generating pwsh scripts

InstituteforDiseaseModeling · Nov 13, 2019 · 3ba0466 · 3ba0466
1 parent f5cafdc
commit 3ba0466
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diff --git a/.gitignore b/.gitignore
@@ -18,6 +18,7 @@ output
 status.txt
 log
 *.temp.json
+Std*.txt
 
 # Python
 .virtualenv

diff --git a/.scenario b/.scenario
@@ -0,0 +1,5 @@
+{
+  "plotAllCharts": {
+    "commandline": ""
+  }
+}
diff --git a/Scenarios/Generic/DensityScaling/.scenario b/Scenarios/Generic/DensityScaling/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "Density Scaling",
+    "report": "output/InsetChart.json"
+  },
+  "plotSIRChannels": {
+    "commandline": "python ../../../bin/plotSIRChannels.py -c I -t \"Density Scaling\" output/InsetChart.json",
+    "script": "plotSIRChannels.py"
+  }
+}
diff --git a/Scenarios/Generic/DensityScaling/plotAllCharts.ps1 b/Scenarios/Generic/DensityScaling/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "Density Scaling"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/HINT_AgeAndAccess/A_BaselineOutbreak/.scenario b/Scenarios/Generic/HINT_AgeAndAccess/A_BaselineOutbreak/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotPropertyReport": {
+    "commandline": "python ../../../../bin/plotPropertyReport.py output/PropertyReport.json",
+    "script": "plotPropertyReport.py"
+  },
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "HINT - Baseline Outbreak",
+    "report": "output/InsetChart.json"
+  }
+}
diff --git a/Scenarios/Generic/HINT_AgeAndAccess/A_BaselineOutbreak/plotAllCharts.ps1 b/Scenarios/Generic/HINT_AgeAndAccess/A_BaselineOutbreak/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "HINT - Baseline Outbreak"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/HINT_AgeAndAccess/B_AgeTargetedVaccine/.scenario b/Scenarios/Generic/HINT_AgeAndAccess/B_AgeTargetedVaccine/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotPropertyReport": {
+    "commandline": "python ../../../../bin/plotPropertyReport.py output/PropertyReport.json",
+    "script": "plotPropertyReport.py"
+  },
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "HINT - Age-Targeted Vaccine",
+    "report": "output/InsetChart.json"
+  }
+}
diff --git a/Scenarios/Generic/HINT_AgeAndAccess/B_AgeTargetedVaccine/plotAllCharts.ps1 b/Scenarios/Generic/HINT_AgeAndAccess/B_AgeTargetedVaccine/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "HINT - Age-Targeted Vaccine"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/HINT_AgeAndAccess/C_AccessTargetedVaccine/.scenario b/Scenarios/Generic/HINT_AgeAndAccess/C_AccessTargetedVaccine/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotPropertyReport": {
+    "commandline": "python ../../../../bin/plotPropertyReport.py output/PropertyReport.json",
+    "script": "plotPropertyReport.py"
+  },
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "HINT - Access-Targeted Vaccine",
+    "report": "output/InsetChart.json"
+  }
+}
diff --git a/Scenarios/Generic/HINT_AgeAndAccess/C_AccessTargetedVaccine/plotAllCharts.ps1 b/Scenarios/Generic/HINT_AgeAndAccess/C_AccessTargetedVaccine/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "HINT - Access-Targeted Vaccine"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/HINT_SeattleCommuting/.scenario b/Scenarios/Generic/HINT_SeattleCommuting/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotPropertyReport": {
+    "commandline": "python ../../../bin/plotPropertyReport.py output/PropertyReport.json -m",
+    "script": "plotPropertyReport.py"
+  },
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "HINT Seattle Commuting",
+    "report": "output/InsetChart.json"
+  }
+}
diff --git a/Scenarios/Generic/HINT_SeattleCommuting/plotAllCharts.ps1 b/Scenarios/Generic/HINT_SeattleCommuting/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "HINT Seattle Commuting"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/SEIR/.scenario b/Scenarios/Generic/SEIR/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "Generic SEIR",
+    "report": "output/InsetChart.json"
+  },
+  "plotSIRChannels": {
+    "commandline": "python ../../../bin/plotSIRChannels.py -c SEIR -t \"Generic SEIR\" output/InsetChart.json",
+    "script": "plotSIRChannels.py"
+  }
+}
diff --git a/Scenarios/Generic/SEIR/plotAllCharts.ps1 b/Scenarios/Generic/SEIR/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "Generic SEIR"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/SEIRS/.scenario b/Scenarios/Generic/SEIRS/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "SEIRS",
+    "report": "output/InsetChart.json"
+  },
+  "plotSIRChannels": {
+    "commandline": "python ../../../bin/plotSIRChannels.py -c SEIRW -t \"SEIRS\" output/InsetChart.json",
+    "script": "plotSIRChannels.py"
+  }
+}
diff --git a/Scenarios/Generic/SEIRS/plotAllCharts.ps1 b/Scenarios/Generic/SEIRS/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "SEIRS"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/SEIR_VitalDynamics/.scenario b/Scenarios/Generic/SEIR_VitalDynamics/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "Generic SEIR with vital dynamics",
+    "report": "output/InsetChart.json"
+  },
+  "plotSIRChannels": {
+    "commandline": "python ../../../bin/plotSIRChannels.py -c SEIR -t \"Generic SEIR with vital dynamics\" output/InsetChart.json",
+    "script": "plotSIRChannels.py"
+  }
+}
diff --git a/Scenarios/Generic/SEIR_VitalDynamics/plotAllCharts.ps1 b/Scenarios/Generic/SEIR_VitalDynamics/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "Generic SEIR with vital dynamics"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/SI/.scenario b/Scenarios/Generic/SI/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "SI",
+    "report": "output/InsetChart.json"
+  },
+  "plotSIRChannels": {
+    "commandline": "python ../../../bin/plotSIRChannels.py -c SI -t \"SI\" output/InsetChart.json",
+    "script": "plotSIRChannels.py"
+  }
+}
diff --git a/Scenarios/Generic/SI/plotAllCharts.ps1 b/Scenarios/Generic/SI/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "SI"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/SIR/.scenario b/Scenarios/Generic/SIR/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "SIR",
+    "report": "output/InsetChart.json"
+  },
+  "plotSIRChannels": {
+    "commandline": "python ../../../bin/plotSIRChannels.py -c SIR -t \"SIR\" output/InsetChart.json",
+    "script": "plotSIRChannels.py"
+  }
+}
diff --git a/Scenarios/Generic/SIR/plotAllCharts.ps1 b/Scenarios/Generic/SIR/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "SIR"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/SIRS/.scenario b/Scenarios/Generic/SIRS/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "SIRS",
+    "report": "output/InsetChart.json"
+  },
+  "plotSIRChannels": {
+    "commandline": "python ../../../bin/plotSIRChannels.py -c SIRW -t \"SIRS\" output/InsetChart.json",
+    "script": "plotSIRChannels.py"
+  }
+}
diff --git a/Scenarios/Generic/SIRS/plotAllCharts.ps1 b/Scenarios/Generic/SIRS/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "SIRS"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/SIS/.scenario b/Scenarios/Generic/SIS/.scenario
@@ -0,0 +1,11 @@
+{
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "SIS",
+    "report": "output/InsetChart.json"
+  },
+  "plotSIRChannels": {
+    "commandline": "python ../../../bin/plotSIRChannels.py -c SI -t \"SIS\" output/InsetChart.json",
+    "script": "plotSIRChannels.py"
+  }
+}
diff --git a/Scenarios/Generic/SIS/plotAllCharts.ps1 b/Scenarios/Generic/SIS/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "SIS"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/Vaccinations/A_BaselineOutbreak/.scenario b/Scenarios/Generic/Vaccinations/A_BaselineOutbreak/.scenario
@@ -0,0 +1,15 @@
+{
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "Vaccinations - Baseline",
+    "report": "output/InsetChart.json"
+  },
+  "plotSIRChannels": {
+    "commandline": "python ../../../../bin/plotSIRChannels.py -c SIR -t \"Vaccinations - Baseline\" output/InsetChart.json",
+    "script": "plotSIRChannels.py"
+  },
+  "plotPropertyReport": {
+    "commandline": "python ../../../../bin/plotPropertyReport.py -n output/PropertyReport.json",
+    "script": "plotPropertyReport.py"
+  }
+}
diff --git a/Scenarios/Generic/Vaccinations/A_BaselineOutbreak/plotAllCharts.ps1 b/Scenarios/Generic/Vaccinations/A_BaselineOutbreak/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "Vaccinations - Baseline"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/Vaccinations/B_Vaccinations/.scenario b/Scenarios/Generic/Vaccinations/B_Vaccinations/.scenario
@@ -0,0 +1,15 @@
+{
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "Vaccinations - Vaccination All",
+    "report": "output/InsetChart.json"
+  },
+  "plotSIRChannels": {
+    "commandline": "python ../../../../bin/plotSIRChannels.py -c SIR -t \"Vaccinations - Vaccination All\" output/InsetChart.json",
+    "script": "plotSIRChannels.py"
+  },
+  "plotPropertyReport": {
+    "commandline": "python ../../../../bin/plotPropertyReport.py -n output/PropertyReport.json",
+    "script": "plotPropertyReport.py"
+  }
+}
diff --git a/Scenarios/Generic/Vaccinations/B_Vaccinations/plotAllCharts.ps1 b/Scenarios/Generic/Vaccinations/B_Vaccinations/plotAllCharts.ps1
@@ -2,7 +2,8 @@ Push-Location -Path $PSScriptRoot
 
