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pd2af
Commit 9eaa7fb8 authored by Denis Shirshov's avatar Denis Shirshov
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parent c3486423
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Showing with 2414 additions and 160 deletions
code/gen-html.rkt
View file @ 9eaa7fb8
......@@ -18,6 +18,7 @@
(define-namespace-anchor a)
(define ns (namespace-anchor->namespace a))
; (write-file "../html/index.html" (process-html-template "../templates/index.t" #:tabtree-root "../knowledge" #:namespace ns))
(write-file "../html/index.html" (process-html-template "../templates/index.t" #:tabtree-root "../knowledge" #:namespace ns))
(write-file "../html/specification.html" (process-html-template "../templates/specification.t" #:tabtree-root "../tests" #:namespace ns))
; (write-file "../html/translator.html" (process-html-template "../templates/translator.t" #:tabtree-root "../knowledge" #:namespace ns))
(write-file "../html/cases.html" (process-html-template "../templates/cases.t" #:tabtree-root "../tests" #:namespace ns))
(write-file "../html/translator.html" (process-html-template "../templates/translator.t" #:tabtree-root "../knowledge" #:namespace ns))
code/template-functions.rkt
View file @ 9eaa7fb8
......@@ -38,6 +38,16 @@
`((change-text ',subst-table)
(read-file "../templates/parts/expandable.part"))))
(define-macro (expandable-cases . args)
(let ((subst-table (for/fold
((res empty))
((arg args))
(append
(list (cons (format "<<~a>>" (first arg)) (~a (second arg))))
res))))
`((change-text ',subst-table)
(read-file "../templates/parts/expandable_cases.part"))))
(define (exists? var)
(and var (non-empty-string? var)))
......
html/cases.html 0 → 100644
View file @ 9eaa7fb8
This diff is collapsed.
html/index.html
View file @ 9eaa7fb8
......@@ -14,7 +14,7 @@
<img src="img/pd2af_logo.png" alt="pd2af logo" />
</div>
<nav>
<a href="index.html" class="current_page_nav">Start</a><a href="specification.html" >Specification</a><a href="translator.html" >Try it!</a>
<a href="index.html" class="current_page_nav">Start</a><a href="specification.html" >Specification</a><a href="cases.html" >Cases</a><a href="translator.html" >Try it!</a>
</nav>
</header>
......@@ -54,7 +54,7 @@
</div>
<footer>
<div>Page generated <b>24.04.2019</b></div>
<div>Page generated <b>30.07.2019</b></div>
</footer>
<!-- Yandex.Metrika counter -->
......
html/specification.html
View file @ 9eaa7fb8
......@@ -17,7 +17,7 @@
<img src="img/pd2af_logo.png" alt="pd2af logo" />
</div>
<nav>
<a href="index.html" >Start</a><a href="specification.html" class="current_page_nav">Specification</a><a href="translator.html" >Try it!</a>
<a href="index.html" >Start</a><a href="specification.html" class="current_page_nav">Specification</a><a href="cases.html" >Cases</a><a href="translator.html" >Try it!</a>
</nav>
</header>
......@@ -2030,7 +2030,7 @@
<div class="placeholder" ng-hide="show1 || show2"></div>
<footer>
<div>Page generated <b>27.05.2019</b></div>
<div>Page generated <b>30.07.2019</b></div>
</footer>
<!-- Yandex.Metrika counter -->
......
