From 68ea5e1701e5a9d7e6992dfc980895ef07c03b91 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ond=C5=99ej=20Huvar?= <492849@mail.muni.cz>
Date: Mon, 2 Sep 2024 20:41:05 +0200
Subject: [PATCH] Prototype for JSON & XML serialization, new internal BMA
structure, many model examples.
---
.../2var_unstable (1).json | 1 +
.../json-export-from-repo/Default Model.json | 1 +
.../json-export-from-repo/E coli Tarfunc.json | 1 +
models/json-export-from-repo/New Model.json | 1 +
.../json-export-from-repo/Resting Neuron.json | 1 +
models/json-export-from-repo/SSkin1D (1).json | 1 +
models/json-export-from-repo/SSkin1D.json | 1 +
models/json-export-from-repo/SSkin1D_TF.json | 1 +
.../SSkin1D_analysis_hang.json | 1 +
.../SSkin2D_3cells_2layers.json | 1 +
models/json-export-from-repo/Skin1D (1).json | 1 +
models/json-export-from-repo/Skin1D (2).json | 1 +
models/json-export-from-repo/Skin1D.json | 1 +
.../Skin1D_TF_analysis_hang.json | 1 +
.../Skin2D_3cells_2layers.json | 1 +
.../Skin2D_3cells_2layers_TF.json | 1 +
...in2D_3cells_2layers_TF_analysis_crash.json | 1 +
models/json-export-from-repo/Skin2D_5X2.json | 1 +
.../json-export-from-repo/Skin2D_5X2_TF.json | 1 +
.../json-export-from-repo/SmallTestCase.json | 1 +
.../json-export-from-repo/ToyModelStable.json | 1 +
.../ToyModelUnstable.json | 1 +
models/json-export-from-repo/VPC_lin15ko.json | 1 +
.../VerySmallTestCase.json | 1 +
models/json-export-from-repo/ion channel.json | 1 +
models/json-export-from-repo/model 1 (1).json | 1 +
models/json-export-from-repo/model 1.json | 1 +
.../Activator-Inhibitor Oscillation.json | 1 +
.../CancerSignalling.json | 1 +
models/json-export-from-tool/Homeostasis.json | 1 +
models/json-export-from-tool/Hyperbolic.json | 1 +
models/json-export-from-tool/Leukaemia.json | 1 +
models/json-export-from-tool/Linear.json | 1 +
.../Metabolism demo.json | 1 +
.../Mutual Inhibition.json | 1 +
.../Oscillatory negative feedback.json | 1 +
.../Perfect Adaptation.json | 1 +
models/json-export-from-tool/Sigmoidal.json | 1 +
models/json-export-from-tool/SkinModel.json | 1 +
.../Substrate depletion oscillations.json | 1 +
.../json-export-from-tool/ToyModelStable.json | 1 +
.../ToyModelUnstable.json | 1 +
models/json-export-from-tool/VPC.json | 1 +
models/json-repo/Race.json | 119 +
models/{json => json-repo}/RestingNeuron.json | 0
.../SimpleBifurcation.json | 0
models/json-repo/Skin1D.json | 1 +
models/json-repo/Skin2D_5X2_AI.json | 3028 +++++++++++++
models/json-repo/SkinModel.json | 1 +
models/json-repo/ToyModelStable.json | 90 +
models/json-repo/ToyModelUnstable.json | 90 +
models/json-repo/ceilFunc.json | 1 +
models/json-repo/ion channel.json | 73 +
models/readme.md | 11 +
models/xml-repo/2var_unstable.xml | 60 +
models/xml-repo/BooleanLoop.xml | 60 +
models/xml-repo/NoLoopFound.xml | 114 +
models/xml-repo/SSkin1D.xml | 680 +++
models/xml-repo/SSkin1D_TF.xml | 680 +++
models/xml-repo/SSkin1D_analysis_hang.xml | 680 +++
models/xml-repo/SSkin2D_3cells_2layers.xml | 913 ++++
models/{xml => xml-repo}/Skin1D.xml | 86 +-
models/xml-repo/Skin1D_TF_analysis_hang.xml | 1508 +++++++
models/xml-repo/Skin2D_3cells_2layers.xml | 1855 ++++++++
models/xml-repo/Skin2D_3cells_2layers_TF.xml | 1837 ++++++++
...kin2D_3cells_2layers_TF_analysis_crash.xml | 1855 ++++++++
models/xml-repo/Skin2D_5X2.xml | 3879 +++++++++++++++++
models/xml-repo/Skin2D_5X2_TF.xml | 3879 +++++++++++++++++
models/xml-repo/SmallTestCase.xml | 78 +
models/xml-repo/VPC_lin15ko.xml | 1939 ++++++++
.../{xml => xml-repo}/VerySmallTestCase.xml | 0
src/bin/load_json.rs | 56 +-
src/bin/load_xml.rs | 53 +-
src/bma_model.rs | 252 ++
src/enums.rs | 14 +
src/json_model.rs | 197 +-
src/lib.rs | 3 +
src/xml_model.rs | 180 +-
78 files changed, 24084 insertions(+), 231 deletions(-)
create mode 100644 models/json-export-from-repo/2var_unstable (1).json
create mode 100644 models/json-export-from-repo/Default Model.json
create mode 100644 models/json-export-from-repo/E coli Tarfunc.json
create mode 100644 models/json-export-from-repo/New Model.json
create mode 100644 models/json-export-from-repo/Resting Neuron.json
create mode 100644 models/json-export-from-repo/SSkin1D (1).json
create mode 100644 models/json-export-from-repo/SSkin1D.json
create mode 100644 models/json-export-from-repo/SSkin1D_TF.json
create mode 100644 models/json-export-from-repo/SSkin1D_analysis_hang.json
create mode 100644 models/json-export-from-repo/SSkin2D_3cells_2layers.json
create mode 100644 models/json-export-from-repo/Skin1D (1).json
create mode 100644 models/json-export-from-repo/Skin1D (2).json
create mode 100644 models/json-export-from-repo/Skin1D.json
create mode 100644 models/json-export-from-repo/Skin1D_TF_analysis_hang.json
create mode 100644 models/json-export-from-repo/Skin2D_3cells_2layers.json
create mode 100644 models/json-export-from-repo/Skin2D_3cells_2layers_TF.json
create mode 100644 models/json-export-from-repo/Skin2D_3cells_2layers_TF_analysis_crash.json
create mode 100644 models/json-export-from-repo/Skin2D_5X2.json
create mode 100644 models/json-export-from-repo/Skin2D_5X2_TF.json
create mode 100644 models/json-export-from-repo/SmallTestCase.json
create mode 100644 models/json-export-from-repo/ToyModelStable.json
create mode 100644 models/json-export-from-repo/ToyModelUnstable.json
create mode 100644 models/json-export-from-repo/VPC_lin15ko.json
create mode 100644 models/json-export-from-repo/VerySmallTestCase.json
create mode 100644 models/json-export-from-repo/ion channel.json
create mode 100644 models/json-export-from-repo/model 1 (1).json
create mode 100644 models/json-export-from-repo/model 1.json
create mode 100644 models/json-export-from-tool/Activator-Inhibitor Oscillation.json
create mode 100644 models/json-export-from-tool/CancerSignalling.json
create mode 100644 models/json-export-from-tool/Homeostasis.json
create mode 100644 models/json-export-from-tool/Hyperbolic.json
create mode 100644 models/json-export-from-tool/Leukaemia.json
create mode 100644 models/json-export-from-tool/Linear.json
create mode 100644 models/json-export-from-tool/Metabolism demo.json
create mode 100644 models/json-export-from-tool/Mutual Inhibition.json
create mode 100644 models/json-export-from-tool/Oscillatory negative feedback.json
create mode 100644 models/json-export-from-tool/Perfect Adaptation.json
create mode 100644 models/json-export-from-tool/Sigmoidal.json
create mode 100644 models/json-export-from-tool/SkinModel.json
create mode 100644 models/json-export-from-tool/Substrate depletion oscillations.json
create mode 100644 models/json-export-from-tool/ToyModelStable.json
create mode 100644 models/json-export-from-tool/ToyModelUnstable.json
create mode 100644 models/json-export-from-tool/VPC.json
create mode 100644 models/json-repo/Race.json
rename models/{json => json-repo}/RestingNeuron.json (100%)
rename models/{json => json-repo}/SimpleBifurcation.json (100%)
create mode 100644 models/json-repo/Skin1D.json
create mode 100644 models/json-repo/Skin2D_5X2_AI.json
create mode 100644 models/json-repo/SkinModel.json
create mode 100644 models/json-repo/ToyModelStable.json
create mode 100644 models/json-repo/ToyModelUnstable.json
create mode 100644 models/json-repo/ceilFunc.json
create mode 100644 models/json-repo/ion channel.json
create mode 100644 models/readme.md
create mode 100644 models/xml-repo/2var_unstable.xml
create mode 100644 models/xml-repo/BooleanLoop.xml
create mode 100644 models/xml-repo/NoLoopFound.xml
