json parsing

build.gradle.kts

@@ -9,7 +9,7 @@ plugins {
 }
 
 group = "org.veupathdb.lib"
-version = "0.4.0"
+version = "0.5.0"
 
 buildscript {
   dependencies {

src/main/kotlin/org/veupathdb/lib/cli/diamond/Diamond.kt

@@ -25,7 +25,7 @@ import org.veupathdb.lib.cli.diamond.commands.BlastX
 import org.veupathdb.lib.cli.diamond.commands.impl.BlastNImpl
 import org.veupathdb.lib.cli.diamond.commands.impl.BlastPImpl
 import org.veupathdb.lib.cli.diamond.commands.impl.BlastXImpl
-import org.veupathdb.lib.cli.diamond.opts.output_format.cacheFormatFields
+import org.veupathdb.lib.cli.diamond.opts.fields.output_format.cacheFormatFields
 import org.veupathdb.lib.jackson.Json
 import java.io.InputStream
 
@@ -39,6 +39,18 @@ object Diamond {
   @DiamondExtras
   fun blastN(): BlastN = BlastNImpl()
 
+  /**
+   * Creates a new, blank [BlastN] CLI configuration instance and passes it to
+   * the given action before returning it.
+   *
+   * @param action Action which may be used to mutate the new `BlastN` instance.
+   *
+   * @return The new `BlastN` instance.
+   */
+  @JvmStatic
+  @DiamondExtras
+  inline fun blastN(action: BlastN.() -> Unit): BlastN = blastN().apply(action)
+
   /**
    * Attempts to parse the given JSON value as a [BlastN] CLI configuration.
    *
@@ -96,6 +108,17 @@ object Diamond {
   @JvmStatic
   fun blastP(): BlastP = BlastPImpl()
 
+  /**
+   * Creates a new, blank [BlastP] CLI configuration instance and passes it to
+   * the given action before returning it.
+   *
+   * @param action Action which may be used to mutate the new `BlastP` instance.
+   *
+   * @return The new `BlastP` instance.
+   */
+  @JvmStatic
+  inline fun blastP(action: BlastP.() -> Unit) = blastP().apply(action)
+
   /**
    * Attempts to parse the given JSON value as a [BlastP] CLI configuration.
    *
@@ -150,6 +173,17 @@ object Diamond {
   @JvmStatic
   fun blastX(): BlastX = BlastXImpl()
 
+  /**
+   * Creates a new, blank [BlastX] CLI configuration instance and passes it to
+   * the given action before returning it.
+   *
+   * @param action Action which may be used to mutate the new `BlastX` instance.
+   *
+   * @return The new `BlastX` instance.
+   */
+  @JvmStatic
+  inline fun blastX(action: BlastX.() -> Unit) = blastX().apply(action)
+
   /**
    * Attempts to parse the given JSON value as a [BlastX] CLI configuration.
    *

src/main/kotlin/org/veupathdb/lib/cli/diamond/commands/DiamondCommandConfig.kt

@@ -1,10 +1,15 @@
 package org.veupathdb.lib.cli.diamond.commands
 
+import com.fasterxml.jackson.annotation.JsonGetter
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize
 import org.veupathdb.lib.cli.diamond.DiamondCommand
+import org.veupathdb.lib.cli.diamond.util.DiamondCommandConfigDeserializer
 
+@JsonDeserialize(using = DiamondCommandConfigDeserializer::class)
 sealed interface DiamondCommandConfig {
   /**
    * Diamond subcommand.
    */
+  @get:JsonGetter("tool")
   val tool: DiamondCommand
 }

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/OutputFormatOptionContainer.kt

@@ -20,7 +20,7 @@ package org.veupathdb.lib.cli.diamond.opts
 import com.fasterxml.jackson.annotation.JsonGetter
 import com.fasterxml.jackson.annotation.JsonSetter
 import io.foxcapades.lib.cli.builder.flag.CliFlag
-import org.veupathdb.lib.cli.diamond.opts.output_format.OutputFormatOptions
+import org.veupathdb.lib.cli.diamond.opts.fields.output_format.OutputFormatOptions
 
 interface OutputFormatOptionContainer {
   /**

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/output_format/BlastTabFormat.kt → src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/fields/output_format/BlastTabFormat.kt

@@ -1,4 +1,4 @@
-package org.veupathdb.lib.cli.diamond.opts.output_format
+package org.veupathdb.lib.cli.diamond.opts.fields.output_format
 
 class BlastTabFormat(override var formatFields: Iterable<FormatField> = emptyList())
   : BlastTabFormatBase<Iterable<FormatField>>(OutputFormat.BlastTab)

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/output_format/BlastTabFormatBase.kt → src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/fields/output_format/BlastTabFormatBase.kt

@@ -1,4 +1,4 @@
-package org.veupathdb.lib.cli.diamond.opts.output_format
+package org.veupathdb.lib.cli.diamond.opts.fields.output_format
 
 import com.fasterxml.jackson.annotation.JsonValue
 import org.veupathdb.lib.jackson.Json

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/output_format/FormatField.fn.kt → src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/fields/output_format/FormatField.fn.kt

@@ -1,4 +1,4 @@
-package org.veupathdb.lib.cli.diamond.opts.output_format
+package org.veupathdb.lib.cli.diamond.opts.fields.output_format
 
 private var formatFieldCache: Map<String, FormatField>? = null
 

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/output_format/FormatField.kt → src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/fields/output_format/FormatField.kt

@@ -1,4 +1,4 @@
-package org.veupathdb.lib.cli.diamond.opts.output_format
+package org.veupathdb.lib.cli.diamond.opts.fields.output_format
 
 import com.fasterxml.jackson.annotation.JsonCreator
 import com.fasterxml.jackson.annotation.JsonValue

