Class GeoScrapeTaskCommand

java.lang.Object
ubic.gemma.core.job.TaskCommand
ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand
All Implemented Interfaces:
Serializable
@Deprecated public class GeoScrapeTaskCommand extends TaskCommand
Deprecated.
Supplanted by the curation agent's own GEO scraping, currently scrape_geo_and_open_triage.py. The agent discovers candidates, decides what is worth preboarding, and opens its own triage ticket, so Gemma no longer needs to run the scrape itself.

Nothing here is removed yet and it still works. What it does that the agent must therefore also do: it creates the PreboardedExperiment rows, writes the GeoScrapeWatermark audit row, and opens ONE SCREENING ticket per batch targeting that watermark -- deliberately not one per candidate.

The preboarded write API the agent uses instead is POST /preboarded + POST /preboarded/{id}/annotation-sets, with GET /workflow/queue?datasetType=preboarded_experiment for the queue.

See Also:

  • Constructor Details

    • GeoScrapeTaskCommand

      public GeoScrapeTaskCommand()
      Deprecated.

  • Method Details

    • getTaskClass

      public Class<? extends Task<? extends TaskCommand>> getTaskClass()
      Deprecated.
      Description copied from class: TaskCommand
      Obtain the class of the Task object that will be run for this command.

      If null, the task command cannot be submitted through TaskRunningService.submitTaskCommand(TaskCommand) and a task object must be explicitly created.

      For now, this how we map from TaskCommand to Task that actually runs it. We have to have this mapping somewhere until we make Tasks themselves serializable. Tasks are not readily serializable because they have dependencies to Spring services. at which point TaskCommand can be deprecated(or remain as TaskContext).

      Overrides:
      getTaskClass in class TaskCommand

    • getSince

      @Nullable public Date getSince()
      Deprecated.

    • getUntil

      @Nullable public Date getUntil()
      Deprecated.

    • getMaxRecords

      @Nullable public Integer getMaxRecords()
      Deprecated.

    • getCriteria

      @Nullable public Collection<String> getCriteria()
      Deprecated.

    • isDryRun

      public boolean isDryRun()
      Deprecated.

    • getStartAt

      @Nullable public String getStartAt()
      Deprecated.
      GEO accession to resume from; see ScrapeRequest.startAt.

    • getSkip

      @Nullable public Integer getSkip()
      Deprecated.
      Records to skip at the start of the resolved window; see ScrapeRequest.skip.

    • setSince

      public void setSince(@Nullable Date since)
      Deprecated.

    • setUntil

      public void setUntil(@Nullable Date until)
      Deprecated.

    • setMaxRecords

      public void setMaxRecords(@Nullable Integer maxRecords)
      Deprecated.

    • setCriteria

      public void setCriteria(@Nullable Collection<String> criteria)
      Deprecated.

    • setDryRun

      public void setDryRun(boolean dryRun)
      Deprecated.

    • setStartAt

      public void setStartAt(@Nullable String startAt)
      Deprecated.
      GEO accession to resume from; see ScrapeRequest.startAt.

    • setSkip

      public void setSkip(@Nullable Integer skip)
      Deprecated.
      Records to skip at the start of the resolved window; see ScrapeRequest.skip.