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[Feature] Modern UI roll out (#236)

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This PR moves all the collection pages into the new UI in a rough push.
I did not put the same amount of care into these as into search, index, and predict.

## Major changes

- All modals are now migrated to a state based alpine.js implementation.
- jQuery is no longer present in the base layout; ajax is replace by native fetch api
- most of the pps.js is now obsolte (as I understand it; the code is not referenced any more @jebus  please double check)
- in-memory pagination for large result lists (set to 50; we can make that configurable later; performance degrades at around 1k) stukk a bit rough tracked in #235

## Minor things

- Sarch and index also use alpine now
- The loading spinner is now CSS animated (not sure if it currently gets correctly called)

## Not done

- Ihave not even cheked the admin pages. Not sure If these need migrations
- The temporary migration pages still use the old template. Not sure what is supposed to happen with those? @jebus

## What I did to test

- opend all pages in browse, and user ; plus all pages reachable from there.
- Interacted and tested the functionality of each modal superfically with exception of the API key modal (no functional test).

---
This PR is massive sorry for that; just did not want to push half-brokenn state.
@jebus @liambrydon I would be glad if you could click around and try to break it :)

Finally closes #133

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#236
Co-authored-by: Tobias O <tobias.olenyi@envipath.com>
Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
This commit is contained in:
Tobias O
2025-11-26 23:16:44 +13:00
committed by jebus
parent 7f6f209b4a
commit 1a2c9bb543
110 changed files with 10784 additions and 9465 deletions
Download Patch File Download Diff File Expand all files Collapse all files

5
templates/actions/collections/compound.html
View File

@ -1,6 +1,9 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#new_compound_modal">
<a
role="button"
onclick="document.getElementById('new_compound_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Compound</a
>
</li>

3
templates/actions/collections/compound_structure.html
View File

@ -2,8 +2,7 @@
<li>
<a
role="button"
data-toggle="modal"
data-target="#new_compound_structure_modal"
onclick="document.getElementById('new_compound_structure_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Compound Structure</a
>

5
templates/actions/collections/edge.html
View File

@ -1,6 +1,9 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#new_edge_modal">
<a
role="button"
onclick="document.getElementById('new_edge_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Edge</a
>
</li>

5
templates/actions/collections/group.html
View File

@ -1,5 +1,8 @@
<li>
<a role="button" data-toggle="modal" data-target="#new_group_modal">
<a
role="button"
onclick="document.getElementById('new_group_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Group</a
>
</li>

5
templates/actions/collections/model.html
View File

@ -1,6 +1,9 @@
{% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
<li>
<a role="button" data-toggle="modal" data-target="#new_model_modal">
<a
role="button"
onclick="document.getElementById('new_model_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Model</a
>
</li>

5
templates/actions/collections/node.html
View File

@ -1,6 +1,9 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#new_node_modal">
<a
role="button"
onclick="document.getElementById('new_node_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Node</a
>
</li>

13
templates/actions/collections/package.html
View File

@ -1,18 +1,23 @@
<li>
<a role="button" data-toggle="modal" data-target="#new_package_modal">
<a
role="button"
onclick="document.getElementById('new_package_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Package</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#import_package_modal">
<a
role="button"
onclick="document.getElementById('import_package_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-import"></span> Import Package from JSON</a
>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#import_legacy_package_modal"
onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-import"></span> Import Package from legacy
JSON</a

5
templates/actions/collections/reaction.html
View File

@ -1,6 +1,9 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#new_reaction_modal">
<a
role="button"
onclick="document.getElementById('new_reaction_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Reaction</a
>
</li>

5
templates/actions/collections/rule.html
View File

@ -1,6 +1,9 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#new_rule_modal">
<a
role="button"
onclick="document.getElementById('new_rule_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Rule</a
>
</li>

5
templates/actions/collections/scenario.html
View File

@ -1,6 +1,9 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#new_scenario_modal">
<a
role="button"
onclick="document.getElementById('new_scenario_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span> New Scenario</a
>
</li>

5
templates/actions/collections/setting.html
View File

@ -1,6 +1,9 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#new_setting_modal">
<a
role="button"
onclick="document.getElementById('new_setting_modal').showModal(); return false;"
>
<span class="glyphicon glyphicon-plus"></span>New Setting</a
>
</li>

33
templates/actions/objects/compound.html
View File

@ -1,42 +1,59 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_compound_modal">
<a
role="button"
onclick="document.getElementById('edit_compound_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Compound</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#add_structure_modal">
<a
role="button"
onclick="document.getElementById('add_structure_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Add Structure</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#generic_set_external_reference_modal"
onclick="document.getElementById('generic_set_external_reference_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a
>
</li>
{% endif %}
<li>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<a
role="button"
onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-duplicate"></i> Copy</a
>
</li>
{% if meta.can_edit %}
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a
>
</li>

21
templates/actions/objects/compound_structure.html
View File

@ -2,33 +2,40 @@
<li>
<a
role="button"
data-toggle="modal"
data-target="#edit_compound_structure_modal"
onclick="document.getElementById('edit_compound_structure_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#generic_set_external_reference_modal"
onclick="document.getElementById('generic_set_external_reference_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a
>
</li>

15
templates/actions/objects/edge.html
View File

@ -1,16 +1,25 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Edge</a
>
</li>

10
templates/actions/objects/group.html
View File

@ -1,11 +1,17 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_group_member_modal">
<a
role="button"
onclick="document.getElementById('edit_group_member_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Group</a
>
</li>

