Merge branch 'develop' into enhancement/licenses

This commit is contained in:
2025-11-12 02:19:13 +13:00
99 changed files with 5496 additions and 1326 deletions

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@ -1,3 +1,4 @@
<div class="modal fade" tabindex="-1" id="new_model_modal" role="dialog" aria-labelledby="new_model_modal"
aria-hidden="true">
<div class="modal-dialog modal-lg">
@ -47,14 +48,14 @@
<option disabled>Reviewed Packages</option>
{% for obj in meta.readable_packages %}
{% if obj.reviewed %}
<option value="{{ obj.url }}">{{ obj.name }}</option>
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
{% endif %}
{% endfor %}
<option disabled>Unreviewed Packages</option>
{% for obj in meta.readable_packages %}
{% if not obj.reviewed %}
<option value="{{ obj.url }}">{{ obj.name }}</option>
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
{% endif %}
{% endfor %}
</select>
@ -68,14 +69,14 @@
<option disabled>Reviewed Packages</option>
{% for obj in meta.readable_packages %}
{% if obj.reviewed %}
<option value="{{ obj.url }}">{{ obj.name }}</option>
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
{% endif %}
{% endfor %}
<option disabled>Unreviewed Packages</option>
{% for obj in meta.readable_packages %}
{% if not obj.reviewed %}
<option value="{{ obj.url }}">{{ obj.name }}</option>
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
{% endif %}
{% endfor %}
</select>

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@ -1,3 +1,4 @@
{% load static %}
<div class="modal fade" tabindex="-1" id="new_pathway_modal" role="dialog" aria-labelledby="new_pathway_modal"
aria-hidden="true" style="overflow-y: auto;">
@ -111,7 +112,7 @@
<select id="settingSelect" name="settingSelect" class="form-control">
{% for setting in available_settings %}
<option value="{{ setting.id }}">{{ setting.name }}</option>
<option value="{{ setting.id }}">{{ setting.name|safe }}</option>
{% endfor %}
</select>
<p></p>

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@ -1,3 +1,4 @@
{% load static %}
<div id="new_prediction_setting_modal" class="modal" tabindex="-1">
@ -40,14 +41,14 @@
<option disabled>Reviewed Packages</option>
{% for obj in meta.readable_packages %}
{% if obj.reviewed %}
<option value="{{ obj.url }}">{{ obj.name }}</option>
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
{% endif %}
{% endfor %}
<option disabled>Unreviewed Packages</option>
{% for obj in meta.readable_packages %}
{% if not obj.reviewed %}
<option value="{{ obj.url }}">{{ obj.name }}</option>
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
{% endif %}
{% endfor %}
</select>
@ -57,7 +58,7 @@
<select id="model-based-prediction-setting-model" name="model-based-prediction-setting-model" class="form-control" data-width='100%'>
<option disabled selected>Select the model</option>
{% for m in models %}
<option value="{{ m.url }}">{{ m.name }}</option>
<option value="{{ m.url }}">{{ m.name|safe }}</option>
{% endfor %}
</select>
<label for="model-based-prediction-setting-threshold">Threshold</label>

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@ -1,3 +1,4 @@
{% load static %}
<div class="modal fade bs-modal-lg" id="add_pathway_edge_modal" tabindex="-1" aria-labelledby="add_pathway_edge_modal"
aria-modal="true"
@ -36,7 +37,7 @@
<select id="add_pathway_edge_substrates" name="edge-substrates"
data-actions-box='true' class="form-control" multiple data-width='100%'>
{% for n in pathway.nodes %}
<option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
<option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
{% endfor %}
</select>
</div>
@ -47,7 +48,7 @@
<select id="add_pathway_edge_products" name="edge-products"
data-actions-box='true' class="form-control" multiple data-width='100%'>
{% for n in pathway.nodes %}
<option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name }}</option>
<option data-smiles="{{ n.default_node_label.smiles }}" value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
{% endfor %}
</select>
</div>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Delete Edge -->
<div id="delete_pathway_edge_modal" class="modal" tabindex="-1">
@ -19,7 +20,7 @@
data-actions-box='true' class="form-control" data-width='100%'>
<option value="" disabled selected>Select Reaction to delete</option>
{% for e in pathway.edges %}
<option value="{{ e.url }}">{{ e.edge_label.name }}</option>
<option value="{{ e.url }}">{{ e.edge_label.name|safe }}</option>
{% endfor %}
</select>
<input type="hidden" id="hidden" name="hidden" value="delete"/>