create mode 100644 models/xml-repo/SSkin1D.xml
create mode 100644 models/xml-repo/SSkin1D_TF.xml
create mode 100644 models/xml-repo/SSkin1D_analysis_hang.xml
create mode 100644 models/xml-repo/SSkin2D_3cells_2layers.xml
rename models/{xml => xml-repo}/Skin1D.xml (97%)
create mode 100644 models/xml-repo/Skin1D_TF_analysis_hang.xml
create mode 100644 models/xml-repo/Skin2D_3cells_2layers.xml
create mode 100644 models/xml-repo/Skin2D_3cells_2layers_TF.xml
create mode 100644 models/xml-repo/Skin2D_3cells_2layers_TF_analysis_crash.xml
create mode 100644 models/xml-repo/Skin2D_5X2.xml
create mode 100644 models/xml-repo/Skin2D_5X2_TF.xml
create mode 100644 models/xml-repo/SmallTestCase.xml
create mode 100644 models/xml-repo/VPC_lin15ko.xml
rename models/{xml => xml-repo}/VerySmallTestCase.xml (100%)
create mode 100644 src/bma_model.rs
create mode 100644 src/enums.rs
diff --git a/models/json-export-from-repo/2var_unstable (1).json b/models/json-export-from-repo/2var_unstable (1).json
new file mode 100644
index 0000000..e6c87e7
--- /dev/null
+++ b/models/json-export-from-repo/2var_unstable (1).json
@@ -0,0 +1 @@
+{"Model":{"Name":"2var_unstable","Variables":[{"Name":"X","Id":1,"RangeFrom":0,"RangeTo":1,"Formula":"var(2)"},{"Name":"Y","Id":2,"RangeFrom":0,"RangeTo":1,"Formula":"var(1)"}],"Relationships":[{"Id":1,"FromVariable":1,"ToVariable":2,"Type":"Activator"},{"Id":0,"FromVariable":2,"ToVariable":1,"Type":"Activator"}]},"Layout":{"Variables":[{"Id":1,"Name":"X","Type":"Default","ContainerId":1,"PositionX":595.8666666666667,"PositionY":358.8857142857143,"CellX":null,"CellY":null,"Angle":0,"Description":""},{"Id":2,"Name":"Y","Type":"Default","ContainerId":1,"PositionX":659.2,"PositionY":424.6,"CellX":null,"CellY":null,"Angle":0,"Description":""}],"Containers":[{"Id":1,"Name":"","Size":1,"PositionX":2,"PositionY":1}],"AnnotatedGridCells":[],"Description":""},"ltl":{"states":[],"operations":[]}}
\ No newline at end of file
diff --git a/models/json-export-from-repo/Default Model.json b/models/json-export-from-repo/Default Model.json
new file mode 100644
index 0000000..00eac4b
--- /dev/null
+++ b/models/json-export-from-repo/Default Model.json
@@ -0,0 +1 @@
+{"Model":{"Name":"Default Model","Variables":[{"Name":"a","Id":5,"RangeFrom":4,"RangeTo":4,"Formula":""},{"Name":"b","Id":1,"RangeFrom":0,"RangeTo":4,"Formula":"var(5)/2 - var(3)"},{"Name":"c","Id":2,"RangeFrom":0,"RangeTo":4,"Formula":"var(1)"},{"Name":"d","Id":4,"RangeFrom":0,"RangeTo":4,"Formula":"var(2)"},{"Name":"e","Id":3,"RangeFrom":0,"RangeTo":4,"Formula":"var(4)"}],"Relationships":[{"Id":1,"FromVariable":5,"ToVariable":1,"Type":"Activator"},{"Id":2,"FromVariable":1,"ToVariable":2,"Type":"Activator"},{"Id":3,"FromVariable":2,"ToVariable":4,"Type":"Activator"},{"Id":5,"FromVariable":3,"ToVariable":1,"Type":"Inhibitor"},{"Id":4,"FromVariable":4,"ToVariable":3,"Type":"Activator"}]},"Layout":{"Variables":[{"Id":5,"Name":"a","Type":"Constant","ContainerId":0,"PositionX":406.6666666666667,"PositionY":107.14285714285714,"CellX":null,"CellY":null,"Angle":0,"Description":""},{"Id":1,"Name":"b","Type":"MembraneReceptor","ContainerId":1,"PositionX":629.0696034252197,"PositionY":3.579843570048979,"CellX":0,"CellY":0,"Angle":0,"Description":""},{"Id":2,"Name":"c","Type":"Default","ContainerId":1,"PositionX":573.0666666666667,"PositionY":102.54285714285714,"CellX":null,"CellY":null,"Angle":0,"Description":""},{"Id":4,"Name":"d","Type":"Default","ContainerId":1,"PositionX":620.5666666666666,"PositionY":168.25714285714287,"CellX":null,"CellY":null,"Angle":0,"Description":""},{"Id":3,"Name":"e","Type":"Default","ContainerId":1,"PositionX":683.9,"PositionY":102.54285714285714,"CellX":null,"CellY":null,"Angle":0,"Description":""}],"Containers":[{"Id":1,"Name":"","Size":1,"PositionX":2,"PositionY":0}],"AnnotatedGridCells":[],"Description":""},"ltl":{"states":[],"operations":[]}}
\ No newline at end of file
diff --git a/models/json-export-from-repo/E coli Tarfunc.json b/models/json-export-from-repo/E coli Tarfunc.json
new file mode 100644
index 0000000..f92584f
--- /dev/null
+++ b/models/json-export-from-repo/E coli Tarfunc.json
@@ -0,0 +1 @@
+{"Model":{"Name":"E coli Tarfunc","Variables":[{"Name":"Aspartate","Id":14,"RangeFrom":0,"RangeTo":4,"Formula":"0"},{"Name":"Nickel","Id":15,"RangeFrom":0,"RangeTo":4,"Formula":"0"},{"Name":"Tar","Id":1,"RangeFrom":0,"RangeTo":4,"Formula":"2*(1-var(14)+var(15))-floor(var(3)*2/3)+var(13)"},{"Name":"CheA","Id":2,"RangeFrom":0,"RangeTo":4,"Formula":"var(1)"},{"Name":"CheY","Id":9,"RangeFrom":0,"RangeTo":4,"Formula":"ceil(var(2)/3)"},{"Name":"Motor","Id":10,"RangeFrom":0,"RangeTo":4,"Formula":""},{"Name":"CheR","Id":13,"RangeFrom":0,"RangeTo":4,"Formula":"1"},{"Name":"CheB","Id":3,"RangeFrom":0,"RangeTo":9,"Formula":""}],"Relationships":[{"Id":6,"FromVariable":2,"ToVariable":9,"Type":"Activator"},{"Id":2,"FromVariable":2,"ToVariable":3,"Type":"Activator"},{"Id":1,"FromVariable":1,"ToVariable":2,"Type":"Activator"},{"Id":11,"FromVariable":13,"ToVariable":1,"Type":"Activator"},{"Id":12,"FromVariable":15,"ToVariable":1,"Type":"Activator"},{"Id":13,"FromVariable":14,"ToVariable":1,"Type":"Inhibitor"},{"Id":14,"FromVariable":3,"ToVariable":1,"Type":"Activator"},{"Id":7,"FromVariable":9,"ToVariable":10,"Type":"Activator"}]},"Layout":{"Variables":[{"Id":14,"Name":"Aspartate","Type":"Constant","ContainerId":0,"PositionX":204.16666666666666,"PositionY":41.42857142857143,"CellX":null,"CellY":null,"Angle":0,"Description":""},{"Id":15,"Name":"Nickel","Type":"Constant","ContainerId":0,"PositionX":188.33333333333334,"PositionY":189.28571428571428,"CellX":null,"CellY":null,"Angle":0,"Description":""},{"Id":1,"Name":"Tar","Type":"MembraneReceptor","ContainerId":1,"PositionX":256.5135611766465,"PositionY":127.33220023058388,"CellX":0,"CellY":0,"Angle":-90,"Description":""},{"Id":2,"Name":"CheA","Type":"Default","ContainerId":1,"PositionX":323.06666666666666,"PositionY":168.25714285714287,"CellX":null,"CellY":null,"Angle":0,"Description":""},{"Id":9,"Name":"CheY","Type":"Default","ContainerId":1,"PositionX":367.4,"PositionY":199.8,"CellX":null,"CellY":null,"Angle":0,"Description":""},{"Id":10,"Name":"Motor","Type":"MembraneReceptor","ContainerId":1,"PositionX":493.4380180393696,"PositionY":126.74981302279934,"CellX":0,"CellY":0,"Angle":90,"Description":""},{"Id":13,"Name":"CheR","Type":"Default","ContainerId":1,"PositionX":351.56666666666666,"PositionY":51.94285714285714,"CellX":null,"CellY":null,"Angle":0,"Description":""},{"Id":3,"Name":"CheB","Type":"Default","ContainerId":1,"PositionX":386.4,"PositionY":102.54285714285714,"CellX":null,"CellY":null,"Angle":0,"Description":""}],"Containers":[{"Id":1,"Name":"C0","Size":1,"PositionX":1,"PositionY":0}],"AnnotatedGridCells":[],"Description":""},"ltl":{"states":[],"operations":[]}}
\ No newline at end of file
diff --git a/models/json-export-from-repo/New Model.json b/models/json-export-from-repo/New Model.json
new file mode 100644
index 0000000..824627d
--- /dev/null
+++ b/models/json-export-from-repo/New Model.json
@@ -0,0 +1 @@
