diff --git a/docs/list_of_procs.rst b/docs/list_of_procs.rst index 48cc0149..2e884cf0 100644 --- a/docs/list_of_procs.rst +++ b/docs/list_of_procs.rst @@ -19,6 +19,7 @@ "**insert_position**", "OUT p_id int(11) unsigned, p_posX long, p_posY long, p_posZ long, p_scale long", "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", "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", "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", "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", "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)", "Insert a row with info about a screening. Returns the ID in p_id" @@ -246,7 +247,9 @@ "**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)", "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", "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", "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_title varchar(255), p_beamlineOperator varchar(45), p_nbShifts int(10) unsigned, p_scheduled tinyint(1), p_usedFlag tinyint(1), p_comments varchar(255), p_externalPkId int(11) unsigned, p_externalPkUUID varchar(32)", "Inserts or updates a session for a proposal with given code and" + "**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_title varchar(255), p_beamlineOperator varchar(45), p_nbShifts int(10) unsigned, p_scheduled tinyint(1), p_usedFlag tinyint(1), p_comments varchar(255), p_externalPkId int(11) unsigned, p_externalPkUUID varchar(32)", "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)", "Inserts or updates info about a session - person association (p_sessionId, p_personId). Mandatory columns: For insert: p_sessionId, p_personId diff --git a/docs/list_of_tables_and_columns.rst b/docs/list_of_tables_and_columns.rst index b6d1a1fe..2d706d7b 100644 --- a/docs/list_of_tables_and_columns.rst +++ b/docs/list_of_tables_and_columns.rst @@ -89,7 +89,6 @@ ``processingEnvironment``,varchar,"Cpus, Nodes,..." ``recordTimeStamp``,datetime,"Creation or last update date/time" ``processingJobId``,int,"" - ``dataCollectionId``,int,"" **AutoProcProgramAttachment**,table,"" ``autoProcProgramAttachmentId``,int,"Primary key (auto-incremented)" ``autoProcProgramId``,int,"Related autoProcProgram item" @@ -133,6 +132,7 @@ ``anomalous``,tinyint,"boolean type:0 noanoum - 1 anoum" ``ccHalf``,float,"information from XDS" ``ccAnomalous``,float,"" + ``resIOverSigI2``,float,"Resolution where I/Sigma(I) equals 2" **AutoProcScaling_has_Int**,table,"" ``autoProcScaling_has_IntId``,int,"Primary key (auto-incremented)" ``autoProcScalingId``,int,"AutoProcScaling item" @@ -409,6 +409,10 @@ ``blSampleId``,int,"" ``energyScanId``,int,"" ``blSampleHasEnergyScanId``,int,"" + **BLSample_has_Positioner**,table,"" + ``blSampleHasPositioner``,int,"" + ``blSampleId``,int,"" + ``positionerId``,int,"" **BLSession**,table,"" ``sessionId``,int,"" ``beamLineSetupId``,int,"" @@ -456,6 +460,10 @@ ``recordTimeStamp``,timestamp,"Creation or last update date/time" ``source``,enum,"" ``type``,varchar,"The type of subsample, i.e. roi (region), poi (point), loi (line)" + **BLSubSample_has_Positioner**,table,"" + ``blSubSampleHasPositioner``,int,"" + ``blSubSampleId``,int,"" + ``positionerId``,int,"" **Buffer**,table,"" ``bufferId``,int,"" ``BLSESSIONID``,int,"" @@ -1497,6 +1505,10 @@ ``X``,double,"" ``Y``,double,"" ``Z``,double,"" + **Positioner**,table,"An arbitrary positioner and its value, could be e.g. a motor. Allows for instance to store some positions with a sample or subsample" + ``positionerId``,int,"" + ``positioner``,varchar,"" + ``value``,float,"" **PreparePhasingData**,table,"" ``preparePhasingDataId``,int,"Primary key (auto-incremented)" ``phasingAnalysisId``,int,"Related phasing analysis item" @@ -1752,6 +1764,7 @@ ``diffractionPlanId``,int,"references DiffractionPlan" ``dataCollectionGroupId``,int,"" ``xmlSampleInformation``,longblob,"" + ``autoProcProgramId``,int,"" **ScreeningInput**,table,"" ``screeningInputId``,int,"" ``screeningId``,int,"" diff --git a/schemas/ispyb/data.sql b/schemas/ispyb/data.sql index 64ebd37b..dfe55fc8 100644 --- a/schemas/ispyb/data.sql +++ b/schemas/ispyb/data.sql @@ -84,7 +84,7 @@ INSERT INTO `AutoProcIntegration` (`autoProcIntegrationId`, `dataCollectionId`, -- /*!40000 ALTER TABLE `AutoProcProgram` DISABLE KEYS */; -INSERT INTO `AutoProcProgram` (`autoProcProgramId`, `processingCommandLine`, `processingPrograms`, `processingStatus`, `processingMessage`, `processingStartTime`, `processingEndTime`, `processingEnvironment`, `recordTimeStamp`, `processingJobId`, `dataCollectionId`) VALUES (56425592,'/dls_sw/apps/fast_dp/2395/src/fast_dp.py -a S -j 0 -J 18 /dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','fast_dp',1,NULL,NULL,NULL,NULL,'2016-01-14 12:46:22',NULL,NULL),(56425944,'xia2 min_images=3 -3dii -xparallel -1 -atom s -blend -project cm14451v1 -crystal xtlysjan41 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 3dii',1,NULL,NULL,NULL,NULL,'2016-01-14 13:09:51',NULL,NULL),(56425952,'xia2 min_images=3 -dials -xparallel -1 -atom s -blend -project cm14451v1 -crystal xtlysjan41 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 dials',1,NULL,NULL,NULL,NULL,'2016-01-14 13:24:22',NULL,NULL),(56425963,'/dls_sw/apps/GPhL/autoPROC/20151214/autoPROC/bin/linux64/process -xml -Id xtlysjan41,/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/,tlys_jan_4_1_####.cbf,1,3600 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_PROCESSORS=12 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_J','autoPROC 1.0.4 (see: http://www.globalphasing.com/autoproc/)',1,NULL,NULL,NULL,NULL,'2016-01-14 13:34:34',NULL,NULL),(56426286,'xia2 min_images=3 -dials -atom s -blend -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/linediffraction_1_0001.cbf image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 dials',1,NULL,NULL,NULL,NULL,'2016-01-14 14:01:57',NULL,NULL),(56426287,'xia2 min_images=3 -3dii -atom s -blend -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/linediffraction_1_0001.cbf image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 3dii',1,NULL,NULL,NULL,NULL,'2016-01-14 14:13:57',NULL,NULL),(56983954,'/dls_sw/apps/fast_dp/2395/src/fast_dp.py -a S -j 0 -J 18 /dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','fast_dp',1,NULL,NULL,NULL,NULL,'2016-01-22 11:34:03',NULL,NULL),(56985584,'xia2 min_images=3 -3d -xparallel -1 -atom s -blend -project cm14451v1 -crystal xins22 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','xia2 3d',1,NULL,NULL,NULL,NULL,'2016-01-22 11:52:36',NULL,NULL),(56985589,'/dls_sw/apps/GPhL/autoPROC/20151214/autoPROC/bin/linux64/process -xml -Id xins22,/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/,ins2_2_####.cbf,1,7200 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_PROCESSORS=12 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_JOBS=4 Sto','autoPROC 1.0.4 (see: http://www.globalphasing.com/autoproc/)',1,NULL,NULL,NULL,NULL,'2016-01-22 11:53:38',NULL,NULL),(56985592,'xia2 min_images=3 -3dii -xparallel -1 -atom s -blend -project cm14451v1 -crystal xins22 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','xia2 3dii',1,NULL,NULL,NULL,NULL,'2016-01-22 11:54:01',NULL,NULL),(56986673,'xia2 min_images=3 -dials -xparallel -1 -atom s -blend -project cm14451v1 -crystal xins22 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','xia2 dials',1,NULL,NULL,NULL,NULL,'2016-01-22 12:01:59',5,NULL); +INSERT INTO `AutoProcProgram` (`autoProcProgramId`, `processingCommandLine`, `processingPrograms`, `processingStatus`, `processingMessage`, `processingStartTime`, `processingEndTime`, `processingEnvironment`, `recordTimeStamp`, `processingJobId`) VALUES (56425592,'/dls_sw/apps/fast_dp/2395/src/fast_dp.py -a S -j 0 -J 18 /dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','fast_dp',1,NULL,NULL,NULL,NULL,'2016-01-14 12:46:22',NULL),(56425944,'xia2 min_images=3 -3dii -xparallel -1 -atom s -blend -project cm14451v1 -crystal xtlysjan41 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 3dii',1,NULL,NULL,NULL,NULL,'2016-01-14 13:09:51',NULL),(56425952,'xia2 min_images=3 -dials -xparallel -1 -atom s -blend -project cm14451v1 -crystal xtlysjan41 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 dials',1,NULL,NULL,NULL,NULL,'2016-01-14 13:24:22',NULL),(56425963,'/dls_sw/apps/GPhL/autoPROC/20151214/autoPROC/bin/linux64/process -xml -Id xtlysjan41,/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/,tlys_jan_4_1_####.cbf,1,3600 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_PROCESSORS=12 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_J','autoPROC 1.0.4 (see: http://www.globalphasing.com/autoproc/)',1,NULL,NULL,NULL,NULL,'2016-01-14 13:34:34',NULL),(56426286,'xia2 min_images=3 -dials -atom s -blend -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/linediffraction_1_0001.cbf image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 dials',1,NULL,NULL,NULL,NULL,'2016-01-14 14:01:57',NULL),(56426287,'xia2 min_images=3 -3dii -atom s -blend -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/linediffraction_1_0001.cbf image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 3dii',1,NULL,NULL,NULL,NULL,'2016-01-14 14:13:57',NULL),(56983954,'/dls_sw/apps/fast_dp/2395/src/fast_dp.py -a S -j 0 -J 18 /dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','fast_dp',1,NULL,NULL,NULL,NULL,'2016-01-22 11:34:03',NULL),(56985584,'xia2 min_images=3 -3d -xparallel -1 -atom s -blend -project cm14451v1 -crystal xins22 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','xia2 3d',1,NULL,NULL,NULL,NULL,'2016-01-22 11:52:36',NULL),(56985589,'/dls_sw/apps/GPhL/autoPROC/20151214/autoPROC/bin/linux64/process -xml -Id xins22,/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/,ins2_2_####.cbf,1,7200 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_PROCESSORS=12 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_JOBS=4 Sto','autoPROC 1.0.4 (see: http://www.globalphasing.com/autoproc/)',1,NULL,NULL,NULL,NULL,'2016-01-22 11:53:38',NULL),(56985592,'xia2 min_images=3 -3dii -xparallel -1 -atom s -blend -project cm14451v1 -crystal xins22 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','xia2 3dii',1,NULL,NULL,NULL,NULL,'2016-01-22 11:54:01',NULL),(56986673,'xia2 min_images=3 -dials -xparallel -1 -atom s -blend -project cm14451v1 -crystal xins22 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','xia2 dials',1,NULL,NULL,NULL,NULL,'2016-01-22 12:01:59',5); /*!40000 ALTER TABLE `AutoProcProgram` ENABLE KEYS */; -- @@ -115,7 +115,7 @@ INSERT INTO `AutoProcScaling` (`autoProcScalingId`, `autoProcId`, `recordTimeSta -- /*!40000 ALTER TABLE `AutoProcScalingStatistics` DISABLE KEYS */; -INSERT INTO `AutoProcScalingStatistics` (`autoProcScalingStatisticsId`, `autoProcScalingId`, `scalingStatisticsType`, `comments`, `resolutionLimitLow`, `resolutionLimitHigh`, `rMerge`, `rMeasWithinIPlusIMinus`, `rMeasAllIPlusIMinus`, `rPimWithinIPlusIMinus`, `rPimAllIPlusIMinus`, `fractionalPartialBias`, `nTotalObservations`, `nTotalUniqueObservations`, `meanIOverSigI`, `completeness`, `multiplicity`, `anomalousCompleteness`, `anomalousMultiplicity`, `recordTimeStamp`, `anomalous`, `ccHalf`, `ccAnomalous`) VALUES (1770617,596133,'outerShell',NULL,1.65,1.61,0.766,NULL,0.789,NULL,NULL,NULL,105090,3089,5.5,97.8,34,96.8,17.8,'2016-01-14 12:46:22',0,91.7,15.8),(1770618,596133,'innerShell',NULL,29.5,7.18,0.061,NULL,0.063,NULL,NULL,NULL,17093,593,61.7,98.6,28.8,100,19.5,'2016-01-14 12:46:22',0,99.9,73.4),(1770619,596133,'overall',NULL,29.5,1.61,0.106,NULL,0.109,NULL,NULL,NULL,1588225,43478,30.2,99.8,36.5,99.8,19.4,'2016-01-14 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13:24:22',0,0.999,0.343),(1770656,596146,'outerShell',NULL,1.476,1.451,1.268,1.314,1.312,0.459,0.33,NULL,42945,2859,2.4,99.2,15,98.9,7.8,'2016-01-14 13:34:35',0,0.633,-0.059),(1770657,596146,'innerShell',NULL,129.722,3.938,0.08,0.078,0.081,0.017,0.014,NULL,103297,3251,50.7,100,31.8,99.7,19.1,'2016-01-14 13:34:35',0,0.993,-0.169),(1770658,596146,'overall',NULL,129.722,1.451,0.138,0.141,0.141,0.032,0.024,NULL,1953227,58523,22.5,100,33.4,100,17.8,'2016-01-14 13:34:35',0,0.996,0.035),(1770659,596147,'outerShell',NULL,1.47,1.43,3.442,NULL,3.711,1.471,1.058,NULL,46996,4388,1.6,99,10.7,97.8,5.5,'2016-01-14 14:01:57',0,0.627,-0.004),(1770660,596147,'innerShell',NULL,129.84,6.4,0.124,NULL,0.129,0.023,0.019,NULL,41147,842,27,100,48.9,100,31.8,'2016-01-14 14:01:57',0,0.996,0.532),(1770661,596147,'overall',NULL,129.84,1.43,0.707,NULL,0.719,0.156,0.114,NULL,2865527,61286,14.1,99.9,46.8,99.8,24.3,'2016-01-14 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`scalingStatisticsType`, `comments`, `resolutionLimitLow`, `resolutionLimitHigh`, `rMerge`, `rMeasWithinIPlusIMinus`, `rMeasAllIPlusIMinus`, `rPimWithinIPlusIMinus`, `rPimAllIPlusIMinus`, `fractionalPartialBias`, `nTotalObservations`, `nTotalUniqueObservations`, `meanIOverSigI`, `completeness`, `multiplicity`, `anomalousCompleteness`, `anomalousMultiplicity`, `recordTimeStamp`, `anomalous`, `ccHalf`, `ccAnomalous`, `resIOverSigI2`) VALUES (1770617,596133,'outerShell',NULL,1.65,1.61,0.766,NULL,0.789,NULL,NULL,NULL,105090,3089,5.5,97.8,34,96.8,17.8,'2016-01-14 12:46:22',0,91.7,15.8,NULL),(1770618,596133,'innerShell',NULL,29.5,7.18,0.061,NULL,0.063,NULL,NULL,NULL,17093,593,61.7,98.6,28.8,100,19.5,'2016-01-14 12:46:22',0,99.9,73.4,NULL),(1770619,596133,'overall',NULL,29.5,1.61,0.106,NULL,0.109,NULL,NULL,NULL,1588225,43478,30.2,99.8,36.5,99.8,19.4,'2016-01-14 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11:53:38',0,1,0.217,NULL),(1792601,603461,'outerShell',NULL,1.38,1.34,3.444,NULL,3.597,0.746,0.545,NULL,57746,1347,1.2,100,42.9,100,21.2,'2016-01-22 11:54:01',0,0.647,0.002,NULL),(1792602,603461,'innerShell',NULL,31.9,6,0.044,NULL,0.046,0.007,0.006,NULL,15773,225,131.2,99.6,70.1,100,40.5,'2016-01-22 11:54:01',0,1,0.654,NULL),(1792603,603461,'overall',NULL,31.9,1.34,0.08,NULL,0.082,0.013,0.009,NULL,1314502,17989,34.2,100,73.1,100,37.3,'2016-01-22 11:54:01',0,1,0.469,NULL),(1792628,603470,'outerShell',NULL,1.36,1.33,3.124,NULL,3.246,0.711,0.515,NULL,53402,1370,1.3,100,39,100,19.2,'2016-01-22 12:01:59',0,0.703,0.017,NULL),(1792629,603470,'innerShell',NULL,39.07,5.95,0.051,NULL,0.053,0.008,0.006,NULL,16799,235,117.7,99.7,71.5,100,41.9,'2016-01-22 12:01:59',0,1,0.654,NULL),(1792630,603470,'overall',NULL,39.07,1.33,0.08,NULL,0.082,0.013,0.009,NULL,1305126,18395,30.9,100,71,100,36.1,'2016-01-22 12:01:59',0,1,0.482,NULL); /*!40000 ALTER TABLE `AutoProcScalingStatistics` ENABLE KEYS */; -- @@ -259,6 +259,13 @@ INSERT INTO `BLSample_has_DataCollectionPlan` (`blSampleId`, `dataCollectionPlan /*!40000 ALTER TABLE `BLSample_has_EnergyScan` DISABLE KEYS */; /*!40000 ALTER TABLE `BLSample_has_EnergyScan` ENABLE KEYS */; +-- +-- Dumping data for table `BLSample_has_Positioner` +-- + +/*!40000 ALTER TABLE `BLSample_has_Positioner` DISABLE KEYS */; +/*!40000 ALTER TABLE `BLSample_has_Positioner` ENABLE KEYS */; + -- -- Dumping data for table `BLSession` -- @@ -282,6 +289,13 @@ INSERT INTO `BLSession` (`sessionId`, `beamLineSetupId`, `proposalId`, `beamCale INSERT INTO `BLSubSample` (`blSubSampleId`, `blSampleId`, `diffractionPlanId`, `blSampleImageId`, `positionId`, `position2Id`, `motorPositionId`, `blSubSampleUUID`, `imgFileName`, `imgFilePath`, `comments`, `recordTimeStamp`, `source`, `type`) VALUES (2,398816,197784,NULL,2,5,NULL,NULL,NULL,NULL,NULL,'2016-09-30 14:25:19','manual',NULL),(5,398819,197784,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-05 10:16:44','manual',NULL); /*!40000 ALTER TABLE `BLSubSample` ENABLE KEYS */; +-- +-- Dumping data for table `BLSubSample_has_Positioner` +-- + +/*!40000 ALTER TABLE `BLSubSample_has_Positioner` DISABLE KEYS */; +/*!40000 ALTER TABLE `BLSubSample_has_Positioner` ENABLE KEYS */; + -- -- Dumping data for table `BeamApertures` -- @@ -955,6 +969,13 @@ INSERT INTO `Person` (`personId`, `laboratoryId`, `siteId`, `personUUID`, `famil INSERT INTO `Position` (`positionId`, `relativePositionId`, `posX`, `posY`, `posZ`, `scale`, `recordTimeStamp`, `X`, `Y`, `Z`) VALUES (2,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(5,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); /*!40000 ALTER TABLE `Position` ENABLE KEYS */; +-- +-- Dumping data for table `Positioner` +-- + +/*!40000 ALTER TABLE `Positioner` DISABLE KEYS */; +/*!40000 ALTER TABLE `Positioner` ENABLE KEYS */; + -- -- Dumping data for table `PreparePhasingData` -- @@ -1199,7 +1220,7 @@ INSERT INTO `ScanParametersModel` (`scanParametersModelId`, `scanParametersServi -- /*!40000 ALTER TABLE `Screening` DISABLE KEYS */; -INSERT INTO `Screening` (`screeningId`, `dataCollectionId`, `bltimeStamp`, `programVersion`, `comments`, `shortComments`, `diffractionPlanId`, `dataCollectionGroupId`, `xmlSampleInformation`) VALUES (1894770,1052494,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm native',NULL,1040398,NULL),(1894773,1052494,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm anomalous',NULL,1040398,NULL),(1894774,1052494,'2016-10-26 08:50:31','EDNA MXv1','Standard Native Dataset Multiplicity=3 I/sig=2 Maxlifespan=202 s','EDNAStrategy1',NULL,1040398,NULL),(1894777,1052494,'2016-10-26 08:50:31','EDNA MXv1','strategy with target multiplicity=16, target I/sig=2 Maxlifespan=202 s','EDNAStrategy3',NULL,1040398,NULL),(1894780,1052494,'2016-10-26 08:50:31','EDNA MXv1','Gentle: Target Multiplicity=2 and target I/Sig 2 and Maxlifespan=20 s','EDNAStrategy4',NULL,1040398,NULL),(1894783,1052494,'2016-10-26 08:50:31','EDNA MXv1','Standard Anomalous Dataset Multiplicity=3 I/sig=2 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60c6b146..538cbac8 100644 --- a/schemas/ispyb/routines.sql +++ b/schemas/ispyb/routines.sql @@ -1655,6 +1655,128 @@ DELIMITER ; /*!50003 SET character_set_client = @saved_cs_client */ ; /*!50003 SET character_set_results = @saved_cs_results */ ; /*!50003 SET collation_connection = @saved_col_connection */ ; +/*!50003 DROP PROCEDURE IF EXISTS `insert_processing_scaling_v2` */; +/*!50003 SET @saved_cs_client = @@character_set_client */ ; +/*!50003 SET @saved_cs_results = @@character_set_results */ ; +/*!50003 SET @saved_col_connection = @@collation_connection */ ; +/*!50003 SET character_set_client = utf8 */ ; +/*!50003 SET character_set_results = utf8 */ ; +/*!50003 SET collation_connection = utf8_general_ci */ ; +/*!50003 SET @saved_sql_mode = @@sql_mode */ ; +/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ; +DELIMITER ;; +CREATE PROCEDURE `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 + ) + MODIFIES SQL DATA + COMMENT 'Inserts 1 row in AutoProcScaling, 3 rows in AutoProcScalingStatistics. Returns: autoProcScalingId value in p_id' +BEGIN + IF p_parentid IS NULL THEN + SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_parentid is NULL'; + ELSE + + START TRANSACTION; + INSERT INTO AutoProcScaling (autoProcId, recordTimeStamp) + VALUES (p_parentId, now()); + + SET p_id = LAST_INSERT_ID(); + + INSERT INTO AutoProcScalingStatistics (autoProcScalingId, scalingStatisticsType, comments, resolutionLimitLow, resolutionLimitHigh, rMerge, + rMeasWithinIPlusIMinus, rMeasAllIPlusIMinus, rPimWithinIPlusIMinus, rPimAllIPlusIMinus, fractionalPartialBias, nTotalObservations, nTotalUniqueObservations, + meanIOverSigI, resIOverSigI2, completeness, multiplicity, anomalous, anomalousCompleteness, anomalousMultiplicity, ccHalf, ccAnomalous, recordTimeStamp) + VALUES (p_id, p_Type1, p_Comments1, p_ResolutionLimitLow1, p_ResolutionLimitHigh1, p_rMerge1, p_rMeasWithinIPlusIMinus1, p_rMeasAllIPlusIMinus1, + p_rPimWithinIPlusIMinus1, p_rPimAllIPlusIMinus1, p_fractionalPartialBias1, p_nTotalObservations1, p_nTotalUniqueObservations1, p_meanIOverSigI1, + p_resIOverSigI21, p_completeness1, p_multiplicity1, p_anomalous1, p_anomalousCompleteness1, p_anomalousMultiplicity1, p_ccHalf1, p_ccAnomalous1, now()); + + INSERT INTO AutoProcScalingStatistics (autoProcScalingId, scalingStatisticsType, comments, resolutionLimitLow, resolutionLimitHigh, rMerge, + rMeasWithinIPlusIMinus, rMeasAllIPlusIMinus, rPimWithinIPlusIMinus, rPimAllIPlusIMinus, fractionalPartialBias, nTotalObservations, nTotalUniqueObservations, + meanIOverSigI, resIOverSigI2, completeness, multiplicity, anomalous, anomalousCompleteness, anomalousMultiplicity, ccHalf, ccAnomalous, recordTimeStamp) + VALUES (p_id, p_Type2, p_Comments2, p_ResolutionLimitLow2, p_ResolutionLimitHigh2, p_rMerge2, p_rMeasWithinIPlusIMinus2, p_rMeasAllIPlusIMinus2, + p_rPimWithinIPlusIMinus2, p_rPimAllIPlusIMinus2, p_fractionalPartialBias2, p_nTotalObservations2, p_nTotalUniqueObservations2, p_meanIOverSigI2, + p_resIOverSigI22, p_completeness2, p_multiplicity2, p_anomalous2, p_anomalousCompleteness2, p_anomalousMultiplicity2, p_ccHalf2, p_ccAnomalous2, now()); + + INSERT INTO AutoProcScalingStatistics (autoProcScalingId, scalingStatisticsType, comments, resolutionLimitLow, resolutionLimitHigh, rMerge, + rMeasWithinIPlusIMinus, rMeasAllIPlusIMinus, rPimWithinIPlusIMinus, rPimAllIPlusIMinus, fractionalPartialBias, nTotalObservations, nTotalUniqueObservations, + meanIOverSigI, resIOverSigI2, completeness, multiplicity, anomalous, anomalousCompleteness, anomalousMultiplicity, ccHalf, ccAnomalous, recordTimeStamp) + VALUES (p_id, p_Type3, p_Comments3, p_ResolutionLimitLow3, p_ResolutionLimitHigh3, p_rMerge3, p_rMeasWithinIPlusIMinus3, p_rMeasAllIPlusIMinus3, + p_rPimWithinIPlusIMinus3, p_rPimAllIPlusIMinus3, p_fractionalPartialBias3, p_nTotalObservations3, p_nTotalUniqueObservations3, p_meanIOverSigI3, + p_resIOverSigI23, p_completeness3, p_multiplicity3, p_anomalous3, p_anomalousCompleteness3, p_anomalousMultiplicity3, p_ccHalf3, p_ccAnomalous3, now()); + COMMIT; + + END IF; + END ;; +DELIMITER ; +/*!50003 SET sql_mode = @saved_sql_mode */ ; +/*!50003 SET character_set_client = @saved_cs_client */ ; +/*!50003 SET character_set_results = @saved_cs_results */ ; +/*!50003 SET collation_connection = @saved_col_connection */ ; /*!50003 DROP PROCEDURE IF EXISTS `insert_quality_indicators` */; /*!50003 SET @saved_cs_client = @@character_set_client */ ; /*!50003 SET @saved_cs_results = @@character_set_results */ ; @@ -10616,7 +10738,7 @@ DELIMITER ; /*!50003 SET character_set_results = utf8 */ ; /*!50003 SET collation_connection = utf8_general_ci */ ; /*!50003 SET @saved_sql_mode = @@sql_mode */ ; -/*!50003 SET sql_mode = '' */ ; +/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ; DELIMITER ;; CREATE PROCEDURE `upsert_session_for_proposal_code_number`( INOUT p_id int(11) unsigned, @@ -10637,41 +10759,58 @@ CREATE PROCEDURE `upsert_session_for_proposal_code_number`( p_externalPkUUID varchar(32) ) MODIFIES SQL DATA - COMMENT 'Inserts or updates a session for a proposal with given code and' + COMMENT 'Inserts or updates a session for a proposal with given code and number.\nMandatory columns: p_id OR (p_proposalCode and p_proposalNumber)\nReturns: Record ID in p_id.' BEGIN - DECLARE row_proposal_id int(10) unsigned DEFAULT NULL; - IF p_id IS NOT NULL OR (p_proposalCode IS NOT NULL AND p_proposalNumber IS NOT NULL) THEN - SELECT min(proposalId) INTO row_proposal_id FROM Proposal WHERE proposalCode=p_proposalCode AND proposalNumber=p_proposalNumber; + DECLARE row_proposal_id int(10) unsigned DEFAULT NULL; + DECLARE row_session_id int(10) unsigned DEFAULT NULL; + + IF p_id IS NOT NULL OR (p_proposalCode IS NOT NULL AND p_proposalNumber IS NOT NULL) THEN + + IF p_proposalCode IS NOT NULL AND p_proposalNumber IS NOT NULL THEN + SELECT min(proposalId) INTO row_proposal_id FROM Proposal WHERE proposalCode=p_proposalCode AND proposalNumber=p_proposalNumber; + IF row_proposal_id IS NULL THEN + SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Proposal given by p_proposalCode + p_proposalNumber does not exist.'; + END IF; + END IF; + + IF p_id IS NULL AND row_proposal_id IS NOT NULL THEN + SELECT sessionId INTO row_session_id FROM BLSession WHERE proposalId = row_proposal_id AND visit_number = p_visitNumber; + ELSEIF p_id IS NOT NULL THEN + SET row_session_id := p_id; + END IF; - IF p_id IS NULL THEN - INSERT INTO BLSession(sessionId, proposalId, visit_number, beamLineSetupId, startDate, endDate, - beamLineName, sessionTitle, beamLineOperator, nbShifts, scheduled, usedFlag, comments, expSessionPk, externalId) - VALUES (p_id, row_proposal_id, p_visitNumber, p_beamLineSetupId, p_startDate, p_endDate, - p_beamlineName, p_title, p_beamlineOperator, p_nbShifts, p_scheduled, p_usedFlag, p_comments, p_externalPkId, unhex(p_externalPkUUID)); - SET p_id = LAST_INSERT_ID(); + IF row_session_id IS NULL THEN + INSERT INTO BLSession(sessionId, proposalId, visit_number, beamLineSetupId, startDate, endDate, + beamLineName, sessionTitle, beamLineOperator, nbShifts, scheduled, usedFlag, comments, expSessionPk, externalId) + VALUES (p_id, row_proposal_id, p_visitNumber, p_beamLineSetupId, p_startDate, p_endDate, + p_beamlineName, p_title, p_beamlineOperator, p_nbShifts, p_scheduled, p_usedFlag, p_comments, p_externalPkId, unhex(p_externalPkUUID)); + SET p_id = LAST_INSERT_ID(); + + ELSE + + UPDATE BLSession + SET + proposalId = IFNULL(row_proposal_id, proposalId), + visit_number = IFNULL(p_visitNumber, visit_number), + beamLineSetupId = IFNULL(p_beamLineSetupId, beamLineSetupId), + startDate = IFNULL(p_startDate, startDate), + endDate = IFNULL(p_endDate, endDate), + beamLineName = IFNULL(p_beamlineName, beamLineName), + sessionTitle = IFNULL(p_title, sessionTitle), + beamLineOperator = IFNULL(p_beamlineOperator, beamLineOperator), + nbShifts = IFNULL(p_nbShifts, nbShifts), + scheduled = IFNULL(p_scheduled, scheduled), + usedFlag = IFNULL(p_usedFlag, usedFlag), + comments = IFNULL(p_comments, comments), + expSessionPk = IFNULL(p_externalPkId, expSessionPk), + externalId = IFNULL(unhex(p_externalPkUUID), externalId) + WHERE sessionId = row_session_id; + SET p_id := row_session_id; - ELSEIF p_id IS NOT NULL THEN - UPDATE BLSession - SET - proposalId = IFNULL(row_proposal_id, proposalId), - visit_number = IFNULL(p_visitNumber, visit_number), - beamLineSetupId = IFNULL(p_beamLineSetupId, beamLineSetupId), - startDate = IFNULL(p_startDate, startDate), - endDate = IFNULL(p_endDate, endDate), - beamLineName = IFNULL(p_beamlineName, beamLineName), - sessionTitle = IFNULL(p_title, sessionTitle), - beamLineOperator = IFNULL(p_beamlineOperator, beamLineOperator), - nbShifts = IFNULL(p_nbShifts, nbShifts), - scheduled = IFNULL(p_scheduled, scheduled), - usedFlag = IFNULL(p_usedFlag, usedFlag), - comments = IFNULL(p_comments, comments), - expSessionPk = IFNULL(p_externalPkId, expSessionPk), - externalId = IFNULL(unhex(p_externalPkUUID), externalId) - WHERE sessionId = p_id; END IF; - ELSE - SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument(s) are NULL: p_id OR (p_proposalCode AND p_proposalNumber) must be non-NULL.'; - END IF; + ELSE + SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument(s) are NULL: p_id OR (p_proposalCode AND p_proposalNumber) must be non-NULL.'; + END IF; END ;; DELIMITER ; /*!50003 SET sql_mode = @saved_sql_mode */ ; @@ -10888,7 +11027,7 @@ DELIMITER ; /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-05-28 15:50:24 +-- Dump completed on 2021-07-23 18:38:10 -- MariaDB dump 10.19 Distrib 10.5.10-MariaDB, for Linux (x86_64) -- -- Host: 10.88.0.5 Database: ispyb_build @@ -10935,4 +11074,4 @@ DELIMITER ; /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-05-28 15:50:24 +-- Dump completed on 2021-07-23 18:38:11 diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index ea37af65..a69556e8 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -245,12 +245,9 @@ CREATE TABLE `AutoProcProgram` ( `processingEnvironment` varchar(255) DEFAULT NULL COMMENT 'Cpus, Nodes,...', `recordTimeStamp` datetime DEFAULT NULL COMMENT 'Creation or last update date/time', `processingJobId` int(11) unsigned DEFAULT NULL, - `dataCollectionId` int(11) unsigned DEFAULT NULL, PRIMARY KEY (`autoProcProgramId`), KEY `AutoProcProgram_FK2` (`processingJobId`), - KEY `AutoProcProgram_fk3` (`dataCollectionId`), - CONSTRAINT `AutoProcProgram_FK2` FOREIGN KEY (`processingJobId`) REFERENCES `ProcessingJob` (`processingJobId`), - CONSTRAINT `AutoProcProgram_fk3` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) + CONSTRAINT `AutoProcProgram_FK2` FOREIGN KEY (`processingJobId`) REFERENCES `ProcessingJob` (`processingJobId`) ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; @@ -344,6 +341,7 @@ CREATE TABLE `AutoProcScalingStatistics` ( `anomalous` tinyint(1) DEFAULT 0 COMMENT 'boolean type:0 noanoum - 1 anoum', `ccHalf` float DEFAULT NULL COMMENT 'information from XDS', `ccAnomalous` float DEFAULT NULL, + `resIOverSigI2` float DEFAULT NULL COMMENT 'Resolution where I/Sigma(I) equals 2', PRIMARY KEY (`autoProcScalingStatisticsId`), KEY `AutoProcScalingStatistics_FKindexType` (`scalingStatisticsType`), KEY `AutoProcScalingStatistics_scalingId_statisticsType` (`autoProcScalingId`,`scalingStatisticsType`), @@ -887,6 +885,25 @@ CREATE TABLE `BLSample_has_EnergyScan` ( ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; +-- +-- Table structure for table `BLSample_has_Positioner` +-- + +DROP TABLE IF EXISTS `BLSample_has_Positioner`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `BLSample_has_Positioner` ( + `blSampleHasPositioner` int(10) unsigned NOT NULL AUTO_INCREMENT, + `blSampleId` int(10) unsigned NOT NULL, + `positionerId` int(10) unsigned NOT NULL, + PRIMARY KEY (`blSampleHasPositioner`), + KEY `BLSampleHasPositioner_ibfk1` (`blSampleId`), + KEY `BLSampleHasPositioner_ibfk2` (`positionerId`), + CONSTRAINT `BLSampleHasPositioner_ibfk1` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`), + CONSTRAINT `BLSampleHasPositioner_ibfk2` FOREIGN KEY (`positionerId`) REFERENCES `Positioner` (`positionerId`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + -- -- Table structure for table `BLSession` -- @@ -991,6 +1008,25 @@ CREATE TABLE `BLSubSample` ( ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; +-- +-- Table structure for table `BLSubSample_has_Positioner` +-- + +DROP TABLE IF EXISTS `BLSubSample_has_Positioner`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `BLSubSample_has_Positioner` ( + `blSubSampleHasPositioner` int(10) unsigned NOT NULL AUTO_INCREMENT, + `blSubSampleId` int(10) unsigned NOT NULL, + `positionerId` int(10) unsigned NOT NULL, + PRIMARY KEY (`blSubSampleHasPositioner`), + KEY `BLSubSampleHasPositioner_ibfk1` (`blSubSampleId`), + KEY `BLSubSampleHasPositioner_ibfk2` (`positionerId`), + CONSTRAINT `BLSubSampleHasPositioner_ibfk1` FOREIGN KEY (`blSubSampleId`) REFERENCES `BLSubSample` (`blSubSampleId`), + CONSTRAINT `BLSubSampleHasPositioner_ibfk2` FOREIGN KEY (`positionerId`) REFERENCES `Positioner` (`positionerId`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + -- -- Table structure for table `BeamApertures` -- @@ -3564,6 +3600,21 @@ CREATE TABLE `Position` ( ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; +-- +-- Table structure for table `Positioner` +-- + +DROP TABLE IF EXISTS `Positioner`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `Positioner` ( + `positionerId` int(10) unsigned NOT NULL AUTO_INCREMENT, + `positioner` varchar(50) NOT NULL, + `value` float NOT NULL, + PRIMARY KEY (`positionerId`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='An arbitrary positioner and its value, could be e.g. a motor. Allows for instance to store some positions with a sample or subsample'; +/*!40101 SET character_set_client = @saved_cs_client */; + -- -- Table structure for table `PreparePhasingData` -- @@ -3890,7 +3941,7 @@ CREATE TABLE `ProposalHasPerson` ( `proposalHasPersonId` int(10) unsigned NOT NULL AUTO_INCREMENT, `proposalId` int(10) unsigned NOT NULL, `personId` int(10) unsigned NOT NULL, - `role` enum('Co-Investigator','Principal Investigator','Alternate Contact','ERA Admin') DEFAULT NULL, + `role` enum('Co-Investigator','Principal Investigator','Alternate Contact','ERA Admin','Associate') DEFAULT NULL, PRIMARY KEY (`proposalHasPersonId`), KEY `fk_ProposalHasPerson_Proposal` (`proposalId`), KEY `fk_ProposalHasPerson_Personal` (`personId`), @@ -4372,10 +4423,13 @@ CREATE TABLE `Screening` ( `diffractionPlanId` int(10) unsigned DEFAULT NULL COMMENT 'references DiffractionPlan', `dataCollectionGroupId` int(11) DEFAULT NULL, `xmlSampleInformation` longblob DEFAULT NULL, + `autoProcProgramId` int(10) unsigned DEFAULT NULL, PRIMARY KEY (`screeningId`), KEY `Screening_FKIndexDiffractionPlanId` (`diffractionPlanId`), KEY `dcgroupId` (`dataCollectionGroupId`), KEY `_Screening_ibfk2` (`dataCollectionId`), + KEY `Screening_fk_autoProcProgramId` (`autoProcProgramId`), + CONSTRAINT `Screening_fk_autoProcProgramId` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE SET NULL ON UPDATE CASCADE, CONSTRAINT `Screening_ibfk_1` FOREIGN KEY (`dataCollectionGroupId`) REFERENCES `DataCollectionGroup` (`dataCollectionGroupId`) ON DELETE NO ACTION ON UPDATE NO ACTION, CONSTRAINT `_Screening_ibfk2` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE ) ENGINE=InnoDB DEFAULT CHARSET=latin1; @@ -4629,7 +4683,7 @@ DROP TABLE IF EXISTS `Session_has_Person`; CREATE TABLE `Session_has_Person` ( `sessionId` int(10) unsigned NOT NULL DEFAULT 0, `personId` int(10) unsigned NOT NULL DEFAULT 0, - `role` enum('Local Contact','Local Contact 2','Staff','Team Leader','Co-Investigator','Principal Investigator','Alternate Contact','Data Access','Team Member','ERA Admin') DEFAULT NULL, + `role` enum('Local Contact','Local Contact 2','Staff','Team Leader','Co-Investigator','Principal Investigator','Alternate Contact','Data Access','Team Member','ERA Admin','Associate') DEFAULT NULL, `remote` tinyint(1) DEFAULT 0, PRIMARY KEY (`sessionId`,`personId`), KEY `Session_has_Person_FKIndex2` (`personId`), @@ -6073,4 +6127,4 @@ CREATE TABLE `zc_ZocaloBuffer` ( /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-07-07 11:36:18 +-- Dump completed on 2021-07-23 18:38:10 diff --git a/schemas/ispyb/updates/2021_07_23_AdminVar_bump_version.sql b/schemas/ispyb/updates/2021_07_23_AdminVar_bump_version.sql new file mode 100644 index 00000000..8eda6946 --- /dev/null +++ b/schemas/ispyb/updates/2021_07_23_AdminVar_bump_version.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2021_07_23_AdminVar_bump_version.sql', 'ONGOING'); + +UPDATE AdminVar SET `value` = '1.24.0' WHERE `name` = 'schemaVersion'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2021_07_23_AdminVar_bump_version.sql';