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@ -1,4 +1,5 @@
{% load static %}
<!-- Delete Node -->
<div id="delete_pathway_node_modal" class="modal" tabindex="-1">
<div class="modal-dialog">
@ -19,7 +20,7 @@
data-actions-box='true' class="form-control" data-width='100%'>
<option value="" disabled selected>Select Compound to delete</option>
{% for n in pathway.nodes %}
<option value="{{ n.url }}">{{ n.default_node_label.name }}</option>
<option value="{{ n.url }}">{{ n.default_node_label.name|safe }}</option>
{% endfor %}
</select>
<input type="hidden" id="hidden" name="hidden" value="delete"/>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Edit Compound -->
<div id="edit_compound_modal" class="modal" tabindex="-1">
@ -15,12 +16,12 @@
{% csrf_token %}
<p>
<label for="compound-name">Name</label>
<input id="compound-name" class="form-control" name="compound-name" value="{{ compound.name}}">
<input id="compound-name" class="form-control" name="compound-name" value="{{ compound.name|safe}}">
</p>
<p>
<label for="compound-description">Description</label>
<input id="compound-description" type="text" class="form-control"
value="{{ compound.description }}"
value="{{ compound.description|safe }}"
name="compound-description">
</p>
</form>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Edit Compound -->
<div id="edit_compound_structure_modal" class="modal" tabindex="-1">
@ -15,12 +16,12 @@
{% csrf_token %}
<p>
<label for="compound-structure-name">Name</label>
<input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ compound_structure.name }}">
<input id="compound-structure-name" class="form-control" name="compound-structure-name" value="{{ compound_structure.name|safe }}">
</p>
<p>
<label for="compound-structure-description">Description</label>
<input id="compound-structure-description" type="text" class="form-control"
value="{{ compound_structure.description }}" name="compound-structure-description">
value="{{ compound_structure.description|safe }}" name="compound-structure-description">
</p>
</form>
</div>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Edit Package Permission -->
<div id="edit_group_member_modal" class="modal" tabindex="-1">
@ -39,7 +40,7 @@
{% endfor %}
<option disabled>Groups</option>
{% for g in groups %}
<option value="{{ g.url }}">{{ g.name }}</option>
<option value="{{ g.url }}">{{ g.name|safe }}</option>
{% endfor %}
</select>
<input type="hidden" name="action" value="add">
@ -81,7 +82,7 @@
accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<div class="col-xs-8">
{{ g.name }}
{{ g.name|safe }}
<input type="hidden" name="member" value="{{ g.url }}"/>
<input type="hidden" name="action" value="remove">
</div>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Edit Model -->
<div id="edit_model_modal" class="modal" tabindex="-1">
@ -16,12 +17,12 @@
<p>
<label for="model-name">Name</label>
<input id="model-name" type="text" class="form-control" name="model-name"
value="{{ model.name }}">
value="{{ model.name|safe }}">
</p>
<p>
<label for="model-description">Description</label>
<input id="model-description" type="text" class="form-control" name="model-description"
value="{{ model.description }}">
value="{{ model.description|safe }}">
</p>
</form>
</div>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Edit Node -->
<div id="edit_node_modal" class="modal" tabindex="-1">
@ -15,12 +16,12 @@
{% csrf_token %}
<p>
<label for="node-name">Name</label>
<input id="node-name" class="form-control" name="node-name" value="{{ node.name}}">
<input id="node-name" class="form-control" name="node-name" value="{{ node.name|safe}}">
</p>
<p>
<label for="node-description">Description</label>
<input id="node-description" type="text" class="form-control"
value="{{ node.description }}"
value="{{ node.description|safe }}"
name="node-description">
</p>
</form>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Edit Package -->
<div id="edit_package_modal" class="modal" tabindex="-1">
@ -15,12 +16,12 @@
{% csrf_token %}
<p>
<label for="package-name">Name</label>
<input id="package-name" class="form-control" name="package-name" value="{{ package.name}}">
<input id="package-name" class="form-control" name="package-name" value="{{ package.name|safe}}">
</p>
<p>
<label for="package-description">Description</label>
<input id="package-description" type="text" class="form-control"
value="{{ package.description }}"
value="{{ package.description|safe }}"
name="package-description">
</p>
</form>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Edit Package Permission -->
<div id="edit_package_permissions_modal" class="modal" tabindex="-1">
@ -46,7 +47,7 @@
{% endfor %}
<option disabled>Groups</option>
{% for g in groups %}
<option value="{{ g.url }}">{{ g.name }}</option>
<option value="{{ g.url }}">{{ g.name|safe }}</option>
{% endfor %}
</select>
</div>
@ -100,7 +101,7 @@
accept-charset="UTF-8" action="" data-remote="true" method="post">
{% csrf_token %}
<div class="col-xs-4">
{{ gp.group.name }}
{{ gp.group.name|safe }}
<input type="hidden" name="grantee" value="{{ gp.group.url }}"/>
</div>
<div class="col-xs-2">