 . ../../../../scripts/helpers.ps1
 
-$chart = (Join-Path "output" "InsetChart.json")
-$pyscript = (Join-Path "$BIN_ROOT" "plotAllCharts.py")
-$pytitle = "Vaccinations - Vaccination All"
-& python $pyscript $chart "$pytitle"
+$sc = (Get-Content -Path ".scenario" | ConvertFrom-Json -AsHashtable)
+$key = (Split-Path $MyInvocation.MyCommand.Name -LeafBase)
+$config = $sc[$key]
+$pyscript = (Join-Path "$BIN_ROOT" $config.script)
+& python $pyscript --title="$($config.title)" $config.report
diff --git a/Scenarios/Generic/Vaccinations/C_TargetedVaccinations/.scenario b/Scenarios/Generic/Vaccinations/C_TargetedVaccinations/.scenario
@@ -0,0 +1,15 @@
+{
+  "plotAllCharts": {
+    "script": "plotAllCharts.py",
+    "title": "Vaccinations - Easy Targeted",
+    "report": "output/InsetChart.json"
+  },
+  "plotSIRChannels": {
+    "commandline": "python ../../../../bin/plotSIRChannels.py -c SIR -t \"Vaccinations - Easy Targeted\" output/InsetChart.json",
+    "script": "plotSIRChannels.py"
+  },
+  "plotPropertyReport": {
+    "commandline": "python ../../../../bin/plotPropertyReport.py -n output/PropertyReport.json",
+    "script": "plotPropertyReport.py"
+  }
+}