%elif users_error is defined%}
+      {{display_error("Users", users_error)}}
+      {%else%}
+      <form action="{{url_for(
+		    'oauth2.resource.assign_role',
+		    resource_id=resource.resource_id)}}"
+	    method="POST" autocomplete="off">
+	<input type="hidden" name="resource_id" value="{{resource_id}}" />
+	<div class="form-group">
+	  <label for="group_role_id" class="form-label">Role</label>
+	  <select class="form-control" name="group_role_id"
+		  id="group_role_id" required="required">
+	    <option value="">Select role</option>
+	    {%for grole in group_roles%}
+	    <option value="{{grole.group_role_id}}">
+	      {{grole.role.role_name}}
+	    </option>
+	    {%endfor%}
+	  </select>
+	</div>
+	<div class="form-group">
+	  <label for="user-email" class="form-label">User Email</label>
+	  <input list="users-list" name="user_email" class="form-control"
+		 {%if users | length == 0%}
+		 disabled="disabled"
+		 {%endif%}
+		 required="required" />
+	  <datalist id="users-list">
+	    {%for user in users%}
+	    <option value="{{user.email}}">{{user.email}} - {{user.name}}</option>
+	    {%endfor%}
+	  </datalist>
+	</div>
+
+	<input type="submit" class="btn btn-primary" value="Assign"
+	       {%if users | length == 0%}
+	       disabled="disabled"
+	       {%endif%} />
+      </form>
+      {%endif%}
+    </div>
+    {%endif%}
+
+  </div>
+
+</div>
+{%endblock%}