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Remove sample tracking manual external service transfer due to security concerns

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This commit is contained in:
Nate Coraor
2016-02-24 11:18:24 -05:00
parent 7c4b8ff747
commit ffcd4fe192
6 changed files with 3 additions and 520 deletions
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templates/admin/requests/select_datasets_to_transfer.mako
-148
View File
@@ -1,148 +0,0 @@
<%inherit file="/base.mako"/>
<%namespace file="/message.mako" import="render_msg" />
<%namespace file="/requests/common/common.mako" import="render_sample_datasets" />
<%namespace file="/requests/common/common.mako" import="common_javascripts" />
<%def name="javascripts()">
${parent.javascripts()}
${common_javascripts()}
</%def>
${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )}
${h.css( "dynatree_skin/ui.dynatree" )}
<script type="text/javascript">
$(function(){
$("#tree").ajaxComplete(function(event, XMLHttpRequest, ajaxOptions) {
_log("debug", "ajaxComplete: %o", this); // dom element listening
});
// --- Initialize sample trees
$("#tree").dynatree({
title: "${scp_configs['data_location']}",
minExpandLevel: 1, // 1: root node is not collapsible
persist: false,
checkbox: true,
selectMode: 3,
onPostInit: function(isReloading, isError) {
//alert("reloading: "+isReloading+", error:"+isError);
logMsg("onPostInit(%o, %o) - %o", isReloading, isError, this);
// Re-fire onActivate, so the text is updated
this.reactivate();
},
fx: { height: "toggle", duration: 200 },
// initAjax is hard to fake, so we pass the children as object array:
initAjax: {url: "${h.url_for( controller='requests_admin', action='open_folder' )}",
dataType: "json",
data: { request_id: "${trans.security.encode_id( request.id )}", external_service_id: "${trans.security.encode_id( external_service.id )}", key: "${scp_configs['data_location']}" },
},
onLazyRead: function(dtnode){
dtnode.appendAjax({
url: "${h.url_for( controller='requests_admin', action='open_folder' )}",
dataType: "json",
data: { request_id: "${trans.security.encode_id( request.id )}", external_service_id: "${trans.security.encode_id( external_service.id )}", key: dtnode.data.key },
});
},
onSelect: function(select, dtnode) {
// Display list of selected nodes
var selNodes = dtnode.tree.getSelectedNodes();
// convert to title/key array
var selKeys = $.map(selNodes, function(node){
return node.data.key;
});
document.select_datasets_to_transfer.selected_datasets_to_transfer.value = selKeys.join(",")
},
onActivate: function(dtnode) {
var cell = $("#file_details");
var selected_value;
if (dtnode.data.key == 'root') {
selected_value = "${scp_configs['data_location']}/";
} else {
selected_value = dtnode.data.key;
};
if (selected_value.charAt(selected_value.length-1) != '/') {
// Make ajax call
$.ajax( {
type: "POST",
url: "${h.url_for( controller='requests_admin', action='get_file_details' )}",
dataType: "json",
data: { request_id: "${trans.security.encode_id(request.id)}", external_service_id: "${trans.security.encode_id(external_service.id)}", folder_path: selected_value },
success : function ( data ) {
cell.html( '<label>'+data+'</label>' )
}
});
} else {
cell.html( '' );
};
},
});
});
</script>
<%
is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
can_transfer_datasets = is_admin and sample.untransferred_dataset_files and sample.library and sample.folder
%>
<br/><br/>
<ul class="manage-table-actions">
<li><a class="action-button" href="${h.url_for( controller='external_service', action='view_external_service', id=trans.security.encode_id( external_service.id ) )}">External service configuration</a></li>
%if can_transfer_datasets:
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', cntrller=cntrller, sample_id=trans.security.encode_id( sample.id ) )}">Transfer datasets</a></li>
%endif
<li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( request.id ) )}">Browse this request</a></li>
</ul>
%if not sample:
<br/>
<font color="red"><b><i>Select a sample before selecting datasets to transfer</i></b></font>
<br/>
%endif
%if request.samples_without_library_destinations:
<p>
<font color="red"><b><i>Select a target data library and folder for a sample before selecting its datasets to transfer from the external service</i></b></font>
</p>
%endif
%if message:
${render_msg( message, status )}
%endif
<div class="toolForm">
<div class="toolFormTitle">Select datasets to transfer from data directory configured for the external service</div>
<form name="select_datasets_to_transfer" id="select_datasets_to_transfer" action="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), request_id=trans.security.encode_id( request.id ))}" method="post" >
<div class="form-row">
<label>Sample:</label>
${sample_id_select_field.get_html()}
<div class="toolParamHelp" style="clear: both;">
Select the sample that was sequenced to produce the datasets you want to transfer.
</div>
</div>
<div class="form-row" >
<label>Select datasets from source data location defined in the external service configuration:</label>
<div id="tree" >
Loading...
</div>
<input id="selected_datasets_to_transfer" name="selected_datasets_to_transfer" type="hidden" size=40"/>
<div class="toolParamHelp" style="clear: both;">
<ul>
<li>Click the <b>external service configuration</b> button and change the <b>Data directory</b> setting to redefine the source data location.</li>
<li>Select a folder to select all of the individual files within that folder.</li>
<li>Click the <b>Select datasets</b> button when desired dataset check boxes are checked.</li>
</ul>
</div>
</div>
<div class="form-row">
<div id="file_details" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div>
</div>
<div class="form-row">
<input type="submit" name="select_datasets_to_transfer_button" value="Select datasets"/>
</div>
</form>
</div>
%if sample and sample.datasets:
<% title = 'All selected datasets for "%s"' % sample.name %>
<p/>
${render_sample_datasets( 'requests_admin', sample, sample.datasets, title )}
%endif
templates/webapps/galaxy/requests/common/common.mako
+1 -11
View File
@@ -333,7 +333,6 @@
can_add_samples = is_unsubmitted
can_delete_samples = not adding_new_samples and request.samples and ( ( is_admin and not is_complete ) or is_unsubmitted )
can_edit_samples = request.samples and ( is_admin or not is_complete )
can_select_datasets = is_admin and displayable_sample_widgets and ( is_submitted or is_complete )
can_transfer_datasets = is_admin and request.samples and not request.is_rejected
display_checkboxes = not adding_new_samples and ( is_complete or is_rejected or is_submitted )
display_bar_code = request.samples and ( is_complete or is_rejected or is_submitted )
@@ -407,7 +406,7 @@
%elif sample:
<tr>
<td>
%if sample.state and ( can_select_datasets or can_transfer_datasets ):
%if sample.state and can_transfer_datasets:
## A sample will have a state only after the request has been submitted.
<%
encoded_id = trans.security.encode_id( sample.id )
@@ -419,14 +418,6 @@
<a class="view-info" href="${h.url_for( controller='requests_common', action='view_sample', cntrller=cntrller, id=trans.security.encode_id( sample.id ) )}">${sample.name | h}</a>
</div>
<div popupmenu="sample-${sample.id}-popup">
%if can_select_datasets:
%for external_service in sample.request.type.get_external_services_for_manual_data_transfer( trans ):
<%
menu_item_label = "Select datasets to transfer using %s" % external_service.name
%>
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', external_service_id=trans.security.encode_id( external_service.id ), request_id=trans.security.encode_id( request.id ), sample_id=trans.security.encode_id( sample.id ) )}">${menu_item_label}</a></li>
%endfor
%endif
%if sample.datasets and len( sample.datasets ) > len( transferred_dataset_files ) and sample.library and sample.folder:
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ) )}">Manage selected datasets</a></li>
%elif sample.datasets and len( sample.datasets ) == len( transferred_dataset_files ):
@@ -665,7 +656,6 @@
is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
is_complete = sample.request.is_complete
is_submitted = sample.request.is_submitted
can_select_datasets = is_admin and ( is_complete or is_submitted )
can_transfer_datasets = is_admin and sample.untransferred_dataset_files
%>
## The transfer status should update only when the request has been submitted or complete
templates/webapps/galaxy/requests/common/view_request_history.mako
-1
View File
@@ -11,7 +11,6 @@
can_add_samples = is_unsubmitted
can_edit_request = ( is_admin and not is_complete ) or is_unsubmitted
can_reject = is_admin and is_submitted
can_select_datasets = is_admin and ( is_complete or is_submitted )
can_submit_request = request.samples and is_unsubmitted
%>
templates/webapps/galaxy/requests/common/view_sample_datasets.mako
-4
View File
@@ -12,7 +12,6 @@
is_admin = cntrller == 'requests_admin' and trans.user_is_admin()
is_complete = sample.request.is_complete
is_submitted = sample.request.is_submitted
can_select_datasets = is_admin and ( is_complete or is_submitted )
can_transfer_datasets = is_admin and sample.untransferred_dataset_files and sample.library and sample.folder
%>
@@ -24,9 +23,6 @@
%endif
<li><a class="action-button" id="sample-${sample.id}-popup" class="menubutton">Dataset Actions</a></li>
<div popupmenu="sample-${sample.id}-popup">
%if can_select_datasets:
<li><a class="action-button" href="${h.url_for( controller='requests_admin', action='select_datasets_to_transfer', cntrller=cntrller, external_service_id=trans.security.encode_id( external_service.id ), request_id=trans.security.encode_id( sample.request.id ), sample_id=trans.security.encode_id( sample.id ) )}">Select more datasets</a></li>
%endif
<li><a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=trans.security.encode_id( sample.library.id ) )}">View target Data Library</a></li>
<li><a class="action-button" href="${h.url_for( controller='requests_common', action='view_request', cntrller=cntrller, id=trans.security.encode_id( sample.request.id ) )}">Browse this request</a></li>
</div>