From 167fbde7dfb275ea38e46aafc0bdbde6a93ae665 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Wed, 7 Jul 2021 11:42:24 +0100 Subject: [PATCH] Bump to v1.23.0, update schema files + documentation --- HISTORY.rst | 22 ++++++++++++++ docs/list_of_procs.rst | 1 + docs/list_of_tables_and_columns.rst | 10 +++++++ schemas/ispyb/data.sql | 21 ++++++++----- schemas/ispyb/lookups.sql | 12 ++++---- schemas/ispyb/tables.sql | 30 +++++++++++++++++-- .../2021_07_07_AdminVar_bump_version.sql | 5 ++++ 7 files changed, 85 insertions(+), 16 deletions(-) create mode 100644 schemas/ispyb/updates/2021_07_07_AdminVar_bump_version.sql diff --git a/HISTORY.rst b/HISTORY.rst index 3c75f2a1..c22cf809 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -4,6 +4,28 @@ History Unreleased / master ------------------- + +1.23.0 (2021-07-07) +------------------- + +New columns: + +* ``DiffractionPlan``: ``qMin``, ``qMax``, ``reductionParametersAveraging`` +* ``ParticleClassification``: ``classDistribution`` +* ``ParticlePicker``: ``summaryImageFullPath`` +* ``BLSampleGroup``: ``proposalId`` (and populate it based on ``BLSampleGroup_has_BLSample -> BLSample -> Crystal -> Protein.proposalId``) + +New tables: + +* ``zc_ZocaloBuffer``: A table for temporary Zocalo data. + +Lookup table data changes: + +* ``SpaceGroup``: Changed a few ``spaceGroupShortName`` values for common spacegroups, and set ``MX_used = 0`` for less commonly used spacegroups. +* ``UserGroup``: Add groups ``detector_admin``, ``prop_admin``, ``goods_handling``, ``imaging_admin``, ``spectroscopy_admin``, ``mm_admin``. + +Additionally, new enum options have been added to DataCollectionGroup.experimentType: Mesh3D, Screening. + 1.22.0 (2021-05-28) ------------------- diff --git a/docs/list_of_procs.rst b/docs/list_of_procs.rst index 7ed8ed75..48cc0149 100644 --- a/docs/list_of_procs.rst +++ b/docs/list_of_procs.rst @@ -196,6 +196,7 @@ "**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", "Update or insert new entry with info about a MX molecular replacements 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)", "Update or insert new entry with info about views (image paths) for an MX molecular replacement 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)", "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)", "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", "Inserts or updates info about a particle classification (p_id). Mandatory columns: For insert: p_particleClassificationGroupId diff --git a/docs/list_of_tables_and_columns.rst b/docs/list_of_tables_and_columns.rst index e8788a69..b6d1a1fe 100644 --- a/docs/list_of_tables_and_columns.rst +++ b/docs/list_of_tables_and_columns.rst @@ -334,6 +334,7 @@ **BLSampleGroup**,table,"" ``blSampleGroupId``,int,"" ``name``,varchar,"Human-readable name" + ``proposalId``,int,"" **BLSampleGroup_has_BLSample**,table,"" ``blSampleGroupId``,int,"" ``blSampleId``,int,"" @@ -953,6 +954,9 @@ ``purificationColumnId``,int,"" ``collectionMode``,enum,"The requested collection mode, possible values are auto, manual" ``priority``,int,"The priority of this sample relative to others in the shipment" + ``qMin``,float,"minimum in qRange, unit: nm^-1, needed for SAXS" + ``qMax``,float,"maximum in qRange, unit: nm^-1, needed for SAXS" + ``reductionParametersAveraging``,enum,"Post processing params for SAXS" **EMMicroscope**,table,"" ``emMicroscopeId``,int,"" ``instrumentName``,varchar,"" @@ -1331,6 +1335,7 @@ ``estimatedResolution``,float,"???, Unit: Angstroms" ``overallFourierCompleteness``,float,"" ``particleClassificationGroupId``,int,"" + ``classDistribution``,float,"Provides