20
templates/actions/objects/model.html
View File

@ -1,21 +1,33 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_model_modal">
<a
role="button"
onclick="document.getElementById('edit_model_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Model</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#evaluate_model_modal">
<a
role="button"
onclick="document.getElementById('evaluate_model_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-ok"></i> Evaluate Model</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#retrain_model_modal">
<a
role="button"
onclick="document.getElementById('retrain_model_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-repeat"></i> Retrain Model</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Model</a
>
</li>

20
templates/actions/objects/node.html
View File

@ -1,21 +1,33 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_node_modal">
<a
role="button"
onclick="document.getElementById('edit_node_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Node</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Node</a
>
</li>

28
templates/actions/objects/package.html
View File

@ -1,35 +1,49 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_package_modal">
<a
role="button"
onclick="document.getElementById('edit_package_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Package</a
>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#edit_package_permissions_modal"
onclick="document.getElementById('edit_package_permissions_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-user"></i> Edit Permissions</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#publish_package_modal">
<a
role="button"
onclick="document.getElementById('publish_package_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#export_package_modal">
<a
role="button"
onclick="document.getElementById('export_package_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_license_modal">
<a
role="button"
onclick="document.getElementById('set_license_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-duplicate"></i> License</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Package</a
>
</li>

54
templates/actions/objects/pathway.html
View File

@ -1,26 +1,34 @@
{% if meta.can_edit %}
<li>
<a class="button" data-toggle="modal" data-target="#add_pathway_node_modal">
<a
class="button"
onclick="document.getElementById('add_pathway_node_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Add Compound</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">
<a
class="button"
onclick="document.getElementById('add_pathway_edge_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Add Reaction</a
>
</li>
<li role="separator" class="divider"></li>
{% endif %}
<li>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<a
role="button"
onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-duplicate"></i> Copy</a
>
</li>
<li>
<a
class="button"
data-toggle="modal"
data-target="#download_pathway_csv_modal"
onclick="document.getElementById('download_pathway_csv_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as CSV</a
>
@ -28,8 +36,7 @@
<li>
<a
class="button"
data-toggle="modal"
data-target="#download_pathway_image_modal"
onclick="document.getElementById('download_pathway_image_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a
>
@ -38,8 +45,7 @@
<li>
<a
class="button"
data-toggle="modal"
data-target="#identify_missing_rules_modal"
onclick="document.getElementById('identify_missing_rules_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-question-sign"></i> Identify Missing
Rules</a
@ -47,30 +53,34 @@
</li>
<li role="separator" class="divider"></li>
<li>
<a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
<a
class="button"
onclick="document.getElementById('edit_pathway_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Pathway</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
{# <li>#}
{# <a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">#}
{# <i class="glyphicon glyphicon-plus"></i> Calculate Compound Properties</a>#}
{# </li>#}
<li role="separator" class="divider"></li>
<li>
<a
class="button"
data-toggle="modal"
data-target="#delete_pathway_node_modal"
onclick="document.getElementById('delete_pathway_node_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a
>
@ -78,14 +88,16 @@
<li>
<a
class="button"
data-toggle="modal"
data-target="#delete_pathway_edge_modal"
onclick="document.getElementById('delete_pathway_edge_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Pathway</a
>
</li>

28
templates/actions/objects/reaction.html
View File

@ -1,37 +1,51 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_reaction_modal">
<a
role="button"
onclick="document.getElementById('edit_reaction_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Reaction</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#generic_set_external_reference_modal"
onclick="document.getElementById('generic_set_external_reference_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a
>
</li>
{% endif %}
<li>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<a
role="button"
onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-duplicate"></i> Copy</a
>
</li>
{% if meta.can_edit %}
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
>
</li>

25
templates/actions/objects/rule.html
View File

@ -1,28 +1,43 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_rule_modal">
<a
role="button"
onclick="document.getElementById('edit_rule_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Edit Rule</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<a
role="button"
onclick="document.getElementById('set_aliases_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<a
role="button"
onclick="document.getElementById('set_scenario_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
{% endif %}
<li>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<a
role="button"
onclick="document.getElementById('generic_copy_object_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-duplicate"></i> Copy</a
>
</li>
{% if meta.can_edit %}
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Rule</a
>
</li>

11
templates/actions/objects/scenario.html
View File

@ -2,8 +2,7 @@
<li>
<a
class="button"
data-toggle="modal"
data-target="#add_additional_information_modal"
onclick="document.getElementById('add_additional_information_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Add Additional Information</a
>
@ -11,14 +10,16 @@
<li>
<a
class="button"
data-toggle="modal"
data-target="#update_scenario_additional_information_modal"
onclick="document.getElementById('update_scenario_additional_information_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Set Additional Information</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Scenario</a
>
</li>

18
templates/actions/objects/user.html
View File

@ -1,19 +1,24 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_user_modal">
<a
role="button"
onclick="document.getElementById('edit_user_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-edit"></i> Update</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#edit_password_modal">
<a
role="button"
onclick="document.getElementById('edit_password_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-lock"></i> Update Password</a
>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#new_prediction_setting_modal"
onclick="document.getElementById('new_prediction_setting_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a
>
@ -23,7 +28,10 @@
{# <i class="glyphicon glyphicon-console"></i> Manage API Token</a>#}
{# </li>#}
<li>
<a role="button" data-toggle="modal" data-target="#generic_delete_modal">
<a
class="button"
onclick="document.getElementById('generic_delete_modal').showModal(); return false;"
>
<i class="glyphicon glyphicon-trash"></i> Delete Account</a
>
</li>