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refactor: large scale formatting/linting

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This commit is contained in:
Tobias O
2025-11-12 15:51:13 +13:00
parent 305fdc41fb
commit 34aed2c7aa
120 changed files with 11389 additions and 7532 deletions
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67
templates/actions/objects/compound.html
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@ -1,32 +1,43 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_compound_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Compound</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#add_structure_modal">
<i class="glyphicon glyphicon-plus"></i> Add Structure</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#edit_compound_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Compound</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#add_structure_modal">
<i class="glyphicon glyphicon-plus"></i> Add Structure</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#generic_set_external_reference_modal"
>
<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">
<i class="glyphicon glyphicon-duplicate"></i> Copy</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<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">
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a
>
</li>
{% endif %}

53
templates/actions/objects/compound_structure.html
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@ -1,22 +1,35 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_compound_structure_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#edit_compound_structure_modal"
>
<i class="glyphicon glyphicon-edit"></i> Edit Compound Structure</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#generic_set_external_reference_modal"
>
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Compound Structure</a
>
</li>
{% endif %}

27
templates/actions/objects/edge.html
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@ -1,14 +1,17 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Edge</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Edge</a
>
</li>
{% endif %}

18
templates/actions/objects/group.html
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@ -1,10 +1,12 @@
{% if meta.can_edit %}
<li>
<li>
<a role="button" data-toggle="modal" data-target="#edit_group_member_modal">
<i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Group</a>
</li>
{% endif %}
<i class="glyphicon glyphicon-trash"></i> Add/Remove Member</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Group</a
>
</li>
{% endif %}

38
templates/actions/objects/model.html
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@ -1,18 +1,22 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_model_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Model</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#evaluate_model_modal">
<i class="glyphicon glyphicon-ok"></i> Evaluate Model</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#retrain_model_modal">
<i class="glyphicon glyphicon-repeat"></i> Retrain Model</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Model</a>
</li>
{% endif %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_model_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Model</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#evaluate_model_modal">
<i class="glyphicon glyphicon-ok"></i> Evaluate Model</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#retrain_model_modal">
<i class="glyphicon glyphicon-repeat"></i> Retrain Model</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Model</a
>
</li>
{% endif %}

36
templates/actions/objects/node.html
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@ -1,18 +1,22 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_node_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Node</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Node</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#edit_node_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Node</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Node</a
>
</li>
{% endif %}

60
templates/actions/objects/package.html
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@ -1,26 +1,36 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_package_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Package</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#edit_package_permissions_modal">
<i class="glyphicon glyphicon-user"></i> Edit Permissions</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#publish_package_modal">
<i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#export_package_modal">
<i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_license_modal">
<i class="glyphicon glyphicon-duplicate"></i> License</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Package</a>
</li>
{% endif %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_package_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Package</a
>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#edit_package_permissions_modal"
>
<i class="glyphicon glyphicon-user"></i> Edit Permissions</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#publish_package_modal">
<i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#export_package_modal">
<i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_license_modal">
<i class="glyphicon glyphicon-duplicate"></i> License</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Package</a
>
</li>
{% endif %}

143
templates/actions/objects/pathway.html
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@ -1,59 +1,92 @@
{% if meta.can_edit %}
<li>
<a class="button" data-toggle="modal" data-target="#add_pathway_node_modal">
<i class="glyphicon glyphicon-plus"></i> Add Compound</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">
<i class="glyphicon glyphicon-plus"></i> Add Reaction</a>
</li>
<li role="separator" class="divider"></li>
<li>
<a class="button" data-toggle="modal" data-target="#add_pathway_node_modal">
<i class="glyphicon glyphicon-plus"></i> Add Compound</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#add_pathway_edge_modal">
<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">
<i class="glyphicon glyphicon-duplicate"></i> Copy</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#download_pathway_csv_modal">
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as CSV</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#download_pathway_image_modal">
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<i class="glyphicon glyphicon-duplicate"></i> Copy</a
>
</li>
<li>
<a
class="button"
data-toggle="modal"
data-target="#download_pathway_csv_modal"
>
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as CSV</a
>
</li>
<li>
<a
class="button"
data-toggle="modal"
data-target="#download_pathway_image_modal"
>
<i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a
>
</li>
{% if meta.can_edit %}
<li>
<a class="button" data-toggle="modal" data-target="#identify_missing_rules_modal">
<i class="glyphicon glyphicon-question-sign"></i> Identify Missing Rules</a>
</li>
<li role="separator" class="divider"></li>
<li>
<a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Pathway</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<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">
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#delete_pathway_edge_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Pathway</a>
</li>
<li>
<a
class="button"
data-toggle="modal"
data-target="#identify_missing_rules_modal"
>
<i class="glyphicon glyphicon-question-sign"></i> Identify Missing
Rules</a
>
</li>
<li role="separator" class="divider"></li>
<li>
<a class="button" data-toggle="modal" data-target="#edit_pathway_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Pathway</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<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"
>
<i class="glyphicon glyphicon-trash"></i> Delete Compound</a
>
</li>
<li>
<a
class="button"
data-toggle="modal"
data-target="#delete_pathway_edge_modal"
>
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Pathway</a
>
</li>
{% endif %}