a figure of merit for the class, higher number is better" **ParticleClassificationGroup**,table,"" ``particleClassificationGroupId``,int,"" ``particlePickerId``,int,"" @@ -1350,6 +1355,7 @@ ``particlePickingTemplate``,varchar,"Cryolo model" ``particleDiameter``,float,"Unit: nm" ``numberOfParticles``,int,"" + ``summaryImageFullPath``,varchar,"Generated summary micrograph image with highlighted particles" **PDB**,table,"" ``pdbId``,int,"" ``name``,varchar,"" @@ -2243,3 +2249,7 @@ ``b``,tinyint,"B colour component" ``blSampleId``,int,"ROIs can be created within the context of a sample" ``scalar``,varchar,"For ROIs that are not an element, i.e. could be a scan counter instead" + **zc_ZocaloBuffer**,table,"" + ``AutoProcProgramID``,int,"Reference to an existing AutoProcProgram" + ``UUID``,int,"AutoProcProgram-specific unique identifier" + ``Reference``,int,"Context-dependent reference to primary key IDs in other ISPyB tables" diff --git a/schemas/ispyb/data.sql b/schemas/ispyb/data.sql index b9f8b9c2..64ebd37b 100644 --- a/schemas/ispyb/data.sql +++ b/schemas/ispyb/data.sql @@ -1,8 +1,8 @@ --- MariaDB dump 10.19 Distrib 10.5.9-MariaDB, for Linux (x86_64) +-- MariaDB dump 10.19 Distrib 10.5.10-MariaDB, for Linux (x86_64) -- -- Host: 10.88.0.5 Database: ispyb_build -- ------------------------------------------------------ --- Server version 10.4.17-MariaDB-1:10.4.17+maria~bionic +-- Server version 10.4.19-MariaDB-1:10.4.19+maria~bionic /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; @@ -188,7 +188,7 @@ INSERT INTO `BLSample` (`blSampleId`, `diffractionPlanId`, `crystalId`, `contain -- /*!40000 ALTER TABLE `BLSampleGroup` DISABLE KEYS */; -INSERT INTO `BLSampleGroup` (`blSampleGroupId`, `name`) VALUES (5,NULL),(6,'foo'),(7,'bar'); +INSERT INTO `BLSampleGroup` (`blSampleGroupId`, `name`, `proposalId`) VALUES (5,NULL,37027),(6,'foo',37027),(7,'bar',37027); /*!40000 ALTER TABLE `BLSampleGroup` ENABLE KEYS */; -- @@ -405,7 +405,7 @@ INSERT INTO `ContainerQueue` (`containerQueueId`, `containerId`, `personId`, `cr -- /*!40000 ALTER TABLE `ContainerQueueSample` DISABLE KEYS */; -INSERT INTO `ContainerQueueSample` (`containerQueueSampleId`, `containerQueueId`, `blSubSampleId`) VALUES (2,2,2); +INSERT INTO `ContainerQueueSample` (`containerQueueSampleId`, `containerQueueId`, `blSubSampleId`, `status`, `startTime`, `endTime`, `dataCollectionPlanId`, `blSampleId`) VALUES (2,2,2,NULL,NULL,NULL,NULL,NULL); /*!40000 ALTER TABLE `ContainerQueueSample` ENABLE KEYS */; -- @@ -471,7 +471,7 @@ INSERT INTO `Crystal` (`crystalId`, `diffractionPlanId`, `proteinId`, `crystalUU -- /*!40000 ALTER TABLE `DataCollection` DISABLE KEYS */; -INSERT INTO `DataCollection` (`dataCollectionId`, `BLSAMPLEID`, `SESSIONID`, `experimenttype`, `dataCollectionNumber`, `startTime`, `endTime`, `runStatus`, `axisStart`, `axisEnd`, `axisRange`, `overlap`, `numberOfImages`, `startImageNumber`, `numberOfPasses`, `exposureTime`, `imageDirectory`, `imagePrefix`, `imageSuffix`, `imageContainerSubPath`, `fileTemplate`, `wavelength`, `resolution`, `detectorDistance`, `xBeam`, `yBeam`, `comments`, `printableForReport`, `CRYSTALCLASS`, `slitGapVertical`, `slitGapHorizontal`, `transmission`, `synchrotronMode`, `xtalSnapshotFullPath1`, `xtalSnapshotFullPath2`, `xtalSnapshotFullPath3`, `xtalSnapshotFullPath4`, `rotationAxis`, `phiStart`, `kappaStart`, `omegaStart`, `chiStart`, `resolutionAtCorner`, `detector2Theta`, `DETECTORMODE`, `undulatorGap1`, `undulatorGap2`, `undulatorGap3`, `beamSizeAtSampleX`, `beamSizeAtSampleY`, `centeringMethod`, `averageTemperature`, `ACTUALSAMPLEBARCODE`, `ACTUALSAMPLESLOTINCONTAINER`, `ACTUALCONTAINERBARCODE`, `ACTUALCONTAINERSLOTINSC`, `actualCenteringPosition`, `beamShape`, `dataCollectionGroupId`, `POSITIONID`, `detectorId`, `FOCALSPOTSIZEATSAMPLEX`, `POLARISATION`, `FOCALSPOTSIZEATSAMPLEY`, `APERTUREID`, `screeningOrigId`, `startPositionId`, `endPositionId`, `flux`, `strategySubWedgeOrigId`, `blSubSampleId`, `flux_end`, `bestWilsonPlotPath`, `processedDataFile`, `datFullPath`, `magnification`, `totalAbsorbedDose`, `binning`, `particleDiameter`, `boxSize_CTF`, `minResolution`, `minDefocus`, `maxDefocus`, `defocusStepSize`, `amountAstigmatism`, `extractSize`, `bgRadius`, `voltage`, `objAperture`, `c1aperture`, `c2aperture`, `c3aperture`, `c1lens`, `c2lens`, `c3lens`, `totalExposedDose`, `nominalMagnification`, `nominalDefocus`, `imageSizeX`, `imageSizeY`, `pixelSizeOnImage`, `phasePlate`) VALUES (993677,374695,55167,NULL,1,'2016-01-14 12:40:34','2016-01-14 12:41:54','DataCollection 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Successful',0,0.4,0.4,-89.6,2,1,1,0.01,'/dls/i03/data/2016/cm14451-2/20160413/test_xtal/','xtal1','cbf',NULL,'xtal1_1_####.cbf',0.976254,1.24362,200,214.33,208.71,'(-703,-47,-74) Aperture: Large',1,NULL,0.059918,0.099937,100,'User','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_1_90.0.png','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_1_0.0.png',NULL,NULL,'Omega',NULL,NULL,0,NULL,NULL,NULL,NULL,5.30095,NULL,NULL,0.08,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1040398,647536,NULL,80,NULL,20,3752,NULL,NULL,NULL,1959830505829.428,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(1052503,NULL,55168,NULL,3,'2016-04-13 12:21:26','2016-04-13 12:21:54','DataCollection Successful',93,0.3,0.3,-44.7,3,1,1,0.01,'/dls/i03/data/2016/cm14451-2/20160413/test_xtal/','xtal1','cbf',NULL,'xtal1_3_####.cbf',0.976253,1.5,266.693,214.372,208.299,'(-703,-47,-74) Aperture: Large',1,NULL,0.059918,0.099937,100,'User','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_1_183.0.png','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_1_93.0.png',NULL,NULL,'Omega',NULL,NULL,93,NULL,NULL,NULL,NULL,5.30095,NULL,NULL,0.08,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1040407,647545,NULL,80,NULL,20,3752,NULL,NULL,NULL,1972385107622.2878,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(1066786,398810,55168,NULL,2,'2016-04-18 11:04:44','2016-04-18 11:04:57','DataCollection Successful',0,0.5,0.5,-44.5,3,1,1,0.1,'/dls/i03/data/2016/cm14451-2/gw/20160418/thau/edna_test/','thau','cbf',NULL,'thau_2_####.cbf',0.976253,1.5,266.693,214.372,208.299,'(-345,-241,-185) Aperture: 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`imagePrefix`, `imageSuffix`, `imageContainerSubPath`, `fileTemplate`, `wavelength`, `resolution`, `detectorDistance`, `xBeam`, `yBeam`, `comments`, `printableForReport`, `CRYSTALCLASS`, `slitGapVertical`, `slitGapHorizontal`, `transmission`, `synchrotronMode`, `xtalSnapshotFullPath1`, `xtalSnapshotFullPath2`, `xtalSnapshotFullPath3`, `xtalSnapshotFullPath4`, `rotationAxis`, `phiStart`, `kappaStart`, `omegaStart`, `chiStart`, `resolutionAtCorner`, `detector2Theta`, `DETECTORMODE`, `undulatorGap1`, `undulatorGap2`, `undulatorGap3`, `beamSizeAtSampleX`, `beamSizeAtSampleY`, `centeringMethod`, `averageTemperature`, `ACTUALSAMPLEBARCODE`, `ACTUALSAMPLESLOTINCONTAINER`, `ACTUALCONTAINERBARCODE`, `ACTUALCONTAINERSLOTINSC`, `actualCenteringPosition`, `beamShape`, `dataCollectionGroupId`, `POSITIONID`, `detectorId`, `FOCALSPOTSIZEATSAMPLEX`, `POLARISATION`, `FOCALSPOTSIZEATSAMPLEY`, `APERTUREID`, `screeningOrigId`, `startPositionId`, `endPositionId`, `flux`, `strategySubWedgeOrigId`, `blSubSampleId`, `flux_end`, `bestWilsonPlotPath`, `processedDataFile`, `datFullPath`, `magnification`, `totalAbsorbedDose`, `binning`, `particleDiameter`, `boxSize_CTF`, `minResolution`, `minDefocus`, `maxDefocus`, `defocusStepSize`, `amountAstigmatism`, `extractSize`, `bgRadius`, `voltage`, `objAperture`, `c1aperture`, `c2aperture`, `c3aperture`, `c1lens`, `c2lens`, `c3lens`, `totalExposedDose`, `nominalMagnification`, `nominalDefocus`, `imageSizeX`, `imageSizeY`, `pixelSizeOnImage`, `phasePlate`, `dataCollectionPlanId`) VALUES (993677,374695,55167,NULL,1,'2016-01-14 12:40:34','2016-01-14 12:41:54','DataCollection Successful',45,0.1,0.1,0,3600,1,1,0.02,'/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/','tlys_jan_4','cbf',NULL,'tlys_jan_4_1_####.cbf',1.28255,1.6,193.087,215.62,208.978,'(-402,345,142) EDNAStrategy4: subWedge:1Aperture: 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`exposureTemperature`, `experimentTypeId`, `purificationColumnId`, `collectionMode`, `priority`) VALUES (197784,NULL,'OSC',NULL,NULL,0.2,NULL,NULL,NULL,NULL,NULL,10.5,10.5,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,0,NULL,NULL,NULL,1.1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-20 23:50:27',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(197788,NULL,NULL,NULL,NULL,10,NULL,NULL,NULL,NULL,NULL,160,100,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-26 15:28:12',NULL,150,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,4,162.5,45,330.6,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(197792,'XPDF-1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2017-03-22 10:56:32',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); +INSERT INTO `DiffractionPlan` (`diffractionPlanId`, `name`, `experimentKind`, `observedResolution`, `minimalResolution`, `exposureTime`, `oscillationRange`, `maximalResolution`, `screeningResolution`, `radiationSensitivity`, `anomalousScatterer`, `preferredBeamSizeX`, `preferredBeamSizeY`, `preferredBeamDiameter`, `comments`, `DIFFRACTIONPLANUUID`, `aimedCompleteness`, `aimedIOverSigmaAtHighestRes`, `aimedMultiplicity`, `aimedResolution`, `anomalousData`, `complexity`, `estimateRadiationDamage`, `forcedSpaceGroup`, `requiredCompleteness`, `requiredMultiplicity`, `requiredResolution`, `strategyOption`, `kappaStrategyOption`, `numberOfPositions`, `minDimAccrossSpindleAxis`, `maxDimAccrossSpindleAxis`, `radiationSensitivityBeta`, `radiationSensitivityGamma`, `minOscWidth`, `recordTimeStamp`, `monochromator`, `energy`, `transmission`, `boxSizeX`, `boxSizeY`, 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08:59:59'),(72,'2020-03','2020-05-22 09:00:00','2020-08-14 08:59:59'); /*!40000 ALTER TABLE `v_run` ENABLE KEYS */; + +-- +-- Dumping data for table `zc_ZocaloBuffer` +-- + +/*!40000 ALTER TABLE `zc_ZocaloBuffer` DISABLE KEYS */; +/*!40000 ALTER TABLE `zc_ZocaloBuffer` ENABLE KEYS */; /*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; /*!40101 SET SQL_MODE=@OLD_SQL_MODE */; @@ -1431,4 +1438,4 @@ INSERT INTO `v_run` (`runId`, `run`, `startDate`, `endDate`) VALUES (1,'2008-01' /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-04-20 17:53:54 +-- Dump completed on 2021-07-07 11:36:19 diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index 9efa38e6..c6938144 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -19,7 +19,7 @@ -- /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */; -INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','1.22.0'); +INSERT INTO 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(`containerTypeId`, `name`, `proposalType`, `active` -- /*!40000 