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Test for script-managed trees, show warning msg #1252

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Test for script-managed trees, show warning msg #1252

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7730fa2
Test for script-managed trees, show warning msg
jimallman Sep 24, 2020
34cd2be
Ignore missing `node` list in script-managed trees.
jimallman Oct 4, 2020
0cba699
Merge branch 'master' into script-managed-trees
jimallman Oct 4, 2020
7700bdb
Shared test for script-managed trees.
jimallman Oct 4, 2020
7a486f2
More tools to skip script-managed trees
jimallman Oct 4, 2020
caeabc9
Block analysis tools if there are no eligible trees.
jimallman Oct 7, 2020
c3f9188
typo
jimallman Oct 7, 2020
570e568
style for no-eligible-trees message
jimallman Oct 7, 2020
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38 changes: 37 additions & 1 deletion curator/static/js/study-editor.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -752,12 +752,16 @@ function loadSelectedStudy() {
},
'tree': {
highestOrdinalNumber: null,
gatherAll: function(nexml) {
gatherAll: function(nexml, options) {
// return an array of all matching elements
if (!options) options = {INCLUDE_SCRIPT_MANAGED_TREES: true};
var allTrees = [];
var allTreesCollections = viewModel.elementTypes.trees.gatherAll(nexml);
$.each(allTreesCollections, function(i, treesCollection) {
$.each(treesCollection.tree, function(i, tree) {
if (!options.INCLUDE_SCRIPT_MANAGED_TREES) {
if (isScriptManagedTree(tree)) return true;
}
allTrees.push( tree );
});
});
Expand Down Expand Up @@ -1167,6 +1171,10 @@ function loadSelectedStudy() {
if ($.isArray(chosenTrees)) {
// it's a list of zero or more trees
$.each( chosenTrees, function(i, tree) {
if (isScriptManagedTree(tree)) {
// ignore "empty" (script-managed) trees
return;
}
// check this tree's nodes for this OTU id
$.each( tree.node, function( i, node ) {
if (node['@otu']) {
Expand Down Expand Up @@ -3033,6 +3041,10 @@ function getRootedStatusForTree( tree ) {
// Let's check for some/all/none with separate functions.
function anyBranchLengthsFoundInTree( tree ) {
var foundBranchWithLength = false;
if (isScriptManagedTree(tree)) {
// ignore "empty" (script-managed) trees
return false;
}
$.each(tree.edge, function(i, edge) {
if ('@length' in edge) {
foundBranchWithLength = true;
Expand All @@ -3043,6 +3055,10 @@ function anyBranchLengthsFoundInTree( tree ) {
}
function allBranchLengthsFoundInTree( tree ) {
var foundBranchWithoutLength = false;
if (isScriptManagedTree(tree)) {
// ignore "empty" (script-managed) trees
return false;
}
$.each(tree.edge, function(i, edge) {
if (!('@length' in edge)) {
foundBranchWithoutLength = true;
Expand Down Expand Up @@ -8974,6 +8990,11 @@ function getAmbiguousLabelsInTree(tree) {
return labelData;
}

if (isScriptManagedTree(tree)) {
// ignore "empty" (script-managed) trees
return labelData;
}

$.each( tree.node, function(i, node) {
if (node['^ot:isLeaf'] === true) {
/* We sometimes save a misspelled taxon name as `node[@label]` so
Expand All @@ -8986,6 +9007,7 @@ function getAmbiguousLabelsInTree(tree) {
labelData[ nodeID ] = node['@label'];
}
});

return labelData;
}
function showAmbiguousLabelsInTreeViewer(tree) {
Expand Down Expand Up @@ -9139,6 +9161,20 @@ function currentStudyVersionContributedToLatestSynthesis() {
return (viewModel.startingCommitSHA === latestSynthesisSHA);
}

function studyContainsScriptManagedTrees() {
// check for signature for this in Nexson (to modify UI, hide/block some features?)
var allTrees = viewModel.elementTypes.tree.gatherAll(viewModel.nexml);
var bigTrees = ko.utils.arrayFilter(
allTrees,
isScriptManagedTree
);
return (bigTrees.length > 0);
}
function isScriptManagedTree(tree) {
// if this property is found (even if it's an empty object), assume it's a huge script-managed tree
return (tree["^ot:external_data"] !== undefined);
}

function getNormalizedStudyPublicationURL() {
// just the bare URL, or '' if not found
var url = $.trim(viewModel.nexml['^ot:studyPublication']['@href']);
Expand Down
31 changes: 27 additions & 4 deletions curator/views/study/edit.html
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -374,6 +374,20 @@ <h4 class="pull-left" style="margin: 5px 1em 0 0">Trees in this study</h4>
</div>
</div>

<!-- ko if: studyContainsScriptManagedTrees() -->
<div class="empty-list-prompt">
This study contains
<a target="_blank"
href="https://github.com/OpenTreeOfLife/script-managed-trees/blob/master/README.md">script-managed trees</a>
that are too large to store in phylesystem.
These cannot be managed in the curation web app, nor can
this study's OTUs, but you can edit the study's metadata
and see its revision history.
</div>

<!-- /ko -->

<!-- ko if: ! studyContainsScriptManagedTrees() -->
<div class="empty-list-prompt" data-bind="visible: viewModel.filteredTrees().pagedItems().length === 0">
No matching trees found! Add new trees or clear the
filter above to see trees in this study.
Expand Down Expand Up @@ -525,6 +539,7 @@ <h4 class="pull-left" style="margin: 5px 1em 0 0">Trees in this study</h4>
</li>
</ul>
</div>
<!-- /ko -->

</div>

Expand Down Expand Up @@ -1612,11 +1627,17 @@ <h4 style="margin-top: 0;">Adding new taxa</h4>
<div class="tab-pane" id="Analyses">
<div class="span8"><!-- main column... -->

<!-- ko if: viewModel.elementTypes.tree.gatherAll(viewModel.nexml, {INCLUDE_SCRIPT_MANAGED_TREES: false}).length === 0 -->
<div class="empty-list-prompt">
<em>This study has no eligible trees.</em>
</div>
<!-- /ko -->
<!-- ko if: viewModel.elementTypes.tree.gatherAll(viewModel.nexml, {INCLUDE_SCRIPT_MANAGED_TREES: false}).length > 0 -->
<form class="form-inline">
<label>Analyze tree</label>
<select id="tree-select"
onchange="(this); return false;"
data-bind="options: viewModel.elementTypes.tree.gatherAll(viewModel.nexml),
data-bind="options: viewModel.elementTypes.tree.gatherAll(viewModel.nexml, {INCLUDE_SCRIPT_MANAGED_TREES: false}),
optionsValue: '@id',
optionsText: '@label',
optionsCaption: 'Choose a tree from this study...',
Expand All @@ -1632,9 +1653,11 @@ <h4 style="margin-top: 0;">Adding new taxa</h4>
<button class="btn btn-info" data-bind="click: fetchAndShowTreeConflictSummary">GO!</button>
</form>

<div id="analysis-results">
<em>Analysis results will appear here...</em>
</div>
<div id="analysis-results">
<em>Analysis results will appear here...</em>
</div>

<!-- /ko -->

</div><!-- end of main column... -->
<div class="span4"><!-- right col -->
Expand Down