Commit e5d6c7a2 authored by Denis Shirshov's avatar Denis Shirshov

15.5

parent cfb90408
......@@ -21,4 +21,4 @@
(write-file "../html/generated/result.sbgn" af-xml)
))
(test-xml "../knowledge/sbgn_examples/metabolismregulation.org/MR012-cAMP.sbgn")
(test-xml "../knowledge/sbgn_examples/metabolismregulation.org/MR100-aspirin-v3A.sbgn")
This diff is collapsed.
......@@ -1731,6 +1731,34 @@
</tr>
</table>
<h3>9.3 Regulation combining 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/regulation_combining_1/pd.png" width="232" /></div>
</td>
<td>
<img src="specification/regulation_combining_1/af.png" width="230" />
</td>
</tr>
<tr style="font-size:90%;" class="links">
<td>
<a href="specification/regulation_combining_1/pd.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/regulation_combining_1/pd.sbgn" target="_blank">Newt</a>
</td>
<td>
<a href="specification/regulation_combining_1/af.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/regulation_combining_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>
......@@ -1738,7 +1766,7 @@
<div class="placeholder" ng-hide="show1 || show2"></div>
<footer>
<div>Page generated <b>14.05.2019</b></div>
<div>Page generated <b>15.05.2019</b></div>
</footer>
<!-- Yandex.Metrika counter -->
......
......@@ -36,19 +36,19 @@
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......@@ -56,32 +56,32 @@
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</glyph>
<arc class="positive influence" id="positive-influence-782" source="and-770-out" target="M2">
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......
......@@ -31,14 +31,14 @@
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</glyph>
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......@@ -54,24 +54,24 @@
<end x="360.0" y="550.0" />
</arc>
<arc class="catalysis" id="catalysis-769" source="or-760-out" target="p1">
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<start x="400.0" y="170.0" />
......
......@@ -24,9 +24,9 @@
</glyph>
</glyph>
<glyph id="and-597" class="and">
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</glyph>
<glyph id="not-598" class="not">
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......@@ -34,16 +34,16 @@
<port id="not-598-out" x="317.0" y="249.5" />
</glyph>
<arc class="negative influence" id="negative-influence-602" source="and-597-out" target="B">
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<end x="215.0" y="132.5" />
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<arc class="logic arc" id="logic-arc-599" source="A" target="not-598-in">
<start x="240.0" y="250.0" />
......
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="activity flow">
<glyph id="R1" class="biological activity">
<label text="R1" />
<bbox x="160.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="R2" class="biological activity">
<label text="R2" />
<bbox x="360.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="R3" class="biological activity">
<label text="R3" />
<bbox x="260.0" y="330.0" 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>
<glyph id="or-1495" class="or">
<bbox x="287.0" y="170.0" w="25" h="25" />
<port id="or-1495-in" x="299.5" y="165.0" />
<port id="or-1495-out" x="299.5" y="200.0" />
</glyph>
<arc class="positive influence" id="positive-influence-1498" source="or-1495-out" target="A2">
<start x="299.5" y="195.0" />
<end x="300.0" y="230.0" />
</arc>
<arc class="logic arc" id="logic-arc-1496" source="R1" target="or-1495-in">
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</arc>
<arc class="negative influence" id="negative-influence-1499" source="R3" target="A2">
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<end x="300.0" y="270.0" />
</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="R1" class="macromolecule">
<label text="R1" />
<bbox x="160.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="R2" class="macromolecule">
<label text="R2" />
<bbox x="360.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="R3" class="macromolecule">
<label text="R3" />
<bbox x="260.0" y="330.0" 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-1493" 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-1494" class="state variable">
<state value="active" variable="" />
<bbox x="430.0" y="222.5" w="15" h="15" />
</glyph>
</glyph>
<glyph id="p" class="process">
<bbox x="288.0" y="238.0" w="24" h="24" />
<port id="p-in" x="283.0" y="250.0" />
<port id="p-out" x="317.0" y="250.0" />
</glyph>
<glyph id="or-1488" class="or">
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</glyph>
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</arc>
<arc class="production" id="production-1487" source="p-out" target="A2">
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</arc>
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<end x="300.0" y="262.0" />
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</map>
</sbgn>
\ No newline at end of file
......@@ -8,7 +8,6 @@
(require "../libs/odysseus_modules/pd2af/pd2pd.rkt")
(require "../libs/odysseus_modules/pd2af/pd2af.rkt")
(require "../libs/odysseus_modules/pd2af/af2af.rkt")
(require "../libs/odysseus_modules/pd2af/af2xml.rkt")
(require "../libs/odysseus_modules/pd2af/translate.rkt")
(require "../libs/odysseus_modules/sbgn/common.rkt")
(require "../libs/odysseus_modules/sbgn/context.rkt")
......
......@@ -20,7 +20,7 @@
<div class="box">
<div class="buttons">
<a ng-class="['button', translate_button? 'selected' : 'action']" ngf-select="refresh_filename($file)" ng-model="file" name="file">[[file_selector_button_text]]</a>
<a class="button action ng-hide" ng-show="translate_button" ng-click="submit()">Translate</a>
<a class="button action ng-hide" ng-show="translate_button" ng-click="submit()">Convert</a>
</div>
</div>
<div ng-show="error" class="box ng-hide error">
......@@ -28,7 +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 ngshow="calculation_img"><img src="img/loading.gif" /></div> -->
<div ng-show="download_button" class="box ng-hide">
<table class="results_table">
<tbody>
......
......@@ -2,20 +2,18 @@
(parameters name:_experiments)
(test-case
(parameters name:hidden_inhibition_1)
(parameters name:a-cat-ss)
(sbgn-pd-context
(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)))
(default:compartment
(C macromolecule q:2-1)
(A macromolecule state:active q:1-2)
(S source-and-sink q:3-2)
(A (process p) S)
(C catalysis p)))
(sbgn-af-context
(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))))
(default:compartment
(C biological-activity q:2-1)
(A biological-activity q:2-2)
(C negative-influence A))))
)
\ No newline at end of file
......@@ -37,4 +37,27 @@
(A2 biological-activity name:A q:3-2)
(M2 biological-activity type:simple-chemical q:3-3)
((C M1) positive-influence (A2 M2)))))
(test-case
(parameters name:regulation_combining_1)
(sbgn-pd-context
(default:compartment
(R1 macromolecule qy:1 qx:1)
(R2 macromolecule qy:1 qx:3)
(R3 macromolecule qy:3 qx:2)
(A1 macromolecule name:A state:inactive1 q:1-2)
(A2 macromolecule name:A state:active q:3-2)
(A1 (process p) A2)
(R1 catalysis p)
(R2 stimulation p)
(R3 inhibition p)))
(sbgn-af-context
(default:compartment
(R1 biological-activity qy:1 qx:1)
(R2 biological-activity qy:1 qx:3)
(R3 biological-activity qy:3 qx:2)
(A2 biological-activity name:A qx:2 qy:2)
((or R1 R2) positive-influence A2)
(R3 negative-influence A2))))
)
\ No newline at end of file
......@@ -64,3 +64,4 @@ tests
new_schemes rule-number:8
currency_metabolites_1 rule-number:1 passed:<t>
noncurrency_metabolites_1 rule-number:2 passed:<t>
regulation_combining_1 rule-number:3 passed:<t>
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