make the generator take named args. Tidy Makefile (#5)

* make the generator take named args. Tidy Makefile

* address comments

Makefile

@@ -4,8 +4,6 @@ SBT=sbt -DARTIFACTORY_USER="${ARTIFACTORY_USER}" -DARTIFACTORY_PWD="${ARTIFACTOR
 SBT_G=sbt -DARTIFACTORY_USER="${ARTIFACTORY_USER}" -DARTIFACTORY_PWD="${ARTIFACTORY_PWD}" -Dversion="${G_VERSION}"
 # Why sed and not grep, you ask? Because grep on mac takes the -E flag, but takes -P on *nix
 BENCH_NUMBER=$(shell echo ${CIRCLE_JOB} | sed 's/benchmark//')
-CORE_FILES=$(shell for i in address Age annotation attachment backboneElement codeableConcept coding contactDetail contactPoint Contributor Count DataRequirement Distance dosage duration element Expression extension humanName identifier meta money ParameterDefinition period quantity range ratio reference RelatedArtifact Resource SampledData Signature timing TriggerDefinition UsageContext; do echo "./generator/src/main/resources/resourceModel/$${i}.json"; done | xargs | sed 's/ /,/g')
-HL7_FILES=$(shell ls generator/src/main/resources/resourceModel/*.json | grep -vE '/(address|Age|annotation|attachment|backboneElement|codeableConcept|coding|contactDetail|contactPoint|Contributor|Count|DataRequirement|Distance|dosage|duration|element|Expression|extension|humanName|identifier|meta|money|ParameterDefinition|period|quantity|range|ratio|reference|RelatedArtifact|Resource|SampledData|Signature|timing|TriggerDefinition|UsageContext).json'  | xargs | sed -E 's:(^| ):\1./:g' | sed 's/ /,/g')
 CORE_MODULES=core hl7
 US_MODULES=usbase uscore
 ALL_MODULES=$(CORE_MODULES) $(US_MODULES)
@@ -76,23 +74,24 @@ publish-all-local:
 	$(SBT) common/publishLocal common/publishM2 macros/publishLocal macros/publishM2 $(foreach i,$(ALL_MODULES),$i/publishLocal $i/publishM2 $iJava/publishLocal $iJava/publishM2)
 
 build-hl7-class-models:
-	$(SBT) 'project generator' 'run "generate" "$(CORE_FILES)" "$(HL7_FILES)" \
-		"./.ignore/dummy=" \
-		"_java" \
-		"./generated_typescript" \
-		"" \
-		true'
+	$(SBT) 'project generator' 'run "generate" \
+		--javaPackageSuffix=_java \
+		--typescriptDir="./generated_typescript"'
 	$(SBT) $(foreach i,$(CORE_MODULES),$i/scalafmtAll)
 	$(SBT) $(foreach i,$(CORE_MODULES),$iJava/javafmt)
 	./apply_patches.sh
 
+build-all-class-models-dry:
+	$(SBT) 'project generator' 'run "generate" \
+		--models="usbase=fhir/spec/hl7.fhir.r4.examples/4.0.1/package/StructureDefinition-*;uscore=fhir/spec/hl7.fhir.us.core/3.1.0/package/StructureDefinition-*" \
+		--javaPackageSuffix=_java \
+		--moduleDependencies="usbase<uscore" \
+		--dryRun'
 build-all-class-models:
-	$(SBT) 'project generator' 'run "generate" "$(CORE_FILES)" "$(HL7_FILES)" \
-		"usbase=fhir/spec/hl7.fhir.r4.examples/4.0.1/package/StructureDefinition-*;uscore=fhir/spec/hl7.fhir.us.core/3.1.0/package/StructureDefinition-*" \
-		"_java" \
-		"./.ignore/typescript" \
-		"usbase<uscore" \
-		true'
+	$(SBT) 'project generator' 'run "generate" \
+		--models="usbase=fhir/spec/hl7.fhir.r4.examples/4.0.1/package/StructureDefinition-*;uscore=fhir/spec/hl7.fhir.us.core/3.1.0/package/StructureDefinition-*" \
+		--javaPackageSuffix=_java \
+		--moduleDependencies="usbase<uscore"'
 	$(SBT) $(foreach i,$(ALL_MODULES),$i/scalafmtAll)
 	$(SBT) $(foreach i,$(ALL_MODULES),$iJava/javafmt)
 	./apply_patches.sh

docs/documentation.md

@@ -244,26 +244,10 @@ If you're using intelliJ the highlighting is misleading here, since it will info
 ## Generation
 