+{"Model":{"Name":"New Model","Variables":[{"Name":"a","Id":1,"RangeFrom":0,"RangeTo":1,"Formula":"var(2)"},{"Name":"b","Id":2,"RangeFrom":0,"RangeTo":1,"Formula":"1-var(1)"}],"Relationships":[{"Id":1,"FromVariable":1,"ToVariable":2,"Type":"Activator"},{"Id":2,"FromVariable":2,"ToVariable":1,"Type":"Activator"}]},"Layout":{"Variables":[{"Id":1,"Name":"a","Type":"Default","ContainerId":1,"PositionX":101.56666666666666,"PositionY":84.8,"CellX":null,"CellY":null,"Angle":0,"Description":""},{"Id":2,"Name":"b","Type":"Default","ContainerId":1,"PositionX":149.06666666666666,"PositionY":134.0857142857143,"CellX":null,"CellY":null,"Angle":0,"Description":""}],"Containers":[{"Id":1,"Name":"","Size":1,"PositionX":0,"PositionY":0}],"AnnotatedGridCells":[],"Description":""},"ltl":{"states":[],"operations":[]}}
\ No newline at end of file
diff --git a/models/json-export-from-repo/Resting Neuron.json b/models/json-export-from-repo/Resting Neuron.json
new file mode 100644
index 0000000..92bb8f4
--- /dev/null
+++ b/models/json-export-from-repo/Resting Neuron.json
@@ -0,0 +1 @@
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diff --git a/models/json-export-from-tool/Oscillatory negative feedback.json b/models/json-export-from-tool/Oscillatory negative feedback.json
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diff --git a/models/json-export-from-tool/Sigmoidal.json b/models/json-export-from-tool/Sigmoidal.json
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index 0000000..755f5d3
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+++ b/models/json-repo/ceilFunc.json
@@ -0,0 +1 @@
+{"Model":{"Name":"E coli Tarfunc","Variables":[{"Id":14,"RangeFrom":0,"RangeTo":4,"Formula":"0"},{"Id":15,"RangeFrom":0,"RangeTo":4,"Formula":"0"},{"Id":1,"RangeFrom":0,"RangeTo":4,"Formula":"2*(1-var(14)+var(15))-floor(var(3)*2/3)+var(13)"},{"Id":2,"RangeFrom":0,"RangeTo":4,"Formula":"var(1)"},{"Id":9,"RangeFrom":0,"RangeTo":4,"Formula":"ceil(var(2)/3)"},{"Id":10,"RangeFrom":0,"RangeTo":4,"Formula":""},{"Id":13,"RangeFrom":0,"RangeTo":4,"Formula":"1"},{"Id":3,"RangeFrom":0,"RangeTo":9,"Formula":""}],"Relationships":[{"Id":6,"FromVariable":2,"ToVariable":9,"Type":"Activator"},{"Id":2,"FromVariable":2,"ToVariable":3,"Type":"Activator"},{"Id":1,"FromVariable":1,"ToVariable":2,"Type":"Activator"},{"Id":11,"FromVariable":13,"ToVariable":1,"Type":"Activator"},{"Id":12,"FromVariable":15,"ToVariable":1,"Type":"Activator"},{"Id":13,"FromVariable":14,"ToVariable":1,"Type":"Inhibitor"},{"Id":14,"FromVariable":3,"ToVariable":1,"Type":"Activator"},{"Id":7,"FromVariable":9,"ToVariable":10,"Type":"Activator"}]},"Layout":{"Variables":[{"Id":14,"Name":"Aspartate","Type":"Constant","ContainerId":0,"PositionX":204.16666666666666,"PositionY":41.42857142857143,"CellX":null,"CellY":null,"Angle":0},{"Id":15,"Name":"Nickel","Type":"Constant","ContainerId":0,"PositionX":188.33333333333334,"PositionY":189.28571428571428,"CellX":null,"CellY":null,"Angle":0},{"Id":1,"Name":"Tar","Type":"MembraneReceptor","ContainerId":1,"PositionX":270.9115781789792,"PositionY":128.87154260827256,"CellX":null,"CellY":null,"Angle":-90},{"Id":2,"Name":"CheA","Type":"Default","ContainerId":1,"PositionX":323.06666666666666,"PositionY":168.25714285714287,"CellX":null,"CellY":null,"Angle":0},{"Id":9,"Name":"CheY","Type":"Default","ContainerId":1,"PositionX":367.4,"PositionY":199.8,"CellX":null,"CellY":null,"Angle":0},{"Id":10,"Name":"Motor","Type":"MembraneReceptor","ContainerId":1,"PositionX":484.0055640954981,"PositionY":127.80506352833035,"CellX":null,"CellY":null,"Angle":90},{"Id":13,"Name":"CheR","Type":"Default","ContainerId":1,"PositionX":351.56666666666666,"PositionY":51.94285714285714,"CellX":null,"CellY":null,"Angle":0},{"Id":3,"Name":"CheB","Type":"Default","ContainerId":1,"PositionX":386.4,"PositionY":102.54285714285714,"CellX":null,"CellY":null,"Angle":0}],"Containers":[{"Id":1,"Name":"","Size":1,"PositionX":1,"PositionY":0}]}}
\ No newline at end of file
diff --git a/models/json-repo/ion channel.json b/models/json-repo/ion channel.json
new file mode 100644
index 0000000..a5f03ac
--- /dev/null
+++ b/models/json-repo/ion channel.json
@@ -0,0 +1,73 @@
+{
+ "Model": {
+ "Name": "ion channel",
+ "Variables": [
+ {
+ "Id": 2,
+ "RangeFrom": 0,
+ "RangeTo": 1,
+ "Formula": ""
+ },
+ {
+ "Id": 3,
+ "RangeFrom": 0,
+ "RangeTo": 1,
+ "Formula": ""
+ }
+ ],
+ "Relationships": [
+ {
+ "Id": 4,
+ "FromVariable": 2,
+ "ToVariable": 3,
+ "Type": "Activator"
+ },
+ {
+ "Id": 5,
+ "FromVariable": 2,
+ "ToVariable": 2,
+ "Type": "Activator"
+ },
+ {
+ "Id": 6,
+ "FromVariable": 3,
+ "ToVariable": 2,
+ "Type": "Inhibitor"
+ }
+ ]
+ },
+ "Layout": {
+ "Variables": [
+ {
+ "Id": 2,
+ "Name": "",
+ "Type": "MembraneReceptor",
+ "ContainerId": 1,
+ "PositionX": 633.4614423293597,
+ "PositionY": -826.802736706546,
+ "CellX": 0,
+ "CellY": 0,
+ "Angle": 3.842338183320199
+ },
+ {
+ "Id": 3,
+ "Name": "",
+ "Type": "Default",
+ "ContainerId": 1,
+ "PositionX": 622.2222222222222,
+ "PositionY": -740.3777779473198,
+ "CellX": 0,
+ "CellY": 0,
+ "Angle": 0
+ }
+ ],
+ "Containers": [
+ {
+ "Id": 1,
+ "Size": 1,
+ "PositionX": 2,
+ "PositionY": -3
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/models/readme.md b/models/readme.md
new file mode 100644
index 0000000..ffc8c37
--- /dev/null
+++ b/models/readme.md
@@ -0,0 +1,11 @@
+We have following sets of model files:
+- `xml-repo` - XML models collected in the Github repository in folder [Models](https://github.com/hallba/BioModelAnalyzer/tree/master/Models)
+- `json-repo` - JSON models collected in the Github repository in folder [BackEndTests](https://github.com/hallba/BioModelAnalyzer/tree/master/src/BackEndTests)
+- `json-export-from-repo` - we took models from `xml-repo` and `json-repo`, uploaded them to the [tool](https://biomodelanalyzer.org/tool.html), and exported them (so that we have the newest supported format)
+- `json-export-from-tool` - selection of all models shown in the [tool](https://biomodelanalyzer.org/tool.html), exported in the newest JSON
+
+Note that models can (by design) be replicated in different folders.
+We just use them to cover wide range of possible formats and model variants, so that we can properly test the parser.
+In future, we should curate them a bit.
+
+Note that model formats might not be the same. For example, the XML and JSON formats differ. Also, JSON models in `json-repo` sometimes differ in specific format.
\ No newline at end of file
diff --git a/models/xml-repo/2var_unstable.xml b/models/xml-repo/2var_unstable.xml
new file mode 100644
index 0000000..8dda654
--- /dev/null
+++ b/models/xml-repo/2var_unstable.xml
@@ -0,0 +1,60 @@
+
+
+ This is the default model.
+ 2012-10-14T15:04:16.301427+01:00
+ 2012-10-14T15:04:16.301427+01:00
+
+ 6
+ 5
+ 44.76
+ 0
+ 428
+
+
+
+ 2
+ 1
+ 1
+
+
+
+
+ 1
+ Default
+ 0
+ 1
+ var(Y)
+ 104
+ 82
+ 2
+ 1
+ 0
+
+
+ 1
+ Default
+ 0
+ 1
+ var(X)
+ 204
+ 182
+ 2
+ 1
+ 0
+
+
+
+
+ 1
+ 1
+ 2
+ Activator
+
+
+ 1
+ 2
+ 1
+ Activator
+
+
+
\ No newline at end of file
diff --git a/models/xml-repo/BooleanLoop.xml b/models/xml-repo/BooleanLoop.xml
new file mode 100644
index 0000000..37ae22a
--- /dev/null
+++ b/models/xml-repo/BooleanLoop.xml
@@ -0,0 +1,60 @@
+
+
+ This is a new model.
+ 2012-10-20T21:18:58.0516882+01:00
+ 2012-10-20T21:18:58.0516882+01:00
+
+ 1
+ 1
+ 4
+ 0
+ 0
+
+
+
+ 0
+ 0
+ 1
+
+
+
+
+ 1
+ Default
+ 0
+ 1
+ var(b)
+ 113
+ 91
+ 0
+ 0
+ 0
+
+
+ 1
+ Default
+ 0
+ 1
+ 1-var(a)
+ 188
+ 166
+ 0
+ 0
+ 0
+
+
+
+
+ 1
+ 1
+ 2
+ Activator
+
+
+ 1
+ 2
+ 1
+ Activator
+
+
+
\ No newline at end of file
diff --git a/models/xml-repo/NoLoopFound.xml b/models/xml-repo/NoLoopFound.xml
new file mode 100644
index 0000000..e95c28a
--- /dev/null
+++ b/models/xml-repo/NoLoopFound.xml
@@ -0,0 +1,114 @@
+
+
+ This is the default model.
