| Name | Params | Users/roles | Comment |
|---|---|---|---|
| clear_container_error | IN p_barcode varchar(10) | ispyb_acquisition | Sets error for p_barcode in automation fault table to resolved s |
| delete_usergroup_has_person_for_login | p_login varchar(45) | none | Deletes all rows from UserGroup_has_Person for personId corresponding to the Person login provided. Mandatory columns: p_login Returns: Nothing. |
| finish_container | IN p_barcode varchar(45) | ispyb_acquisition | Set the completedTimeStamp in the ContainerQueue table for the container with this barcode |
| finish_container_for_id | IN p_id int(10) unsigned | ispyb_processing | Set the completedTimeStamp in the ContainerQueue table for the container with this containerId |
| insert_aperture | OUT p_id int(10) unsigned p_sizeX float |
ispyb_gda_mxcx | Inserts a row into the Aperture table |
| insert_beamline_action | OUT p_id int(11) unsigned p_proposalCode varchar(3), p_proposalNumber int(10) p_sessionNumber int(10) p_startTime timestamp p_endTime timestamp p_message varchar(255) p_parameter varchar(50) p_value varchar(50) p_logLevel enum('DEBUG','CRITICAL','INFO') p_status enum('PAUSED','RUNNING','TERMINATED','COMPLETE','ERROR','EPICSFAIL') |
ispyb_gda_scm | Insert a beamline action row for session p_proposalCode + p_prop |
| insert_container_error | IN p_barcode varchar(45) p_error varchar(255) p_severity int, p_stack_trace text |
ispyb_acquisition | Inserts row with info about container loading-related error into |
| insert_container_inspections | p_containerId int(11) unsigned p_scheduleName varchar(10) |
none | Inserts records into ContainerInspection |
| insert_cryoem_initial_model | OUT p_id int unsigned p_particleClassificationId int unsigned, p_resolution float p_numberOfParticles int unsigned |
ispyb_processing | Inserts or updates info about a (cryoEM) initial model for a given particle classification (p_particleClassificationId). Mandatory columns: p_particleClassificationId Returns: Record ID in p_id. |
| insert_crystal | OUT p_id int(11) unsigned p_diffractionPlanId int(11) unsigned, p_proteinId int(11) unsigned p_crystalUUID varchar(45) p_name varchar(255) p_spaceGroup varchar(20) p_morphology varchar(255), p_color varchar(45) p_size_x long p_size_y long p_size_z long, p_cell_a long p_cell_b long p_cell_c long p_cell_alpha long, p_cell_beta long p_cell_gamma long p_comments varchar(255), p_recordTimeStamp varchar(1024) p_abundance float p_theoreticalDensity float |
ispyb_gda_mxcx | Inserts information into the Crystal table. Returns Record ID in p_id. |
| insert_dc_plan | OUT p_id int(11) unsigned p_name varchar(20) p_experimentKind varchar(25) p_observedResolution float p_minimalResolution float, p_exposuretime float p_oscillationRange float p_maximalResolution float p_screeningResolution float p_radiationSensitivity float, p_anomalousScatterer varchar(255) p_preferredBeamSizeX float, p_preferredBeamSizeY float p_preferredBeamDiameter float p_comments varchar(1024) p_DiffractionPlanUUID varchar(1000) p_aimedCompleteness double p_aimedIOverSigmaAtHighestRes double p_aimedMultiplicity double p_aimedResolution double p_anomalousData tinyint(1), p_complexity varchar(45) p_estimateRadiationDamage tinyint(1), p_forcedSpaceGroup varchar(45) p_requiredCompleteness double, p_requiredMultiplicity double p_requiredResolution double, p_strategyOption varchar(200) p_kappaStrategyOption varchar(45), p_numberOfPositions int(11) p_minDimAccrossSpindleAxis double, p_maxDimAccrossSpindleAxis double p_radiationSensitivityBeta double, p_radiationSensitivityGamma double p_minOscWidth float, p_recordTimeStamp timestamp p_monochromator varchar(8) p_energy float, p_transmission float p_boxSizeX float p_boxSizeY float p_kappaStart float p_axisStart float p_axisRange float p_numberOfImages mediumint(9) p_beamLineName varchar(45) p_detectorId int(11), p_distance double p_orientation double p_monoBandwidth double, p_centringMethod varchar(20) p_userPath varchar(100), p_robotPlateTemperature float p_exposureTemperature float, p_collectionMode varchar(10) p_priority int(4) |
ispyb_gda_mxcx | Inserts a row into the DiffractionPlan table. Returns Record ID in p_id. |
| insert_phasing_analysis_results | OUT p_id int(11) unsigned IN p_phasing_result JSON IN p_autoProcScalingId int(10) unsigned |
ispyb_processing | Insert all the results from a phasing into the relevant database tables. Returns the top-level phasing ID in p_id. |
| insert_position | OUT p_id int(11) unsigned p_posX long p_posY long p_posZ long, p_scale long |
ispyb_gda_mxcx | Inserts information into the Position table. Returns Record ID in p_id. |
| insert_processing_scaling | OUT p_id integer unsigned p_parentId integer unsigned p_Type1 enum('overall','innerShell','outerShell') p_Comments1 varchar(255), p_ResolutionLimitLow1 float p_ResolutionLimitHigh1 float p_rMerge1 float p_rMeasWithinIPlusIMinus1 float p_rMeasAllIPlusIMinus1 float, p_rPimWithinIPlusIMinus1 float p_rPimAllIPlusIMinus1 float, p_fractionalPartialBias1 float p_nTotalObservations1 integer, p_nTotalUniqueObservations1 integer p_meanIOverSigI1 float, p_completeness1 float p_multiplicity1 float p_anomalous1 boolean, p_anomalousCompleteness1 float p_anomalousMultiplicity1 float, p_ccHalf1 float p_ccAnomalous1 float p_Type2 enum('overall','innerShell','outerShell') p_Comments2 varchar(255), p_ResolutionLimitLow2 float p_ResolutionLimitHigh2 float p_rMerge2 float p_rMeasWithinIPlusIMinus2 float p_rMeasAllIPlusIMinus2 float, p_rPimWithinIPlusIMinus2 float p_rPimAllIPlusIMinus2 float, p_fractionalPartialBias2 float p_nTotalObservations2 integer, p_nTotalUniqueObservations2 integer p_meanIOverSigI2 float, p_completeness2 float p_multiplicity2 float p_anomalous2 boolean, p_anomalousCompleteness2 float p_anomalousMultiplicity2 float, p_ccHalf2 float p_ccAnomalous2 float p_Type3 enum('overall','innerShell','outerShell') p_Comments3 varchar(255), p_ResolutionLimitLow3 float p_ResolutionLimitHigh3 float p_rMerge3 float p_rMeasWithinIPlusIMinus3 float p_rMeasAllIPlusIMinus3 float, p_rPimWithinIPlusIMinus3 float p_rPimAllIPlusIMinus3 float, p_fractionalPartialBias3 float p_nTotalObservations3 integer, p_nTotalUniqueObservations3 integer p_meanIOverSigI3 float, p_completeness3 float p_multiplicity3 float p_anomalous3 boolean, p_anomalousCompleteness3 float p_anomalousMultiplicity3 float, p_ccHalf3 float p_ccAnomalous3 float |
ispyb_processing | Inserts 1 row in AutoProcScaling 3 rows in AutoProcScalingStati |
| insert_processing_scaling_v2 | OUT p_id integer unsigned p_parentId integer unsigned p_Type1 enum('overall','innerShell','outerShell') p_Comments1 varchar(255), p_ResolutionLimitLow1 float p_ResolutionLimitHigh1 float p_rMerge1 float p_rMeasWithinIPlusIMinus1 float p_rMeasAllIPlusIMinus1 float, p_rPimWithinIPlusIMinus1 float p_rPimAllIPlusIMinus1 float, p_fractionalPartialBias1 float p_nTotalObservations1 integer, p_nTotalUniqueObservations1 integer p_meanIOverSigI1 float, p_resIOverSigI21 float p_completeness1 float p_multiplicity1 float, p_anomalous1 boolean p_anomalousCompleteness1 float, p_anomalousMultiplicity1 float p_ccHalf1 float p_ccAnomalous1 float, p_Type2 enum('overall','innerShell','outerShell') p_Comments2 varchar(255) p_ResolutionLimitLow2 float p_ResolutionLimitHigh2 float, p_rMerge2 float p_rMeasWithinIPlusIMinus2 float p_rMeasAllIPlusIMinus2 float p_rPimWithinIPlusIMinus2 float p_rPimAllIPlusIMinus2 float, p_fractionalPartialBias2 float p_nTotalObservations2 integer, p_nTotalUniqueObservations2 integer p_meanIOverSigI2 float, p_resIOverSigI22 float p_completeness2 float p_multiplicity2 float, p_anomalous2 boolean p_anomalousCompleteness2 float, p_anomalousMultiplicity2 float p_ccHalf2 float p_ccAnomalous2 float, p_Type3 enum('overall','innerShell','outerShell') p_Comments3 varchar(255) p_ResolutionLimitLow3 float p_ResolutionLimitHigh3 float, p_rMerge3 float p_rMeasWithinIPlusIMinus3 float p_rMeasAllIPlusIMinus3 float p_rPimWithinIPlusIMinus3 float p_rPimAllIPlusIMinus3 float, p_fractionalPartialBias3 float p_nTotalObservations3 integer, p_nTotalUniqueObservations3 integer p_meanIOverSigI3 float, p_resIOverSigI23 float p_completeness3 float p_multiplicity3 float, p_anomalous3 boolean p_anomalousCompleteness3 float, p_anomalousMultiplicity3 float p_ccHalf3 float p_ccAnomalous3 float |
