diff options
Diffstat (limited to 'gn2/wqflask/templates')
22 files changed, 369 insertions, 227 deletions
diff --git a/gn2/wqflask/templates/base.html b/gn2/wqflask/templates/base.html index 26b75230..6c545646 100644 --- a/gn2/wqflask/templates/base.html +++ b/gn2/wqflask/templates/base.html @@ -188,7 +188,7 @@ </span> <span style="padding: 5px;margin-left: 65px;" > - <a style="text-decoration: none" target="_blank" href="https://issues.genenetwork.org/topics/xapian/xapian-search-queries"> + <a style="text-decoration: none" target="_blank" href="/search-syntax"> <i style="text-align: center;color:#336699;;" class="fa fa-question-circle fa-2x" title="see more search hints" aria-hidden="true"></i> </a> </span> diff --git a/gn2/wqflask/templates/collections/list.html b/gn2/wqflask/templates/collections/list.html index c3d5d2a4..dc725fb6 100644 --- a/gn2/wqflask/templates/collections/list.html +++ b/gn2/wqflask/templates/collections/list.html @@ -57,8 +57,8 @@ <td align="center" style="padding: 0px;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td> <td align="right">{{ loop.index }} <td><a class="collection_name" href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td> - <td>{{ uc.created_timestamp }}</td> - <td>{{ uc.changed_timestamp }}</td> + <td>{{ uc.created }}</td> + <td>{{ uc.changed }}</td> <td align="right">{{ uc.num_members }}</td> </tr> {% endfor %} @@ -88,8 +88,8 @@ <td align="center" style="padding: 0px;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td> <td align="right">{{ loop.index }} <td><a class="collection_name" href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td> - <td>{{ uc.created_timestamp }}</td> - <td>{{ uc.changed_timestamp }}</td> + <td>{{ uc.created }}</td> + <td>{{ uc.changed }}</td> <td align="right">{{ uc.num_members }}</td> </tr> {% endfor %} diff --git a/gn2/wqflask/templates/collections/view.html b/gn2/wqflask/templates/collections/view.html index 7e74442f..55669f09 100644 --- a/gn2/wqflask/templates/collections/view.html +++ b/gn2/wqflask/templates/collections/view.html @@ -214,9 +214,9 @@ 'render': function(data) { if (Object.hasOwn(data, 'description')){ try { - return decodeURIComponent(escape(data.description)) + return decodeURIComponent(data.description) } catch(err){ - return escape(data.description) + return data.description } } else if (Object.hasOwn(data, 'location')){ return data.location diff --git a/gn2/wqflask/templates/correlation_page.html b/gn2/wqflask/templates/correlation_page.html index 24eaff1f..07118145 100644 --- a/gn2/wqflask/templates/correlation_page.html +++ b/gn2/wqflask/templates/correlation_page.html @@ -69,8 +69,8 @@ <input type="text" name="r_less_select" value="1.0" size="6" maxlength="10">, with mean > <input type="text" name="mean_greater_select" value="0" size="6" maxlength="10"> <select id="mean_and_or" size="1"> - <option value="and" selected>AND</option> - <option value="or">OR</option> + <option value="and">AND</option> + <option value="or" selected>OR</option> </select> mean < <input type="text" name="mean_less_select" value="100" size="6" maxlength="10"> diff --git a/gn2/wqflask/templates/dataset.html b/gn2/wqflask/templates/dataset.html index 096a3724..62fac650 100644 --- a/gn2/wqflask/templates/dataset.html +++ b/gn2/wqflask/templates/dataset.html @@ -40,31 +40,6 @@ .panel-metadata dt::after { content: ":"; } - - .search { - width: 50%; - margin: 1em auto; - } - .has-search .form-control-feedback { - right: initial; - left: 0; - color: #ccc; - } - - .has-search .form-control { - padding-right: 12px; - padding-left: 34px; - } - - .search { - transform: scale(1.5, 1.5); - } - .search input { - min-width: 17em; - } - .dataset-search { - padding: 0 17%; - } </style> {% endblock %} @@ -348,7 +323,7 @@ </div> {% else %} -<div class="container dataset-search"> +<div class="container"> <p class="lead">We appreciate your interest, but unfortunately, we don't have any additional