html/specification/complex_association/af.sbgn
View file @ 9eaa7fb8
......@@ -4,7 +4,7 @@
<glyph id="C1" class="biological activity">
<label text="A-B" />
<bbox x="360.0" y="330.0" w="80" h="40" />
<glyph id="C1-uoi-1308" class="unit of information">
<glyph id="C1-uoi-3115" class="unit of information">
<label text="" />
<entity name="complex" />
<bbox x="380.0" y="325.0" w="40" h="10" />
......@@ -18,20 +18,20 @@
<label text="B" />
<bbox x="160.0" y="430.0" w="80" h="40" />
</glyph>
<glyph id="and-1304" class="and">
<glyph id="and-3111" class="and">
<bbox x="254.0" y="337.0" w="25" h="25" />
<port id="and-1304-in" x="249.0" y="349.5" />
<port id="and-1304-out" x="284.0" y="349.5" />
<port id="and-3111-in" x="249.0" y="349.5" />
<port id="and-3111-out" x="284.0" y="349.5" />
</glyph>
<arc class="positive influence" id="positive-influence-1307" source="and-1304-out" target="C1">
<arc class="positive influence" id="positive-influence-3114" source="and-3111-out" target="C1">
<start x="279.0" y="349.5" />
<end x="360.0" y="350.0" />
</arc>
<arc class="logic arc" id="logic-arc-1305" source="A1" target="and-1304-in">
<arc class="logic arc" id="logic-arc-3112" source="A1" target="and-3111-in">
<start x="200.0" y="270.0" />
<end x="249.0" y="349.5" />
</arc>
<arc class="logic arc" id="logic-arc-1306" source="B1" target="and-1304-in">
<arc class="logic arc" id="logic-arc-3113" source="B1" target="and-3111-in">
<start x="200.0" y="430.0" />
<end x="249.0" y="349.5" />
</arc>
......
html/specification/complex_association/pd.sbgn
View file @ 9eaa7fb8
......@@ -25,15 +25,15 @@
<port id="p1-in" x="253.0" y="361.0" />
<port id="p1-out" x="287.0" y="361.0" />
</glyph>
<arc class="consumption" id="consumption-1301" source="A1" target="p1-in">
<arc class="consumption" id="consumption-3108" source="A1" target="p1-in">
<start x="200.0" y="270.0" />
<end x="253.0" y="361.0" />
</arc>
<arc class="consumption" id="consumption-1302" source="B1" target="p1-in">
<arc class="consumption" id="consumption-3109" source="B1" target="p1-in">
<start x="200.0" y="430.0" />
<end x="253.0" y="361.0" />
</arc>
<arc class="production" id="production-1303" source="p1-out" target="C1">
<arc class="production" id="production-3110" source="p1-out" target="C1">
<start x="287.0" y="361.0" />
<end x="360.0" y="385.0" />
</arc>
......
html/specification/complex_association_regulated/af.sbgn
View file @ 9eaa7fb8
......@@ -4,7 +4,7 @@
<glyph id="C1" class="biological activity">
<label text="A-B" />
<bbox x="360.0" y="330.0" w="80" h="40" />
<glyph id="C1-uoi-1337" class="unit of information">
<glyph id="C1-uoi-3144" class="unit of information">
<label text="" />
<entity name="complex" />
<bbox x="380.0" y="325.0" w="40" h="10" />
......@@ -22,24 +22,24 @@
<label text="B" />
<bbox x="160.0" y="430.0" w="80" h="40" />
</glyph>
<glyph id="and-1332" class="and">
<glyph id="and-3139" class="and">
<bbox x="262.0" y="287.0" w="25" h="25" />
<port id="and-1332-in" x="257.0" y="299.5" />
<port id="and-1332-out" x="292.0" y="299.5" />
<port id="and-3139-in" x="257.0" y="299.5" />
<port id="and-3139-out" x="292.0" y="299.5" />
</glyph>
<arc class="positive influence" id="positive-influence-1336" source="and-1332-out" target="C1">
<arc class="positive influence" id="positive-influence-3143" source="and-3139-out" target="C1">
<start x="274.5" y="312.0" />
<end x="400.0" y="330.0" />
</arc>
<arc class="logic arc" id="logic-arc-1333" source="R" target="and-1332-in">
<arc class="logic arc" id="logic-arc-3140" source="R" target="and-3139-in">
<start x="300.0" y="170.0" />
<end x="257.0" y="299.5" />
</arc>
<arc class="logic arc" id="logic-arc-1334" source="A1" target="and-1332-in">
<arc class="logic arc" id="logic-arc-3141" source="A1" target="and-3139-in">
<start x="200.0" y="270.0" />
<end x="257.0" y="299.5" />
</arc>
<arc class="logic arc" id="logic-arc-1335" source="B1" target="and-1332-in">
<arc class="logic arc" id="logic-arc-3142" source="B1" target="and-3139-in">
<start x="200.0" y="430.0" />
<end x="257.0" y="299.5" />
</arc>
......
