diff --git a/core/pom.xml b/core/pom.xml
index 4b5ed6fb..29a1c06f 100644
--- a/core/pom.xml
+++ b/core/pom.xml
@@ -23,7 +23,7 @@
mysql
mysql-connector-java
- 8.0.12
+ 8.0.16
org.hibernate
@@ -112,7 +112,7 @@
mysql
mysql-connector-java
- 8.0.12
+ 8.0.16
diff --git a/web/src/main/webapp/js/ctd2.js b/web/src/main/webapp/js/ctd2.js
index 222eec6e..b31aff51 100644
--- a/web/src/main/webapp/js/ctd2.js
+++ b/web/src/main/webapp/js/ctd2.js
@@ -509,11 +509,11 @@
$.fancybox.open(
this.template(this.model), {
- 'autoDimensions': false,
- 'centerOnScroll': true,
- 'transitionIn': 'none',
- 'transitionOut': 'none'
- }
+ 'autoDimensions': false,
+ 'centerOnScroll': true,
+ 'transitionIn': 'none',
+ 'transitionOut': 'none'
+ }
);
return this;
@@ -536,11 +536,11 @@
$.fancybox.open(
this.template({}), {
- 'autoDimensions': false,
- 'centerOnScroll': true,
- 'transitionIn': 'none',
- 'transitionOut': 'none'
- }
+ 'autoDimensions': false,
+ 'centerOnScroll': true,
+ 'transitionIn': 'none',
+ 'transitionOut': 'none'
+ }
);
return this;
@@ -754,119 +754,119 @@
/// TODO: encode these into the DB instead
const ecoMappings = [{
- "evidence": "file",
- "role": "background",
- "eco_term": "inference from background scientific knowledge",
- "eco_id": "ECO:0000001"
- },
- {
- "evidence": "file",
- "role": "computed",
- "eco_term": "computational combinatorial evidence",
- "eco_id": "ECO:0000053"
- },
- {
- "evidence": "file",
- "role": "literature",
- "eco_term": "traceable author statement",
- "eco_id": "ECO:0000033"
- },
- {
- "evidence": "file",
- "role": "measured",
- "eco_term": "direct assay evidence",
- "eco_id": "ECO:0000002"
- },
- {
- "evidence": "file",
- "role": "observed",
- "eco_term": "experimental phenotypic evidence",
- "eco_id": "ECO:0000059"
- },
- {
- "evidence": "file",
- "role": "written",
- "eco_term": "author statement",
- "eco_id": "ECO:0000204"
- },
- {
- "evidence": "label",
- "role": "background",
- "eco_term": "inference from background scientific knowledge",
- "eco_id": "ECO:0000001"
- },
- {
- "evidence": "label",
- "role": "computed",
- "eco_term": "computational combinatorial evidence",
- "eco_id": "ECO:0000053"
- },
- {
- "evidence": "label",
- "role": "observed",
- "eco_term": "ad-hoc qualitative phenotype observation evidence",
- "eco_id": "ECO:0005673"
- },
- {
- "evidence": "label",
- "role": "species",
- "eco_term": "biological system reconstruction evidence by experimental evidence from single species",
- "eco_id": "ECO:0005553"
- },
- {
- "evidence": "numeric",
- "role": "background",
- "eco_term": "inference from background scientific knowledge",
- "eco_id": "ECO:0000001"
- },
- {
- "evidence": "numeric",
- "role": "computed",
- "eco_term": "computational combinatorial evidence",
- "eco_id": "ECO:0000053"
- },
- {
- "evidence": "numeric",
- "role": "measured",
- "eco_term": "experimental phenotypic evidence",
- "eco_id": "ECO:0000059"
- },
- {
- "evidence": "numeric",
- "role": "observed",
- "eco_term": "ad-hoc quantitative phenotype observation evidence",
- "eco_id": "ECO:0005675"
- },
- {
- "evidence": "url",
- "role": "computed",
- "eco_term": "computational combinatorial evidence",
- "eco_id": "ECO:0000053"
- },
- {
- "evidence": "url",
- "role": "link",
- "eco_term": "combinatorial evidence",
- "eco_id": "ECO:0000212"
- },
- {
- "evidence": "url",
- "role": "measured",
- "eco_term": "experimental phenotypic evidence",
- "eco_id": "ECO:0000059"
- },
- {
- "evidence": "url",
- "role": "reference",
- "eco_term": "traceable author statement",
- "eco_id": "ECO:0000033"
- },
- {
- "evidence": "url",
- "role": "resource",
- "eco_term": "imported information",
- "eco_id": "ECO:0000311"
- }
+ "evidence": "file",
+ "role": "background",
