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pd2af
Commit 7f3e1bea authored by Denis Shirshov's avatar Denis Shirshov
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code/template-functions.rkt
View file @ 7f3e1bea
......@@ -91,43 +91,6 @@
(format "(af (default:compartment ~a ~a))" af-coors af-str)))))
af-full-str))
(define-catch (create-sbgn-ml-files basepath item)
(let* (
; (_ (--- "rules.html.t" (hash-pretty-string item) "\n"))
(folder ($ folder item))
(folder-path (str basepath "/" folder))
(pd-coors ($ pd-coors item))
(pd-str ($ pd item))
(compartments ($ compartments item))
(pd-full ($ pd-full item))
(pd-file ($ pd-file item))
(diagram-files-in-folder ($ diagram-files-in-folder item))
(pd-full-str (or
(and pd-full (format "(pd ~a)" pd-full))
(and pd-file (read-file pd-file))
(and diagram-files-in-folder (read-file (str folder-path "/diagram.pd")))
(if compartments
(format "(pd ~a ~a)" pd-coors pd-str)
(format "(pd (default:compartment ~a ~a))" pd-coors pd-str))))
(pd-xml (eval (preprocess-lisp-sbgn pd-full-str) ns))
(af-coors ($ af-coors item))
(af-str ($ af item))
(af-full ($ af-full item))
(af-file ($ af-file item))
(af-full-str (or
(and af-full (format "(af ~a)" af-full))
(and af-file (read-file af-file))
(and diagram-files-in-folder (read-file (str folder-path "/diagram.af")))
(if compartments
(format "(af ~a)" af-str)
(format "(af (default:compartment ~a ~a))" af-coors af-str))))
(af-xml (eval (preprocess-lisp-sbgn af-full-str) ns))
)
(write-file-to-dir #:dir folder-path #:file "pd.sbgn" pd-xml)
(write-file-to-dir #:dir folder-path #:file "af.sbgn" af-xml)
))
(define (calculate-img-width img-path)
(if (file-exists? img-path)
(let* ((image-geometry (get-image-geometry img-path))
......
code/test-xml.rkt
View file @ 7f3e1bea
......@@ -21,4 +21,5 @@
(write-file "../html/generated/result.sbgn" af-xml)
))
(test-xml "../knowledge/sbgn_examples/metabolismregulation.org/MR007-inos.sbgn")
(test-xml "../knowledge/sbgn_examples/metabolismregulation.org/F100-aspirin-V003A_2.sbgn")
; (test-xml "../knowledge/sbgn_examples/bigger_maps/mastcellv40.sbgn")
html/generated/result.sbgn
View file @ 7f3e1bea
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html/specification.html
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html/specification/MR001-glycolysis/af.sbgn
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html/specification/MR001-glycolysis/pd.sbgn
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html/specification/MR002-glycolysis-alt/af.sbgn
View file @ 7f3e1bea
......@@ -8,7 +8,7 @@
<glyph id="ATP" class="biological activity">
<label text="ATP" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="ATP-uoi-506" class="unit of information">
<glyph id="ATP-uoi-2044" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
......@@ -17,7 +17,7 @@
<glyph id="cAMP" class="biological activity">
<label text="cAMP" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="cAMP-uoi-507" class="unit of information">
<glyph id="cAMP-uoi-2045" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
......@@ -35,10 +35,19 @@
<label text="PFKFB2-P" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="α-D-glucose-6P" class="biological activity">
<label text="α-D-glucose-6P" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="α-D-glucose-6P-uoi-2046" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="β-D-fructose-6P" class="biological activity">
<label text="β-D-fructose-6P" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="β-D-fructose-6P-uoi-508" class="unit of information">
<glyph id="β-D-fructose-6P-uoi-2047" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
......@@ -47,7 +56,7 @@
<glyph id="β-D-fructose-1-6P2" class="biological activity">
<label text="β-D-fructose-1-6P2" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="β-D-fructose-1-6P2-uoi-509" class="unit of information">
<glyph id="β-D-fructose-1-6P2-uoi-2048" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
......@@ -56,7 +65,7 @@
<glyph id="β-D-fructose-2-6P2" class="biological activity">
<label text="β-D-fructose-2-6P2" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="β-D-fructose-2-6P2-uoi-510" class="unit of information">
<glyph id="β-D-fructose-2-6P2-uoi-2049" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
......@@ -74,104 +83,117 @@
<label text="PFK1" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="and-482" class="and">
<glyph id="and-2017" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-2017-in" x="39.5" y="37.0" />
<port id="and-2017-out" x="39.5" y="2.0" />
</glyph>
<glyph id="and-2024" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-482-in" x="39.5" y="37.0" />
<port id="and-482-out" x="39.5" y="2.0" />
<port id="and-2024-in" x="39.5" y="37.0" />
<port id="and-2024-out" x="39.5" y="2.0" />
</glyph>
<glyph id="and-489" class="and">
<glyph id="and-2028" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-489-in" x="39.5" y="37.0" />
<port id="and-489-out" x="39.5" y="2.0" />
<port id="and-2028-in" x="39.5" y="37.0" />
<port id="and-2028-out" x="39.5" y="2.0" />
</glyph>
<glyph id="and-493" class="and">
