fix_result_options_and_refresh.py

from bika.lims import api
from nmrl.lims.scripts import setup_script_environment
from senaite.core.catalog import SETUP_CATALOG, SAMPLE_CATALOG
import transaction


def fix_services():
    services = api.search({"portal_type": "AnalysisService"}, SETUP_CATALOG)
    print("Total services found: {}".format(len(services)))

    updated_keywords = set()
    batch = 0

    for brain in services:
        service = api.get_object(brain)
        result_type = service.getResultType()
        result_options = service.getResultOptions()

        if result_type == "numeric" and result_options:
            print("Updating {} from 'numeric' to 'select'".format(service.Title()))
            service.setResultType("select")
            service.reindexObject()
            updated_keywords.add(service.getKeyword())
            batch += 1

            if batch >= 10:
                transaction.commit()
                print("Committed batch of 10 service updates")
                batch = 0

    if batch:
        transaction.commit()
        print("Final commit of remaining {} service updates".format(batch))

    print("Total services fixed: {}".format(len(updated_keywords)))
    return list(updated_keywords)


def search_service(keyword):
    results = api.search({
        "portal_type": "AnalysisService",
        "getKeyword": keyword
    }, SETUP_CATALOG)
    return api.get_object(results[0]) if results else None


def refresh_samples(app, updated_keywords, commit_interval=10):
    query = {
        "portal_type": "AnalysisRequest",
        "review_state": "sample_received",
        "sort_on": "created",
        "sort_order": "ascending",
    }

    brains = api.search(query, SAMPLE_CATALOG)
    print("\nFound {} samples in 'sample_received'".format(len(brains)))

    updated_count = 0

    for brain in brains:
        sample = api.get_object(brain)
        analyses = sample.getAnalyses()

        if not analyses:
            continue

        print("\nSample: {} with {} analyses".format(sample.getId(), len(analyses)))

        to_delete = []
        refresh_keywords = []
        keep_services = []

        for a_brain in analyses:
            analysis = api.get_object(a_brain)
            state = api.get_review_status(analysis)

            if state not in ["received", "unassigned", "assigned"]:
                print("  Skipping sample: {} (analysis not in allowed state)".format(sample.getId()))
                to_delete = []
                break

            # TODO: handle worksheets - unassign first but keep position then reassign later to same position

            service = analysis.getAnalysisService()
            keyword = service.getKeyword()

            if keyword in updated_keywords:
                to_delete.append(analysis.getId())
                refresh_keywords.append(keyword)
            else:
                keep_services.append(service)

        if not to_delete:
            continue

        # Delete outdated analyses
        print("  Deleting: {}".format(to_delete))
        sample.manage_delObjects(to_delete)

        # Re-attach updated services
        refreshed_services = []
        for keyword in refresh_keywords:
            service = search_service(keyword)
            if service:
                refreshed_services.append(service)
            else:
                print("  Missing service for keyword: {}".format(keyword))

        final_services = refreshed_services + keep_services

        if final_services:
            try:
                sample.setAnalyses(final_services)
                sample.reindexObject()
                print("  Refreshed Sample {} with services: {}".format(
                    sample.getId(),
                    [s.getKeyword() for s in final_services]
                ))
            except Exception as e:
                print("  Failed to update sample {}: {}".format(sample.getId(), str(e)))
                continue

        updated_count += 1

        if updated_count % commit_interval == 0:
            transaction.commit()
            print("  Committed after {} refreshed samples".format(updated_count))

    transaction.commit()
    print("\nDone. Total refreshed samples: {}".format(updated_count))


def main(app):
    setup_script_environment(app)
    updated_keywords = fix_services()

    if updated_keywords:
        refresh_samples(app, updated_keywords)
    else:
        print("No services were modified. No samples refreshed.")


if __name__ == "__main__":
    main(app)