information available for: <strong>{{ name }}</strong>. If you have other inquiries or need assistance with something else, please don't hesitate to get in touch with us. </div> diff --git a/gn2/wqflask/templates/gnqa.html b/gn2/wqflask/templates/gnqa.html index 8b50fe43..b3bc74fd 100644 --- a/gn2/wqflask/templates/gnqa.html +++ b/gn2/wqflask/templates/gnqa.html @@ -93,7 +93,7 @@ AI Search <small> <sup> - <button class="search-hist-btn" hx-get="/gnqna/hist/" hx-target="#swap" hx-swap="innerHTML" > + <button class="search-hist-btn" hx-get="/gnqna/hist" hx-target="#swap" hx-swap="innerHTML"> [Search History] </button> </sup> @@ -107,7 +107,7 @@ <button class="btn btn-default btn-sm col-xs-1 col-sm-1 col-sm-offset-3" hx-post="/gnqna" hx-target="#swap" - hx-swap="innerHTML" + hx-swap="innerHTML" hx-indicator="#indicator"> <i class="fa fa-search fa-3x" aria-hidden="true" title="Search"></i> <img id="indicator" class="htmx-indicator" src="/static/gif/loader.gif"/> diff --git a/gn2/wqflask/templates/gnqa_answer.html b/gn2/wqflask/templates/gnqa_answer.html index 0ddcfde7..41c1b338 100644 --- a/gn2/wqflask/templates/gnqa_answer.html +++ b/gn2/wqflask/templates/gnqa_answer.html @@ -3,10 +3,10 @@ <div class="row container gnqa-answer" style="margin-bottom: 1em"> <p class="row lead"> <mark style="font-family: 'Linux Libertine','Georgia','Times','Source Serif Pro',serif;"><b><i>{{ query }}</i></b></mark><br/> - {{ answer }} + {{ answer|safe }} </p> <div class="rating row" data-doc-id="{{query}}"> - <button class="btn" id="upvote" data-toggle="tooltip" data-placement="top" title="Vote Up"><i class="fa fa-thumbs-up fa-sm fa-1x" aria-hidden="true"></i></button> + <button class="btn" id="upvote" data-toggle="tooltip" data-placement="top" title="Vote Up"><i class="fa fa-thumbs-up fa-sm fa-1x" aria-hidden="true"></i></button> <button class="btn" id="downvote" data-toggle="tooltip" data-placement="top" title="Vote Down"><i class="fa fa-thumbs-down fa-sm fa-1x" aria-hidden="true"></i></button> <sub id="rate" class="text-info"> </sub> @@ -32,7 +32,7 @@ </div> <div id="collapse{{reference.doc_id}}" class="panel-collapse collapse in" role="tabpanel" aria-labelledby="heading{{reference.doc_id}}"> <div class="panel-body"> - <p class="node-references">{{ reference.comboTxt }}</p> + <p class="node-references">{{ reference.comboTxt|safe }}</p> <div> {% if reference.pubmed %} <details open> @@ -60,7 +60,7 @@ </div> <div id="collapse{{reference.doc_id}}" class="panel-collapse collapse" role="tabpanel" aria-labelledby="heading{{reference.doc_id}}"> <div class="panel-body"> - <p class="node-references">{{reference.comboTxt}}</p> + <p class="node-references">{{ reference.comboTxt|safe }}</p> <div> {% if reference.pubmed %} <details > @@ -93,20 +93,27 @@ {% block js %} <script> + function updateRatingHandler(target, responseObj, args){ + let {status, response} = responseObj.xhr + if (status==200 && args == "upvote"){ + htmx.toggleClass(htmx.find('#upvote'), 'btn-success'); + htmx.removeClass(htmx.find("#downvote"), "btn-danger"); + } + else if(status == 200 && args == "downvote") { + htmx.toggleClass(htmx.find('#downvote'), 'btn-danger'); + htmx.removeClass(htmx.find("#upvote"), "btn-success"); + } + else { + alert(`Error occurred with status ${status} and Error ${response}` ) +}} var query = {{ query|tojson }}; var answer = {{ answer|tojson }} var {task_id} = {{ task_id|tojson }} - htmx.on("#upvote", "click", function(evt){ +htmx.on("#upvote", "click", function(evt){ vote_count = htmx.find(".btn-success") ? 0 : 1 - htmx.ajax("POST", `/gnqna/rating/${task_id}/${vote_count}`, {target: "#rate", swap:"innerHTML",values: {'query': query, 'answer': answer}}).then(()=>{ - htmx.toggleClass(htmx.find('#upvote'), 'btn-success'); - htmx.removeClass(htmx.find("#downvote"), "btn-danger"); -})}); + htmx.ajax("POST", `/gnqna/rating/${task_id}/${vote_count}`, {target: "#rate", handler: (target,obj)=> updateRatingHandler(target,obj,"upvote"), swap:"innerHTML",values: {'query': query, 'answer': answer}})}); htmx.on("#downvote", "click", function(evt){ vote_count = htmx.find(".btn-danger") ? 