58
templates/actions/objects/reaction.html
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@ -1,28 +1,38 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_reaction_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Reaction</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#generic_set_external_reference_modal">
<i class="glyphicon glyphicon-plus"></i> Set External Reference</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#edit_reaction_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Reaction</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#generic_set_external_reference_modal"
>
<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">
<i class="glyphicon glyphicon-duplicate"></i> Copy</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<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">
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
>
</li>
{% endif %}

45
templates/actions/objects/rule.html
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@ -1,24 +1,29 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_rule_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Rule</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#edit_rule_modal">
<i class="glyphicon glyphicon-edit"></i> Edit Rule</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_aliases_modal">
<i class="glyphicon glyphicon-plus"></i> Set Aliases</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#set_scenario_modal">
<i class="glyphicon glyphicon-plus"></i> Set Scenarios</a
>
</li>
{% endif %}
<li>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<i class="glyphicon glyphicon-duplicate"></i> Copy</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#generic_copy_object_modal">
<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">
<i class="glyphicon glyphicon-trash"></i> Delete Rule</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Rule</a
>
</li>
{% endif %}

37
templates/actions/objects/scenario.html
View File

@ -1,14 +1,25 @@
{% if meta.can_edit %}
<li>
<a class="button" data-toggle="modal" data-target="#add_additional_information_modal">
<i class="glyphicon glyphicon-trash"></i> Add Additional Information</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#update_scenario_additional_information_modal">
<i class="glyphicon glyphicon-trash"></i> Set Additional Information</a>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Scenario</a>
</li>
{% endif %}
<li>
<a
class="button"
data-toggle="modal"
data-target="#add_additional_information_modal"
>
<i class="glyphicon glyphicon-trash"></i> Add Additional Information</a
>
</li>
<li>
<a
class="button"
data-toggle="modal"
data-target="#update_scenario_additional_information_modal"
>
<i class="glyphicon glyphicon-trash"></i> Set Additional Information</a
>
</li>
<li>
<a class="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Scenario</a
>
</li>
{% endif %}

50
templates/actions/objects/user.html
View File

@ -1,22 +1,30 @@
{% if meta.can_edit %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_user_modal">
<i class="glyphicon glyphicon-edit"></i> Update</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#edit_password_modal">
<i class="glyphicon glyphicon-lock"></i> Update Password</a>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#new_prediction_setting_modal">
<i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a>
</li>
{# <li>#}
{# <a role="button" data-toggle="modal" data-target="#manage_api_token_modal">#}
{# <i class="glyphicon glyphicon-console"></i> Manage API Token</a>#}
{# </li>#}
<li>
<a role="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Account</a>
</li>
{% endif %}
<li>
<a role="button" data-toggle="modal" data-target="#edit_user_modal">
<i class="glyphicon glyphicon-edit"></i> Update</a
>
</li>
<li>
<a role="button" data-toggle="modal" data-target="#edit_password_modal">
<i class="glyphicon glyphicon-lock"></i> Update Password</a
>
</li>
<li>
<a
role="button"
data-toggle="modal"
data-target="#new_prediction_setting_modal"
>
<i class="glyphicon glyphicon-plus"></i> New Prediction Setting</a
>
</li>
{# <li>#}
{# <a role="button" data-toggle="modal" data-target="#manage_api_token_modal">#}
{# <i class="glyphicon glyphicon-console"></i> Manage API Token</a>#}
{# </li>#}
<li>
<a role="button" data-toggle="modal" data-target="#generic_delete_modal">
<i class="glyphicon glyphicon-trash"></i> Delete Account</a
>
</li>
{% endif %}