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@ -1,3 +1,4 @@
{% load static %}
<!-- Edit Pathway -->
<div id="edit_pathway_modal" class="modal" tabindex="-1">
@ -15,12 +16,12 @@
{% csrf_token %}
<p>
<label for="pathway-name">Name</label>
<input id="pathway-name" class="form-control" name="pathway-name" value="{{ pathway.name }}">
<input id="pathway-name" class="form-control" name="pathway-name" value="{{ pathway.name|safe }}">
</p>
<p>
<label for="pathway-description">Description</label>
<textarea id="pathway-description" type="text" class="form-control" name="pathway-description"
rows="10">{{ pathway.description }}</textarea>
rows="10">{{ pathway.description|safe }}</textarea>
</p>
</form>
</div>

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@ -32,7 +32,7 @@
<td colspan="2">
<select id="model" name="model" class="form-control" data-width='100%'>
{% for m in models %}
<option value="{{ m.id }}" {% if user.prediction_settings.model.url == m.url %}selected{% endif %}>{{ m.name }}</option>
<option value="{{ m.id }}" {% if user.prediction_settings.model.url == m.url %}selected{% endif %}>{{ m.name|safe }}</option>
{% endfor %}
</select>
</td>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Edit Reaction -->
<div id="edit_reaction_modal" class="modal" tabindex="-1">
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{% csrf_token %}
<p>
<label for="reaction-name">Name</label>
<input id="reaction-name" class="form-control" name="reaction-name" value="{{ reaction.name }}">
<input id="reaction-name" class="form-control" name="reaction-name" value="{{ reaction.name|safe }}">
</p>
<p>
<label for="reaction-description">Description</label>
<input id="reaction-description" type="text" class="form-control"
value="{{ reaction.description }}" name="reaction-description">
value="{{ reaction.description|safe }}" name="reaction-description">
</p>
</form>
</div>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Edit Rule -->
<div id="edit_rule_modal" class="modal" tabindex="-1">
@ -14,12 +15,12 @@
{% csrf_token %}
<p>
<label for="rule-name">Name</label>
<input id="rule-name" class="form-control" name="rule-name" value="{{ rule.name }}">
<input id="rule-name" class="form-control" name="rule-name" value="{{ rule.name|safe }}">
</p>
<p>
<label for="rule-description">Description</label>
<input id="rule-description" type="text" class="form-control"
value="{{ rule.description }}" name="rule-description">
value="{{ rule.description|safe }}" name="rule-description">
</p>
</form>
</div>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Edit User -->
<div id="edit_user_modal" class="modal" tabindex="-1">
@ -18,7 +19,7 @@
<select id="default-package" name="default-package" class="form-control" data-width='100%'>
<option disabled>Select a Package</option>
{% for p in meta.writeable_packages %}
<option value="{{ p.url }}" {% if p.id == meta.user.default_package.id %}selected{% endif %}>{{ p.name }}</option>
<option value="{{ p.url }}" {% if p.id == meta.user.default_package.id %}selected{% endif %}>{{ p.name|safe }}</option>
{% endfor %}
</select>
</p>
@ -27,7 +28,7 @@
<select id="default-group" name="default-group" class="form-control" data-width='100%'>
<option disabled>Select a Group</option>
{% for g in meta.available_groups %}
<option value="{{ g.url }}" {% if g.id == meta.user.default_group.id %}selected{% endif %}>{{ g.name }}</option>
<option value="{{ g.url }}" {% if g.id == meta.user.default_group.id %}selected{% endif %}>{{ g.name|safe }}</option>
{% endfor %}
</select>
</p>
@ -36,7 +37,7 @@
<select id="default-prediction-setting" name="default-prediction-setting" class="form-control" data-width='100%'>
<option disabled>Select a Setting</option>
{% for s in meta.available_settings %}
<option value="{{ s.url }}" {% if s.id == meta.user.default_setting.id %}selected{% endif %}>{{ s.name }}</option>
<option value="{{ s.url }}" {% if s.id == meta.user.default_setting.id %}selected{% endif %}>{{ s.name|safe }}</option>
{% endfor %}
</select>
</p>