+ 2012-10-01T09:34:01.9209266+01:00
+ 2012-10-16T12:33:04.3040693+01:00
+
+ 6
+ 5
+ 0
+ 901
+ 0
+
+
+
+ 2
+ 0
+ 1
+
+
+
+
+ 0
+ Constant
+ 4
+ 4
+
+ 200
+ 125
+ 1
+ 0
+ 0
+
+
+ 1
+ MembraneReceptor
+ 0
+ 4
+ var(a)/2 - var(e)
+ 156
+ -20
+ 2
+ 0
+ 0
+
+
+ 1
+ Default
+ 0
+ 4
+ var(b)
+ 68
+ 118
+ 2
+ 0
+ 0
+
+
+ 1
+ Default
+ 0
+ 4
+ var(c)
+ 143
+ 218
+ 2
+ 0
+ 0
+
+
+ 1
+ Default
+ 0
+ 4
+ var(d)
+ 243
+ 118
+ 2
+ 0
+ 0
+
+
+
+
+ 0
+ 5
+ 1
+ Activator
+
+
+ 1
+ 1
+ 2
+ Activator
+
+
+ 1
+ 2
+ 4
+ Activator
+
+
+ 1
+ 3
+ 1
+ Inhibitor
+
+
+ 1
+ 4
+ 3
+ Activator
+
+
+
\ No newline at end of file
diff --git a/models/xml-repo/SSkin1D.xml b/models/xml-repo/SSkin1D.xml
new file mode 100644
index 0000000..a18ee31
--- /dev/null
+++ b/models/xml-repo/SSkin1D.xml
@@ -0,0 +1,680 @@
+
+
+ Description
+ 2012-10-27T13:57:40.3364976+01:00
+ 2012-10-27T13:57:40.3364976+01:00
+
+ 6
+ 5
+ 82.49
+ 0
+ 300
+
+
+
+ 0
+ 2
+ 1
+
+
+ 1
+ 2
+ 1
+
+
+ 2
+ 2
+ 1
+
+
+ 3
+ 2
+ 1
+
+
+ 4
+ 2
+ 1
+
+
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 0
+ 1
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 1
+ 1
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 3
+ 1
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 4
+ 1
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 0
+ 3
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 1
+ 3
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 2
+ 3
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 2
+ 1
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 3
+ 3
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 4
+ 3
+ 0
+
+
+ 1
+ Default
+ 0
+ 4
+
+ 209
+ 84
+ 0
+ 2
+ 0
+
+
+ 1
+ MembraneReceptor
+ 0
+ 4
+
+ 156
+ 344
+ 0
+ 2
+ 180
+
+
+ 1
+ MembraneReceptor
+ 0
+ 4
+
+ 258
+ 298
+ 0
+ 2
+ 135
+
+
+ 1
+ Default
+ 0
+ 4
+ min(var(Notch), var(Ligand-in))
+ 204
+ 182
+ 0
+ 2
+ 0
+
+
+ 2
+ Default
+ 0
+ 4
+
+ 209
+ 84
+ 1
+ 2
+ 0
+
+
+ 2
+ MembraneReceptor
+ 0
+ 4
+
+ 156
+ 344
+ 1
+ 2
+ 180
+
+
+ 2
+ MembraneReceptor
+ 0
+ 4
+
+ 258
+ 298
+ 1
+ 2
+ 135
+
+
+ 2
+ Default
+ 0
+ 4
+ min(var(Notch), var(Ligand-in))
+ 209
+ 184
+ 1
+ 2
+ 0
+
+
+ 3
+ Default
+ 0
+ 4
+
+ 209
+ 84
+ 2
+ 2
+ 0
+
+
+ 3
+ MembraneReceptor
+ 0
+ 4
+
+ 258
+ 298
+ 2
+ 2
+ 135
+
+
+ 3
+ MembraneReceptor
+ 0
+ 4
+
+ 156
+ 344
+ 2
+ 2
+ 180
+
+
+ 3
+ Default
+ 0
+ 4
+ min(var(Notch), var(Ligand-in))
+ 204
+ 182
+ 2
+ 2
+ 0
+
+
+ 4
+ Default
+ 0
+ 4
+
+ 209
+ 84
+ 3
+ 2
+ 0
+
+
+ 4
+ MembraneReceptor
+ 0
+ 4
+
+ 156
+ 344
+ 3
+ 2
+ 180
+
+
+ 4
+ MembraneReceptor
+ 0
+ 4
+
+ 258
+ 298
+ 3
+ 2
+ 135
+
+
+ 4
+ Default
+ 0
+ 4
+ min(var(Notch), var(Ligand-in))
+ 204
+ 182
+ 3
+ 2
+ 0
+
+
+ 5
+ Default
+ 0
+ 4
+
+ 209
+ 84
+ 4
+ 2
+ 0
+
+
+ 5
+ MembraneReceptor
+ 0
+ 4
+
+ 156
+ 344
+ 4
+ 2
+ 180
+
+
+ 5
+ MembraneReceptor
+ 0
+ 4
+
+ 258
+ 298
+ 4
+ 2
+ 135
+
+
+ 5
+ Default
+ 0
+ 4
+ min(var(Notch), var(Ligand-in))
+ 204
+ 182
+ 4
+ 2
+ 0
+
+
+
+
+ 2
+ 14
+ 1
+ Activator
+
+
+ 1
+ 12
+ 2
+ Activator
+
+
+ 3
+ 16
+ 2
+ Activator
+
+
+ 2
+ 14
+ 9
+ Activator
+
+
+ 4
+ 18
+ 9
+ Activator
+
+
+ 3
+ 16
+ 4
+ Activator
+
+
+ 5
+ 20
+ 4
+ Activator
+
+
+ 4
+ 18
+ 5
+ Activator
+
+
+ 0
+ 6
+ 32
+ Activator
+
+
+ 0
+ 7
+ 33
+ Activator
+
+
+ 0
+ 8
+ 34
+ Activator
+
+
+ 0
+ 10
+ 35
+ Activator
+
+
+ 0
+ 11
+ 36
+ Activator
+
+
+ 1
+ 32
+ 12
+ Inhibitor
+
+
+ 2
+ 33
+ 14
+ Inhibitor
+
+
+ 3
+ 34
+ 16
+ Inhibitor
+
+
+ 4
+ 35
+ 18
+ Inhibitor
+
+
+ 5
+ 36
+ 20
+ Inhibitor
+
+
+ 0
+ 1
+ 24
+ Activator
+
+
+ 1
+ 24
+ 7
+ Activator
+
+
+ 1
+ 32
+ 24
+ Activator
+
+
+ 0
+ 6
+ 25
+ Activator
+
+
+ 1
+ 25
+ 32
+ Activator
+
+
+ 0
+ 2
+ 26
+ Activator
+
+
+ 2
+ 26
+ 6
+ Activator
+
+
+ 2
+ 26
+ 8
+ Activator
+
+
+ 2
+ 33
+ 26
+ Activator
+
+
+ 0
+ 7
+ 27
+ Activator
+
+
+ 2
+ 27
+ 33
+ Activator
+
+
+ 0
+ 8
+ 22
+ Activator
+
+
+ 3
+ 22
+ 10
+ Activator
+
+
+ 3
+ 22
+ 34
+ Activator
+
+
+ 0
+ 9
+ 23
+ Activator
+
+
+ 3
+ 23
+ 7
+ Activator
+
+
+ 3
+ 34
+ 23
+ Activator
+
+
+ 0
+ 4
+ 28
+ Activator
+
+
+ 4
+ 28
+ 8
+ Activator
+
+
+ 4
+ 28
+ 11
+ Activator
+
+
+ 4
+ 35
+ 28
+ Activator
+
+
+ 0
+ 10
+ 29
+ Activator
+
+
+ 4
+ 29
+ 35
+ Activator
+
+
+ 0
+ 5
+ 30
+ Activator
+
+
+ 5
+ 30
+ 10
+ Activator
+
+
+ 5
+ 36
+ 30
+ Activator
+
+
+ 0
+ 11
+ 31
+ Activator
+
+
+ 5
+ 31
+ 36
+ Activator
+
+
+
\ No newline at end of file
diff --git a/models/xml-repo/SSkin1D_TF.xml b/models/xml-repo/SSkin1D_TF.xml
new file mode 100644
index 0000000..16ae281
--- /dev/null
+++ b/models/xml-repo/SSkin1D_TF.xml
@@ -0,0 +1,680 @@
+
+
+ Description
+ 2012-10-27T14:10:08.1815447+01:00
+ 2012-10-27T14:10:08.1815447+01:00
+
+ 6
+ 5
+ 28.42
+ 0
+ 701
+
+
+
+ 0
+ 2
+ 1
+
+
+ 1
+ 2
+ 1
+
+
+ 2
+ 2
+ 1
+
+
+ 3
+ 2
+ 1
+
+
+ 4
+ 2
+ 1
+
+
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 0
+ 1
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+ var(Wnt)+var(Wnt)
+ 159
+ 179
+ 1
+ 1
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+ var(Wnt)+var(Wnt)
+ 159
+ 179
+ 3
+ 1
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 4
+ 1
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 0
+ 3
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 1
+ 3
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 2
+ 3
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+ var(Wnt)+var(Wnt)
+ 159
+ 179
+ 2
+ 1
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 3
+ 3
+ 0
+
+
+ 0
+ Constant
+ 0
+ 4
+
+ 159
+ 179
+ 4
+ 3
+ 0
+
+
+ 1
+ Default
+ 0
+ 4
+
+ 209
+ 84
+ 0
+ 2
+ 0
+
+
+ 1
+ MembraneReceptor
+ 0
+ 4
+ var(Wnt-ext)+var(Notch-IC)
+ 156
+ 344
+ 0
+ 2
+ 180
+
+
+ 1
+ MembraneReceptor
+ 0
+ 4
+
+ 258
+ 298
+ 0
+ 2
+ 135
+
+
+ 1
+ Default
+ 0
+ 4
+ min(var(Notch), var(Ligand-in))
+ 204
+ 182
+ 0
+ 2
+ 0
+
+
+ 2
+ Default
+ 0
+ 4
+
+ 209
+ 84
+ 1
+ 2
+ 0
+
+
+ 2
+ MembraneReceptor
+ 0
+ 4
+ var(Wnt-ext)+var(Notch-IC)
+ 156
+ 344
+ 1
+ 2
+ 180
+
+
+ 2
+ MembraneReceptor
+ 0
+ 4
+
+ 258
+ 298
+ 1
+ 2
+ 135
+
+
+ 2
+ Default
+ 0
+ 4
+ min(var(Notch), var(Ligand-in))
+ 209
+ 184
+ 1
+ 2
+ 0
+
+
+ 3
+ Default
+ 0
+ 4
+
+ 209
+ 84
+ 2
+ 2
+ 0
+
+
+ 3
+ MembraneReceptor
+ 0
+ 4
+
+ 258
+ 298
+ 2
+ 2
+ 135
+
+
+ 3
+ MembraneReceptor
+ 0
+ 4
+ var(Wnt-ext)+var(Notch-IC)
+ 156
+ 344
+ 2
+ 2
+ 180
+
+
+ 3
+ Default
+ 0
+ 4
+ min(var(Notch), var(Ligand-in))
+ 204
+ 182
+ 2
+ 2
+ 0
+
+
+ 4
+ Default
+ 0
+ 4
+
+ 209
+ 84
+ 3
+ 2
+ 0
+
+
+ 4
+ MembraneReceptor
+ 0
+ 4
+ var(Notch-IC)+var(Wnt-ext)
+ 156
+ 344
+ 3
+ 2
+ 180
+
+
+ 4
+ MembraneReceptor
+ 0
+ 4
+
+ 258
+ 298
+ 3
+ 2
+ 135
+
+
+ 4
+ Default
+ 0
+ 4
+ min(var(Notch), var(Ligand-in))
+ 204
+ 182
+ 3
+ 2
+ 0
+
+
+ 5
+ Default
+ 0
+ 4
+
+ 209
+ 84
+ 4
+ 2
+ 0
+
+
+ 5
+ MembraneReceptor
+ 0
+ 4
+ var(Notch-IC)+var(Wnt-ext)
+ 156
+ 344
+ 4
+ 2
+ 180
+
+
+ 5
+ MembraneReceptor
+ 0
+ 4
+
+ 258
+ 298
+ 4
+ 2
+ 135
+
+
+ 5
+ Default
+ 0
+ 4
+ min(var(Notch), var(Ligand-in))
+ 204
+ 182
+ 4
+ 2
+ 0
+
+
+
+
+ 2
+ 14
+ 1
+ Activator
+
+
+ 1
+ 12
+ 2
+ Activator
+
+
+ 3
+ 16
+ 2
+ Activator
+
+
+ 2
+ 14
+ 9
+ Activator
+
+
+ 4
+ 18
+ 9
+ Activator
+
+
+ 3
+ 16
+ 4
+ Activator
+
+
+ 5
+ 20
+ 4
+ Activator
+
+
+ 4
+ 18
+ 5
+ Activator
+
+
+ 0
+ 6
+ 32
+ Activator
+
+
+ 0
+ 7
+ 33
+ Activator
+
+
+ 0
+ 8
+ 34
+ Activator
+
+
+ 0
+ 10
+ 35
+ Activator
+
+
+ 0
+ 11
+ 36
+ Activator
+
+
+ 1
+ 32
+ 12
+ Inhibitor
+