0 : -1 - htmx.ajax("POST", `/gnqna/rating/${task_id}/${vote_count}`, {target: "#rate", swap:"innerHTML",values: {'query': query, 'answer': answer}}).then(()=>{ - htmx.toggleClass(htmx.find('#downvote'), 'btn-danger'); - htmx.removeClass(htmx.find("#upvote"), "btn-success") - })}); + htmx.ajax("POST", `/gnqna/rating/${task_id}/${vote_count}`, {target: "#rate",handler: (target,obj)=> updateRatingHandler(target,obj,"downvote") , swap:"innerHTML",values: {'query': query, 'answer': answer}})}); </script> {% endblock %} diff --git a/gn2/wqflask/templates/gnqa_search_history.html b/gn2/wqflask/templates/gnqa_search_history.html index 2c07b8c0..976fd7fd 100644 --- a/gn2/wqflask/templates/gnqa_search_history.html +++ b/gn2/wqflask/templates/gnqa_search_history.html @@ -1,42 +1,52 @@ -<section class="container-fluid gnqa-copy"> +<section class="container-fluid gnqa-copy" id="search-hist"> <header class="row"> - <div class="panel panel default col-sm-6 col-sm-offset-3"> <div class="panel panel-default"> <div class="panel-heading"> <div> - <h4 class="text-primary">You search History </h4> + <h4 class="text-secondary" style="font-family: 'Linux Libertine','Georgia','Times','Source Serif Pro',serif;font-size:2.3rem">Your AI search History </h4> </div> </div> </div> </div> </header> <div class="container row"> - <div class="panel panel-default col-sm-6 col-sm-offset-3 "> - {% for record in prev_queries %} - <div class="panel-body"> - <div class="row"> - <input name="" type="checkbox" value="" class="col-sm-1"> + <div> + <div class="col-sm-6 col-sm-offset-3" style="margin-bottom:10px"> + <button type="button" class="btn btn-danger" id="delete-btn">Delete Selected </button> + </div> + <div > + <div class="panel panel-default col-sm-6 col-sm-offset-3 "> + <div> + <ul class="list-group list-group-flush" style="overflow-y:scroll"> + {% for item in prev_queries %} + <li class="row list-group-item"> + <input name="" type="checkbox" value="{{item['task_id']}}" class="col-sm-1" style="height: 20px; + width: 20px;"> <div class="col-sm-10"> - {% for id,val in record.items() %} <button - hx-get="/gnqna/hist/search/{{id}}" + hx-get="/gnqna/hist?query={{item['query']}}&search_term={{item['task_id']}}" hx-target="#swap" hx-swap="innerHTML" hx-trigger= "click" data-bs-toggle="tooltip" data-bs-placement="left" - title="/gnqna/hist/search?{{id}}" + title="/gnqna/hist?query={{item['query']}}&search_term={{item['task_id']}}" style="background:transparent;border:none;cursor:pointer" > - <b class="text-info">{{val}} </b> + <p class="text-info">{{item.get('query')}} </p> </button> - {% endfor %} - </div> - </div> - </div> - {% endfor %} + </div> + </li> + {% endfor %} + </ul> </div> </div> </div> - </section> +</section> +<script> + htmx.on("#delete-btn", "click", function(evt){ + htmx.ajax("DELETE","/gnqna/hist", {target: "#search-hist","swap" :"outerHTML", + values: Array.from(htmx.findAll("input[type=checkbox]:checked"), e => e.value)}) + }) +</script> diff --git a/gn2/wqflask/templates/gsearch_gene.html b/gn2/wqflask/templates/gsearch_gene.html index 50b48401..3432662d 100644 --- a/gn2/wqflask/templates/gsearch_gene.html +++ b/gn2/wqflask/templates/gsearch_gene.html @@ -258,8 +258,12 @@ "scroller": true {% endif %} } - - create_table(tableId, traitsJson, columnDefs, tableSettings); + + if (traitsJson.length > 0) { + create_table(tableId, traitsJson, columnDefs, tableSettings); + } else { + $("#" + tableId +" td").replaceWith("<td>No data</td>") + } }); diff --git a/gn2/wqflask/templates/oauth2/confirm-resource-role-unassign-privilege.html b/gn2/wqflask/templates/oauth2/confirm-resource-role-unassign-privilege.html new file mode 100644 index 00000000..988cf3b4 --- /dev/null +++ b/gn2/wqflask/templates/oauth2/confirm-resource-role-unassign-privilege.html @@ -0,0 +1,34 @@ +{%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"> + {{profile_nav(uipages, user_privileges)}} + {{flash_me()}} + + <form id="frm_confirm_resource_role_unassign_privilege" + method="POST" + action="{{url_for('oauth2.resource.unassign_privilege_from_resource_role', + resource_id=resource.resource_id, + role_id=role.role_id)}}"> + <p> + Are you sure you want to unassign the privilege to + '{{privilege.privilege_description}}' from the role '{{role.role_name}}' + on resource '{{resource.resource_name}}'?