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@ -1,3 +1,4 @@
<div class="modal fade" tabindex="-1" id="evaluate_model_modal" role="dialog" aria-labelledby="evaluate_model_modal"
aria-hidden="true">
<div class="modal-dialog modal-lg">
@ -24,14 +25,14 @@
<option disabled>Reviewed Packages</option>
{% for obj in meta.readable_packages %}
{% if obj.reviewed %}
<option value="{{ obj.url }}">{{ obj.name }}</option>
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
{% endif %}
{% endfor %}
<option disabled>Unreviewed Packages</option>
{% for obj in meta.readable_packages %}
{% if not obj.reviewed %}
<option value="{{ obj.url }}">{{ obj.name }}</option>
<option value="{{ obj.url }}">{{ obj.name|safe }}</option>
{% endif %}
{% endfor %}
</select>

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@ -1,3 +1,4 @@
{% load static %}
<!-- Copy Object -->
<div id="generic_copy_object_modal" class="modal" tabindex="-1">
@ -18,7 +19,7 @@
data-width='100%'>
<option disabled selected>Select Target Package</option>
{% for p in meta.writeable_packages %}
<option value="{{ p.url }}">{{ p.name }}</option>`
<option value="{{ p.url }}">{{ p.name|safe }}</option>`
{% endfor %}
</select>
<input type="hidden" name="hidden" value="copy">

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@ -1,3 +1,4 @@
{% load static %}
<style>
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<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
<h4 class="modal-title">Set Aliases for {{ current_object.name }}</h4>
<h4 class="modal-title">Set Aliases for {{ current_object.name|safe }}</h4>
</div>
<div class="modal-body">
<form id="set_aliases_modal_form" accept-charset="UTF-8" action="{{ current_object.url }}"

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@ -1,3 +1,4 @@
{% load static %}
<!-- Delete Object -->
<div id="generic_set_external_reference_modal" class="modal" tabindex="-1">
@ -23,7 +24,7 @@
{% if entity == object_type %}
{% for db in databases %}
<option id="db-select-{{ db.database.pk }}" data-input-placeholder="{{ db.placeholder }}"
value="{{ db.database.id }}">{{ db.database.name }}</option>`
value="{{ db.database.id }}">{{ db.database.name|safe }}</option>`
{% endfor %}
{% endif %}
{% endfor %}

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@ -1,3 +1,4 @@
{% load static %}
<div class="modal fade bs-modal-lg" id="set_scenario_modal" tabindex="-1" aria-labelledby="set_scenario_modal"
aria-modal="true" role="dialog">
@ -7,7 +8,7 @@
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
<h4 class="modal-title">Set Scenarios for {{ current_object.name }}</h4>
<h4 class="modal-title">Set Scenarios for {{ current_object.name|safe }}</h4>
</div>
<div class="modal-body">
<div id="loading_scenario_div" class="text-center"></div>

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@ -1,3 +1,4 @@
<div class="modal fade"
tabindex="-1"
id="manage_api_token_modal"
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<div class="input-group">
<input type="hidden" name="hidden" value="delete">
<input type="hidden" name="token-id" value="{{ t.pk }}">
<input type="text" class="form-control" value="{{ t.name }}" disabled>
<input type="text" class="form-control" value="{{ t.name|safe }}" disabled>
<span class="input-group-btn">
<button type="submit" class="btn btn-danger">Delete</button>
</span>

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@ -56,7 +56,7 @@
<option disabled>Select a Setting</option>
{% for s in meta.available_settings %}
<option value="{{ s.url }}"{% if s.id == meta.user.default_setting.id %}selected{% endif %}>
{{ s.name }}{% if s.id == meta.user.default_setting.id %} <i>(User default)</i>{% endif %}
{{ s.name|safe }}{% if s.id == meta.user.default_setting.id %} <i>(User default)</i>{% endif %}
</option>
{% endfor %}
</select>