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\ No newline at end of file
diff --git a/models/xml-repo/SSkin1D_analysis_hang.xml b/models/xml-repo/SSkin1D_analysis_hang.xml
new file mode 100644
index 0000000..b19ccea
--- /dev/null
+++ b/models/xml-repo/SSkin1D_analysis_hang.xml
@@ -0,0 +1,680 @@
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+
+ Description
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+ 2012-10-27T13:59:01.0563644+01:00
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\ No newline at end of file
diff --git a/models/xml-repo/SSkin2D_3cells_2layers.xml b/models/xml-repo/SSkin2D_3cells_2layers.xml
new file mode 100644
index 0000000..29e67d8
--- /dev/null
+++ b/models/xml-repo/SSkin2D_3cells_2layers.xml
@@ -0,0 +1,913 @@
+
+
+ Description
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+ 2012-10-27T14:16:13.0007404+01:00
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+ 25
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+
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+
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+
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+
+
\ No newline at end of file
diff --git a/models/xml/Skin1D.xml b/models/xml-repo/Skin1D.xml
similarity index 97%
rename from models/xml/Skin1D.xml
rename to models/xml-repo/Skin1D.xml
index 352e7ec..795ddaf 100644
--- a/models/xml/Skin1D.xml
+++ b/models/xml-repo/Skin1D.xml
@@ -1,14 +1,14 @@

Description
- 2012-05-30T10:14:04.4761834+01:00
- 2012-05-30T12:15:31.1964861+01:00
+ 2012-10-27T13:16:01.6519909+01:00
+ 2012-10-27T13:16:01.6519909+01:00
6
5
- 100
- 646
- 402
+ 98.76
+ 0
+ 95
@@ -115,7 +115,7 @@
Constant
0
4
- (4+var(Wnt))/2
+
159
179
1
@@ -127,7 +127,7 @@
Constant
0
4
- (2+var(Jagged))/2
+
159
179
1
@@ -139,7 +139,7 @@
Constant
0
4
- var(Wnt)/2
+
159
179
5
@@ -151,7 +151,7 @@
Constant
0
4
- (2+var(Jagged))/2
+
159
179
5
@@ -247,7 +247,7 @@
Default
0
4
- 4
+
159
109
2
@@ -259,7 +259,7 @@
Default
0
4
- 4
+
159
184
2
@@ -415,7 +415,7 @@
Default
0
4
- 4
+
159
109
3
@@ -427,7 +427,7 @@
Default
0
4
- 4
+
159
184
3
@@ -571,7 +571,7 @@
Default
0
4
- 4
+
159
109
4
@@ -583,7 +583,7 @@
Default
0
4
- 4
+
159
184
4
@@ -715,7 +715,7 @@
Default
0
4
- 4
+
159
109
1
@@ -727,7 +727,7 @@
Default
0
4
- 4
+
159
184
1
@@ -883,7 +883,7 @@
Default
0
4
- 4
+
159
109
5
@@ -895,7 +895,7 @@
Default
0
4
- 4
+
159
184
5
@@ -1234,36 +1234,18 @@
92
Activator
-
- 3
- 33
- 75
- Activator
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index 0000000..da6547c
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\ No newline at end of file
diff --git a/models/xml-repo/Skin2D_3cells_2layers.xml b/models/xml-repo/Skin2D_3cells_2layers.xml
new file mode 100644
index 0000000..3a1ef60
--- /dev/null
+++ b/models/xml-repo/Skin2D_3cells_2layers.xml
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\ No newline at end of file
diff --git a/models/xml-repo/Skin2D_3cells_2layers_TF.xml b/models/xml-repo/Skin2D_3cells_2layers_TF.xml
new file mode 100644
index 0000000..c06c7b3
--- /dev/null
+++ b/models/xml-repo/Skin2D_3cells_2layers_TF.xml
@@ -0,0 +1,1837 @@
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\ No newline at end of file
diff --git a/models/xml-repo/Skin2D_3cells_2layers_TF_analysis_crash.xml b/models/xml-repo/Skin2D_3cells_2layers_TF_analysis_crash.xml
new file mode 100644
index 0000000..4bc129a
--- /dev/null
+++ b/models/xml-repo/Skin2D_3cells_2layers_TF_analysis_crash.xml
@@ -0,0 +1,1855 @@
+
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+ Description
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\ No newline at end of file
diff --git a/models/xml-repo/Skin2D_5X2.xml b/models/xml-repo/Skin2D_5X2.xml
new file mode 100644
index 0000000..aec8931
--- /dev/null
+++ b/models/xml-repo/Skin2D_5X2.xml
@@ -0,0 +1,3879 @@
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\ No newline at end of file
diff --git a/models/xml-repo/Skin2D_5X2_TF.xml b/models/xml-repo/Skin2D_5X2_TF.xml
new file mode 100644
index 0000000..924e2f2
--- /dev/null
+++ b/models/xml-repo/Skin2D_5X2_TF.xml
@@ -0,0 +1,3879 @@
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+
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+
+
\ No newline at end of file
diff --git a/models/xml-repo/SmallTestCase.xml b/models/xml-repo/SmallTestCase.xml
new file mode 100644
index 0000000..a27633c
--- /dev/null
+++ b/models/xml-repo/SmallTestCase.xml
@@ -0,0 +1,78 @@
+
+
+ This is a new model.
+ 2012-09-11T12:59:28.7119993+01:00
+ 2012-09-11T13:01:16.9361558+01:00
+
+ 6
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+ 0
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+
+ 1
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+
+
+ 1
+ 3
+ 1
+ Inhibitor
+
+
+
\ No newline at end of file
diff --git a/models/xml-repo/VPC_lin15ko.xml b/models/xml-repo/VPC_lin15ko.xml
new file mode 100644
index 0000000..0b31745
--- /dev/null
+++ b/models/xml-repo/VPC_lin15ko.xml
@@ -0,0 +1,1939 @@
+
+
+ Description
+ 2012-10-14T15:16:20.1478286+01:00
+ 2012-10-16T14:21:25.1469644+01:00
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+
+
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+ 33
+ 32
+ Inhibitor
+
+
+ 7
+ 31
+ 34
+ Activator
+
+
+ 8
+ 37
+ 38
+ Activator
+
+
+ 8
+ 38
+ 39
+ Activator
+
+
+ 8
+ 39
+ 40
+ Activator
+
+
+ 8
+ 40
+ 41
+ Activator
+
+
+ 8
+ 42
+ 41
+ Activator
+
+
+ 8
+ 37
+ 43
+ Inhibitor
+
+
+ 8
+ 43
+ 38
+ Inhibitor
+
+
+ 8
+ 43
+ 39
+ Inhibitor
+
+
+ 8
+ 43
+ 40
+ Inhibitor
+
+
+ 8
+ 43
+ 42
+ Inhibitor
+
+
+ 8
+ 41
+ 44
+ Activator
+
+
+ 9
+ 47
+ 48
+ Activator
+
+
+ 9
+ 48
+ 49
+ Activator
+
+
+ 9
+ 49
+ 50
+ Activator
+
+
+ 9
+ 50
+ 51
+ Activator
+
+
+ 9
+ 52
+ 51
+ Activator
+
+
+ 9
+ 47
+ 53
+ Inhibitor
+
+
+ 9
+ 53
+ 48
+ Inhibitor
+
+
+ 9
+ 53
+ 49
+ Inhibitor
+
+
+ 9
+ 53
+ 50
+ Inhibitor
+
+
+ 9
+ 53
+ 52
+ Inhibitor
+
+
+ 9
+ 51
+ 54
+ Activator
+
+
+ 10
+ 57
+ 58
+ Activator
+
+
+ 10
+ 58
+ 59
+ Activator
+
+
+ 10
+ 59
+ 60
+ Activator
+
+
+ 10
+ 60
+ 61
+ Activator
+
+
+ 10
+ 62
+ 61
+ Activator
+
+
+ 10
+ 57
+ 63
+ Inhibitor
+
+
+ 10
+ 63
+ 58
+ Inhibitor
+
+
+ 10
+ 63
+ 59
+ Inhibitor
+
+
+ 10
+ 63
+ 60
+ Inhibitor
+
+
+ 10
+ 63
+ 62
+ Inhibitor
+
+
+ 10
+ 61
+ 64
+ Activator
+
+
+ 11
+ 67
+ 68
+ Activator
+
+
+ 11
+ 68
+ 69
+ Activator
+
+
+ 11
+ 69
+ 70
+ Activator
+
+
+ 11
+ 70
+ 71
+ Activator
+
+
+ 11
+ 72
+ 71
+ Activator
+
+
+ 11
+ 67
+ 73
+ Inhibitor
+
+
+ 11
+ 73
+ 68
+ Inhibitor
+
+
+ 11
+ 73
+ 69
+ Inhibitor
+
+
+ 11
+ 73
+ 70
+ Inhibitor
+
+
+ 11
+ 73
+ 72
+ Inhibitor
+
+
+ 11
+ 71
+ 74
+ Activator
+
+
+ 12
+ 76
+ 75
+ Inhibitor
+
+
+ 13
+ 80
+ 79
+ Inhibitor
+
+
+ 14
+ 84
+ 83
+ Inhibitor
+
+
+ 15
+ 88
+ 87
+ Inhibitor
+
+
+ 16
+ 92
+ 91
+ Inhibitor
+
+
+ 6
+ 24
+ 8
+ Activator
+
+
+ 6
+ 21
+ 3
+ Activator
+
+
+ 12
+ 78
+ 52
+ Activator
+
+
+ 12
+ 75
+ 47
+ Activator
+
+
+ 13
+ 82
+ 62
+ Activator
+
+
+ 13
+ 79
+ 57
+ Activator
+
+
+ 14
+ 86
+ 72
+ Activator
+
+
+ 14
+ 83
+ 67
+ Activator
+
+
+ 15
+ 90
+ 32
+ Activator
+
+
+ 15
+ 87
+ 27
+ Activator
+
+
+ 16
+ 94
+ 42
+ Activator
+
+
+ 16
+ 91
+ 37
+ Activator
+
+
+ 10
+ 64
+ 86
+ Activator
+
+
+ 10
+ 61
+ 85
+ Activator
+
+
+ 11
+ 71
+ 81
+ Activator
+
+
+ 11
+ 74
+ 82
+ Activator
+
+
+ 10
+ 64
+ 78
+ Activator
+
+
+ 10
+ 61
+ 77
+ Activator
+
+
+ 9
+ 51
+ 81
+ Activator