</p> + <input type="hidden" + name="privilege_id" + value="{{privilege.privilege_id}}" /> + + <input type="submit" + name="confirm" + value="Cancel" + class="btn btn-success" /> + + <input type="submit" + name="confirm" + value="Unassign" + class="btn btn-danger" /> + </form> +</div> +{%endblock%} diff --git a/gn2/wqflask/templates/oauth2/create-role.html b/gn2/wqflask/templates/oauth2/create-role.html index f2bff7b4..6cf0bb78 100644 --- a/gn2/wqflask/templates/oauth2/create-role.html +++ b/gn2/wqflask/templates/oauth2/create-role.html @@ -7,31 +7,43 @@ {{profile_nav("roles", user_privileges)}} <h3>Create Role</h3> - {{flash_me()}} + <p>Create a new role to act on resource "{{resource.resource_name}}"</p> - {%if group_privileges_error is defined%} - {{display_error("Group Privileges", group_privileges_error)}} + {%if resource_role_error is defined%} + {{display_error("Resource Role", resource_role_error)}} {%else%} - {%if "group:role:create-role" in user_privileges%} - <form method="POST" action="{{url_for('oauth2.role.create_role')}}"> - <legend>Create Group Role</legend> + {%if "resource:role:create-role" in (user_privileges|map(attribute="privilege_id")) %} + <form method="POST" action="{{url_for('oauth2.resource.create_resource_role', + resource_id=resource.resource_id)}}"> + <legend>create resource role</legend> + + {{flash_me()}} + <div class="form-group"> <label for="role_name" class="form-label">Name</label> - <input type="text" id="role_name" name="role_name" required="required" - class="form-control" - {%if prev_role_name is defined and prev_role_name is not none%} - value="{{prev_role_name}}" - {%endif%} /> + <div class="input-group"> + <span class="input-group-addon"> + {{resource.resource_name|replace(" ", "_")}}:: + </span> + <input type="text" id="role_name" name="role_name" required="required" + class="form-control" + {%if prev_role_name is defined and prev_role_name is not none%} + value="{{prev_role_name}}" + {%endif%} /> + </div> + <span class="form-text text-muted"> + The name of the role will have the resource's name appended. + </span> </div> <label class="form-label">Privileges</label> - {%for priv in group_privileges%} + {%for priv in user_privileges%} <div class="checkbox"> - <label for="chk:{{priv.privilege_id}}"> - <input type="checkbox" id="chk:{{priv.privilege_id}}" + <label for="chk-{{priv.privilege_id}}"> + <input type="checkbox" id="chk-{{priv.privilege_id}}" name="privileges[]" value={{priv.privilege_id}} /> <span style="text-transform: capitalize;"> {{priv.privilege_description}} - </span> ({{priv.privilege_id}}) + </span> </label> </div> {%endfor%} diff --git a/gn2/wqflask/templates/oauth2/data-list-mrna.html b/gn2/wqflask/templates/oauth2/data-list-mrna.html index 728e95d4..c5c1c27e 100644 --- a/gn2/wqflask/templates/oauth2/data-list-mrna.html +++ b/gn2/wqflask/templates/oauth2/data-list-mrna.html @@ -92,7 +92,7 @@ <div class="row"> <span id="search-messages" class="alert-danger" style="display:none"></span> <form id="frm-search" - action="{{search_uri}}" + action="{{url_for('oauth2.data.json_search_mrna')}}" method="POST"> <legend>Search: mRNA Assay</legend> <input type="hidden" value="{{species_name}}" name="species" diff --git a/gn2/wqflask/templates/oauth2/data-list-phenotype.html b/gn2/wqflask/templates/oauth2/data-list-phenotype.html index e5172c70..d355f3f9 100644 --- a/gn2/wqflask/templates/oauth2/data-list-phenotype.html +++ b/gn2/wqflask/templates/oauth2/data-list-phenotype.html @@ -113,7 +113,8 @@ <form id="frm-search-traits" action="#" method="POST" - data-gn-server-url="{{gn_server_url}}"> + data-search-endpoint="{{search_endpoint}}" + data-pheno-results-template="{{pheno_results_template}}"> {%if dataset_type == "mrna"%} <legend>mRNA: Search</legend> {%else%} diff --git a/gn2/wqflask/templates/oauth2/profile_nav.html b/gn2/wqflask/templates/oauth2/profile_nav.html index aa752905..c79bccbc 100644 --- a/gn2/wqflask/templates/oauth2/profile_nav.html +++ b/gn2/wqflask/templates/oauth2/profile_nav.html @@ -17,13 +17,6 @@ </li> <li role="presentation" - {%if calling_page == "roles"%} - class="active" - {%endif%}> - <a href="{{url_for('oauth2.role.user_roles')}}">Roles</a> - </li> - - <li role="presentation" {%if calling_page == "resources"%} class="active" {%endif%}> diff --git a/gn2/wqflask/templates/oauth2/view-group-role.html b/gn2/wqflask/templates/oauth2/view-group-role.html deleted file mode 100644 index 5da023bf..00000000 --- a/gn2/wqflask/templates/oauth2/view-group-role.html +++ /dev/null @@ -1,102 +0,0 @@ -{%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("roles", user_privileges)}} - <h3>View Group Role</h3> - - {{flash_me()}} - - <div class="container-fluid"> - <div class="row"> - <h3>Role Details</h3> - {%if group_role_error is defined%} - {{display_error("Group Role", group_role_error)}} - {%else%} - <table class="table"> - <caption>Details for '{{group_role.role.role_name}}' Role</caption> - <thead> - <tr> - <th>Privilege</th> - <th>Description</th> - <th>Action</th> - </tr> - </thead> - <tbody> - {%for privilege in group_role.role.privileges%} - <tr> - <td>{{privilege.privilege_id}}</td> - <td>{{privilege.privilege_description}}</td> - <td> - <form action="{{url_for( - 'oauth2.group.delete_privilege_from_role', - group_role_id=group_role.group_role_id)}}" - method="POST"> - <input type="hidden" name="privilege_id" - value="{{privilege.privilege_id}}" /> - <input type="submit" class="btn btn-danger" - value="Remove" - {%if not group_role.role.user_editable%} - disabled="disabled" - {%endif%} /> - </form> - </td> - </tr> - {%endfor%} - </tbody> - </table> - {%endif%} - </div> - - <div class="row"> - <h3>Other Privileges</h3> - <table class="table"> - <caption>Other Privileges not Assigned to this Role</caption> - <thead> - <tr> - <th>Privilege</th> - <th>Description</th> - <th>Action</th> - </tr> - </thead> - - <tbody> - {%for priv in group_privileges%} - <tr> - <td>{{priv.privilege_id}}</td> - <td>{{priv.privilege_description}}</td> - <td> - <form action="{{url_for( - 'oauth2.group.add_privilege_to_role', - group_role_id=group_role.group_role_id)}}" - method="POST"> - <input type="hidden" name="privilege_id" - value="{{priv.privilege_id}}" /> - <input type="submit" class="btn btn-warning" - value="Add to Role" - {%if not group_role.role.user_editable%} - disabled="disabled" - {%endif%} /> - </form> - </td> - </tr> - {%else%} - <tr> - <td colspan="3"> - <span class="glyphicon glyphicon-info-sign text-info"> - </span> - - <span class="text-info">All privileges assigned!</span> - </td> - </tr> - {%endfor%} - </tbody> - </table> - </div> - - </div> - -</div> -{%endblock%} diff --git a/gn2/wqflask/templates/oauth2/view-resource-role.html b/gn2/wqflask/templates/oauth2/view-resource-role.html new file mode 100644 index 00000000..4bd0ab45 --- /dev/null +++ b/gn2/wqflask/templates/oauth2/view-resource-role.html @@ -0,0 +1,149 @@ +{%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%} + +{%macro unassign_button(resource_id, role_id, privilege_id)%} +<form method="GET" + action="{{url_for('oauth2.resource.unassign_privilege_from_resource_role', + resource_id=resource_id, + role_id=role_id)}}" + id="frm_unlink_privilege_{{privilege_id}}"> + <input type="hidden" name="resource_id" value="{{resource_id}}" /> + <input