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@ -0,0 +1,535 @@
{% load static %}
<dialog id="search_modal" class="modal @max-sm:modal-top justify-center">
<div class="modal-box w-lvw sm:w-[85vw] sm:max-w-5xl h-full sm:h-8/12 p-1" >
<!-- Search Input and Mode Selector -->
<div class="form-control mb-4 flex-shrink-0 w-full">
<div class="join w-full m-0 p-3 items-center">
<label class="input join-item input-ghost grow">
<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round" class="lucide lucide-search-icon lucide-search"><path d="m21 21-4.34-4.34"/><circle cx="11" cy="11" r="8"/></svg>
<input type="text" autofocus
id="modal_searchbar"
placeholder="Benfuracarb"
class="grow" aria-label="Search" />
</label>
<!-- Mode Dropdown -->
<div>
<button type="button"
tabindex="0"
id="modal_mode_button"
popovertarget="search_dropdown_menu" style="anchor-name:--anchor-1"
class="btn join-item btn-ghost">
Text
<svg class="w-4 h-4 ml-1" fill="none" stroke="currentColor" viewBox="0 0 24 24">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M19 9l-7 7-7-7"/>
</svg>
</button>
<ul tabindex="0"" class="dropdown dropdown-end menu bg-base-200 rounded-box z-[100] w-64 p-2 shadow-lg" popover id="search_dropdown_menu" style="position-anchor:--anchor-1">
<li class="menu-title">Text</li>
<li>
<a id="modal_dropdown_text"
class="tooltip tooltip-left"
data-tip="Search on object names and descriptions">
Text
</a>
</li>
<li class="menu-title">SMILES</li>
<li>
<a id="modal_dropdown_smiles_default"
class="tooltip tooltip-left"
data-tip="Ignores stereochemistry and charge">
Default
</a>
</li>
<li>
<a id="modal_dropdown_smiles_canonical"
class="tooltip tooltip-left"
data-tip="Ignores stereochemistry, preserves charge">
Canonical
</a>
</li>
<li>
<a id="modal_dropdown_smiles_exact"
class="tooltip tooltip-left"
data-tip="Exact match for stereochemistry and charge">
Exact
</a>
</li>
<li class="menu-title">InChI</li>
<li>
<a id="modal_dropdown_inchikey"
class="tooltip tooltip-left"
data-tip="Search by InChIKey">
InChIKey
</a>
</li>
</ul>
</div>
<button type="button" id="modal_search_button" class="btn btn-xs btn-ghost join-item">
<kbd class="kbd kbd-sm p-1 text-base-content/50">
<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round" class="lucide lucide-corner-down-left-icon lucide-corner-down-left"><path d="M20 4v7a4 4 0 0 1-4 4H4"/><path d="m9 10-5 5 5 5"/></svg>
</kbd>
</button>
</div>
</div>
<!-- Package Selector with Pills -->
<div class="form-control mb-4 flex-shrink-0">
<!-- Pills Container -->
<div id="modal_package_pills_container"
class="flex flex-wrap gap-2 p-3 border-2 border-dashed border-base-300 rounded-lg m-3 min-h-[3rem] items-center">
<!-- Pills will be added here dynamically -->
</div>
<!-- Package Dropdown Menu -->
<ul class="dropdown dropdown-end menu bg-base-200 rounded-box z-[100] w-80 max-h-96 overflow-y-auto p-2 shadow-lg"
popover
id="package_dropdown_menu"
style="position-anchor:--anchor-packages">
{% if unreviewed_packages %}
<li class="menu-title">Reviewed Packages</li>
{% for obj in reviewed_packages %}
<li>
<a class="package-option flex justify-between items-center"
data-package-url="{{ obj.url }}"
data-package-name="{{ obj.name }}">
<span>{{ obj.name }}</span>
<svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4 package-checkmark hidden" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M5 13l4 4L19 7"/>
</svg>
</a>
</li>
{% endfor %}
<li class="menu-title">Unreviewed Packages</li>
{% for obj in unreviewed_packages %}
<li>
<a class="package-option flex justify-between items-center"
data-package-url="{{ obj.url }}"
data-package-name="{{ obj.name }}">
<span>{{ obj.name }}</span>
<svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4 package-checkmark hidden" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M5 13l4 4L19 7"/>
</svg>
</a>
</li>
{% endfor %}
{% else %}
<li class="menu-title">Reviewed Packages</li>
{% for obj in reviewed_packages %}
<li>
<a class="package-option flex justify-between items-center"
data-package-url="{{ obj.url }}"
data-package-name="{{ obj.name }}">
<span>{{ obj.name }}</span>
<svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4 package-checkmark hidden" fill="none" viewBox="0 0 24 24" stroke="currentColor">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M5 13l4 4L19 7"/>
</svg>
</a>
</li>
{% endfor %}
{% endif %}
</ul>
</div>
<!-- Loading Indicator -->
<div id="search_loading" class="hidden justify-center py-8 flex-shrink-0">
<span class="loading loading-spinner loading-lg text-primary"></span>
</div>
<!-- Results Container - scrollable -->
<div id="search_results" class="flex-1 overflow-y-auto min-h-0 p-2"></div>
</div>
<!-- Backdrop to close -->
<form method="dialog" class="modal-backdrop">
<button>close</button>
</form>
</dialog>
<script>
(function() {
// Package Selector Module - Data-driven multiselect package selection
const PackageSelector = {
// Single source of truth: array of selected packages
selectedPackages: [],
elements: {
pillsContainer: null,
packageDropdown: null,
packageOptions: null
},
init() {