ispyb_processing | Inserts 1 row in AutoProcScaling 3 rows in AutoProcScalingStatistics. Returns: autoProcScalingId value in p_id |
| insert_quality_indicators | OUT p_id int(11) unsigned p_dataCollectionId int(11) unsigned, p_autoProcProgramId int(10) unsigned p_imageNumber mediumint(8) unsigned p_spotTotal int(10) p_inResTotal int(10), p_goodBraggCandidates int(10) p_iceRings int(10) p_method1Res float, p_method2Res float p_maxUnitCell float p_pctSaturationTop50Peaks float p_inResolutionOvrlSpots int(10) p_binPopCutOffMethod2Res float, p_totalIntegratedSignal double p_driftFactor float |
ispyb_processing | Inserts a row into the image quality indicators table |
| insert_sample_image_auto_score | OUT p_id int(11) unsigned p_imageFullPath varchar(255), p_schemaName varchar(25) p_scoreClass varchar(15) p_probability float |
none | Insert a row with the auto scored probability for a given sample image using a certain class and schema. Returns the ID in p_id. |
| insert_screening | OUT p_id int(11) unsigned p_dcgId int(11) unsigned p_dcId int(11) unsigned p_programVersion varchar(45) p_shortComments varchar(20), p_comments varchar(255) |
ispyb_processing | Insert a row with info about a screening. Returns the ID in p_id |
| insert_screening_input | OUT p_id int(11) unsigned p_screeningId int(10) unsigned p_beamX float p_beamY float p_rmsErrorLimits float p_minFractionIndexed float p_maxFractionRejected float p_minSignalToNoise float |
ispyb_processing | Insert a row with info about a screening input. Returns the ID i |
| insert_screening_output | OUT p_id int(11) unsigned p_screeningId int(10) unsigned, p_statusDescription varchar(1024) p_rejectedReflections int(10) unsigned p_resolutionObtained float p_spotDeviationR float, p_spotDeviationTheta float p_beamShiftX float p_beamShiftY float, p_numSpotsFound int(10) unsigned p_numSpotsUsed int(10) unsigned, p_numSpotsRejected int(10) unsigned p_mosaicity float p_iOverSigma float p_diffractionRings boolean p_mosaicityEstimated boolean, p_rankingResolution double p_program varchar(45) p_doseTotal double, p_totalExposureTime double p_totalRotationRange double, p_totalNumberOfImages int(11) p_rFriedel double p_indexingSuccess boolean p_strategySuccess boolean |
ispyb_processing | Insert a row with info about a screening output. Returns the ID |
| insert_screening_output_lattice | OUT p_id int(10) unsigned p_screeningOutputId int(10) unsigned, p_spaceGroup varchar(45) p_pointGroup varchar(45) p_bravaisLattice varchar(45) p_rawOrientationMatrix_a_x float, p_rawOrientationMatrix_a_y float p_rawOrientationMatrix_a_z float, p_rawOrientationMatrix_b_x float p_rawOrientationMatrix_b_y float, p_rawOrientationMatrix_b_z float p_rawOrientationMatrix_c_x float, p_rawOrientationMatrix_c_y float p_rawOrientationMatrix_c_z float, p_unitCell_a float p_unitCell_b float p_unitCell_c float, p_unitCell_alpha float p_unitCell_beta float p_unitCell_gamma float, p_labelitIndexing boolean |
ispyb_processing | Insert a row with info about a screening output lattice. Returns |
| insert_screening_output_v2 | OUT p_id int(11) unsigned p_screeningId int(10) unsigned, p_statusDescription varchar(1024) p_rejectedReflections int(10) unsigned p_resolutionObtained float p_spotDeviationR float, p_spotDeviationTheta float p_beamShiftX float p_beamShiftY float, p_numSpotsFound int(10) unsigned p_numSpotsUsed int(10) unsigned, p_numSpotsRejected int(10) unsigned p_mosaicity float p_iOverSigma float p_diffractionRings boolean p_mosaicityEstimated boolean, p_rankingResolution double p_program varchar(45) p_doseTotal double, p_totalExposureTime double p_totalRotationRange double, p_totalNumberOfImages int(11) p_rFriedel double p_indexingSuccess boolean p_strategySuccess boolean p_alignmentSuccess boolean |
ispyb_processing | Insert a row with info about a screening output. Returns the ID in p_id. |
| insert_screening_strategy | OUT p_id int(10) unsigned p_screeningOutputId int(10) unsigned, p_phiStart float p_phiEnd float p_rotation float p_exposureTime float p_resolution float p_completeness float p_multiplicity float, p_anomalous float p_program varchar(45) p_rankingResolution float, p_transmission float |
ispyb_processing | Insert a row with info about a screening strategy. Returns the I |
| insert_screening_strategy_sub_wedge | OUT p_id int(10) unsigned p_screeningStrategyWedgeId int(10) unsigned p_subWedgeNumber int(10) unsigned p_rotationAxis varchar(45), p_axisStart float p_axisEnd float p_exposureTime float p_transmission float p_oscillationRange float p_completeness float p_multiplicity float p_resolution float p_doseTotal float p_numberOfImages int(10) unsigned p_comments varchar(255) |
ispyb_processing | Insert a row with info about a screening strategy sub-wedge. Returns the ID in p_id. |
| insert_screening_strategy_wedge | OUT p_id int(10) unsigned p_screeningStrategyId int(10) unsigned, p_wedgeNumber int(10) unsigned p_resolution float p_completeness float p_multiplicity float p_doseTotal float p_numberOfImages int(10) unsigned p_phi float p_kappa float p_chi float p_comments varchar(255) p_wavelength double |
ispyb_processing | Insert a row with info about a screening strategy wedge. Returns |
| insert_screening_v2 | OUT p_id int(11) unsigned p_dcgId int(11) unsigned p_dcId int(11) unsigned p_programVersion varchar(45) p_shortComments varchar(20), p_comments varchar(255) p_autoProcProgramId int(10) unsigned |
ispyb_processing | Insert a row with info about a screening. Returns the ID in p_id. |
| insert_subsample_for_image_full_path | OUT p_id int(11) unsigned p_imageFullPath varchar(255) p_source varchar(10) p_position1x double p_position1y double p_position2x double p_position2y double |
ispyb_import | Returns subsample ID in p_id. |
| insert_subsample_for_image_full_path_v2 | OUT p_id int(11) unsigned p_imageFullPath varchar(255) p_source varchar(10) p_position1x double p_position1y double p_position2x double p_position2y double p_experiment_type varchar(20) |
ispyb_import | Returns subsample ID in p_id. |
| insert_usergroup_has_person_for_ug_and_login | p_ug_name varchar(31) p_login varchar(45) |
none | Inserts a row in UserGroup_has_Person corresponding to the Person login and the UserGroup name provided. Mandatory columns: p_usergroup, p_login Returns: Nothing. |
| retrieve_apertures_using_size | p_sizeX double | ispyb_gda_mxcx | Return a multi-row result set with info about Apertures identified by aperture size. |
| retrieve_associated_dc_ids | IN p_dc_id INT | none | |
| retrieve_components_for_sample_type | IN p_sampleTypeId int unsigned | none | Return multi-row result-set with component ID and other info abo |
| retrieve_component_lattices_for_component | IN p_componentId int unsigned | none | Return multi-row result-set with component lattices for componen |
| retrieve_container | p_id int unsigned p_useContainerSession boolean p_authLogin varchar(45) |
ispyb_gda_mxcx | Returns a single-row result-set with the container for the given Id |
| retrieve_containers_on_beamline_with_status | IN p_beamline varchar(20) IN p_status varchar(40) |
ispyb_acquisition | Returns a multi-row result-set with info about when containers o |
| retrieve_containers_submitted_non_ls | IN p_beamline varchar(15) | ispyb_processing | Returns multi-row result-set with info about submitted not comp |
| retrieve_container_for_barcode | IN p_barcode varchar(45) | ispyb_import | Return single-row result set with info about a Container identified by p_barcode |
| retrieve_container_for_inspection_id | IN p_containerInspectionId int(11) unsigned | ispyb_import | Return single-row result set with info about a Container identified by p_containerInspectionId |
| retrieve_container_for_sample_id | p_id int unsigned p_authLogin varchar(45) |
ispyb_processing | Returns a single-row result-set with the container and its processing pipeline info for the given ID |
| retrieve_container_info | IN p_barcode varchar(45) | ispyb_acquisition | Returns single row result-set with info about the container with |
| retrieve_container_info_for_id | IN p_containerId int unsigned | none | Return single-row result set with info about a Container identif |