 Lit can be used to generate new class models from your existing fhir profiles. Simply specify the module name and the location of the profiles in the args for the generator, when running it. Module dependencies can also be specified, in case your profiles depend on ones defined outside of the core and hl7 modules. e.g.
-// TODO: this really hammers home the issues with how the generator is currently called. At the very least we need to have a saner directory structure the core files, named args, and default arguments.
 ```
-# Should just be generator/src/main/resources/resourceModel/core/*.json 
-CORE_FILES=$(for i in address Age annotation attachment backboneElement codeableConcept coding contactDetail contactPoint Contributor Count DataRequirement Distance dosage duration element Expression extension humanName identifier meta money ParameterDefinition period quantity range ratio reference RelatedArtifact Resource SampledData Signature timing TriggerDefinition UsageContext; do echo "./generator/src/main/resources/resourceModel/$${i}.json"; done | xargs | sed 's/ /,/g')
-# Should just be generator/src/main/resources/resourceModel/hl7/*.json
-HL7_FILES=$(ls generator/src/main/resources/resourceModel/*.json | grep -vE '/(address|Age|annotation|attachment|backboneElement|codeableConcept|coding|contactDetail|contactPoint|Contributor|Count|DataRequirement|Distance|dosage|duration|element|Expression|extension|humanName|identifier|meta|money|ParameterDefinition|period|quantity|range|ratio|reference|RelatedArtifact|Resource|SampledData|Signature|timing|TriggerDefinition|UsageContext).json'  | xargs | sed -E 's:(^| ):\1./:g' | sed 's/ /,/g')
-
 'project generator' 'run \
-    # might be redundant, but might not. Not too bad. Think I'll keep it
     "generate" \
-    # should be --modelOverrides="core=$(CORE_FILES);hl7=$(HL7_FILES)" and also be the default, and thus be omittable.
-    "$(CORE_FILES)" "$(HL7_FILES)" \
-    # should be --models="..."
-    "usbase=fhir/spec/hl7.fhir.r4.examples/4.0.1/package/StructureDefinition-*;uscore=fhir/spec/hl7.fhir.us.core/3.1.0/package/StructureDefinition-*" \
-    # should be --javaPackageSuffix=_java, and when unspecified we shouldn't generate java code
-    "_java" \
-    # should be --typescriptDir=...; when unspecified, we shouldn't generate typescript code -- this .ignore hack shouldn't be necessary
-    "./.ignore/typescript" \
-    # should be --modelDependencies="usbase<uscore"; should default to empty string
-    "usbase<uscore" \
-    # should be inverted as `--dryRun=false`, default to false, and be specifiable as just `--dryRun`
-    true'
+    --models="usbase=fhir/spec/hl7.fhir.r4.examples/4.0.1/package/StructureDefinition-*;uscore=fhir/spec/hl7.fhir.us.core/3.1.0/package/StructureDefinition-*" \
+    --javaPackageSuffix=_java \
+    --moduleDependencies="usbase<uscore"
 ```

generator/src/main/scala/com/babylonhealth/lit/Autogenerator.scala

@@ -11,8 +11,8 @@ import io.circe.parser.decode
 import com.babylonhealth.lit.ElementTreee._
 import com.babylonhealth.lit.core.serdes.objectDecoder
 import com.babylonhealth.lit.hl7.BINDING_STRENGTH
-import com.babylonhealth.lit.hl7.model.{ElementDefinition, StructureDefinition}
-import com.babylonhealth.lit.languages.{JavaGenerator, ScalaCodegen, TypescriptCodegen}
+import com.babylonhealth.lit.hl7.model.{ ElementDefinition, StructureDefinition }
+import com.babylonhealth.lit.languages.{ JavaGenerator, ScalaCodegen, TypescriptCodegen }
 
 trait FHIRFetcher {}
 
@@ -126,15 +126,11 @@ object Autogenerator extends Commonish with Logging with FileUtils with JavaGene
   }
 
   def getStrings(
-      overridingModels: Seq[SourceFile],
-      resourceModels: Seq[SourceFile],
-      javaDirSuffix: String,
-      typescriptOutputLocation: Option[String],
-      moduleDependencies: ModuleDependencies,
+      args: MainArgs,
       extensions: Map[String, Seq[ClassGenInfo]],
       fetchValueSet: (String, BINDING_STRENGTH) => Option[CodeValueSet]): AllGeneratedFiles = {
 
-    val sortedLocations = sortLocationsByBase(overridingModels, resourceModels)
+    val sortedLocations = sortLocationsByBase(args.modelOverrides, args.models)
     println("Sorted models")
     val modules = sortedLocations.foldLeft(Seq.empty[String]) { (acc, n) =>
       val currModule = acc.lastOption contains n.targetModule
@@ -166,7 +162,7 @@ object Autogenerator extends Commonish with Logging with FileUtils with JavaGene
     val valueSetDecls: ValueSetDecls = ValueSetDecls(topLevelClasses.classes.flatMap {
       _._2.flatMap { case (pkg, x) => x.valueSets.map { case (k, v) => (pkg, k, v) } }
     }.toSeq).stripVersions
-    val valueSetEarliestDeclarations: ValueSetDecls = valueSetDecls.earliestDeclarations(moduleDependencies)
+    val valueSetEarliestDeclarations: ValueSetDecls = valueSetDecls.earliestDeclarations(args.moduleDependencies)
 
     val scalaClassGenInfo: Seq[ClassGenInfo] = {
 
@@ -187,9 +183,9 @@ object Autogenerator extends Commonish with Logging with FileUtils with JavaGene
                 element,
                 backboneElement,
                 topLevelClasses,
-                moduleDependencies,
+                args.moduleDependencies,
                 pkgAndValueSet,
-                ElementTreee.getUnionTypes.values.map(moduleDependencies leastCommon _._1.toSet).toSet
+                ElementTreee.getUnionTypes.values.map(args.moduleDependencies leastCommon _._1.toSet).toSet
               ))
           catch {
             case NonFatal(ex) =>
@@ -200,24 +196,18 @@ object Autogenerator extends Commonish with Logging with FileUtils with JavaGene
         }.toSeq
       }
       allFHIRClasses ++ valueSetFiles ++ extensions("scala") ++
-      ScalaCodegen.genPackageObjectFiles(moduleDependencies, ElementTreee.getUnionTypes)
+      ScalaCodegen.genPackageObjectFiles(args.moduleDependencies, ElementTreee.getUnionTypes)
     }
 
-    val javaClassGenInfo: JavaClassGenInfo = {
+    val javaClassGenInfo: Option[JavaClassGenInfo] = args.javaPackageSuffix.map { j =>
       val bar: Seq[ClassGenInfo] = valueSetEarliestDeclarations.byPackage.flatMap { case (pkg, ps) =>
-        generateCodeAliases(pkg, javaDirSuffix, ps.toMap)
+        generateCodeAliases(pkg, j, ps.toMap)
       }.toSeq
       JavaClassGenInfo(
         topLevelClasses.classes.toSeq.flatMap { case (o, m) =>
           m.flatMap { case (p, k) =>
-            val javaPackageStr = (s"com.babylonhealth.lit.$p$javaDirSuffix")
-            try genTheJavaForClass(
-              k,
-              javaPackageStr,
-              p,
-              valueSetEarliestDeclarations,
-              moduleDependencies,
-              javaDirSuffix)
+            val javaPackageStr = (s"com.babylonhealth.lit.$p$j")
+            try genTheJavaForClass(k, javaPackageStr, p, valueSetEarliestDeclarations, args.moduleDependencies, j)
             catch {
               case NonFatal(ex) =>
                 log.error(s"Unable to gen Java file for $p.$o", ex)
@@ -229,7 +219,7 @@ object Autogenerator extends Commonish with Logging with FileUtils with JavaGene
       )
     }
 
-    val typescriptClassGenInfo: Option[Seq[ClassGenInfo]] = typescriptOutputLocation.map { o =>
+    val typescriptClassGenInfo: Option[Seq[ClassGenInfo]] = args.typescriptDir.map { o =>
       topLevelClasses.classes.toSeq.flatMap { case (o, m) =>
         m.flatMap { case (p, k) =>
           try TypescriptCodegen.genTypescriptForClass(k)
@@ -245,32 +235,18 @@ object Autogenerator extends Commonish with Logging with FileUtils with JavaGene
     AllGeneratedFiles(scalaClassGenInfo, javaClassGenInfo, typescriptClassGenInfo)
   }
   def generateAndWriteOutput(
-      overridingModels: Seq[SourceFile],
-      resourceModels: Seq[SourceFile],
-      javaDirSuffix: String,
-      typescriptOutputLocation: Option[String],
-      moduleDependencies: ModuleDependencies,
-      writeCode: Boolean,
+      args: MainArgs,
       extensions: Map[String, Seq[ClassGenInfo]],
       fetchValueSet: (String, BINDING_STRENGTH) => Option[CodeValueSet]): Unit = {
     println("Trying to generate files")
     val AllGeneratedFiles(scalaClassGenInfo, javaClassGenInfo, typescriptClassGenInfo) =
-      getStrings(
-        overridingModels,
-        resourceModels,
-        javaDirSuffix,
-        typescriptOutputLocation,
-        moduleDependencies,
-        extensions,
-        fetchValueSet)
-    def javaOutputLocation(pkg: String): String =
-      s"./$pkg$javaDirSuffix/src/main/java/com/babylonhealth/lit/$pkg$javaDirSuffix"
-    def javaOutputLocations(pkg: String): Seq[String] = {
-      val dir = javaOutputLocation(pkg)
-      Seq(s"$dir/builders", s"$dir/codes")
-    }
+      getStrings(args, extensions, fetchValueSet)
+    def javaOutputLocation(pkg: String): Option[String] =
+      args.javaPackageSuffix.map(j => s"./$pkg$j/src/main/java/com/babylonhealth/lit/$pkg$j")
+    def javaOutputLocations(pkg: String): Seq[String] =
+      javaOutputLocation(pkg).toSeq.flatMap(dir => Seq(s"$dir/builders", s"$dir/codes"))
     println("Successfully generated files")
-    if (writeCode) { // create the directories fresh
+    if (!args.dryRun) { // create the directories fresh
       scalaClassGenInfo
         .map(_.pkg)
         .distinct
@@ -281,19 +257,15 @@ object Autogenerator extends Commonish with Logging with FileUtils with JavaGene
       scalaClassGenInfo foreach { case ClassGenInfo(fc, fileName, pkg) =>
         write(s"$pkg/src/main/scala/com/babylonhealth/lit/$pkg/model/$fileName.scala", fc)
       }
-      javaClassGenInfo.builders foreach { case ClassGenInfo(fc, fileName, pkg) =>
-        if (pkg == null) println(s"NULL WAT??? 111 ${fileName} :: ${pkg}")
-        else
-          write(s"${javaOutputLocation(pkg)}/builders/$fileName.java", fc)
+      javaClassGenInfo.toSeq.flatMap(_.builders) foreach { case ClassGenInfo(fc, fileName, pkg) =>
+        write(s"${javaOutputLocation(pkg).get}/builders/$fileName.java", fc)
       }
-      javaClassGenInfo.codes foreach { case ClassGenInfo(fc, fileName, pkg) =>
-        if (pkg == null) println(s"NULL WAT 222 ${fileName} :: ${pkg}??? ")
-        else
-          write(s"${javaOutputLocation(pkg)}/codes/$fileName.java", fc)
+      javaClassGenInfo.toSeq.flatMap(_.codes) foreach { case ClassGenInfo(fc, fileName, pkg) =>
+        write(s"${javaOutputLocation(pkg).get}/codes/$fileName.java", fc)
       }
-      if (typescriptClassGenInfo.nonEmpty) new File(typescriptOutputLocation.get).mkdirs()
+      if (typescriptClassGenInfo.nonEmpty) new File(args.typescriptDir.get).mkdirs()
       typescriptClassGenInfo.foreach(c =>
-        write(s"${typescriptOutputLocation.get}/DomainModel.ts", c.map(_.fileContents).mkString("\n\n")))
+        write(s"${args.typescriptDir.get}/DomainModel.ts", c.map(_.fileContents).mkString("\n\n")))
     }
   }
 }

generator/src/main/scala/com/babylonhealth/lit/FileUtils.scala

@@ -9,6 +9,7 @@ import scala.util.Try
 import io.circe.Json
 import io.circe.parser.parse
 
+object FileUtils extends FileUtils
 trait FileUtils extends common.FileUtils {
   def getFileAsJson(file: File): Json =
     if (!file.exists()) {