this.cacheElements();
this.loadInitialSelection();
this.attachEventListeners();
this.render();
},
cacheElements() {
this.elements.pillsContainer = document.getElementById('modal_package_pills_container');
this.elements.packageDropdown = document.getElementById('package_dropdown_menu');
this.elements.packageOptions = document.querySelectorAll('.package-option');
},
loadInitialSelection() {
// Load pre-selected packages from server-rendered pills
const existingPills = this.elements.pillsContainer.querySelectorAll('.badge');
existingPills.forEach(pill => {
this.selectedPackages.push({
url: pill.dataset.packageUrl,
name: pill.dataset.packageName
});
});
// If no pills found, select all reviewed packages by default
if (this.selectedPackages.length === 0) {
// Iterate through all menu items and collect reviewed packages
const menuItems = this.elements.packageDropdown.querySelectorAll('li');
for (const item of menuItems) {
// Check if this is the "Unreviewed Packages" menu title
if (item.classList.contains('menu-title') &&
item.textContent.trim() === 'Unreviewed Packages') {
break; // Stop processing after this point
}
// Check for package options (only reviewed packages reach here)
const packageOption = item.querySelector('.package-option');
if (packageOption) {
this.selectedPackages.push({
url: packageOption.dataset.packageUrl,
name: packageOption.dataset.packageName
});
}
}
}
},
attachEventListeners() {
// Toggle package selection on dropdown item click
this.elements.packageOptions.forEach(option => {
option.addEventListener('click', (e) => {
e.preventDefault();
e.stopPropagation(); // Prevent dropdown from closing
const packageUrl = option.dataset.packageUrl;
const packageName = option.dataset.packageName;
this.togglePackageSelection(packageUrl, packageName);
});
});
// Remove package when X is clicked (using event delegation)
this.elements.pillsContainer.addEventListener('click', (e) => {
if (e.target.classList.contains('package-remove-btn') || e.target.closest('.package-remove-btn')) {
const pill = e.target.closest('.badge');
if (pill) {
const packageUrl = pill.dataset.packageUrl;
this.removePackage(packageUrl);
}
}
});
},
togglePackageSelection(packageUrl, packageName) {
const index = this.selectedPackages.findIndex(pkg => pkg.url === packageUrl);
if (index !== -1) {
// Remove from selection
this.selectedPackages.splice(index, 1);
} else {
// Add to selection
this.selectedPackages.push({ url: packageUrl, name: packageName });
}
this.render();
},
removePackage(packageUrl) {
const index = this.selectedPackages.findIndex(pkg => pkg.url === packageUrl);
if (index !== -1) {
this.selectedPackages.splice(index, 1);
this.render();
}
},
render() {
this.renderPills();
this.renderAddButton();
this.renderCheckmarks();
},
renderPills() {
// Clear existing pills and button (except placeholder)
const pills = this.elements.pillsContainer.querySelectorAll('.badge');
pills.forEach(pill => pill.remove());
const existingButton = this.elements.pillsContainer.querySelector('#modal_package_add_button');
if (existingButton) {
existingButton.remove();
}
// Create pills from data
this.selectedPackages.forEach(pkg => {
const pill = this.createPillElement(pkg.url, pkg.name);
this.elements.pillsContainer.appendChild(pill);
});
},
renderAddButton() {
// Only render button if there are packages available
if (this.elements.packageOptions.length === 0) {
return;
}
const button = document.createElement('button');
button.type = 'button';
button.id = 'modal_package_add_button';
button.setAttribute('popovertarget', 'package_dropdown_menu');
button.style.cssText = 'anchor-name:--anchor-packages';
button.className = 'btn btn-sm btn-ghost gap-2 text-base-content/50';
button.innerHTML = `
<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round" class="lucide lucide-plus-icon lucide-plus"><path d="M5 12h14"/><path d="M12 5v14"/></svg>
Add Package
`;
this.elements.pillsContainer.appendChild(button);
},
createPillElement(packageUrl, packageName) {
const pill = document.createElement('span');
pill.className = 'badge badge-outline gap-2 max-w-xs';
pill.dataset.packageUrl = packageUrl;
pill.dataset.packageName = packageName;
pill.innerHTML = `
<span class="truncate" title="${packageName}">${packageName}</span>
<svg xmlns="http://www.w3.org/2000/svg"
class="h-4 w-4 cursor-pointer hover:text-error package-remove-btn flex-shrink-0 rotate-45"
viewBox="0 0 24 24"
fill="none" stroke="currentColor"
stroke-width="2"
stroke-linecap="round"
stroke-linejoin="round"
>
<path d="M5 12h14"/><path d="M12 5v14"/>
</svg>
`;
return pill;
},
renderCheckmarks() {
// Update all checkmarks based on selected packages
this.elements.packageOptions.forEach(option => {
const packageUrl = option.dataset.packageUrl;
const isSelected = this.selectedPackages.some(pkg => pkg.url === packageUrl);
const checkmark = option.querySelector('.package-checkmark');
if (checkmark) {
checkmark.classList.toggle('hidden', !isSelected);
}
});
},
getSelectedPackages() {
return this.selectedPackages.map(pkg => pkg.url);
}
};
// Modal and Search Management