+
+
+ 9
+ 54
+ 82
+ Activator
+
+
+ 9
+ 51
+ 23
+ Activator
+
+
+ 9
+ 54
+ 24
+ Activator
+
+
+ 1
+ 7
+ 77
+ Activator
+
+
+ 1
+ 10
+ 78
+ Activator
+
+
+ 1
+ 7
+ 89
+ Activator
+
+
+ 1
+ 10
+ 90
+ Activator
+
+
+ 7
+ 31
+ 23
+ Activator
+
+
+ 7
+ 34
+ 24
+ Activator
+
+
+ 7
+ 31
+ 93
+ Activator
+
+
+ 7
+ 34
+ 94
+ Activator
+
+
+ 8
+ 41
+ 89
+ Activator
+
+
+ 8
+ 44
+ 90
+ Activator
+
+
+ 1
+ 1
+ 3
+ Activator
+
+
+ 1
+ 1
+ 10
+ Activator
+
+
+ 0
+ 95
+ 1
+ Activator
+
+
+ 1
+ 2
+ 9
+ Activator
+
+
+ 1
+ 7
+ 2
+ Inhibitor
+
+
+ 6
+ 23
+ 2
+ Activator
+
+
+ 7
+ 25
+ 27
+ Activator
+
+
+ 7
+ 25
+ 34
+ Activator
+
+
+ 0
+ 95
+ 25
+ Activator
+
+
+ 7
+ 26
+ 33
+ Activator
+
+
+ 7
+ 31
+ 26
+ Inhibitor
+
+
+ 15
+ 89
+ 26
+ Activator
+
+
+ 8
+ 35
+ 37
+ Activator
+
+
+ 8
+ 35
+ 44
+ Activator
+
+
+ 0
+ 95
+ 35
+ Activator
+
+
+ 8
+ 36
+ 43
+ Activator
+
+
+ 8
+ 41
+ 36
+ Inhibitor
+
+
+ 16
+ 93
+ 36
+ Activator
+
+
+ 9
+ 45
+ 47
+ Activator
+
+
+ 9
+ 45
+ 54
+ Activator
+
+
+ 0
+ 95
+ 45
+ Activator
+
+
+ 9
+ 46
+ 53
+ Activator
+
+
+ 9
+ 51
+ 46
+ Inhibitor
+
+
+ 12
+ 77
+ 46
+ Activator
+
+
+ 10
+ 55
+ 57
+ Activator
+
+
+ 10
+ 55
+ 64
+ Activator
+
+
+ 0
+ 95
+ 55
+ Activator
+
+
+ 10
+ 56
+ 63
+ Activator
+
+
+ 10
+ 61
+ 56
+ Inhibitor
+
+
+ 13
+ 81
+ 56
+ Activator
+
+
+ 11
+ 65
+ 67
+ Activator
+
+
+ 11
+ 65
+ 74
+ Activator
+
+
+ 0
+ 95
+ 65
+ Activator
+
+
+ 11
+ 66
+ 73
+ Activator
+
+
+ 11
+ 71
+ 66
+ Inhibitor
+
+
+ 14
+ 85
+ 66
+ Activator
+
+
+
\ No newline at end of file
diff --git a/models/xml/VerySmallTestCase.xml b/models/xml-repo/VerySmallTestCase.xml
similarity index 100%
rename from models/xml/VerySmallTestCase.xml
rename to models/xml-repo/VerySmallTestCase.xml
diff --git a/src/bin/load_json.rs b/src/bin/load_json.rs
index 268fdc3..fcf1b65 100644
--- a/src/bin/load_json.rs
+++ b/src/bin/load_json.rs
@@ -1,15 +1,49 @@
+use biodivine_lib_bma_data::bma_model::BmaModel;
use biodivine_lib_bma_data::json_model::JsonBmaModel;
-use std::fs::read_to_string;
+use std::fs::{read_dir, read_to_string};
+
+/// Iterate through all models and see if they are parse without error.
+/// Results are printed, one line per model.
+fn test_parse_all_models_in_dir(models_dir: &str) {
+ let model_paths = read_dir(models_dir)
+ .expect("Unable to read directory")
+ .map(|entry| entry.expect("Unable to read entry").path())
+ .collect::>();
+
+ // Iterate over each JSON file and try to parse it
+ for model_path in model_paths {
+ let model_path_str = model_path.to_str().expect("Invalid path");
+ let json_data = read_to_string(&model_path)
+ .unwrap_or_else(|_| panic!("Unable to read file: {}", model_path_str));
+
+ let json_model: Result = serde_json::from_str(&json_data);
+
+ match json_model {
+ Ok(_) => {
+ println!("Successfully parsed model: `{model_path_str}`.");
+ }
+ Err(e) => {
+ println!("Failed to parse JSON file `{}`: {:?}.", model_path_str, e);
+ }
+ }
+ }
+ println!();
+}
fn main() {
- let json_data =
- read_to_string("models/json/SimpleBifurcation.json").expect("Unable to read file");
- let resting_neuron: JsonBmaModel =
- serde_json::from_str(&json_data).expect("JSON was not well-formatted");
- println!("{:?}", resting_neuron);
-
- let json_data = read_to_string("models/json/RestingNeuron.json").expect("Unable to read file");
- let resting_neuron: JsonBmaModel =
- serde_json::from_str(&json_data).expect("JSON was not well-formatted");
- println!("{:?}", resting_neuron);
+ // 1) first, let's just check the small example and print the internal structure
+ let selected_model_paths = vec!["models/json-repo/SimpleBifurcation.json"];
+ for model_path in selected_model_paths {
+ println!("Parsing selected model {:?}:", model_path);
+ let json_data = read_to_string(model_path).expect("Unable to read file");
+ let json_model: JsonBmaModel =
+ serde_json::from_str(&json_data).expect("JSON was not well-formatted");
+ let model = BmaModel::from(json_model);
+ println!("Internal structure:\n{:?}\n", model);
+ }
+
+ // 2) now let's iterate through all models and see if they at least parse without error
+ test_parse_all_models_in_dir("models/json-repo/");
+ test_parse_all_models_in_dir("models/json-export-from-repo/");
+ test_parse_all_models_in_dir("models/json-export-from-tool/");
}
diff --git a/src/bin/load_xml.rs b/src/bin/load_xml.rs
index 4b6fc6c..2744d16 100644
--- a/src/bin/load_xml.rs
+++ b/src/bin/load_xml.rs
@@ -1,14 +1,47 @@
+use biodivine_lib_bma_data::bma_model::BmaModel;
use biodivine_lib_bma_data::xml_model::XmlBmaModel;
-use std::fs::read_to_string;
+use std::fs::{read_dir, read_to_string};
+
+/// Iterate through all models and see if they are parse without error.
+/// Results are printed, one line per model.
+fn test_parse_all_models_in_dir(models_dir: &str) {
+ let model_paths = read_dir(models_dir)
+ .expect("Unable to read directory")
+ .map(|entry| entry.expect("Unable to read entry").path())
+ .collect::>();
+
+ // Iterate over each XML file and try to parse it
+ for model_path in model_paths {
+ let model_path_str = model_path.to_str().expect("Invalid path");
+ let xml_data = read_to_string(&model_path)
+ .unwrap_or_else(|_| panic!("Unable to read file: {}", model_path_str));
+
+ let xml_model: Result = serde_xml_rs::from_str(&xml_data);
+
+ match xml_model {
+ Ok(_) => {
+ println!("Successfully parsed model: `{model_path_str}`.");
+ }
+ Err(e) => {
+ println!("Failed to parse XML file `{}`: {:?}.", model_path_str, e);
+ }
+ }
+ }
+ println!();
+}
fn main() {
- let xml_data = read_to_string("models/xml/VerySmallTestCase.xml").expect("Unable to read file");
- let xml_model: XmlBmaModel =
- serde_xml_rs::from_str(&xml_data).expect("XML was not well-formatted");
- println!("{:?}", xml_model);
-
- let xml_data = read_to_string("models/xml/Skin1D.xml").expect("Unable to read file");
- let xml_model: XmlBmaModel =
- serde_xml_rs::from_str(&xml_data).expect("XML was not well-formatted");
- println!("{:?}", xml_model);
+ // 1) first, let's just check the small example and print the internal structure
+ let selected_model_paths = vec!["models/xml-repo/VerySmallTestCase.xml"];
+ for model_path in selected_model_paths {
+ println!("Parsing selected model {:?}:", model_path);
+ let xml_data = read_to_string(model_path).expect("Unable to read file");
+ let xml_model: XmlBmaModel =
+ serde_xml_rs::from_str(&xml_data).expect("XML was not well-formatted");
+ let model = BmaModel::from(xml_model);
+ println!("Internal structure:\n{:?}\n", model);
+ }
+
+ // 2) now let's iterate through all models and see if they at least parse without error
+ test_parse_all_models_in_dir("models/xml-repo/");
}
diff --git a/src/bma_model.rs b/src/bma_model.rs
new file mode 100644
index 0000000..88a67e0
--- /dev/null
+++ b/src/bma_model.rs
@@ -0,0 +1,252 @@
+use crate::enums::{RelationshipType, VariableType};
+use crate::json_model::JsonBmaModel;
+use crate::xml_model::XmlBmaModel;
+use serde::{Deserialize, Serialize};
+use std::collections::HashMap;
+
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct BmaModel {
+ /// Main data with variables and relationships.
+ pub model: Model,
+ /// Layout information (variable positions, containers, ...).
+ pub layout: Layout,
+ /// Stores additional metadata like description, biocheck_version, etc.
