Commit 669e3a93 authored by Denis Shirshov's avatar Denis Shirshov

15

parent f2dc7540
......@@ -21,4 +21,4 @@
(write-file "../html/generated/result.sbgn" af-xml)
))
(test-xml "../knowledge/sbgn_examples/metabolismregulation.org/MR009-phosphoinositides.valid.sbgn")
(test-xml "../knowledge/sbgn_examples/metabolismregulation.org/MR012-cAMP.sbgn")
......@@ -12,6 +12,7 @@ angular
$scope.delayed = {};
$scope.download_button = false;
$scope.file_selector_button_text = "Select file";
$scope.calculation_img = false;
$scope.refresh_filename = function(file) {
$scope.translate_button = true;
......@@ -33,6 +34,7 @@ angular
url: 'http://localhost/translate',
data: {'file': file, 'action': 'parse', 'filename': $scope.filename}
}).then(function(response) {
$scope.calculation_img = false;
var result = response.data;
if (result.error_message) {
$scope.error = true;
......@@ -50,6 +52,7 @@ angular
}, function (response) {
console.log('Error status: ' + response);
}, function (evt) {
$scope.calculation_img = true;
var progressPercentage = parseInt(100.0 * evt.loaded / evt.total);
// console.log('progress: ' + progressPercentage + '% ' + evt.config.data.file.name);
});
......
This diff is collapsed.
......@@ -1663,6 +1663,74 @@
</tr>
</table>
</div>
</div>
<div class="expandable_block">
<div class="expandable_header skipped" ng-class="{set_failed: bugs[9], set_passed: !bugs[9] && passed[9] > 0}">
<div class="window_button maximize" ng-hide="show[9]" ng-click="toggle_show(9)"></div>
<div class="window_button minimize" ng-show="show[9]" ng-click="toggle_show(9)"></div>
<!--(define tabtree (parse-tab-tree "../tests/test-results.tree"))-->
<h2>New Schemes <span>#(failed[9])#/#(passed[9])#</span></h2>
</div>
<div class="expandable_body" ng-show="show[9]">
<h3>9.1 Currency metabolites 1</h3>
<div><div class="test_button passed" ng-init="increment_passed(9)"></div>
</div>
<table class="rules-table">
<tr>
<td>
<div><img src="specification/currency_metabolites_1/pd.png" width="232" /></div>
</td>
<td>
<img src="specification/currency_metabolites_1/af.png" width="70" />
</td>
</tr>
<tr style="font-size:90%;" class="links">
<td>
<a href="specification/currency_metabolites_1/pd.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=%http://pd2af.rusvegia.com/specification%/currency_metabolites_1/pd.sbgn" target="_blank">Newt</a>
</td>
<td>
<a href="specification/currency_metabolites_1/af.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=%http://pd2af.rusvegia.com/specification%/currency_metabolites_1/af.sbgn" target="_blank">Newt</a>
</td>
</tr>
<tr style="line-height: 3em;">
<td colspan="2" style="text-align:left;"></td>
</tr>
<tr style="line-height: 3em;">
<td colspan="2" style="text-align:left;"></td>
</tr>
</table>
<h3>9.2 Noncurrency metabolites 1</h3>
<div><div class="test_button passed" ng-init="increment_passed(9)"></div>
</div>
<table class="rules-table">
<tr>
<td>
<div><img src="specification/noncurrency_metabolites_1/pd.png" width="232" /></div>
</td>
<td>
<img src="specification/noncurrency_metabolites_1/af.png" width="290" />
</td>
</tr>
<tr style="font-size:90%;" class="links">
<td>
<a href="specification/noncurrency_metabolites_1/pd.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=%http://pd2af.rusvegia.com/specification%/noncurrency_metabolites_1/pd.sbgn" target="_blank">Newt</a>
</td>
<td>
<a href="specification/noncurrency_metabolites_1/af.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=%http://pd2af.rusvegia.com/specification%/noncurrency_metabolites_1/af.sbgn" target="_blank">Newt</a>
</td>
</tr>
<tr style="line-height: 3em;">
<td colspan="2" style="text-align:left;"></td>
</tr>
<tr style="line-height: 3em;">
<td colspan="2" style="text-align:left;"></td>
</tr>
</table>
</div>
</div>
......@@ -1670,7 +1738,7 @@
<div class="placeholder" ng-hide="show1 || show2"></div>
<footer>
<div>Page generated <b>07.05.2019</b></div>
<div>Page generated <b>14.05.2019</b></div>
</footer>
<!-- Yandex.Metrika counter -->
......
