Packages

class OrphanetGeneSet extends ETLP

Linear Supertypes
ETLP, ETLSingleDestination, ETL, Runnable, AnyRef, Any
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Inherited
  1. OrphanetGeneSet
  2. ETLP
  3. ETLSingleDestination
  4. ETL
  5. Runnable
  6. AnyRef
  7. Any
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Visibility
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Instance Constructors

  1. new OrphanetGeneSet()(implicit conf: Configuration)

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. val HGNC_gene_id: (Node) ⇒ Option[String]
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. val association_status: (Node) ⇒ Option[String]
  7. val association_type: (Node) ⇒ Option[String]
  8. val association_type_id: (Node) ⇒ Option[Long]
  9. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  10. implicit val conf: Configuration
    Definition Classes
    ETL
  11. val defaultRepartition: (DataFrame) ⇒ DataFrame
    Definition Classes
    OrphanetGeneSet → ETL
  12. def defaultSampling: PartialFunction[String, (DataFrame) ⇒ DataFrame]
    Definition Classes
    ETL
  13. val ensembl_gene_id: (Node) ⇒ Option[String]
  14. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  16. def extract(lastRunDateTime: LocalDateTime, currentRunDateTime: LocalDateTime)(implicit spark: SparkSession): Map[String, DataFrame]

    Reads data from a file system and produce a Map[DatasetConf, DataFrame].

    Reads data from a file system and produce a Map[DatasetConf, DataFrame]. This method should avoid transformation and joins but can implement filters in order to make the ETL more efficient.

    spark

    an instance of SparkSession

    returns

    all the data needed to pass to the transform method and produce the desired output.

    Definition Classes
    OrphanetGeneSet → ETL
  17. val genatlas_gene_id: (Node) ⇒ Option[String]
  18. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  19. def getLastRunDateFor(ds: DatasetConf)(implicit spark: SparkSession): LocalDateTime

    If possible, fetch the last run date time from the dataset passed in argument

    If possible, fetch the last run date time from the dataset passed in argument

    ds

    dataset

    spark

    a spark session

    returns

    the last run date or the minDateTime

    Definition Classes
    ETL
  20. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  21. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  22. def lastReleaseId(implicit spark: SparkSession): String
    Definition Classes
    ETLP
  23. final def load(data: Map[String, DataFrame], lastRunDateTime: LocalDateTime, currentRunDateTime: LocalDateTime, repartition: (DataFrame) ⇒ DataFrame)(implicit spark: SparkSession): Map[String, DataFrame]

    Loads the output data into a persistent storage.

    Loads the output data into a persistent storage. The output destination can be any of: object store, database or flat files...

    data

    output data produced by the transform method.

    spark

    an instance of SparkSession

    Definition Classes
    ETLSingleDestination → ETL
  24. def loadDataset(df: DataFrame, ds: DatasetConf, repartition: (DataFrame) ⇒ DataFrame)(implicit spark: SparkSession): DataFrame
    Definition Classes
    ETL
  25. def loadSingle(data: DataFrame, lastRunDateTime: LocalDateTime = minDateTime, currentRunDateTime: LocalDateTime = LocalDateTime.now(), repartition: (DataFrame) ⇒ DataFrame = defaultRepartition)(implicit spark: SparkSession): DataFrame
    Definition Classes
    ETLSingleDestination
  26. val log: Logger
    Definition Classes
    ETL
  27. val mainDestination: DatasetConf
    Definition Classes
    OrphanetGeneSet → ETL
  28. val maxDateTime: LocalDateTime
    Definition Classes
    ETL
  29. val minDateTime: LocalDateTime
    Definition Classes
    ETL
  30. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  31. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  32. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  33. val omim_gene_id: (Node) ⇒ Option[String]
  34. val orphanet_disease_history: DatasetConf
  35. val orphanet_gene_association: DatasetConf
  36. def parseProduct6XML(doc: Elem): Seq[OrphanetGeneAssociation]
  37. def parseProduct9XML(doc: Elem): Seq[OrphanetDiseaseHistory]
  38. def publish()(implicit spark: SparkSession): Unit

    OPTIONAL - Contains all actions needed to be done in order to make the data available to users like creating a view with the data.

    OPTIONAL - Contains all actions needed to be done in order to make the data available to users like creating a view with the data.

    spark

    an instance of SparkSession

    Definition Classes
    ETLP → ETL
  39. val reactome_gene_id: (Node) ⇒ Option[String]
  40. def replaceWhere: Option[String]

    replaceWhere is used in for OverWriteStaticPartition load.

    replaceWhere is used in for OverWriteStaticPartition load. It avoids to compute dataframe to infer which partitions to replace. Most of the time, these partitions can be inferred statically. Always prefer that to dynamically overwrite partitions.

    Definition Classes
    ETL
  41. def reset()(implicit spark: SparkSession): Unit

    Reset the ETL by removing the destination dataset.

    Reset the ETL by removing the destination dataset.

    Definition Classes
    ETL
  42. def run(runSteps: Seq[RunStep] = RunStep.default_load, lastRunDateTime: Option[LocalDateTime] = None, currentRunDateTime: Option[LocalDateTime] = None)(implicit spark: SparkSession): Map[String, DataFrame]

    Entry point of the etl - execute this method in order to run the whole ETL

    Entry point of the etl - execute this method in order to run the whole ETL

    spark

    an instance of SparkSession

    Definition Classes
    ETL → Runnable
  43. def sampling: PartialFunction[String, (DataFrame) ⇒ DataFrame]

    Logic used when the ETL is run as a SAMPLE_LOAD

    Logic used when the ETL is run as a SAMPLE_LOAD

    Definition Classes
    ETL
  44. val swiss_prot_gene_id: (Node) ⇒ Option[String]
  45. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  46. def toMain(df: ⇒ DataFrame): Map[String, DataFrame]
    Definition Classes
    ETL
  47. def toString(): String
    Definition Classes
    AnyRef → Any
  48. final def transform(data: Map[String, DataFrame], lastRunDateTime: LocalDateTime = minDateTime, currentRunDateTime: LocalDateTime = LocalDateTime.now())(implicit spark: SparkSession): Map[String, DataFrame]

    Takes a Map[DatasetConf, DataFrame] as input and apply a set of transformation to it to produce the ETL output.

    Takes a Map[DatasetConf, DataFrame] as input and apply a set of transformation to it to produce the ETL output. It is recommended to not read any additional data but to use the extract() method instead to inject input data.

    data

    input data

    spark

    an instance of SparkSession

    Definition Classes
    ETLSingleDestination → ETL
  49. def transformSingle(data: Map[String, DataFrame], lastRunDateTime: LocalDateTime, currentRunDateTime: LocalDateTime)(implicit spark: SparkSession): DataFrame

    Takes aDataFrame as input and apply a set of transformation to it to produce the ETL output.

    Takes aDataFrame as input and apply a set of transformation to it to produce the ETL output. It is recommended to not read any additional data but to use the extract() method instead to inject input data.

    data

    input data

    spark

    an instance of SparkSession

    Definition Classes
    OrphanetGeneSet → ETLSingleDestination
  50. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  51. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  52. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

Inherited from ETLP

Inherited from ETLSingleDestination

Inherited from ETL

Inherited from Runnable

Inherited from AnyRef

Inherited from Any

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