+ pub metadata: HashMap,
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct Model {
+ pub name: String,
+ pub variables: Vec,
+ pub relationships: Vec,
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct Variable {
+ pub id: u32,
+ pub name: String,
+ pub variable_type: VariableType, // Corresponds to "Type" in JSON/XML
+ pub range_from: u32,
+ pub range_to: u32,
+ pub formula: String,
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct Relationship {
+ pub id: u32,
+ pub from_variable: u32,
+ pub to_variable: u32,
+ pub relationship_type: RelationshipType, // Corresponds to "Type" in JSON/XML
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct Layout {
+ pub variables: Vec,
+ pub containers: Vec,
+ pub zoom_level: Option,
+ pub pan_x: Option,
+ pub pan_y: Option,
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct LayoutVariable {
+ pub id: u32,
+ pub container_id: u32,
+ pub position_x: f64,
+ pub position_y: f64,
+ pub cell_x: Option,
+ pub cell_y: Option,
+ pub angle: f64,
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct Container {
+ id: u32,
+ pub name: Option, // Optional, as some containers may not have a name
+ pub size: u32,
+ pub position_x: f64,
+ pub position_y: f64,
+}
+
+impl From for BmaModel {
+ fn from(json_model: JsonBmaModel) -> Self {
+ // Create a mapping from variable IDs to their names from the layout
+ let layout_var_names: HashMap = json_model
+ .layout
+ .as_ref()
+ .map(|layout| {
+ layout
+ .variables
+ .iter()
+ .filter(|layout_var| layout_var.name.is_some())
+ .map(|layout_var| (layout_var.id, layout_var.name.clone().unwrap()))
+ .collect()
+ })
+ .unwrap_or_default();
+
+ // Convert the model
+ let model = Model {
+ name: json_model.model.name,
+ variables: json_model
+ .model
+ .variables
+ .into_iter()
+ .map(|var| Variable {
+ id: var.id,
+ name: var
+ .name
+ .unwrap_or(layout_var_names.get(&var.id).cloned().unwrap_or_default()), // Use the name from layout
+ variable_type: json_model
+ .layout
+ .as_ref()
+ .and_then(|layout| layout.variables.iter().find(|v| v.id == var.id))
+ .map(|v| v.r#type)
+ .unwrap_or(VariableType::Default), // Use the type from layout if available
+ range_from: var.range_from,
+ range_to: var.range_to,
+ formula: var.formula,
+ })
+ .collect(),
+ relationships: json_model
+ .model
+ .relationships
+ .into_iter()
+ .map(|rel| Relationship {
+ id: rel.id,
+ from_variable: rel.from_variable,
+ to_variable: rel.to_variable,
+ relationship_type: rel.r#type,
+ })
+ .collect(),
+ };
+
+ // Convert the layout
+ let layout = json_model
+ .layout
+ .map(|layout| Layout {
+ variables: layout
+ .variables
+ .into_iter()
+ .map(|var| LayoutVariable {
+ id: var.id,
+ container_id: var.container_id,
+ position_x: var.position_x,
+ position_y: var.position_y,
+ cell_x: var.cell_x,
+ cell_y: var.cell_y,
+ angle: var.angle,
+ })
+ .collect(),
+ containers: layout
+ .containers
+ .into_iter()
+ .map(|container| Container {
+ id: container.id,
+ name: container.name,
+ size: container.size,
+ position_x: container.position_x,
+ position_y: container.position_y,
+ })
+ .collect(),
+ zoom_level: None,
+ pan_x: None,
+ pan_y: None,
+ })
+ .unwrap_or_else(|| Layout {
+ variables: vec![],
+ containers: vec![],
+ zoom_level: None,
+ pan_x: None,
+ pan_y: None,
+ });
+
+ // metadata not present in JsonBmaModel
+ let metadata = HashMap::new();
+
+ BmaModel {
+ model,
+ layout,
+ metadata,
+ }
+ }
+}
+
+impl From for BmaModel {
+ fn from(xml_model: XmlBmaModel) -> Self {
+ // Convert the model
+ let model = Model {
+ name: xml_model.name,
+ variables: xml_model
+ .variables
+ .variable
+ .clone()
+ .into_iter()
+ .map(|var| Variable {
+ id: var.id,
+ name: var.name,
+ variable_type: var.r#type,
+ range_from: var.range_from,
+ range_to: var.range_to,
+ formula: var.formula,
+ })
+ .collect(),
+ relationships: xml_model
+ .relationships
+ .relationship
+ .into_iter()
+ .map(|rel| Relationship {
+ id: rel.id,
+ from_variable: rel.from_variable_id,
+ to_variable: rel.to_variable_id,
+ relationship_type: rel.r#type,
+ })
+ .collect(),
+ };
+
+ // Convert the layout
+ let layout = Layout {
+ variables: xml_model
+ .variables
+ .variable
+ .into_iter()
+ .map(|var| LayoutVariable {
+ id: var.id,
+ container_id: var.container_id,
+ position_x: var.position_x,
+ position_y: var.position_y,
+ cell_x: Some(var.cell_x),
+ cell_y: Some(var.cell_y),
+ angle: var.angle,
+ })
+ .collect(),
+ containers: xml_model
+ .containers
+ .container
+ .into_iter()
+ .map(|container| Container {
+ id: container.id,
+ name: Some(container.name),
+ size: container.size,
+ position_x: container.position_x,
+ position_y: container.position_y,
+ })
+ .collect(),
+ zoom_level: Some(xml_model.layout.zoom_level),
+ pan_x: Some(xml_model.layout.pan_x),
+ pan_y: Some(xml_model.layout.pan_y),
+ };
+
+ // Metadata can be constructed from various XML fields
+ let mut metadata = HashMap::new();
+ metadata.insert("biocheck_version".to_string(), xml_model.biocheck_version);
+ metadata.insert("description".to_string(), xml_model.description);
+ metadata.insert("created_date".to_string(), xml_model.created_date);
+ metadata.insert("modified_date".to_string(), xml_model.modified_date);
+
+ BmaModel {
+ model,
+ layout,
+ metadata,
+ }
+ }
+}
diff --git a/src/enums.rs b/src/enums.rs
new file mode 100644
index 0000000..c365a9e
--- /dev/null
+++ b/src/enums.rs
@@ -0,0 +1,14 @@
+use serde::{Deserialize, Serialize};
+
+#[derive(Serialize, Deserialize, Debug, Clone, Copy)]
+pub enum VariableType {
+ Default,
+ Constant,
+ MembraneReceptor,
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone, Copy)]
+pub enum RelationshipType {
+ Activator,
+ Inhibitor,
+}
diff --git a/src/json_model.rs b/src/json_model.rs
index e6fba09..c79fd57 100644
--- a/src/json_model.rs
+++ b/src/json_model.rs
@@ -1,87 +1,140 @@
+use crate::enums::{RelationshipType, VariableType};
use serde::{Deserialize, Serialize};
+use std::str::FromStr;
-#[derive(Serialize, Deserialize, Debug)]
-struct Model {
- #[serde(rename = "Name")]
- name: String,
- #[serde(rename = "Variables")]
- variables: Vec,
- #[serde(rename = "Relationships")]
- relationships: Vec,
+#[derive(Deserialize)]
+#[serde(untagged)]
+enum StrOrNum<'a> {
+ Str(&'a str),
+ Num(u32),
}
-#[derive(Serialize, Deserialize, Debug)]
-struct Variable {
- #[serde(rename = "Id")]
- id: u32,
- #[serde(rename = "RangeFrom")]
- range_from: f64,
- #[serde(rename = "RangeTo")]
- range_to: f64,
- #[serde(rename = "Formula")]
- formula: String,
+/// Custom deserializer function for (potentially) quoted integers (like "42").
+///
+/// For some reason, this is JSON-specific, and we have to use different variant for XMP.
+pub fn deser_quoted_int<'de, D>(deserializer: D) -> Result
+where
+ D: serde::Deserializer<'de>,
+{
+ let raw = StrOrNum::deserialize(deserializer)?;
+
+ match raw {
+ StrOrNum::Str(s) => {
+ let trimmed = s.trim_matches('"');
+ u32::from_str(trimmed).map_err(serde::de::Error::custom)
+ }
+ StrOrNum::Num(num) => Ok(num),
+ }
}
-#[derive(Serialize, Deserialize, Debug)]
-struct Relationship {
- #[serde(rename = "Id")]
- id: u32,
- #[serde(rename = "FromVariable")]
- from_variable: u32,
- #[serde(rename = "ToVariable")]
- to_variable: u32,
- #[serde(rename = "Type")]
- r#type: String,
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct JsonBmaModel {
+ #[serde(rename = "Model", alias = "model")]
+ pub model: JsonModel,
+ #[serde(rename = "Layout", alias = "layout")]
+ pub layout: Option,
}
-#[derive(Serialize, Deserialize, Debug)]
-struct Layout {
- #[serde(rename = "Variables")]
- variables: Vec,
- #[serde(rename = "Containers")]
- containers: Vec,
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct JsonModel {
+ #[serde(rename = "Name", alias = "name")]
+ pub name: String,
+ #[serde(rename = "Variables", alias = "variables")]
+ pub variables: Vec,
+ #[serde(rename = "Relationships", alias = "relationships")]
+ pub relationships: Vec,
}
-#[derive(Serialize, Deserialize, Debug)]
-struct LayoutVariable {
- #[serde(rename = "Id")]
- id: u32,
- #[serde(rename = "Name")]
- name: String,
- #[serde(rename = "Type")]
- r#type: String,
- #[serde(rename = "ContainerId")]
- container_id: u32,
- #[serde(rename = "PositionX")]
- position_x: f64,
- #[serde(rename = "PositionY")]
- position_y: f64,
- #[serde(rename = "CellX")]
- cell_x: Option,
- #[serde(rename = "CellY")]
- cell_y: Option,
- #[serde(rename = "Angle")]
- angle: f64,
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct JsonVariable {
+ #[serde(rename = "Id", alias = "id", deserialize_with = "deser_quoted_int")]
+ pub id: u32,
+ #[serde(rename = "Id", alias = "id")]
+ pub name: Option,
+ #[serde(
+ rename = "RangeFrom",
+ alias = "rangeFrom",
+ deserialize_with = "deser_quoted_int"
+ )]
+ pub range_from: u32,
+ #[serde(
+ rename = "RangeTo",
+ alias = "rangeTo",
+ deserialize_with = "deser_quoted_int"
+ )]
+ pub range_to: u32,
+ #[serde(rename = "Formula", alias = "formula")]
+ pub formula: String,
}
-#[derive(Serialize, Deserialize, Debug)]
-struct Container {
- #[serde(rename = "Id")]
- id: u32,
- #[serde(rename = "Name")]
- name: Option,
- #[serde(rename = "Size")]
- size: u32,
- #[serde(rename = "PositionX")]
- position_x: f64,
- #[serde(rename = "PositionY")]
- position_y: f64,
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct JsonRelationship {
+ #[serde(rename = "Id", alias = "id", deserialize_with = "deser_quoted_int")]
+ pub id: u32,
+ #[serde(
+ rename = "FromVariable",
+ alias = "fromVariable",
+ alias = "fromVariableId",
+ alias = "FromVariableId",
+ deserialize_with = "deser_quoted_int"
+ )]
+ pub from_variable: u32,
+ #[serde(
+ rename = "ToVariable",
+ alias = "toVariable",
+ alias = "toVariableId",
+ alias = "ToVariableId",
+ deserialize_with = "deser_quoted_int"
+ )]
+ pub to_variable: u32,
+ #[serde(rename = "Type", alias = "type")]
+ pub r#type: RelationshipType,
}
-#[derive(Serialize, Deserialize, Debug)]
-pub struct JsonBmaModel {
- #[serde(rename = "Model")]
- model: Model,
- #[serde(rename = "Layout")]
- layout: Option,
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct JsonLayout {
+ #[serde(rename = "Variables", alias = "variables")]
+ pub variables: Vec,
+ #[serde(rename = "Containers", alias = "containers")]
+ pub containers: Vec,
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct JsonLayoutVariable {
+ #[serde(rename = "Id", alias = "id", deserialize_with = "deser_quoted_int")]
+ pub id: u32,
+ #[serde(rename = "Name", alias = "name")]
+ pub name: Option,
+ #[serde(rename = "Type", alias = "type")]
+ pub r#type: VariableType,
+ #[serde(
+ rename = "ContainerId",
+ alias = "containerId",
+ deserialize_with = "deser_quoted_int"
+ )]
+ pub container_id: u32,
+ #[serde(rename = "PositionX", alias = "positionX")]
+ pub position_x: f64,
+ #[serde(rename = "PositionY", alias = "positionY")]
+ pub position_y: f64,
+ #[serde(rename = "CellX", alias = "cellX")]
+ pub cell_x: Option,
+ #[serde(rename = "CellY", alias = "cellY")]
+ pub cell_y: Option,
+ #[serde(rename = "Angle", alias = "angle")]
+ pub angle: f64,
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct JsonContainer {
+ #[serde(rename = "Id", alias = "id", deserialize_with = "deser_quoted_int")]
+ pub id: u32,
+ #[serde(rename = "Name", alias = "name")]
+ pub name: Option,
+ #[serde(rename = "Size", alias = "size", deserialize_with = "deser_quoted_int")]
+ pub size: u32,
+ #[serde(rename = "PositionX", alias = "positionX")]
+ pub position_x: f64,
+ #[serde(rename = "PositionY", alias = "positionY")]
+ pub position_y: f64,
}
diff --git a/src/lib.rs b/src/lib.rs
index d652c1a..93680b7 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -1,4 +1,7 @@
//! Rust library for working with models in BMA format.