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="activity flow">
<glyph id="C" class="biological activity">
<label text="C" />
<bbox x="260.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="A2" class="biological activity">
<label text="A" />
<bbox x="260.0" y="230.0" w="80" h="40" />
</glyph>
<arc class="positive influence" id="positive-influence-1419" source="C" target="A2">
<start x="300.0" y="170.0" />
<end x="300.0" y="230.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="process description">
<glyph id="C" class="macromolecule">
<label text="C" />
<bbox x="260.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="A1" class="macromolecule">
<label text="A" />
<bbox x="160.0" y="230.0" w="80" h="40" />
<glyph id="A1-state-variable-1417" class="state variable">
<state value="inactive1" variable="" />
<bbox x="230.0" y="222.5" w="15" h="15" />
</glyph>
</glyph>
<glyph id="A2" class="macromolecule">
<label text="A" />
<bbox x="360.0" y="230.0" w="80" h="40" />
<glyph id="A2-state-variable-1418" class="state variable">
<state value="active" variable="" />
<bbox x="430.0" y="222.5" w="15" h="15" />
</glyph>
</glyph>
<glyph id="ATP" class="simple chemical">
<label text="ATP" />
<bbox x="160.0" y="330.0" w="80" h="40" />
</glyph>
<glyph id="ADP" class="simple chemical">
<label text="ADP" />
<bbox x="360.0" y="330.0" w="80" h="40" />
</glyph>
<glyph id="p" class="process">
<bbox x="288.0" y="288.0" w="24" h="24" />
<port id="p-in" x="283.0" y="300.0" />
<port id="p-out" x="317.0" y="300.0" />
</glyph>
<arc class="consumption" id="consumption-1412" source="A1" target="p-in">
<start x="200.0" y="270.0" />
<end x="283.0" y="300.0" />
</arc>
<arc class="consumption" id="consumption-1413" source="ATP" target="p-in">
<start x="200.0" y="330.0" />
<end x="283.0" y="300.0" />
</arc>
<arc class="production" id="production-1414" source="p-out" target="A2">
<start x="317.0" y="300.0" />
<end x="400.0" y="270.0" />
</arc>
<arc class="production" id="production-1415" source="p-out" target="ADP">
<start x="317.0" y="300.0" />
<end x="400.0" y="330.0" />
</arc>
<arc class="stimulation" id="stimulation-1416" source="C" target="p">
<start x="300.0" y="170.0" />
<end x="300.0" y="288.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="activity flow">
<glyph id="C" class="biological activity">
<label text="C" />
<bbox x="260.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="M1" class="biological activity">
<label text="M1" />
<bbox x="160.0" y="330.0" w="80" h="40" />
<glyph id="M1-uoi-1452" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="180.0" y="325.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="A2" class="biological activity">
<label text="A" />
<bbox x="360.0" y="230.0" w="80" h="40" />
</glyph>
<glyph id="M2" class="biological activity">
<label text="M2" />
<bbox x="360.0" y="330.0" w="80" h="40" />
<glyph id="M2-uoi-1453" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="380.0" y="325.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="and-1447" class="and">
<bbox x="312.0" y="262.0" w="25" h="25" />
<port id="and-1447-in" x="307.0" y="274.5" />
<port id="and-1447-out" x="342.0" y="274.5" />
</glyph>
<arc class="positive influence" id="positive-influence-1450" source="and-1447-out" target="A2">
<start x="337.0" y="274.5" />
