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[ADAM-941] Automatically generate projection enums.
Resolves #941.
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adam-codegen/src/main/scala/org/bdgenomics/adam/codegen/DumpSchemasToProjectionEnums.scala
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| /** | ||
| * Licensed to Big Data Genomics (BDG) under one | ||
| * or more contributor license agreements. See the NOTICE file | ||
| * distributed with this work for additional information | ||
| * regarding copyright ownership. The BDG licenses this file | ||
| * to you under the Apache License, Version 2.0 (the | ||
| * "License"); you may not use this file except in compliance | ||
| * with the License. You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package org.bdgenomics.adam.codegen | ||
|
|
||
| import java.io.{ File, FileWriter } | ||
| import org.apache.avro.Schema | ||
| import org.apache.avro.reflect.ReflectData | ||
| import scala.collection.JavaConversions._ | ||
|
|
||
| object DumpSchemasToProjectionEnums { | ||
|
|
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| def main(args: Array[String]) { | ||
| new DumpSchemasToProjectionEnums()(args) | ||
| } | ||
| } | ||
|
|
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| class DumpSchemasToProjectionEnums extends Generator { | ||
|
|
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| private def fields(schema: Schema): Seq[String] = { | ||
| schema.getFields() | ||
| .map(field => field.name) | ||
| .toSeq | ||
| } | ||
|
|
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| private def generateClassDump(className: String): String = { | ||
|
|
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| // get schema | ||
| val schema = ReflectSchema.getSchemaByReflection(className) | ||
|
|
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| // get class name without package | ||
| val classNameNoPackage = className.split('.').last | ||
|
|
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| "\n\nobject %sField extends FieldEnumeration(%s.SCHEMA$) {\n val %s = SchemaValue\n}".format( | ||
| classNameNoPackage, | ||
| className, | ||
| fields(schema).mkString(", ")) | ||
| } | ||
|
|
||
| def apply(args: Array[String]) { | ||
|
|
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| if (args.length < 3) { | ||
| println("DumpSchemasToProjectionEnums <package-name> <class-to-dump> ... <file-to-dump-to>") | ||
| System.exit(1) | ||
| } else { | ||
|
|
||
| // drop the file to write and the package name | ||
| val classesToDump = args.drop(1).dropRight(1) | ||
|
|
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| // open the file to write | ||
| val dir = new File(args.last).getParentFile | ||
| if (!dir.exists()) { | ||
| dir.mkdirs() | ||
| } | ||
| val fw = new FileWriter(args.last) | ||
|
|
||
| // write the header | ||
| writeHeader(fw, args.head) | ||
|
|
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| // loop and dump the classes | ||
| classesToDump.foreach(className => { | ||
| val dumpString = generateClassDump(className) | ||
|
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| fw.write("\n") | ||
| fw.write(dumpString) | ||
| }) | ||
|
|
||
| // we are done, so close and flush | ||
| fw.close() | ||
| } | ||
| } | ||
| } |
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50
adam-codegen/src/main/scala/org/bdgenomics/adam/codegen/Generator.scala
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| /** | ||
| * Licensed to Big Data Genomics (BDG) under one | ||
| * or more contributor license agreements. See the NOTICE file | ||
| * distributed with this work for additional information | ||
| * regarding copyright ownership. The BDG licenses this file | ||
| * to you under the Apache License, Version 2.0 (the | ||
| * "License"); you may not use this file except in compliance | ||
| * with the License. You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package org.bdgenomics.adam.codegen | ||
|
|
||
| import java.io.FileWriter | ||
|
|
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| trait Generator { | ||
|
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| protected def writeHeader(fw: FileWriter, packageName: String) { | ||
| val hdr = Seq( | ||
| "/**", | ||
| "* Licensed to Big Data Genomics (BDG) under one", | ||
| "* or more contributor license agreements. See the NOTICE file", | ||
| "* distributed with this work for additional information", | ||
| "* regarding copyright ownership. The BDG licenses this file", | ||
| "* to you under the Apache License, Version 2.0 (the", | ||
| "* \"License\"); you may not use this file except in compliance", | ||
| "* with the License. You may obtain a copy of the License at", | ||
| "*", | ||
| "* http://www.apache.org/licenses/LICENSE-2.0", | ||
| "*", | ||
| "* Unless required by applicable law or agreed to in writing, software", | ||
| "* distributed under the License is distributed on an \"AS IS\" BASIS,", | ||
| "* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.", | ||
| "* See the License for the specific language governing permissions and", | ||
| "* limitations under the License.", | ||
| "*/", | ||
| "package %s".format(packageName), | ||
| "", | ||
| "import scala.collection.JavaConversions._", | ||
| "import scala.collection.JavaConverters._").mkString("\n") | ||
|
|
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| fw.write(hdr) | ||
| } | ||
| } |
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28 changes: 0 additions & 28 deletions
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adam-core/src/main/scala/org/bdgenomics/adam/projections/AlignmentRecordField.scala
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adam-core/src/main/scala/org/bdgenomics/adam/projections/ContigField.scala
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adam-core/src/main/scala/org/bdgenomics/adam/projections/DbxrefField.scala
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adam-core/src/main/scala/org/bdgenomics/adam/projections/FeatureField.scala
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