+pub mod bma_model;
pub mod json_model;
pub mod xml_model;
+
+mod enums;
diff --git a/src/xml_model.rs b/src/xml_model.rs
index 21269da..6b16805 100644
--- a/src/xml_model.rs
+++ b/src/xml_model.rs
@@ -1,138 +1,128 @@
+use crate::enums::{RelationshipType, VariableType};
use serde::{Deserialize, Serialize};
+use std::str::FromStr;
-#[derive(Serialize, Deserialize, Debug)]
+/// Custom deserializer function for (potentially) quoted integers (like "42").
+///
+/// For some reason, this is XML-specific, and we have to use different variant for JSON.
+pub fn deser_quoted_int<'de, D>(deserializer: D) -> Result
+where
+ D: serde::Deserializer<'de>,
+{
+ let s: String = String::deserialize(deserializer)?;
+ let trimmed = s.trim_matches('"');
+ u32::from_str(trimmed).map_err(serde::de::Error::custom)
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone)]
#[serde(rename = "Model")]
-struct Model {
- #[serde(rename = "Id")]
- id: u32,
+pub struct XmlBmaModel {
+ #[serde(rename = "Id", deserialize_with = "deser_quoted_int")]
+ pub id: u32,
#[serde(rename = "Name")]
- name: String,
+ pub name: String,
#[serde(rename = "BioCheckVersion")]
- biocheck_version: String,
+ pub biocheck_version: String,
#[serde(rename = "Description")]
- description: String,
+ pub description: String,
#[serde(rename = "CreatedDate")]
- created_date: String,
+ pub created_date: String,
#[serde(rename = "ModifiedDate")]
- modified_date: String,
+ pub modified_date: String,
#[serde(rename = "Layout")]
- layout: Layout,
+ pub layout: XmlLayout,
#[serde(rename = "Containers")]
- containers: Containers,
+ pub containers: XmlContainers,
#[serde(rename = "Variables")]
- variables: Variables,
+ pub variables: XmlVariables,
#[serde(rename = "Relationships")]
- relationships: Relationships,
+ pub relationships: XmlRelationships,
}
-#[derive(Serialize, Deserialize, Debug)]
-struct Layout {
- #[serde(rename = "Columns")]
- columns: u32,
- #[serde(rename = "Rows")]
- rows: u32,
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct XmlLayout {
+ #[serde(rename = "Columns", deserialize_with = "deser_quoted_int")]
+ pub columns: u32,
+ #[serde(rename = "Rows", deserialize_with = "deser_quoted_int")]
+ pub rows: u32,
#[serde(rename = "ZoomLevel")]
- zoom_level: u32,
+ pub zoom_level: f32,
#[serde(rename = "PanX")]
- pan_x: i32,
+ pub pan_x: i32,
#[serde(rename = "PanY")]
- pan_y: i32,
+ pub pan_y: i32,
}
-#[derive(Serialize, Deserialize, Debug)]
-struct Containers {
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct XmlContainers {
#[serde(rename = "Container")]
- container: Vec,
+ pub container: Vec,
}
-#[derive(Serialize, Deserialize, Debug)]
-struct Container {
- #[serde(rename = "Id")]
- id: u32,
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct XmlContainer {
+ #[serde(rename = "Id", deserialize_with = "deser_quoted_int")]
+ pub id: u32,
#[serde(rename = "Name")]
- name: String,
+ pub name: String,
#[serde(rename = "PositionX")]
- position_x: f64,
+ pub position_x: f64,
#[serde(rename = "PositionY")]
- position_y: f64,
- #[serde(rename = "Size")]
- size: u32,
+ pub position_y: f64,
+ #[serde(rename = "Size", deserialize_with = "deser_quoted_int")]
+ pub size: u32,
}
-#[derive(Serialize, Deserialize, Debug)]
-struct Variables {
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct XmlVariables {
#[serde(rename = "Variable")]
- variable: Vec,
+ pub variable: Vec,
}
-#[derive(Serialize, Deserialize, Debug)]
-struct Variable {
- #[serde(rename = "Id")]
- id: u32,
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct XmlVariable {
+ #[serde(rename = "Id", deserialize_with = "deser_quoted_int")]
+ pub id: u32,
#[serde(rename = "Name")]
- name: String,
- #[serde(rename = "ContainerId")]
- container_id: u32,
+ pub name: String,
+ #[serde(rename = "ContainerId", deserialize_with = "deser_quoted_int")]
+ pub container_id: u32,
#[serde(rename = "Type")]
- r#type: String,
- #[serde(rename = "RangeFrom")]
- range_from: f64,
- #[serde(rename = "RangeTo")]
- range_to: f64,
+ pub r#type: VariableType,
+ #[serde(rename = "RangeFrom", deserialize_with = "deser_quoted_int")]
+ pub range_from: u32,
+ #[serde(rename = "RangeTo", deserialize_with = "deser_quoted_int")]
+ pub range_to: u32,
#[serde(rename = "Formula")]
- formula: String,
+ pub formula: String,
#[serde(rename = "PositionX")]
- position_x: f64,
+ pub position_x: f64,
#[serde(rename = "PositionY")]
- position_y: f64,
- #[serde(rename = "CellX")]
- cell_x: u32,
- #[serde(rename = "CellY")]
- cell_y: u32,
+ pub position_y: f64,
+ #[serde(rename = "CellX", deserialize_with = "deser_quoted_int")]
+ pub cell_x: u32,
+ #[serde(rename = "CellY", deserialize_with = "deser_quoted_int")]
+ pub cell_y: u32,
#[serde(rename = "Angle")]
- angle: f64,
+ pub angle: f64,
}
-#[derive(Serialize, Deserialize, Debug)]
-struct Relationships {
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct XmlRelationships {
#[serde(rename = "Relationship")]
- relationship: Vec,
+ pub relationship: Vec,
}
-#[derive(Serialize, Deserialize, Debug)]
-struct Relationship {
- #[serde(rename = "Id")]
- id: u32,
- #[serde(rename = "ContainerId")]
- container_id: u32,
- #[serde(rename = "FromVariableId")]
- from_variable_id: u32,
- #[serde(rename = "ToVariableId")]
- to_variable_id: u32,
+#[derive(Serialize, Deserialize, Debug, Clone)]
+pub struct XmlRelationship {
+ #[serde(rename = "Id", deserialize_with = "deser_quoted_int")]
+ pub id: u32,
+ #[serde(rename = "ContainerId", deserialize_with = "deser_quoted_int")]
+ pub container_id: u32,
+ #[serde(rename = "FromVariableId", deserialize_with = "deser_quoted_int")]
+ pub from_variable_id: u32,
+ #[serde(rename = "ToVariableId", deserialize_with = "deser_quoted_int")]
+ pub to_variable_id: u32,
#[serde(rename = "Type")]
- r#type: String,
-}
-
-#[derive(Serialize, Deserialize, Debug)]
-pub struct XmlBmaModel {
- #[serde(rename = "Id")]
- id: u32,
- #[serde(rename = "Name")]
- name: String,
- #[serde(rename = "BioCheckVersion")]
- biocheck_version: String,
- #[serde(rename = "Description")]
- description: String,
- #[serde(rename = "CreatedDate")]
- created_date: String,
- #[serde(rename = "ModifiedDate")]
- modified_date: String,
- #[serde(rename = "Layout")]
- layout: Layout,
- #[serde(rename = "Containers")]
- containers: Containers,
- #[serde(rename = "Variables")]
- variables: Variables,
- #[serde(rename = "Relationships")]
- relationships: Relationships,
+ pub r#type: RelationshipType,
}