const modal = document.getElementById('search_modal');
const searchbar = document.getElementById('modal_searchbar');
const searchButton = document.getElementById('modal_search_button');
const modeButton = document.getElementById('modal_mode_button');
const resultsDiv = document.getElementById('search_results');
const loadingDiv = document.getElementById('search_loading');
// MutationObserver to detect when modal opens
const observer = new MutationObserver((mutations) => {
mutations.forEach((mutation) => {
if (mutation.attributeName === 'open' && modal.open) {
PackageSelector.render();
// Delay focus to allow CSS transitions to complete (modal has 0.3s transition)
setTimeout(() => {
searchbar.focus();
}, 320);
}
});
});
observer.observe(modal, { attributes: true });
// Clear results when modal closes
modal.addEventListener('close', function() {
resultsDiv.innerHTML = '';
loadingDiv.classList.add('hidden');
searchbar.value = '';
});
// Mode dropdown handlers
const dropdownMenu = document.getElementById('search_dropdown_menu');
const modeButtons = [
{ id: 'modal_dropdown_text', text: 'Text' },
{ id: 'modal_dropdown_smiles_default', text: 'Default' },
{ id: 'modal_dropdown_smiles_canonical', text: 'Canonical' },
{ id: 'modal_dropdown_smiles_exact', text: 'Exact' },
{ id: 'modal_dropdown_inchikey', text: 'InChIKey' }
];
modeButtons.forEach(({ id, text }) => {
document.getElementById(id).addEventListener('click', function(e) {
e.preventDefault();
modeButton.innerHTML = text + ` <svg class="w-4 h-4 ml-1" fill="none" stroke="currentColor" viewBox="0 0 24 24">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M19 9l-7 7-7-7"/>
</svg>`;
// Close dropdown using popover API
if (dropdownMenu && typeof dropdownMenu.hidePopover === 'function') {
dropdownMenu.hidePopover();
}
});
});
// Initialize Package Selector
PackageSelector.init();
// Search Response Handler
function handleSearchResponse(data) {
resultsDiv.innerHTML = '';
function makeContent(objs) {
let links = '';
objs.forEach(obj => {
links += `<a href="${obj.url}" class="block px-4 py-2 hover:bg-base-300 rounded-lg transition-colors">${obj.name}</a>`;
});
return links;
}
let allEmpty = true;
let content = '';
// Category order for better UX
const categoryOrder = ['Compounds', 'Compound Structures', 'Rules', 'Reactions', 'Pathways'];
categoryOrder.forEach(key => {
if (!data[key] || data[key].length < 1) {
return;
}
allEmpty = false;
content += `
<div class="collapse collapse-arrow bg-base-200 mb-2">
<input type="checkbox" checked />
<div class="collapse-title font-medium">
${key} <span class="badge badge-neutral badge-sm ml-2">${data[key].length}</span>
</div>
<div class="collapse-content">
${makeContent(data[key])}
</div>
</div>
`;
});
if (allEmpty) {
resultsDiv.innerHTML = `
<div class="alert alert-warning">
<svg class="w-6 h-6" fill="none" stroke="currentColor" viewBox="0 0 24 24">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M12 9v2m0 4h.01m-6.938 4h13.856c1.54 0 2.502-1.667 1.732-3L13.732 4c-.77-1.333-2.694-1.333-3.464 0L3.34 16c-.77 1.333.192 3 1.732 3z"/>
</svg>
<span>No results found</span>
</div>
`;
} else {
resultsDiv.innerHTML = `
<div class="mb-2">
<div class="text-sm font-semibold text-base-content/70 mb-2">Results</div>
${content}
</div>
`;
}
}
// Search Execution
function performSearch(e) {
e.preventDefault();
const query = searchbar.value.trim();
if (!query) {
console.log('Search phrase empty, won\'t do search');
return;
}
const selPacks = PackageSelector.getSelectedPackages();
if (selPacks.length < 1) {
console.log('No package selected, won\'t do search');
resultsDiv.innerHTML = `
<div class="alert alert-info">
<svg class="w-6 h-6" fill="none" stroke="currentColor" viewBox="0 0 24 24">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"/>
</svg>
<span>Please select at least one package</span>
</div>
`;
return;
}
const mode = modeButton.textContent.trim().toLowerCase();
const params = new URLSearchParams();
selPacks.forEach(pack => params.append('packages', pack));
params.append('search', query);
params.append('mode', mode);
// Show loading
loadingDiv.classList.remove('hidden');
resultsDiv.innerHTML = '';
fetch(`{{ SERVER_BASE }}/search?${params.toString()}`, {
method: 'GET',
headers: {
'Accept': 'application/json'
}
})
.then(response => {
if (!response.ok) {
throw new Error('Search request failed');
}
return response.json();
})
.then(result => {
loadingDiv.classList.add('hidden');
handleSearchResponse(result);
})
.catch(error => {
loadingDiv.classList.add('hidden');
console.error('Search error:', error);
resultsDiv.innerHTML = `
<div class="alert alert-error">
<svg class="w-6 h-6" fill="none" stroke="currentColor" viewBox="0 0 24 24">
<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M12 8v4m0 4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"/>
</svg>
<span>Search failed. Please try again.</span>
</div>
`;
});
}
// Event listeners for search
searchButton.addEventListener('click', performSearch);
searchbar.addEventListener('keydown', function(e) {
if (e.key === 'Enter') {
performSearch(e);
}
});
})();
</script>