<glyph id="and-2032" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-493-in" x="39.5" y="37.0" />
<port id="and-493-out" x="39.5" y="2.0" />
<port id="and-2032-in" x="39.5" y="37.0" />
<port id="and-2032-out" x="39.5" y="2.0" />
</glyph>
<glyph id="and-498" class="and">
<glyph id="and-2036" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-498-in" x="39.5" y="37.0" />
<port id="and-498-out" x="39.5" y="2.0" />
<port id="and-2036-in" x="39.5" y="37.0" />
<port id="and-2036-out" x="39.5" y="2.0" />
</glyph>
<glyph id="and-502" class="and">
<glyph id="and-2040" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-502-in" x="39.5" y="37.0" />
<port id="and-502-out" x="39.5" y="2.0" />
<port id="and-2040-in" x="39.5" y="37.0" />
<port id="and-2040-out" x="39.5" y="2.0" />
</glyph>
<arc class="positive influence" id="positive-influence-485" source="and-482-out" target="cAMP">
<arc class="positive influence" id="positive-influence-2020" source="and-2017-out" target="cAMP">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-483" source="ADCY" target="and-482-in">
<arc class="logic arc" id="logic-arc-2018" source="ADCY" target="and-2017-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-484" source="ATP" target="and-482-in">
<arc class="logic arc" id="logic-arc-2019" source="ATP" target="and-2017-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="positive influence" id="positive-influence-486" source="cAMP" target="PKA">
<arc class="positive influence" id="positive-influence-2021" source="cAMP" target="PKA">
<start x="80.0" y="20.0" />
<end x="0" y="20.0" />
</arc>
<arc class="negative influence" id="negative-influence-487" source="PKA" target="PFKFB2">
<arc class="negative influence" id="negative-influence-2022" source="PKA" target="PFKFB2">
<start x="80.0" y="20.0" />
<end x="0" y="20.0" />
</arc>
<arc class="positive influence" id="positive-influence-488" source="PKA" target="PFKFB2-P">
<arc class="positive influence" id="positive-influence-2023" source="PKA" target="PFKFB2-P">
<start x="80.0" y="20.0" />
<end x="0" y="20.0" />
</arc>
<arc class="positive influence" id="positive-influence-492" source="and-489-out" target="β-D-fructose-2-6P2">
<arc class="positive influence" id="positive-influence-2027" source="and-2024-out" target="β-D-fructose-2-6P2">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-490" source="β-D-fructose-6P" target="and-489-in">
<arc class="logic arc" id="logic-arc-2025" source="β-D-fructose-6P" target="and-2024-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-491" source="PFKFB2" target="and-489-in">
<arc class="logic arc" id="logic-arc-2026" source="PFKFB2" target="and-2024-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="positive influence" id="positive-influence-496" source="and-493-out" target="β-D-fructose-6P">
<arc class="positive influence" id="positive-influence-2031" source="and-2028-out" target="β-D-fructose-6P">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-494" source="β-D-fructose-2-6P2" target="and-493-in">
<arc class="logic arc" id="logic-arc-2029" source="β-D-fructose-2-6P2" target="and-2028-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-495" source="PFKFB2-P" target="and-493-in">
<arc class="logic arc" id="logic-arc-2030" source="PFKFB2-P" target="and-2028-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="positive influence" id="positive-influence-497" source="GPI" target="β-D-fructose-6P">
<start x="80.0" y="20.0" />
<end x="0" y="20.0" />
<arc class="positive influence" id="positive-influence-2035" source="and-2032-out" target="β-D-fructose-6P">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-2033" source="GPI" target="and-2032-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-2034" source="α-D-glucose-6P" target="and-2032-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="positive influence" id="positive-influence-501" source="and-498-out" target="β-D-fructose-6P">
<arc class="positive influence" id="positive-influence-2039" source="and-2036-out" target="β-D-fructose-6P">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-499" source="F1-6BP" target="and-498-in">
<arc class="logic arc" id="logic-arc-2037" source="F1-6BP" target="and-2036-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-500" source="β-D-fructose-1-6P2" target="and-498-in">
<arc class="logic arc" id="logic-arc-2038" source="β-D-fructose-1-6P2" target="and-2036-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="positive influence" id="positive-influence-505" source="and-502-out" target="β-D-fructose-1-6P2">
<arc class="positive influence" id="positive-influence-2043" source="and-2040-out" target="β-D-fructose-1-6P2">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-503" source="β-D-fructose-6P" target="and-502-in">
<arc class="logic arc" id="logic-arc-2041" source="β-D-fructose-6P" target="and-2040-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-504" source="PFK1" target="and-502-in">
<arc class="logic arc" id="logic-arc-2042" source="PFK1" target="and-2040-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
......