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/output_format/JsonFlatFormat.kt → src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/fields/output_format/JsonFlatFormat.kt

@@ -1,4 +1,4 @@
-package org.veupathdb.lib.cli.diamond.opts.output_format
+package org.veupathdb.lib.cli.diamond.opts.fields.output_format
 
 class JsonFlatFormat(override var formatFields: Iterable<FormatField> = emptyList())
   : BlastTabFormatBase<Iterable<FormatField>>(OutputFormat.BlastTab)

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/output_format/OutFormatFormatter.kt → src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/fields/output_format/OutFormatFormatter.kt

@@ -1,4 +1,4 @@
-package org.veupathdb.lib.cli.diamond.opts.output_format
+package org.veupathdb.lib.cli.diamond.opts.fields.output_format
 
 import io.foxcapades.lib.cli.builder.arg.Argument
 import io.foxcapades.lib.cli.builder.arg.format.ArgumentFormatter

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/output_format/OutputFormat.kt → src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/fields/output_format/OutputFormat.kt

@@ -1,4 +1,4 @@
-package org.veupathdb.lib.cli.diamond.opts.output_format
+package org.veupathdb.lib.cli.diamond.opts.fields.output_format
 
 import com.fasterxml.jackson.annotation.JsonCreator
 import com.fasterxml.jackson.annotation.JsonValue

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/output_format/OutputFormatDeserializer.kt → src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/fields/output_format/OutputFormatDeserializer.kt

@@ -1,4 +1,4 @@
-package org.veupathdb.lib.cli.diamond.opts.output_format
+package org.veupathdb.lib.cli.diamond.opts.fields.output_format
 
 import com.fasterxml.jackson.core.JsonParser
 import com.fasterxml.jackson.databind.DeserializationContext

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/output_format/OutputFormatOptions.fn.kt → src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/fields/output_format/OutputFormatOptions.fn.kt

@@ -1,4 +1,4 @@
-package org.veupathdb.lib.cli.diamond.opts.output_format
+package org.veupathdb.lib.cli.diamond.opts.fields.output_format
 
 import com.fasterxml.jackson.databind.JsonNode
 import com.fasterxml.jackson.databind.node.ArrayNode

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/output_format/OutputFormatOptions.kt → src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/fields/output_format/OutputFormatOptions.kt

@@ -1,4 +1,4 @@
-package org.veupathdb.lib.cli.diamond.opts.output_format
+package org.veupathdb.lib.cli.diamond.opts.fields.output_format
 
 import com.fasterxml.jackson.databind.annotation.JsonDeserialize
 

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/output_format/SimpleOutputFormat.kt → src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/fields/output_format/SimpleOutputFormat.kt

@@ -1,4 +1,4 @@
-package org.veupathdb.lib.cli.diamond.opts.output_format
+package org.veupathdb.lib.cli.diamond.opts.fields.output_format
 
 import com.fasterxml.jackson.annotation.JsonCreator
 import com.fasterxml.jackson.annotation.JsonValue

src/main/kotlin/org/veupathdb/lib/cli/diamond/opts/impl/OutputFormatOptionContainerImpl.kt

@@ -3,8 +3,8 @@ package org.veupathdb.lib.cli.diamond.opts.impl
 import io.foxcapades.lib.cli.builder.flag.flag
 import io.foxcapades.lib.cli.builder.flag.toggleFlag
 import org.veupathdb.lib.cli.diamond.opts.OutputFormatOptionContainer
-import org.veupathdb.lib.cli.diamond.opts.output_format.OutFormatFormatter
-import org.veupathdb.lib.cli.diamond.opts.output_format.OutputFormatOptions
+import org.veupathdb.lib.cli.diamond.opts.fields.output_format.OutFormatFormatter
+import org.veupathdb.lib.cli.diamond.opts.fields.output_format.OutputFormatOptions
 
 internal class OutputFormatOptionContainerImpl : OutputFormatOptionContainer {
   override var outputFormat by flag<OutputFormatOptions> { formatter = OutFormatFormatter }

src/main/kotlin/org/veupathdb/lib/cli/diamond/util/DiamondCommandConfigDeserializer.kt

@@ -0,0 +1,31 @@
+package org.veupathdb.lib.cli.diamond.util
+
+import com.fasterxml.jackson.core.JsonParser
+import com.fasterxml.jackson.databind.DeserializationContext
+import com.fasterxml.jackson.databind.JsonDeserializer
+import com.fasterxml.jackson.databind.JsonMappingException
+import com.fasterxml.jackson.databind.node.ObjectNode
+import com.fasterxml.jackson.module.kotlin.contains
+import org.veupathdb.lib.cli.diamond.DiamondCommand
+import org.veupathdb.lib.cli.diamond.commands.DiamondCommandConfig
+import org.veupathdb.lib.cli.diamond.commands.impl.BlastPImpl
+import org.veupathdb.lib.cli.diamond.commands.impl.BlastXImpl
+import org.veupathdb.lib.jackson.Json
+
+internal class DiamondCommandConfigDeserializer : JsonDeserializer<DiamondCommandConfig>() {
+  override fun deserialize(p: JsonParser, ctxt: DeserializationContext): DiamondCommandConfig {
+    val obj = p.readValueAs(ObjectNode::class.java)
+
+    if ("tool" !in obj)
+      throw JsonMappingException(
+        p,
+        "cannot deserialize given JSON into a DIAMOND command configuration; the given object has no \"tool\" property"
+      )
+
+    return when (DiamondCommand.fromJson(obj["tool"])) {
+      DiamondCommand.BlastP -> Json.parse<BlastPImpl>(obj)
+      DiamondCommand.BlastX -> Json.parse<BlastXImpl>(obj)
+      else -> TODO("unsupported type")
+    }
+  }
+}