<end x="360.0" y="250.0" />
</arc>
<arc class="positive influence" id="positive-influence-1451" source="and-1447-out" target="M2">
<start x="324.5" y="287.0" />
<end x="400.0" y="330.0" />
</arc>
<arc class="logic arc" id="logic-arc-1448" source="C" target="and-1447-in">
<start x="300.0" y="170.0" />
<end x="307.0" y="274.5" />
</arc>
<arc class="logic arc" id="logic-arc-1449" source="M1" target="and-1447-in">
<start x="200.0" y="330.0" />
<end x="307.0" y="274.5" />
</arc>
</map>
</sbgn>
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="process description">
<glyph id="C" class="macromolecule">
<label text="C" />
<bbox x="260.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="A1" class="macromolecule">
<label text="A" />
<bbox x="160.0" y="230.0" w="80" h="40" />
<glyph id="A1-state-variable-1445" class="state variable">
<state value="inactive1" variable="" />
<bbox x="230.0" y="222.5" w="15" h="15" />
</glyph>
</glyph>
<glyph id="A2" class="macromolecule">
<label text="A" />
<bbox x="360.0" y="230.0" w="80" h="40" />
<glyph id="A2-state-variable-1446" class="state variable">
<state value="active" variable="" />
<bbox x="430.0" y="222.5" w="15" h="15" />
</glyph>
</glyph>
<glyph id="M1" class="simple chemical">
<label text="M1" />
<bbox x="160.0" y="330.0" w="80" h="40" />
</glyph>
<glyph id="M2" class="simple chemical">
<label text="M2" />
<bbox x="360.0" y="330.0" w="80" h="40" />
</glyph>
<glyph id="p" class="process">
<bbox x="288.0" y="288.0" w="24" h="24" />
<port id="p-in" x="283.0" y="300.0" />
<port id="p-out" x="317.0" y="300.0" />
</glyph>
<arc class="consumption" id="consumption-1440" source="A1" target="p-in">
<start x="200.0" y="270.0" />
<end x="283.0" y="300.0" />
</arc>
<arc class="consumption" id="consumption-1441" source="M1" target="p-in">
<start x="200.0" y="330.0" />
<end x="283.0" y="300.0" />
</arc>
<arc class="production" id="production-1442" source="p-out" target="A2">
<start x="317.0" y="300.0" />
<end x="400.0" y="270.0" />
</arc>
<arc class="production" id="production-1443" source="p-out" target="M2">
<start x="317.0" y="300.0" />
<end x="400.0" y="330.0" />
</arc>
<arc class="stimulation" id="stimulation-1444" source="C" target="p">
<start x="300.0" y="170.0" />
<end x="300.0" y="288.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
......@@ -40,6 +40,7 @@
<span>[[error_message]]</span>
<div class="box"><a class="button reset" ng-click="reset()">Reset</a></div>
</div>
<div ng-show="calculation_img"><img src="img/loading.gif" /></div>
<div ng-show="download_button" class="box ng-hide">
<table class="results_table">
<tbody>
......@@ -59,7 +60,7 @@
</section>
</form>
<footer>
<div>Page generated <b>24.04.2019</b></div>
<div>Page generated <b>14.05.2019</b></div>
</footer>
<!-- Yandex.Metrika counter -->
......
Subproject commit a6938382108c83ce561e9da09d9838f069b97960
Subproject commit d8b66d2d16c17ac3248aed37632909ddd9872415
Subproject commit d6a88bf4db4f6f7981ce72afbb2524ac6d9f4b0c
Subproject commit 99f8afc044b5bfc124518fe5c7c0480be92d8af0
......@@ -26,6 +26,7 @@
%%(expandable (scheme hidden_inhibition) (n 6))%%
%%(expandable (scheme patterns) (n 7))%%
%%(expandable (scheme simple_schemes) (n 8))%%
%%(expandable (scheme new_schemes) (n 9))%%
<div class="placeholder" ng-hide="show1 || show2"></div>
......