html/specification/complex_association_regulated/pd.sbgn
View file @ 9eaa7fb8
......@@ -29,19 +29,19 @@
<port id="p1-in" x="253.0" y="361.0" />
<port id="p1-out" x="287.0" y="361.0" />
</glyph>
<arc class="consumption" id="consumption-1328" source="A1" target="p1-in">
<arc class="consumption" id="consumption-3135" source="A1" target="p1-in">
<start x="200.0" y="270.0" />
<end x="253.0" y="361.0" />
</arc>
<arc class="consumption" id="consumption-1329" source="B1" target="p1-in">
<arc class="consumption" id="consumption-3136" source="B1" target="p1-in">
<start x="200.0" y="430.0" />
<end x="253.0" y="361.0" />
</arc>
<arc class="production" id="production-1330" source="p1-out" target="C1">
<arc class="production" id="production-3137" source="p1-out" target="C1">
<start x="287.0" y="361.0" />
<end x="360.0" y="385.0" />
</arc>
<arc class="catalysis" id="catalysis-1331" source="R" target="p1">
<arc class="catalysis" id="catalysis-3138" source="R" target="p1">
<start x="300.0" y="170.0" />
<end x="270.0" y="349.0" />
</arc>
......
html/specification/complex_association_with_complex_name/af.sbgn
View file @ 9eaa7fb8
......@@ -4,7 +4,7 @@
<glyph id="C1" class="biological activity">
<label text="C" />
<bbox x="360.0" y="330.0" w="80" h="40" />
<glyph id="C1-uoi-1286" class="unit of information">
<glyph id="C1-uoi-3093" class="unit of information">
<label text="" />
<entity name="complex" />
<bbox x="380.0" y="325.0" w="40" h="10" />
......@@ -18,20 +18,20 @@
<label text="B" />
<bbox x="160.0" y="430.0" w="80" h="40" />
</glyph>
<glyph id="and-1282" class="and">
<glyph id="and-3089" class="and">
<bbox x="254.0" y="337.0" w="25" h="25" />
<port id="and-1282-in" x="249.0" y="349.5" />
<port id="and-1282-out" x="284.0" y="349.5" />
<port id="and-3089-in" x="249.0" y="349.5" />
<port id="and-3089-out" x="284.0" y="349.5" />
</glyph>
<arc class="positive influence" id="positive-influence-1285" source="and-1282-out" target="C1">
<arc class="positive influence" id="positive-influence-3092" source="and-3089-out" target="C1">
<start x="279.0" y="349.5" />
<end x="360.0" y="350.0" />
</arc>
<arc class="logic arc" id="logic-arc-1283" source="A1" target="and-1282-in">
<arc class="logic arc" id="logic-arc-3090" source="A1" target="and-3089-in">
<start x="200.0" y="270.0" />
<end x="249.0" y="349.5" />
</arc>
<arc class="logic arc" id="logic-arc-1284" source="B1" target="and-1282-in">
<arc class="logic arc" id="logic-arc-3091" source="B1" target="and-3089-in">
<start x="200.0" y="430.0" />
<end x="249.0" y="349.5" />
</arc>
......