ALTER TABLE `ExperimentType` DISABLE KEYS */; -INSERT INTO `ExperimentType` (`experimentTypeId`, `name`, `proposalType`, `active`) VALUES (1,'Default',NULL,1),(2,'MXPressE','mx',1),(3,'MXPressO','mx',1),(4,'MXPressE_SAD','mx',1),(5,'MXScore','mx',1),(6,'MXPressM','mx',1),(7,'MAD','mx',1),(8,'SAD','mx',1),(9,'Fixed','mx',1),(10,'Ligand binding','mx',1),(11,'Refinement','mx',1),(12,'OSC','mx',1),(13,'MAD - Inverse Beam','mx',1),(14,'SAD - Inverse Beam','mx',1),(15,'MESH','mx',1),(16,'XFE','mx',1),(17,'Stepped transmission','mx',1),(18,'XChem High Symmetry','mx',1),(19,'XChem Low Symmetry','mx',1),(20,'Commissioning','mx',1),(21,'HPLC','saxs',1),(22,'Robot','saxs',1),(23,'Rack','saxs',1),(24,'Grid','saxs',1),(25,'Solids','saxs',1),(26,'Powder','saxs',1),(27,'Peltier','saxs',1),(28,'Spectroscopy','saxs',1),(29,'CD Spectroscopy','saxs',1),(30,'Microscopy','saxs',1),(31,'Imaging','saxs',1),(32,'CD Thermal Melt','saxs',1),(33,'Fixed Energy At Ambient With Robot','saxs',1); +INSERT INTO `ExperimentType` (`experimentTypeId`, `name`, `proposalType`, `active`) VALUES (1,'Default',NULL,1),(2,'MXPressE','mx',1),(3,'MXPressO','mx',1),(4,'MXPressE_SAD','mx',1),(5,'MXScore','mx',1),(6,'MXPressM','mx',1),(7,'MAD','mx',1),(8,'SAD','mx',1),(9,'Fixed','mx',1),(10,'Ligand binding','mx',1),(11,'Refinement','mx',1),(12,'OSC','mx',1),(13,'MAD - Inverse Beam','mx',1),(14,'SAD - Inverse Beam','mx',1),(15,'MESH','mx',1),(16,'XFE','mx',1),(17,'Stepped transmission','mx',1),(18,'XChem High Symmetry','mx',1),(19,'XChem Low Symmetry','mx',1),(20,'Commissioning','mx',1),(21,'HPLC','saxs',1),(22,'Robot','saxs',1),(23,'Rack','saxs',1),(24,'Grid','saxs',1),(25,'Solids','saxs',1),(26,'Powder','saxs',1),(27,'Peltier','saxs',1),(28,'Spectroscopy','saxs',1),(29,'CD Spectroscopy','saxs',1),(30,'Microscopy','saxs',1),(31,'Imaging','saxs',1),(32,'CD Thermal Melt','saxs',1),(33,'Fixed Energy At Ambient With 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-3 c1',NULL,NULL,NULL,NULL,1),(229,229,'Im-3m','Im -3 m',NULL,NULL,NULL,NULL,1),(230,230,'Ia-3d1','Ia -3 d1',NULL,NULL,NULL,NULL,1); +INSERT INTO `SpaceGroup` (`spaceGroupId`, `spaceGroupNumber`, `spaceGroupShortName`, `spaceGroupName`, `bravaisLattice`, `bravaisLatticeName`, `pointGroup`, `geometryClassnameId`, `MX_used`) VALUES (1,1,'P1','P 1','aP',NULL,NULL,NULL,1),(2,2,'P-1','P-1',NULL,NULL,NULL,NULL,1),(3,3,'P2','P 12 1','mP',NULL,NULL,NULL,1),(4,4,'P21','P 121 1','mP',NULL,NULL,NULL,1),(5,5,'C2','C 12 1','mC,mI',NULL,NULL,NULL,1),(6,6,'P1m1','P 1m 1',NULL,NULL,NULL,NULL,0),(7,7,'P1c1','P 1c 1',NULL,NULL,NULL,NULL,0),(8,8,'C1m1','C 1m 1',NULL,NULL,NULL,NULL,0),(9,9,'C1c1','C 1c 1',NULL,NULL,NULL,NULL,0),(10,10,'P12/m1','P 12/m 1',NULL,NULL,NULL,NULL,0),(11,11,'P121/m1','P 121/m 1',NULL,NULL,NULL,NULL,0),(12,12,'C12/m1','C 12/m 1',NULL,NULL,NULL,NULL,0),(13,13,'P12/c1','P 12/c 1',NULL,NULL,NULL,NULL,0),(14,14,'P121/c1','P 121/c 1',NULL,NULL,NULL,NULL,0),(15,15,'C12/c1','C 12/c 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m1',NULL,NULL,NULL,NULL,0),(58,58,'Pnnm1','P nn m1',NULL,NULL,NULL,NULL,0),(59,59,'Pmmn1','P mm n1',NULL,NULL,NULL,NULL,0),(60,60,'Pbcn1','P bc n1',NULL,NULL,NULL,NULL,0),(61,61,'Pbca1','P bc a1',NULL,NULL,NULL,NULL,0),(62,62,'Pnma1','P nm a1',NULL,NULL,NULL,NULL,0),(63,63,'Cmcm1','C mc m1',NULL,NULL,NULL,NULL,0),(64,64,'Cmca1','C mc a1',NULL,NULL,NULL,NULL,0),(65,65,'Cmmm','C mm m',NULL,NULL,NULL,NULL,0),(66,66,'Cccm','C cc m',NULL,NULL,NULL,NULL,0),(67,67,'Cmma','C mm a',NULL,NULL,NULL,NULL,0),(68,68,'Ccca','C cc a',NULL,NULL,NULL,NULL,0),(69,69,'Fmmm','F