......@@ -28,6 +28,7 @@
<span>[[error_message]]</span>
<div class="box"><a class="button reset" ng-click="reset()">Reset</a></div>
</div>
<div ng-show="calculation_img"><img src="img/loading.gif" /></div>
<div ng-show="download_button" class="box ng-hide">
<table class="results_table">
<tbody>
......
......@@ -2,24 +2,20 @@
(parameters name:_experiments)
(test-case
(parameters name:logical_gates)
(parameters name:hidden_inhibition_1)
(sbgn-pd-context
(default:compartment
(M1 simple-chemical q:1-5)
(M2 simple-chemical q:3-5)
(A macromolecule q:2-1)
(C macromolecule q:3-1)
(D macromolecule q:5-2)
(M1 (process p1) M2)
((or A D (not (or C (B macromolecule q:4-1)))) catalysis p1)))
(default:compartment
(A1 macromolecule name:A state:inactive1 q:1-2)
(A2 macromolecule name:A state:inactive2 q:3-2)
(A3 macromolecule name:A state:active q:5-2)
(R1 macromolecule q:2-1)
(A2 (process p1) A1)
(A2 (process p2) A3)
(R1 catalysis p1)))
(sbgn-af-context
(default:compartment
(M1 biological-activity type:simple-chemical q:1-5)
(M2 biological-activity type:simple-chemical q:3-5)
(A biological-activity q:2-1)
(B biological-activity q:4-1)
(C biological-activity q:3-1)
(D biological-activity q:5-2)
((M1 (or A D (not (or C B)))) positive-influence M2))))
(default:compartment
(R1 biological-activity type:macromolecule q:1-1)
(A-active biological-activity name:A type:macromolecule q:1-2)
(R1 negative-influence A-active))))
)
\ No newline at end of file
;;;; TRANSLOCATION
(test-suite
(parameters name:new_schemes)
(test-case
(parameters name:currency_metabolites_1)
(sbgn-pd-context
(default:compartment
(C macromolecule q:2-1)
(A1 macromolecule name:A state:inactive1 q:1-2)
(A2 macromolecule name:A state:active q:3-2)
(ATP simple-chemical name:ATP q:1-3)
(ADP simple-chemical name:ADP q:3-3)
((A1 ATP) (process p) (A2 ADP))
(C stimulation p)))
(sbgn-af-context
(default:compartment
(C biological-activity q:2-1)
(A2 biological-activity name:A q:2-2)
(C positive-influence A2))))
(test-case
(parameters name:noncurrency_metabolites_1)
(sbgn-pd-context
(default:compartment
(C macromolecule q:2-1)
(A1 macromolecule name:A state:inactive1 q:1-2)
(A2 macromolecule name:A state:active q:3-2)
(M1 simple-chemical name:M1 q:1-3)
(M2 simple-chemical name:M2 q:3-3)
((A1 M1) (process p) (A2 M2))
(C stimulation p)))
(sbgn-af-context
(default:compartment
(C biological-activity q:2-1)
(M1 biological-activity type:simple-chemical q:1-3)
(A2 biological-activity name:A q:3-2)
(M2 biological-activity type:simple-chemical q:3-3)
((C M1) positive-influence (A2 M2)))))
)
\ No newline at end of file
......@@ -61,3 +61,6 @@ tests
simple_schemes rule-number:7
raf-mek-erk rule-number:1 passed:<t>
elk_signalling rule-number:2 passed:<t>
new_schemes rule-number:8
currency_metabolites_1 rule-number:1 passed:<t>
noncurrency_metabolites_1 rule-number:2 passed:<t>
(test-epic
(parameters output-folder:../html/specification knowledge-file:../tests/test-results.tree)
(load-test-suite "_experiments.pdafer" #f)
; (load-test-suite "_experiments.pdafer")
(load-test-suite "elementary_regulation.pdafer")
(load-test-suite "source_and_sinks.pdafer")
......@@ -10,4 +10,5 @@
(load-test-suite "complexes.pdafer")
(load-test-suite "hidden_inhibition.pdafer")
(load-test-suite "simple_schemes.pdafer")
(load-test-suite "new_schemes.pdafer")
)
\ No newline at end of file
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment