From 290adf6aaab858db681ab9deb4a5ccb80f79abfd Mon Sep 17 00:00:00 2001 From: Salih Altun Date: Tue, 1 Jun 2021 09:37:13 +0300 Subject: [PATCH] Rename source and sink to empty set #658 --- .../{source-and-sink.svg => empty-set.svg} | 2 +- app/img/pd-legend.svg | 2 +- app/js/app-menu.js | 2 +- app/js/app-utilities.js | 32 +++++++++---------- app/js/inspector-utilities.js | 4 +-- app/resources/libsbgn-0.3.xsd | 2 +- ..._stat1alpha_induction_of_the_irf1_gene.nwt | 4 +-- app/samples/drosophila_cell_cycle.nwt | 30 ++++++++--------- app/samples/pd_learners_card.nwt | 8 ++--- app/samples/polyq_proteins_interference.nwt | 2 +- app/samples/two_gene_system_behavior.nwt | 14 ++++---- index.html | 6 ++-- package-lock.json | 4 +-- templatelibsbgn.xslt | 18 +++++------ 14 files changed, 65 insertions(+), 65 deletions(-) rename app/img/nodes/{source-and-sink.svg => empty-set.svg} (99%) diff --git a/app/img/nodes/source-and-sink.svg b/app/img/nodes/empty-set.svg similarity index 99% rename from app/img/nodes/source-and-sink.svg rename to app/img/nodes/empty-set.svg index 7837ee5ca..fb8a18416 100644 --- a/app/img/nodes/source-and-sink.svg +++ b/app/img/nodes/empty-set.svg @@ -14,7 +14,7 @@ id="svg2" version="1.1" inkscape:version="0.91 r13725" - sodipodi:docname="source-and-sink.svg" + sodipodi:docname="empty-set.svg" inkscape:export-filename="C:\Users\ugur\Desktop\node-legend.2016.04.01.png" inkscape:export-xdpi="300" inkscape:export-ydpi="300"> diff --git a/app/img/pd-legend.svg b/app/img/pd-legend.svg index 6d2ce0058..65264c537 100644 --- a/app/img/pd-legend.svg +++ b/app/img/pd-legend.svg @@ -851,7 +851,7 @@ y="430.32028" x="62.120743" id="tspan6268" - sodipodi:role="line">source or sinkempty set To fix, reverse the consumption arc:

"; } */ else if(errors[currentPage].pattern == "pd10103") { - html += "

To fix, split the source and sink glyph for each consumption arc:

"; + html += "

To fix, split the empty set glyph for each consumption arc:

"; }else if(radioButtonRules.includes(errors[currentPage].pattern)) { var params = { handled: handled }; html= inspectorUtilities.handleRadioButtons(errors[currentPage].pattern,html,eles,cy,params); @@ -1437,7 +1437,7 @@ inspectorUtilities.fixRadioButtons = function (errorCode,eles,cy) { } else if(errors[currentPage].pattern == "pd10107") { - html += "

To fix, split the source and sink glyph for each production arc:

"; + html += "

To fix, split the empty set glyph for each production arc:

"; var connectedEdges = eles.connectedEdges().filter('[class="production"]'); for (var i = 0; i < connectedEdges.length; i++) { viewUtilitilesInstance.highlight(connectedEdges[i], 1); diff --git a/app/resources/libsbgn-0.3.xsd b/app/resources/libsbgn-0.3.xsd index 5c803e7d4..9e6e0e05c 100644 --- a/app/resources/libsbgn-0.3.xsd +++ b/app/resources/libsbgn-0.3.xsd @@ -663,7 +663,7 @@ - + diff --git a/app/samples/activated_stat1alpha_induction_of_the_irf1_gene.nwt b/app/samples/activated_stat1alpha_induction_of_the_irf1_gene.nwt index 917815fce..e374ce61b 100644 --- a/app/samples/activated_stat1alpha_induction_of_the_irf1_gene.nwt +++ b/app/samples/activated_stat1alpha_induction_of_the_irf1_gene.nwt @@ -73,7 +73,7 @@ using logical operators true - + @@ -89,7 +89,7 @@ using logical operators - + diff --git a/app/samples/drosophila_cell_cycle.nwt b/app/samples/drosophila_cell_cycle.nwt index 67ef9af1b..1ad3f81e6 100644 --- a/app/samples/drosophila_cell_cycle.nwt +++ b/app/samples/drosophila_cell_cycle.nwt @@ -193,7 +193,7 @@ - + @@ -222,7 +222,7 @@ - + @@ -248,7 +248,7 @@ - + @@ -260,7 +260,7 @@ - + @@ -268,7 +268,7 @@ - + @@ -281,7 +281,7 @@ - + @@ -289,7 +289,7 @@ - + @@ -297,7 +297,7 @@ - + @@ -315,10 +315,10 @@ - + - + @@ -400,7 +400,7 @@ - + @@ -408,7 +408,7 @@ - + @@ -416,7 +416,7 @@ - + @@ -461,7 +461,7 @@ - + @@ -479,7 +479,7 @@ - + diff --git a/app/samples/pd_learners_card.nwt b/app/samples/pd_learners_card.nwt index bb122e024..602759e76 100644 --- a/app/samples/pd_learners_card.nwt +++ b/app/samples/pd_learners_card.nwt @@ -326,7 +326,7 @@ - + @@ -558,7 +558,7 @@ - + @@ -657,7 +657,7 @@ - + @@ -684,7 +684,7 @@ - + diff --git a/app/samples/polyq_proteins_interference.nwt b/app/samples/polyq_proteins_interference.nwt index 4ed1faad8..691703b7e 100644 --- a/app/samples/polyq_proteins_interference.nwt +++ b/app/samples/polyq_proteins_interference.nwt @@ -126,7 +126,7 @@ - + diff --git a/app/samples/two_gene_system_behavior.nwt b/app/samples/two_gene_system_behavior.nwt index 6c83b5e02..fdd9e5dfd 100644 --- a/app/samples/two_gene_system_behavior.nwt +++ b/app/samples/two_gene_system_behavior.nwt @@ -130,10 +130,10 @@ doi:10.1038/nrg3885 - + - + @@ -141,10 +141,10 @@ doi:10.1038/nrg3885 - + - + @@ -164,7 +164,7 @@ doi:10.1038/nrg3885 - + @@ -177,7 +177,7 @@ doi:10.1038/nrg3885 - + @@ -250,7 +250,7 @@ doi:10.1038/nrg3885 - + diff --git a/index.html b/index.html index ba93a044c..08c6a41a3 100644 --- a/index.html +++ b/index.html @@ -608,7 +608,7 @@
-
+
@@ -2838,7 +2838,7 @@

SBGN Bricks

- + diff --git a/package-lock.json b/package-lock.json index 65347ad71..2a25c2214 100644 --- a/package-lock.json +++ b/package-lock.json @@ -2358,7 +2358,7 @@ "dev": true }, "chise": { - "version": "github:iVis-at-Bilkent/chise.js#36835c9f67d9846dd45c282396f726ceaf3dabdb", + "version": "github:iVis-at-Bilkent/chise.js#522b431c9ff4d3f3b0c2961fb4d09ccfd8306a10", "from": "github:iVis-at-Bilkent/chise.js#unstable", "requires": { "lodash.isequal": "^4.5.0" @@ -6889,7 +6889,7 @@ "integrity": "sha512-NqVDv9TpANUjFm0N8uM5GxL36UgKi9/atZw+x7YFnQ8ckwFGKrl4xX4yWtrey3UJm5nP1kUbnYgLopqWNSRhWw==" }, "sbgnviz": { - "version": "github:iVis-at-Bilkent/sbgnviz.js#ee7c4a7b69aa845293acdf0dfe144ea83df12937", + "version": "github:iVis-at-Bilkent/sbgnviz.js#ed33cfc653ea7558e340f7bad1cb35aa66743cc7", "from": "github:iVis-at-Bilkent/sbgnviz.js#unstable", "requires": { "libsbgn.js": "github:sbgn/libsbgn.js#develop", diff --git a/templatelibsbgn.xslt b/templatelibsbgn.xslt index e988626ce..37cc88df7 100644 --- a/templatelibsbgn.xslt +++ b/templatelibsbgn.xslt @@ -75,7 +75,7 @@ -pd10101errorArc with class consumption must have source reference to glyph of EPN classes +pd10101errorArc with class consumption must have source reference to glyph of EPN classes @@ -98,10 +98,10 @@ - + -pd10103errorThe source and sink glyph can be connected to at most one consumption glyph +pd10103errorThe empty set glyph can be connected to at most one consumption glyph @@ -139,7 +139,7 @@ -pd10106errorArc with class production must have target reference to glyph of EPN classes +pd10106errorArc with class production must have target reference to glyph of EPN classes @@ -149,10 +149,10 @@ - + -pd10107errorThe source and sink glyph can be connected to at most one production glyph +pd10107errorThe empty set glyph can be connected to at most one production glyph @@ -214,7 +214,7 @@ - + pd10112errorIf there are compartments defined, top-level glyphs must have a compartment reference @@ -267,7 +267,7 @@ -pd10127errorArc with class equivalence arc must have source reference to glyph of EPN classes +pd10127errorArc with class equivalence arc must have source reference to glyph of EPN classes @@ -301,7 +301,7 @@ - + pd10131errorEPNs should not be orphaned (i.e. they must be associated with at least one arc)