type="hidden" name="role_id" value="{{role_id}}" /> + <input type="hidden" name="privilege_id" value="{{privilege_id}}" /> + <input type="submit" value="Unassign" class="btn btn-danger" /> +</form> +{%endmacro%} + +<div class="container"> + <div class="row"> + {{profile_nav(uipages, user_privileges)}} + {{flash_me()}} + {%if resource_error is defined%} + {{display_error("Resource", resource_error)}} + {%else%} + <h3>Role for Resource '{{resource.resource_name}}'</h3> + {%if role_error is defined%} + {{display_error("Role", role_error)}} + {%else%} + <table class="table"> + <caption>Role '{{role.role_name}}' for resource '{{resource.resource_name}}'</caption> + <thead> + <tr> + <th>Role Name</th> + <th>Privilege</th> + <th>Action</th> + </tr> + </thead> + + <tbody> + {%for priv in role.privileges%} + {%if loop.index0 == 0%} + <tr> + <td rowspan="{{role.privileges | length}}" + style="text-align: center;vertical-align: middle;"> + {{role.role_name}}</td> + <td>{{priv.privilege_description}}</td> + <td>{{unassign_button(resource.resource_id, role.role_id, priv.privilege_id)}}</td> + </tr> + {%else%} + <tr> + <td>{{priv.privilege_description}}</td> + <td>{{unassign_button(resource.resource_id, role.role_id, priv.privilege_id)}}</td> + </tr> + {%endif%} + {%else%} + <tr> + <td colspan="3"> + <p class="text-info"> + <span class="glyphicon glyphicon-info-sign text-info"></span> + + This role has no privileges. + </p> + </td> + </tr> + {%endfor%} + </tbody> + </table> + </div> + + <div class="row"> + <form id="frm_assign_privileges" method="POST" action="#"> + <input type="hidden" name="resource_id" value="{{resource_id}}" /> + <input type="hidden" name="role_id" value="{{role_id}}" /> + {%if unassigned_privileges | length == 0%} + <p class="text-info"> + <strong>{{title}}</strong>: + <span class="glyphicon glyphicon-info-sign text-info"></span> + + There are no more privileges left to assign. + </p> + {%else%} + <fieldset> + <legend>Select privileges to assign to this role</legend> + {%for priv in unassigned_privileges%} + <div class="checkbox"> + <label for="rdo_{{priv.privilege_id}}"> + <input type="checkbox" value="{{priv.privilege_id}}" /> + {{priv.privilege_description}} + </label> + </div> + {%endfor%} + </fieldset> + + <input type="submit" class="btn btn-primary" value="Assign" /> + {%endif%} + </form> + </div> + + {%if user_error is defined%} + {{display_error("Users", user_error)}} + {%endif%} + + {%if users is defined and users | length > 0%} + <div class="row"> + <h3>Users</h3> + + <table class="table"> + <caption> + Users assigned role '{{role.role_name}}' on resource + '{{resource.resource_name}}' + </caption> + + <thead> + <tr> + <th>Email</th> + <th>Name</th> + </tr> + </thead> + + <tbody> + {%for user in users%} + <tr> + <td>{{user.email}}</td> + <td>{{user.name}}</td> + </tr> + {%endfor%} + </tbody> + </table> + </div> + {%endif%} + + {%if users is defined and users | length == 0%} + <div class="row"> + <h3>Delete this role</h3> + <p class="text-danger"> + <strong>Delete Role</strong>: + <span class="glyphicon glyphicon-exclamation-sign text-danger"></span> + + This will delete this role, and you will no longer have access to it. + </p> + </div> + {%endif%} + {%endif%} + {%endif%} +</div> + +{%endblock%} diff --git a/gn2/wqflask/templates/oauth2/view-resource.html b/gn2/wqflask/templates/oauth2/view-resource.html index 275fcb24..0788e30c 100644 --- a/gn2/wqflask/templates/oauth2/view-resource.html +++ b/gn2/wqflask/templates/oauth2/view-resource.html @@ -2,6 +2,10 @@ {%from "oauth2/profile_nav.html" import profile_nav%} {%from "oauth2/display_error.html" import display_error%} {%block title%}View User{%endblock%} +{%block css%} +<link rel="stylesheet" href="/static/new/css/pills.css" /> +<link rel="stylesheet" href="/static/new/css/resource-roles.css" /> +{%endblock%} {%block content%} <div class="container" style="min-width: 