| retrieve_container_ls_position | IN p_barcode varchar(45) | ispyb_acquisition | Returns single row single column result-set with the position o |
| retrieve_container_ls_queue | IN p_beamline varchar(45) | ispyb_acquisition | Returns a multi-row result-set with info about when containers o |
| retrieve_container_on_gonio | IN p_beamline varchar(45) | ispyb_acquisition | Returns multi-row result-set with info about the containers on p |
| retrieve_container_queue_most_recent_completed_timestamp | IN p_barcode varchar(45) | ispyb_acquisition | Returns a single-row result-set with the most recent timestamp o |
| retrieve_container_queue_timestamp | IN p_barcode varchar(45) | ispyb_acquisition | Returns a single-column single-row result-set with timestamp of |
| retrieve_container_subsamples | IN p_barcode varchar(45) | ispyb_acquisition | Returns a mutli-row result-set with general info about submitted |
| retrieve_container_subsamples_v2 | IN p_barcode varchar(45) | ispyb_acquisition | Returns a mutli-row result-set with general info about submitted subsamples on submitted container p_barcode |
| retrieve_current_cm_sessions | IN p_beamline varchar(15) | ispyb_processing | |
| retrieve_current_sessions | IN p_beamline varchar(15) IN p_tolerance_minutes int |
ispyb_processing | Returns a multi-row result-set with the current (within tolerance
p_tolerance_minutes) session(s) (mx12345-123) their start and end dates for beamline p_beamline |
| retrieve_current_sessions_for_person | IN p_beamline varchar(15) IN p_fed_id varchar(24) IN p_tolerance_minutes int |
ispyb_processing | Returns a multi-row result-set with the current (within tolerance
p_tolerance_minutes) session(s) (mx12345-123) their start and end dates for person p_fed_id and beamline p_beamline |
| retrieve_dc | p_id int unsigned p_authLogin varchar(45) |
ispyb_gda_mxcx ispyb_processing |
Returns a single-row result-set with the data collection for the given ID |
| retrieve_dcs_for_sample | p_id int unsigned | ispyb_gda_mxcx | Return a multi-row result-set with the data-collection-main compatible records for the given sample ID |
| retrieve_dc_group | p_id int unsigned | ispyb_acquisition ispyb_gda_scm |
Returns a single-row result-set with the columns for the given data collection group id |
| retrieve_dc_group_v2 | p_id int unsigned p_authLogin varchar(45) |
ispyb_acquisition ispyb_gda_scm ispyb_processing |
Returns a single-row result-set with the columns for the given data collection group id |
| retrieve_dc_infos_for_subsample | p_id int | ispyb_acquisition | |
| retrieve_dc_main | p_id int unsigned | ispyb_processing | Returns a single-row result-set with the main data collection in |
| retrieve_dc_main_v2 | p_id int unsigned p_authLogin varchar(45) |
ispyb_processing | Returns a single-row result-set with the main data collection info for the given ID |
| retrieve_dc_plans_for_sample | IN p_sampleId int unsigned | none | Return multi-row result-set with info about data collection plan |
| retrieve_dc_plan_groups | IN p_session varchar(15) | none | |
| retrieve_dc_plan_info | IN p_id int | none | |
| retrieve_detector | IN p_serialNumber varchar(15) | ispyb_gda_scm | |
| retrieve_dewars_for_proposal_code_number | p_proposalCode varchar(3) p_proposalNumber int unsigned |
ispyb_processing | Return multi-row result-set with dewar ID + other dewar info ass |
| retrieve_dewars_for_proposal_code_number_v2 | p_proposalCode varchar(3) p_proposalNumber int unsigned, p_authLogin varchar(45) |
ispyb_processing | Return multi-row result-set with dewar ID + other dewar info
associated with shipments in a given proposal specified by proposal
code proposal_number |
| retrieve_expired_sessions_for_instrument_and_period | IN p_instrument varchar(15) IN p_startDate datetime IN p_endDate datetime |
ispyb_processing | Returns a multi-row result-set with the sessions that ended within the window defined by p_startDate and p_endDate on instrument given by p_instrument (can contain wildcards) |
| retrieve_grid_info_for_dc | IN p_dcId int unsigned p_authLogin varchar(45) |
ispyb_processing | Return multi-row result-set with grid info values for the dc |
| retrieve_grid_info_for_dcg | IN p_dcgId int unsigned | ispyb_processing | Return multi-row result-set with grid info values for the dcg |
| retrieve_grid_info_for_dcg_v2 | IN p_dcgId int unsigned p_authLogin varchar(45) |
ispyb_processing | Return multi-row result-set with grid info values for the dcg |
| retrieve_grid_info_for_dc_ids | IN p_dcIds TEXT | none | Return multi-row result-set with dc ID grid info and some addit |
| retrieve_grid_info_for_dc_v2 | IN p_dcId int unsigned p_authLogin varchar(45) |
ispyb_processing | Return multi-row result-set with grid info values for the dc |
| retrieve_lcs_for_session | p_proposal_code varchar(5) p_proposal_number int p_session_number int |
none | |
| retrieve_most_recent_session | IN p_beamline varchar(15) IN p_proposal_code varchar(5) |
ispyb_processing | Returns a single-row result-set with the session (mx12345-123) its start and end dates for beamline p_beamline and proposal code p_proposal_code (e.g. cm mx nt in ee) |
| retrieve_pdbs_for_component | IN p_componentId int unsigned | none | Return multi-row result set with PDB columns for component p_com |
| retrieve_persons_for_proposal | p_proposal_code varchar(5) p_proposal_number int |
ispyb_processing | Returns a multi-row result-set with info about the persons for |
| retrieve_persons_for_session | p_proposal_code varchar(5) p_proposal_number int p_visit_number int |
ispyb_processing | Returns a multi-row result-set with info about the persons for
session identified by p_proposal_code p_proposal_number, p_visit_number |
| retrieve_processing_job | p_id int unsigned | none | Returns a single-row result-set with info about the processing j |
| retrieve_processing_job_image_sweeps | p_id int unsigned | none | Returns a multi-row result-set with sweep info for the given pro |
| retrieve_processing_job_image_sweeps_v2 | p_id int unsigned p_authLogin varchar(45) |
ispyb_processing | Returns a multi-row result-set with sweep info for the given processing job ID |
| retrieve_processing_job_parameters | p_id int unsigned | none | Returns a multi-row result-set (max 1000) with parameters for th |
| retrieve_processing_job_parameters_v2 | p_id int unsigned p_authLogin varchar(45) |
ispyb_processing | Returns a multi-row result-set (max 1000) with parameters for the given processing job ID |
| retrieve_processing_job_v2 | p_id int unsigned p_authLogin varchar(45) |
ispyb_processing | Returns a single-row result-set with info about the processing job for the given ID |
| retrieve_processing_programs_for_job_id | p_id int unsigned | ispyb_processing | Returns a multi-row result-set with processing program instances for the given processing job ID |
| retrieve_processing_programs_for_job_id_v2 | p_id int unsigned p_authLogin varchar(45) |
ispyb_processing | Returns a multi-row result-set with processing program instances for the given processing job ID |
| retrieve_processing_program_attachments_for_dc_group_and_program | p_id int unsigned p_program varchar(255) |
ispyb_processing | Returns a multi-row result-set with the processing program attachments for the given DC group ID |
| retrieve_processing_program_attachments_for_dc_group_program_v2 | p_id int unsigned p_program varchar(255) p_authLogin varchar(45) |
ispyb_processing | Returns a multi-row result-set with the processing program attachments for the given DC group ID |
| retrieve_processing_program_attachments_for_program_id | p_id int unsigned | ispyb_processing | Returns a multi-row result-set with the processing program attachments for the given processing program id |
| retrieve_processing_program_attachments_for_program_id_v2 | p_id int unsigned p_authLogin varchar(45) |
ispyb_processing | Returns a multi-row result-set with the processing program attachments for the given processing program id |
| retrieve_proposal_title | p_proposal_code varchar(5) p_proposal_number int |
ispyb_processing | Returns a single-row single-column result set with the title of the proposal p_proposal_code + p_proposal_number |
| retrieve_proposal_title | p_proposal_code varchar(5) p_proposal_number int p_authLogin varchar(45) |