html/specification/MR002-glycolysis-alt/pd.sbgn
View file @ 7f3e1bea
......@@ -16,7 +16,7 @@
<glyph id="PKA-1" class="macromolecule">
<label text="PKA" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="PKA-1-state-variable-478" class="state variable">
<glyph id="PKA-1-state-variable-2013" class="state variable">
<state value="inactive" variable="" />
<bbox x="70" y="-7.5" w="15" h="15" />
</glyph>
......@@ -24,7 +24,7 @@
<glyph id="PKA-2" class="macromolecule">
<label text="PKA" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="PKA-2-state-variable-479" class="state variable">
<glyph id="PKA-2-state-variable-2014" class="state variable">
<state value="active" variable="" />
<bbox x="70" y="-7.5" w="15" h="15" />
</glyph>
......@@ -32,7 +32,7 @@
<glyph id="PFKFB2" class="macromolecule">
<label text="PFKFB2" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="PFKFB2-state-variable-480" class="state variable">
<glyph id="PFKFB2-state-variable-2015" class="state variable">
<state value="" variable="S36" />
<bbox x="70" y="-7.5" w="30" h="15" />
</glyph>
......@@ -40,7 +40,7 @@
<glyph id="PFKFB2-P" class="macromolecule">
<label text="PFKFB2" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="PFKFB2-P-state-variable-481" class="state variable">
<glyph id="PFKFB2-P-state-variable-2016" class="state variable">
<state value="P" variable="S36" />
<bbox x="70" y="-7.5" w="30" h="15" />
</glyph>
......@@ -88,7 +88,7 @@
<port id="p4-in" x="40.0" y="37.0" />
<port id="p4-out" x="40.0" y="3.0" />
</glyph>
<glyph id="p5" class="reversible process">
<glyph id="p5" class="process">
<bbox x="28.0" y="8.0" w="24" h="24" />
<port id="p5-in" x="40.0" y="37.0" />
<port id="p5-out" x="40.0" y="3.0" />
......@@ -113,99 +113,99 @@
<port id="p7-2-in" x="40.0" y="37.0" />
<port id="p7-2-out" x="40.0" y="3.0" />
</glyph>
<arc class="consumption" id="consumption-454" source="ATP" target="p1-in">
<arc class="consumption" id="consumption-1989" source="ATP" target="p1-in">
<start x="80.0" y="20.0" />
<end x="40.0" y="37.0" />
</arc>
<arc class="production" id="production-455" source="p1-out" target="cAMP">
<arc class="production" id="production-1990" source="p1-out" target="cAMP">
<start x="40.0" y="3.0" />
<end x="0" y="20.0" />
</arc>
<arc class="catalysis" id="catalysis-456" source="ADCY" target="p1">
<arc class="catalysis" id="catalysis-1991" source="ADCY" target="p1">
<start x="80.0" y="20.0" />
<end x="28.0" y="20.0" />
</arc>
<arc class="consumption" id="consumption-457" source="PKA-1" target="p2-in">
<arc class="consumption" id="consumption-1992" source="PKA-1" target="p2-in">
<start x="80.0" y="20.0" />
<end x="40.0" y="37.0" />
</arc>
<arc class="production" id="production-458" source="p2-out" target="PKA-2">
<arc class="production" id="production-1993" source="p2-out" target="PKA-2">
<start x="40.0" y="3.0" />
<end x="0" y="20.0" />
</arc>
<arc class="stimulation" id="stimulation-459" source="cAMP" target="p2">
<arc class="stimulation" id="stimulation-1994" source="cAMP" target="p2">
<start x="80.0" y="20.0" />
<end x="28.0" y="20.0" />
</arc>
<arc class="consumption" id="consumption-460" source="PFKFB2" target="p4-in">
<arc class="consumption" id="consumption-1995" source="PFKFB2" target="p4-in">