html/specification/complex_association_with_complex_name/pd.sbgn
View file @ 9eaa7fb8
......@@ -26,15 +26,15 @@
<port id="p1-in" x="253.0" y="361.0" />
<port id="p1-out" x="287.0" y="361.0" />
</glyph>
<arc class="consumption" id="consumption-1279" source="A1" target="p1-in">
<arc class="consumption" id="consumption-3086" source="A1" target="p1-in">
<start x="200.0" y="270.0" />
<end x="253.0" y="361.0" />
</arc>
<arc class="consumption" id="consumption-1280" source="B1" target="p1-in">
<arc class="consumption" id="consumption-3087" source="B1" target="p1-in">
<start x="200.0" y="430.0" />
<end x="253.0" y="361.0" />
</arc>
<arc class="production" id="production-1281" source="p1-out" target="C1">
<arc class="production" id="production-3088" source="p1-out" target="C1">
<start x="287.0" y="361.0" />
<end x="360.0" y="385.0" />
</arc>
......
html/specification/complex_dissociation/af.sbgn
View file @ 9eaa7fb8
......@@ -4,7 +4,7 @@
<glyph id="C1" class="biological activity">
<label text="A-B" />
<bbox x="160.0" y="330.0" w="80" h="40" />
<glyph id="C1-uoi-1357" class="unit of information">
<glyph id="C1-uoi-3164" class="unit of information">
<label text="" />
<entity name="complex" />
<bbox x="180.0" y="325.0" w="40" h="10" />
......@@ -18,20 +18,20 @@
<label text="B" />
<bbox x="360.0" y="430.0" w="80" h="40" />
</glyph>
<glyph id="hyperarc-1346" class="and">
<glyph id="hyperarc-3153" class="and">
<bbox x="320.0" y="337.0" w="25" h="25" />
<port id="hyperarc-1346-in" x="315.0" y="349.5" />
<port id="hyperarc-1346-out" x="350.0" y="349.5" />
<port id="hyperarc-3153-in" x="315.0" y="349.5" />
<port id="hyperarc-3153-out" x="350.0" y="349.5" />
</glyph>
<arc class="positive influence" id="positive-influence-1355" source="hyperarc-1346-out" target="A2">
<arc class="positive influence" id="positive-influence-3162" source="hyperarc-3153-out" target="A2">
<start x="332.5" y="337.0" />
<end x="400.0" y="270.0" />
</arc>
<arc class="positive influence" id="positive-influence-1356" source="hyperarc-1346-out" target="B2">
<arc class="positive influence" id="positive-influence-3163" source="hyperarc-3153-out" target="B2">
<start x="332.5" y="362.0" />
<end x="400.0" y="430.0" />
</arc>
<arc class="logic arc" id="logic-arc-1354" source="C1" target="hyperarc-1346-in">
<arc class="logic arc" id="logic-arc-3161" source="C1" target="hyperarc-3153-in">
<start x="240.0" y="350.0" />
<end x="315.0" y="349.5" />
</arc>
......
html/specification/complex_dissociation/pd.sbgn
View file @ 9eaa7fb8
......@@ -25,15 +25,15 @@
<port id="p1-in" x="319.0" y="361.0" />
<port id="p1-out" x="353.0" y="361.0" />
</glyph>
<arc class="consumption" id="consumption-1351" source="C1" target="p1-in">
<arc class="consumption" id="consumption-3158" source="C1" target="p1-in">
<start x="260.0" y="385.0" />
<end x="319.0" y="361.0" />
</arc>
<arc class="production" id="production-1352" source="p1-out" target="A2">
<arc class="production" id="production-3159" source="p1-out" target="A2">
<start x="353.0" y="361.0" />
<end x="400.0" y="270.0" />
</arc>
<arc class="production" id="production-1353" source="p1-out" target="B2">
<arc class="production" id="production-3160" source="p1-out" target="B2">
<start x="353.0" y="361.0" />
<end x="400.0" y="430.0" />
</arc>
......