mm m',NULL,NULL,NULL,NULL,0),(70,70,'Fddd','F dd d',NULL,NULL,NULL,NULL,0),(71,71,'Immm','I mm m',NULL,NULL,NULL,NULL,0),(72,72,'Ibam','I ba m',NULL,NULL,NULL,NULL,0),(73,73,'Ibca1','I b c a1',NULL,NULL,NULL,NULL,0),(74,74,'Imma1','I mm 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2',NULL,NULL,NULL,NULL,0),(117,117,'P-4b2','P-4 b 2',NULL,NULL,NULL,NULL,0),(118,118,'P-4n2','P-4 n 2',NULL,NULL,NULL,NULL,0),(119,119,'I-4m2','I-4 m 2',NULL,NULL,NULL,NULL,0),(120,120,'I-4c2','I-4 c 2',NULL,NULL,NULL,NULL,0),(121,121,'I-42m','I-4 2 m',NULL,NULL,NULL,NULL,0),(122,122,'I-42d','I-4 2 d',NULL,NULL,NULL,NULL,0),(123,123,'P4/mmm','P4/m m m',NULL,NULL,NULL,NULL,0),(124,124,'P4/mcc','P4/m c c',NULL,NULL,NULL,NULL,0),(125,125,'P4/nbm','P4/n b m',NULL,NULL,NULL,NULL,0),(126,126,'P4/nnc','P4/n n c',NULL,NULL,NULL,NULL,0),(127,127,'P4/mbm1','P4/m b m1',NULL,NULL,NULL,NULL,0),(128,128,'P4/mnc1','P4/m n c1',NULL,NULL,NULL,NULL,0),(129,129,'P4/nmm1','P4/n m m1',NULL,NULL,NULL,NULL,0),(130,130,'P4/ncc1','P4/n c c1',NULL,NULL,NULL,NULL,0),(131,131,'P42/mmc','P42/m m c',NULL,NULL,NULL,NULL,0),(132,132,'P42/mcm','P42/m c m',NULL,NULL,NULL,NULL,0),(133,133,'P42/nbc','P42/n b c',NULL,NULL,NULL,NULL,0),(134,134,'P42/nnm','P42/n n m',NULL,NULL,NULL,NULL,0),(135,135,'P42/mbc','P42/m b 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2',NULL,NULL,NULL,NULL,0),(189,189,'P-62m','P-6 2 m',NULL,NULL,NULL,NULL,0),(190,190,'P-62c','P-6 2 c',NULL,NULL,NULL,NULL,0),(191,191,'P6/mmm','P6/m m m',NULL,NULL,NULL,NULL,0),(192,192,'P6/mcc','P6/m c c',NULL,NULL,NULL,NULL,0),(193,193,'P63/mcm','P63/m c m',NULL,NULL,NULL,NULL,0),(194,194,'P63/mmc','P63/m m c',NULL,NULL,NULL,NULL,0),(195,195,'P23','P2 3','cP',NULL,NULL,NULL,1),(196,196,'F23','F2 3','cF',NULL,NULL,NULL,1),(197,197,'I23','I2 3','cI',NULL,NULL,NULL,1),(198,198,'P213','P21 3','cP',NULL,NULL,NULL,1),(199,199,'I213','I21 3','cI',NULL,NULL,NULL,1),(200,200,'Pm-3','Pm -3',NULL,NULL,NULL,NULL,0),(201,201,'Pn-3','Pn -3',NULL,NULL,NULL,NULL,0),(202,202,'Fm-3','Fm -3',NULL,NULL,NULL,NULL,0),(203,203,'Fd-3','Fd -3',NULL,NULL,NULL,NULL,0),(204,204,'Im-3','Im -3',NULL,NULL,NULL,NULL,0),(205,205,'Pa-31','Pa -31',NULL,NULL,NULL,NULL,0),(206,206,'Ia-31','Ia -31',NULL,NULL,NULL,NULL,0),(207,207,'P432','P4 3 2','cP',NULL,NULL,NULL,1),(208,208,'P4232','P42 3 2','cP',NULL,NULL,NULL,1),(209,209,'F432','F4 3 2','cF',NULL,NULL,NULL,1),(210,210,'F4132','F41 3 2','cF',NULL,NULL,NULL,1),(211,211,'I432','I4 3 2','cI',NULL,NULL,NULL,1),(212,212,'P4332','P43 3 2','cP',NULL,NULL,NULL,1),(213,213,'P4132','P41 3 2','cP',NULL,NULL,NULL,1),(214,214,'I4132','I41 3 2','cI',NULL,NULL,NULL,1),(215,215,'P-43m','P-4 3 m',NULL,NULL,NULL,NULL,0),(216,216,'F-43m','F-4 3 m',NULL,NULL,NULL,NULL,0),(217,217,'I-43m','I-4 3 m',NULL,NULL,NULL,NULL,0),(218,218,'P-43n','P-4 3 n',NULL,NULL,NULL,NULL,0),(219,219,'F-43c','F-4 3 c',NULL,NULL,NULL,NULL,0),(220,220,'I-43d','I-4 3 d',NULL,NULL,NULL,NULL,0),(221,221,'Pm-3m','Pm -3 m',NULL,NULL,NULL,NULL,0),(222,222,'Pn-3n','Pn -3 n',NULL,NULL,NULL,NULL,0),(223,223,'Pm-3n1','Pm -3 n1',NULL,NULL,NULL,NULL,0),(224,224,'Pn-3m1','Pn -3 m1',NULL,NULL,NULL,NULL,0),(225,225,'Fm-3m','Fm -3 m',NULL,NULL,NULL,NULL,0),(226,226,'Fm-3c','Fm -3 c',NULL,NULL,NULL,NULL,0),(227,227,'Fd-3m1','Fd -3 m1',NULL,NULL,NULL,NULL,0),(228,228,'Fd-3c1','Fd -3 c1',NULL,NULL,NULL,NULL,0),(229,229,'Im-3m','Im -3 m',NULL,NULL,NULL,NULL,0),(230,230,'Ia-3d1','Ia -3 d1',NULL,NULL,NULL,NULL,0); /*!40000 ALTER TABLE `SpaceGroup` ENABLE KEYS */; -- @@ -213,7 +213,7 @@ INSERT INTO `PurificationColumn` (`purificationColumnId`, `name`, `active`) VALU -- /*!40000 