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 - 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\ 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 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\ 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 + 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+ + 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 + 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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/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 + 2012-10-27T14:16:13.0007404+01:00 + 2012-10-27T14:16:13.0007404+01:00 + + 6 + 5 + 76 + 197 + 878 + + + + 0 + 2 + 1 + + + 2 + 2 + 1 + + + 4 + 2 + 1 + + + 0 + 4 + 1 + + + 2 + 4 + 1 + + + 4 + 4 + 1 + + + + + 0 + Constant + 0 + 4 + + 159 + 179 + 0 + 3 + 0 + + + 0 + Constant + 0 + 4 + + 159 + 179 + 2 + 3 + 0 + + + 0 + Constant + 0 + 4 + + 159 + 179 + 4 + 3 + 0 + + + 0 + Constant + 0 + 4 + + 159 + 179 + 1 + 2 + 0 + + + 0 + Constant + 0 + 4 + + 159 + 179 + 3 + 2 + 0 + + + 0 + Constant + 0 + 4 + + 159 + 179 + 5 + 2 + 0 + + + 0 + Constant + 0 + 4 + + 159 + 179 + 1 + 4 + 0 + + + 0 + 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+ + 0 + 68 + 63 + Activator + + + \ 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 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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, }