<start x="80.0" y="20.0" />
<end x="40.0" y="37.0" />
</arc>
<arc class="production" id="production-461" source="p4-out" target="PFKFB2-P">
<arc class="production" id="production-1996" source="p4-out" target="PFKFB2-P">
<start x="40.0" y="3.0" />
<end x="0" y="20.0" />
</arc>
<arc class="catalysis" id="catalysis-462" source="PKA-2" target="p4">
<arc class="catalysis" id="catalysis-1997" source="PKA-2" target="p4">
<start x="80.0" y="20.0" />
<end x="28.0" y="20.0" />
</arc>
<arc class="production" id="production-463" source="p5-in" target="α-D-glucose-6P">
<arc class="production" id="production-1998" source="p5-in" target="α-D-glucose-6P">
<start x="40.0" y="3.0" />
<end x="0" y="20.0" />
</arc>
<arc class="production" id="production-464" source="p5-out" target="β-D-fructose-6P">
<arc class="production" id="production-1999" source="p5-out" target="β-D-fructose-6P">
<start x="40.0" y="3.0" />
<end x="0" y="20.0" />
</arc>
<arc class="catalysis" id="catalysis-465" source="GPI" target="p5">
<arc class="catalysis" id="catalysis-2000" source="GPI" target="p5">
<start x="80.0" y="20.0" />
<end x="28.0" y="20.0" />
</arc>
<arc class="consumption" id="consumption-466" source="β-D-fructose-6P" target="p6-1-in">
<arc class="consumption" id="consumption-2001" source="β-D-fructose-6P" target="p6-1-in">
<start x="80.0" y="20.0" />
<end x="40.0" y="37.0" />
</arc>
<arc class="production" id="production-467" source="p6-1-out" target="β-D-fructose-1-6P2">
<arc class="production" id="production-2002" source="p6-1-out" target="β-D-fructose-1-6P2">
<start x="40.0" y="3.0" />
<end x="0" y="20.0" />
</arc>
<arc class="catalysis" id="catalysis-468" source="PFK1" target="p6-1">
<arc class="catalysis" id="catalysis-2003" source="PFK1" target="p6-1">
<start x="80.0" y="20.0" />
<end x="28.0" y="20.0" />
</arc>
<arc class="consumption" id="consumption-469" source="β-D-fructose-1-6P2" target="p6-2-in">
<arc class="consumption" id="consumption-2004" source="β-D-fructose-1-6P2" target="p6-2-in">
<start x="80.0" y="20.0" />
<end x="40.0" y="37.0" />
</arc>
<arc class="production" id="production-470" source="p6-2-out" target="β-D-fructose-6P">
<arc class="production" id="production-2005" source="p6-2-out" target="β-D-fructose-6P">
<start x="40.0" y="3.0" />
<end x="0" y="20.0" />
</arc>
<arc class="catalysis" id="catalysis-471" source="F1-6BP" target="p6-2">
<arc class="catalysis" id="catalysis-2006" source="F1-6BP" target="p6-2">
<start x="80.0" y="20.0" />
<end x="28.0" y="20.0" />
</arc>
<arc class="consumption" id="consumption-472" source="β-D-fructose-6P" target="p7-1-in">
<arc class="consumption" id="consumption-2007" source="β-D-fructose-6P" target="p7-1-in">
<start x="80.0" y="20.0" />
<end x="40.0" y="37.0" />
</arc>
<arc class="production" id="production-473" source="p7-1-out" target="β-D-fructose-2-6P2">
<arc class="production" id="production-2008" source="p7-1-out" target="β-D-fructose-2-6P2">
<start x="40.0" y="3.0" />
<end x="0" y="20.0" />
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html/specification/MR003-eicosanoids/af.sbgn
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html/specification/MR003-eicosanoids/pd.sbgn
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