ALTER TABLE `UserGroup` DISABLE KEYS */; -INSERT INTO `UserGroup` (`userGroupId`, `name`) VALUES (39,'autocollect'),(17,'bag_stats'),(20,'bl_stats'),(8,'developers'),(9,'ehc'),(6,'em_admin'),(10,'fault_admin'),(2,'mx_admin'),(14,'pdb_stats'),(4,'powder_admin'),(3,'saxs_admin'),(28,'ship_manage'),(12,'sm_admin'),(1,'super_admin'),(24,'temp_mx_admin'),(5,'tomo_admin'),(11,'vmxi'),(34,'xpdf_admin'); +INSERT INTO `UserGroup` (`userGroupId`, `name`) VALUES (39,'autocollect'),(17,'bag_stats'),(20,'bl_stats'),(45,'detector_admin'),(8,'developers'),(9,'ehc'),(6,'em_admin'),(10,'fault_admin'),(50,'goods_handling'),(53,'imaging_admin'),(59,'mm_admin'),(2,'mx_admin'),(14,'pdb_stats'),(4,'powder_admin'),(47,'prop_admin'),(3,'saxs_admin'),(28,'ship_manage'),(12,'sm_admin'),(56,'spectroscopy_admin'),(1,'super_admin'),(24,'temp_mx_admin'),(5,'tomo_admin'),(11,'vmxi'),(34,'xpdf_admin'); /*!40000 ALTER TABLE `UserGroup` ENABLE KEYS */; -- @@ -248,4 +248,4 @@ INSERT INTO `ScanParametersService` (`scanParametersServiceId`, `name`, `descrip /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-05-28 16:46:57 +-- Dump completed on 2021-07-07 11:36:19 diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index a3773cf0..ea37af65 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -642,7 +642,10 @@ DROP TABLE IF EXISTS `BLSampleGroup`; CREATE TABLE `BLSampleGroup` ( `blSampleGroupId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(100) DEFAULT NULL COMMENT 'Human-readable name', - PRIMARY KEY (`blSampleGroupId`) + `proposalId` int(10) unsigned DEFAULT NULL, + PRIMARY KEY (`blSampleGroupId`), + KEY `BLSampleGroup_fk_proposalId` (`proposalId`), + CONSTRAINT `BLSampleGroup_fk_proposalId` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE SET NULL ON UPDATE CASCADE ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; @@ -1888,7 +1891,7 @@ CREATE TABLE `DataCollectionGroup` ( `sessionId` int(10) unsigned NOT NULL COMMENT 'references Session table', `comments` varchar(1024) DEFAULT NULL COMMENT 'comments', `blSampleId` int(10) unsigned DEFAULT NULL COMMENT 'references BLSample table', - `experimentType` enum('SAD','SAD - Inverse Beam','OSC','Collect - Multiwedge','MAD','Helical','Multi-positional','Mesh','Burn','MAD - Inverse Beam','Characterization','Dehydration','tomo','experiment','EM','PDF','PDF+Bragg','Bragg','single particle','Serial Fixed','Serial Jet','Standard','Time Resolved','Diamond Anvil High Pressure','Custom','XRF map','Energy scan','XRF spectrum','XRF map xas') DEFAULT NULL COMMENT 'Standard: Routine structure determination experiment. Time Resolved: Investigate the change of a system over time. Custom: Special or non-standard data collection.', + `experimentType` enum('SAD','SAD - Inverse Beam','OSC','Collect - Multiwedge','MAD','Helical','Multi-positional','Mesh','Burn','MAD - Inverse Beam','Characterization','Dehydration','tomo','experiment','EM','PDF','PDF+Bragg','Bragg','single particle','Serial Fixed','Serial Jet','Standard','Time Resolved','Diamond Anvil High Pressure','Custom','XRF map','Energy scan','XRF spectrum','XRF map xas','Mesh3D','Screening') DEFAULT NULL COMMENT 'Standard: Routine structure determination experiment. Time Resolved: Investigate the change of a system over time. Custom: Special or non-standard data collection.', `startTime` datetime DEFAULT NULL COMMENT 'Start time of the dataCollectionGroup', `endTime` datetime DEFAULT NULL COMMENT 'end time of the dataCollectionGroup', `crystalClass` varchar(20) DEFAULT NULL COMMENT 'Crystal Class for industrials users', @@ -2215,6 +2218,9 @@ CREATE TABLE `DiffractionPlan` ( `purificationColumnId` int(10) unsigned DEFAULT NULL, `collectionMode` enum('auto','manual') DEFAULT NULL COMMENT 'The requested collection mode, possible values are auto, manual', `priority` int(4) DEFAULT NULL COMMENT 'The priority of this sample relative to others in the shipment', + `qMin` float DEFAULT NULL COMMENT 'minimum in qRange, unit: nm^-1, needed for SAXS', + `qMax` float DEFAULT NULL COMMENT 'maximum in qRange, unit: nm^-1, needed for SAXS', + `reductionParametersAveraging` enum('All','Fastest Dimension','1D') DEFAULT NULL COMMENT 'Post processing params for SAXS', PRIMARY KEY (`diffractionPlanId`), KEY `DiffractionPlan_ibfk1` (`presetForProposalId`), KEY `DataCollectionPlan_ibfk3` (`detectorId`), @@ -3216,6 +3222,7 @@ CREATE TABLE `ParticleClassification` ( `estimatedResolution` float DEFAULT NULL COMMENT '???, Unit: Angstroms', `overallFourierCompleteness` float DEFAULT NULL, `particleClassificationGroupId` int(10) unsigned DEFAULT NULL, + `classDistribution` float DEFAULT NULL COMMENT 'Provides a figure of merit for the class, higher number is better', PRIMARY KEY (`particleClassificationId`), KEY `ParticleClassification_fk_particleClassificationGroupId` (`particleClassificationGroupId`), CONSTRAINT `ParticleClassification_fk_particleClassificationGroupId` FOREIGN KEY (`particleClassificationGroupId`) REFERENCES `ParticleClassificationGroup` (`particleClassificationGroupId`) ON DELETE CASCADE ON UPDATE CASCADE @@ -3277,6 +3284,7 @@ CREATE TABLE `ParticlePicker` ( `particlePickingTemplate` varchar(255) DEFAULT NULL COMMENT 'Cryolo model', `particleDiameter` float DEFAULT NULL COMMENT 'Unit: nm', `numberOfParticles` int(10) unsigned DEFAULT NULL, + `summaryImageFullPath` varchar(255) DEFAULT NULL COMMENT 'Generated summary micrograph image with highlighted particles', PRIMARY KEY (`particlePickerId`), KEY `ParticlePicker_fk_particlePickerProgramId` (`programId`), KEY `ParticlePicker_fk_motionCorrectionId` (`firstMotionCorrectionId`), @@ -5603,6 +5611,22 @@ SET character_set_client = utf8; ) ENGINE=MyISAM */; SET character_set_client = @saved_cs_client; +-- +-- Table structure for table `zc_ZocaloBuffer` +-- + +DROP TABLE IF EXISTS `zc_ZocaloBuffer`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `zc_ZocaloBuffer` ( + `AutoProcProgramID` int(10) unsigned NOT NULL COMMENT 'Reference to an existing AutoProcProgram', + `UUID` int(10) unsigned NOT NULL COMMENT 'AutoProcProgram-specific unique identifier', + `Reference` int(10) unsigned DEFAULT NULL COMMENT 'Context-dependent reference to primary key IDs in other ISPyB tables', + PRIMARY KEY (`AutoProcProgramID`,`UUID`), + CONSTRAINT `AutoProcProgram_fk_AutoProcProgramId` FOREIGN KEY (`AutoProcProgramID`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE CASCADE ON UPDATE CASCADE +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + -- -- Final view structure for view `v_Log4Stat` -- @@ -6049,4 +6073,4 @@ SET character_set_client = @saved_cs_client; /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2021-05-14 17:23:07 +-- Dump completed on 2021-07-07 11:36:18 diff --git a/schemas/ispyb/updates/2021_07_07_AdminVar_bump_version.sql b/schemas/ispyb/updates/2021_07_07_AdminVar_bump_version.sql new file mode 100644 index 00000000..f6197e91 --- /dev/null +++ b/schemas/ispyb/updates/2021_07_07_AdminVar_bump_version.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2021_07_07_AdminVar_bump_version.sql', 'ONGOING'); + +UPDATE AdminVar SET `value` = '1.23.0' WHERE `name` = 'schemaVersion'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2021_07_07_AdminVar_bump_version.sql';