1250px;"> {{profile_nav("resources", user_privileges)}} @@ -230,7 +234,27 @@ </div> <div class="row"> - <h3>User Roles</h3> + <h3>Available Resource Roles</h3> + <div class="resource_roles"> + {%for role in resource_roles%} + <a class="pill" + href="{{url_for('oauth2.resource.view_resource_role', + resource_id=resource.resource_id, + role_id=role.role_id)}}" + title="Role page for role named '{{role.role_name}}'"> + {{role.role_name}} + </a> + {%endfor%} + </div> + <hr /> + <a title="create a new role for this resource" + href="{{url_for('oauth2.resource.create_resource_role', + resource_id=resource.resource_id)}}" + class="btn btn-info">New Role</a> + </div> + + <div class="row"> + <h3>Users: Assigned Roles</h3> {%if users_n_roles_error is defined%} {{display_error("Users and Roles", users_n_roles_error)}} {%else%} @@ -254,14 +278,14 @@ <th>Role</th> <th>Action</th> </tr> - {%for grole in user_row.roles%} + {%for role 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}} + role_id=role.role_id)}}" + title="Details for '{{role.role_name}}' role"> + {{role.role_name}} </a> </td> <td> @@ -270,8 +294,8 @@ 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="hidden" name="role_id" + value="{{role.role_id}}"> <input type="submit" value="Unassign" class="btn btn-danger" @@ -301,8 +325,8 @@ <div class="row"> <h3>Assign</h3> - {%if group_roles_error is defined%} - {{display_error("Group Roles", group_roles_error)}} + {%if resource_roles_error is defined%} + {{display_error("Resource Roles", resource_roles_error)}} {%elif users_error is defined%} {{display_error("Users", users_error)}} {%else%} @@ -312,13 +336,13 @@ 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}} + <label for="role_id" class="form-label">Role</label> + <select class="form-control" name="role_id" + id="role_id" required="required"> + <option value="">Select role</option>> + {%for rrole in resource_roles%} + <option value="{{rrole.role_id}}"> + {{rrole.role_name}} </option> {%endfor%} </select> diff --git a/gn2/wqflask/templates/search-syntax.html b/gn2/wqflask/templates/search-syntax.html new file mode 100644 index 00000000..52538826 --- /dev/null +++ b/gn2/wqflask/templates/search-syntax.html @@ -0,0 +1,24 @@ +{% extends "base.html" %} + +{% block title %}Global Search Syntax{% endblock %} + +{% block css %} +<link rel="stylesheet" type="text/css" href="/static/new/css/markdown.css" /> +{% endblock %} + +{% block content %} + + <div class="github-btn-container"> + <div class="github-btn"> + <a href="https://github.com/genenetwork/gn-docs/blob/master/general/search/xapian_syntax.md"> + Edit Text + <img src="/static/images/edit.png"> + </a> + </div> +</div> +<div id="markdown" class="container"> + {{ rendered_markdown|safe }} + +</div> + +{% endblock %} \ No newline at end of file diff --git a/gn2/wqflask/templates/search_result_page.html b/gn2/wqflask/templates/search_result_page.html index 934b6a9d..fccda1ae 100644 --- a/gn2/wqflask/templates/search_result_page.html +++ b/gn2/wqflask/templates/search_result_page.html @@ -224,7 +224,8 @@ 'type': "natural", 'width': "{{ max_widths.symbol * 8 }}px", 'targets': 3, - 'data': "symbol" + 'data': "symbol", + 'defaultContent': "N/A" }, { 'title': "Description", @@ -237,9 +238,9 @@ description = data.description.slice(0, 200) + '...' } try { - return decodeURIComponent(escape(description)) + return decodeURIComponent(description) } catch(err){ - return escape(description) + return description } } }, @@ -248,14 +249,16 @@ 'type': "natural-minus-na", 'width': "130px", 'targets': 5, - 'data': "location" + 'data': "location", + 'defaultContent': "N/A" }, { 'title': "<div style='text-align: right;'>Mean</div>", 'type': "natural-minus-na", 'width': "40px", - 'data': "mean", 'targets': 6, + 'data': "mean", + 'defaultContent': "N/A", 'orderSequence': [ "desc", "asc"] }, { @@ -279,6 +282,7 @@ 'data': "additive", 'width': "65px", 'targets': 9, + 'defaultContent': "N/A", 'orderSequence': [ "desc", "asc"] }{% elif dataset.type == 'Publish' %}, { @@ -294,6 +298,7 @@ { 'title': "Description", 'type': "natural", + 'width': "500px", 'data': null, 'targets': 3, 'render': function(data) { @@ -302,9 +307,9 @@ description = data.description.slice(0, 200) + '...' } try { - return decodeURIComponent(escape(description)) + return decodeURIComponent(description) } catch(err){ - return escape(description) + return description } } }, @@ -312,8 +317,9 @@ 'title': "<div style='text-align: right;'>Mean</div>", 'type': "natural-minus-na", 'width': "60px", - 'data': "mean", 'targets': 4, + 'data': "mean", + 'defaultContent': "N/A", 'orderSequence': [ "desc", "asc"] }, { diff --git a/gn2/wqflask/templates/show_trait_transform_and_filter.html b/gn2/wqflask/templates/show_trait_transform_and_filter.html index e61e1248..8a7cd8a5 100644 --- a/gn2/wqflask/templates/show_trait_transform_and_filter.html +++ b/gn2/wqflask/templates/show_trait_transform_and_filter.html @@ -5,7 +5,7 @@ needed. </p> <div id="blockMenuSpan" class="input-append block-div"> - <label for="remove_samples_field">Block samples by index:</label> + <label for="remove_samples_field">Filter samples by index:</label> <input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12"> <select id="block_group" size="1"> <option value="primary"> @@ -23,7 +23,7 @@ </div> {% if categorical_attr_exists == "true" %} <div class="input-append block-div-2"> - <label for="exclude_column">Block samples by group:</label> + <label for="exclude_column">Filter samples by group:</label> <select id="exclude_column" size=1> {% for attribute in sample_groups[0].attributes %} {% if sample_groups[0].attributes[attribute].distinct_values|length <= 500 and sample_groups[0].attributes[attribute].distinct_values|length > 1 %} diff --git a/gn2/wqflask/templates/tool_buttons.html b/gn2/wqflask/templates/tool_buttons.html index c6d1476c..3e716d70 100644 --- a/gn2/wqflask/templates/tool_buttons.html +++ b/gn2/wqflask/templates/tool_buttons.html @@ -18,6 +18,10 @@ BNW </button> +<button id="send_to_genecup" class="btn btn-primary submit_special" data-url="/genecup" > + GeneCup +</button> + <button id="wgcna_setup" class="btn btn-primary submit_special" data-url="/wgcna_setup" title="WGCNA Analysis" > WGCNA </button> diff --git a/gn2/wqflask/templates/tutorials.html b/gn2/wqflask/templates/tutorials.html index 870dba1a..6281291f 100644 --- a/gn2/wqflask/templates/tutorials.html +++ b/gn2/wqflask/templates/tutorials.html @@ -221,11 +221,12 @@ $('#myTable3').dataTable( { </tr> </thead> <tbody> - <tr><td><a href="https://www.biorxiv.org/content/10.1101/2020.12.23.424047v1">GeneNetwork: a continuously updated tool for systems genetics analyses</a></td></tr> - <tr><td><a href="https://doi.org/10.3390/genes13040614">New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork</a></td> - <tr><td><a href="https://www.opar.io/pdf/Rat_HRDP_Brain_Proteomics_Wang_WIlliams_08Oct2021.pdf">A Primer on Brain Proteomics and protein-QTL Analysis for Substance Use Disorders</a></td></tr> - - </tbody> + <tr><td><a href="https://www.opar.io/pdf/Ashbrook_ExperimentalPrecisionMedicineMouseModels_2023.pdf">Experimental precision medicine: Mouse models in which to test precision medicine</a></td> + <tr><td><a href="https://www.opar.io/pdf/Williams_ResourcesForSystemsGenetics_2017.pdf">Systems Genetics. Methods and Protocols</a></td></tr> + <tr><td><a href="https://www.biorxiv.org/content/10.1101/2020.12.23.424047v1">GeneNetwork: a continuously updated tool for systems genetics analyses</a></td></tr> + <tr><td><a href="https://doi.org/10.3390/genes13040614">New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork</a></td> + <tr><td><a href="https://www.opar.io/pdf/Rat_HRDP_Brain_Proteomics_Wang_WIlliams_08Oct2021.pdf">A Primer on Brain Proteomics and protein-QTL Analysis for Substance Use Disorders</a></td></tr> + </tbody> </table> <script> $('#myTable4').dataTable( { |