Class GeoScrapeServiceImpl

java.lang.Object

ubic.gemma.core.geoscrape.GeoScrapeServiceImpl

All Implemented Interfaces:

GeoScrapeService

@Service
public class GeoScrapeServiceImpl
extends Object
implements GeoScrapeService

Default GeoScrapeService implementation.

Pages through GeoBrowser results, filters to expression-profiling records on the allowed taxa, evaluates each registered GeoRecordMatcher against each record, and creates a PreboardedExperiment for any record at least one matcher flagged. Tracks progress on a single GeoScrapeWatermark row per invocation.

The watermark is written via a short-lived programmatic transaction so IN_PROGRESS / COMPLETED / FAILED / CANCELLED state changes are visible to the GET /admin/geo-scrape/last endpoint even while a scrape is in flight. Preboarded creation routes through PreboardedExperimentService which handles dedupe + audit emission.

Author:

phase 3 geo-scrape pipeline

Nested Class Summary

Nested classes/interfaces inherited from interface GeoScrapeService

GeoScrapeService.DryRunResult, GeoScrapeService.ScrapeRequest

Constructor Summary

Constructors

Constructor	Description
GeoScrapeServiceImpl(SessionFactory sessionFactory, PreboardedExperimentService preboardedExperimentService, List<GeoRecordMatcher> matchers, org.springframework.transaction.PlatformTransactionManager transactionManager, TicketService ticketService, UserManager userManager)

Method Summary

Modifier and Type	Method	Description
GeoScrapeWatermark	getLastWatermark()
GeoScrapeWatermark	scrape(GeoScrapeService.ScrapeRequest req)	Run a scrape.
GeoScrapeService.DryRunResult	scrapeDryRun(GeoScrapeService.ScrapeRequest req)	Evaluate matchers against the same window GeoScrapeService.scrape(ScrapeRequest) would inspect, but persist nothing — no watermark row, no PreboardedExperiment row, no ticket.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

GeoScrapeServiceImpl

@Autowired
public GeoScrapeServiceImpl(SessionFactory sessionFactory,
 PreboardedExperimentService preboardedExperimentService,
 List<GeoRecordMatcher> matchers,
 org.springframework.transaction.PlatformTransactionManager transactionManager,
 TicketService ticketService,
 UserManager userManager)

Method Details

scrape

public GeoScrapeWatermark scrape(GeoScrapeService.ScrapeRequest req)

Description copied from interface: GeoScrapeService

Run a scrape. Synchronous; intended to be invoked from a GeoScrapeTaskCommand running on the task-runner. Honors Thread.interrupted() between pages — the watermark row is marked GeoScrapeWatermark.Status.CANCELLED if the worker is interrupted mid-scan.

Specified by:

scrape in interface GeoScrapeService

Returns:

the persisted watermark row covering this run (so the caller can summarize counts/timings).

scrapeDryRun

public GeoScrapeService.DryRunResult scrapeDryRun(GeoScrapeService.ScrapeRequest req)

Description copied from interface: GeoScrapeService

Evaluate matchers against the same window GeoScrapeService.scrape(ScrapeRequest) would inspect, but persist nothing — no watermark row, no PreboardedExperiment row, no ticket. Intended for downstream callers (currently gemma-curation-agents) that mock-persist the results locally to evaluate curation methods without writing to prod gemd. Wire shape per candidate mirrors the existing preboarded GET response so the dry-run flag can flip off later without a shape change.

Specified by:

scrapeDryRun in interface GeoScrapeService

Returns:

the candidate list in scan order; dryRun on the request is ignored (treated as true by contract).

getLastWatermark

@Nullable
public GeoScrapeWatermark getLastWatermark()

Specified by:

getLastWatermark in interface GeoScrapeService

Returns:

the most recent GeoScrapeWatermark row, or null if no scrape has ever been run.