View File

@ -1,110 +0,0 @@
<div class="modal fade bs-modal-sm" id="signupmodal" tabindex="-1" role="dialog" aria-labelledby="mySmallModalLabel"
aria-hidden="true">
<div class="modal-dialog modal-sm">
<div class="modal-content">
<br>
<div class="bs-example bs-example-tabs">
<ul id="myTab" class="nav nav-tabs">
<li class="active">
<a href="#signin" data-toggle="tab">Sign In</a>
</li>
<li class="">
<a href="#signup" data-toggle="tab">Register</a>
</li>
<li class="">
<a href="#why" data-toggle="tab">Why?</a>
</li>
</ul>
</div>
<div class="modal-body">
<div id="myTabContent" class="tab-content">
<div class="tab-pane fade active in" id="signin">
<form class="form-horizontal" method="post" action="{% url 'login' %}">
{% csrf_token %}
<fieldset>
<input type="hidden" name="login" id="login" value="true"/>
<div class="control-group">
<label class="control-label" for="username">Username:</label>
<div class="controls">
<input required id="username" name="username" type="text" class="form-control"
placeholder="username" autocomplete="username">
</div>
<label class="control-label" for="passwordinput">Password:</label>
<div class="controls">
<input required id="passwordinput" name="password" class="form-control"
type="password" placeholder="********" autocomplete="current-password">
</div>
</div>
<!-- Button -->
<div class="control-group">
<label class="control-label" for="signin"></label>
<div class="controls">
<button id="signin" name="signin" class="btn btn-success">Sign In</button>
</div>
</div>
</fieldset>
</form>
</div>
<!-- Why tab -->
<div class="tab-pane fade in" id="why">
<p>After you register, you have more permissions on
this site, e.g., can create your own
packages, submit data for review, and set access
permissions to your data.</p>
<p></p>
<p>
<br> Please
contact <a href="mailto:admin@envipath.org">admin@envipath.org</a>
if you have any questions.</p>
</div>
<!-- Register -->
<div class="tab-pane fade"
id="signup">
<div id="passwordGuideline" class="alert alert-info">
The password must contain 8 to 30 characters<br>
The following characters are allowed:
- Upper and lower case characters<br>
- Digits<br>
- Special characters _, -, +<br>
</div>
<form id="signup-action" class="form-horizontal" action="{% url 'login' %}" method="post">
{% csrf_token %}
<input type="hidden" name="register" id="register" value="true"/>
<label class="control-label" for="userid">Username:</label>
<input id="userid" name="username" class="form-control" type="text" placeholder="user" required autocomplete="username">
<label class="control-label" for="email">Email:</label>
<input id="email" name="email" class="form-control" type="email" placeholder="user@envipath.org" required>
<label class="control-label" for="password">Password:</label>
<input id="password" name="password" class="form-control" type="password" placeholder="********" required autocomplete="new-password">
<label class="control-label" for="rpassword">Repeat Password:</label>
<input id="rpassword" name="rpassword" class="form-control" type="password" placeholder="********" required autocomplete="new-password">
<div class="control-group">
<label class="control-label" for="confirmsignup"></label>
<div class="controls">
<button id="confirmsignup" name="confirmsignup" class="btn btn-success">Sign Up
</button>
</div>
</div>
</form>
</div>
</div>
</div>
<div class="modal-footer">
<center>
<button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
</center>
</div>
</div>
</div>
</div>