ispyb_processing | Returns a single-row single-column result set with the title of the proposal p_proposal_code + p_proposal_number |
| retrieve_quality_indicators | p_dataCollectionId int unsigned p_imageNumber int unsigned |
ispyb_gda_mxcx | Returns a single-row result set with the image quality indicators for a given data collection id and image number. |
| retrieve_reprocessing_by_dc | p_dcId int(11) unsigned | ispyb_processing | Retrieves reprocessing requests for a data collection (p_dcId). |
| retrieve_robot_actions_for_sample | p_id int unsigned p_useRobotActionSession boolean p_authLogin varchar(45) |
ispyb_gda_mxcx | Returns a multi-row result-set with the robot actions for the given sample ID. |
| retrieve_sample | p_id int unsigned p_useContainerSession boolean p_authLogin varchar(45) |
ispyb_acquisition | Returns a single-row result-set with the sample for the given ID |
| retrieve_samples_assigned_for_proposal | IN p_proposalCode varchar(3) IN p_proposalNumber int |
none | Retrieve the user friendly name and ID of all assigned instances |
| retrieve_samples_for_sample_group | IN p_sampleGroupId int unsigned | none | Return multi-row result set with sample IDs order in the group |
| retrieve_samples_not_loaded_for_container_reg_barcode | p_barcode varchar(20) | ispyb_processing | |
| retrieve_sample_for_container_id_and_location | IN p_containerId int(11) unsigned p_location varchar(45) |
ispyb_import | Return single-row result set with info about a BLSample identified by p_containerId and p_location |
| retrieve_sample_groups_for_sample | IN p_sampleId int unsigned | none | Return multi-row result-set with sample group IDs order in the |
| retrieve_sample_type_for_sample | IN p_sampleId int unsigned | none | Return single-row result set with sample type columns for sample |
| retrieve_scm_container | p_id int unsigned p_useContainerSession boolean p_authLogin varchar(45) |
ispyb_gda_scm | Returns a single-row result-set with the container for the given ID |
| retrieve_scm_containers_for_session | p_proposalCode varchar(45) p_proposalNumber varchar(45), p_sessionNumber int unsigned p_status varchar(45) p_authLogin varchar(45) |
ispyb_gda_scm | Returns a multi-row result-set with the containers for the given
session defined by proposal code proposal number and session number |
| retrieve_scm_container_for_barcode | p_barcode varchar(45) p_useContainerSession boolean p_authLogin varchar(45) |
ispyb_gda_scm | Returns a single-row result-set with the container for the given barcode |
| retrieve_scm_sample | p_id int unsigned p_useContainerSession boolean p_authLogin varchar(45) |
ispyb_gda_scm | Returns a single-row result-set with the sample for the given ID |
| retrieve_scm_samples_for_container_id | p_containerId int unsigned p_useContainerSession boolean, p_authLogin varchar(45) |
ispyb_gda_scm | Returns a multi-row result-set with the samples for the given container ID |
| retrieve_scm_sample_for_container_barcode_and_location | p_barcode varchar(45) p_location varchar(45) p_useContainerSession boolean p_authLogin varchar(45) |
ispyb_gda_scm | Returns a single-row result-set (although can be multi-row if multiple samples per location in a container) with the sample for the given container barcode and sample location. |
| retrieve_screenings_for_sample | p_id int unsigned | ispyb_gda_mxcx | Returns multi-row result set with the screening for the given sampleId |
| retrieve_sessions_for_beamline_and_run | IN p_beamline varchar(15) IN p_run varchar(7) |
ispyb_processing | Returns a multi-row result-set with the sessions (mx12345-123),
their start and end dates for beamline p_beamline and run p_run. If
called with NULL for p_run then use the current run. |
| retrieve_sessions_for_person_login | p_login varchar(45) | ispyb_processing | Returns a multi-row result-set with info about the sessions associated with a person with login=p_login |
| retrieve_session_id | p_session varchar(15) OUT p_id int |
ispyb_acquisition | |
| retrieve_session_id_v2 | p_session varchar(15) p_authLogin varchar(45) |
ispyb_processing | Returns the session ID (an integer) for p_session (e.g. mx12345-123) |
| retrieve_sleeve | p_id tinyint unsigned | ispyb_acquisition | |
| retrieve_sleeves | ispyb_acquisition | ||
| retrieve_test | ispyb_acquisition | For testing the connection | |
| retrieve_xfe_fluo_ids_for_sample | p_id int unsigned | ispyb_gda_mxcx | Returns a multi-row result-set with the fluorescence spectrum ids for the given sample id. |
| update_container_assign | IN p_beamline varchar(20) IN p_registry_barcode varchar(45) IN p_position int |
ispyb_processing ispyb_touchscreen |
Toggles assign status of container (p_barcode). Sets the s.c. position and beamline. If assigned then: 1) Also assign its dewar and shipping. 2) Unassigns other containers in the same proposal on that beamline and s.c. position. If unassign then: |
| update_container_current_dewar_id | IN p_id int unsigned IN p_dewarId int unsigned |
ispyb_touchscreen | For Container with containerId==p_id: Sets currentDewarId=p_dewarId and inserts row into ContainerHistory with that currentDewarId. |
| update_container_dispose | IN p_barcode varchar(45) | ispyb_touchscreen | Update the Container with barcode p_barcode: Set containerStatus to disposed and imagerId to NULL. Also add a row in ContainerHistory with status = disposed. |
| update_container_ls_position | IN p_barcode varchar(45) IN p_position int |
ispyb_acquisition | Updates container sampleChangerLocation for barcode = p_barcode, |
| update_container_session_id | IN p_containerId int unsigned IN p_proposalCode varchar(10) IN p_proposalNumber int IN p_sessionNumber int IN p_authLogin varchar(45) |
ispyb_touchscreen | Updates sessionId in the Container (given by p_containerId). If
p_authLogin is given it must be authorised. |
| update_container_status | IN p_barcode varchar(45) IN p_status varchar(45) |
ispyb_acquisition | Set container containerStatus = p_status for barcode = p_barcode. Only a defined range of statuses are accepted. |
| update_container_unassign_all_for_beamline | IN p_beamline varchar(20) | ispyb_processing ispyb_touchscreen |
Unassigns all containers on a given beamline one by one by calling update_container_assign on each. |
| update_container_unqueue | IN p_barcode varchar(45) | ispyb_acquisition | Find the containerQueueId for the non-completed rows in ContainerQueue associated with barcode p_barcode. Remove the association to that ContainerQueue row for the from sub sample queue and remove the ContainerQueue row for the container with this barcode |
| update_dc_append_comments | p_id int(11) unsigned p_comments varchar(1024) p_separator varchar(5) |
ispyb_acquisition ispyb_processing |
Appends text to DataCollection.comments for dataCollectionId=p_id. |
| update_dc_experiment | p_id int(11) unsigned p_slitGapVertical float p_slitGapHorizontal float p_transmission float p_exposureTime float p_xBeam float, p_yBeam float p_axisStart float p_axisEnd float p_axisRange float, p_overlap float p_flux double p_fluxEnd double p_rotationAxis varchar(10) p_phiStart float p_kappaStart float p_omegaStart float, p_wavelength float p_resolution float p_detectorDistance float, p_bestWilsonPlotPath varchar(255) p_beamSizeAtSampleX float, p_beamSizeAtSampleY float p_focalSpotSizeAtSampleX float, p_focalSpotSizeAtSampleY float p_apertureSizeX float |
ispyb_acquisition | |
| update_dc_experiment_v2 | p_id int(11) unsigned p_slitGapVertical float p_slitGapHorizontal float p_transmission float p_exposureTime float p_xBeam float, p_yBeam float p_axisStart float p_axisEnd float p_axisRange float, p_overlap float p_flux double p_fluxEnd double p_rotationAxis varchar(10) p_phiStart float p_kappaStart float p_omegaStart float, p_wavelength float p_resolution float p_detectorDistance float, p_detector2Theta float p_bestWilsonPlotPath varchar(255), p_beamSizeAtSampleX float p_beamSizeAtSampleY float, p_focalSpotSizeAtSampleX float p_focalSpotSizeAtSampleY float, p_apertureSizeX float |
ispyb_acquisition ispyb_gda_scm |
|
| update_dc_machine | p_id int(11) unsigned p_synchrotronMode varchar(20), p_undulatorGap1 float p_undulatorGap2 float p_undulatorGap3 float |
ispyb_acquisition ispyb_gda_scm |
|
| update_dc_plans | IN p_shippingId int unsigned IN p_dewarId int unsigned IN p_containerId int unsigned IN p_sampleId int unsigned IN p_strategyOption varchar(200) IN p_priority int IN p_minimalResolution float IN p_requiredResolution double IN p_experimentKind varchar(20), IN p_energy float IN p_anomalousScatterer varchar(255) IN p_centringMethod varchar(20) IN p_useNulls boolean IN p_useProposalType varchar(10) |
ispyb_touchscreen | Updates the DiffractionPlan strategyOption and priority for a given
shipment. If p_shippingId is set then update for all plans in the shipment. If p_dewarId is set then update for all plans in the dewar. If p_containerId is set then update for all plans in the container. If p_sampleId is set then update for all plans in the sample. If p_useNulls is true then use plan parameter values as given otherwise only set them if they are not-null. p_useProposalType should be a value used in the proposalType column in the ExperimentType table. |
| update_dc_position | p_dcId int(11) unsigned p_posX double p_posY double p_posZ double p_scale double |
ispyb_acquisition ispyb_gda_scm ispyb_processing |
Sets the Position for the data collection (p_id). |
| update_dewar_comments_json_merge | IN p_id int(10) unsigned p_comments JSON |
ispyb_touchscreen | Merges in additional JSON into the comments column on a dewar/parcel (p_id). Mandatory columns: p_id Returns: Nothing |
| update_processing_program_for_id_range | p_startId int unsigned p_endId int unsigned |
none | Maintenance procedure to update processingPrograms based on contents of processingCommandLine |
| update_reg_container_barcode | IN p_oldBarcode varchar(20) IN p_newBarcode varchar(20) |
none | For Registered Container with barcode==p_oldBarcode: Sets barcode=p_newBarcode |
| update_reprocessing_status | p_id int(11) unsigned p_status enum('submitted' 'running', 'finished' 'failed') p_startedTimeStamp timestamp p_lastUpdateMessage varchar(80) |
ispyb_processing | Updates the reprocessing status |
| update_sample_append_staff_comments | p_id int(11) unsigned p_staffComments varchar(1024) p_separator varchar(5) |
none | Appends text to BLSample.staffComments for blSampleId=p_id. |
| update_session_archived | IN p_proposalCode varchar(3) IN p_proposalNumber int IN p_sessionNumber int IN p_archived boolean |
none | Updates the session archived column
for session specified by p_proposalCode p_proposalNumber, p_sessionNumber |
| update_session_enddate | p_id int(11) unsigned p_endDate datetime |
none | Updates the end date for a session. Mandatory params: p_id and p_endDate. |
| update_session_paths | p_proposalCode varchar(3) p_proposalNumber int(10) p_sessionNumber int(10) p_oldRoot varchar(255) p_newRoot varchar(255) |
none | Attempts to update the root (the leftmost part) of all paths related to session p_proposalCode + p_proposalNumber + p_sessionNumber from p_oldRoot to p_newRoot. NOTE: We assume that p_oldRoot and p_newRoot both contain a trailing / |
| upsert_adminvar | p_name varchar(32) p_value varchar(1024) |
none | |
| upsert_container_report | INOUT p_id int(11) unsigned p_containerRegistryBarcode varchar(20), p_login varchar(45) p_report text |
none | Inserts or updates a ContainerReport (p_barcode). Returns: Record ID in p_id. |
| upsert_ctf | INOUT p_ctfId int(11) unsigned p_motionCorrectionId int(11) unsigned p_autoProcProgramId int(11) unsigned p_boxSizeX float, p_boxSizeY float p_minResolution float p_maxResolution float, p_minDefocus float p_maxDefocus float p_defocusStepSize float, p_astigmatism float p_astigmatismAngle float p_estimatedResolution float p_estimatedDefocus float p_amplitudeContrast float p_ccValue float p_fftTheoreticalFullPath varchar(255) p_comments varchar(255) |
ispyb_processing | |
| upsert_dc | INOUT p_id int(11) unsigned p_dcgId int(11) unsigned p_sessionId int(11) unsigned p_sampleId int(11) unsigned p_detectorid int(11) unsigned p_positionid int(11) unsigned p_apertureid int(11) unsigned, p_datacollectionNumber int(10) unsigned p_starttime datetime p_endtime datetime p_runStatus varchar(45) p_axisStart float p_axisEnd float, p_axisRange float p_overlap float p_numberOfImages int(10) unsigned, p_startImageNumber int(10) unsigned p_numberOfPasses int(10) unsigned, p_exposureTime float p_imageDirectory varchar(255) p_imagePrefix varchar(45) p_imageSuffix varchar(45) p_imageContainerSubPath varchar(255) p_fileTemplate varchar(255) p_wavelength float, p_resolution float p_detectorDistance float p_xbeam float p_ybeam float p_comments varchar(1024) p_slitgapVertical float, p_slitgapHorizontal float p_transmission float p_synchrotronMode varchar(20) p_xtalSnapshotFullPath1 varchar(255), p_xtalSnapshotFullPath2 varchar(255) p_xtalSnapshotFullPath3 varchar(255) p_xtalSnapshotFullPath4 varchar(255) p_rotationAxis enum('Omega','Kappa','Phi') p_phistart float p_kappastart float, p_omegastart float p_resolutionAtCorner float p_detector2theta float, p_undulatorGap1 float p_undulatorGap2 float p_undulatorGap3 float, p_beamSizeAtSampleX float p_beamSizeAtSampleY float, p_averageTemperature float p_actualCenteringPosition varchar(255), p_beamShape varchar(45) p_focalSpotSizeAtSampleX float, p_focalSpotSizeAtSampleY float p_polarisation float p_flux double, p_processedDataFile varchar(255) p_datFullPath varchar(255), p_magnification int(11) p_totalAbsorbedDose float p_binning tinyint(1) p_particleDiameter float p_boxSize_CTF float, p_minResolution float p_minDefocus float p_maxDefocus float, p_defocusStepSize float p_amountAstigmatism float p_extractSize float, p_bgRadius float p_voltage float p_objAperture float p_c1aperture float p_c2aperture float p_c3aperture float p_c1lens float p_c2lens float p_c3lens float |
ispyb_acquisition ispyb_processing ispyb_ssx_writer |
Inserts or updates info about a data collection (p_id). Mandatory columns: For insert: p_dcgId For update: p_id Returns: Record ID in p_id. |
| upsert_dc | p_Id int(11) unsigned p_parentId int(11) unsigned p_visitId int(11) unsigned p_sampleId int(11) unsigned p_detectorid int(11) unsigned p_positionid int(11) unsigned p_apertureid int(11) unsigned, p_datacollectionNumber int(10) unsigned p_starttime datetime p_endtime datetime p_runStatus varchar(45) p_axisStart float p_axisEnd float, p_axisRange float p_overlap float p_numberOfImages int(10) unsigned, p_startImageNumber int(10) unsigned p_numberOfPasses int(10) unsigned, p_exposureTime float p_imageDirectory varchar(255) p_imagePrefix varchar(45) p_imageSuffix varchar(45) p_fileTemplate varchar(255), p_wavelength float p_resolution float p_detectorDistance float, p_xbeam float p_ybeam float p_comments varchar(1024), p_slitgapVertical float p_slitgapHorizontal float p_transmission float p_synchrotronMode varchar(20) p_xtalSnapshotFullPath1 varchar(255) p_xtalSnapshotFullPath2 varchar(255), p_xtalSnapshotFullPath3 varchar(255) p_xtalSnapshotFullPath4 varchar(255) p_rotationAxis enum('Omega','Kappa','Phi') p_phistart float p_kappastart float p_omegastart float p_resolutionAtCorner float p_detector2theta float p_undulatorGap1 float p_undulatorGap2 float p_undulatorGap3 float p_beamSizeAtSampleX float, p_beamSizeAtSampleY float p_averageTemperature float, p_actualCenteringPosition varchar(255) p_beamShape varchar(45), p_focalSpotSizeAtSampleX float p_focalSpotSizeAtSampleY float, p_polarisation float p_flux float p_processedDataFile varchar(255), p_datFullPath varchar(255) p_magnification int(11) p_totalAbsorbedDose float p_binning tinyint(1) p_particleDiameter float p_boxSize_CTF float p_minResolution float p_minDefocus float p_maxDefocus float, p_defocusStepSize float p_amountAstigmatism float p_extractSize float, p_bgRadius float p_voltage float p_objAperture float p_c1aperture float p_c2aperture float p_c3aperture float p_c1lens float p_c2lens float p_c3lens float |
ispyb_acquisition ispyb_processing ispyb_ssx_writer |
Inserts or updates info about a data collection (p_id). Mandatory columns: For insert: p_dcgId For update: p_id Returns: Record ID in p_id. |
| upsert_dcg_grid | INOUT p_id int(11) unsigned p_dcgId int(11) unsigned p_dxInMm double p_dyInMm double p_stepsX double p_stepsY double p_meshAngle double p_pixelsPerMicronX float p_pixelsPerMicronY float, p_snapshotOffsetXPixel float p_snapshotOffsetYPixel float, p_orientation enum('vertical','horizontal') p_snaked boolean |
ispyb_acquisition ispyb_gda_scm ispyb_processing |
|
| upsert_dc_file_attachment | INOUT p_id int(11) unsigned p_dataCollectionId int(11) unsigned, p_fileFullPath varchar(255) p_fileType varchar(45) |
ispyb_processing | Inserts or updates info about a file attachmet for a data collection. Returns: The PK value in p_id. |
| upsert_dc_grid | INOUT p_id int(11) unsigned p_dcId int(11) unsigned p_dxInMm double p_dyInMm double p_stepsX double p_stepsY double p_meshAngle double p_pixelsPerMicronX float p_pixelsPerMicronY float, p_snapshotOffsetXPixel float p_snapshotOffsetYPixel float, p_orientation enum('vertical','horizontal') p_snaked boolean |
ispyb_acquisition ispyb_gda_scm ispyb_processing |
|
| upsert_dc_grid_v2 | INOUT p_id int(11) unsigned p_dcId int(11) unsigned p_dxInMm double p_dyInMm double p_stepsX double p_stepsY double p_meshAngle double p_micronsPerPixelX float p_micronsPerPixelY float, p_snapshotOffsetXPixel float p_snapshotOffsetYPixel float, p_orientation enum('vertical','horizontal') p_snaked boolean |
ispyb_acquisition | |
| upsert_dc_group | INOUT p_id int(11) unsigned p_proposalCode varchar(3), p_proposalNumber int(10) p_sessionNumber int(10) p_sampleId int(10) unsigned p_sampleBarcode varchar(45) p_experimenttype varchar(45), p_starttime datetime p_endtime datetime p_crystalClass varchar(20), p_detectorMode varchar(255) p_actualSampleBarcode varchar(45), p_actualSampleSlotInContainer integer(10) p_actualContainerBarcode varchar(45) p_actualContainerSlotInSC integer(10) p_comments varchar(1024) |
ispyb_acquisition | Inserts or updates info about data collection group (p_id). Mand |
| upsert_dc_group_v2 | INOUT p_id int(11) unsigned p_sessionId int(10) unsigned, p_proposalCode varchar(3) p_proposalNumber int(10) p_sessionNumber int(10) p_sampleId int(10) unsigned p_sampleBarcode varchar(45), p_experimenttype varchar(45) p_starttime datetime p_endtime datetime, p_crystalClass varchar(20) p_detectorMode varchar(255), p_actualSampleBarcode varchar(45) p_actualSampleSlotInContainer integer(10) p_actualContainerBarcode varchar(45), p_actualContainerSlotInSC integer(10) p_comments varchar(1024), p_xtalSnapshotFullPath varchar(255) |
ispyb_acquisition ispyb_processing |
Inserts or updates info about data collection group (p_id). Mand |
| upsert_dc_group_v3 | INOUT p_id int(11) unsigned p_sessionId int(10) unsigned, p_proposalCode varchar(3) p_proposalNumber int(10) p_sessionNumber int(10) p_sampleId int(10) unsigned p_sampleBarcode varchar(45), p_experimenttype varchar(45) p_starttime datetime p_endtime datetime, p_crystalClass varchar(20) p_detectorMode varchar(255), p_actualSampleBarcode varchar(45) p_actualSampleSlotInContainer integer(10) p_actualContainerBarcode varchar(45), p_actualContainerSlotInSC integer(10) p_comments varchar(1024), p_xtalSnapshotFullPath varchar(255) p_scanParameters longtext CHARACTER SET utf8mb4 COLLATE utf8mb4_bin |
ispyb_acquisition ispyb_gda_scm ispyb_processing, ispyb_ssx_writer |
Inserts or updates info about data collection group (p_id).
Mandatory columns: For insert: Either p_sessionId or a valid session
described by (p_proposalCode p_proposalNumber p_sessionNumber) For update: p_id Note: In order to associate the data collection group with a sample one of the following sets of parameters are required: * p_sampleId * p_proposalCode p_proposalNumber p_sessionNumber + p_sampleBarcode * p_actualContainerBarcode + p_actualSampleSlotInContainer Returns: Record ID in p_id. |
| upsert_dc_main | INOUT p_id int(11) unsigned p_groupId int(11) unsigned, p_detectorId int(11) p_dcNumber int(10) unsigned p_startTime datetime, p_endTime datetime p_status varchar(45) p_noImages int(10) unsigned, p_startImgNumber int(10) unsigned p_noPasses int(10) unsigned p_imgDir varchar(255) p_imgPrefix varchar(45) p_imgSuffix varchar(45), p_fileTemplate varchar(255) p_snapshot1 varchar(255) p_snapshot2 varchar(255) p_snapshot3 varchar(255) p_snapshot4 varchar(255), p_comments varchar(1024) |
ispyb_acquisition | |
| upsert_dc_main_v2 | INOUT p_id int(11) unsigned p_groupId int(11) unsigned, p_detectorId int(11) p_blSubSampleId int(11) unsigned p_dcNumber int(10) unsigned p_startTime datetime p_endTime datetime p_status varchar(45) p_noImages int(10) unsigned p_startImgNumber int(10) unsigned p_noPasses int(10) unsigned p_imgDir varchar(255), p_imgPrefix varchar(45) p_imgSuffix varchar(45) p_fileTemplate varchar(255) p_snapshot1 varchar(255) p_snapshot2 varchar(255), p_snapshot3 varchar(255) p_snapshot4 varchar(255) p_comments varchar(1024) |
ispyb_acquisition | Inserts (if p_id not provided) or updates a row in DataCollectio |
| upsert_dc_main_v3 | INOUT p_id int(11) unsigned p_groupId int(11) unsigned, p_detectorId int(11) p_blSubSampleId int(11) unsigned p_dcNumber int(10) unsigned p_startTime datetime p_endTime datetime p_status varchar(45) p_noImages int(10) unsigned p_startImgNumber int(10) unsigned p_noPasses int(10) unsigned p_imgDir varchar(255), p_imgPrefix varchar(45) p_imgSuffix varchar(45) p_imgContainerSubPath varchar(255) p_fileTemplate varchar(255) p_snapshot1 varchar(255), p_snapshot2 varchar(255) p_snapshot3 varchar(255) p_snapshot4 varchar(255) p_comments varchar(1024) |
ispyb_acquisition ispyb_gda_scm |
Inserts (if p_id not provided) or updates a row in DataCollection, returns ID in p_id. |
| upsert_dewar | INOUT p_id int(10) unsigned p_shippingId int(10) unsigned p_name varchar(45) p_comments tinytext p_storageLocation varchar(45), p_status varchar(45) p_isStorageDewar tinyint(1) p_barcode varchar(45) p_firstSessionId int(10) unsigned p_customsValue int(11) unsigned p_transportValue int(11) unsigned, p_trackingNumberToSynchrotron varchar(30), p_trackingNumberFromSynchrotron varchar(30) p_type varchar(40), p_facilityCode varchar(20) p_weight float p_deliveryAgentBarcode varchar(30) |
ispyb_processing | Inserts or updates info about a dewar/parcel (p_id). Mandatory columns: For insert: none For update: p_id Returns: Record ID in p_id. |
| upsert_dewar_v2 | INOUT p_id int(10) unsigned p_authLogin varchar(45) p_shippingId int(10) unsigned p_name varchar(45) p_comments tinytext, p_storageLocation varchar(45) p_status varchar(45) p_isStorageDewar tinyint(1) p_barcode varchar(45) p_firstSessionId int(10) unsigned, p_customsValue int(11) unsigned p_transportValue int(11) unsigned, p_trackingNumberToSynchrotron varchar(30), p_trackingNumberFromSynchrotron varchar(30) p_type varchar(40), p_facilityCode varchar(20) p_weight float p_deliveryAgentBarcode varchar(30) |
ispyb_processing | Inserts or updates info about a dewar/parcel (p_id). Mandatory columns: For insert: none For update: p_id Returns: Record ID in p_id. |
| upsert_dewar_v3 | INOUT p_id int(10) unsigned p_authLogin varchar(45) p_shippingId int(10) unsigned p_name varchar(45) p_comments tinytext, p_storageLocation varchar(45) p_status varchar(45) p_isStorageDewar tinyint(1) p_barcode varchar(45) p_firstSessionId int(10) unsigned, p_customsValue int(11) unsigned p_transportValue int(11) unsigned, p_trackingNumberToSynchrotron varchar(30), p_trackingNumberFromSynchrotron varchar(30) p_facilityCode varchar(20), p_weight float p_deliveryAgentBarcode varchar(30) |
none | Inserts or updates info about a dewar/parcel (p_id). Mandatory columns: For insert: none For update: p_id Returns: Record ID in p_id. |
| upsert_energy_scan | INOUT p_id int(11) unsigned p_sessionId int(10) unsigned, p_sampleId int(10) unsigned p_subSampleId int(11) unsigned p_startTime datetime p_endTime datetime p_startEnergy float p_endEnergy float, p_detector varchar(40) p_element varchar(10) p_edgeEnergy varchar(10), p_synchrotronCurrent float p_temperature float p_peakEnergy float, p_peakFPrime float p_peakFDoublePrime float p_inflectionEnergy float, p_inflectionFPrime float p_inflectionFDoublePrime float, p_choochFileFullPath varchar(255) p_jpegChoochFileFullPath varchar(255) p_scanFileFullPath varchar(255) p_beamSizeHorizontal float p_beamSizeVertical float p_exposureTime float p_transmission float p_flux double p_fluxEnd double p_comments varchar(1024) |
ispyb_processing | Inserts or updates info about an energy scan (p_id). Mandatory c |
| upsert_fluo_mapping | INOUT p_id int(11) unsigned p_xrfFluorescenceMappingROIId int(11), p_gridInfoId int(11) unsigned p_dataFormat varchar(15) p_data longblob p_points int(11) p_opacity float p_colourMap varchar(20), p_min int(3) p_max int(3) p_autoProcProgramId int(10) unsigned |
ispyb_processing | Inserts or updates info about a fluorescence spectrum mapping (p_id). Mandatory columns: For insert: For update: p_id Returns: Record ID in p_id. |
| upsert_fluo_mapping_roi | INOUT p_id int(11) unsigned p_startEnergy float p_endEnergy float, p_element varchar(2) p_edge varchar(15) p_r tinyint(3) unsigned p_g tinyint(3) unsigned p_b tinyint(3) unsigned p_blSampleId int(10) unsigned p_scalar varchar(50) |
ispyb_processing | Inserts or updates info about a fluorescence spectrum mapping region of interest (p_id). Mandatory columns: For update: p_id Returns: Record ID in p_id. |
| upsert_motion_correction | INOUT p_motionCorrectionId int(11) unsigned p_movieId int(11) unsigned p_autoProcProgramId int(11) unsigned p_imageNumber smallint unsigned p_firstFrame smallint unsigned p_lastFrame smallint unsigned, p_dosePerFrame float p_totalMotion float p_averageMotionPerFrame float p_driftPlotFullPath varchar(255) p_micrographFullPath varchar(255) p_micrographSnapshotFullPath varchar(255) p_fftFullPath varchar(255) p_fftCorrectedFullPath varchar(255) p_patchesUsedX mediumint unsigned p_patchesUsedY mediumint unsigned p_comments varchar(255) |
ispyb_processing | |
| upsert_movie | INOUT p_movieId int(11) unsigned p_dataCollectionId int(11) unsigned p_movieNumber mediumint unsigned p_movieFullPath varchar(255) p_createdTimeStamp timestamp p_positionX float, p_positionY float p_nominalDefocus float unsigned |
ispyb_processing | |
| upsert_mrrun | INOUT p_id integer p_parentId integer p_success boolean p_message varchar(255) p_pipeline varchar(50) p_inputCoordFile varchar(255), p_outputCoordFile varchar(255) p_inputMTZFile varchar(255), p_outputMTZFile varchar(255) p_runDirectory varchar(255) p_logFile varchar(255) p_commandLine varchar(255) p_rValueStart float , p_rValueEnd float p_rFreeValueStart float p_rFreeValueEnd float , p_starttime datetime p_endtime datetime |
ispyb_processing | Update or insert new entry with info about a MX molecular
replacements run e.g. Dimple |
| upsert_mrrun | p_id integer p_parentId integer p_success boolean p_message varchar(255) p_pipeline varchar(50) p_inputCoordFile varchar(255), p_outputCoordFile varchar(255) p_inputMTZFile varchar(255), p_outputMTZFile varchar(255) p_runDirectory varchar(255) p_logFile varchar(255) p_commandLine varchar(255) p_rValueStart float , p_rValueEnd float p_rFreeValueStart float p_rFreeValueEnd float , p_starttime datetime p_endtime datetime |
ispyb_processing | Update or insert new entry with info about a MX molecular
replacements run e.g. Dimple |
| upsert_mrrun_blob | INOUT p_id integer p_parentId integer p_view1 varchar(255), p_view2 varchar(255) p_view3 varchar(255) |
ispyb_processing | Update or insert new entry with info about views (image paths) for
an MX molecular replacement run e.g. Dimple. |
| upsert_mrrun_blob | p_Id integer p_parentId integer p_view1 varchar(255) p_view2 varchar(255) p_view3 varchar(255) |
ispyb_processing | Update or insert new entry with info about views (image paths) for
an MX molecular replacement run e.g. Dimple. |
| upsert_mx_sample | INOUT p_sampleId int(10) unsigned p_authLogin varchar(45), p_containerId int(10) unsigned p_dataCollectionPlanId int(10) unsigned, p_crystalId int(10) unsigned p_positionId int(10) unsigned, p_sampleName varchar(45) p_sampleCode varchar(45) p_sampleComments varchar(1024) p_publicationComments varchar(255) p_sampleLocation varchar(45) p_sampleSubLocation smallint(5) unsigned, p_isInSampleChanger tinyint(1) p_lastKnownCenteringPosition varchar(255) p_holderLength double p_loopLength double p_loopType varchar(45) p_wireWidth double p_sampleStatus varchar(20), p_completionStage varchar(45) p_structureStage varchar(45), p_publicationStage varchar(45) |
ispyb_gda_mxcx | Inserts or updates info about a sample. |
| upsert_particle_classification | INOUT p_id int unsigned p_particleClassificationGroupId int unsigned p_classNumber int unsigned p_classImageFullPath varchar(255), p_particlesPerClass int unsigned p_rotationAccuracy float, p_translationAccuracy float p_estimatedResolution float, p_overallFourierCompleteness float |
ispyb_processing | Inserts or updates info about a particle classification (p_id). Mandatory columns: For insert: p_particleClassificationGroupId For update: p_id Returns: Record ID in p_id. |
| upsert_particle_classification_group | INOUT p_id int(11) unsigned p_particlePickerId int(11) unsigned, p_programId int(11) unsigned p_type varchar(10) p_batchNumber int unsigned p_numberOfParticlesPerBatch int unsigned, p_numberOfClassesPerBatch int unsigned p_symmetry varchar(20) |
ispyb_processing | Inserts or updates info about a particle classification group (p_id). Mandatory columns: For insert: p_particlePickerId For update: p_id Returns: Record ID in p_id. |
| upsert_particle_classification_v2 | INOUT p_id int unsigned p_particleClassificationGroupId int unsigned p_classNumber int unsigned p_classImageFullPath varchar(255), p_particlesPerClass int unsigned p_classDistribution float, p_rotationAccuracy float p_translationAccuracy float, p_estimatedResolution float p_overallFourierCompleteness float |
ispyb_processing | Inserts or updates info about a particle classification (p_id). Mandatory columns: For insert: p_particleClassificationGroupId For update: p_id Returns: Record ID in p_id. |
| upsert_particle_picker | INOUT p_id int(11) unsigned p_firstMotionCorrectionId int(11) unsigned p_programId int(11) unsigned p_particlePickingTemplate varchar(255) p_particleDiameter float p_numberOfParticles int unsigned |
ispyb_processing | Inserts or updates info about a particle picker (p_id). Mandatory columns: For insert: p_firstMotionCorrectionId For update: p_id Returns: Record ID in p_id. |
| upsert_particle_picker_v2 | INOUT p_id int(11) unsigned p_firstMotionCorrectionId int(11) unsigned p_programId int(11) unsigned p_particlePickingTemplate varchar(255) p_particleDiameter float p_numberOfParticles int unsigned p_summaryImageFullPath varchar(255) |
ispyb_processing | Inserts or updates info about a particle picker (p_id). Mandatory columns: For insert: p_firstMotionCorrectionId For update: p_id Returns: Record ID in p_id. |
| upsert_person | INOUT p_id int(10) unsigned p_laboratoryId int(10) unsigned, p_familyName varchar(100) p_givenName varchar(45) p_title varchar(45), p_emailAddress varchar(60) p_phoneNumber varchar(45) p_login varchar(45) p_externalPkId int(11) unsigned p_externalPkUUID varchar(32) |
ispyb_processing | Inserts or updates info about a person (p_id). Mandatory columns: For insert: login For update: p_id Returns: Record ID in p_id. |
| upsert_processing | INOUT p_id int(10) unsigned p_parentId int(10) unsigned, p_spacegroup varchar(45) p_refinedcell_a float p_refinedcell_b float, p_refinedcell_c float p_refinedcell_alpha float p_refinedcell_beta float p_refinedcell_gamma float |
ispyb_processing | Inserts or updates existing row in AutoProc. |
| upsert_processing | p_id int(10) p_parentId int(10) p_spacegroup varchar(45), p_refinedcell_a float p_refinedcell_b float p_refinedcell_c float, p_refinedcell_alpha float p_refinedcell_beta float p_refinedcell_gamma float |
ispyb_processing | Inserts or updates existing row in AutoProc. |
| upsert_processing_integration | INOUT p_id integer unsigned p_parentId integer unsigned, p_datacollectionId integer unsigned p_programRunId integer unsigned, p_startImageNumber integer p_endImageNumber integer, p_refinedDetectorDistance float p_refinedXBeam float p_refinedYBeam float p_rotationAxisX float p_rotationAxisY float p_rotationAxisZ float p_beamVectorX float p_beamVectorY float p_beamVectorZ float, p_cell_a float p_cell_b float p_cell_c float p_cell_alpha float, p_cell_beta float p_cell_gamma float p_anomalous float |
ispyb_processing | Inserts/updates row in AutoProcIntegration ID returned in p_id. |
| upsert_processing_job | INOUT p_id int(11) unsigned p_dataCollectionId int(11) unsigned, p_displayName varchar(80) p_comments varchar(255) p_recipe varchar(50) p_automatic tinyint(1) |
ispyb_processing | If p_id is not provided inserts new row. Otherwise updates exis |
| upsert_processing_job_image_sweep | INOUT p_id int(11) unsigned p_processingJobId int(11) unsigned, p_dataCollectionId int(11) unsigned p_startImage mediumint(8) unsigned, p_endImage mediumint(8) unsigned |
ispyb_processing | If p_id is not provided inserts new row. Otherwise updates exis |
| upsert_processing_job_parameter | INOUT p_id int(11) unsigned p_processingJobId int(11) unsigned, p_parameterKey varchar(80) p_parameterValue varchar(1024) |
ispyb_processing | If p_id is not provided inserts new row. Otherwise updates existing row. |
| upsert_processing_program | INOUT p_id int(11) unsigned p_commandLine varchar(255) p_programs varchar(255) p_status int(11) p_updateMessage varchar(80), p_startTimestamp datetime p_updateTimestamp datetime p_environment varchar(255) p_processingJobId int(11) unsigned p_recordTimestamp datetime |
ispyb_processing | If p_id is not provided inserts new row. Otherwise updates existing row if uts processingStatus is NULL + other conditions. |
| upsert_processing_program_attachment | INOUT p_id int(10) unsigned p_parentid int(10) unsigned p_name varchar(255) p_path varchar(255) p_type enum('Log','Result','Graph') |
ispyb_processing | Inserts or updates existing row in AutoProcProgramAttachment. Pa |
| upsert_processing_program_attachment_v2 | INOUT p_id int(10) unsigned p_parentid int(10) unsigned p_name varchar(255) p_path varchar(255) p_type enum('Log','Result','Graph', 'Debug') p_importanceRank tinyint unsigned |
ispyb_processing | Inserts or updates existing row in AutoProcProgramAttachment. Pa |
| upsert_processing_program_message | INOUT p_id int(10) unsigned p_programId int(10) unsigned, p_severity varchar(255) p_message varchar(255) p_description text |
ispyb_processing | Inserts or updates existing row in AutoProcProgramMessage. |
| upsert_processing_program_v2 | INOUT p_id int(11) unsigned p_commandLine varchar(255) p_programs varchar(255) p_status int(11) p_updateMessage varchar(80), p_startTimestamp datetime p_updateTimestamp datetime p_environment varchar(255) p_processingJobId int(11) unsigned p_processingPipelineId int(11) unsigned p_recordTimestamp datetime |
ispyb_processing | If p_id is not provided inserts new row. Otherwise updates existing row if uts processingStatus is NULL + other conditions. |
| upsert_proposal | INOUT p_id int(11) unsigned p_personId int(11) unsigned p_title varchar(200) p_proposalCode varchar(45) p_proposalNumber int(11) unsigned p_proposalType varchar(2) p_externalPkUUID varchar(32) |
ispyb_processing | Inserts or updates info about a proposal (p_id). Mandatory columns: For insert: p_personId AND p_proposalCode AND p_proposalNumber For update: p_id Returns: Record ID in p_id. |
| upsert_proposal_has_person | INOUT p_id int(10) unsigned p_proposalId int(10) unsigned, p_personId int(10) unsigned p_role varchar(100) |
ispyb_processing | Inserts or updates info about a proposal - person association
(p_id). Mandatory columns: For insert: p_proposalId p_personId For update: p_id Returns: Record ID in p_id. |
| upsert_quality_indicators | OUT p_id int(11) unsigned p_dataCollectionId int(11) unsigned, p_autoProcProgramId int(10) unsigned p_imageNumber mediumint(8) unsigned p_spotTotal int(10) p_inResTotal int(10), p_goodBraggCandidates int(10) p_iceRings int(10) p_method1Res float, p_method2Res float p_maxUnitCell float p_pctSaturationTop50Peaks float p_inResolutionOvrlSpots int(10) p_binPopCutOffMethod2Res float, p_totalIntegratedSignal double p_dozorScore double p_driftFactor float |
ispyb_processing | Inserts into or updates a row in the image quality indicators table |
| upsert_quality_indicators_dozor_score | OUT p_id int(11) unsigned p_dataCollectionId int(11) unsigned, p_imageNumber mediumint(8) unsigned p_dozorScore double |
none | Inserts into or updates a row in the image quality indicators table |
| upsert_robot_action | INOUT p_id int(11) unsigned p_sessionId int(11) unsigned, p_sampleId int(11) unsigned p_actionType varchar(15) p_startTimestamp timestamp p_endTimestamp timestamp p_status varchar(24) p_message varchar(255) p_containerLocation smallint p_dewarLocation smallint, p_sampleBarcode varchar(45) p_snapshotBefore varchar(255), p_snapshotAfter varchar(255) |
ispyb_processing | Inserts or updates info about a robot action (p_id). Mandatory c |
| upsert_sample | INOUT p_id int(10) unsigned p_authLogin varchar(45) p_crystalId int(10) unsigned p_containerId int(10) unsigned p_name varchar(45), p_code varchar(45) p_location varchar(45) p_holderLength float, p_loopLength float p_loopType varchar(45) p_wireWidth float, p_comments varchar(1024) p_blSampleStatus varchar(20), p_isInSampleChanger boolean |
ispyb_processing | Inserts or updates info about sample (p_id). |
| upsert_sample | p_id int(10) unsigned p_crystalId int(10) unsigned p_containerId int(10) unsigned p_name varchar(45) p_code varchar(45) p_location varchar(45) p_holderLength float p_loopLength float p_loopType varchar(45) p_wireWidth float p_comments varchar(1024), p_blSampleStatus varchar(20) p_isInSampleChanger boolean |
ispyb_processing | Inserts or updates info about sample (p_id). |
| upsert_sample_image | INOUT p_id int(11) unsigned p_sampleId int(11) unsigned, p_containerInspectionId int(11) unsigned p_micronsPerPixelX float, p_micronsPerPixelY float p_imageFullPath varchar(255) p_comments varchar(255) |
ispyb_import | If p_id is not provided inserts new row and returns ID in p_id. Otherwise updates existing row. |
| upsert_sample_image_analysis | INOUT p_id int(11) unsigned p_containerBarcode varchar(45), p_sampleLocation varchar(45) p_oavSnapshotBefore varchar(255), p_oavSnapshotAfter varchar(255) p_deltaX int p_deltaY int, p_goodnessOfFit float p_scaleFactor float p_resultCode varchar(15), p_matchStartTS timestamp p_matchEndTS timestamp |
ispyb_acquisition | Insert or update info about the sample image analysis for the mo |
| upsert_sample_image_auto_score | p_imageFullPath varchar(255) p_schemaName varchar(25) p_scoreClass varchar(15) p_probability float |
ispyb_import ispyb_processing |
Insert or update a row with the auto scored probability for a given sample image with a certain class and schema. Returns nothing. |
| upsert_session_for_proposal_code_number | INOUT p_id int(11) unsigned p_proposalCode varchar(3), p_proposalNumber int(11) p_visitNumber int(10) unsigned, p_beamLineSetupId int(10) unsigned p_startDate datetime p_endDate datetime p_beamlineName varchar(45) p_beamlineOperator varchar(45), p_nbShifts int(10) unsigned p_scheduled tinyint(1) p_usedFlag tinyint(1) p_comments varchar(255) p_externalPkUUID varchar(32) |
ispyb_processing | Inserts or updates a session for a proposal with given code and number. Mandatory columns: p_id OR (p_proposalCode and p_proposalNumber) Returns: Record ID in p_id. |
| upsert_session_has_person | p_sessionId int(10) unsigned p_personId int(10) unsigned p_role varchar(100) p_remote tinyint(1) |
ispyb_processing | Inserts or updates info about a session - person association
(p_sessionId p_personId). Mandatory columns: For insert: p_sessionId, p_personId For update: p_sessionId p_personId Returns: Nothing. |
| upsert_session_has_person_for_session_and_login | p_proposalCode varchar(45) p_proposalNumber int(11) unsigned, p_visit_number int(10) unsigned p_login varchar(45) p_role varchar(100) p_remote tinyint(1) |
none | Inserts or updates info about a session - person association
(p_sessionId p_personId). Mandatory columns: p_proposalCode, p_proposalNumber p_visit_number p_login Returns: Nothing. |
| upsert_sleeve | INOUT p_id tinyint unsigned p_location tinyint unsigned, p_lastMovedToFreezer datetime p_lastMovedFromFreezer datetime |
ispyb_acquisition | |
| upsert_xfe_fluo_spectrum | INOUT p_id int(11) unsigned p_sessionId int(10) unsigned, p_sampleId int(10) unsigned p_subSampleId int(11) unsigned p_startTime datetime p_endTime datetime p_energy float p_fileName varchar(255), p_annotatedPymcaSpectrum varchar(255) p_fittedDataFileFullPath varchar(255) p_jpegScanFileFullPath varchar(255) p_scanFileFullPath varchar(255) p_beamSizeHorizontal float p_beamSizeVertical float, p_exposureTime float p_transmission float p_flux double p_fluxEnd double p_comments varchar(1024) |
ispyb_processing | Inserts or updates info about a fluorescence spectrum measuremen |
| Warnings | none |