html/specification/dimerization/af.sbgn 0 → 100644
View file @ 9eaa7fb8
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="activity flow">
<glyph id="A1" class="biological activity">
<label text="A" />
<bbox x="160.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="A2" class="biological activity">
<label text="A-dimer" />
<bbox x="160.0" y="330.0" w="80" h="40" />
</glyph>
<arc class="positive influence" id="positive-influence-3056" source="A1" target="A2">
<start x="200.0" y="170.0" />
<end x="200.0" y="330.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
html/specification/dimerization/pd.sbgn 0 → 100644
View file @ 9eaa7fb8
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="process description">
<glyph id="A1" class="macromolecule">
<label text="A" />
<bbox x="160.0" y="130.0" w="80" h="40" />
</glyph>
<glyph id="A2" class="macromolecule multimer">
<label text="A" />
<bbox x="160.0" y="330.0" w="80" h="40" />
<glyph id="A2-uoi-3055" class="unit of information">
<label text="N:2" />
<bbox x="180.0" y="325.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="p" class="process">
<bbox x="188.0" y="238.0" w="24" h="24" />
<port id="p-in" x="200.0" y="233.0" />
<port id="p-out" x="200.0" y="267.0" />
</glyph>
<arc class="consumption" id="consumption-3053" source="A1" target="p-in">
<start x="200.0" y="170.0" />
<end x="200.0" y="233.0" />
</arc>
<arc class="production" id="production-3054" source="p-out" target="A2">
<start x="200.0" y="267.0" />
<end x="200.0" y="330.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
html/specification/empty_set_1/af.sbgn 0 → 100644
View file @ 9eaa7fb8
<?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="A" 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-3283" source="C" target="A">
<start x="300.0" y="170.0" />
<end x="300.0" y="230.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
html/specification/empty_set_1/pd.sbgn 0 → 100644
View file @ 9eaa7fb8
<?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="S" class="source and sink">
<bbox x="175.0" y="225.0" w="50" h="50" />
</glyph>
<glyph id="A" class="macromolecule">
<label text="A" />
<bbox x="360.0" y="230.0" w="80" h="40" />
<glyph id="A-state-variable-3282" class="state variable">
<state value="inactive" 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>
<arc class="consumption" id="consumption-3279" source="S" target="p-in">
<start x="225.0" y="250.0" />
<end x="283.0" y="250.0" />
</arc>
<arc class="production" id="production-3280" source="p-out" target="A">
<start x="317.0" y="250.0" />
<end x="360.0" y="250.0" />
</arc>
<arc class="stimulation" id="stimulation-3281" source="C" target="p">
<start x="300.0" y="170.0" />
<end x="300.0" y="238.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
html/specification/empty_set_2/af.sbgn 0 → 100644
View file @ 9eaa7fb8
<?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="A" class="biological activity">
<label text="A" />
<bbox x="260.0" y="230.0" w="80" h="40" />
</glyph>
<arc class="negative influence" id="negative-influence-3303" source="C" target="A">
<start x="300.0" y="170.0" />
<end x="300.0" y="230.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
html/specification/empty_set_2/pd.sbgn 0 → 100644
View file @ 9eaa7fb8
<?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="A" class="macromolecule">
<label text="A" />
<bbox x="160.0" y="230.0" w="80" h="40" />
<glyph id="A-state-variable-3302" class="state variable">
<state value="active" variable="" />
<bbox x="230.0" y="222.5" w="15" h="15" />
</glyph>
</glyph>
<glyph id="S" class="source and sink">
<bbox x="375.0" y="225.0" w="50" h="50" />
</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>
<arc class="consumption" id="consumption-3299" source="A" target="p-in">
<start x="240.0" y="250.0" />
<end x="283.0" y="250.0" />
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html/specification/gene_expression/af.sbgn 0 → 100644
View file @ 9eaa7fb8
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html/specification/gene_expression/pd.sbgn 0 → 100644
View file @ 9eaa7fb8
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