+ "eco_term": "inference from background scientific knowledge",
+ "eco_id": "ECO:0000001"
+ },
+ {
+ "evidence": "file",
+ "role": "computed",
+ "eco_term": "computational combinatorial evidence",
+ "eco_id": "ECO:0000053"
+ },
+ {
+ "evidence": "file",
+ "role": "literature",
+ "eco_term": "traceable author statement",
+ "eco_id": "ECO:0000033"
+ },
+ {
+ "evidence": "file",
+ "role": "measured",
+ "eco_term": "direct assay evidence",
+ "eco_id": "ECO:0000002"
+ },
+ {
+ "evidence": "file",
+ "role": "observed",
+ "eco_term": "experimental phenotypic evidence",
+ "eco_id": "ECO:0000059"
+ },
+ {
+ "evidence": "file",
+ "role": "written",
+ "eco_term": "author statement",
+ "eco_id": "ECO:0000204"
+ },
+ {
+ "evidence": "label",
+ "role": "background",
+ "eco_term": "inference from background scientific knowledge",
+ "eco_id": "ECO:0000001"
+ },
+ {
+ "evidence": "label",
+ "role": "computed",
+ "eco_term": "computational combinatorial evidence",
+ "eco_id": "ECO:0000053"
+ },
+ {
+ "evidence": "label",
+ "role": "observed",
+ "eco_term": "ad-hoc qualitative phenotype observation evidence",
+ "eco_id": "ECO:0005673"
+ },
+ {
+ "evidence": "label",
+ "role": "species",
+ "eco_term": "biological system reconstruction evidence by experimental evidence from single species",
+ "eco_id": "ECO:0005553"
+ },
+ {
+ "evidence": "numeric",
+ "role": "background",
+ "eco_term": "inference from background scientific knowledge",
+ "eco_id": "ECO:0000001"
+ },
+ {
+ "evidence": "numeric",
+ "role": "computed",
+ "eco_term": "computational combinatorial evidence",
+ "eco_id": "ECO:0000053"
+ },
+ {
+ "evidence": "numeric",
+ "role": "measured",
+ "eco_term": "experimental phenotypic evidence",
+ "eco_id": "ECO:0000059"
+ },
+ {
+ "evidence": "numeric",
+ "role": "observed",
+ "eco_term": "ad-hoc quantitative phenotype observation evidence",
+ "eco_id": "ECO:0005675"
+ },
+ {
+ "evidence": "url",
+ "role": "computed",
+ "eco_term": "computational combinatorial evidence",
+ "eco_id": "ECO:0000053"
+ },
+ {
+ "evidence": "url",
+ "role": "link",
+ "eco_term": "combinatorial evidence",
+ "eco_id": "ECO:0000212"
+ },
+ {
+ "evidence": "url",
+ "role": "measured",
+ "eco_term": "experimental phenotypic evidence",
+ "eco_id": "ECO:0000059"
+ },
+ {
+ "evidence": "url",
+ "role": "reference",
+ "eco_term": "traceable author statement",
+ "eco_id": "ECO:0000033"
+ },
+ {
+ "evidence": "url",
+ "role": "resource",
+ "eco_term": "imported information",
+ "eco_id": "ECO:0000311"
+ }
];
const class2imageData = {
@@ -1099,11 +1099,11 @@
_.template($("#cytoscape-tmpl").html())({
description: sifDesc
}), {
- touch: false,
- 'autoDimensions': false,
- 'transitionIn': 'none',
- 'transitionOut': 'none'
- }
+ touch: false,
+ 'autoDimensions': false,
+ 'transitionIn': 'none',
+ 'transitionOut': 'none'
+ }
);
// load cytoscape
@@ -1257,14 +1257,17 @@
result.eco =
_.chain(ecoMappings)
- .filter(function (m) {
- return m.evidence == mEvidence && m.role == result.observedEvidenceRole.evidenceRole.displayName;
- })
- .first()
- .value();
+ .filter(function (m) {
+ return m.evidence == mEvidence && m.role == result.observedEvidenceRole.evidenceRole.displayName;
+ })
+ .first()
+ .value();
if (result.eco == undefined) {
result.eco = wildcard_evidence_codes[result.observedEvidenceRole.evidenceRole.displayName];
}
+ if (result.eco == undefined) {
+ result.eco = { eco_term: '', eco_id: '' };
+ }
this.template = _.template($(templateId).html());
$(this.el).append(this.template(result));
@@ -1312,8 +1315,8 @@
$.ajax("count/submission/?filterBy=" + aCenter.id).done(function (count) {
const cntContent = _.template(
$("#count-submission-tmpl").html())({
- count: count
- });
+ count: count
+ });
const countCellId = "#submission-count-" + aCenter.id;
$(countCellId).html(cntContent);
@@ -1340,19 +1343,19 @@
"iDisplayLength": 25,
"orderFixed": [4, "desc"],
columnDefs: [{
- targets: [0, 2],
- orderable: false,
- }, {
- targets: 3,
- orderDataType: "submission-count",
- type: "numeric"
- },
- {
- "visible": false,
- "sortable": false,
- "searchable": false,
- "targets": 4
- },
+ targets: [0, 2],
+ orderable: false,
+ }, {
+ targets: 3,
+ orderDataType: "submission-count",
+ type: "numeric"
+ },
+ {
+ "visible": false,
+ "sortable": false,
+ "searchable": false,
+ "targets": 4
+ },
],
}).fnSort([
[1, 'asc']
@@ -1391,15 +1394,15 @@
});
$('#stories-list').dataTable({
columns: [{
- type: "string"
- },
+ type: "string"
+ },
null,
- {
- orderDataType: "text-date-order"
- },
- {
- "orderable": false
- },
+ {
+ orderDataType: "text-date-order"
+ },
+ {
+ "orderable": false
+ },
],
order: [
[2, 'desc']
@@ -1447,18 +1450,18 @@
'data': table_data,
"deferRender": true,
"columns": [{
- class: "wrapok"
- },
+ class: "wrapok"
+ },
null,
- {
- "type": "observation-count"
- },
- {
- "type": "observation-count"
- },
- {
- "type": "observation-count"
- }
+ {
+ "type": "observation-count"
+ },
+ {
+ "type": "observation-count"
+ },
+ {
+ "type": "observation-count"
+ }
],
'buttons': [{
extend: 'excelHtml5',
@@ -1584,8 +1587,8 @@
'dom': '',
"sPaginationType": "bootstrap",
"columns": [{
- "orderDataType": "dashboard-date"
- },
+ "orderDataType": "dashboard-date"
+ },
null,
null,
null
@@ -2313,8 +2316,8 @@
"#count-observations-tmpl";
submission.details = _.template(
$(tmplName).html())({
- count: count
- });
+ count: count
+ });
});
centerSubmissionRowView.render();
@@ -2336,8 +2339,8 @@
"drawCallback": function (settings) {
const api = this.api();
api.column(1, {
- page: 'all'
- })
+ page: 'all'
+ })
.data()
.each(function (group, i) {
const project_url = group.toLowerCase().replace(/[^a-zA-Z0-9]/g, "-");
@@ -2349,8 +2352,8 @@
}).nodes();
let last = null;
api.column(1, {
- page: 'current'
- })
+ page: 'current'
+ })
.data()
.each(function (group, i) {
if (last != group) {
@@ -2735,8 +2738,8 @@
// some of the elements will be hidden in the pagination. Use magic-scoping!
const cntContent = _.template(
$("#count-observations-tmpl").html())({
- count: model.observationCount
- });
+ count: model.observationCount
+ });
$("#subject-observation-count-" + result.id).html(cntContent);
return this;
@@ -2874,8 +2877,8 @@
"#count-observations-tmpl";
const cntContent = _.template(
$(tmplName).html())({
- count: submission.observationCount
- });
+ count: submission.observationCount
+ });
$("#search-observation-count-" + submission.dashboardEntity.id).html(cntContent);
const centerId = submission.dashboardEntity.observationTemplate.submissionCenter.id;
centerCounter.add(centerId);
@@ -3026,11 +3029,11 @@
_.template($("#mra-cytoscape-tmpl").html())({
description: mraDesc
}), {
- touch: false,
- 'autoDimensions': false,
- 'transitionIn': 'none',
- 'transitionOut': 'none'
- }
+ touch: false,
+ 'autoDimensions': false,
+ 'transitionIn': 'none',
+ 'transitionOut': 'none'
+ }
);
window.cy = this;
@@ -3396,7 +3399,7 @@
target: ["background", "biomarker", "candidate master regulator", "interactor", "master regulator", "oncogene", "target"],
compound: ["candidate drug", "control compound", "perturbagen"],
context: ["disease", "metastasis", "tissue"],
- cellline: ["cell line", ],
+ cellline: ["cell line",],
};
const subjectType = {
@@ -4061,11 +4064,11 @@
description: description,
svgHtml: svgHtml
}), {
- touch: false,
- 'autoDimensions': false,
- 'transitionIn': 'none',
- 'transitionOut': 'none'
- }
+ touch: false,
+ 'autoDimensions': false,
+ 'transitionIn': 'none',
+ 'transitionOut': 'none'
+ }
);
cytoscape({